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  • Overview: module code
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- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/biofluxes.html b/pr-preview/pr-63/_modules/jobs/biofluxes.html deleted file mode 100644 index 6576d481..00000000 --- a/pr-preview/pr-63/_modules/jobs/biofluxes.html +++ /dev/null @@ -1,230 +0,0 @@ - - - - - - jobs.biofluxes — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
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Source code for jobs.biofluxes

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Prepare biofluxes files for COSMO simulations.
-
-    Copies biofluxes files from the project folder (:attr:`cfg.vprm['dir']`)
-    to the int2lm input folder on scratch (:attr:`cfg.int2lm_input`/vprm).
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-
-    scratch_path = os.path.join(cfg.int2lm_input, 'vprm')
-
-    tools.create_dir(scratch_path, "biofluxes input")
-
-    for time in tools.iter_hours(cfg.startdate_sim, cfg.enddate_sim):
-        logging.info(time)
-
-        for prefix in cfg.vprm['prefix']:
-            filename = os.path.join(cfg.vprm['dir'],
-                                    prefix + time.strftime('%Y%m%d%H.nc'))
-            filename_sc = os.path.join(scratch_path,
-                                       prefix + time.strftime('%Y%m%d%H.nc'))
-            if not (os.path.isfile(filename)):
-                logging.error(
-                    "File %s not found. Consider using the vprmsplit.py script prior",
-                    filename)
-                #tools.vprmsplit.main(time.strftime("%Y%m%d%H"),cfg.vprm['dir']_orig,cfg.vprm['dir']_proc,cfg)
-
-            tools.copy_file(filename, scratch_path)
-
-            if not os.path.isfile(filename_sc):
-                logging.error(
-                    "Splitting or copying of GPP or/and RA files to scratch failed."
-                )

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- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/check_output.html b/pr-preview/pr-63/_modules/jobs/check_output.html deleted file mode 100644 index 1caed8e8..00000000 --- a/pr-preview/pr-63/_modules/jobs/check_output.html +++ /dev/null @@ -1,1081 +0,0 @@ - - - - - - jobs.check_output — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
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- -
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-
- -

Source code for jobs.check_output

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import os
-from os.path import dirname, realpath, basename
-import shutil
-from distutils.dir_util import copy_tree
-import datetime as dt
-import glob
-import numpy as np
-import xarray as xr
-import pandas as pd
-import cartopy.crs as ccrs
-import cartopy.feature as cfeature
-import sys
-import multiprocessing
-import subprocess
-from matplotlib import gridspec
-from PIL import Image
-
-import matplotlib.pyplot as plt
-
-plt.switch_backend('Agg')
-
-try:
-    from . import tools
-except ImportError:
-    import tools
-
-BASIC_PYTHON_JOB = True
-
-
-def pkl_path(folder, pid=None):
-    """ Returns the path (and creates it, if necessary) to the stored
-    pandas data file.
-
-    Parameters
-    ----------	
-    folder : str
-        Path to the chain_root or the output_root
-    pid : int
-        Process ID in case of parallel exectution
-
-    Returns
-    -------
-    output_path : str
-        Full file path to pickle file
-    
-    """
-    if pid is None:
-        # Main file with complete content
-        filename = 'data.pkl'
-    else:
-        # Split file per process
-        filename = 'data_' + str(pid) + '.pkl'
-
-    if pid is None:
-        output_folder = os.path.join(folder, 'check_output')
-    else:
-        output_folder = os.path.join(folder, 'check_output', 'data')
-    tools.create_dir(output_folder, 'check_output')
-    output_path = os.path.join(output_folder, filename)
-
-    return output_path
-
-
-def timeseries_path(cfg):
-    """ Returns the path (and creates it, if necessary) to the timeseries
-    plots.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-
-    Returns
-    -------
-    output_path : str
-        Full file path to timeseries directory
-    """
-    output_folder = os.path.join(cfg.output_root, 'check_output', 'timeseries')
-    tools.create_dir(output_folder, 'timeseries')
-    output_path = os.path.join(cfg.output_root, 'check_output', 'timeseries')
-
-    return output_path
-
-
-def maps_path(cfg):
-    """ Returns the path (and creates it, if necessary) to the map plots.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-
-    Returns
-    -------
-    output_folder : str
-        Full file path to maps directory
-    """
-    output_folder = os.path.join(cfg.chain_root, 'check_output', 'maps')
-    tools.create_dir(output_folder, 'check_output maps')
-
-    return output_folder
-
-
-def animations_path(cfg):
-    """ Returns the path (and creates it, if necessary) to the animations.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-
-    Returns
-    -------
-    output_folder : str
-        Full file path to animations directory
-    """
-    output_folder = os.path.join(cfg.output_root, 'check_output', 'animations')
-    tools.create_dir(output_folder, 'animations')
-    output_path = os.path.join(cfg.output_root, 'check_output', 'animations')
-
-    return output_path
-
-
-def tracername2gas(tracername):
-    """ Returns the chemical symbol from the COSMO tracer name to be 
-    recognized by the helper convert_unit() function.
-
-    Parameters
-    ----------	
-    tracername : str
-        Full name of the tracer in COSMO output file
-
-    Returns
-    -------
-    gas : str
-        Chemical symbol as used in helper
-    """
-    gas = tracername.split('_')[0]
-    if gas == 'NOX':
-        gas = 'NO2'
-    elif gas == 'C14':
-        gas = '14CO2'
-
-    return gas
-
-
-def get_variable_names(cols):
-    """ Get unique variable names from dataframe.
-    
-    Parameters
-    ----------	
-    cols : list of str
-        List of column names from dataframe 
-
-    Returns
-    -------
-    varnames : list of str
-        List of unique variable names (e.g., CO2_A, NOX_BG, ...)
-    
-    """
-    todels = ['max', 'min', 'ground', 'mean', 'std']
-    varnames = []
-    for col in cols:
-        split_col = col.split('_')
-        for todel in todels:
-            split_col = list(filter(lambda x: x != todel, split_col))
-        varnames.append('_'.join(split_col))
-    varnames = list(dict.fromkeys(varnames))
-
-    return varnames
-
-
-def get_units(infiles, varnames):
-    """ Get units of variables from netCDF files.
-
-    Parameters
-    ----------
-    infiles : list of str
-        List of netCDF files 
-    varnames : list of str
-        List of unique variable names (e.g., CO2_A, NOX_BG, ...)
-
-    Returns
-    -------
-    units : dict
-        Dictionary containing units of variable names
-    
-    """
-    DS = xr.open_dataset(infiles[0])
-    starttime = DS.time.values[-1].astype(dt.datetime)
-    units = {}
-    for infile in infiles:
-        DS = xr.open_dataset(infile)
-        time = DS.time.values[-1].astype(dt.datetime)
-        if time > starttime:
-            break
-        for varname in varnames:
-            try:
-                if not varname in units:
-                    units[varname] = DS[varname].units
-            except KeyError:
-                continue
-
-    return units
-
-
-def plot_timeseries(cfg, units):
-    """ Plot of the min, max, mean and std values as time series. 
-    
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-    units : dict
-        Dictionary containing units os variables
-    
-    """
-    data_path = pkl_path(cfg.output_root)
-    df = pd.read_pickle(data_path)
-    ts_path = timeseries_path(cfg)
-
-    varnames = get_variable_names(df.columns.values)
-
-    # Tweak figure properties
-    style_label = 'seaborn-whitegrid'
-    (fig_width, fig_height) = plt.rcParams['figure.figsize']
-    fig_size = [fig_width * 2.2, fig_height * 1.8]
-
-    for varname in varnames:
-        logging.info('Plotting %s.png' % varname)
-
-        # Get diagnostic values
-        vmean = df[varname + '_mean']
-        vstd = df[varname + '_std']
-        vmin = df[varname + '_min']
-        vmax = df[varname + '_max']
-
-        # Unit conversion
-        if (varname.startswith('CO2_') or varname.startswith('CO_')
-                or varname.startswith('CH4_') or varname.startswith('C14_')
-                or varname.startswith('NOX_') or varname.startswith('NO2_')):
-            gas = tracername2gas(varname)
-            in_unit = units[varname]
-            out_unit = tools.helper.common_unit(gas)
-            vmean = tools.helper.convert_unit(vmean, in_unit, out_unit, gas)
-            vstd = tools.helper.convert_unit(vstd, in_unit, out_unit, gas)
-            vmin = tools.helper.convert_unit(vmin, in_unit, out_unit, gas)
-            vmax = tools.helper.convert_unit(vmax, in_unit, out_unit, gas)
-        else:
-            out_unit = units[varname]
-
-        # Figure options
-        fig, axes = plt.subplots(ncols=1,
-                                 nrows=3,
-                                 num=style_label,
-                                 figsize=fig_size,
-                                 squeeze=True)
-        fig.suptitle(cfg.casename)
-
-        axes[0].plot(df.index, vmean, linestyle='-')
-        axes[0].set_title('Ground-level mean values')
-
-        axes[1].plot(df.index, vmin, linestyle='-')
-        axes[1].set_title('Global minimum values')
-
-        axes[2].plot(df.index, vmax, linestyle='-')
-        axes[2].set_title('Global maximum values')
-
-        for ax in axes:
-            ylabel = '%s (%s)' % (varname, out_unit)
-            ax.set_ylabel(ylabel)
-            ax.grid()
-
-        axes[2].set_xlabel('Datetime')
-
-        fig.tight_layout(rect=[0, 0, 1, 0.95])
-        plt.savefig(os.path.join(ts_path, varname + '.png'))
-
-        plt.close('all')
-
-
-def get_data_single_file(infile, chain_src_dir, casename, chain_root):
-    """Fetches the diagnostic data from COSMO output files.
-
-    Parameters
-    ----------
-    infile : str
-        Full file name to be read
-    chain_src_dir : str
-        Path to the directory where the processing chain is ran
-    casename : str
-        Name of the current case
-    chain_root : str
-        Path to the processing chain directory
-    """
-    logging.info(infile)
-
-    DS = xr.open_dataset(infile)
-
-    ground_level = DS.level.values[-1]
-    nctime = DS.time.values[-1]
-
-    # Read values from variables.csv
-    alternate_csv_file = os.path.join(chain_src_dir, 'cases', casename,
-                                      'variables.csv')
-    variables = tools.helper.find_variables_file(alternate_csv_file)
-
-    # Drop variables without min/max values
-    variables['min_value'].replace('', np.nan, inplace=True)
-    variables['max_value'].replace('', np.nan, inplace=True)
-    variables['min_value'].replace(' ', np.nan, inplace=True)
-    variables['max_value'].replace(' ', np.nan, inplace=True)
-    variables.dropna(subset=['min_value'], inplace=True)
-    variables.dropna(subset=['max_value'], inplace=True)
-
-    # Get variable names
-    varnames = variables.index.values
-
-    data_values = dict()
-
-    # Loop over variables
-    for varname in varnames:
-        try:
-            da = DS[varname].sel(time=nctime).values
-        except KeyError:
-            #logging.warning('%s: Variable not in output file \n%s' %(varname,infile))
-            continue
-        if 'level' in DS[varname].dims:
-            da_ground = DS[varname].sel(level=ground_level, time=nctime)\
-                        .values.flatten()
-        else:
-            da_ground = da.flatten()
-
-        da = da.flatten()
-        minval = float(variables.loc[varname, 'min_value'])
-        maxval = float(variables.loc[varname, 'max_value'])
-        logging.info("{:10s} (min: {:11.4e}, max: {:11.4e})".format(
-            varname, minval, maxval))
-
-        varmin = np.nanmin(da)
-        varmax = np.nanmax(da)
-        varmin_ground = np.nanmin(da_ground)
-        varmax_ground = np.nanmax(da_ground)
-        varmean = np.mean(da_ground)
-        varstd = np.std(da_ground)
-
-        data_values[varname + '_min'] = varmin
-        data_values[varname + '_max'] = varmax
-        data_values[varname + '_min_ground'] = varmin_ground
-        data_values[varname + '_max_ground'] = varmax_ground
-        data_values[varname + '_mean'] = varmean
-        data_values[varname + '_std'] = varstd
-
-        if np.isnan(da).any():
-            error_msg = ('Variable %s in file %s has NaNs!' %
-                         (varname, infile))
-            logging.error(error_msg)
-        if (varmin < minval):
-            error_msg = ('Variable %s in file %s falls below minimum value!\n'
-                         'Allowed min = %e\n'
-                         'Actual min = %e' % (varname, infile, minval, varmin))
-            logging.error(error_msg)
-        if (varmax > maxval):
-            error_msg = ('Variable %s in file %s exceeds maximum value!\n'
-                         'Allowed max = %e\n'
-                         'Actual max = %e' % (varname, infile, maxval, varmax))
-            logging.error(error_msg)
-
-    # Get the time from the name
-    time_str = os.path.basename(infile)[4:14]
-    ctime = dt.datetime.strptime(time_str, '%Y%m%d%H')
-
-    data = pd.DataFrame(data_values, index=[ctime])
-
-    # Store the time series of min and max in a pandas file format.
-    pid = os.getpid()
-    logging.info('Storing data to %s' % pkl_path(chain_root, pid))
-    store_data(data, chain_root, pid)
-
-
-def merge_data(cfg):
-    """ Merges multiple pickle files into one.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-
-    Returns
-    -------
-    data : pandas.DataFrame
-        Dataframe containing the whole diagnostic data 
-    """
-    output_path = pkl_path(cfg.output_root)
-    input_path = os.path.join(cfg.chain_root, 'check_output', 'data')
-    infiles = sorted(glob.glob(os.path.join(input_path, "data_*.pkl")))
-    for infile in infiles:
-        data = pd.read_pickle(infile)
-        os.remove(infile)
-        if os.path.exists(output_path):
-            history = pd.read_pickle(output_path)
-            history = history.combine_first(data)
-            history.sort_index(inplace=True)
-            history.to_pickle(output_path)
-        else:
-            data.sort_index(inplace=True)
-            data.to_pickle(output_path)
-
-    data = pd.read_pickle(output_path)
-
-    return data
-
-
-def store_data(data, folder, pid=None):
-    """ Stores the time series diagnostic data in a pandas dataframe.
-    Appends it to the existing file, without overwriting the previous dates. 
-    This is useful if this is a continuous run with a spin-up period or 
-    when using binary restart files.
-
-    Parameters
-    ----------	
-    data: pandas.DataFrame
-        Dataframe containing diagnostic values for each variable
-    folder : str
-        Path to the folder where the results are stored
-    pid : int
-        Process ID in case of parallel exectution
-    """
-    output_path = pkl_path(folder, pid)
-
-    if os.path.exists(output_path):
-        history = pd.read_pickle(output_path)
-        history = history.combine_first(data)
-        history.sort_index(inplace=True)
-        history.to_pickle(output_path)
-    else:
-        data.sort_index(inplace=True)
-        data.to_pickle(output_path)
-
-
-def write_footnotetext(field):
-    """ Formats the footnote text for map plots.
-    
-    Parameter
-    ---------
-    field : numpy.array
-        Two-dimensional field of data to be shown in the plot
-
-    Returns
-    -------
-    footnotetext : str
-        Formatted footnote text with min/max/mean values of the field
-    """
-    fmin = np.min(field)
-    fmax = np.max(field)
-    fmean = np.mean(field)
-
-    footnotetext = 'min: ' + "{:.1f}".format(fmin) + \
-                   '  max: ' + "{:.1f}".format(fmax) + \
-                   '  mean: ' + "{:.1f}".format(fmean)
-
-    return footnotetext
-
-
-def get_infiles(path):
-    """ Returns a sorted file list of COSMO output files without *c.nc file. 
-
-    Parameter
-    ---------
-    path : str
-        Path to the COSMO output folder
-
-    Returns
-    -------
-    infiles : list of str
-        Sorted List of filenames of COSMO ouputs
-    """
-    infiles = sorted(glob.glob(os.path.join(path, "lffd*.nc")))
-    infiles = [
-        infile for infile in infiles
-        if os.path.split(infile)[1].split('lffd', 1)[1][10] != 'c'
-    ]
-
-    # If this is a spin-up simulation, skip the first output files
-    timestr = basename(dirname(dirname(realpath(path))))
-    times = timestr.split("_")
-    spinup_time = int(times[1])
-    start = dt.datetime.strptime(times[0], '%Y%m%d%H')
-
-    if spinup_time < 0:
-        for f in infiles.copy():
-            fname = basename(f)
-            ftime = dt.datetime.strptime(fname[4:14], '%Y%m%d%H')
-            if ftime < start:
-                infiles.remove(f)
-
-    return infiles
-
-
-def plot_single_map(data, infile, output_path, varnames):
-    """ Plots 2D maps of certain variables from a netCDF file.
-
-    Parameters
-    ----------	
-    data: pandas.DataFrame
-        Dataframe containing diagnostic values for each variable
-    infile : str
-        Full file name to be read
-    output_path: str
-        Full path where output files should be generated
-    varnames : list of str
-        Names of variables to be processed
-    """
-    # Read in files
-    logging.info(infile)
-
-    DS = xr.open_dataset(infile)
-
-    ground_level = DS.level.values[-1]
-    nctime = DS.time.values[-1]
-    ts = nctime.astype(dt.datetime)
-    ts = dt.datetime.utcfromtimestamp(ts / 1e9)
-    timestr = ts.strftime("%Y%m%d%H")
-
-    rlon = DS['rlon'].values
-    rlat = DS['rlat'].values
-    lon = DS['lon'].values
-    lat = DS['lat'].values
-    pollon = DS["rotated_pole"].attrs["grid_north_pole_longitude"]
-    pollat = DS["rotated_pole"].attrs["grid_north_pole_latitude"]
-    startlon = rlon[0]
-    endlon = rlon[-1]
-    startlat = rlat[0]
-    endlat = rlat[-1]
-
-    domain = tools.helper.Domain('COSMO',
-                                 startlon,
-                                 startlat,
-                                 endlon,
-                                 endlat,
-                                 pollon=pollon,
-                                 pollat=pollat)
-
-    # Check for rotated pole coordinates
-    if not isinstance(domain.proj, ccrs.RotatedPole):
-        raise NotImplementedError('domain needs to use rotated pole coords')
-
-    for varname in varnames:
-        try:
-            field = DS[varname].sel(time=nctime).values
-        except KeyError:
-            logging.warning('%s: Variable not in output file \n%s' %
-                            (varname, infile))
-            continue
-        if len(np.shape(field)) == 3:
-            field = DS[varname].sel(level=ground_level, time=nctime).values
-
-        convert = False
-        # Unit conversion
-        if (varname.startswith('CO2_') or varname.startswith('CO_')
-                or varname.startswith('CH4_') or varname.startswith('C14_')
-                or varname.startswith('NOX_') or varname.startswith('NO2_')):
-            convert = True
-            gas = tracername2gas(varname)
-            in_unit = DS[varname].units
-            out_unit = tools.helper.common_unit(gas)
-            field = tools.helper.convert_unit(field, in_unit, out_unit, gas)
-        else:
-            out_unit = DS[varname].units
-
-        # Set min/max for colorbar and convert if needed
-        vmin = data[varname + "_min_ground"].min()
-        vmax = data[varname + "_max_ground"].max()
-        if convert:
-            vmin = tools.helper.convert_unit(vmin, in_unit, out_unit, gas)
-            vmax = tools.helper.convert_unit(vmax, in_unit, out_unit, gas)
-
-        # Set manual min/max range in case they are equal
-        if vmax == vmin:
-            vmax == vmin + 1
-
-        # Create figure and axes objects
-        fig = plt.figure()
-        gs = gridspec.GridSpec(1, 2, width_ratios=[9, 1])
-        ax = plt.subplot(gs[0], projection=domain.proj)
-        cax = plt.subplot(gs[1])
-
-        # Dimensions
-        dlon = rlon[1] - rlon[0]
-        left = rlon[0] - dlon / 2.0
-        right = rlon[-1] + dlon / 2.0
-        dlat = rlat[1] - rlat[0]
-        bottom = rlat[0] - dlat / 2.0
-        top = rlat[-1] + dlat / 2.0
-        ax.set_xlim(domain.startlon, domain.stoplon)
-        ax.set_ylim(domain.startlat, domain.stoplat)
-
-        # Annotations
-        ax.set_title(varname, loc='left', pad=10.0)
-        ax.set_title(timestr, loc='right', pad=10.0)
-        footnotetext = write_footnotetext(field)
-        ax.annotate(footnotetext, (0, 0), (0, -4),
-                    xycoords='axes fraction',
-                    textcoords='offset points',
-                    va='top')
-
-        # Add coastlines
-        ax.coastlines(resolution='10m', color="black", linewidth=1)
-        lines = cfeature.NaturalEarthFeature(
-            category='cultural',
-            name='admin_0_boundary_lines_land',
-            scale='10m',
-        )
-        ax.add_feature(lines,
-                       edgecolor="grey",
-                       facecolor='none',
-                       linewidth=0.75)
-
-        # Fill the plot
-        im = ax.imshow(field,
-                       vmin=vmin,
-                       vmax=vmax,
-                       cmap='viridis',
-                       extent=(left, right, bottom, top),
-                       interpolation=None,
-                       transform=domain.proj)
-
-        # Colorbar
-        cax.cla()
-        ticks = np.linspace(vmin, vmax, 8, endpoint=True)
-        cb = plt.colorbar(im, cax=cax, ticks=ticks)
-        cb.ax.set_yticklabels(["{:.1f}".format(i) for i in ticks])
-        cb.ax.set_title(out_unit)
-
-        # Save figure
-        output_folder = os.path.join(output_path, varname)
-        fig.savefig(os.path.join(output_folder,
-                                 varname + '_' + timestr + '.png'),
-                    bbox_inches='tight')
-        plt.close('all')
-
-
-def create_map_directories(cfg, data, units):
-    """Create folders for the 2D maps of variables.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-    data: pandas.DataFrame
-        Dataframe containing diagnostic values for each variable
-    units : dict
-        Dictionary of units per variable name
-    """
-    output_path = maps_path(cfg)
-    data_path = pkl_path(cfg.output_root)
-    df = pd.read_pickle(data_path)
-
-    # Get variable names
-    varnames = get_variable_names(df.columns.values)
-    # Create directories per variable for map plots
-    for varname in varnames:
-        output_folder = os.path.join(output_path, varname)
-        tools.create_dir(output_folder, varname)
-
-
-def create_animations(cfg):
-    """Creates animated *.gif files from map plots.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-    """
-    data_path = pkl_path(cfg.output_root)
-    df = pd.read_pickle(data_path)
-
-    # Get variable names
-    varnames = get_variable_names(df.columns.values)
-
-    map_path = os.path.join(cfg.output_root, 'check_output', 'maps')
-    output_path = animations_path(cfg)
-    for varname in varnames:
-        infile_path = os.path.join(map_path, varname)
-        infiles = sorted(glob.glob(os.path.join(infile_path, "*.png")))
-        frames = []
-        for i in infiles:
-            new_frame = Image.open(i)
-            frames.append(new_frame)
-
-        # Save into a GIF file
-        outfile = os.path.join(output_path, varname + '.gif')
-        frames[0].save(outfile,
-                       format='GIF',
-                       append_images=frames[1:],
-                       save_all=True,
-                       duration=300)
-
-
-
[docs]def main(cfg):
-    """Check output variables for physical reasonability and create plots.
-
-    This function checks the output variables to ensure they are in a physically
-    reasonable range. It stores the time series of the minimum, maximum, mean, and
-    standard deviation of the variables as a pandas object into a pickle file.
-
-    It also creates per-variable plots from the stored time series data.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    date = dt.datetime.today()
-
-    to_print = """check_output
-
-=====================================================
-============== POST PROCESSING BEGINS ===============
-============== StartTime: %s 
-=====================================================""" % date.strftime("%s")
-
-    logging.info(to_print)
-
-    # if cfg.compute_host!="daint":
-    #     logging.error("The check_output script is supposed to be run on daint only, "
-    #                   "not on %s" % cfg.compute_host)
-    #     sys.exit(1)
-    """Wait for Cosmo to finish first"""
-    tools.check_job_completion(cfg.log_finished_dir, "cosmo",
-                               waittime=300)  # check every 30 seconds
-
-    # Get list of files
-    logging.info('Getting list of input files')
-    infiles = get_infiles(cfg.cosmo_output)
-
-    # Get data from COSMO output files
-    logging.info('Getting data from COSMO output files')
-    to_write = """#!/usr/bin/env bash
-#SBATCH --partition=debug
-#SBATCH --account=em05
-#SBATCH --job-name="check_output_{cfg.startdate_sim_yyyymmddhh}_{cfg.forecasttime}"
-#SBATCH --open-mode=append
-#SBATCH --time=00:30:00
-#SBATCH --constraint=mc
-#SBATCH --ntasks=1
-#SBATCH --output={cfg.logfile}
-
-
-export EASYBUILD_PREFIX=/store/empa/em05/easybuild
-export ECCODES_DEFINITION_PATH=/store/empa/em05/easybuild/software/ecCodes/2.12.5-CrayGNU-19.10/share/eccodes/definitions/
-
-module load daint-mc
-module load EasyBuild-custom
-
-module load daint-mc
-module load EasyBuild-custom
-
-module load cray-python/3.8.5.0
-module load PyExtensions/python3-CrayGNU-20.11
-
-module load GEOS
-module load PROJ/4.9.3-CrayGNU-20.11
-module load ecCodes
-#module load GDAL                         # FIXME: currently easybuild install is not working
-
-# source /store/empa/em05/pyvenv-3.8/bin/activate
-source ~/python/stem2/bin/activate
-
-srun python jobs/check_output.py {casename} {cosmo_output} {output_root} {chain} {chain_root} {action}
-"""
-    to_write_fmt = to_write.format(cfg=cfg,
-                                   casename=cfg.casename,
-                                   cosmo_output=cfg.cosmo_output,
-                                   output_root=cfg.output_root,
-                                   work_log=cfg.log_working_dir,
-                                   logfile=cfg.logfile,
-                                   chain=cfg.chain_src_dir,
-                                   chain_root=cfg.chain_root,
-                                   action='get_data')
-
-    output_file = os.path.join(cfg.cosmo_work, "get_data.job")
-
-    with open(output_file, 'w') as outf:
-        outf.write(to_write_fmt)
-
-    result = subprocess.run(["sbatch", "--wait", output_file])
-    exitcode = result.returncode
-
-    if exitcode != 0:
-        raise RuntimeError("sbatch returned exitcode {}".format(exitcode))
-
-    # Merge data to single pickle file
-    logging.info('Merging data to single pickle file')
-    data = merge_data(cfg)
-
-    # Get variable names
-    logging.info('Getting variable names')
-    varnames = get_variable_names(data.columns.values)
-    logging.info(varnames)
-
-    # Get units
-    logging.info('Reading units')
-    units = get_units(infiles, varnames)
-    logging.info(units)
-
-    # Plots
-    logging.info('Creating timeseries plots in %s' % timeseries_path(cfg))
-    plot_timeseries(cfg, units)
-
-    logging.info('Creating map plots in %s' % maps_path(cfg))
-    create_map_directories(cfg, data, units)
-
-    to_write_fmt = to_write.format(cfg=cfg,
-                                   casename=cfg.casename,
-                                   cosmo_output=cfg.cosmo_output,
-                                   output_root=cfg.output_root,
-                                   logfile=cfg.logfile,
-                                   chain=cfg.chain_src_dir,
-                                   chain_root=cfg.chain_root,
-                                   action='plot_maps')
-
-    output_file = os.path.join(cfg.cosmo_work, "plot_maps.job")
-
-    with open(output_file, 'w') as outf:
-        outf.write(to_write_fmt)
-
-    result = subprocess.run(["sbatch", "--wait", output_file])
-    exitcode = result.returncode
-
-    if exitcode != 0:
-        raise RuntimeError("sbatch returned exitcode {}".format(exitcode))
-
-    # Move map plots to output directory
-    src_folder = os.path.join(cfg.chain_root, 'check_output', 'maps')
-    dest_folder = os.path.join(cfg.output_root, 'check_output')
-    logging.info('Move map plots to %s' % dest_folder)
-    try:
-        shutil.move(src_folder, dest_folder)
-    except:
-        for varname in varnames:
-            fromDirectory = os.path.join(src_folder, varname)
-            toDirectory = os.path.join(dest_folder, 'maps', varname)
-            copy_tree(fromDirectory, toDirectory)
-
-    # Animations
-    logging.info('Creating animations in %s' % animations_path(cfg))
-    create_animations(cfg)
-
-    date = dt.datetime.today()
-    to_print = """=====================================================
-============== POST PROCESSING ENDS ==================
-============== EndTime: %s
-=====================================================""" % date.strftime("%s")
-    logging.info(to_print)
-
-    # Check for errors
-    with open(cfg.logfile) as f:
-        if 'ERROR' in f.read():
-            raise RuntimeError('Logfile containing errors! See %s' %
-                               cfg.logfile)

-
-
-if __name__ == '__main__':
-    args = sys.argv
-
-    casename = args[1]
-    cosmo_output = args[2]
-    output_root = args[3]
-    chain_src_dir = args[4]
-    chain_root = args[5]
-    action = args[6]
-
-    output_folder = os.path.join(chain_root, 'check_output')
-    data_path = os.path.join(output_root, 'check_output', 'data.pkl')
-    infiles = get_infiles(cosmo_output)
-
-    nthread = 36
-
-    if action == 'plot_maps':
-        with multiprocessing.Pool(nthread) as pool:
-            data = pd.read_pickle(data_path)
-            # Get variable names
-            output_path = os.path.join(output_folder, 'maps')
-            varnames = get_variable_names(data.columns.values)
-            pool.starmap(plot_single_map,
-                         [(data, infile, output_path, varnames)
-                          for infile in infiles])
-
-    elif action == 'get_data':
-        # Loop over all files and check values
-        with multiprocessing.Pool(nthread) as pool:
-            pool.starmap(get_data_single_file,
-                         [(infile, chain_src_dir, casename, chain_root)
-                          for infile in infiles])
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/cosmo.html b/pr-preview/pr-63/_modules/jobs/cosmo.html deleted file mode 100644 index a1cc0002..00000000 --- a/pr-preview/pr-63/_modules/jobs/cosmo.html +++ /dev/null @@ -1,376 +0,0 @@ - - - - - - jobs.cosmo — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.cosmo

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import os
-import subprocess
-from pathlib import Path
-
-from datetime import datetime
-from .tools import write_cosmo_input_ghg
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Setup the namelists for a COSMO run and submit the job to the queue.
-
-    Create necessary directory structure to run COSMO (run, output, and
-    restart directories, defined in ``cfg.cosmo_run``, ``cfg.cosmo_output``,
-    and ``cfg.cosmo_restart_out``).
-
-    Copy the COSMO-executable from
-    ``cfg.cosmo['binary_file']`` to ``cfg.cosmo_run/cfg.cosmo['execname']``.
-
-    Convert the tracer csv file to a COSMO namelist file.
-
-    Format the COSMO namelist templates using the information in ``cfg``.
-
-    Format the runscript template and submit the job.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-
-    logging.info("Setup the namelist for a COSMO tracer run and "
-                 "submit the job to the queue")
-
-    # Create directories
-    tools.create_dir(cfg.cosmo_run, "cosmo_run")
-    tools.create_dir(cfg.cosmo_output, "cosmo_output")
-
-    # Total number of processes
-    np_tot = int(cfg.cosmo['np_x'] * cfg.cosmo['np_y'] /
-                 cfg.ntasks_per_node) + cfg.cosmo['np_io']
-
-    # If an laf* file is used for initialization,
-    # copy this to to 'cosmo/input/initial/' or merge with fieldextra
-    if hasattr(cfg, 'laf_startfile'):
-        tools.create_dir(cfg.cosmo_input, "cosmo_input")
-        ini_dir = os.path.join(cfg.cosmo_input, "initial")
-        tools.create_dir(ini_dir, "cosmo_input_initial")
-        startfiletime = datetime.strptime(cfg.laf_startfile[-10:], "%Y%m%d%H")
-        if cfg.startdate_sim >= startfiletime:
-            work_root = os.path.dirname(os.path.dirname(cfg.chain_root))
-            last_output_path = os.path.join(work_root, cfg.casename,
-                                            cfg.chunk_id_prev, 'cosmo',
-                                            'output')
-            laf_output_refdate = cfg.startdate_sim.strftime("%Y%m%d%H")
-            last_laf_filename = "laf" + laf_output_refdate
-            # At the beginning, use original laf_startfile
-            if cfg.startdate_sim == startfiletime:
-                last_laf_startfile = cfg.laf_startfile
-            else:
-                last_laf_startfile = os.path.join(last_output_path,
-                                                  last_laf_filename)
-
-            # Check if fieldextra is used
-            if hasattr(cfg, 'fieldextra_bin') and \
-            hasattr(cfg, 'fieldextra_control_file'):
-                # Check if merge should be done for initial file
-                if not hasattr(cfg, 'do_merge_at_start'):
-                    setattr(cfg, 'do_merge_at_start', False)
-                if cfg.startdate_sim == startfiletime and not cfg.do_merge_at_start:
-                    # Just copy the existing laf file
-                    tools.copy_file(last_laf_startfile, ini_dir)
-                else:
-                    out_file = os.path.join(ini_dir, last_laf_filename)
-                    ifs_in_file = os.path.join(cfg.int2lm_output,
-                                               last_laf_filename)
-                    # Write control file for fieldextra script (merge.ctl)
-                    with open(cfg.fieldextra_control_file) as input_file:
-                        to_write = input_file.read()
-
-                    output_file_merge = os.path.join(ini_dir, "merge.ctl")
-                    with open(output_file_merge, "w") as outf:
-                        outf.write(
-                            to_write.format(
-                                cfg=cfg,
-                                in_file=last_laf_startfile,
-                                ifs_in_file=ifs_in_file,
-                                out_file=out_file,
-                                laf_output_refdate=laf_output_refdate,
-                            ))
-                    # Execute fieldextra
-                    with open(cfg.logfile, "a+") as log:
-                        result = subprocess.run(
-                            [cfg.fieldextra_bin, output_file_merge],
-                            stdout=log)
-                        exitcode = result.returncode
-                    if exitcode != 0:
-                        raise RuntimeError(
-                            "Fieldextra returned exitcode {}".format(exitcode))
-            else:
-                # Just copy the existing laf file
-                tools.copy_file(last_laf_startfile, ini_dir)
-        else:
-            raise ValueError(
-                "Start time %s must not be smaller than in laf_starttime %s." %
-                (str(cfg.starttime_sim), str(startfiletime)))
-
-    # Create restart directory if feature is present and
-    # if there is no spinup
-    if 'restart' in cfg.workflow['features'] and not \
-       hasattr(cfg, 'spinup'):
-        tools.create_dir(cfg.cosmo_restart_out, "cosmo_restart_out")
-
-    # Copy cosmo executable
-    cfg.cosmo_execname = Path(cfg.cosmo['binary_file']).name
-    tools.copy_file(cfg.cosmo['binary_file'],
-                    cfg.cosmo_run / cfg.cosmo_execname)
-
-    # Prepare namelist and submit job
-    tracer_csvfile = os.path.join(cfg.chain_src_dir, 'cases', cfg.casename,
-                                  'cosmo_tracers.csv')
-    if hasattr(cfg, 'cams') or hasattr(cfg, 'mozart'):
-        namelist_names = ['AF', 'ORG', 'IO', 'DYN', 'GHG', 'PHY', 'DIA', 'ASS']
-    elif hasattr(cfg, 'photo_rate'):
-        namelist_names = [
-            'ART', 'ASS', 'DIA', 'DYN', 'EPS', 'INI', 'IO', 'ORG', 'PHY'
-        ]
-        if hasattr(cfg, 'oem_dir'):
-            # When doing online emissions in COSMO-ART, an additional
-            # namelist is required
-            namelist_names += ['OAE']
-    elif hasattr(cfg, 'cosmo'):
-        namelist_names = ['ORG', 'IO', 'DYN', 'PHY', 'DIA', 'ASS', 'SAT']
-
-    for section in namelist_names:
-        namelist_file = os.path.join(
-            cfg.chain_src_dir, 'cases', cfg.casename,
-            cfg.cosmo['namelist_prefix'] + section + ".cfg")
-        with open(namelist_file) as input_file:
-            cosmo_namelist = input_file.read()
-
-        output_file = os.path.join(cfg.cosmo_run, "INPUT_" + section)
-        with open(output_file, "w") as outf:
-            if hasattr(cfg, 'spinup'):
-                # no built-in restarts
-                cosmo_namelist = cosmo_namelist.format(cfg=cfg,
-                                                       **cfg.cosmo,
-                                                       **cfg.oem,
-                                                       restart_start=12,
-                                                       restart_stop=0,
-                                                       restart_step=12)
-            else:
-                # built-in restarts
-                cosmo_namelist = cosmo_namelist.format(
-                    cfg=cfg,
-                    **cfg.cosmo,
-                    **cfg.oem,
-                    restart_start=0,
-                    restart_stop=cfg.restart_step_hours,
-                    restart_step=cfg.restart_step_hours)
-            outf.write(cosmo_namelist)
-
-    # Append INPUT_GHG namelist with tracer definitions from csv file
-    if os.path.isfile(tracer_csvfile):
-        if hasattr(cfg, 'cams') or hasattr(cfg, 'mozart'):
-            input_ghg_filename = os.path.join(cfg.cosmo_run, 'INPUT_GHG')
-
-            write_cosmo_input_ghg.main(tracer_csvfile, input_ghg_filename, cfg)
-
-    # Write run script (run.job)
-    runscript_file = os.path.join(cfg.chain_src_dir, 'cases', cfg.casename,
-                                  cfg.cosmo['runjob_filename'])
-    with open(runscript_file) as input_file:
-        cosmo_runscript = input_file.read()
-
-    Path(cfg.cosmo_run).mkdir(parents=True, exist_ok=True)
-    script = (cfg.cosmo_run / 'run_cosmo.job')
-    with open(script, "w") as outf:
-        outf.write(
-            cosmo_runscript.format(cfg=cfg,
-                                   **cfg.cosmo,
-                                   np_tot=np_tot,
-                                   logfile=cfg.logfile,
-                                   logfile_finish=cfg.logfile_finish))
-
-    # Submit job
-    cfg.submit('cosmo', script)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/emissions.html b/pr-preview/pr-63/_modules/jobs/emissions.html deleted file mode 100644 index 382de31e..00000000 --- a/pr-preview/pr-63/_modules/jobs/emissions.html +++ /dev/null @@ -1,253 +0,0 @@ - - - - - - jobs.emissions — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.emissions

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Copy emission files to the int2lm input directory.
-
-    Necessary for both COSMO and COSMOART simulations.
-
-    Copy emission files from project folder (``cfg.emissions['dir']``) to
-    int2lm input folder on scratch (``cfg.int2lm_input/emissions``).
-
-    For COSMO simulations, converts the netCDF-variable-names 
-    from ``string`` to ``char`` (necessary for int2lm).
-
-    If there are multiple emission-datasets (cfg.emissions['dir'] is a list of
-    paths), they are copied as follows::
-
-        cfg.emissions['dir'][0]/cfg.emissions['gridname'][0]YYYYMMDD.nc -> int2lm_input/emissions/emis_YYYYMMDD.nc
-        cfg.emissions['dir'][1]/cfg.emissions['gridname'][1]YYYYMMDD.nc -> int2lm_input/emissions2/emis_YYYYMMDD.nc
-        cfg.emissions['dir'][2]/cfg.emissions['gridname'][2]YYYYMMDD.nc -> int2lm_input/emissions3/emis_YYYYMMDD.nc
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-    dest_prefix = "emis_"
-
-    if not isinstance(cfg.emissions['dir'], list):
-        emis_dirs = [cfg.emissions['dir']]
-    else:
-        emis_dirs = cfg.emissions['dir']
-    if not isinstance(cfg.emissions['gridname'], list):
-        emis_prefixes = [cfg.emissions['gridname']]
-    else:
-        emis_prefixes = cfg.emissions['gridname']
-
-    assert len(emis_dirs) == len(emis_prefixes), (
-        "Different number of cfg.emissions['dir'] and cfg.emissions['gridname']"
-    )
-
-    for i, (emis_dir, emis_prefix) in enumerate(zip(emis_dirs, emis_prefixes)):
-        # create directory
-        if i == 0:
-            target_dir = os.path.join(cfg.int2lm_input, "emissions")
-            tools.create_dir(target_dir, "emissions input")
-        else:
-            target_dir = os.path.join(cfg.int2lm_input,
-                                      "emissions" + str(i + 1))
-            tools.create_dir(target_dir, "emissions input")
-        # copy data
-        for time in tools.iter_hours(cfg.startdate_sim, cfg.enddate_sim):
-            logging.info(time)
-            filename_ending = time.strftime('%Y%m%d%H.nc')
-            source_path = os.path.join(emis_dir, emis_prefix + filename_ending)
-            dest_path = os.path.join(target_dir, dest_prefix + filename_ending)
-            tools.copy_file(source_path, dest_path)
-
-            # convert grid_mapping_name from string (NF90_STRING) to char
-            # (NF90_CHAR) (needed for int2lm to work)
-            if hasattr(cfg, 'cosmo'):
-                tools.string2char.main(dest_path)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/icon.html b/pr-preview/pr-63/_modules/jobs/icon.html deleted file mode 100644 index 4260b16b..00000000 --- a/pr-preview/pr-63/_modules/jobs/icon.html +++ /dev/null @@ -1,240 +0,0 @@ - - - - - - jobs.icon — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.icon

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-from pathlib import Path
-from . import tools, prepare_icon
-
-BASIC_PYTHON_JOB = False
-
-
-
[docs]def main(cfg):
-    """Setup the namelists for an ICON run and submit the job to
-    the queue.
-
-    Copy the ICON-executable from
-    ``cfg.icon_binary_file`` to ``cfg.icon_work/icon.exe``.
-
-    Format the ICON-namelist-templates:
-    ``icon_master.namelist.cfg, icon_NAMELIST_NWP.cfg``,
-    using the information in ``cfg``.
-
-    Format the runscript-template and submit the job.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    prepare_icon.set_cfg_variables(cfg)
-    tools.change_logfile(cfg.logfile)
-
-    logging.info("Setup the namelist for an ICON run and "
-                 "submit the job to the queue")
-
-    # Copy icon executable
-    cfg.icon_execname = Path(cfg.icon['binary_file']).name
-    tools.create_dir(cfg.icon_work, "icon_work")
-    tools.copy_file(cfg.icon_binary_file, cfg.icon_work / cfg.icon_execname)
-
-    # Symlink the restart file to the last run into the icon/run folder
-    if cfg.lrestart == '.TRUE.':
-        tools.symlink_file(cfg.restart_file, cfg.restart_file_scratch)
-
-    # Get name of initial file
-    if hasattr(cfg, 'inicond_filename'):
-        inidata_filename = cfg.icon_input_icbc / cfg.inicond_filename
-    else:
-        inidata_filename = cfg.icon_input_icbc / str(
-            cfg.startdate_sim.strftime(cfg.meteo['prefix'] +
-                                       cfg.meteo['nameformat']) + '.nc')
-
-    # Write run script (run_icon.job)
-    template = (cfg.case_path / cfg.icon_runjob_filename).read_text()
-    script_str = template.format(cfg=cfg, inidata_filename=inidata_filename)
-    script = (cfg.icon_work / 'run_icon.job')
-    script.write_text(script_str)
-
-    # Submit run script
-    cfg.submit('icon', script)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/icontools.html b/pr-preview/pr-63/_modules/jobs/icontools.html deleted file mode 100644 index 3fbc1608..00000000 --- a/pr-preview/pr-63/_modules/jobs/icontools.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - jobs.icontools — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.icontools

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import os
-import xarray as xr
-import numpy as np
-from . import tools, prepare_icon
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """
-    - Add GEOSP to all meteo files
-    - Submit the runscript for the DWD ICON tools to remap the meteorological files.
-    - All runscripts specified in ``cfg.icontools_runjobs`` are submitted.
-    - The meteorological files are read from the original input directory
-      (``cfg.input_root_meteo``), and the remapped meteorological files are saved
-      in the input folder on scratch (``cfg.icon_input/icbc``).
-    """
-    prepare_icon.set_cfg_variables(cfg)
-    tools.change_logfile(cfg.logfile)
-
-    #-----------------------------------------------------
-    # Create LBC datafile lists (each at 00 UTC and others)
-    #-----------------------------------------------------
-    datafile_list = []
-    datafile_list_rest = []
-    datafile_list_chem = []
-    for time in tools.iter_hours(cfg.startdate_sim, cfg.enddate_sim,
-                                 cfg.meteo['inc']):
-        meteo_file = cfg.icon_input_icbc / (
-            cfg.meteo['prefix'] + time.strftime(cfg.meteo['nameformat']))
-        if hasattr(cfg, 'art_input_folder'):
-            chem_file = cfg.icon_input_icbc / (
-                cfg.chem['prefix'] + time.strftime(cfg.chem_nameformat))
-            datafile_list_chem.append(str(chem_file) + cfg.chem['suffix'])
-        if str(meteo_file).endswith('00'):
-            datafile_list.append(str(meteo_file) + cfg.meteo['suffix'])
-        else:
-            datafile_list_rest.append(str(meteo_file) + cfg.meteo['suffix'])
-    datafile_list = ' '.join([str(v) for v in datafile_list])
-    datafile_list_rest = ' '.join([str(v) for v in datafile_list_rest])
-    datafile_list_chem = ' '.join([str(v) for v in datafile_list_chem])
-
-    #-----------------------------------------------------
-    # Write and submit ICONTOOLS runscripts
-    #-----------------------------------------------------
-    dep_id = None
-    for runscript in cfg.icontools_runjobs:
-        with (cfg.case_path / runscript).open() as input_file:
-            to_write = input_file.read()
-        runscript_path = cfg.icon_work / f"{runscript}.job"
-        with runscript_path.open("w") as outf:
-            outf.write(
-                to_write.format(cfg=cfg,
-                                meteo=cfg.meteo,
-                                logfile=cfg.logfile,
-                                logfile_finish=cfg.logfile_finish,
-                                datafile_list=datafile_list,
-                                datafile_list_rest=datafile_list_rest,
-                                datafile_list_chem=datafile_list_chem))
-
-        # Submitting icontools runscripts sequentially
-        logging.info(f" Starting icontools runscript {runscript}.")
-        dep_id = cfg.submit('icontools', runscript_path, add_dep=dep_id)
-
-    logging.info("Add GEOSP to all meteo files")
-    for time in tools.iter_hours(cfg.startdate_sim, cfg.enddate_sim,
-                                 cfg.meteo['inc']):
-        # Specify file names
-        geosp_filename = time.replace(
-            hour=0).strftime(cfg.meteo['prefix'] +
-                             cfg.meteo['nameformat']) + '_lbc.nc'
-        geosp_file = os.path.join(cfg.icon_input_icbc, geosp_filename)
-        src_filename = time.strftime(cfg.meteo['prefix'] +
-                                     cfg.meteo['nameformat']) + '_lbc.nc'
-        src_file = os.path.join(cfg.icon_input_icbc, src_filename)
-        merged_filename = time.strftime(cfg.meteo['prefix'] +
-                                        cfg.meteo['nameformat']) + '_merged.nc'
-        merged_file = os.path.join(cfg.icon_input_icbc, merged_filename)
-
-        # Copy GEOSP file from last run if not present
-        if hasattr(cfg,
-                   'icon_input_icbc_prev') and not os.path.exists(geosp_file):
-            geosp_src_file = os.path.join(cfg.icon_input_icbc_prev,
-                                          geosp_filename)
-            tools.copy_file(geosp_src_file,
-                            cfg.icon_input_icbc,
-                            output_log=True)
-
-        # Load GEOSP data array as da_geosp at time 00:
-        ds = xr.open_dataset(src_file)
-        ds_geosp = xr.open_dataset(geosp_file)
-        da_geosp = ds_geosp['GEOSP']
-
-        # Merge GEOSP-dataset with other timesteps
-        if (time.hour != 0):
-            # Change values of time dimension to current time
-            da_geosp = da_geosp.assign_coords(time=[np.datetime64(time)])
-            # Merge GEOSP into temporary file
-            ds_merged = xr.merge([ds, da_geosp])
-            ds_merged.attrs = ds.attrs
-            ds_merged.to_netcdf(merged_file)
-            # Logging info for merging GEOSP
-            logging.info("Added GEOSP to file {}".format(merged_file))
-            # Rename file to get original file name
-            tools.rename_file(merged_file, src_file)
-    logging.info('OK')

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/int2lm.html b/pr-preview/pr-63/_modules/jobs/int2lm.html deleted file mode 100644 index 5f928448..00000000 --- a/pr-preview/pr-63/_modules/jobs/int2lm.html +++ /dev/null @@ -1,336 +0,0 @@ - - - - - - jobs.int2lm — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.int2lm

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-import shutil
-import pytz
-
-from datetime import datetime
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Setup the namelist for int2lm and submit the job to the queue.
-
-    Necessary for both COSMO and COSMOART simulations.
-
-    Decide if the soil model should be TERRA or TERRA multi-layer depending on
-    `startdate` of the simulation.
-
-    Create necessary directory structure to run int2lm (run and output
-    directories, defined in ``cfg.int2lm`` and ``cfg.int2lm['output']``).
-
-    Copy the int2lm-executable from ``cfg.int2lm['binary_file']`` to 
-    ``cfg.int2lm['work']/int2lm``.
-
-    Copy the extpar-file ``cfg.int2lm['extpar_file']`` to
-    ``cfg.int2lm_run/work``.
-
-    COSMOART: Copy the ``libgrib_api`` files to
-    ``cfg.int2lm['work']/libgrib_api``.
-
-    COSMO: Convert the tracer-csv-files into an int2lm-namelist file.
-
-    Format the int2lm-namelist-template using the information in ``cfg``.
-
-    Format the runscript-template and submit the job.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-
-    # Total number of processes
-    np_tot = cfg.int2lm['np_x'] * cfg.int2lm['np_y']
-
-    # Set folder names
-    int2lm_run = os.path.join(cfg.int2lm_run)
-    int2lm_output = os.path.join(cfg.int2lm_output)
-
-    # Create int2lm directories
-    tools.create_dir(int2lm_run, "int2lm_run")
-    tools.create_dir(int2lm_output, "int2lm_output")
-
-    tools.copy_file(cfg.int2lm['binary_file'],
-                    os.path.join(int2lm_run, "int2lm"))
-
-    # Copy extpar file to input/extpar directory
-    extpar_dir = os.path.join(cfg.int2lm_input, "extpar")
-    tools.create_dir(extpar_dir, "int2lm extpar")
-    tools.copy_file(
-        os.path.join(cfg.int2lm['extpar_dir'], cfg.int2lm['extpar_filename']),
-        extpar_dir)
-
-    # Copy landuse and plant-functional-type files
-    if hasattr(cfg, 'photo_rate'):
-        lu_file_src = cfg.int2lm['lu_file']
-        lu_file_dst = os.path.join(extpar_dir, 'landuse.nc')
-        tools.copy_file(lu_file_src, lu_file_dst)
-
-        pft_file_src = cfg.int2lm['pft_file']
-        pft_file_dst = os.path.join(extpar_dir, 'pft.nc')
-        tools.copy_file(pft_file_src, pft_file_dst)
-
-        # Copy libgrib_api
-        dest = os.path.join(cfg.int2lm['work'], 'libgrib_api')
-        try:
-            # delete so no error when forcing this job
-            shutil.rmtree(dest)
-        except FileNotFoundError:
-            pass
-        try:
-            shutil.copytree(src=cfg.int2lm['libgrib_dir'],
-                            dst=dest,
-                            symlinks=True)
-        except FileNotFoundError:
-            logging.error("libgrib_api directory not found")
-            raise
-        except (PermissionError, OSError):
-            logging.error("Copying libgrib_api failed")
-            raise
-
-    # Write INPUT_ART from csv file if present
-    tracer_csvfile = os.path.join(cfg.chain_src_dir, 'cases', cfg.casename,
-                                  'int2lm_tracers.csv')
-    if os.path.isfile(tracer_csvfile):
-        datasets_csvfile = os.path.join(cfg.chain_src_dir, 'cases',
-                                        cfg.casename, 'int2lm_datasets.csv')
-        input_art_filename = os.path.join(int2lm_run, 'INPUT_ART')
-
-        tools.write_int2lm_input_art.main(tracer_csvfile, datasets_csvfile,
-                                          input_art_filename)
-
-    # Change of soil model from TERRA to TERRA multi-layer on 2 Aug 2007
-    if cfg.startdate_sim < datetime(2007, 8, 2, tzinfo=pytz.UTC):
-        multi_layer = ".FALSE."
-    else:
-        multi_layer = ".TRUE."
-
-    # Prepare namelist
-    with open(os.path.join(cfg.case_path,
-                           cfg.int2lm['namelist_filename'])) as input_file:
-        int2lm_namelist = input_file.read()
-
-    # Int2lm processing always starts at hstart=0, thus modifying inidate
-    hstart_int2lm = 0
-    hstop_int2lm = cfg.forecasttime
-
-    output_file = os.path.join(int2lm_run, "INPUT")
-    with open(output_file, "w") as outf:
-        outf.write(
-            int2lm_namelist.format(
-                cfg=cfg,
-                **cfg.int2lm,
-                hstart_int2lm=hstart_int2lm,
-                hstop_int2lm=hstop_int2lm,
-                multi_layer=multi_layer,
-                meteo_prefix=cfg.meteo['prefix'],
-            ))
-
-    # Prepare runscript
-    with open(os.path.join(cfg.case_path,
-                           cfg.int2lm['runjob_filename'])) as input_file:
-        int2lm_runscript = input_file.read()
-
-    script = (cfg.int2lm_run / 'run_int2lm.job')
-    with open(script, "w") as outf:
-        outf.write(
-            int2lm_runscript.format(cfg=cfg,
-                                    **cfg.int2lm,
-                                    int2lm_run=int2lm_run,
-                                    ini_day=cfg.startdate_sim_yyyymmddhh[0:8],
-                                    ini_hour=cfg.startdate_sim_yyyymmddhh[8:],
-                                    np_tot=np_tot,
-                                    hstop_int2lm=hstop_int2lm,
-                                    logfile=cfg.logfile,
-                                    logfile_finish=cfg.logfile_finish))
-
-    # Submit job
-    cfg.submit('int2lm', script)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/obs_nudging.html b/pr-preview/pr-63/_modules/jobs/obs_nudging.html deleted file mode 100644 index 460e5781..00000000 --- a/pr-preview/pr-63/_modules/jobs/obs_nudging.html +++ /dev/null @@ -1,241 +0,0 @@ - - - - - - jobs.obs_nudging — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.obs_nudging

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-
-from datetime import timedelta
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Copy and rename the obs_nudging files to the **COSMO** input directory.
-
-    In the folder ``cfg.obs_nudging_dir``, the files are saved in the format
-    ``{prefix}-YYYYMMDD000000-YYYYMMDD000000``. **COSMO** expects files in the 
-    format ``{prefix}x``, where ``x`` is ``[nothing], .2, .3, .4, ...``. This 
-    job handles this filename-change and copies them to the **COSMO** input 
-    folder on scratch (``cfg.cosmo_input/obs_nudging``).
-
-    Missing observation files are ignored.
-
-    Also copies the blacklist-file blklsttmp.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    dest_dir = os.path.join(cfg.cosmo_input, "obs_nudging")
-    tools.create_dir(dest_dir, "obs nudging input")
-
-    logging.info("Copying obs_nudging files from {} to {}".format(
-        cfg.obs_nudging_dir, dest_dir))
-
-    for i, t in enumerate(
-            tools.iter_hours(cfg.startdate_sim, cfg.enddate_sim, step=24)):
-        i += 1
-        for prefix in cfg.obs_nudging_prefixes:
-            src_filename = (
-                prefix + t.strftime(cfg.obs_nudging_date_format) +
-                (t + timedelta(days=1)).strftime(cfg.obs_nudging_date_format))
-            src_path = os.path.join(cfg.obs_nudging_dir, src_filename)
-            if i == 1:
-                dest_path = os.path.join(dest_dir, prefix)
-            else:
-                dest_path = os.path.join(dest_dir, "{}.{}".format(prefix, i))
-
-            try:
-                tools.copy_file(src_path, dest_path)
-            except BlockingIOError:
-                continue
-            logging.info("Copied file {} to {}".format(src_filename,
-                                                       dest_path))
-
-    tools.copy_file(os.path.join(cfg.obs_nudging_dir, 'blklsttmp'), dest_dir)
-
-    logging.info("Copied blacklist-file to {}".format(dest_dir))

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/octe.html b/pr-preview/pr-63/_modules/jobs/octe.html deleted file mode 100644 index e52d55f2..00000000 --- a/pr-preview/pr-63/_modules/jobs/octe.html +++ /dev/null @@ -1,373 +0,0 @@ - - - - - - jobs.octe — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.octe

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-
-import numpy as np
-
-from os import scandir
-from os.path import join, basename
-from netCDF4 import Dataset
-
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-def create_dir_and_copy_input(dest_dir, lambdas_src, maps_src):
-    """Create a directory at dest_dir (**COSMO** input) and copy src there.
-
-    lambdas_src -> dest_dir/lambdas.nc
-    maps_src   -> dest_dir/maps.nc
-
-    Parameters
-    ----------
-    dest_dir : str
-    lambdas_src : str
-    maps_src : str
-    """
-    tools.create_dir(dest_dir, "input data for OCTE")
-    tools.copy_file(lambdas_src, join(dest_dir, 'lambdas.nc'))
-    tools.copy_file(maps_src, join(dest_dir, 'maps.nc'))
-
-
-def read_lambdas(nc_dataset):
-    """Read the lambda values from the nc_dataset.
-
-    The relevant lambda values are the last ones along the
-    dimension ~nparam~. They are returned in a list of length
-    ~nensembles~.
-
-    Parameters
-    ----------
-    nc_dataset : netCDF4.Dataset
-        Contains a variable called ~lambda~ with dimensions,
-        ~(nensembles, nparam)~
-
-    Returns
-    -------
-    list(float)
-    """
-    lambda_var = nc_dataset['lambda']
-    assert len(lambda_var.dimensions) == 2, (
-        "Number of dimensions of 'lambda' variable doesn't match")
-    # this would not be a problem in python, but COSMO breaks if
-    # this doesn't hold:
-    assert lambda_var.dimensions[1] == 'nparam', (
-        "Dimension ordering of 'lambda' variable incorrect")
-
-    return list(lambda_var[:, -1])
-
-
-def perturb_bg_in_dataset(nc_dataset, lambdas):
-    """Create BG fields from lambdas in nc_dataset.
-
-    Perturb the background CO2 field in nc_dataset based on lambda values in
-    lambdas.
-    The pertubation is just a global scaling of the field by one
-    of the lambda values. For each ensemble member (=each lambda), a new
-    variable is created.
-
-    The perturbed fields are created by multiplying the values of
-    a variable called ~CO2_BG~ with one of the lambda-values. The new
-    field is stored in a newly created variable called ~CO2_BGnnn~,
-    where ~nnn~ runs from ~001~ to ~{nensembles:03d}~.
-
-    If there is no variable ~CO2_BG~ in nc_dataset, do nothing.
-
-    Parameters
-    ----------
-    nc_dataset : netCDF4.Dataset
-        If this doesn't contain a variable ~CO2_BG~, do nothing. If it does,
-        create a new variable for each lambda value with the original field
-        scaled.
-    lambdas : list(float)
-        For each value in the list, create an ensemble member
-    """
-    basevar_name = 'CO2_BG'
-    filename = basename(nc_dataset.filepath())
-
-    if basevar_name not in nc_dataset.variables:
-        logging.info("No BG in dataset {}, doing nothing".format(filename))
-        return
-
-    basevar = nc_dataset[basevar_name]
-
-    field = np.array(basevar[:])
-    dtype = basevar.datatype
-    dims = basevar.dimensions
-    attr_names = basevar.ncattrs()
-    try:
-        # Remove fill value from ncattrs because setting it after
-        # construction is not possible
-        attr_names.remove('_FillValue')
-        fill_value = basevar.getncattr('_FillValue')
-    except ValueError:
-        fill_value = None
-
-    attrs = dict((name, basevar.getncattr(name)) for name in attr_names)
-
-    for i, lambda_ in enumerate(lambdas):
-        name = basevar_name + '{:03d}'.format(i + 1)
-        var = nc_dataset.createVariable(varname=name,
-                                        datatype=dtype,
-                                        dimensions=dims,
-                                        fill_value=fill_value)
-        var[:] = field * lambda_
-        for attrname, attrval in attrs.items():
-            var.setncattr(name=attrname, value=attrval)
-
-    logging.info("Created BG ensemble in dataset {}".format(filename))
-
-
-def perturb_bgs_in_dir(lambdas_nc, directory):
-    """Create perturbed BG fields from read lambda values in all NetCDF-files
-    in the directory.
-
-    Perturb the background CO2 field in all the NetCDF-files
-    found in directory based on lambda values from lambdas_nc.
-    The pertubation is just a global scaling of the field by one
-    lambda value. For each ensemble, a new variable is created.
-
-    Lambda values and the number of ensembles are read from the file
-    lambdas_nc. The lambda-value for the BG is assumed to be the last
-    value along the ~nparam~-dimension of the ~lambda~-variable.
-
-    The perturbed fields are then created by multiplying the values of
-    a variable called ~CO2_BG~ with one of the lambda-values. The new
-    field is stored in a newly created variable called ~CO2_BGnnn~,
-    where ~nnn~ runs from ~001~ to ~{nensembles:03d}~
-
-    Parameters
-    ----------
-    lambdas_nc : str
-        Path to the file storing the lambda-values.
-        Contains a variable called ~lambda~ with dimensions,
-        ~(nensembles, nparam)~.
-    directory : str
-        Path to the output-dir of int2lm. Add perturbed BG-fields to all
-        netcdf-files there containing a variable called ~CO2_BG~.
-
-    """
-    with Dataset(lambdas_nc) as lambdas_file:
-        lambdas = read_lambdas(lambdas_file)
-
-    with scandir(directory) as dir_iterator:
-        for entry in dir_iterator:
-            if not entry.name.startswith('.') and entry.is_file():
-                try:
-                    with Dataset(entry.path, 'a') as nc_dataset:
-                        perturb_bg_in_dataset(nc_dataset, lambdas)
-                except OSError:
-                    logging.info("File {} is not a netCDF-file.".format(
-                        entry.name))
-
-
-
[docs]def main(cfg):
-    """Copy necessary input files for **COSMO** and perturb BG.
-
-    Copies the NetCDF-files found at ``cfg.octe_maps`` and ``cfg.octe_lambdas`` to
-    the **COSMO** input-directory.
-
-    Perturbs the background tracer field. To do that, it reads the lambda-value
-    from the ``cfg.octe_lambdas`` (last value along the nparam-dimension) and
-    scales the BG-field produced by int2lm, creating a new variable for each
-    ensemble.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    dest_dir = join(cfg.cosmo_input, 'octe')
-    create_dir_and_copy_input(dest_dir=dest_dir,
-                              lambdas_src=cfg.octe_lambdas,
-                              maps_src=cfg.octe_maps)
-    logging.info("Copied OCTE files {} and {} to {}".format(
-        cfg.octe_lambdas, cfg.octe_maps, dest_dir))
-
-    logging.info("Starting to create BG-ensembles in " + cfg.int2lm_output)
-    perturb_bgs_in_dir(cfg.octe_lambdas, cfg.int2lm_output)
-    logging.info("Finished creating BG-ensembles")

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/oem.html b/pr-preview/pr-63/_modules/jobs/oem.html deleted file mode 100644 index ae2d44b8..00000000 --- a/pr-preview/pr-63/_modules/jobs/oem.html +++ /dev/null @@ -1,268 +0,0 @@ - - - - - - jobs.oem — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.oem

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Copy emission and profile files to the **cosmo** or **icon** input
-    directory.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-
-    Raises
-    ------
-    RuntimeError
-        If an error occurs during the process.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-
-    oem_dir = cfg.oem['dir']
-    oem_gridded_emissions_nc = os.path.join(oem_dir,
-                                            cfg.oem['gridded_emissions_nc'])
-    oem_vertical_profiles_nc = os.path.join(oem_dir,
-                                            cfg.oem['vertical_profiles_nc'])
-
-    # Temporal profiles can be given as hourofday, dayofweek, monthofyear
-    # AND/OR as hourofyear. We copy all files indicated in cfg, but make
-    # sure at least one type is present
-    hod_tps = True
-    hoy_tps = True
-    try:
-        oem_hourofday_nc = os.path.join(oem_dir, cfg.oem['hourofday_nc'])
-        oem_dayofweek_nc = os.path.join(oem_dir, cfg.oem['dayofweek_nc'])
-        oem_monthofyear_nc = os.path.join(oem_dir, cfg.oem['monthofyear_nc'])
-    except AttributeError:
-        hod_tps = False
-    try:
-        oem_hourofyear_nc = os.path.join(oem_dir, cfg.oem['hourofyear_nc'])
-    except AttributeError:
-        hoy_tps = False
-
-    if not (hod_tps or hoy_tps):
-        raise RuntimeError("At least one of (hod/dow/moy) or (hoy) netcdfs "
-                           " have to be given for online emissions")
-
-    if hasattr(cfg, 'icon'):
-        input_dir = cfg.icon_input
-    elif hasattr(cfg, 'cosmo'):
-        input_dir = cfg.cosmo_input
-    dest_dir = os.path.join(input_dir, "oem")
-    tools.create_dir(dest_dir, "online emissions input")
-
-    logging.info("Copying oem files from {} to {}".format(oem_dir, dest_dir))
-
-    if hod_tps:
-        tools.copy_file(
-            oem_gridded_emissions_nc,
-            os.path.join(dest_dir, cfg.oem['gridded_emissions_nc']))
-        tools.copy_file(
-            oem_vertical_profiles_nc,
-            os.path.join(dest_dir, cfg.oem['vertical_profiles_nc']))
-        tools.copy_file(oem_hourofday_nc,
-                        os.path.join(dest_dir, cfg.oem['hourofday_nc']))
-        tools.copy_file(oem_dayofweek_nc,
-                        os.path.join(dest_dir, cfg.oem['dayofweek_nc']))
-        tools.copy_file(oem_monthofyear_nc,
-                        os.path.join(dest_dir, cfg.oem['monthofyear_nc']))
-    if hoy_tps:
-        tools.copy_file(oem_hourofyear_nc,
-                        os.path.join(dest_dir, cfg.oem['hourofyear_nc']))
-
-    # Additional files for ICON simulations
-    if cfg.oem.get('ens_reg_nc') is not None:
-        tools.copy_file(os.path.join(oem_dir, cfg.oem['ens_reg_nc']),
-                        os.path.join(dest_dir, cfg.oem['ens_reg_nc']))
-    if cfg.oem.get('oem_ens_lambda_nc') is not None:
-        tools.copy_file(os.path.join(oem_dir, cfg.oem['ens_lambda_nc']),
-                        os.path.join(dest_dir, cfg.oem['ens_lambda_nc']))

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/online_vprm.html b/pr-preview/pr-63/_modules/jobs/online_vprm.html deleted file mode 100644 index 9c4ad219..00000000 --- a/pr-preview/pr-63/_modules/jobs/online_vprm.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - jobs.online_vprm — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.online_vprm

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Copy MODIS surface reflectance data and vegetation class fraction file
-    to the **cosmo** input directory.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-    dest_modis = 'modis.nc'
-    dest_vegetation = 'vegetation.nc'
-
-    src_dir = cfg.online_vprm['dir']
-    dest_dir = os.path.join(cfg.cosmo_input, "vprm")
-    tools.create_dir(dest_dir, "input data for vprm")
-
-    modis_data_nc = os.path.join(src_dir, cfg.online_vprm['modis_filename'])
-    logging.info("Copying MODIS file from {} to {}".format(src_dir, dest_dir))
-    tools.copy_file(modis_data_nc, os.path.join(dest_dir, dest_modis))
-
-    vegetation_data_nc = os.path.join(src_dir,
-                                      cfg.online_vprm['vegetation_filename'])
-    logging.info("Copying vegetation class fraction file from {} to {}".format(
-        src_dir, dest_dir))
-    tools.copy_file(vegetation_data_nc, os.path.join(dest_dir,
-                                                     dest_vegetation))

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/photo_rate.html b/pr-preview/pr-63/_modules/jobs/photo_rate.html deleted file mode 100644 index cdf545f4..00000000 --- a/pr-preview/pr-63/_modules/jobs/photo_rate.html +++ /dev/null @@ -1,220 +0,0 @@ - - - - - - jobs.photo_rate — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.photo_rate

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Copy photolysis-rate file to the **COSMOART** input directory.
-
-    Only necessary for **COSMOART** simulations.
-
-    Copy the photolysis-rate file from the project (`cfg.photo_rate_file`) to
-    the **COSMOART** input folder on scratch (`cfg.cosmo_input/art_photolysis`).
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-
-    logging.info("Copying photolysis-rate file from {} to {}".format(
-        cfg.photo_rate_file,
-        os.path.join(cfg.cosmo_input, "art_photolysis", "papa_data.p")))
-
-    tools.create_dir(os.path.join(cfg.cosmo_input, "art_photolysis"),
-                     "photolysis rate input")
-
-    src_file = cfg.photo_rate_file
-    dest_path = os.path.join(cfg.cosmo_input, 'art_photolysis', 'papa_data.d')
-
-    tools.copy_file(src_file, dest_path)
-
-    logging.info("Finished")

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/post_cosmo.html b/pr-preview/pr-63/_modules/jobs/post_cosmo.html deleted file mode 100644 index a8446134..00000000 --- a/pr-preview/pr-63/_modules/jobs/post_cosmo.html +++ /dev/null @@ -1,306 +0,0 @@ - - - - - - jobs.post_cosmo — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.post_cosmo

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import os
-import datetime
-
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-def logfile_header_template():
-    """Returns a template for the logfile-header"""
-    return ("\n=====================================================\n"
-            "============== POST PROCESSING {}\n"
-            "============== {}\n"
-            "=====================================================\n\n")
-
-
-def runscript_header_template():
-    """Returns a template for the runscript-header (#SBATCH-directives)"""
-    return '\n'.join([
-        "#SBATCH --job-name=post_cosmo", "#SBATCH --partition=xfer",
-        "#SBATCH --constraint={constraint}",
-        "#SBATCH --account={compute_account}", "#SBATCH --output={logfile}",
-        "#SBATCH --open-mode=append", "#SBATCH --chdir={cosmo_run}",
-        "#SBATCH --time=00:30:00", "", ""
-    ])
-
-
-def runscript_commands_template():
-    """Return a template for the commands in the runscript.
-
-    To ensure the bash-commands have the intended behaviour, make sure to strip
-    trailing slashes from the directory names (they are added as needed in the
-    template).
-    """
-    commands = list()
-
-    return '\n'.join([
-        "srun cp -Rafv {int2lm_run_src}/. {int2lm_run_dest}/",
-        "srun cp -Rafv {cosmo_run_src}/. {cosmo_run_dest}/",
-        "srun cp -Rafv {cosmo_output_src}/. {cosmo_output_dest}/",
-        "srun cp -Rafv {logs_src}/. {logs_dest}/", "unset SLURM_MEM_PER_CPU"
-    ])
-
-
-
[docs]def main(cfg):
-    """Copy the output of a **COSMO**-run to a user-defined position.
-
-    Write a runscript to copy all files (**COSMO** settings & output,
-    **int2lm** settings, logfiles) from ``cfg.cosmo_run``,
-    ``cfg.cosmo_output``, ``cfg.int2lm_run``, ``cfg.log_finished_dir`` to
-    ``cfg.output_root/...``.
-    If the job ``reduce_output`` has been run before ``post_cosmo``, a 
-    directory ``cfg.cosmo_output_reduced`` is created. In this case,
-    ``cfg.cosmo_output_reduced`` is copied instead of ``cfg.cosmo_output``.
-    
-    Submit the job to the xfer-queue.
-    
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    tools.change_logfile(cfg.logfile)
-    prepare_cosmo.set_cfg_variables(cfg)
-
-    copy_path = os.path.join(
-        cfg.post_cosmo['output_root'],
-        cfg.startdate_sim_yyyymmddhh + "_" + cfg.enddate_sim_yyyymmddhh)
-
-    logging.info(logfile_header_template().format(
-        "STARTS", str(datetime.datetime.today())))
-
-    # Prepare the runscript
-    runscript_content = "#!/bin/bash\n"
-    runscript_content += runscript_header_template().format(
-        compute_account=cfg.compute_account,
-        logfile=cfg.logfile,
-        constraint=cfg.constraint,
-        cosmo_run=cfg.cosmo_run)
-
-    if os.path.isdir(cfg.cosmo_output_reduced):
-        cosmo_output_src = str(cfg.cosmo_output_reduced).rstrip('/')
-        cosmo_output_dest = os.path.join(copy_path,
-                                         "cosmo_output_reduced").rstrip('/')
-    else:
-        cosmo_output_src = str(cfg.cosmo_output).rstrip('/')
-        cosmo_output_dest = os.path.join(copy_path, "cosmo_output").rstrip('/')
-
-    # Create new directories
-    os.makedirs(os.path.join(copy_path, "int2lm_run"), exist_ok=True)
-    os.makedirs(os.path.join(copy_path, "cosmo_run"), exist_ok=True)
-    os.makedirs(cosmo_output_dest, exist_ok=True)
-    os.makedirs(os.path.join(copy_path, "logs"), exist_ok=True)
-
-    int2lm_run_path = os.path.abspath(os.path.join(copy_path, "int2lm_run"))
-    cosmo_run_path = os.path.abspath(os.path.join(copy_path, "cosmo_run"))
-    cosmo_output_dest_path = os.path.abspath(cosmo_output_dest)
-    logs_path = os.path.abspath(os.path.join(copy_path, "logs"))
-
-    # Format the runscript
-    runscript_content += runscript_commands_template().format(
-        target_dir=copy_path.rstrip('/'),
-        int2lm_run_src=str(cfg.int2lm_run).rstrip('/'),
-        int2lm_run_dest=int2lm_run_path.rstrip('/'),
-        cosmo_run_src=str(cfg.cosmo_run).rstrip('/'),
-        cosmo_run_dest=cosmo_run_path.rstrip('/'),
-        cosmo_output_src=cosmo_output_src,
-        cosmo_output_dest=cosmo_output_dest_path,
-        logs_src=str(cfg.log_finished_dir).rstrip('/'),
-        logs_dest=logs_path.rstrip('/'))
-
-    os.makedirs(cfg.cosmo_run, exist_ok=True)
-    script = (cfg.cosmo_run / 'run_post_cosmo.job')
-    with open(script, "w") as outf:
-        outf.write(runscript_content)
-
-    logging.info("Submitting the copy job to the xfer queue")
-    logging.info("Make sure you have the module 'xalt' unloaded!")
-
-    # Submit job
-    cfg.submit('post_cosmo', script)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/post_int2lm.html b/pr-preview/pr-63/_modules/jobs/post_int2lm.html deleted file mode 100644 index a7ac48ca..00000000 --- a/pr-preview/pr-63/_modules/jobs/post_int2lm.html +++ /dev/null @@ -1,338 +0,0 @@ - - - - - - jobs.post_int2lm — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.post_int2lm

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import os
-import glob
-import netCDF4 as nc
-
-from datetime import datetime, timedelta
-from . import tools, prepare_cosmo
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """Combine multiple **int2lm** tracer-output files into a single one for
-    **COSMO**.
-
-    Only necessary for **COSMO** simulations.
-
-    **int2lm** puts tracers into different netCDF files. Combine the files
-    specified in ``cfg.post_int2lm_species`` into a single netCDF file for
-    **COSMO**.
-
-    If ``cfg.spinup`` and ``cfg.post_int2lm_species_spinup`` are present,
-    also read in the specified variables and take them as an input for 
-    **COSMO**.
-    
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-    prepare_cosmo.set_cfg_variables(cfg)
-    tools.change_logfile(cfg.logfile)
-
-    # Int2lm processing always starts at hstart=0, thus modifying inidate
-    inidate_int2lm_yyyymmddhh = cfg.startdate_sim_yyyymmddhh
-
-    chem_list = cfg.post_int2lm['species']
-
-    date = datetime.today()
-
-    to_print = """POST_INT2LM
-
-=====================================================
-============== POST PROCESSING BEGINS ===============
-============== StartTime: %s 
-=====================================================""" % date.strftime('%s')
-
-    logging.info(to_print)
-
-    logging.info(
-        'BOUNDARY CONDITIONS: Adding tracers from lbfd*t.nc files to regular int2lm files.'
-    )
-    # Add background tracers in all 'lbfd**t.nc' files to
-    # normal lbfd files, because CAMS tracers are only every 3 hours.
-    # We add it 4 times to hour-1, hour+0, hour+1 and hour+2
-    for f in sorted(glob.glob(os.path.join(cfg.int2lm_output, 'lbfd*t.nc'))):
-        logging.info(f'Reading tracer file {f}')
-        yyyymmddhh_str = os.path.basename(f)[4:-4]
-        yyyymmddhh = datetime.strptime(yyyymmddhh_str, '%Y%m%d%H')
-        yyyymmddhh_prev = yyyymmddhh - timedelta(hours=1)
-        yyyymmddhh_next2 = yyyymmddhh + timedelta(hours=2)
-
-        for hour in tools.iter_hours(yyyymmddhh_prev, yyyymmddhh_next2, 1):
-            outfile = os.path.join(cfg.int2lm_output,
-                                   hour.strftime('lbfd%Y%m%d%H' + '.nc'))
-            if os.path.exists(outfile):
-                with nc.Dataset(outfile, 'a') as outf, nc.Dataset(f) as inf:
-                    for chem in chem_list:
-                        try:
-                            outf.createVariable(chem, inf[chem].dtype,
-                                                inf[chem].dimensions)
-                            for attr in inf[chem].ncattrs():
-                                outf[chem].setncattr(attr,
-                                                     inf[chem].getncattr(attr))
-                            logging.info(f'Variable {chem} added to {outfile}')
-                        except RuntimeError:
-                            logging.warning(
-                                'Variable {} already present in {}'.format(
-                                    chem, outfile))
-                        outf[chem][:] = inf[chem][:]
-    logging.info("OK")
-
-    # Meteo spinup simulation with tracer recycling
-    if hasattr(cfg, 'spinup') and \
-    cfg.post_int2lm.get('species_spinup') is not None and not cfg.first_one:
-        var_list = cfg.post_int2lm['species_spinup']
-        logging.info(
-            'INITIAL CONDITIONS (RECYCLING): Adding tracers %s from last COSMO run (%s) to regular int2lm files.'
-            % (str(var_list), cfg.last_cosmo_output))
-
-        infile_name = 'lffd' + cfg.startdate_sim_yyyymmddhh + '*.nc'
-        infile_paths = sorted(
-            glob.glob(os.path.join(cfg.last_cosmo_output, infile_name)))
-        outfile_name = 'laf' + inidate_int2lm_yyyymmddhh + '.nc'
-        outfile_path = os.path.join(cfg.int2lm_output, outfile_name)
-
-        for infile_path in infile_paths:
-            with nc.Dataset(infile_path) as inf, nc.Dataset(outfile_path,
-                                                            'a') as outf:
-                for var in var_list:
-                    if var in inf.variables.keys():
-                        if var in outf.variables.keys():
-                            logging.warning(
-                                'Recycling: Variable {} already present in {}'.
-                                format(var, outfile_path))
-                        else:
-                            outf.createVariable(varname=var,
-                                                datatype=inf[var].dtype,
-                                                dimensions=inf[var].dimensions)
-                            logging.info('Recycled variable ' + var +
-                                         ' from ' + infile_path)
-                            logging.info('into ' + outfile_path)
-                        outf[var][:] = inf[var][:]
-                        for attr in inf[var].ncattrs():
-                            outf[var].setncattr(attr, inf[var].getncattr(attr))
-    # Normal run
-    else:
-        logging.info(
-            'INITIAL CONDITIONS: Adding tracers from laf*t.nc files to regular int2lm files.'
-        )
-        infile = os.path.join(cfg.int2lm_output,
-                              "laf" + inidate_int2lm_yyyymmddhh + "t.nc")
-        if os.path.exists(infile):
-            outfile = infile[:-4] + ".nc"
-            try:
-                with nc.Dataset(infile) as inf, nc.Dataset(outfile,
-                                                           "a") as outf:
-                    for chem in chem_list:
-                        if chem in outf.variables.keys():
-                            logging.warning(
-                                'Variable %s already present in file %s' %
-                                (chem, outfile))
-                        else:
-                            outf.createVariable(chem, inf[chem].dtype,
-                                                inf[chem].dimensions)
-                            outf[chem][:] = inf[chem][:]
-                            for attr in inf[chem].ncattrs():
-                                outf[chem].setncattr(attr,
-                                                     inf[chem].getncattr(attr))
-                            logging.info(
-                                'Variable %s added as initial condition.' %
-                                chem)
-            except:
-                logging.error(
-                    'Appending tracers %s from file %s to file %s failed.' %
-                    (str(chem_list), infile, outfile))
-
-    date = datetime.today()
-    to_print = """=====================================================
-============== POST PROCESSING ENDS ==================
-============== EndTime: %s
-=====================================================""" % date.strftime('%s')
-
-    logging.info(to_print)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/prepare_cosmo.html b/pr-preview/pr-63/_modules/jobs/prepare_cosmo.html deleted file mode 100644 index 919a758e..00000000 --- a/pr-preview/pr-63/_modules/jobs/prepare_cosmo.html +++ /dev/null @@ -1,428 +0,0 @@ - - - - - - jobs.prepare_cosmo — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.prepare_cosmo

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from pathlib import Path
-import logging
-import csv
-import os
-from datetime import timedelta
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-def set_cfg_variables(cfg):
-    cfg.int2lm_root = cfg.chain_root / 'int2lm'
-    cfg.int2lm_input = cfg.int2lm_root / 'input'
-    cfg.int2lm_run = cfg.chain_root / 'int2lm' / 'run'
-    cfg.int2lm_output = cfg.chain_root / 'int2lm' / 'output'
-
-    cfg.cosmo_base = cfg.chain_root / 'cosmo'
-    cfg.cosmo_input = cfg.chain_root / 'cosmo' / 'input'
-    cfg.cosmo_run = cfg.chain_root / 'cosmo' / 'run'
-    cfg.cosmo_output = cfg.chain_root / 'cosmo' / 'output'
-    cfg.cosmo_output_reduced = cfg.chain_root / 'cosmo' / 'output_reduced'
-
-    # Number of tracers
-    if 'tracers' in cfg.workflow['features']:
-        tracer_csvfile = cfg.chain_src_dir / 'cases' / cfg.casename / 'cosmo_tracers.csv'
-        if tracer_csvfile.is_file():
-            with open(tracer_csvfile, 'r') as csv_file:
-                reader = csv.DictReader(csv_file, delimiter=',')
-                reader = [r for r in reader if r[''] != '#']
-                cfg.in_tracers = len(reader)
-        else:
-            raise FileNotFoundError(f"File not found: {tracer_csvfile}")
-
-        # tracer_start namelist parameter for spinup simulation
-        if hasattr(cfg, 'spinup'):
-            if cfg.first_one:
-                cfg.tracer_start = 0
-            else:
-                cfg.tracer_start = cfg.spinup
-        else:
-            cfg.tracer_start = 0
-
-    # asynchronous I/O
-    if hasattr(cfg, 'cfg.cosmo_np_io'):
-        if cfg.cosmo_np_io == 0:
-            cfg.lasync_io = '.FALSE.'
-            cfg.num_iope_percomm = 0
-        else:
-            cfg.lasync_io = '.TRUE.'
-            cfg.num_iope_percomm = 1
-
-    # If nested run: use output of mother-simulation
-    if 'nesting' in cfg.workflow['features'] and not os.path.isdir(
-            cfg.meteo.dir):
-        # if ifs_hres_dir doesn't point to a directory,
-        # it is the name of the mother run
-        mother_name = cfg.meteo.dir
-        cfg.meteo.dir = cfg.work_root / mother_name / cfg.chunk_id / 'cosmo' / 'output'
-        cfg.meteo.inc = 1
-        cfg.meteo.prefix = 'lffd'
-
-
-
[docs]def main(cfg):
-    """
-    **COSMO Data Preparation**
-
-    This function prepares input data for COSMO simulations by creating necessary directories,
-    copying meteorological files, and handling specific data processing.
-
-    - Copy meteorological files to **int2lm** input.
-    - Create the necessary directory ``cfg.int2lm_input/meteo``.
-    - Copy meteorological files from the project directory (``cfg.meteo['dir']/cfg.meteo['prefix']YYYYMMDDHH``)
-      to the int2lm input folder on scratch (``cfg.int2lm_input/meteo``).
-    - For nested runs (meteorological files are COSMO output: ``cfg.meteo['prefix'] == 'lffd'``),
-      also copy the ``*c.nc``-file with constant parameters.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-
-    Raises
-    ------
-    RuntimeError
-        If any subprocess returns a non-zero exit code during execution.
-    """
-    set_cfg_variables(cfg)
-    tools.change_logfile(cfg.logfile)
-
-    logging.info('COSMO analysis data for IC/BC')
-
-    dest_path = cfg.int2lm_input / 'meteo'
-    tools.create_dir(dest_path, "meteo input")
-
-    source_nameformat = cfg.meteo['nameformat']
-    if cfg.meteo['prefix'] == 'lffd':
-        # nested runs use cosmoart-output as meteo data
-        # have to copy the *c.nc-file
-        src_file = (cfg.meteo['dir'] /
-                    cfg.startdate_sim.strftime(source_nameformat + 'c.nc'))
-
-        tools.copy_file(src_file, dest_path, output_log=True)
-
-        logging.info("Copied constant-param file from {} to {}".format(
-            src_file, dest_path))
-
-        # extend nameformat with ending to match cosmo-output
-        source_nameformat += '.nc'
-
-    if cfg.meteo['prefix'] == 'efsf':
-        source_nameformat = cfg.meteo['prefix'] + '%y%m%d%H'
-
-    num_steps = 0
-    meteo_dir = cfg.meteo['dir']
-    subdir = meteo_dir / cfg.startdate_sim.strftime('%y%m%d%H')
-    for time in tools.iter_hours(cfg.startdate_sim, cfg.enddate_sim,
-                                 cfg.meteo['inc']):
-        dest_path = cfg.int2lm_input / 'meteo'
-        src_file = meteo_dir / time.strftime(source_nameformat)
-
-        if cfg.meteo['prefix'] == 'efsf':
-            if time == cfg.startdate_sim:
-                src_file = subdir / ('eas' + time.strftime('%Y%m%d%H'))
-                if not src_file.exists() and cfg.meteo.get('dir_alt') \
-                    is not None:
-                    meteo_dir = cfg.meteo['dir_alt']
-                    subdir = meteo_dir / cfg.startdate_sim.strftime('%y%m%d%H')
-                    src_file = subdir / ('eas' + time.strftime('%Y%m%d%H'))
-                dest_path = cfg.int2lm_input / 'meteo' / (cfg.meteo['prefix'] +
-                                                          '00000000')
-            else:
-                td = time - cfg.startdate_sim - timedelta(hours=6 * num_steps)
-                days = str(td.days).zfill(2)
-                hours = str(td.seconds // 3600).zfill(2)
-                td_total = time - cfg.startdate_sim
-                days_total = str(td_total.days).zfill(2)
-                hours_total = str(td_total.seconds // 3600).zfill(2)
-
-                src_file = subdir / (cfg.meteo['prefix'] + days + hours +
-                                     '0000')
-                dest_path = cfg.int2lm_input / 'meteo' / (
-                    cfg.meteo['prefix'] + days_total + hours_total + '0000')
-
-                # Next time, change directory
-                checkdir = meteo_dir / time.strftime('%y%m%d%H')
-                if checkdir.is_dir():
-                    num_steps += 1
-                    subdir = checkdir
-                elif cfg.meteo.get('dir_alt') is not None:
-                    checkdir = cfg.meteo['dir_alt'] / time.strftime('%y%m%d%H')
-                    if checkdir.is_dir():
-                        num_steps += 1
-                        subdir = checkdir
-                        meteo_dir = cfg.meteo['dir_alt']
-                        logging.info(
-                            "Switching to other input directory from {} to {}".
-                            format(cfg.meteo['dir'], cfg.meteo['dir_alt']))
-        elif not src_file.exists():
-            # special case for MeteoSwiss COSMO-7 data
-            archive = Path('/store/mch/msopr/owm/COSMO-7')
-            yy = time.strftime("%y")
-            path = archive / 'ANA' + yy
-            src_file = path / time.strftime(source_nameformat)
-
-        # copy meteo file from project folder to
-        tools.copy_file(src_file, dest_path, output_log=True)
-
-        logging.info("Copied file from {} to {}".format(src_file, dest_path))
-
-    # Other IC/BC data
-    inv_to_process = []
-    if hasattr(cfg, 'cams'):
-        try:
-            CAMS = dict(fullname="CAMS",
-                        nickname="cams",
-                        executable="cams4int2cosmo",
-                        indir=cfg.cams['dir_orig'],
-                        outdir=cfg.cams['dir_proc'],
-                        param=[{
-                            'inc': cfg.cams['inc'],
-                            'suffix': cfg.cams['suffix']
-                        }])
-            inv_to_process.append(CAMS)
-        except AttributeError:
-            pass
-        try:
-            CT = dict(fullname="CarbonTracker",
-                      nickname="ct",
-                      executable="ctnoaa4int2cosmo",
-                      indir=cfg.ct_dir_orig,
-                      outdir=cfg.ct_dir_proc,
-                      param=cfg.ct_parameters)
-            inv_to_process.append(CT)
-        except AttributeError:
-            pass
-    elif hasattr(cfg, 'mozart'):
-        try:
-            MOZART = dict(fullname='MOZART',
-                          nickname='mozart',
-                          executable='mozart2int2lm',
-                          indir=cfg.mozart_file_orig,
-                          outdir=cfg.mozart_dir_proc,
-                          param=[{
-                              'inc': cfg.mozart_inc,
-                              'suffix': cfg.mozart_prefix
-                          }])
-            inv_to_process.append(MOZART)
-        except AttributeError:
-            pass
-
-    if inv_to_process:
-        logging.info("Processing " +
-                     ", ".join([i["fullname"]
-                                for i in inv_to_process]) + " data")
-
-        scratch_path = cfg.int2lm_input / 'icbc'
-        tools.create_dir(scratch_path, "icbc input")
-
-        for inv in inv_to_process:
-            logging.info(inv["fullname"] + " files")
-            tools.create_dir(inv["outdir"], "processed " + inv["fullname"])
-
-            for p in inv["param"]:
-                inc = p["inc"]
-                for time in tools.iter_hours(cfg.startdate_sim,
-                                             cfg.enddate_sim, inc):
-                    logging.info(time)
-
-                    filename = inv["outdir"] / (
-                        p["suffix"] + "_" + time.strftime("%Y%m%d%H") + ".nc")
-                    if not filename.exists():
-                        logging.info(filename)
-                        try:
-                            to_call = getattr(tools, inv["executable"])
-                            to_call.main(time, inv["indir"], inv["outdir"], p)
-                        except:
-                            logging.error("Preprocessing " + inv["fullname"] +
-                                          " data failed")
-                            raise
-
-                    # copy to (temporary) run input directory
-                    tools.copy_file(filename, scratch_path, output_log=True)
-
-                    logging.info("OK")

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/prepare_icon.html b/pr-preview/pr-63/_modules/jobs/prepare_icon.html deleted file mode 100644 index 8467a57d..00000000 --- a/pr-preview/pr-63/_modules/jobs/prepare_icon.html +++ /dev/null @@ -1,291 +0,0 @@ - - - - - - jobs.prepare_icon — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.prepare_icon

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from pathlib import Path
-import logging
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-def set_cfg_variables(cfg):
-    cfg.icon_base = cfg.chain_root / 'icon'
-    cfg.icon_input = cfg.icon_base / 'input'
-    cfg.icon_input_icbc = cfg.icon_input / 'icbc'
-    cfg.icon_work = cfg.icon_base / 'run'
-    cfg.icon_output = cfg.icon_base / 'output'
-    cfg.icon_output_reduced = cfg.icon_base / 'output_reduced'
-    cfg.icon_restart_out = cfg.icon_base / 'restart'
-    if cfg.chunk_id_prev:
-        cfg.icon_restart_in = cfg.chain_root_prev / 'icon' / 'run'
-        cfg.icon_input_icbc_prev = cfg.chain_root_prev / 'icon' / 'input' / 'icbc'
-
-    cfg.input_files_scratch = {}
-    for dsc, file in cfg.input_files.items():
-        cfg.input_files[dsc] = (p := Path(file))
-        cfg.input_files_scratch[dsc] = cfg.icon_input / p.name
-
-    cfg.create_vars_from_dicts()
-
-    cfg.ini_datetime_string = cfg.startdate.strftime('%Y-%m-%dT%H:00:00Z')
-    cfg.end_datetime_string = cfg.enddate.strftime('%Y-%m-%dT%H:00:00Z')
-
-    if cfg.lrestart == '.TRUE.':
-        cfg.restart_filename = 'restart_atm_DOM01.nc'
-        cfg.restart_file = cfg.icon_restart_in / cfg.restart_filename
-        cfg.restart_file_scratch = cfg.icon_work / cfg.restart_filename
-
-    # Nudge type (global or nothing)
-    cfg.nudge_type = 2 if hasattr(cfg,
-                                  'era5') and cfg.era5_global_nudging else 0
-    # Time step for global nudging in seconds
-    cfg.nudging_step_seconds = cfg.nudging_step * 3600 if hasattr(
-        cfg, 'nudging_step') else None
-    # Prescribed initial conditions for CH4, CO and/or OH
-    cfg.iart_init_gas = 4 if hasattr(
-        cfg, 'species_inicond') and cfg.species_inicond else 0
-
-    cfg.startdate_sim_yyyymmdd_hh = cfg.startdate_sim.strftime('%Y%m%d_%H')
-
-
-
[docs]def main(cfg):
-    """
-    **ICON Data Preparation**
-
-    This function prepares input data for ICON simulations by creating necessary directories,
-    copying meteorological files, and handling specific data processing.
-
-    - Create working directories and copy input files
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-
-    Raises
-    ------
-    RuntimeError
-        If any subprocess returns a non-zero exit code during execution.
-    """
-    set_cfg_variables(cfg)
-    tools.change_logfile(cfg.logfile)
-
-    # Create directories
-    tools.create_dir(cfg.icon_work, "icon_work")
-    tools.create_dir(cfg.icon_input_icbc, "icon_input_icbc")
-    tools.create_dir(cfg.icon_output, "icon_output")
-    tools.create_dir(cfg.icon_restart_out, "icon_restart_out")
-
-    logging.info('Copy ICON input data (IC/BC) to working directory')
-    # Copy input files to scratch
-    if cfg.machine == 'daint':
-        script_lines = [
-            '#!/usr/bin/env bash',
-            f'#SBATCH --job-name="copy_input_{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.enddate_sim_yyyymmddhh}"',
-            f'#SBATCH --account={cfg.compute_account}',
-            '#SBATCH --time=00:10:00',
-            f'#SBATCH --partition={cfg.compute_queue}',
-            f'#SBATCH --constraint={cfg.constraint}', '#SBATCH --nodes=1',
-            f'#SBATCH --output={cfg.logfile}', '#SBATCH --open-mode=append',
-            f'#SBATCH --chdir={cfg.icon_work}', ''
-        ]
-    elif cfg.machine == 'euler':
-        script_lines = [
-            '#!/usr/bin/env bash',
-            f'#SBATCH --job-name="copy_input_{cfg.casename}_{cfg.startdate_sim_yyyymmddhh}_{cfg.enddate_sim_yyyymmddhh}"',
-            '#SBATCH --time=00:10:00',
-            f'#SBATCH --partition={cfg.compute_queue}',
-            f'#SBATCH --constraint={cfg.constraint}', '#SBATCH --ntasks=1',
-            f'#SBATCH --output={cfg.logfile}', '#SBATCH --open-mode=append',
-            f'#SBATCH --chdir={cfg.icon_work}', ''
-        ]
-    for target, destination in zip(cfg.input_files.values(),
-                                   cfg.input_files_scratch.values()):
-        script_lines.append(f'rsync -av {target} {destination}')
-
-    with (script := cfg.icon_work / 'copy_input.job').open('w') as f:
-        f.write('\n'.join(script_lines))
-
-    cfg.submit('prepare_icon', script)
-    logging.info("OK")

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/reduce_output.html b/pr-preview/pr-63/_modules/jobs/reduce_output.html deleted file mode 100644 index 5a7df864..00000000 --- a/pr-preview/pr-63/_modules/jobs/reduce_output.html +++ /dev/null @@ -1,350 +0,0 @@ - - - - - - jobs.reduce_output — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.reduce_output

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import logging
-import os
-import sys
-import shutil
-import datetime as dt
-import glob
-import netCDF4 as nc
-import subprocess
-import numpy as np
-from datetime import datetime
-import math
-
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-
[docs]def main(cfg):
-    """
-    Calculates 2D column data and writes them into a new netCDF file.
-    Only a fixed number of levels from **COSMO** output are considered.
-    Those files are written into a new directory ``cosmo_output_reduced``.
-
-    The number of levels is set by the configuration variable
-    ``cfg.reduce_output['output_levels']`` (default = all levels).
-    
-    **Important**: If several ``GRIBOUT`` sections are used to split the output
-    data, then this code only works in case of the following:
-    The tracers, for which the column-averaged dry-air (``X``) and
-    moist-air (``Y``) mole fractions are calculated, have to be
-
-        1. saved in a separate output file and
-        2. the output file appears alphabetically **after** the meteorological
-           variables.
-
-    For example, use a GRIBOUT section suffix ``_met`` for standard **COSMO**
-    output, and ``_trc`` for tracers.
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-    """
-    tools.change_logfile(cfg.logfile)
-    cosmo_output = cfg.cosmo_output
-    output_path = cfg.cosmo_output_reduced
-
-    date = dt.datetime.today()
-
-    to_print = """reduce_output
-
-=====================================================
-============== POST PROCESSING BEGINS ===============
-============== StartTime: %s 
-=====================================================""" % date.strftime("%s")
-
-    logging.info(to_print)
-
-    tools.create_dir(output_path, "output")
-
-    if cfg.compute_host != "daint":
-        logging.error(
-            "The reduce_output script is supposed to be run on daint only, "
-            "not on %s" % cfg.compute_host)
-        sys.exit(1)
-
-    # Wait for Cosmo to finish first
-    tools.check_job_completion(cfg.log_finished_dir, "cosmo")
-
-    # Number of levels and switch for unit conversion for 'reduce_output' job
-    if not hasattr(cfg, 'output_levels'):
-        cfg.output_levels = -1
-    if not hasattr(cfg, 'convert_gas'):
-        cfg.convert_gas = True
-    """Get list of constant files"""
-    cfiles = []
-    read_cfile = False
-    for infile in sorted(
-            glob.glob(os.path.join(cosmo_output, "lffd*[0-9]c*.nc"))):
-        cfiles.append(infile)
-        if not read_cfile:
-            # Read the first constant file and store height value
-            logging.info(infile)
-            with nc.Dataset(infile) as inf:
-                h = np.array(inf.variables['HHL'][0])
-            read_cfile = True
-            logging.info('Successfully read constant file %s' % infile)
-
-    if not read_cfile:
-        logging.error('Constant file could not be read')
-    """Copy constant file directly"""
-    if os.path.exists(cfiles[0]):
-        shutil.copy(cfiles[0], output_path)
-        logging.info('Copied constant file %s to %s.' %
-                     (cfiles[0], output_path))
-    else:
-        logging.error('Constant file could not be copied.')
-    """Get list of files"""
-    infiles = sorted(glob.glob(os.path.join(cosmo_output, "lffd*.nc")))
-    mytimes = []
-    for infile in list(infiles):
-        basename = os.path.split(infile)[1]
-        timestr = basename.split('lffd', 1)[1][:10]
-        mytimes.append(datetime.strptime(timestr, '%Y%m%d%H'))
-
-    str_startdate = mytimes[0].strftime('%Y-%m-%d %H')
-    str_enddate = mytimes[-1].strftime('%Y-%m-%d %H')
-    """Compute time step for parallel tasks"""
-    ncores = 36
-    total_time = mytimes[-1] - mytimes[0]
-    nout_times = int(total_time.total_seconds() // 3600) + 1
-    output_step = int(max(math.ceil(nout_times / ncores), 2))
-    """Execute parallel bash script"""
-    dir_path = os.path.dirname(os.path.realpath(__file__))
-    tool_path = os.path.join(dir_path, 'tools')
-    bash_file = os.path.join(tool_path, 'reduce_output_parallel.bash')
-    py_file = os.path.join(tool_path, 'reduce_output_start_end.py')
-    alternate_csv_file = os.path.join(cfg.chain_src_dir, 'cases', cfg.casename,
-                                      'variables.csv')
-    logging.info('Submitting job to the queue...')
-
-    result = subprocess.run([
-        "sbatch", '--output=' + cfg.logfile, '--open-mode=append', '--wait',
-        bash_file, py_file, cosmo_output, output_path, str_startdate,
-        str_enddate,
-        str(cfg.reduce_output['output_levels']),
-        str(output_step), alternate_csv_file,
-        str(cfg.reduce_output['convert_gas'])
-    ])
-    exitcode = result.returncode
-
-    if exitcode != 0:
-        raise RuntimeError("sbatch returned exitcode {}".format(exitcode))
-    """Check if all files have been processed"""
-    cfile_names = []
-    for cfile in cfiles:
-        cfile_names.append(os.path.basename(cfile))
-    files_cosmo = sorted([
-        name for name in os.listdir(cosmo_output)
-        if os.path.isfile(os.path.join(cosmo_output, name))
-        and name not in cfile_names
-    ])
-    files_reduced = sorted([
-        name for name in os.listdir(output_path)
-        if os.path.isfile(os.path.join(output_path, name))
-        and name not in cfile_names
-    ])
-
-    if not files_cosmo == files_reduced:
-        logging.error(set(files_cosmo).symmetric_difference(files_reduced))
-        logging.error('Reduced output files differ from original output!')
-        raise RuntimeError('Error in reduce_output job')
-    """Check for corrupted files"""
-    for f in [
-            os.path.join(output_path, name) for name in os.listdir(output_path)
-    ]:
-        with nc.Dataset(f) as _:
-            logging.info('File %s is not corrupted' % f)
-
-    date = dt.datetime.today()
-    to_print = """=====================================================
-============== POST PROCESSING ENDS ==================
-============== EndTime: %s
-=====================================================""" % date.strftime("%s")
-
-    logging.info(to_print)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/cams4int2cosmo.html b/pr-preview/pr-63/_modules/jobs/tools/cams4int2cosmo.html deleted file mode 100644 index 9025ad4a..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/cams4int2cosmo.html +++ /dev/null @@ -1,557 +0,0 @@ - - - - - - jobs.tools.cams4int2cosmo — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.cams4int2cosmo

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-#
-# Author: Dominik Brunner (DB), Empa, Switzerland
-#       DB, 15 May 2017: first implementation on daint.cscs.ch
-#       DB, 06 Jun 2017: modified to add surface pressure fields
-#       hjm, 22 Jun 2018: Translated to Python
-######################
-## Problems:
-## - when comparing to the "processed2" icbc form Gerrit, PSURF is slightly different
-## - when checking the website, the b levels are not the same as in CAMS
-## - It is not possible to delete a variable from a netcdf4 file, so resort to calling ncks at the end
-
-import argparse
-import os
-import logging
-import shutil
-import netCDF4 as nc
-import numpy as np
-from subprocess import call
-import sys
-import importlib
-
-###############################
-##  Constants : CAMS levels  ##
-###############################
-# hybrid coefficients of the 137 model level version
-# http://www.ecmwf.int/en/forecasts/documentation-and-support/137-model-levels
-a_half_137 = [
-    0.0000000000e+00, 2.0003650188e+00, 3.1022410393e+00, 4.6660838127e+00,
-    6.8279771805e+00, 9.7469663620e+00, 1.3605423927e+01, 1.8608930588e+01,
-    2.4985717773e+01, 3.2985710144e+01, 4.2879241943e+01, 5.4955463409e+01,
-    6.9520576477e+01, 8.6895881653e+01, 1.0741574097e+02, 1.3142550659e+02,
-    1.5927940369e+02, 1.9133856201e+02, 2.2796894836e+02, 2.6953958130e+02,
-    3.1642074585e+02, 3.6898236084e+02, 4.2759249878e+02, 4.9261602783e+02,
-    5.6441345215e+02, 6.4333990479e+02, 7.2974414062e+02, 8.2396783447e+02,
-    9.2634490967e+02, 1.0372011719e+03, 1.1568536377e+03, 1.2856103516e+03,
-    1.4237701416e+03, 1.5716229248e+03, 1.7294489746e+03, 1.8975192871e+03,
-    2.0760959473e+03, 2.2654316406e+03, 2.4657705078e+03, 2.6773481445e+03,
-    2.9003913574e+03, 3.1351193848e+03, 3.3817436523e+03, 3.6404682617e+03,
-    3.9114904785e+03, 4.1949306641e+03, 4.4908173828e+03, 4.7991494141e+03,
-    5.1198950195e+03, 5.4529907227e+03, 5.7983447266e+03, 6.1560742188e+03,
-    6.5269467773e+03, 6.9118706055e+03, 7.3118691406e+03, 7.7274121094e+03,
-    8.1593540039e+03, 8.6085253906e+03, 9.0764003906e+03, 9.5626826172e+03,
-    1.0065978516e+04, 1.0584631836e+04, 1.1116662109e+04, 1.1660067383e+04,
-    1.2211547852e+04, 1.2766873047e+04, 1.3324668945e+04, 1.3881331055e+04,
-    1.4432139648e+04, 1.4975615234e+04, 1.5508256836e+04, 1.6026115234e+04,
-    1.6527322266e+04, 1.7008789062e+04, 1.7467613281e+04, 1.7901621094e+04,
-    1.8308433594e+04, 1.8685718750e+04, 1.9031289062e+04, 1.9343511719e+04,
-    1.9620042969e+04, 1.9859390625e+04, 2.0059931641e+04, 2.0219664062e+04,
-    2.0337863281e+04, 2.0412308594e+04, 2.0442078125e+04, 2.0425718750e+04,
-    2.0361816406e+04, 2.0249511719e+04, 2.0087085938e+04, 1.9874025391e+04,
-    1.9608572266e+04, 1.9290226562e+04, 1.8917460938e+04, 1.8489707031e+04,
-    1.8006925781e+04, 1.7471839844e+04, 1.6888687500e+04, 1.6262046875e+04,
-    1.5596695312e+04, 1.4898453125e+04, 1.4173324219e+04, 1.3427769531e+04,
-    1.2668257812e+04, 1.1901339844e+04, 1.1133304688e+04, 1.0370175781e+04,
-    9.6175156250e+03, 8.8804531250e+03, 8.1633750000e+03, 7.4703437500e+03,
-    6.8044218750e+03, 6.1685312500e+03, 5.5643828125e+03, 4.9937968750e+03,
-    4.4573750000e+03, 3.9559609375e+03, 3.4892343750e+03, 3.0572656250e+03,
-    2.6591406250e+03, 2.2942421875e+03, 1.9615000000e+03, 1.6594765625e+03,
-    1.3875468750e+03, 1.1432500000e+03, 9.2650781250e+02, 7.3499218750e+02,
-    5.6806250000e+02, 4.2441406250e+02, 3.0247656250e+02, 2.0248437500e+02,
-    1.2210156250e+02, 6.2781250000e+01, 2.2835937500e+01, 3.7578129768e+00,
-    0.0000000000e+00, 0.0000000000e+00
-]
-b_half_137 = [
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 3.8199999608e-08, 6.7607002165e-06,
-    2.4348000807e-05, 5.8921999880e-05, 1.1191429803e-04, 1.9857739971e-04,
-    3.4037968726e-04, 5.6155532366e-04, 8.8969792705e-04, 1.3528055279e-03,
-    1.9918379840e-03, 2.8571242001e-03, 3.9709536359e-03, 5.3778146394e-03,
-    7.1333767846e-03, 9.2614600435e-03, 1.1806022376e-02, 1.4815628529e-02,
-    1.8318451941e-02, 2.2354844958e-02, 2.6963520795e-02, 3.2176095992e-02,
-    3.8026399910e-02, 4.4547960162e-02, 5.1773015410e-02, 5.9728413820e-02,
-    6.8448252976e-02, 7.7958308160e-02, 8.8285736740e-02, 9.9461667240e-02,
-    1.1150465161e-01, 1.2444812804e-01, 1.3831289113e-01, 1.5312503278e-01,
-    1.6891041398e-01, 1.8568944931e-01, 2.0349121094e-01, 2.2233286500e-01,
-    2.4224400520e-01, 2.6324188709e-01, 2.8535401821e-01, 3.0859845877e-01,
-    3.3293908834e-01, 3.5825419426e-01, 3.8436332345e-01, 4.1112476587e-01,
-    4.3839120865e-01, 4.6600329876e-01, 4.9380031228e-01, 5.2161920071e-01,
-    5.4930114746e-01, 5.7669216394e-01, 6.0364806652e-01, 6.3003581762e-01,
-    6.5573596954e-01, 6.8064302206e-01, 7.0466899872e-01, 7.2773873806e-01,
-    7.4979656935e-01, 7.7079755068e-01, 7.9071676731e-01, 8.0953603983e-01,
-    8.2725608349e-01, 8.4388113022e-01, 8.5943180323e-01, 8.7392926216e-01,
-    8.8740754128e-01, 8.9990049601e-01, 9.1144818068e-01, 9.2209565639e-01,
-    9.3188077211e-01, 9.4085955620e-01, 9.4906443357e-01, 9.5654952526e-01,
-    9.6335172653e-01, 9.6951341629e-01, 9.7507840395e-01, 9.8007160425e-01,
-    9.8454189301e-01, 9.8849952221e-01, 9.9198400974e-01, 9.9500250816e-01,
-    9.9763011932e-01, 1.0000000000e+00
-]
-
-# hybrid coefficients of the 60 model level version
-# http://www.ecmwf.int/en/forecasts/documentation-and-support/60-model-levels
-a_half_60 = [
-    0.0000000000e+00, 2.0000000000e+01, 3.8425338745e+01, 6.3647796631e+01,
-    9.5636962891e+01, 1.3448330688e+02, 1.8058435059e+02, 2.3477905273e+02,
-    2.9849584961e+02, 3.7397192383e+02, 4.6461816406e+02, 5.7565112305e+02,
-    7.1321801758e+02, 8.8366040039e+02, 1.0948347168e+03, 1.3564746094e+03,
-    1.6806403809e+03, 2.0822739258e+03, 2.5798886719e+03, 3.1964216309e+03,
-    3.9602915039e+03, 4.9067070312e+03, 6.0180195312e+03, 7.3066328125e+03,
-    8.7650546875e+03, 1.0376125000e+04, 1.2077445312e+04, 1.3775324219e+04,
-    1.5379804688e+04, 1.6819472656e+04, 1.8045183594e+04, 1.9027695312e+04,
-    1.9755109375e+04, 2.0222203125e+04, 2.0429863281e+04, 2.0384480469e+04,
-    2.0097402344e+04, 1.9584328125e+04, 1.8864750000e+04, 1.7961359375e+04,
-    1.6899468750e+04, 1.5706449219e+04, 1.4411125000e+04, 1.3043218750e+04,
-    1.1632757812e+04, 1.0209500000e+04, 8.8023554688e+03, 7.4388046875e+03,
-    6.1443164062e+03, 4.9417773438e+03, 3.8509133301e+03, 2.8876965332e+03,
-    2.0637797852e+03, 1.3859125977e+03, 8.5536181641e+02, 4.6733349609e+02,
-    2.1039389038e+02, 6.5889236450e+01, 7.3677425385e+00, 0.0000000000e+00,
-    0.0000000000e+00
-]
-b_half_60 = [
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00, 0.0000000000e+00,
-    7.5823496445e-05, 4.6139489859e-04, 1.8151560798e-03, 5.0811171532e-03,
-    1.1142909527e-02, 2.0677875727e-02, 3.4121163189e-02, 5.1690407097e-02,
-    7.3533833027e-02, 9.9674701691e-02, 1.3002252579e-01, 1.6438430548e-01,
-    2.0247590542e-01, 2.4393314123e-01, 2.8832298517e-01, 3.3515489101e-01,
-    3.8389211893e-01, 4.3396294117e-01, 4.8477154970e-01, 5.3570991755e-01,
-    5.8616840839e-01, 6.3554745913e-01, 6.8326860666e-01, 7.2878581285e-01,
-    7.7159661055e-01, 8.1125342846e-01, 8.4737491608e-01, 8.7965691090e-01,
-    9.0788388252e-01, 9.3194031715e-01, 9.5182150602e-01, 9.6764522791e-01,
-    9.7966271639e-01, 9.8827010393e-01, 9.9401944876e-01, 9.9763011932e-01,
-    1.0000000000e+00
-]
-
-
-
[docs]def main(date, inpath, outpath, param):
-    """Prepare CAMS CO2, CO and NOx boundary conditions for 
-    **int2lm/int2cosmo** for the project SMARTCARB.
-
-    The CAMS data consists of
-    
-    -   CO2 and CO fields of experiment gf39, class RD (approx. 15 km 
-        resolution, 137 levels). See
-        https://atmosphere.copernicus.eu/change-log-gf39
-    -   NO and NO2 from the CAMS operational product, exp 0001, class MC
-        (60 km resolution)
-
-    The data sets are retrieved as individual 3-hourly files from the MARS
-    archive at ECMWF with names::
-    
-        cams_0001_2015010500.nc   # for NO and NO2
-        sfc_0001_2015010500.nc    # for log of surface pressure
-        cams_gf39_2015010500.nc   # for CO and CO2
-        sfc_gf39_2015010500.nc    # for log of surface pressure
-
-    The path to the directory of the CAMS data can optionally be supplied, 
-    otherwise the script should be invoked in the directory of the CAMS data.
-
-    The script generates 8 individual 3-hourly IC/BC files::
-    
-        cams_nox_yyyymmddhh.nc
-        cams_co2_yyyymmddhh.nc
-
-    Usage::
-    
-        python cams4int2cosmo.py date [-i inpath -o outpath]
-        
-    Output:
-
-         ``cams_NOX_YYYYMMDD00.nc`` to ``cams_NOX_YYYYMMDD21.nc``
-         ``cams_CO2_YYYYMMDD00.nc`` to ``cams_CO2_YYYYMMDD21.nc``
-
-    Parameters
-    ----------
-    date : str
-        date in format YYYYMMDD
-    inpath : str
-        path of original CAMS files (default is current path)
-    outpath : str
-        path where output files should be generated (default is current path)
-    param : dict
-    """
-    try:
-        os.makedirs(outpath, exist_ok=True)
-    except (OSError, PermissionError):
-        logging.error("Creating output directory failed")
-        raise
-
-    tracer2dict = {
-        'CO2': dict(name="CO2_BG",
-                    short_name="co2",
-                    long_name="carbon_dioxide"),
-        'CO': dict(name="CO_BG", short_name="co", long_name="carbon_monoxide"),
-        'CH4': dict(name="CH4_BG", short_name="ch4", long_name="methane"),
-        'NOX': dict(name="NOX_BG",
-                    short_name="NOx",
-                    long_name="nitrogen_oxide"),
-    }
-
-    species = []
-    for s in param["species"]:
-        logging.info(s)
-        logging.info(tracer2dict[s])
-        try:
-            species.append(tracer2dict[s])
-        except KeyError:
-            logging.error("Variable " + s +
-                          " is not part of the available list of variables.")
-
-    main_process(date, inpath, outpath, species, param)

-
-
-def main_process(date, inpath, outpath, species, param):
-    if param["lev"] == 137:
-        a_half = a_half_137  #defined globally
-        b_half = b_half_137  #defined globally
-        offset = 37  # only levels 38 to 137 are retrieved from MARS
-    elif param["lev"] == 60:
-        a_half = a_half_60  #defined globally
-        b_half = b_half_60  #defined globally
-        offset = 0  # all levels
-    else:
-        logging.error(
-            "The list of hybrid parameters for the amount of levels " +
-            param["lev"] + "is not defined.")
-        raise
-
-    hyam = [(a_half[i] + a_half[i + 1]) / 2.
-            for i in range(offset,
-                           len(a_half) - 1)]
-    hybm = [(b_half[i] + b_half[i + 1]) / 2.
-            for i in range(offset,
-                           len(a_half) - 1)]
-
-    to_print = ",".join(
-        [species[i]["short_name"] for i in range(len(species))])
-    logging.info('Processing ' + to_print + ' for time ' +
-                 date.strftime("%Y%m%d%H"))
-
-    infile = os.path.join(
-        inpath, param["prefix1"] + "_" + date.strftime("%Y%m%d%H") + ".nc")
-    sfcfile = os.path.join(
-        inpath, param["prefix2"] + "_" + date.strftime("%Y%m%d%H") + ".nc")
-
-    outfile = os.path.join(
-        outpath, param["suffix"] + "_" + date.strftime("%Y%m%d%H") + ".nc")
-
-    try:
-        shutil.copy(infile, outfile)
-    except FileNotFoundError:
-        logging.error("file " + infile + " not found")
-        raise
-    except (PermissionError, OSError):
-        logging.error("Copying file " + infile + " failed")
-        raise
-
-    with nc.Dataset(outfile, "a", format="NETCDF4") as outf:
-        # copy surface pressure from surface file
-        with nc.Dataset(sfcfile, "r") as inf:
-            lnsp = inf.variables["lnsp"]
-            outf.createVariable("PSURF", "f8", lnsp.dimensions)
-            outf.variables["PSURF"][:] = np.exp(lnsp[:])
-            outf["PSURF"].setncattr("long_name", "surface pressure")
-            outf["PSURF"].setncattr("units", "Pa")
-
-        # change the calender attribute to proleptic_gregorian
-        outf["time"].setncattr("calendar", "proleptic_gregorian")
-
-        # rename fields according to Carbosense4D definitions
-        for s in species:
-            if s["name"] != "NOX_BG":
-                outf.renameVariable(s["short_name"], s["name"])
-            else:
-                # Create NOX from NO and NO2
-                outf.createVariable("NOX_BG", "f8", outf["no"].dimensions)
-                outf["NOX_BG"][:] = outf["no"][:] + outf["no2"][:]
-
-        outf.renameDimension("latitude", "lat")
-        outf.renameDimension("longitude", "lon")
-        outf.renameVariable("latitude", "lat")
-        outf.renameVariable("longitude", "lon")
-
-        # Reverse latitude for all fields so that startlat < endlat
-        for v in outf.variables:
-            dims = outf[v].dimensions
-            if 'lat' in dims:
-                lat_ind = dims.index('lat')
-                if lat_ind == 0:
-                    outf[v][:] = outf[v][::-1]
-                elif lat_ind == 1:
-                    outf[v][:] = outf[v][:, ::-1]
-                elif lat_ind == 2:
-                    outf[v][:] = outf[v][:, :, ::-1]
-                elif lat_ind == 3:
-                    outf[v][:] = outf[v][:, :, :, ::-1]
-                elif lat_ind == 4:
-                    outf[v][:] = outf[v][:, :, :, :, ::-1]
-
-        # Add the units; these must match those in $int2cosmo/src/trcr_gribtabs.f90
-        for s in species:
-            chem = s["name"]
-            long = s["long_name"]
-            outf[chem].setncattr("units", "kg kg-1")
-            outf[chem].setncattr("units_desc",
-                                 "kg of substance per kg of dry air")
-            outf[chem].setncattr(
-                "long_name",
-                "mass mixing ratio of " + chem[:-3] + " from outside domain")
-            outf[chem].setncattr("standard_name",
-                                 "mass_fraction_of_" + long + "_in_air")
-
-        # Add hybrid coefficients
-        outf.createVariable("hyam", np.float64, "level")
-        outf.createVariable("hybm", np.float64, "level")
-        outf["hyam"][:] = hyam
-        outf["hybm"][:] = hybm
-        outf["hyam"].setncattr("units", "Pa")
-        outf["hybm"].setncattr("units", "1")
-        outf["hyam"].setncattr("long_name",
-                               "hybrid A coefficient at layer midpoints")
-        outf["hybm"].setncattr("long_name",
-                               "hybrid B coefficient at layer midpoints")
-
-        # create new dimension lev1
-        outf.createDimension("lev1", 1)
-        outf.createVariable("P0", float, "lev1")
-        outf["P0"][:] = [1]
-        outf["P0"].setncattr("units", "Pa")
-        outf["P0"].setncattr("long_name", "reference pressure")
-
-        #  if NOX_BG, delete no and no2
-        for s in species:
-            if s["name"] == "NOX_BG":
-                if "no" in outf.variables and "no2" in outf.variables:
-                    call([
-                        "ncks", "--overwrite", "-x", "-v", "no,no2", outfile,
-                        outfile
-                    ])
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description=
-        "Prepare CAMS CO2, CO, CH4 and NOx boundary conditions for int2lm/int2cosmo",
-        formatter_class=argparse.RawTextHelpFormatter)
-
-    parser.add_argument('date', type=str, help='date in format YYYYMMDD')
-    parser.add_argument('param', type=str, help='dictionary of the parameters')
-    parser.add_argument(
-        '-i',
-        type=str,
-        metavar="inpath",
-        help='path of original CAMS files (default is current path)',
-        default=os.getcwd())
-    parser.add_argument(
-        '-o',
-        type=str,
-        metavar="outpath",
-        help=
-        "path where output files should be generated (default is inpath/processed)",
-    )
-
-    indir = parser.get_default("i")
-    parser.set_defaults(o=os.path.join(indir, "processed"))
-
-    args = parser.parse_args()
-
-    main(args.date, args.i, args.o, args.param)
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/check_model.html b/pr-preview/pr-63/_modules/jobs/tools/check_model.html deleted file mode 100644 index 3c672b7c..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/check_model.html +++ /dev/null @@ -1,204 +0,0 @@ - - - - - - jobs.tools.check_model — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.check_model

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-
-
[docs]def check_model(cfg, model='COSMO'):
-    """Check that the model specified in cfg matched the prescribed model.
-
-    Check that cfg.workflow_name == model. If not, raises a value-error.
-    Ignores capitalization of the strings
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-
-    model : str
-        Prescribed model
-    """
-    #don't care about capitalization
-    if not cfg.workflow_name.lower() == model.lower():
-        raise ValueError("The model specified in the configuration file is {}"
-                         ", but the job only applies to {}.".format(
-                             cfg.workflow_name, model))

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/comp_nc.html b/pr-preview/pr-63/_modules/jobs/tools/comp_nc.html deleted file mode 100644 index 0dc1814b..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/comp_nc.html +++ /dev/null @@ -1,319 +0,0 @@ - - - - - - jobs.tools.comp_nc — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.comp_nc

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Compare two netCDF-files
-
-# Author: dao, david.ochsner@empa.ch
-
-import argparse
-import netCDF4 as nc
-import numpy as np
-
-colors = {"green": '\033[32m', "red": '\033[31m', "yellow": '\033[33m'}
-
-
-def ccprint(text, color=None, verbose=True):
-    """Print-wrapper that Conditionally prints Colored text
-
-    Parameters
-    ----------
-    text : str
-        Text to print
-    color : str
-        Color of the text
-        One of 'red','green' or 'yellow', or 'None' for black
-    verbose : bool
-        If 'True' the text is printed, if 'False' nothing happens
-    """
-    if not verbose:
-        return
-
-    if color is not None:
-        try:
-            print(colors[color] + text + '\033[0m')
-        except KeyError:
-            raise ValueError("Unrecognized color")
-    else:
-        print(text)
-
-
-def import_data(path):
-    """Imports the data at path into a netCDF4-Dataset
-
-    Parameters
-    ----------
-    path : str
-        Path to the .nc file
-    """
-    return nc.Dataset(path)
-
-
-
[docs]def datasets_equal(dataset1, dataset2, variables, verbose=True):
-    """Compare the contents of dataset1 and dataset2
-
-    Compare with numpy.isclose whether the two datasets are equal. No check for
-    equality (of the values or bitwise of the files) is performed, as numerical
-    errors can produce slightly different files for essentially identical
-    computations. Rather, the values are compared to absolute and relative
-    tolerances, check np.isclose documentation for more detail.
-
-    If variables is not empty, only the provided variables are compared.
-
-    Parameters
-    ----------
-    dataset1 : netCDF4.Dataset
-    dataset2 : netCDF4.Dataset
-    variables : list of str
-        List of the variables to be compared. If it is empty, all variables
-        are compared.
-    verbose : bool
-        If True, results will be printed to stdout.
-    Returns
-    -------
-    bool
-        True if the datasets, or if provided the selected variables, are equal,
-        False otherwise.
-    """
-    if not variables:
-        variables = set(dataset1.variables.keys())
-        variables2 = set(dataset2.variables.keys())
-
-        if not variables == variables2:
-            ccprint("Files don't contain the same variables.", "red", verbose)
-            ccprint("The following variables are in only "
-                    "one of the files:", None, verbose)
-            ccprint(variables.symmetric_difference(variables2), None, verbose)
-            ccprint("The common variables are:", None, verbose)
-            ccprint(variables.intersection(variables2), None, verbose)
-            return False
-    else:
-        assert set(dataset1.variables.keys()).issuperset(variables), (
-            "Dataset 1 doesn't contain all variables that should be compared")
-        assert set(dataset2.variables.keys()).issuperset(variables), (
-            "Dataset 2 doesn't contain all variables that should be compared")
-
-    result = True
-    for var in variables:
-        if not dataset1[var].dtype == dataset2[var].dtype:
-            ccprint("{} has different types.".format(var), "red", verbose)
-            result = False
-
-        if (dataset1[var].dtype in np.sctypes['float']
-                or dataset1[var].dtype in np.sctypes['int']):
-            if np.allclose(dataset1[var], dataset2[var]):
-                ccprint("{} is equal.".format(var), None, verbose)
-            else:
-                ccprint("{} is not equal".format(var), "red", verbose)
-                result = False
-        else:
-            ccprint(
-                "{} is not a numeric type "
-                "and not compared.".format(var), None, verbose)
-
-    return result

-
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser("Compare two netCDF files.")
-    parser.add_argument("Dataset1",
-                        type=str,
-                        help="Path to the first dataset.")
-    parser.add_argument("Dataset2",
-                        type=str,
-                        help="Path to the second dataset.")
-    parser.add_argument("-v",
-                        "--variables",
-                        nargs='*',
-                        default=[],
-                        dest="variables",
-                        help="Variables to be compared. If "
-                        "none are given, all variables in the files are "
-                        "compared.")
-    args = parser.parse_args()
-
-    if datasets_equal(import_data(args.Dataset1), import_data(args.Dataset2),
-                      args.variables):
-        ccprint("Provided files are equal", color="green")
-    else:
-        ccprint("Provided files are not equal", color="red")
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/ctnoaa4int2cosmo.html b/pr-preview/pr-63/_modules/jobs/tools/ctnoaa4int2cosmo.html deleted file mode 100644 index 81707f46..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/ctnoaa4int2cosmo.html +++ /dev/null @@ -1,376 +0,0 @@ - - - - - - jobs.tools.ctnoaa4int2cosmo — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.ctnoaa4int2cosmo

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import sys
-import numpy as np
-from netCDF4 import Dataset
-import argparse
-import os
-
-half_a = (0, 7.367743, 210.39389, 855.361755, 2063.779785, 3850.91333,
-          6144.314941, 8802.356445, 11632.75879, 14411.12402, 16899.46875,
-          18864.75, 20097.40234, 20429.86328, 19755.10938, 18045.18359,
-          15379.80566, 12077.44629, 8765.053711, 6018.019531, 3960.291504,
-          1680.640259, 713.218079, 298.495789, 95.636963, 0)
-half_b = (1, 0.99401945, 0.97966272, 0.95182151, 0.90788388, 0.84737492,
-          0.77159661, 0.68326861, 0.58616841, 0.48477158, 0.38389215,
-          0.28832296, 0.2024759, 0.13002251, 0.07353383, 0.03412116,
-          0.01114291, 0.00181516, 0.00007582, 0, 0, 0, 0, 0, 0, 0)
-
-
-
[docs]def main(date, indir, outdir, param):
-    """Process all CarbonTracker files of a single date to a format
-    compatible with int2lm
-
-    Parameters
-    ----------
-    date : str
-        date in format YYYYMMDD.
-    indir : str
-        directory of original CarbonTracker files (default is current path).
-    outdir : str
-        utput directory of processed files (default is indir/processed).
-    param : dict
-        dictionary of the parameters
-    """
-    try:
-        os.makedirs(outdir, exist_ok=True)
-    except (OSError, PermissionError):
-        logging.error("Creating output directory failed")
-        raise
-
-    ifile = Dataset(
-        os.path.join(indir, param["prefix"] + "_" + date.strftime('%Y-%m-%d') +
-                     '.nc'), 'r')
-    levs = ifile.variables['level'][:]
-    lats = ifile.variables['latitude'][:]
-    lons = ifile.variables['longitude'][:]
-
-    co2 = np.squeeze(ifile.variables['co2'][:])
-    p_bound = np.squeeze(ifile.variables['pressure'][:])
-    ifile.close()
-
-    lats_tf = (lats <= 63.) & (lats >= 35.)
-    lons_tf = (lons <= 34.5) & (lons >= -10.5)
-    lats = lats[np.logical_and(lats >= 35., lats <= 63.)]
-    lons = lons[np.logical_and(lons >= -10.5, lons <= 34.5)]
-
-    co2 = co2[:, :, lats_tf, :][:, :, :,
-                                lons_tf] * 0.04401 / 0.02896  # * mmCO2/mmAir
-    p_bound = p_bound[:, :, lats_tf, :][:, :, :, lons_tf]
-    p = np.empty(shape=(8, 25, 15, 16))
-    for i in range(0, 24):
-        p[:, i, :, :] = (p_bound[:, i, :, :] + p_bound[:, i + 1, :, :]) / 2.
-    sp = np.squeeze(p[:, 0, :, :])
-
-    hyam = np.empty(len(half_a) - 1)
-    hybm = np.empty(len(half_a) - 1)
-    for i in range(len(hyam) - 1):
-        hyam[i] = (half_a[i] + half_a[i + 1]) / 2.
-        hybm[i] = (half_b[i] + half_b[i + 1]) / 2.
-
-    ttt = ("00", "03", "06", "09", "12", "15", "18", "21")
-
-    for ti, tt in enumerate(ttt):
-
-        with Dataset(os.path.join(
-                outdir,
-                param["suffix"] + "_" + date.strftime('%Y%m%d') + tt + '.nc'),
-                     mode='w') as ofile:
-
-            olev = ofile.createDimension('level', len(levs))
-            olat = ofile.createDimension('lat', len(lats))
-            olon = ofile.createDimension('lon', len(lons))
-            odate = ofile.createDimension('date', 1)
-
-            olat = ofile.createVariable('lat', np.float64, ('lat', ))
-            olon = ofile.createVariable('lon', np.float64, ('lon', ))
-            olev = ofile.createVariable('level', np.float64, ('level', ))
-            otime = ofile.createVariable('time', np.float64, ('date', ))
-            odate = ofile.createVariable('date', np.float64, ('date', ))
-
-            ohyam = ofile.createVariable('hyam', np.float32, ('level', ))
-            ohybm = ofile.createVariable('hybm', np.float32, ('level', ))
-
-            oco2 = ofile.createVariable('CO2_BG',
-                                        np.float32,
-                                        ('date', 'level', 'lat', 'lon'),
-                                        fill_value=-999.99)
-            op = ofile.createVariable('pressure',
-                                      np.float32,
-                                      ('date', 'level', 'lat', 'lon'),
-                                      fill_value=-999.99)
-            osp = ofile.createVariable('PSURF',
-                                       np.float32, ('date', 'lat', 'lon'),
-                                       fill_value=-999.99)
-            op0 = ofile.createVariable('P0',
-                                       np.float32, ('date'),
-                                       fill_value=-999.99)
-
-            odate.comment = 'time-interval average, centered on times in the date axis'
-            odate.long_name = 'UTC dates and times'
-            odate.units = 'days since ' + date.strftime('%Y%m%d') + ' 00:00:00'
-            #    otime.dtype = 'double'
-
-            otime.units = 'seconds since ' + date.strftime(
-                '%Y%m%d') + ' 00:00:00'
-            otime.calendar = 'proleptic_gregorian'
-
-            olat.standard_name = 'latitude'
-            olat.long_name = 'latitude'
-            olat.units = 'degree_north'
-            olat.axis = 'Y'
-
-            olon.standard_name = 'longitude'
-            olon.long_name = 'longitude'
-            olon.units = 'degree_east'
-            olon.axis = 'X'
-
-            ohyam.long_name = 'hybrid A coefficient at layer midpoints'
-            ohyam.units = 'Pa'
-
-            ohybm.long_name = 'hybrid B coefficient at layer midpoints'
-            ohybm.units = '1'
-
-            olev.positive = 'up'
-            olev.units = 'levels'
-
-            oco2.standard_name = 'mass_fraction_of_carbon_dioxide_in_air'
-            oco2.long_name = 'mass mixing ratio of CO2 from outside Europe'
-            oco2.units = 'kg kg-1'
-
-            op.long_name = 'pressure_at_center_levels'
-            op.units = 'Pa'
-            op.standard_name = 'air pressure'
-
-            op0.units = 'Pa'
-
-            osp.cell_methods = 'level:mean'
-            osp.units = 'Pa'
-            osp.long_name = 'surface pressure'
-            osp.table = '128'
-            osp.lev = '1'
-
-            olat[:] = lats
-            olon[:] = lons
-            olev[:] = levs
-            odate[:] = 3. * ti / 24.
-            otime[:] = ti * 3 * 3600
-
-            oco2[:] = co2[ti, :]
-            osp[:] = sp[ti, :]
-            op[:] = p[ti, :]
-            op0[:] = 1.
-            ohyam[:] = hyam
-            ohybm[:] = hybm

-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description=
-        "Process all CarbonTracker files of a single date to a format compatible with int2lm",
-        formatter_class=argparse.RawTextHelpFormatter)
-    parser.add_argument('date', type=str, help='date in format YYYYMMDD')
-    parser.add_argument('param', help='dictionary of the parameters')
-    parser.add_argument(
-        '-i',
-        type=str,
-        metavar="indir",
-        help=
-        'directory of original CarbonTracker files (default is current path)',
-        default=os.getcwd())
-    parser.add_argument(
-        '-o',
-        type=str,
-        metavar="outdir",
-        help="output directory of processed files (default is indir/processed)"
-    )
-
-    indir = parser.get_default("i")
-    parser.set_defaults(o=os.path.join(indir, "processed"))
-
-    args = parser.parse_args()
-
-    print(args.param)
-    main(args.date, args.i, args.o, args.param)
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/mozart2int2lm.html b/pr-preview/pr-63/_modules/jobs/tools/mozart2int2lm.html deleted file mode 100644 index 50dee303..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/mozart2int2lm.html +++ /dev/null @@ -1,456 +0,0 @@ - - - - - - jobs.tools.mozart2int2lm — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.mozart2int2lm

-import numpy as np
-
-from datetime import time, date, datetime
-from netCDF4 import Dataset
-from os.path import join
-
-from .nc_operations import VariableCreator, VariableCopier, DimensionCopier
-
-
-def date_from_days_since_0(days_since_00000101):
-    """Convert a float counting days since days since 0000-01-01 00:00:00
-    to a datetime object.
-    """
-
-    def add_years(d, years):
-        """Return a date that's `years` years after the date (or datetime)
-        object `d`. Return the same calendar date (month and day) in the
-        destination year, if it exists, otherwise use the following day
-        (thus changing February 29 to March 1).
-        """
-        # from https://stackoverflow.com/a/15743908
-        try:
-            return d.replace(year=d.year + years)
-        except ValueError:
-            return d + (date(d.year + years, 1, 1) - date(d.year, 1, 1))
-
-    full_days = int(days_since_00000101)
-    # fromordinal starts from day 0
-    timestamp_date = date.fromordinal(full_days + 1)
-    # fromordinal starts at year 1
-    timestamp_date = add_years(timestamp_date, -1)
-
-    hours = int((days_since_00000101 - full_days) * 24)
-    assert hours == (days_since_00000101 - full_days) * 24, (
-        "Can't convert to time at not full hour.")  # too lazy
-    timestamp_time = time(hour=hours)
-
-    return datetime.combine(timestamp_date, timestamp_time)
-
-
-def extract_data(in_path, time_index, dim_ops, var_ops, out_path_template):
-    """Extract and transform indicated data from time_index to
-    out_path_template.
-
-    Create a new netcdf-file at out_path_template after replacing the
-    placeholders with the date from the time_index in in_path.
-
-    Create a 'time' dimension and variable of size 1.
-    Add the ncattr calendar: 'proleptic_gregorian' to the time-variable.
-
-    Copy and transform the dimensions specified in the dim_ops.
-
-    Copy and transform the variables specified in the var_ops.
-
-    Adjust longitude from [0, 360) to (-180, 180].
-    """
-    with Dataset(in_path) as inf:
-        timestamp = date_from_days_since_0(inf.variables['time'][time_index])
-
-        out_path = timestamp.strftime(out_path_template)
-
-        with Dataset(out_path, 'w') as of:
-            of.createDimension(dimname='time', size=1)
-
-            # Create time variable
-            (VariableCreator(
-                var_args={
-                    'varname': 'time',
-                    'datatype': 'f8'
-                },
-                var_attrs={
-                    'axis': 'T',
-                    'calendar': 'proleptic_gregorian',
-                    'long_name': 'simulation_time',
-                    'standard_name': 'time',
-                    'units':
-                    timestamp.strftime('seconds since %Y-%m-%d %H:%M:%S')
-                },
-                var_vals=0).apply_to(of))
-
-            # Create date variable
-            (VariableCreator(var_args={
-                'varname': 'date',
-                'datatype': 'i4',
-                'dimensions': ('time', )
-            },
-                             var_attrs={
-                                 'long_name': ('current date as 8 digit'
-                                               ' integer (YYYYMMDD)')
-                             },
-                             var_vals=int(
-                                 timestamp.strftime('%Y%m%d'))).apply_to(of))
-
-            # Create datesec variable
-            sec_from_midnight = ((timestamp - timestamp.replace(
-                hour=0, minute=0, second=0, microsecond=0)).total_seconds())
-            (VariableCreator(var_args={
-                'varname': 'datesec',
-                'datatype': 'i4',
-                'dimensions': ('time', )
-            },
-                             var_attrs={
-                                 'long_name':
-                                 ('seconds to complete', 'current date'),
-                                 'units':
-                                 's'
-                             },
-                             var_vals=sec_from_midnight).apply_to(of))
-
-            # Transfer specified dimensions and variables
-            for op in dim_ops + var_ops:
-                op.apply_to(inf, of)
-
-            # Transform longitude: [0,360) -> [-180,180)
-            for i in range(len(of['lon'])):
-                if of['lon'][i] > 180:
-                    of['lon'][i] -= 360
-
-
-
[docs]def main(_, infile, outdir, params):
-    """Extract each timeslice from infile into seperate file in outdir.
-
-    Copies dimensions, renaming 'lev' -> 'level'.
-
-    Copies, renames and combines variables (see source code for specifics).
-
-    Transforms 'lon' to [-180, 180) range.
-
-    Parameters
-    ----------
-    _
-        Ignored
-    infile : str
-        Path to file to extract from
-    outdir : str
-        Path to the directory where the output files are written to
-    params : dict
-        Only entry: 'suffix'
-        Processed files are stored as ``outdir/{suffix}_YYYYMMDDHH.nc``
-    """
-    outname_template = join(outdir, params['suffix'] + '_%Y%m%d%H.nc')
-
-    dimpairs = [
-        (
-            'lev',  # name in src
-            'level'),  # name in dst
-        ('lat', 'lat'),
-        ('lon', 'lon'),
-        ('ilev', 'ilev')
-    ]
-
-    dim_copiers = [
-        DimensionCopier(src_name, dst_name) for src_name, dst_name in dimpairs
-    ]
-
-    varpairs_to_copy = [
-        (['CH3CHO_VMR_inst', 'GLYALD_VMR_inst'], 'ALD'),
-        (
-            'CO_VMR_inst',  # name in src, lists added toghether
-            'CO'),  # name in dst
-        ('CRESOL_VMR_inst', 'CSL'),
-        ('C2H6_VMR_inst', 'ETH'),
-        ('GLYOXAL_VMR_inst', 'GLY'),
-        ('H2O2_VMR_inst', 'H2O2'),
-        ('C3H8_VMR_inst', 'HC3'),
-        ('HNO3_VMR_inst', 'HNO3'),
-        ('BIGALK_VMR_inst', 'HC5'),
-        ('CH2O_VMR_inst', 'HCHO'),
-        ('HO2NO2_VMR_inst', 'HNO4'),
-        ('HO2_VMR_inst', 'HO2'),
-        ('ISOP_VMR_inst', 'ISO'),
-        (['CH3COCH3_VMR_inst', 'HYAC_VMR_inst', 'MEK_VMR_inst'], 'KET'),
-        (['MVK_VMR_inst', 'MACR_VMR_inst'], 'MACR'),
-        ('CH3COCHO_VMR_inst', 'MGLY'),
-        ('MPAN_VMR_inst', 'MPAN'),
-        ('N2O5_VMR_inst', 'N2O5'),
-        ('NH3_VMR_inst', 'NH3'),
-        ('NO_VMR_inst', 'NO'),
-        ('NO2_VMR_inst', 'NO2'),
-        ('NO3_VMR_inst', 'NO3'),
-        ('OH_VMR_inst', 'OH'),
-        ('C2H4_VMR_inst', 'OL2'),
-        ('ONIT_VMR_inst', 'ONIT'),
-        ('CH3OOH_VMR_inst', 'OP1'),
-        ('C2H5OOH_VMR_inst', 'OP2'),
-        ('CH3COOH_VMR_inst', 'ORA2'),
-        ('O3_VMR_inst', 'OZONE'),
-        ('CH3COOOH_VMR_inst', 'PAA'),
-        ('PAN_VMR_inst', 'PAN'),
-        ('SO2_VMR_inst', 'SO2'),
-        ('T', 'T'),
-        ('TOLUENE_VMR_inst', 'TOL'),
-        ('DUST1', 'VSOILA'),
-        ('DUST2', 'VSOILB'),
-        ('DUST3', 'VSOILC')
-    ]
-
-    varpairs_to_copy_dimchange = [('NH4_VMR_inst', 'VNH4Jm'),
-                                  (['OC1_VMR_inst',
-                                    'OC2_VMR_inst'], 'VORG1Jm'),
-                                  ('SO4_VMR_inst', 'VSO4Jm'),
-                                  (['CB1_VMR_inst', 'CB2_VMR_inst'], 'VSOOTJ')]
-
-    for time_index in range(Dataset(infile).dimensions['time'].size):
-        # Have to give dimensions explicitly because 'lev' changes to 'level'
-        # Have to give var_val_indices explicitly because we only copy one
-        # time index
-        spacial_variable_options = {
-            'var_args': {
-                'dimensions': ('time', 'level', 'lat', 'lon')
-            },
-            'var_val_indices': np.s_[time_index, :]
-        }
-
-        # 3D variables that simply get copied
-        var_opts = [{
-            'src_names': src,
-            'dst_name': dst,
-            **spacial_variable_options
-        } for src, dst in varpairs_to_copy]
-
-        # 3D variables with dimchange to mol/mol
-        var_opts += [{
-            'src_names': src,
-            'dst_name': dst,
-            'var_attrs': {
-                'units': 'mol/mol'
-            },
-            **spacial_variable_options
-        } for src, dst in varpairs_to_copy_dimchange]
-
-        # Others
-        var_opts += [{
-            'src_names': 'lat',
-            'dst_name': 'lat'
-        }, {
-            'src_names': 'lev',
-            'dst_name': 'level',
-            'var_args': {
-                'dimensions': ('level', )
-            }
-        }, {
-            'src_names': 'lon',
-            'dst_name': 'lon'
-        }, {
-            'src_names': 'P0',
-            'dst_name': 'P0'
-        }, {
-            'src_names': 'PS',
-            'dst_name': 'PSURF',
-            'var_args': {
-                'dimensions': ('time', 'lat', 'lon')
-            },
-            'var_val_indices': np.s_[time_index, :]
-        }, {
-            'src_names': 'hyam',
-            'dst_name': 'hyam',
-            'var_args': {
-                'dimensions': ('level', )
-            }
-        }, {
-            'src_names': 'hybm',
-            'dst_name': 'hybm',
-            'var_args': {
-                'dimensions': ('level', )
-            }
-        }, {
-            'src_names': 'ilev',
-            'dst_name': 'ilev'
-        }]
-
-        var_copiers = [VariableCopier(**kwargs) for kwargs in var_opts]
-
-        extract_data(infile, time_index, dim_copiers, var_copiers,
-                     outname_template)

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/reduce_output_start_end.html b/pr-preview/pr-63/_modules/jobs/tools/reduce_output_start_end.html deleted file mode 100644 index e569447d..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/reduce_output_start_end.html +++ /dev/null @@ -1,501 +0,0 @@ - - - - - - jobs.tools.reduce_output_start_end — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Module code
    • -
  • jobs.tools.reduce_output_start_end
    • -
  • -
    • -
-
-
-
-
- -

Source code for jobs.tools.reduce_output_start_end

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""
-Script used by `reduce_output` job
-
-Author: Michael Jaehn (jae), Empa, Switzerland
-"""
-
-from __future__ import print_function
-
-import sys
-import numpy as np
-import netCDF4 as nc
-from datetime import datetime
-from datetime import timedelta
-import glob
-import os
-import shutil
-import csv
-
-import helper
-
-import logging
-
-logging.basicConfig(level=logging.DEBUG)
-
-
-def get_attrs(v):
-    return dict((k, v.getncattr(k)) for k in v.ncattrs())
-
-
-def str2char(s):
-    return np.array(list(s), 'c')
-
-
-def search_met(infile, fname_met):
-    """
-    Checks which file contains the meteorology data
-    """
-    time = None
-    tocheck = []
-    print(infile)
-    for f in infile:
-        basename = os.path.split(f)[1]
-        print(basename)
-        timestr = basename.split('lffd', 1)[1][:10]
-        mytime = datetime.strptime(timestr, '%Y%m%d%H')
-        if time is None:
-            time = mytime
-        if mytime == time:
-            tocheck.append(f)
-
-    for f in tocheck:
-        with nc.Dataset(f, 'r') as inf:
-            for var in ['T', 'P', 'PS', 'QV']:
-                if var in inf.variables:
-                    basename = os.path.split(f)[1]
-                    fileending = basename.split('lffd', 1)[1][10:-3]
-                    fname_met[var] = fileending
-
-    return fname_met
-
-
-def append_variable(nc, name, values, attrs=None):
-    """\
-    Append variable (name, values) to netCDF file.
-    """
-
-    from six import string_types
-
-    if attrs is None:
-        attrs = {}
-
-    var = nc.createVariable(name,
-                            values.dtype, ('time', 'rlat', 'rlon'),
-                            zlib=True)
-    var[0] = values
-
-    # add or update attributes
-    for key, value in attrs.items():
-        if isinstance(value, string_types):
-            var.setncattr(key, str2char(value))
-        else:
-            var.setncattr(key, value)
-
-
-def reduce_output(infile, cfiles, h, nout_levels, output_path, fname_met, lsd,
-                  convert):
-    dtime = infile.split('lffd', 1)[1][0:10]
-    """Get path and filename for output file"""
-    path, output_filename = os.path.split(infile)
-    outfile = os.path.join(output_path, output_filename)
-    with nc.Dataset(infile, 'r') as inf, \
-         nc.Dataset(outfile, 'w') as outf:
-        # Copy global attributes all at once via dictionary
-        outf.setncatts(inf.__dict__)
-        # Copy dimensions
-        for name, dimension in inf.dimensions.items():
-            outf.createDimension(
-                name,
-                (len(dimension) if not dimension.isunlimited() else None))
-
-        # Get level information
-        level = len(inf.dimensions['level'])
-        level1 = len(inf.dimensions['level1'])
-
-        # Create new dimension level2
-        if nout_levels == -1:
-            nout_levels = level
-        else:
-            outf.createDimension('level2', nout_levels)
-
-        # Copy variables
-        for varname in inf.variables.keys():
-            logging.info('%s: %s' % (output_filename, varname))
-            var = inf.variables[varname]
-            attrs = get_attrs(var)
-            if len(var.dimensions) == 4:
-                if var.dimensions[1] == 'level':
-                    var_dimensions = list(var.dimensions)
-                    var_dimensions[1] = 'level' + '2' * (nout_levels != level)
-                elif var.dimensions[1] == 'level1':
-                    var_dimensions = list(var.dimensions)
-                    var_dimensions[1] = 'level' + '2' * (
-                        nout_levels != level) + '1' * (nout_levels == level)
-                else:
-                    var_dimensions = var.dimensions
-            else:
-                var_dimensions = var.dimensions
-
-            if len(var.dimensions) > 2:
-                if (varname in lsd):
-                    if '_FillValue' in var.ncattrs():
-                        fill_value = inf[varname].getncattr('_FillValue')
-                        outf.createVariable(
-                            varname,
-                            var.dtype,
-                            var_dimensions,
-                            zlib=True,
-                            fill_value=fill_value,
-                            least_significant_digit=lsd[varname])
-                    else:
-                        outf.createVariable(
-                            varname,
-                            var.dtype,
-                            var_dimensions,
-                            zlib=True,
-                            least_significant_digit=lsd[varname])
-                else:
-                    if '_FillValue' in var.ncattrs():
-                        fill_value = inf[varname].getncattr('_FillValue')
-                        outf.createVariable(varname,
-                                            var.dtype,
-                                            var_dimensions,
-                                            zlib=True,
-                                            fill_value=fill_value)
-                    else:
-                        outf.createVariable(varname,
-                                            var.dtype,
-                                            var_dimensions,
-                                            zlib=True)
-            else:
-                outf.createVariable(varname,
-                                    var.dtype,
-                                    var_dimensions,
-                                    zlib=True)
-
-            for attr in var.ncattrs():
-                if attr != '_FillValue':
-                    outf[varname].setncattr(attr, inf[varname].getncattr(attr))
-
-            gas = None
-            if varname != 'rotated_pole':
-                # Check for 3D data and extract only lower_levels
-                if 'level1' in var.dimensions and \
-                    len(var.dimensions) == 4:
-                    lstart = -nout_levels - (nout_levels == level)
-                elif 'level' in var.dimensions and \
-                    len(var.dimensions) == 4:
-                    lstart = -nout_levels
-                else:
-                    outf[varname][:] = inf[varname][:]
-
-            if (varname.startswith('CO2_') or varname.startswith('CO_') or
-                varname.startswith('CH4_') or varname.startswith('C14_') or
-                varname.startswith('NOX_') or varname.startswith('NO2_')) and \
-                len(var.dimensions) == 4:
-                outvar = outf.variables[varname]
-                gas = varname.split('_')[0]
-                if gas == 'NOX':
-                    attrs['standard_name'] = attrs['standard_name'].replace(
-                        'NOX', 'NO2')
-                    gas = 'NO2'
-                field = inf[varname][:, lstart:, :, :]
-                unit = attrs['units']
-
-                if convert:
-                    outvar.units = helper.common_unit(gas)
-                    if gas == 'C14':
-                        outf[varname][:] = helper.convert_unit(
-                            field, unit, outvar.units, 45.993e-3)
-                    else:
-                        outf[varname][:] = helper.convert_unit(
-                            field, unit, outvar.units, gas)
-                else:
-                    outvar.units = unit
-                    outf[varname][:] = field
-
-                attrs['standard_name'] = attrs['standard_name'].replace(
-                    '%s_mass_fraction' % gas, 'X%s' % gas)
-                attrs['units'] = outvar.units
-                attrs2 = attrs.copy()
-                attrs2['standard_name'] = attrs2['standard_name'].replace(
-                    'X%s' % gas, 'Y%s' % gas)
-            elif varname != 'rotated_pole' and len(var.dimensions) == 4 and \
-            ('level1' in var.dimensions or 'level' in var.dimensions):
-                outf[varname][:] = inf[varname][:, lstart:, :, :]
-
-            if gas:
-                fname_met_base = os.path.split(
-                    infile)[0] + '/' + os.path.split(infile)[1][:14]
-                with nc.Dataset(fname_met_base+fname_met['QV']+'.nc', 'r') as inf_qv, \
-                     nc.Dataset(fname_met_base+fname_met['T']+'.nc', 'r') as inf_t, \
-                     nc.Dataset(fname_met_base+fname_met['PS']+'.nc', 'r') as inf_ps, \
-                     nc.Dataset(fname_met_base+fname_met['P']+'.nc', 'r') as inf_p:
-                    qv = np.array(inf_qv.variables['QV'][0])
-                    t = np.array(inf_t.variables['T'][0])
-                    ps = np.array(inf_ps.variables['PS'][0])
-                    p = np.array(inf_p.variables['P'][0])
-
-                    xm = np.array(inf.variables[varname][0])
-                    mair = helper.calculate_mair(p, ps, h)
-
-                    # Column-averaged dry-air mole fraction
-                    column = helper.calculate_xgas(xm, mair, gas, qv)
-                    column = column.astype('f4')
-                    logging.info('%s: X%s' % (output_filename, varname))
-                    append_variable(outf, 'X%s' % varname, column, attrs=attrs)
-
-                    # Column-averaged moist-air mole fraction
-                    column2 = helper.calculate_xgas(xm, mair, gas, 0.0)
-                    column2 = column2.astype('f4')
-                    logging.info('%s: Y%s' % (output_filename, varname))
-                    append_variable(outf,
-                                    'Y%s' % varname,
-                                    column2,
-                                    attrs=attrs2)
-
-    return fname_met
-
-
-
[docs]def main(indir, outdir, strdate_start, strdate_end, nout_levels, csvfile,
-         convert_gas):
-    """
-    Script to reduce output.
-    
-    Output: TODO
-
-    Parameters (TODO)
-    ----------
-    opath : str
-        Output path where the processed data is going to be written
-    """
-    """Get list of constant files"""
-    cfiles = []
-    read_cfile = False
-    for infile in sorted(glob.glob(os.path.join(indir, "lffd*[0-9]c*.nc"))):
-        cfiles.append(infile)
-        if not read_cfile:
-            # Read the first constant file and store height value
-            logging.info(infile)
-            with nc.Dataset(infile) as inf:
-                h = np.array(inf.variables['HHL'][0])
-            read_cfile = True
-
-    if not read_cfile:
-        logging.error('Constant file could not be read')
-    """Get list of files"""
-    infiles = sorted(glob.glob(os.path.join(indir, "lffd*.nc")))
-    """Remove constant files from file list"""
-    for cfile in cfiles:
-        if cfile in infiles:
-            infiles.remove(cfile)
-
-    date_start = datetime.strptime(strdate_start, '%Y%m%d%H')
-    date_end = datetime.strptime(strdate_end, '%Y%m%d%H')
-    """Only take relevant date period into account"""
-    for infile in list(infiles):
-        basename = os.path.split(infile)[1]
-        timestr = basename.split('lffd', 1)[1][:10]
-        mytime = datetime.strptime(timestr, '%Y%m%d%H')
-        if mytime < date_start or mytime > date_end:
-            infiles.remove(infile)
-    """Initialize dict to remember file name for meteo variables"""
-    fname_met = {
-        'T': None,
-        'P': None,
-        'PS': None,
-        'QV': None,
-    }
-    fname_met = search_met(infiles, fname_met)
-    """Translate csv file to dict"""
-    variables = helper.find_variables_file(csvfile)
-    lsd = variables['lsd'].to_dict()
-    """Loop over all input files and apply output reduction"""
-    for infile in infiles:
-        fname_met = reduce_output(infile, cfiles, h, int(nout_levels), outdir,
-                                  fname_met, lsd, convert_gas == 'True')

-
-
-if __name__ == '__main__':
-    indir = sys.argv[1]
-    outdir = sys.argv[2]
-    strdate_start = sys.argv[3]
-    strdate_end = sys.argv[4]
-    nout_levels = sys.argv[5]
-    csvfile = sys.argv[6]
-    convert_gas = sys.argv[7]
-    main(indir, outdir, strdate_start, strdate_end, nout_levels, csvfile,
-         convert_gas)
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/string2char.html b/pr-preview/pr-63/_modules/jobs/tools/string2char.html deleted file mode 100644 index ef061182..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/string2char.html +++ /dev/null @@ -1,226 +0,0 @@ - - - - - - jobs.tools.string2char — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.string2char

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""\
-Convert string to char for attributes globally and for variables.
-"""
-
-from __future__ import print_function
-
-import sys
-import numpy as np
-import netCDF4
-
-if (sys.version_info.major) >= 3:
-    basestring = (str, bytes)
-
-
-def string2char(nc, name, value):
-    if isinstance(value, basestring):
-        value = np.array(list(value), 'c')
-        nc.setncattr(name, value)
-
-
-
[docs]def main(filename):
-    """Convert the variable names of a netcdf-file from strings to a 
-    ``np.array`` of chars.
-    
-    Parameters
-    ----------
-    filename : str
-        Path to the netcdf-file
-    """
-    with netCDF4.Dataset(filename, 'a') as nc:
-        for name in nc.ncattrs():
-            value = nc.getncattr(name)
-            string2char(nc, name, value)
-
-        for v in nc.variables:
-            var = nc.variables[v]
-            for name in var.ncattrs():
-                value = var.getncattr(name)
-                string2char(var, name, value)

-
-
-if __name__ == '__main__':
-    main(sys.argv[1])
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/vprmsplit.html b/pr-preview/pr-63/_modules/jobs/tools/vprmsplit.html deleted file mode 100644 index 514a6ea2..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/vprmsplit.html +++ /dev/null @@ -1,336 +0,0 @@ - - - - - - jobs.tools.vprmsplit — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.tools.vprmsplit

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-"""
-Script to extract VPRM emissions for a single day
-and to convert the output into an int2lm compatible format.
-
-Authors: Dominik Brunner (brd), Empa, Switzerland
-         Michael Jaehn (jae), Empa, Switzerland
-
-History:
-    brd, 23 Jul 2013: first implementation
-    brd, 20 Aug 2014: modified to handle files with gpp and ra provided
-                      separately
-    brd, 12 Jul 2015: corrected for grid coordinate shift by +0.5 grid cells
-                      (since cell coordinates are given for lower left corner)
-                      and added option to specify CO2 name
-    brd, 15 Jan 2017: slightly adapted for hypatia and project SmartCarb
-    jae, 17 Aug 2018: translated to Python
-
-TODOs:
-    - use logging
-"""
-
-from __future__ import print_function
-
-import sys
-import numpy as np
-from netCDF4 import Dataset
-from datetime import datetime
-from datetime import timedelta
-import logging
-
-
-
[docs]def main(year, ipath, opath):
-    """
-    Script to extract VPRM emissions for a single day
-    and to convert the output into an int2lm compatible format.
-    
-    Output:
-    The script generates individual 1-hour emission files for the specified
-    year::
-
-        gpp_yyyymmddhh.nc
-        ra_yyyymmddhh.nc
-
-    Parameters
-    ----------
-    year : str
-        Year (YYYY) of data to be processed
-        The original VPRM input file (e.g., VPRM_ECMWF_*_2017.nc for 2017
-        fluxes) needs to be present in the input directory 'ipath'
-    ipath : str
-        Input path where the VPRM input file is located
-    opath : str
-        Output path where the processed data is going to be written
-    """
-    m_co2 = 44.01
-
-    filename_gee = ''.join([ipath, '/VPRM_ECMWF_GEE_', year[:4], '.nc'])
-    filename_resp = ''.join([ipath, '/VPRM_ECMWF_RESP_', year[:4], '.nc'])
-
-    print('Opening VPRM GEE file', filename_gee)
-    ifile_gee = Dataset(filename_gee, mode='r')
-    print('Opening VPRM RESP file', filename_resp)
-    ifile_resp = Dataset(filename_resp, mode='r')
-
-    lat = ifile_gee.variables['lat'][:]
-    lon = ifile_gee.variables['lon'][:]
-    hours = ifile_gee.variables['time'][:]
-    gpp = ifile_gee.variables['GEE'][:]
-    resp = ifile_resp.variables['RESP'][:]
-    ifile_gee.close()
-    ifile_resp.close()
-
-    # Get grid spacing of VPRM grid
-    dx = lat[1] - lat[0]
-    dy = lon[1] - lon[0]
-
-    # Change fluxes from umol m-2 s-1 to kg m-2 s-1 for GPP
-    gpp *= 1e-9 * m_co2
-
-    # Switch the sign and avoid negative values
-    gpp *= -1.0
-    gpp[gpp <= 0.0] = 0.0
-
-    # Change fluxes from umol m-2 s-1 to kg m-2 s-1 for RESP
-    resp *= 1e-9 * m_co2
-
-    print(hours)
-    for ti, hour in enumerate(hours):
-
-        begin_of_year_dt = datetime.strptime(year[:4] + '0101', '%Y%m%d')
-        curdate_dt = begin_of_year_dt + timedelta(hours=int(hour))
-        curdate_str = datetime.strftime(curdate_dt, '%Y%m%d%H')
-        print(curdate_dt)
-
-        ofile_gpp = Dataset(opath + '/gpp_' + curdate_str + '.nc', mode='w')
-
-        olat = ofile_gpp.createDimension('lat', len(lat))
-        olon = ofile_gpp.createDimension('lon', len(lon))
-        otime = ofile_gpp.createDimension('time', 1)
-
-        olat = ofile_gpp.createVariable('lat', np.float64, ('lat', ))
-        olon = ofile_gpp.createVariable('lon', np.float64, ('lon', ))
-        otime = ofile_gpp.createVariable('time', np.float64, ('time', ))
-        otime.units = ''.join(['seconds since ', year, '-01-01 00:00:00'])
-        otime.calendar = 'proleptic_gregorian'
-
-        ogpp = ofile_gpp.createVariable('CO2_GPP_F',
-                                        np.float32, ('time', 'lat', 'lon'),
-                                        fill_value=-999.99)
-        ogpp.units = 'kg m-2 s-1'
-        ogpp.long_name = 'surface upward mass flux of GPP CO2'
-        ogpp.standard_name = 'surface_upward_mass_flux_of_gpp_carbon_dioxide'
-
-        olat[:] = lat + dx / 2.
-        olon[:] = lon + dy / 2.
-        otime[:] = int((curdate_dt - begin_of_year_dt).total_seconds())
-        ogpp[:] = gpp[ti, :]
-
-        ofile_gpp.close()
-
-        ofile_resp = Dataset(opath + '/ra_' + curdate_str + '.nc', mode='w')
-
-        olat = ofile_resp.createDimension('lat', len(lat))
-        olon = ofile_resp.createDimension('lon', len(lon))
-        otime = ofile_resp.createDimension('time', 1)
-
-        olat = ofile_resp.createVariable('lat', np.float64, ('lat', ))
-        olon = ofile_resp.createVariable('lon', np.float64, ('lon', ))
-        otime = ofile_resp.createVariable('time', np.float64, ('time', ))
-        otime.units = ''.join(['seconds since ', year, '-01-01 00:00:00'])
-        otime.calendar = 'proleptic_gregorian'
-
-        oresp = ofile_resp.createVariable('CO2_RA_F',
-                                          np.float32, ('time', 'lat', 'lon'),
-                                          fill_value=-999.99)
-        oresp.units = 'kg m-2 s-1'
-        oresp.long_name = 'surface upward mass flux of respiration CO2'
-        oresp.standard_name = 'surface_upward_mass_flux_of_respiration_carbon_dioxide'
-
-        olat[:] = lat + dx / 2.
-        olon[:] = lon + dy / 2.
-        otime[:] = int((curdate_dt - begin_of_year_dt).total_seconds())
-        oresp[:] = resp[ti, :]
-
-        ofile_resp.close()

-
-
-if __name__ == '__main__':
-
-    year = sys.argv[1]
-    ipath = sys.argv[2]
-    opath = sys.argv[3]
-    main(year, ipath, opath)
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/write_cosmo_input_ghg.html b/pr-preview/pr-63/_modules/jobs/tools/write_cosmo_input_ghg.html deleted file mode 100644 index efdd7483..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/write_cosmo_input_ghg.html +++ /dev/null @@ -1,299 +0,0 @@ - - - - - - jobs.tools.write_cosmo_input_ghg — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Module code
    • -
  • jobs.tools.write_cosmo_input_ghg
    • -
  • -
    • -
-
-
-
-
- -

Source code for jobs.tools.write_cosmo_input_ghg

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import csv
-import sys
-from .. import tools
-
-STR2INT = {
-    'ytype_adv': {
-        'off': 0,
-        'on': 1
-    },
-    'ytype_diff': {
-        'off': 0,
-        'on': 1
-    },
-    'ytype_turbmix': {
-        'off': 0,
-        '1D': 1,
-        '3D': 2
-    },
-    'ytype_passconv': {
-        'off': 0,
-        'on': 1
-    },
-    'ytype_ini': {
-        'zero': 0,
-        'file': 1,
-        'user': 2
-    },
-    'ytype_lbc': {
-        'zero': 0,
-        'file': 1,
-        'constant': 2,
-        'zero_gradient': 3,
-        'user': 4
-    },
-    'ytype_bbc': {
-        'zero_flux': 0,
-        'zero_value': 1,
-        'surface_value': 2
-    },
-    'ytype_relax': {
-        'off': 0,
-        'full': 1,
-        'inflow': 2
-    },
-    'ytype_damp': {
-        'off': 0,
-        'on': 1
-    },
-    'ytype_clip': {
-        'off': 0,
-        'on': 1
-    }
-}
-
-# Read initial conditions from file (= 1) in case of spinup simluation
-STR2INT_recycling = STR2INT.copy()
-STR2INT_recycling["ytype_ini"] = {'zero': 1, 'file': 1, 'user': 2}
-
-
-def group2text(group, recycling=False):
-
-    lines = ['&TRACER']
-    for key, value in group.items():
-
-        if key == '' or value == '':
-            continue
-
-        if key in STR2INT:
-            if recycling:
-                value = STR2INT_recycling[key][value]
-            else:
-                value = STR2INT[key][value]
-            key = 'i%s' % key[1:]
-
-        if key[0] == 'y':
-            value = "'%s'" % value
-
-        if key == 'ycatl' or key == 'ytpl' or key == 'yvpl':
-            value = value.replace('\'\'', '\'')
-        lines.append('  %s = %s,' % (key, value))
-    lines.append('/\n')
-
-    return '\n'.join(lines)
-
-
-
[docs]def main(csv_filename, namelist_filename, cfg=None):
-    """Convert a table (``.csv`` file) to namelist file (``INPUT_GHG``)
-    read by **COSMO**.
-    
-    Parameters
-    ----------
-    csv_filename : str
-        Path to the source csv-file
-    namelist_filename : str
-        Path to the namelist file that will be created
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    """
-
-    with open(csv_filename, 'r') as csv_file:
-        reader = csv.DictReader(csv_file, delimiter=',')
-        reader = [r for r in reader if r[''] != '#']
-
-        with open(namelist_filename, 'a') as nml_file:
-            for group in reader:
-                if hasattr(cfg, 'spinup') and not cfg.first_one:
-                    nml_file.write(group2text(group, recycling=True))
-                else:
-                    nml_file.write(group2text(group))

-
-
-if __name__ == '__main__':
-    input_filename = sys.argv[1]  # csv file with tracers
-    output_filename = sys.argv[2]  # filename (INPUT_TRCR) read by COSMO
-    main(input_filename, output_filename)
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/tools/write_int2lm_input_art.html b/pr-preview/pr-63/_modules/jobs/tools/write_int2lm_input_art.html deleted file mode 100644 index c6034bc6..00000000 --- a/pr-preview/pr-63/_modules/jobs/tools/write_int2lm_input_art.html +++ /dev/null @@ -1,301 +0,0 @@ - - - - - - jobs.tools.write_int2lm_input_art — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
-
    -
    • -
  • Module code
    • -
  • jobs.tools.write_int2lm_input_art
    • -
  • -
    • -
-
-
-
-
- -

Source code for jobs.tools.write_int2lm_input_art

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from __future__ import print_function
-
-import argparse
-import csv
-import sys
-
-
-def art_control(nart_ds, nart_trcr, hstart=0):
-    lines = [
-        "&ARTCONTROL",
-        "  nart_ds = %d," % nart_ds,  # number of dataset groups
-        "  nart_trcr = %d," % nart_trcr,  # number of tracers groups
-        "  hstart = %d," % hstart,
-        "/"
-    ]
-    return '\n'.join(lines)
-
-
-def make_group(keys, values, group):
-    lines = ['&%s' % group]
-    for key, value in zip(keys, values):
-        if value:
-            if key == 'yvarlist':
-                value = ','.join('"%s"' % v.strip() for v in value.split(","))
-                lines.append('  %s = %s,' % (key, value))
-            elif key[0] == 'y':
-                lines.append('  %s = "%s",' % (key, value))
-            else:
-                lines.append('  %s = %s,' % (key, value))
-    lines.append('/\n')
-    return '\n'.join(lines)
-
-
-def read_file(filename):
-    with open(filename, 'r') as csv_file:
-        lines = [
-            line[1:] for line in csv.reader(csv_file)
-            if not line[0].startswith('#')
-        ]
-
-    return lines[0], lines[1:]
-
-
-
[docs]def main(trcr_filename, set_filename, nml_filename, hstart=0):
-    """Write the INPUT_ART namelist file for int2lm from ``.csv`` files
-    
-    Parameters
-    ----------
-    trcr_filename : str
-        csv file with tracer definitions
-    set_filename : str
-        csv file with tracer datasets
-    nml_filename : str
-        output filename (INPUT_ART)
-    hstart : int
-        meteorology spin up in hours
-    """
-    # art tracers
-    if trcr_filename is None:
-        tracer_values = []
-        n_tracers = 0
-    else:
-        tracer_keys, tracer_values = read_file(trcr_filename)
-        n_tracers = len(tracer_values)
-
-    # art datasets
-    if set_filename is None:
-        set_values = []
-        n_sets = 0
-    else:
-        set_keys, set_values = read_file(set_filename)
-        n_sets = len(set_values)
-
-    # write namelist file
-    with open(nml_filename, 'w') as nml:
-
-        nml.write(art_control(n_sets, n_tracers, hstart))
-        nml.write('\n')
-
-        for values in tracer_values:
-            text = make_group(tracer_keys, values, 'ARTTRACER')
-            nml.write(text)
-            nml.write('\n')
-
-        for values in set_values:
-            text = make_group(set_keys, values, 'ARTDATASET')
-            nml.write(text)
-            nml.write('\n')

-
-
-if __name__ == '__main__':
-    parser = argparse.ArgumentParser(description='Write INPUT_ART for int2lm.')
-
-    parser.add_argument('-t',
-                        dest='trcr_filename',
-                        default=None,
-                        type=str,
-                        help='filename of csv file with tracers')
-    parser.add_argument('-d',
-                        dest='datasets_filename',
-                        default=None,
-                        type=str,
-                        help='filename of csv file with datasets')
-    parser.add_argument('-o',
-                        dest='nml_filename',
-                        default='INPUT_ART',
-                        type=str,
-                        help='output filename (INPUT_ART)')
-    parser.add_argument('-m',
-                        dest='meteo_spinup',
-                        default=0,
-                        type=float,
-                        help='meteorology spin up')
-
-    args = parser.parse_args()
-    main(args.trcr_filename, args.datasets_filename, args.nml_filename,
-         args.meteo_spinup)
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/jobs/verify_chain.html b/pr-preview/pr-63/_modules/jobs/verify_chain.html deleted file mode 100644 index 1d2eef2e..00000000 --- a/pr-preview/pr-63/_modules/jobs/verify_chain.html +++ /dev/null @@ -1,253 +0,0 @@ - - - - - - jobs.verify_chain — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for jobs.verify_chain

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-import os
-import logging
-import netCDF4 as nc
-
-from . import tools
-
-BASIC_PYTHON_JOB = True
-
-
-def comp_data(dataset1, dataset2, variables):
-    """Use tools.helper.datasets_equal to compare the datasets.
-    """
-    tools.helper.datasets_equal(dataset1, dataset2, variables, verbose=True)
-
-
-
[docs]def main(cfg):
-    """Compare outputs of the chain to a reference.
-
-    Looks for the reference-file in ``cfg.verify_chain['reference_dir']``.
-    
-    Looks for the output file in ``cfg.verify_chain['output_dir']`` (if not ``None``), else it
-    goes to the output directory created by the **COSMO**-job.
-    
-    In the dict ``cfg.verify_chain['values_to_check']``, the user specifies the names of the
-    files to be compared as keys, and the variables to compare as a list.
-
-    To compare the temperatures of the last output of the example case, the
-    following variables should be added to the ``config.yaml`` file: ::
-
-        verify_chain['reference_dir'] = os.path.join(input_root, "reference_output")
-        verify_chain['output_dir'] = None
-        verify_chain['values_to_check'] = {("reference_lffd2015010200.nc","lffd2015010200.nc"):
-              ['T']}
-
-    Parameters
-    ----------	
-    cfg : Config
-        Object holding all user-configuration parameters as attributes
-    """
-    tools.change_logfile(cfg.logfile)
-    logging.info("Started verification")
-    for (ref_file,
-         run_file), variables in cfg.verify_chain['values_to_check'].items():
-        logging.info("Comparing " + str(variables))
-
-        # reference file location
-        ref_file_path = os.path.join(cfg.verify_chain['reference_dir'],
-                                     ref_file)
-
-        # run data location
-        if cfg.verify_chain['output_dir'] is None:
-            # Standard output location
-            run_file_path = os.path.join(
-                cfg.output_root, cfg.startdate_sim_yyyymmddhh + "_" +
-                cfg.enddate_sim_yyyymmddhh, "cosmo_output", run_file)
-        else:
-            # User-provided output location
-            run_file_path = os.path.join(cfg.verify_chain['output_dir'],
-                                         run_file)
-
-        logging.info("Output file: " + str(run_file_path))
-        logging.info("Reference file: " + str(ref_file_path))
-
-        # compare data
-        with nc.Dataset(ref_file_path) as ref_data, nc.Dataset(
-                run_file_path) as run_data:
-            comp_data(ref_data, run_data, variables)
-
-    logging.info("Finished verification")

-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_modules/run_chain.html b/pr-preview/pr-63/_modules/run_chain.html deleted file mode 100644 index b64c89e1..00000000 --- a/pr-preview/pr-63/_modules/run_chain.html +++ /dev/null @@ -1,541 +0,0 @@ - - - - - - run_chain — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

Source code for run_chain

-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-from datetime import datetime, timedelta
-import pytz
-import logging
-import shutil
-import argparse
-
-import jobs
-from jobs import tools
-from config import Config
-
-
-def parse_arguments():
-    """Parse command line arguments for the Processing Chain script.
-
-    Parses and retrieves command line arguments, allowing users to specify
-    run identifiers, jobs to execute, and various options to control the
-    execution of the Processing Chain.
-
-    Returns
-    -------
-    argparse.Namespace
-        A namespace object containing parsed command line arguments.
-    """
-    parser = argparse.ArgumentParser(description="Run the Processing Chain.")
-
-    parser.add_argument("casenames",
-                        nargs='+',
-                        help="List of identifiers for the runs. "
-                        "The config-files for each run is assumed "
-                        "to be in cases/<casename>/. The runs are executed "
-                        "sequentially in the order they're given here.")
-
-    jobs_help = ("List of job names to be executed. A job is a .py "
-                 "file in jobs/ with a main()-function which "
-                 "handles one aspect of the Processing Chain, for "
-                 "example copying meteo-input data or launching a "
-                 "job for int2lm. "
-                 "Jobs are executed in the order in which they are "
-                 "given here. "
-                 "If no jobs are given, default jobs will be executed"
-                 "as defined in config/workflows.yaml.")
-    parser.add_argument("-j",
-                        "--jobs",
-                        nargs='*',
-                        dest="job_list",
-                        help=jobs_help,
-                        default=None)
-
-    chunks_help = ("List of chunks to be executed. A chunk is time"
-                   "frame within the total simulation period."
-                   "It has the format `YYYYMMDDHH_YYYYMMDDHH`."
-                   "If no chunks are given, all chunks within the"
-                   "simulation period will be executed.")
-    parser.add_argument("-c",
-                        "--chunks",
-                        nargs='*',
-                        dest="chunk_list",
-                        help=chunks_help,
-                        default=None)
-
-    sync_help = ("Force synchronous execution.")
-    parser.add_argument("-s",
-                        "--force-sync",
-                        action='store_true',
-                        help=sync_help)
-
-    no_logging_help = ("Disable logging for chain_status.log.")
-    parser.add_argument("--no-logging",
-                        action='store_false',
-                        dest="enable_logging",
-                        default=True,
-                        help=no_logging_help)
-
-    force_help = ("Force the processing chain to redo all specified jobs,"
-                  " even if they have been started already or were finished"
-                  " previously. WARNING: Only logfiles get deleted,"
-                  " other effects of a given job (copied files etc.)"
-                  " are simply overwritten. This may cause errors"
-                  " or unexpected behavior.")
-    parser.add_argument("-f", "--force", action='store_true', help=force_help)
-
-    resume_help = (
-        "Resume the Processing Chain by restarting the last unfinished job."
-        " WARNING: Only the logfile gets deleted,"
-        " other effects of a given job (copied files etc.)"
-        " are simply overwritten. This may cause errors."
-        " or unexpected behavior.")
-    parser.add_argument("-r",
-                        "--resume",
-                        help=resume_help,
-                        dest="resume",
-                        action='store_true')
-
-    args = parser.parse_args()
-
-    return args
-
-
-
[docs]def run_chunk(cfg, force, resume):
-    """Run a chunk of the processing chain, managing job execution and logging.
-
-    This function sets up and manages the execution of a Processing Chain, handling
-    job execution, logging, and various configuration settings.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding user-defined configuration parameters as attributes.
-    force : bool
-        If True, it will force the execution of jobs regardless of their completion status.
-    resume : bool
-        If True, it will resume the last unfinished job.
-
-    Raises
-    ------
-    RuntimeError
-        If an error or timeout occurs during job execution.
-
-    Notes
-    -----
-    - This function sets various configuration values based on the provided parameters.
-    - It checks for job completion status and resumes or forces execution accordingly.
-    - Job log files are managed, and errors or timeouts are handled with notifications.
-    """
-    # Set forecast time
-    cfg.forecasttime = (cfg.enddate_sim -
-                        cfg.startdate_sim).total_seconds() / 3600
-
-    # Logging
-    cfg.chain_root = cfg.work_root / cfg.casename / cfg.chunk_id
-    cfg.log_working_dir = cfg.chain_root / 'checkpoints' / 'working'
-    cfg.log_finished_dir = cfg.chain_root / 'checkpoints' / 'finished'
-
-    # Create working directories
-    tools.create_dir(cfg.chain_root, "chain_root")
-    tools.create_dir(cfg.log_working_dir, "log_working")
-    tools.create_dir(cfg.log_finished_dir, "log_finished")
-
-    # Config variables for spinup and restart runs
-    cfg.cosmo_restart_in = ''
-    cfg.cosmo_restart_out = ''
-    if hasattr(cfg, 'spinup'):
-        if cfg.chunk_id_prev:
-            cfg.chain_root_prev = cfg.work_root / cfg.casename / cfg.chunk_id_prev
-            cfg.last_cosmo_output = cfg.chain_root_prev / 'cosmo' / 'output'
-    elif 'restart' in cfg.workflow['features']:
-        if cfg.chunk_id_prev:
-            cfg.chain_root_prev = cfg.work_root / cfg.casename / cfg.chunk_id_prev
-            cfg.cosmo_restart_in = cfg.chain_root_prev / 'cosmo' / 'restart'
-        cfg.cosmo_restart_out = cfg.chain_root / 'cosmo' / 'restart'
-
-    if not cfg.force_sync:
-        # Empty curent job ids
-        cfg.job_ids['current'] = {}
-
-        # Submit current chunk
-        for job_name in cfg.jobs:
-            if (cfg.log_finished_dir / job_name).exists() and not force:
-                # Skip job if already finished
-                print(f'    └── Skipping "{job_name}" job')
-                skip = True
-            else:
-                print(f'    └── Submitting "{job_name}" job')
-
-                # Logfile settings
-                cfg.logfile = cfg.log_working_dir / job_name
-                cfg.logfile_finish = cfg.log_finished_dir / job_name
-
-                # Submit the job
-                job = getattr(jobs, job_name)
-                if hasattr(job, 'BASIC_PYTHON_JOB') and job.BASIC_PYTHON_JOB:
-                    cfg.submit_basic_python(job_name)
-                else:
-                    job.main(cfg)
-
-        # Wait for previous chunk jobs, monitor them and cycle info
-        cfg.cycle()
-
-    else:  # For nested run_chain.py
-        for job_name in cfg.jobs:
-            print(f'    └── Process "{job_name}" for chunk "{cfg.chunk_id}"')
-            try:
-                # Change the log file
-                cfg.logfile = cfg.log_working_dir / job_name
-                cfg.logfile_finish = cfg.log_finished_dir / job_name
-
-                # Launch the job
-                to_call = getattr(jobs, job_name)
-                to_call.main(cfg)
-
-                shutil.copy(cfg.logfile, cfg.logfile_finish)
-
-                exitcode = 0
-            except Exception:
-                exitcode = 1
-                subject = "ERROR or TIMEOUT in job '%s' for chunk '%s'" % (
-                    job_name, cfg.chunk_id)
-                logging.exception(subject)
-                if cfg.user_mail:
-                    message = tools.prepare_message(cfg.log_working_dir /
-                                                    job_name)
-                    logging.info('Sending log file to %s' % cfg.user_mail)
-                    tools.send_mail(cfg.user_mail, subject, message)
-
-            if exitcode != 0 or not (cfg.log_finished_dir / job_name).exists():
-                subject = "ERROR or TIMEOUT in job '%s' for chunk '%s'" % (
-                    job_name, cfg.chunk_id)
-                if cfg.user_mail:
-                    message = tools.prepare_message(cfg.log_working_dir /
-                                                    job_name)
-                    logging.info('Sending log file to %s' % cfg.user_mail)
-                    tools.send_mail(cfg.user_mail, subject, message)
-                raise RuntimeError(subject)

-
-
-
[docs]def restart_runs(cfg, force, resume):
-    """Start subchains in specified intervals and manage restarts.
-
-    This function slices the total runtime of the processing chain according to the
-    `cfg.restart_step_hours` configuration. It calls `run_chunk()` for each
-    specified interval.
-
-    Parameters
-    ----------
-    cfg : Config
-        Object holding all user-configuration parameters as attributes.
-    force : bool
-        If True, it will force the execution of jobs regardless of their completion status.
-    resume : bool
-        If True, it will resume the last unfinished job.
-
-    Notes
-    -----
-    - The function iterates over specified intervals, calling `run_chunk()` for each.
-    - It manages restart settings and logging for each subchain.
-    """
-
-    for chunk_id in cfg.chunks:
-        cfg.chunk_id = chunk_id
-        cfg.get_previous_chunk_id(cfg.chunk_id)
-        cfg.startdate_sim_yyyymmddhh = cfg.chunk_id[0:10]
-        cfg.enddate_sim_yyyymmddhh = cfg.chunk_id[-10:]
-        cfg.startdate_sim = datetime.strptime(
-            cfg.startdate_sim_yyyymmddhh, "%Y%m%d%H").replace(tzinfo=pytz.UTC)
-        cfg.enddate_sim = datetime.strptime(
-            cfg.enddate_sim_yyyymmddhh, "%Y%m%d%H").replace(tzinfo=pytz.UTC)
-
-        if 'spinup' in cfg.workflow['features'] and hasattr(cfg, 'spinup'):
-            if cfg.startdate_sim == cfg.startdate:
-                cfg.first_one = True
-                cfg.second_one = False
-                cfg.lrestart = '.FALSE.'
-            elif cfg.startdate_sim == cfg.startdate + timedelta(
-                    hours=cfg.restart_step_hours):
-                cfg.first_one = False
-                cfg.second_one = True
-                cfg.lrestart = '.TRUE.'
-            else:
-                cfg.first_one = False
-                cfg.second_one = False
-                cfg.lrestart = '.TRUE.'
-        else:
-            # Set restart variable (only takes effect for ICON)
-            cfg.lrestart = ".FALSE." if cfg.startdate_sim == cfg.startdate else ".TRUE."
-
-        print(f'└── Starting chunk "{cfg.chunk_id}"')
-
-        run_chunk(cfg=cfg, force=force, resume=resume)

-
-
-def main():
-    """Main script for running a processing chain.
-
-    This script handles the execution of a processing chain for one or more
-    specified cases. It loads model configurations, prepares the environment,
-    and starts the chain based on the provided settings.
-
-    Parameters
-    ----------
-    None (Command-line arguments are parsed internally)
-
-    Notes
-    -----
-    - This script uses command-line arguments to specify cases and job lists.
-    - It loads model configurations, converts paths to absolute, sets restart 
-      settings, and starts the chain.
-    - Depending on the model's features, it may run with or without restarts
-      or utilize spin-up restarts.
-    """
-    args = parse_arguments()
-
-    for casename in args.casenames:
-        # Load configs
-        cfg = Config(casename)
-
-        # Convert relative to absolute paths
-        cfg.convert_paths_to_absolute()
-
-        # Set restart step in hours
-        cfg.set_restart_step_hours()
-
-        # Duplicate variables in the form of <dict>_<value> for better
-        # access within namelist template.
-        # E.g.: cfg.meteo['dir'] -> cfg.meteo_dir
-        cfg.create_vars_from_dicts()
-
-        # Check if jobs are set or if default ones are used
-        if args.job_list is None:
-            cfg.jobs = cfg.workflow['jobs']
-        else:
-            cfg.jobs = args.job_list
-
-        # Check sync is forced
-        if args.force_sync:
-            cfg.force_sync = True
-        else:
-            cfg.force_sync = False
-
-        # Check constraint
-        if cfg.constraint and cfg.machine == 'daint':
-            assert cfg.constraint in ['gpu', 'mc'], ("Unknown constraint, use"
-                                                     "gpu or mc")
-
-        # Get complete chunk list
-        cfg.get_chunk_list()
-
-        # Print config before chain starts
-        cfg.print_config()
-
-        # Get custom chunks if specified
-        cfg.chunks = args.chunk_list if args.chunk_list else cfg.chunk_list
-
-        tools.create_dir(cfg.case_root, "case_root")
-
-        print("╔════════════════════════════════════════╗")
-        print("║       Starting Processing Chain        ║")
-        print("╠════════════════════════════════════════╣")
-        print(f"║      Case: {casename: <27} ║")
-        print(f"║  Workflow: {cfg.workflow_name: <27} ║")
-        print("╚════════════════════════════════════════╝")
-
-        # Check for restart compatibility and spinup
-        if 'restart' in cfg.workflow['features']:
-            restart_runs(cfg=cfg, force=args.force, resume=args.resume)
-        else:
-            print("No restarts are used.")
-            cfg.startdate_sim = cfg.startdate
-            cfg.enddate_sim = cfg.enddate
-            run_chunk(cfg=cfg, force=args.force, resume=args.resume)
-
-    print("╔════════════════════════════════════════╗")
-    print("║       Processing Chain Completed       ║")
-    print("╚════════════════════════════════════════╝")
-
-
-if __name__ == '__main__':
-    main()
-
- -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/_sources/code-structure.rst.txt b/pr-preview/pr-63/_sources/code-structure.rst.txt deleted file mode 100644 index 9a7ee7ab..00000000 --- a/pr-preview/pr-63/_sources/code-structure.rst.txt +++ /dev/null @@ -1,55 +0,0 @@ -.. _code-structure-section: - -Code Structure --------------- - -The Processing Chain code is structured as follows: - -.. code-block:: bash - - $ tree -L 3 -F --dirsfirst - . - ├── cases/ # folder where all cases are stored - │ ├── cosmo-ghg-spinup-test/ # COSMO-GHG test case with spinup restart - │ │ ├── config.yaml # case configuration file - │ │ ├── *.cfg # templates for namelists & batch jobs - │ │ └── *.csv # CSV files with tracer information - │ ├── cosmo-ghg-test/ # COSMO-GHG testcase with standard restart - │ │ ├── config.yaml - │ │ ├── *.cfg - │ │ └── *.csv - │ ├── icon-art-global-test/ # ICON-ART test case (global domain) - │ │ ├── config.yaml - │ │ ├── icon_runjob.cfg # template for ICON-ART runjob - │ │ ├── *.sh # pre-processing scripts - │ │ └── mypartab - │ ├── icon-art-oem-test/ # ICON-ART test case with online emissions - │ │ ├── config.yaml - │ │ └── *.cfg - │ └── icon-test/ # ICON test case - │ ├── config.yaml - │ └── *.cfg - ├── docs/ # folder for Sphinx documentation - │ ├── _static/ # folder for static assets - │ │ ├── custom.css # custom CSS styles - │ │ └── *.png|ico # additional image assets - │ ├── tables/ # folder for tables used in documentation - │ │ └── *.csv # CSV files containing table data - │ ├── conf.py # configuration file for the Sphinx builder - │ └── *.rst # documentation files (reStructuredText) - ├── env/ - │ └── environment.yml # conda environment file - ├── ext/ # folder for other code (spack, models, etc.) - ├── jenkins/ # automated Jenkins testing - │ ├── scripts/ - │ │ └── *.sh # individual Shell scripts for testing - │ └── Jenkinsfile # text file containing the Jenkins pipeline - ├── jobs/ - │ ├── tools/ - │ │ └── *.py # tool scripts - │ └── *.py # job scripts - ├── LICENSE # license file - ├── README.md # README file - ├── config.py # file containing the Config class - ├── run_chain.py # main script - └── workflows.yaml # file to store workflows with job dependencies diff --git a/pr-preview/pr-63/_sources/config.rst.txt b/pr-preview/pr-63/_sources/config.rst.txt deleted file mode 100644 index f38ef329..00000000 --- a/pr-preview/pr-63/_sources/config.rst.txt +++ /dev/null @@ -1,190 +0,0 @@ -.. _config-section: - -The Processing Chain uses cases to describe a simulation. A case is a -subdirectory in ``cases/``, containing a ``config.yaml`` and several -`namelist` (e.g., ``int2lm_INPUT.cfg``) and `runscripts` (e.g., -``icon_runjob.cfg``) :ref:`templates`, -which define the simulation. - -.. _config.yaml: - -Configuration File ------------------- - -The case-dependent configuration file ``/config.yaml`` contains most -of the information that the :ref:`jobs` need to prepare -and run the simulation, for example the location of the input data. -This configuration file is loaded in ``run_chain.py`` as an instance -of the ``Config()`` class in ``config.py``. - -Configuration Variables -~~~~~~~~~~~~~~~~~~~~~~~ - -This is a non-exhaustive list containing the most important configuration variables: - -+------------------------+-------------------------------------------------------------------------+ -| Variable | Description | -+========================+=========================================================================+ -|| ``case_path`` || The path to the case directory under ``cases/`` for the specified | -|| || casename. | -+------------------------+-------------------------------------------------------------------------+ -| ``casename`` | The name of the case. Derived from the folder name under ``case_path``. | -+------------------------+-------------------------------------------------------------------------+ -|| ``chain_src_dir`` || The source directory for the processing chain, typically the current | -|| || working directory. | -+------------------------+-------------------------------------------------------------------------+ -| ``compute_account`` | The compute account to be used based on user information. | -+------------------------+-------------------------------------------------------------------------+ -| ``constraint`` | The computational constraint (``gpu`` or ``mc``). | -+------------------------+-------------------------------------------------------------------------+ -|| ``email`` || The user's email address, initially set to None and updated using the | -|| || set_email method. | -+------------------------+-------------------------------------------------------------------------+ -|| ``enddate`` || The end date of the simulation in ISO 8601 format | -|| || (``YYYY-MM-DDTHH:mm:ssZ``). | -+------------------------+-------------------------------------------------------------------------+ -| ``jobs`` | List of job-names to be executed. | -+------------------------+-------------------------------------------------------------------------+ -| ``log_finished_dir`` | The directory for finished log files. | -+------------------------+-------------------------------------------------------------------------+ -| ``log_working_dir`` | The directory for working log files. | -+------------------------+-------------------------------------------------------------------------+ -| ``ntasks_per_node`` | The number of tasks per node, based on the node type. | -+------------------------+-------------------------------------------------------------------------+ -| ``restart_step`` | The restart step in ISO 8601 format. | -+------------------------+-------------------------------------------------------------------------+ -| ``restart_step_hours`` | The restart step in hours, derived from the ``restart_step`` attribute. | -+------------------------+-------------------------------------------------------------------------+ -| ``run_on`` | The architecture the model runs on (``cpu`` or ``gpu``). | -+------------------------+-------------------------------------------------------------------------+ -| ``spinup`` | Spin-up duration in hours. Activates spinup behavior if set. | -+------------------------+-------------------------------------------------------------------------+ -|| ``startdate`` || The start date of the simulation in ISO 8601 format | -|| || (``YYYY-MM-DDTHH:mm:ssZ``). | -+------------------------+-------------------------------------------------------------------------+ -| ``user_mail`` | The user's email address, determined based on system configuration. | -+------------------------+-------------------------------------------------------------------------+ -|| ``user_name`` || Your email address to receive notifications. Either provide it | -|| || directly here or in ``~/.forward``. | -+------------------------+-------------------------------------------------------------------------+ -| ``workflow`` | The name of the workflow from ``workflows.yaml`` or a self-defined one. | -+------------------------+-------------------------------------------------------------------------+ -|| ``work_root`` || The working directory where all output is stored. Should be somewhere | -|| || on ``$SCRATCH$``. By default, it is set to ``/work``. | -+------------------------+-------------------------------------------------------------------------+ - - -Variables to Set in ``config.yaml`` -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Here are two examples of which general variables should be set by the user in the -case configuration file. - -Header of ``config.yaml`` for the ``cosmo-ghg-spinup-test`` case -================================================================ - -.. code-block:: yaml - - workflow: cosmo-ghg - constraint: gpu - ntasks_per_node: 12 - restart_step: PT6H - spinup: 3 - startdate: 2015-01-01T00:00:00Z - enddate: 2015-01-01T18:00:00Z - -Header of ``config.yaml`` for the ``icon-art-oem-test`` case -============================================================ - -.. code-block:: yaml - - workflow: icon-art-oem - constraint: gpu - run_on: cpu - compute_queue: normal - ntasks_per_node: 12 - restart_step: PT6H - startdate: 2018-01-01T00:00:00Z - enddate: 2018-01-01T12:00:00Z - - eccodes_dir: ./input/eccodes_definitions - iconremap_bin: iconremap - iconsub_bin: iconsub - latbc_filename: ifs__lbc.nc - inidata_prefix: ifs_init_ - inidata_nameformat: '%Y%m%d%H' - inidata_filename_suffix: .nc - output_filename: icon-art-oem-test - filename_format: _DOM_ - lateral_boundary_grid_order: lateral_boundary - art_input_folder: ./input/icon-art-oem/ART - -Further variables -================= - -Furthermore, there are additional variables to set that are tied to the individual jobs. -These config variables themselves are dictionaries. Let's have a look at and example -for the the ``cfg.meteo`` variable: - -.. code-block:: yaml - - meteo: - dir: ./input/cosmo-ghg/meteo - prefix: laf - nameformat: laf%Y%m%d%H - inc: 1 - -These config variables can be accessed via ``cfg.meteo['dir']``, ``cfg.meteo['prefix']``, etc. -as they are Python dictionaries. - -.. hint:: - In :ref:`namelist and runscript template` files - (see next section), this accessing does not work because of how the ``.format()`` - method is implemented in Python. For that reason, the Processing Chain automatically - creates new variables in the form of ``cfg.meteo_dir``, ``cfg.meteo_prefix``, etc. - at the start to make them accessible for namelist and runjob templates. - -List of dictionary variables -**************************** - -The following is a list of dictionary variables that exist for the Processing Chain. -For the individual elements of those variables, please refer to the ``config.yaml`` -files within the test cases. - -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| Dictionary variable | Used in job | -+=======================+=====================================================================================================================================+ -| ``meteo`` | ``prepare_cosmo``, ``prepare_icon``, ``icontools``, ``int2lm``, ``icon`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``icontools_runjobs`` | ``icontools`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``input_files`` | ``prepare_icon`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``chem`` | ``prepare_icon`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``era5`` | ``prepare_icon`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``cams`` | ``prepare_cosmo`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``emissions`` | ``emissions`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``vprm`` | ``biofluxes`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``oem`` | ``oem``, ``cosmo`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``online_vprm`` | ``online_vprm`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``int2lm`` | ``prepare_cosmo``, ``emissions``, ``biofluxes``, ``octe``, ``int2lm``, ``post_int2lm``, ``cosmo``, ``post_cosmo`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``post_int2lm`` | ``post_int2lm`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``cosmo`` | ``reduce_output``, ``oem``, ``photo_rate``, ``octe``, ``check_output``, ``post_cosmo``, ``cosmo``, ``obs_nudging``, ``online_vprm`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``reduce_output`` | ``reduce_output`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``post_cosmo`` | ``post_cosmo`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``verify_chain`` | ``verify_chain`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ -| ``icon`` | ``oem``, ``prepare_icon``, ``icon`` | -+-----------------------+-------------------------------------------------------------------------------------------------------------------------------------+ diff --git a/pr-preview/pr-63/_sources/environment.rst.txt b/pr-preview/pr-63/_sources/environment.rst.txt deleted file mode 100644 index 58707f7a..00000000 --- a/pr-preview/pr-63/_sources/environment.rst.txt +++ /dev/null @@ -1,62 +0,0 @@ -.. _environment-section: - -Conda Environment -================= - -The following steps allow you to create and use your own virtual environment to run the Processing Chain. We recommend using a conda environment for the usage of the provided scripts. Please follow the instructions for the installation. The following steps only need to be performed once. - -1. Install Miniconda -~~~~~~~~~~~~~~~~~~~~ - -Install Miniconda as user-specific Miniconda, e.g., in your ``$HOME`` directory, which is the default location. - -.. note:: - Only conda itself should be installed in your ``$HOME``. All environments should be stored in your ``$PROJECT`` directory; otherwise, you risk filling up your ``$HOME`` directory. See below for instructions. - -To install the latest Miniconda, type: - -.. code-block:: bash - - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh - bash Miniconda3-latest-Linux-x86_64.sh - -Further details on Miniconda can be found on the `Miniconda documentation page `_. - -2. Create the Conda Environment -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -Create a conda environment ``proc-chain`` and install the requirements: - -.. code-block:: bash - - conda env create --prefix $PROJECT/envs/proc-chain -f env/environment.yml - -To be able to activate your conda environment by simply using ``conda activate proc-chain`` instead of the full path, add the following to your ``.bashrc``: - -.. code-block:: bash - - export CONDA_ENVS_PATH=$PROJECT/envs - -Activate the environment (use "source activate" in case "conda activate" does not work): - -.. code-block:: bash - - conda activate proc-chain - -If you already have the environment but want to update it: - -.. code-block:: bash - - conda env update --file env/environment.yml --prune - -3. Store user-specific data -~~~~~~~~~~~~~~~~~~~~~~~~~~~ - -To register your email address and standard project account, store them in these files within your home directory: - -.. code-block:: bash - - echo > ~/.acct - echo > ~/.forward - -These settings are optional. The Processing Chain will first check the content of those files. If desired, the corresponding variables can be overridden by setting the ``compute_account`` and ``user_mail`` variables in the ``config.yaml`` file. diff --git a/pr-preview/pr-63/_sources/features.rst.txt b/pr-preview/pr-63/_sources/features.rst.txt deleted file mode 100644 index c0f14d0a..00000000 --- a/pr-preview/pr-63/_sources/features.rst.txt +++ /dev/null @@ -1,13 +0,0 @@ -.. _features-section: - -Feature Overview -================ - -- Asynchronous submission of compute jobs to the HPC queue -- Intuitive definition of job dependencies -- Automatic cycling over time periods including folder structure creation -- Various jobs for pre- and post-processing steps -- Using model built-in restarts or custom spinup -- Nested runs possible -- Easy creation of own cases and workflows -- Various examples for COSMO and ICON workflows available \ No newline at end of file diff --git a/pr-preview/pr-63/_sources/functions.rst.txt b/pr-preview/pr-63/_sources/functions.rst.txt deleted file mode 100644 index 4305a932..00000000 --- a/pr-preview/pr-63/_sources/functions.rst.txt +++ /dev/null @@ -1,155 +0,0 @@ -.. _functions-section: - -Jobs ----- - -* :func:`jobs.biofluxes.main` -* :func:`jobs.check_output.main` -* :func:`jobs.cosmo.main` -* :func:`jobs.emissions.main` -* :func:`jobs.icon.main` -* :func:`jobs.icontools.main` -* :func:`jobs.int2lm.main` -* :func:`jobs.obs_nudging.main` -* :func:`jobs.octe.main` -* :func:`jobs.oem.main` -* :func:`jobs.online_vprm.main` -* :func:`jobs.photo_rate.main` -* :func:`jobs.post_cosmo.main` -* :func:`jobs.post_int2lm.main` -* :func:`jobs.prepare_cosmo.main` -* :func:`jobs.prepare_icon.main` -* :func:`jobs.reduce_output.main` -* :func:`jobs.verify_chain.main` - -------------------------------------------- - -.. autofunction:: jobs.biofluxes.main - -------------------------------------------- - -.. autofunction:: jobs.check_output.main - -------------------------------------------- - -.. autofunction:: jobs.cosmo.main - -------------------------------------------- - -.. autofunction:: jobs.emissions.main - -------------------------------------------- - -.. autofunction:: jobs.icon.main - -------------------------------------------- - -.. autofunction:: jobs.icontools.main - -------------------------------------------- - -.. autofunction:: jobs.int2lm.main - -------------------------------------------- - -.. autofunction:: jobs.obs_nudging.main - -------------------------------------------- - -.. autofunction:: jobs.octe.main - -------------------------------------------- - -.. autofunction:: jobs.oem.main - -------------------------------------------- - -.. autofunction:: jobs.online_vprm.main - -------------------------------------------- - -.. autofunction:: jobs.photo_rate.main - -------------------------------------------- - -.. autofunction:: jobs.post_cosmo.main - -------------------------------------------- - -.. autofunction:: jobs.post_int2lm.main - -------------------------------------------- - -.. autofunction:: jobs.prepare_cosmo.main - -------------------------------------------- - -.. autofunction:: jobs.prepare_icon.main - -------------------------------------------- - -.. autofunction:: jobs.reduce_output.main - -------------------------------------------- - -.. autofunction:: jobs.verify_chain.main - - -Tools ------ - -The tools are a collection of functions used by the jobs. Most of those -functions are well documented and listed here. For others, one may take -a look into ``jobs/tools`` directly. - -* :func:`jobs.tools.cams4int2cosmo.main` -* :func:`jobs.tools.check_model.check_model` -* :func:`jobs.tools.comp_nc.datasets_equal` -* :func:`jobs.tools.ctnoaa4int2cosmo.main` -* :func:`jobs.tools.mozart2int2lm.main` -* :func:`jobs.tools.reduce_output_start_end.main` -* :func:`jobs.tools.string2char.main` -* :func:`jobs.tools.vprmsplit.main` -* :func:`jobs.tools.write_cosmo_input_ghg.main` -* :func:`jobs.tools.write_int2lm_input_art.main` - - -------------------------------------------- - -.. autofunction:: jobs.tools.cams4int2cosmo.main - -------------------------------------------- - -.. autofunction:: jobs.tools.check_model.check_model - -------------------------------------------- - -.. autofunction:: jobs.tools.comp_nc.datasets_equal - -------------------------------------------- - -.. autofunction:: jobs.tools.ctnoaa4int2cosmo.main - -------------------------------------------- - -.. autofunction:: jobs.tools.mozart2int2lm.main - -------------------------------------------- - -.. autofunction:: jobs.tools.reduce_output_start_end.main - -------------------------------------------- - -.. autofunction:: jobs.tools.string2char.main - -------------------------------------------- - -.. autofunction:: jobs.tools.vprmsplit.main - -------------------------------------------- - -.. autofunction:: jobs.tools.write_cosmo_input_ghg.main - -------------------------------------------- - -.. autofunction:: jobs.tools.write_int2lm_input_art.main diff --git a/pr-preview/pr-63/_sources/howtorun.rst.txt b/pr-preview/pr-63/_sources/howtorun.rst.txt deleted file mode 100644 index 9d074ee7..00000000 --- a/pr-preview/pr-63/_sources/howtorun.rst.txt +++ /dev/null @@ -1,245 +0,0 @@ -.. _howtorun-section: - -How to Run -========== - -The Python file ``run_chain.py`` in the root directory is the main script of the -Processing Chain. -It reads the user's input from the command line and from the ``config.yaml`` file of the -respective case. -Then it will start the Processing Chain. - -Starting the Chain ------------------- - -The chain has to be run with the following command: - -.. code-block:: bash - - $ ./run_chain.py - -Here, ```` is the name of a directory in the ``cases/``-directory where -there is a ``config.yaml``-file specifying the configuration, as well as templates -for the necessary namelist files for **int2lm**, **COSMO** or **ICON**. It may also -contain additional runscripts to be submitted via ``sbatch``. - -.. hint:: - Technically, you can run several cases (instead of a single case) in one command, - which is useful for nested runs, for example. This can be achieved by running - ``./run_chain.py ``. With that, the full chain is executed for - ``case1`` first, and afterwards for ``case2``. - -There are several optional arguments available to change the behavior of the chain: - -.. code-block:: bash - - $ ./run_chain.py -h - -* ``-h``, ``--help`` - Show this help message and exit. -* ``-j [JOB_LIST ...]``, ``--jobs [JOB_LIST ...]`` - List of job names to be executed. - A job is a ``.py`` file in i``jobs/`` with a ``main()`` function, which - handles one aspect of the Processing Chain, for - example copying ``meteo`` input data or launching a - job for ``int2lm``. Jobs are executed in the order - in which they are given here. If no jobs are - given, default jobs will be executed as defined - in ``config/models.yaml``. -* ``-f``, ``--force`` - Force the Processing Chain to redo all specified - jobs, even if they have been started already or - were finished previously. WARNING: Only logfiles - get deleted, other effects of a given job - (copied files etc.) are simply overwritten. This - may cause errors or unexpected behavior. -* ``-r``, ``--resume`` - Resume the Processing Chain by restarting the - last unfinished job. WARNING: Only the logfile - gets deleted, other effects of a given job - (copied files etc.) are simply overwritten. This - may cause errors or unexpected behavior. - -What it Does ------------- - -The script ``run_chain.py`` reads the command line arguments and the config file -from the specified case. -It then calls the function :func:`run_chain.restart_runs`, which divides the -simulation time according to the specified restart steps. Then it calls -:func:`run_chain.run_chunk` for each part (chunk) of the simulation workflow. -This function sets up the directory structure of the chain and then submits the -specified :ref:`jobs` via ``sbatch`` to the Slurm workload manager, -taking job dependencies into account. - -Test Cases ----------- - -The following test cases are available: - -* ``cosmo-ghg-spinup-test`` -* ``cosmo-ghg-test`` -* ``icon-test`` -* ``icon-art-oem-test`` -* ``icon-art-global-test`` - -To be able to run these test cases, it is necessary to provide the input data, -to setup spack and to compile the models and tools. All this is automized via -the script:: - - $ ./jenkins/scripts/jenkins.sh - -This will run all the individual scripts in ``jenkins/scripts/``, which -can also be launched separately if desired. - -These cases undergo regulary testing to ensure that the Processing Chain runs -correctly. A corresponding Jenkins plan is launched on a weekly basis and -when triggered within a GitHub pull request. - -Directory Structure -------------------- - -The directory structure generated by the Processing Chain for a ``cosmo-ghg`` -run looks like this: - -.. code-block:: bash - - cfg.work_root/cfg.casename/ - └── cfg.chain_root/ - ├── checkpoints/ - │ ├── cfg.log_working_dir/ - │ ├── cfg.log_finished_dir/ - ├── cfg.cosmo_base/ - │ ├── cfg.cosmo_work/ - │ ├── cfg.cosmo_output/ - │ ├── cfg.cosmo_restart_out/ - └── cfg.int2lm_base/ - ├── cfg.int2lm_input/ - ├── cfg.int2lm_work/ - └── cfg.int2lm_output/ - -As one can see, it creates working directories for both the ``int2lm`` preprocessor -and ``cosmo``. Additionally, and this is always the case, the ``checkpoints`` -directory holds all the job logfiles. Whenever a job has successfully finished, -the logfile is copied from the ``working`` to the ``finished`` sub-directory. - -Running the ``cosmo-ghg-test`` case therefore produces the following -directories and files (showing four levels of directories deep): - -.. code-block:: bash - - work/cosmo-ghg-test - ├── 2015010100_2015010106/ - │ ├── checkpoints/ - │ │ ├── finished/ - │ │ │ ├── biofluxes - │ │ │ ├── cosmo - │ │ │ ├── emissions - │ │ │ ├── int2lm - │ │ │ ├── oem - │ │ │ ├── online_vprm - │ │ │ ├── post_cosmo - │ │ │ ├── post_int2lm - │ │ │ └── prepare_cosmo - │ │ └── working/ - │ │ ├── biofluxes - │ │ ├── cosmo - │ │ ├── emissions - │ │ ├── int2lm - │ │ ├── oem - │ │ ├── online_vprm - │ │ ├── post_cosmo - │ │ ├── post_int2lm - │ │ └── prepare_cosmo - │ ├── cosmo/ - │ │ ├── input/ - │ │ │ ├── oem/ - │ │ │ └── vprm/ - │ │ ├── output/ - │ │ │ └── lffd*.nc - │ │ ├── restart/ - │ │ │ └── lrff00060000o.nc - │ │ └── run/ - │ │ ├── cosmo-ghg - │ │ ├── INPUT_* - │ │ ├── post_cosmo.job - │ │ ├── run.job - │ │ └── YU* - │ └── int2lm/ - │ ├── input/ - │ │ ├── emissions - │ │ ├── extpar - │ │ ├── icbc - │ │ ├── meteo - │ │ └── vprm - │ ├── output/ - │ │ ├── laf*.nc - │ │ └── lbfd*.nc - │ └── run/ - │ ├── INPUT - │ ├── INPUT_ART - │ ├── int2lm - │ ├── OUTPUT - │ ├── run.job - │ └── YU* - └── 2015010106_2015010112/ - ├── checkpoints/ - │ ├── finished/ - │ │ ├── biofluxes - │ │ ├── cosmo - │ │ ├── emissions - │ │ ├── int2lm - │ │ ├── oem - │ │ ├── online_vprm - │ │ ├── post_cosmo - │ │ ├── post_int2lm - │ │ └── prepare_cosmo - │ └── working/ - │ ├── biofluxes - │ ├── cosmo - │ ├── emissions - │ ├── int2lm - │ ├── oem - │ ├── online_vprm - │ ├── post_cosmo - │ ├── post_int2lm - │ └── prepare_cosmo - ├── cosmo/ - │ ├── input/ - │ │ ├── oem - │ │ └── vprm - │ ├── output/ - │ │ └── lffd*.nc - │ ├── restart/ - │ │ └── lrff00060000o.nc - │ └── run/ - │ ├── cosmo-ghg - │ ├── INPUT_* - │ ├── post_cosmo.job - │ ├── run.job - │ └── YU* - └── int2lm/ - ├── input/ - │ ├── emissions - │ ├── extpar - │ ├── icbc - │ ├── meteo - │ └── vprm - ├── output/ - │ ├── laf*.nc - │ └── lbfd*.nc - └── run/ - ├── INPUT - ├── INPUT_ART - ├── int2lm - ├── OUTPUT - ├── run.job - └── YU* - -------------------------------------------- - -.. autofunction:: run_chain.run_chunk - -------------------------------------------- - -.. autofunction:: run_chain.restart_runs diff --git a/pr-preview/pr-63/_sources/index.rst.txt b/pr-preview/pr-63/_sources/index.rst.txt deleted file mode 100644 index 169bf730..00000000 --- a/pr-preview/pr-63/_sources/index.rst.txt +++ /dev/null @@ -1,50 +0,0 @@ -.. Processing Chain documentation master file, created by - sphinx-quickstart on Thu Sep 27 14:11:04 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Processing Chain -================ - -The Processing Chain is a Python-based workflow tool designed to streamline -weather and climate simulations. -It facilitates the preparation of essential input data, submission of compute -jobs to the queue on CSCS HPC systems, and the implementation of post-processing -steps. -In addition to supporting standard versions of the COSMO and ICON models, -it is equipped to handle various model variants, notably COSMO-GHG -(Greenhouse Gas Extension) and ICON-ART (Aerosols and Reactive Trace Gases) - -The Processing Chain can be easily customized to meet your specific requirements. -This includes defining custom workflows, creating your own simulation cases, -and integrating new jobs and auxiliary scripts. - -.. toctree:: - :maxdepth: 2 - :caption: Getting Started - - features - environment - howtorun - -.. toctree:: - :maxdepth: 2 - :caption: Configuration - - code-structure - config - namelists - - -.. toctree:: - :maxdepth: 2 - :caption: Jobs & Workflows - - jobs - -.. toctree:: - :maxdepth: 2 - :caption: API - - functions - diff --git a/pr-preview/pr-63/_sources/jobs.rst.txt b/pr-preview/pr-63/_sources/jobs.rst.txt deleted file mode 100644 index 96cae42b..00000000 --- a/pr-preview/pr-63/_sources/jobs.rst.txt +++ /dev/null @@ -1,79 +0,0 @@ -.. _jobs-section: - -Overview --------- - -Jobs have to be part of the respective workflow. They are submitted via ``sbatch`` -to the Slurm workload manager. - -The order of job submission is based on the list given in ``workflows.yaml`` -(or in ``config.yaml`` in case a custom, user-defined workflow is used.) - -Let's have a look at the ``icon-art`` example: - -.. code-block:: yaml - - icon-art: - features: - - restart - jobs: - - prepare_icon - - icontools - - prepare_art - - icon - -This workflow consists of four jobs: ``prepare_icon``, ``icontools``, -``prepare_art`` and ``icon``. - -These jobs will be submitted, however, they are not starting at the same time, -because some of them depend on others: - -.. code-block:: yaml - - dependencies: - icontools: - current: - - prepare_icon - prepare_art: - current: - - icontools - icon: - current: - - prepare_icon - - icontools - - prepare_art - previous: - - icon - -Since ``icontools`` depends on ``prepare_icon``, and ``prepare_art`` depends -on ``icontools``, the order of execution is ``prepare_icon`` --> ``icontools`` ---> ``prepare_art``. Note that if we had another job in there without dependencies, -it would run in parallel to the others. - -Since ``icon`` depends on all other jobs, it will be executed last. Note that -these dependencies are all listed under the ``current`` keyword, targeting -the current chunk. For ``icon``, there is an additional ``previous`` keyword. -This means that an ``icon`` simulation will always wait until the simulation -from the last chunk is finished (because the restart file has to be available). - -Another effect of this workflow definition is that the ``prepare_icon``, -``icontools`` and ``prepare_art`` jobs will also be launched for the next chunk, -as they are not dependent on their previous ones. - -.. figure:: _static/processing_chain_workflow_icon_art.png - :alt: Flowchart for the ``icon-art`` workflow. - - Flowchart for the ``icon-art`` workflow. - - -Adding New Jobs ---------------- - -Adding a new job to the chain is simple: - -1. In the directory ``jobs/``, create a file called ``.py`` containing - a function called ``main`` which takes the same arguments as every other job. - Make sure the function is documented with a docstring. -2. Import it in ``jobs/__init__.py`` to make it accessible to ``run_chain.py``. -3. Add the job to your workflow. - diff --git a/pr-preview/pr-63/_sources/namelists.rst.txt b/pr-preview/pr-63/_sources/namelists.rst.txt deleted file mode 100644 index 20da47ca..00000000 --- a/pr-preview/pr-63/_sources/namelists.rst.txt +++ /dev/null @@ -1,34 +0,0 @@ -.. _namelists-section: - -Namelist and Runscript Templates --------------------------------- - -The namelists and run jobs for **int2lm** and **COSMO**, as well as for **icontools** and **ICON** are dynamically generated -using templates located in the ``cases/`` directory. These templates are essentially -text files containing "normal" namelist parameters alongside Python variables enclosed in curly braces. - -During runtime, these template files are read by their respective jobs. -The resulting strings are formatted through Python's ``.format()`` function, facilitating the -substitution of Python variables with their corresponding value. -Subsequently, the formatted strings are then saved as the actual namelist and run scripts in the -run directory of their respective jobs. - -.. code-block:: - - cases/example/example_namelist.cfg -> [read file] -> - "namelist_var = '{cfg.prefix}{cfg.suffix}'" -> ["".format(cfg)] -> - "namelist_var = 'pref_suff.nc'" -> [write to disk] -> - int2lm/run/example_namelist - -A special case is ``INPUT_ART`` for **int2lm** and ``INPUT_GHG`` for **COSMO** . These namelists are -generated by :func:`jobs.tools.write_int2lm_input_art.main` and :func:`jobs.tools.write_cosmo_input_ghg.main` -from ``.csv``-files containing all necessary information. - ----------------------------------------------------- - -.. autofunction:: jobs.tools.write_int2lm_input_art.main - ----------------------------------------------------- - -.. autofunction:: jobs.tools.write_cosmo_input_ghg.main - diff --git a/pr-preview/pr-63/_static/_sphinx_javascript_frameworks_compat.js b/pr-preview/pr-63/_static/_sphinx_javascript_frameworks_compat.js deleted file mode 100644 index 81415803..00000000 --- a/pr-preview/pr-63/_static/_sphinx_javascript_frameworks_compat.js +++ /dev/null @@ -1,123 +0,0 @@ -/* Compatability shim for jQuery and underscores.js. - * - * Copyright Sphinx contributors - * Released under the two clause BSD licence - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. 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-} - -:not(li) > ol > li:last-child > :last-child, -:not(li) > ul > li:last-child > :last-child { - margin-bottom: 0px; -} - -ol.simple ol p, -ol.simple ul p, -ul.simple ol p, -ul.simple ul p { - margin-top: 0; -} - -ol.simple > li:not(:first-child) > p, -ul.simple > li:not(:first-child) > p { - margin-top: 0; -} - -ol.simple p, -ul.simple p { - margin-bottom: 0; -} - -aside.footnote > span, -div.citation > span { - float: left; -} -aside.footnote > span:last-of-type, -div.citation > span:last-of-type { - padding-right: 0.5em; -} -aside.footnote > p { - margin-left: 2em; -} -div.citation > p { - margin-left: 4em; -} -aside.footnote > p:last-of-type, -div.citation > p:last-of-type { - margin-bottom: 0em; -} -aside.footnote > p:last-of-type:after, -div.citation > p:last-of-type:after { - content: ""; - clear: both; -} - -dl.field-list { - display: grid; - grid-template-columns: fit-content(30%) auto; -} - -dl.field-list > dt { - font-weight: bold; - word-break: break-word; - padding-left: 0.5em; - padding-right: 5px; -} - -dl.field-list > dd { - padding-left: 0.5em; - margin-top: 0em; - margin-left: 0em; - margin-bottom: 0em; -} - -dl { - margin-bottom: 15px; -} - -dd > :first-child { - margin-top: 0px; -} - -dd ul, dd table { - margin-bottom: 10px; -} - -dd { - margin-top: 3px; - margin-bottom: 10px; - margin-left: 30px; -} - -.sig dd { - margin-top: 0px; - margin-bottom: 0px; -} - -.sig dl { - margin-top: 0px; - margin-bottom: 0px; -} - -dl > dd:last-child, -dl > dd:last-child > :last-child { - margin-bottom: 0; -} - -dt:target, span.highlighted { - background-color: #fbe54e; -} - -rect.highlighted { - fill: #fbe54e; -} - -dl.glossary dt { - font-weight: bold; - font-size: 1.1em; -} - -.versionmodified { - font-style: italic; -} - -.system-message { - background-color: #fda; - padding: 5px; - border: 3px solid red; -} - -.footnote:target { - background-color: #ffa; -} - -.line-block { - display: block; - margin-top: 1em; - margin-bottom: 1em; -} - -.line-block .line-block { - margin-top: 0; - margin-bottom: 0; - margin-left: 1.5em; -} - -.guilabel, .menuselection { - font-family: sans-serif; -} - -.accelerator { - text-decoration: underline; -} - -.classifier { - font-style: oblique; -} - -.classifier:before { - font-style: normal; - margin: 0 0.5em; - content: ":"; - display: inline-block; -} - -abbr, acronym { - border-bottom: dotted 1px; - cursor: help; -} - -.translated { - background-color: rgba(207, 255, 207, 0.2) -} - -.untranslated { - background-color: rgba(255, 207, 207, 0.2) -} - -/* -- code displays --------------------------------------------------------- */ - -pre { - overflow: auto; - overflow-y: hidden; /* fixes display issues on Chrome browsers */ -} - -pre, div[class*="highlight-"] { - clear: both; -} - -span.pre { - -moz-hyphens: none; - -ms-hyphens: none; - -webkit-hyphens: none; - hyphens: none; - white-space: nowrap; -} - -div[class*="highlight-"] { - margin: 1em 0; -} - -td.linenos pre { - border: 0; - background-color: transparent; - color: #aaa; -} - -table.highlighttable { - display: block; -} - -table.highlighttable tbody { - display: block; -} - -table.highlighttable tr { - display: flex; -} - -table.highlighttable td { - margin: 0; - padding: 0; -} - -table.highlighttable td.linenos { - padding-right: 0.5em; -} - -table.highlighttable td.code { - flex: 1; - overflow: hidden; -} - -.highlight .hll { - display: block; -} - -div.highlight pre, -table.highlighttable pre { - margin: 0; -} - -div.code-block-caption + div { - margin-top: 0; -} - -div.code-block-caption { - margin-top: 1em; - padding: 2px 5px; - font-size: small; -} - -div.code-block-caption code { - background-color: transparent; -} - -table.highlighttable td.linenos, -span.linenos, -div.highlight span.gp { /* gp: Generic.Prompt */ - user-select: none; - -webkit-user-select: text; /* Safari fallback only */ - -webkit-user-select: none; /* Chrome/Safari */ - -moz-user-select: none; /* Firefox */ - -ms-user-select: none; /* IE10+ */ -} - -div.code-block-caption span.caption-number { - padding: 0.1em 0.3em; - font-style: italic; -} - -div.code-block-caption span.caption-text { -} - -div.literal-block-wrapper { - margin: 1em 0; -} - -code.xref, a code { - background-color: transparent; - font-weight: bold; -} - -h1 code, h2 code, h3 code, h4 code, h5 code, h6 code { - background-color: transparent; -} - -.viewcode-link { - float: right; -} - -.viewcode-back { - float: right; - font-family: sans-serif; -} - -div.viewcode-block:target { - margin: -1px -10px; - padding: 0 10px; -} - -/* -- math display ---------------------------------------------------------- */ - -img.math { - vertical-align: middle; -} - -div.body div.math p { - text-align: center; -} - -span.eqno { - float: right; -} - -span.eqno a.headerlink { - position: absolute; - z-index: 1; -} - -div.math:hover a.headerlink { - visibility: visible; -} - -/* -- printout stylesheet --------------------------------------------------- */ - -@media print { - div.document, - div.documentwrapper, - div.bodywrapper { - margin: 0 !important; - width: 100%; - } - - div.sphinxsidebar, - div.related, - div.footer, - #top-link { - display: none; - } -} \ No newline at end of file diff --git a/pr-preview/pr-63/_static/check-solid.svg b/pr-preview/pr-63/_static/check-solid.svg deleted file mode 100644 index 92fad4b5..00000000 --- a/pr-preview/pr-63/_static/check-solid.svg +++ /dev/null @@ -1,4 +0,0 @@ - - - - diff --git a/pr-preview/pr-63/_static/clipboard.min.js b/pr-preview/pr-63/_static/clipboard.min.js deleted file mode 100644 index 54b3c463..00000000 --- a/pr-preview/pr-63/_static/clipboard.min.js +++ /dev/null @@ -1,7 +0,0 @@ -/*! - * clipboard.js v2.0.8 - * https://clipboardjs.com/ - * - * Licensed MIT © Zeno Rocha - */ -!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return o}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),c=n.n(e);function a(t){try{return document.execCommand(t)}catch(t){return}}var f=function(t){t=c()(t);return a("cut"),t};var l=function(t){var e,n,o,r=1 - - - - diff --git a/pr-preview/pr-63/_static/copybutton.css b/pr-preview/pr-63/_static/copybutton.css deleted file mode 100644 index f1916ec7..00000000 --- a/pr-preview/pr-63/_static/copybutton.css +++ /dev/null @@ -1,94 +0,0 @@ -/* Copy buttons */ -button.copybtn { - position: absolute; - display: flex; - top: .3em; - right: .3em; - width: 1.7em; - height: 1.7em; - opacity: 0; - transition: opacity 0.3s, border .3s, background-color .3s; - user-select: none; - padding: 0; - border: none; - outline: none; - border-radius: 0.4em; - /* The colors that GitHub uses */ - border: #1b1f2426 1px solid; - background-color: #f6f8fa; - color: #57606a; -} - -button.copybtn.success { - border-color: #22863a; - color: #22863a; -} - -button.copybtn svg { - stroke: currentColor; - width: 1.5em; - height: 1.5em; - padding: 0.1em; -} - -div.highlight { - position: relative; -} - -/* Show the copybutton */ -.highlight:hover button.copybtn, button.copybtn.success { - opacity: 1; -} - -.highlight button.copybtn:hover { - background-color: rgb(235, 235, 235); -} - -.highlight button.copybtn:active { - background-color: rgb(187, 187, 187); -} - -/** - * A minimal CSS-only tooltip copied from: - * https://codepen.io/mildrenben/pen/rVBrpK - * - * To use, write HTML like the following: - * - *

Short

- */ - .o-tooltip--left { - position: relative; - } - - .o-tooltip--left:after { - opacity: 0; - visibility: hidden; - position: absolute; - content: attr(data-tooltip); - padding: .2em; - font-size: .8em; - left: -.2em; - background: grey; - color: white; - white-space: nowrap; - z-index: 2; - border-radius: 2px; - transform: translateX(-102%) translateY(0); - transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); -} - -.o-tooltip--left:hover:after { - display: block; - opacity: 1; - visibility: visible; - transform: translateX(-100%) translateY(0); - transition: opacity 0.2s cubic-bezier(0.64, 0.09, 0.08, 1), transform 0.2s cubic-bezier(0.64, 0.09, 0.08, 1); - transition-delay: .5s; -} - -/* By default the copy button shouldn't show up when printing a page */ -@media print { - button.copybtn { - display: none; - } -} diff --git a/pr-preview/pr-63/_static/copybutton.js b/pr-preview/pr-63/_static/copybutton.js deleted file mode 100644 index 863baa29..00000000 --- a/pr-preview/pr-63/_static/copybutton.js +++ /dev/null @@ -1,248 +0,0 @@ -// Localization support -const messages = { - 'en': { - 'copy': 'Copy', - 'copy_to_clipboard': 'Copy to clipboard', - 'copy_success': 'Copied!', - 'copy_failure': 'Failed to copy', - }, - 'es' : { - 'copy': 'Copiar', - 'copy_to_clipboard': 'Copiar al portapapeles', - 'copy_success': '¡Copiado!', - 'copy_failure': 'Error al copiar', - }, - 'de' : { - 'copy': 'Kopieren', - 'copy_to_clipboard': 'In die Zwischenablage kopieren', - 'copy_success': 'Kopiert!', - 'copy_failure': 'Fehler beim Kopieren', - }, - 'fr' : { - 'copy': 'Copier', - 'copy_to_clipboard': 'Copier dans le presse-papier', - 'copy_success': 'Copié !', - 'copy_failure': 'Échec de la copie', - }, - 'ru': { - 'copy': 'Скопировать', - 'copy_to_clipboard': 'Скопировать в буфер', - 'copy_success': 'Скопировано!', - 'copy_failure': 'Не удалось скопировать', - }, - 'zh-CN': { - 'copy': '复制', - 'copy_to_clipboard': '复制到剪贴板', - 'copy_success': '复制成功!', - 'copy_failure': '复制失败', - }, - 'it' : { - 'copy': 'Copiare', - 'copy_to_clipboard': 'Copiato negli appunti', - 'copy_success': 'Copiato!', - 'copy_failure': 'Errore durante la copia', - } -} - -let locale = 'en' -if( document.documentElement.lang !== undefined - && messages[document.documentElement.lang] !== undefined ) { - locale = document.documentElement.lang -} - -let doc_url_root = DOCUMENTATION_OPTIONS.URL_ROOT; -if (doc_url_root == '#') { - doc_url_root = ''; -} - -/** - * SVG files for our copy buttons - */ -let iconCheck = ` - ${messages[locale]['copy_success']} - - -` - -// If the user specified their own SVG use that, otherwise use the default -let iconCopy = ``; -if (!iconCopy) { - iconCopy = ` - ${messages[locale]['copy_to_clipboard']} - - - -` -} - -/** - * Set up copy/paste for code blocks - */ - -const runWhenDOMLoaded = cb => { - if (document.readyState != 'loading') { - cb() - } else if (document.addEventListener) { - document.addEventListener('DOMContentLoaded', cb) - } else { - document.attachEvent('onreadystatechange', function() { - if (document.readyState == 'complete') cb() - }) - } -} - -const codeCellId = index => `codecell${index}` - -// Clears selected text since ClipboardJS will select the text when copying -const clearSelection = () => { - if (window.getSelection) { - window.getSelection().removeAllRanges() - } else if (document.selection) { - document.selection.empty() - } -} - -// Changes tooltip text for a moment, then changes it back -// We want the timeout of our `success` class to be a bit shorter than the -// tooltip and icon change, so that we can hide the icon before changing back. -var timeoutIcon = 2000; -var timeoutSuccessClass = 1500; - -const temporarilyChangeTooltip = (el, oldText, newText) => { - el.setAttribute('data-tooltip', newText) - el.classList.add('success') - // Remove success a little bit sooner than we change the tooltip - // So that we can use CSS to hide the copybutton first - setTimeout(() => el.classList.remove('success'), timeoutSuccessClass) - setTimeout(() => el.setAttribute('data-tooltip', oldText), timeoutIcon) -} - -// Changes the copy button icon for two seconds, then changes it back -const temporarilyChangeIcon = (el) => { - el.innerHTML = iconCheck; - setTimeout(() => {el.innerHTML = iconCopy}, timeoutIcon) -} - -const addCopyButtonToCodeCells = () => { - // If ClipboardJS hasn't loaded, wait a bit and try again. This - // happens because we load ClipboardJS asynchronously. - if (window.ClipboardJS === undefined) { - setTimeout(addCopyButtonToCodeCells, 250) - return - } - - // Add copybuttons to all of our code cells - const COPYBUTTON_SELECTOR = 'div.highlight pre'; - const codeCells = document.querySelectorAll(COPYBUTTON_SELECTOR) - codeCells.forEach((codeCell, index) => { - const id = codeCellId(index) - codeCell.setAttribute('id', id) - - const clipboardButton = id => - `` - codeCell.insertAdjacentHTML('afterend', clipboardButton(id)) - }) - -function escapeRegExp(string) { - return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string -} - -/** - * Removes excluded text from a Node. - * - * @param {Node} target Node to filter. - * @param {string} exclude CSS selector of nodes to exclude. - * @returns {DOMString} Text from `target` with text removed. - */ -function filterText(target, exclude) { - const clone = target.cloneNode(true); // clone as to not modify the live DOM - if (exclude) { - // remove excluded nodes - clone.querySelectorAll(exclude).forEach(node => node.remove()); - } - return clone.innerText; -} - -// Callback when a copy button is clicked. Will be passed the node that was clicked -// should then grab the text and replace pieces of text that shouldn't be used in output -function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { - var regexp; - var match; - - // Do we check for line continuation characters and "HERE-documents"? - var useLineCont = !!lineContinuationChar - var useHereDoc = !!hereDocDelim - - // create regexp to capture prompt and remaining line - if (isRegexp) { - regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') - } else { - regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') - } - - const outputLines = []; - var promptFound = false; - var gotLineCont = false; - var gotHereDoc = false; - const lineGotPrompt = []; - for (const line of textContent.split('\n')) { - match = line.match(regexp) - if (match || gotLineCont || gotHereDoc) { - promptFound = regexp.test(line) - lineGotPrompt.push(promptFound) - if (removePrompts && promptFound) { - outputLines.push(match[2]) - } else { - outputLines.push(line) - } - gotLineCont = line.endsWith(lineContinuationChar) & useLineCont - if (line.includes(hereDocDelim) & useHereDoc) - gotHereDoc = !gotHereDoc - } else if (!onlyCopyPromptLines) { - outputLines.push(line) - } else if (copyEmptyLines && line.trim() === '') { - outputLines.push(line) - } - } - - // If no lines with the prompt were found then just use original lines - if (lineGotPrompt.some(v => v === true)) { - textContent = outputLines.join('\n'); - } - - // Remove a trailing newline to avoid auto-running when pasting - if (textContent.endsWith("\n")) { - textContent = textContent.slice(0, -1) - } - return textContent -} - - -var copyTargetText = (trigger) => { - var target = document.querySelector(trigger.attributes['data-clipboard-target'].value); - - // get filtered text - let exclude = '.linenos'; - - let text = filterText(target, exclude); - return formatCopyText(text, '\\$ ', true, true, true, true, '', '') -} - - // Initialize with a callback so we can modify the text before copy - const clipboard = new ClipboardJS('.copybtn', {text: copyTargetText}) - - // Update UI with error/success messages - clipboard.on('success', event => { - clearSelection() - temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_success']) - temporarilyChangeIcon(event.trigger) - }) - - clipboard.on('error', event => { - temporarilyChangeTooltip(event.trigger, messages[locale]['copy'], messages[locale]['copy_failure']) - }) -} - -runWhenDOMLoaded(addCopyButtonToCodeCells) \ No newline at end of file diff --git a/pr-preview/pr-63/_static/copybutton_funcs.js b/pr-preview/pr-63/_static/copybutton_funcs.js deleted file mode 100644 index dbe1aaad..00000000 --- a/pr-preview/pr-63/_static/copybutton_funcs.js +++ /dev/null @@ -1,73 +0,0 @@ -function escapeRegExp(string) { - return string.replace(/[.*+?^${}()|[\]\\]/g, '\\$&'); // $& means the whole matched string -} - -/** - * Removes excluded text from a Node. - * - * @param {Node} target Node to filter. - * @param {string} exclude CSS selector of nodes to exclude. - * @returns {DOMString} Text from `target` with text removed. - */ -export function filterText(target, exclude) { - const clone = target.cloneNode(true); // clone as to not modify the live DOM - if (exclude) { - // remove excluded nodes - clone.querySelectorAll(exclude).forEach(node => node.remove()); - } - return clone.innerText; -} - -// Callback when a copy button is clicked. Will be passed the node that was clicked -// should then grab the text and replace pieces of text that shouldn't be used in output -export function formatCopyText(textContent, copybuttonPromptText, isRegexp = false, onlyCopyPromptLines = true, removePrompts = true, copyEmptyLines = true, lineContinuationChar = "", hereDocDelim = "") { - var regexp; - var match; - - // Do we check for line continuation characters and "HERE-documents"? - var useLineCont = !!lineContinuationChar - var useHereDoc = !!hereDocDelim - - // create regexp to capture prompt and remaining line - if (isRegexp) { - regexp = new RegExp('^(' + copybuttonPromptText + ')(.*)') - } else { - regexp = new RegExp('^(' + escapeRegExp(copybuttonPromptText) + ')(.*)') - } - - const outputLines = []; - var promptFound = false; - var gotLineCont = false; - var gotHereDoc = false; - const lineGotPrompt = []; - for (const line of textContent.split('\n')) { - match = line.match(regexp) - if (match || gotLineCont || gotHereDoc) { - promptFound = regexp.test(line) - lineGotPrompt.push(promptFound) - if (removePrompts && promptFound) { - outputLines.push(match[2]) - } else { - outputLines.push(line) - } - gotLineCont = line.endsWith(lineContinuationChar) & useLineCont - if (line.includes(hereDocDelim) & useHereDoc) - gotHereDoc = !gotHereDoc - } else if (!onlyCopyPromptLines) { - outputLines.push(line) - } else if (copyEmptyLines && line.trim() === '') { - outputLines.push(line) - } - } - - // If no lines with the prompt were found then just use original lines - if (lineGotPrompt.some(v => v === true)) { - textContent = outputLines.join('\n'); - } - - // Remove a trailing newline to avoid auto-running when pasting - if (textContent.endsWith("\n")) { - textContent = textContent.slice(0, -1) - } - return textContent -} diff --git a/pr-preview/pr-63/_static/css/badge_only.css b/pr-preview/pr-63/_static/css/badge_only.css deleted file mode 100644 index c718cee4..00000000 --- a/pr-preview/pr-63/_static/css/badge_only.css +++ /dev/null @@ -1 +0,0 @@ -.clearfix{*zoom:1}.clearfix:after,.clearfix:before{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-style:normal;font-weight:400;src:url(fonts/fontawesome-webfont.eot?674f50d287a8c48dc19ba404d20fe713?#iefix) format("embedded-opentype"),url(fonts/fontawesome-webfont.woff2?af7ae505a9eed503f8b8e6982036873e) format("woff2"),url(fonts/fontawesome-webfont.woff?fee66e712a8a08eef5805a46892932ad) format("woff"),url(fonts/fontawesome-webfont.ttf?b06871f281fee6b241d60582ae9369b9) format("truetype"),url(fonts/fontawesome-webfont.svg?912ec66d7572ff821749319396470bde#FontAwesome) format("svg")}.fa:before{font-family:FontAwesome;font-style:normal;font-weight:400;line-height:1}.fa:before,a .fa{text-decoration:inherit}.fa:before,a .fa,li .fa{display:inline-block}li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-.8em}ul.fas li 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Can be overridden in ``sphinx.search`` with a - * custom function per language. - * - * The regular expression works by splitting the string on consecutive characters - * that are not Unicode letters, numbers, underscores, or emoji characters. - * This is the same as ``\W+`` in Python, preserving the surrogate pair area. - */ -if (typeof splitQuery === "undefined") { - var splitQuery = (query) => query - .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) - .filter(term => term) // remove remaining empty strings -} - -/** - * Search Module - */ -const Search = { - _index: null, - _queued_query: null, - _pulse_status: -1, - - htmlToText: (htmlString) => { - const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); - const docContent = htmlElement.querySelector('[role="main"]'); - if (docContent !== undefined) return docContent.textContent; - console.warn( - "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." - ); - return ""; - }, - - init: () => { - const query = new URLSearchParams(window.location.search).get("q"); - document - .querySelectorAll('input[name="q"]') - .forEach((el) => (el.value = query)); - if (query) Search.performSearch(query); - }, - - loadIndex: (url) => - (document.body.appendChild(document.createElement("script")).src = url), - - setIndex: (index) => { - Search._index = index; - if (Search._queued_query !== null) { - const query = Search._queued_query; - Search._queued_query = null; - Search.query(query); - } - }, - - hasIndex: () => Search._index !== null, - - deferQuery: (query) => (Search._queued_query = query), - - stopPulse: () => (Search._pulse_status = -1), - - startPulse: () => { - if (Search._pulse_status >= 0) return; - - const pulse = () => { - Search._pulse_status = (Search._pulse_status + 1) % 4; - Search.dots.innerText = ".".repeat(Search._pulse_status); - if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); - }; - pulse(); - }, - - /** - * perform a search for something (or wait until index is loaded) - */ - performSearch: (query) => { - // create the required interface elements - const searchText = document.createElement("h2"); - searchText.textContent = _("Searching"); - const searchSummary = document.createElement("p"); - searchSummary.classList.add("search-summary"); - searchSummary.innerText = ""; - const searchList = document.createElement("ul"); - searchList.classList.add("search"); - - const out = document.getElementById("search-results"); - Search.title = out.appendChild(searchText); - Search.dots = Search.title.appendChild(document.createElement("span")); - Search.status = out.appendChild(searchSummary); - Search.output = out.appendChild(searchList); - - const searchProgress = document.getElementById("search-progress"); - // Some themes don't use the search progress node - if (searchProgress) { - searchProgress.innerText = _("Preparing search..."); - } - Search.startPulse(); - - // index already loaded, the browser was quick! - if (Search.hasIndex()) Search.query(query); - else Search.deferQuery(query); - }, - - /** - * execute search (requires search index to be loaded) - */ - query: (query) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - const allTitles = Search._index.alltitles; - const indexEntries = Search._index.indexentries; - - // stem the search terms and add them to the correct list - const stemmer = new Stemmer(); - const searchTerms = new Set(); - const excludedTerms = new Set(); - const highlightTerms = new Set(); - const objectTerms = new Set(splitQuery(query.toLowerCase().trim())); - splitQuery(query.trim()).forEach((queryTerm) => { - const queryTermLower = queryTerm.toLowerCase(); - - // maybe skip this "word" - // stopwords array is from language_data.js - if ( - stopwords.indexOf(queryTermLower) !== -1 || - queryTerm.match(/^\d+$/) - ) - return; - - // stem the word - let word = stemmer.stemWord(queryTermLower); - // select the correct list - if (word[0] === "-") excludedTerms.add(word.substr(1)); - else { - searchTerms.add(word); - highlightTerms.add(queryTermLower); - } - }); - - if (SPHINX_HIGHLIGHT_ENABLED) { // set in sphinx_highlight.js - localStorage.setItem("sphinx_highlight_terms", [...highlightTerms].join(" ")) - } - - // console.debug("SEARCH: searching for:"); - // console.info("required: ", [...searchTerms]); - // console.info("excluded: ", [...excludedTerms]); - - // array of [docname, title, anchor, descr, score, filename] - let results = []; - _removeChildren(document.getElementById("search-progress")); - - const queryLower = query.toLowerCase(); - for (const [title, foundTitles] of Object.entries(allTitles)) { - if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) { - for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) - results.push([ - docNames[file], - titles[file] !== title ? `${titles[file]} > ${title}` : title, - id !== null ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - - // search for explicit entries in index directives - for (const [entry, foundEntries] of Object.entries(indexEntries)) { - if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) { - for (const [file, id] of foundEntries) { - let score = Math.round(100 * queryLower.length / entry.length) - results.push([ - docNames[file], - titles[file], - id ? "#" + id : "", - null, - score, - filenames[file], - ]); - } - } - } - - // lookup as object - objectTerms.forEach((term) => - results.push(...Search.performObjectSearch(term, objectTerms)) - ); - - // lookup as search terms in fulltext - results.push(...Search.performTermsSearch(searchTerms, excludedTerms)); - - // let the scorer override scores with a custom scoring function - if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item))); - - // now sort the results by score (in opposite order of appearance, since the - // display function below uses pop() to retrieve items) and then - // alphabetically - results.sort((a, b) => { - const leftScore = a[4]; - const rightScore = b[4]; - if (leftScore === rightScore) { - // same score: sort alphabetically - const leftTitle = a[1].toLowerCase(); - const rightTitle = b[1].toLowerCase(); - if (leftTitle === rightTitle) return 0; - return leftTitle > rightTitle ? -1 : 1; // inverted is intentional - } - return leftScore > rightScore ? 1 : -1; - }); - - // remove duplicate search results - // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept - let seen = new Set(); - results = results.reverse().reduce((acc, result) => { - let resultStr = result.slice(0, 4).concat([result[5]]).map(v => String(v)).join(','); - if (!seen.has(resultStr)) { - acc.push(result); - seen.add(resultStr); - } - return acc; - }, []); - - results = results.reverse(); - - // for debugging - //Search.lastresults = results.slice(); // a copy - // console.info("search results:", Search.lastresults); - - // print the results - _displayNextItem(results, results.length, searchTerms); - }, - - /** - * search for object names - */ - performObjectSearch: (object, objectTerms) => { - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const objects = Search._index.objects; - const objNames = Search._index.objnames; - const titles = Search._index.titles; - - const results = []; - - const objectSearchCallback = (prefix, match) => { - const name = match[4] - const fullname = (prefix ? prefix + "." : "") + name; - const fullnameLower = fullname.toLowerCase(); - if (fullnameLower.indexOf(object) < 0) return; - - let score = 0; - const parts = fullnameLower.split("."); - - // check for different match types: exact matches of full name or - // "last name" (i.e. last dotted part) - if (fullnameLower === object || parts.slice(-1)[0] === object) - score += Scorer.objNameMatch; - else if (parts.slice(-1)[0].indexOf(object) > -1) - score += Scorer.objPartialMatch; // matches in last name - - const objName = objNames[match[1]][2]; - const title = titles[match[0]]; - - // If more than one term searched for, we require other words to be - // found in the name/title/description - const otherTerms = new Set(objectTerms); - otherTerms.delete(object); - if (otherTerms.size > 0) { - const haystack = `${prefix} ${name} ${objName} ${title}`.toLowerCase(); - if ( - [...otherTerms].some((otherTerm) => haystack.indexOf(otherTerm) < 0) - ) - return; - } - - let anchor = match[3]; - if (anchor === "") anchor = fullname; - else if (anchor === "-") anchor = objNames[match[1]][1] + "-" + fullname; - - const descr = objName + _(", in ") + title; - - // add custom score for some objects according to scorer - if (Scorer.objPrio.hasOwnProperty(match[2])) - score += Scorer.objPrio[match[2]]; - else score += Scorer.objPrioDefault; - - results.push([ - docNames[match[0]], - fullname, - "#" + anchor, - descr, - score, - filenames[match[0]], - ]); - }; - Object.keys(objects).forEach((prefix) => - objects[prefix].forEach((array) => - objectSearchCallback(prefix, array) - ) - ); - return results; - }, - - /** - * search for full-text terms in the index - */ - performTermsSearch: (searchTerms, excludedTerms) => { - // prepare search - const terms = Search._index.terms; - const titleTerms = Search._index.titleterms; - const filenames = Search._index.filenames; - const docNames = Search._index.docnames; - const titles = Search._index.titles; - - const scoreMap = new Map(); - const fileMap = new Map(); - - // perform the search on the required terms - searchTerms.forEach((word) => { - const files = []; - const arr = [ - { files: terms[word], score: Scorer.term }, - { files: titleTerms[word], score: Scorer.title }, - ]; - // add support for partial matches - if (word.length > 2) { - const escapedWord = _escapeRegExp(word); - Object.keys(terms).forEach((term) => { - if (term.match(escapedWord) && !terms[word]) - arr.push({ files: terms[term], score: Scorer.partialTerm }); - }); - Object.keys(titleTerms).forEach((term) => { - if (term.match(escapedWord) && !titleTerms[word]) - arr.push({ files: titleTerms[word], score: Scorer.partialTitle }); - }); - } - - // no match but word was a required one - if (arr.every((record) => record.files === undefined)) return; - - // found search word in contents - arr.forEach((record) => { - if (record.files === undefined) return; - - let recordFiles = record.files; - if (recordFiles.length === undefined) recordFiles = [recordFiles]; - files.push(...recordFiles); - - // set score for the word in each file - recordFiles.forEach((file) => { - if (!scoreMap.has(file)) scoreMap.set(file, {}); - scoreMap.get(file)[word] = record.score; - }); - }); - - // create the mapping - files.forEach((file) => { - if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1) - fileMap.get(file).push(word); - else fileMap.set(file, [word]); - }); - }); - - // now check if the files don't contain excluded terms - const results = []; - for (const [file, wordList] of fileMap) { - // check if all requirements are matched - - // as search terms with length < 3 are discarded - const filteredTermCount = [...searchTerms].filter( - (term) => term.length > 2 - ).length; - if ( - wordList.length !== searchTerms.size && - wordList.length !== filteredTermCount - ) - continue; - - // ensure that none of the excluded terms is in the search result - if ( - [...excludedTerms].some( - (term) => - terms[term] === file || - titleTerms[term] === file || - (terms[term] || []).includes(file) || - (titleTerms[term] || []).includes(file) - ) - ) - break; - - // select one (max) score for the file. - const score = Math.max(...wordList.map((w) => scoreMap.get(file)[w])); - // add result to the result list - results.push([ - docNames[file], - titles[file], - "", - null, - score, - filenames[file], - ]); - } - return results; - }, - - /** - * helper function to return a node containing the - * search summary for a given text. keywords is a list - * of stemmed words. - */ - makeSearchSummary: (htmlText, keywords) => { - const text = Search.htmlToText(htmlText); - if (text === "") return null; - - const textLower = text.toLowerCase(); - const actualStartPosition = [...keywords] - .map((k) => textLower.indexOf(k.toLowerCase())) - .filter((i) => i > -1) - .slice(-1)[0]; - const startWithContext = Math.max(actualStartPosition - 120, 0); - - const top = startWithContext === 0 ? "" : "..."; - const tail = startWithContext + 240 < text.length ? "..." : ""; - - let summary = document.createElement("p"); - summary.classList.add("context"); - summary.textContent = top + text.substr(startWithContext, 240).trim() + tail; - - return summary; - }, -}; - -_ready(Search.init); diff --git a/pr-preview/pr-63/_static/sphinx_highlight.js b/pr-preview/pr-63/_static/sphinx_highlight.js deleted file mode 100644 index aae669d7..00000000 --- a/pr-preview/pr-63/_static/sphinx_highlight.js +++ /dev/null @@ -1,144 +0,0 @@ -/* Highlighting utilities for Sphinx HTML documentation. */ -"use strict"; - -const SPHINX_HIGHLIGHT_ENABLED = true - -/** - * highlight a given string on a node by wrapping it in - * span elements with the given class name. - */ -const _highlight = (node, addItems, text, className) => { - if (node.nodeType === Node.TEXT_NODE) { - const val = node.nodeValue; - const parent = node.parentNode; - const pos = val.toLowerCase().indexOf(text); - if ( - pos >= 0 && - !parent.classList.contains(className) && - !parent.classList.contains("nohighlight") - ) { - let span; - - const closestNode = parent.closest("body, svg, foreignObject"); - const isInSVG = closestNode && closestNode.matches("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.classList.add(className); - } - - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - parent.insertBefore( - span, - parent.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling - ) - ); - node.nodeValue = val.substr(0, pos); - - if (isInSVG) { - const rect = document.createElementNS( - "http://www.w3.org/2000/svg", - "rect" - ); - const bbox = parent.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute("class", className); - addItems.push({ parent: parent, target: rect }); - } - } - } else if (node.matches && !node.matches("button, select, textarea")) { - node.childNodes.forEach((el) => _highlight(el, addItems, text, className)); - } -}; -const _highlightText = (thisNode, text, className) => { - let addItems = []; - _highlight(thisNode, addItems, text, className); - addItems.forEach((obj) => - obj.parent.insertAdjacentElement("beforebegin", obj.target) - ); -}; - -/** - * Small JavaScript module for the documentation. - */ -const SphinxHighlight = { - - /** - * highlight the search words provided in localstorage in the text - */ - highlightSearchWords: () => { - if (!SPHINX_HIGHLIGHT_ENABLED) return; // bail if no highlight - - // get and clear terms from localstorage - const url = new URL(window.location); - const highlight = - localStorage.getItem("sphinx_highlight_terms") - || url.searchParams.get("highlight") - || ""; - localStorage.removeItem("sphinx_highlight_terms") - url.searchParams.delete("highlight"); - window.history.replaceState({}, "", url); - - // get individual terms from highlight string - const terms = highlight.toLowerCase().split(/\s+/).filter(x => x); - if (terms.length === 0) return; // nothing to do - - // There should never be more than one element matching "div.body" - const divBody = document.querySelectorAll("div.body"); - const body = divBody.length ? divBody[0] : document.querySelector("body"); - window.setTimeout(() => { - terms.forEach((term) => _highlightText(body, term, "highlighted")); - }, 10); - - const searchBox = document.getElementById("searchbox"); - if (searchBox === null) return; - searchBox.appendChild( - document - .createRange() - .createContextualFragment( - '

' + - '' + - _("Hide Search Matches") + - "

" - ) - ); - }, - - /** - * helper function to hide the search marks again - */ - hideSearchWords: () => { - document - .querySelectorAll("#searchbox .highlight-link") - .forEach((el) => el.remove()); - document - .querySelectorAll("span.highlighted") - .forEach((el) => el.classList.remove("highlighted")); - localStorage.removeItem("sphinx_highlight_terms") - }, - - initEscapeListener: () => { - // only install a listener if it is really needed - if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) return; - - document.addEventListener("keydown", (event) => { - // bail for input elements - if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; - // bail with special keys - if (event.shiftKey || event.altKey || event.ctrlKey || event.metaKey) return; - if (DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS && (event.key === "Escape")) { - SphinxHighlight.hideSearchWords(); - event.preventDefault(); - } - }); - }, -}; - -_ready(SphinxHighlight.highlightSearchWords); -_ready(SphinxHighlight.initEscapeListener); diff --git a/pr-preview/pr-63/code-structure.html b/pr-preview/pr-63/code-structure.html deleted file mode 100644 index ac0688ce..00000000 --- a/pr-preview/pr-63/code-structure.html +++ /dev/null @@ -1,238 +0,0 @@ - - - - - - - Code Structure — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

Code Structure

-

The Processing Chain code is structured as follows:

-
$ tree -L 3 -F --dirsfirst
-.
-├── cases/                      # folder where all cases are stored
-│   ├── cosmo-ghg-spinup-test/  # COSMO-GHG test case with spinup restart
-│   │   ├── config.yaml         # case configuration file
-│   │   ├── *.cfg               # templates for namelists & batch jobs
-│   │   └── *.csv               # CSV files with tracer information
-│   ├── cosmo-ghg-test/         # COSMO-GHG testcase with standard restart
-│   │   ├── config.yaml
-│   │   ├── *.cfg
-│   │   └── *.csv
-│   ├── icon-art-global-test/   # ICON-ART test case (global domain)
-│   │   ├── config.yaml
-│   │   ├── icon_runjob.cfg     # template for ICON-ART runjob
-│   │   ├── *.sh                # pre-processing scripts
-│   │   └── mypartab
-│   ├── icon-art-oem-test/      # ICON-ART test case with online emissions
-│   │   ├── config.yaml
-│   │   └── *.cfg
-│   └── icon-test/              # ICON test case
-│       ├── config.yaml
-│       └── *.cfg
-├── docs/                       # folder for Sphinx documentation
-│   ├── _static/                # folder for static assets
-│   │   ├── custom.css          # custom CSS styles
-│   │   └── *.png|ico           # additional image assets
-│   ├── tables/                 # folder for tables used in documentation
-│   │   └── *.csv               # CSV files containing table data
-│   ├── conf.py                 # configuration file for the Sphinx builder
-│   └── *.rst                   # documentation files (reStructuredText)
-├── env/
-│   └── environment.yml         # conda environment file
-├── ext/                        # folder for other code (spack, models, etc.)
-├── jenkins/                    # automated Jenkins testing
-│   ├── scripts/
-│   │   └── *.sh                # individual Shell scripts for testing
-│   └── Jenkinsfile             # text file containing the Jenkins pipeline
-├── jobs/
-│   ├── tools/
-│   │   └── *.py                # tool scripts
-│   └── *.py                    # job scripts
-├── LICENSE                     # license file
-├── README.md                   # README file
-├── config.py                   # file containing the Config class
-├── run_chain.py                # main script
-└── workflows.yaml              # file to store workflows with job dependencies
-
-
-
- - -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/config.html b/pr-preview/pr-63/config.html deleted file mode 100644 index 78e49e57..00000000 --- a/pr-preview/pr-63/config.html +++ /dev/null @@ -1,459 +0,0 @@ - - - - - - - Configuration File — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -

The Processing Chain uses cases to describe a simulation. A case is a -subdirectory in cases/, containing a config.yaml and several -namelist (e.g., int2lm_INPUT.cfg) and runscripts (e.g., -icon_runjob.cfg) templates, -which define the simulation.

-
-

Configuration File

-

The case-dependent configuration file <casename>/config.yaml contains most -of the information that the jobs need to prepare -and run the simulation, for example the location of the input data. -This configuration file is loaded in run_chain.py as an instance -of the Config() class in config.py.

-
-

Configuration Variables

-

This is a non-exhaustive list containing the most important configuration variables:

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Variable

Description

-
case_path
-

-
-
-
The path to the case directory under cases/ for the specified
-
casename.
-
-

casename

The name of the case. Derived from the folder name under case_path.

-
chain_src_dir
-

-
-
-
The source directory for the processing chain, typically the current
-
working directory.
-
-

compute_account

The compute account to be used based on user information.

constraint

The computational constraint (gpu or mc).

-
email
-

-
-
-
The user’s email address, initially set to None and updated using the
-
set_email method.
-
-
-
enddate
-

-
-
-
The end date of the simulation in ISO 8601 format
-
(YYYY-MM-DDTHH:mm:ssZ).
-
-

jobs

List of job-names to be executed.

log_finished_dir

The directory for finished log files.

log_working_dir

The directory for working log files.

ntasks_per_node

The number of tasks per node, based on the node type.

restart_step

The restart step in ISO 8601 format.

restart_step_hours

The restart step in hours, derived from the restart_step attribute.

run_on

The architecture the model runs on (cpu or gpu).

spinup

Spin-up duration in hours. Activates spinup behavior if set.

-
startdate
-

-
-
-
The start date of the simulation in ISO 8601 format
-
(YYYY-MM-DDTHH:mm:ssZ).
-
-

user_mail

The user’s email address, determined based on system configuration.

-
user_name
-

-
-
-
Your email address to receive notifications. Either provide it
-
directly here or in ~/.forward.
-
-

workflow

The name of the workflow from workflows.yaml or a self-defined one.

-
work_root
-

-
-
-
The working directory where all output is stored. Should be somewhere
-
on $SCRATCH$. By default, it is set to <chain_src_dir>/work.
-
-
-
-
-

Variables to Set in config.yaml

-

Here are two examples of which general variables should be set by the user in the -case configuration file.

-
-

Header of config.yaml for the cosmo-ghg-spinup-test case

-
workflow: cosmo-ghg
-constraint: gpu
-ntasks_per_node: 12
-restart_step: PT6H
-spinup: 3
-startdate: 2015-01-01T00:00:00Z
-enddate: 2015-01-01T18:00:00Z
-
-
-
-
-

Header of config.yaml for the icon-art-oem-test case

-
workflow: icon-art-oem
-constraint: gpu
-run_on: cpu
-compute_queue: normal
-ntasks_per_node: 12
-restart_step: PT6H
-startdate: 2018-01-01T00:00:00Z
-enddate: 2018-01-01T12:00:00Z
-
-eccodes_dir: ./input/eccodes_definitions
-iconremap_bin: iconremap
-iconsub_bin: iconsub
-latbc_filename: ifs_<y><m><d><h>_lbc.nc
-inidata_prefix: ifs_init_
-inidata_nameformat: '%Y%m%d%H'
-inidata_filename_suffix: .nc
-output_filename: icon-art-oem-test
-filename_format: <output_filename>_DOM<physdom>_<ddhhmmss>
-lateral_boundary_grid_order: lateral_boundary
-art_input_folder: ./input/icon-art-oem/ART
-
-
-
-
-

Further variables

-

Furthermore, there are additional variables to set that are tied to the individual jobs. -These config variables themselves are dictionaries. Let’s have a look at and example -for the the cfg.meteo variable:

-
meteo:
-    dir: ./input/cosmo-ghg/meteo
-    prefix: laf
-    nameformat: laf%Y%m%d%H
-    inc: 1
-
-
-

These config variables can be accessed via cfg.meteo['dir'], cfg.meteo['prefix'], etc. -as they are Python dictionaries.

-
-

Hint

-

In namelist and runscript template files -(see next section), this accessing does not work because of how the .format() -method is implemented in Python. For that reason, the Processing Chain automatically -creates new variables in the form of cfg.meteo_dir, cfg.meteo_prefix, etc. -at the start to make them accessible for namelist and runjob templates.

-
-
-

List of dictionary variables

-

The following is a list of dictionary variables that exist for the Processing Chain. -For the individual elements of those variables, please refer to the config.yaml -files within the test cases.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Dictionary variable

Used in job

meteo

prepare_cosmo, prepare_icon, icontools, int2lm, icon

icontools_runjobs

icontools

input_files

prepare_icon

chem

prepare_icon

era5

prepare_icon

cams

prepare_cosmo

emissions

emissions

vprm

biofluxes

oem

oem, cosmo

online_vprm

online_vprm

int2lm

prepare_cosmo, emissions, biofluxes, octe, int2lm, post_int2lm, cosmo, post_cosmo

post_int2lm

post_int2lm

cosmo

reduce_output, oem, photo_rate, octe, check_output, post_cosmo, cosmo, obs_nudging, online_vprm

reduce_output

reduce_output

post_cosmo

post_cosmo

verify_chain

verify_chain

icon

oem, prepare_icon, icon

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Conda Environment

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The following steps allow you to create and use your own virtual environment to run the Processing Chain. We recommend using a conda environment for the usage of the provided scripts. Please follow the instructions for the installation. The following steps only need to be performed once.

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-

1. Install Miniconda

-

Install Miniconda as user-specific Miniconda, e.g., in your $HOME directory, which is the default location.

-
-

Note

-

Only conda itself should be installed in your $HOME. All environments should be stored in your $PROJECT directory; otherwise, you risk filling up your $HOME directory. See below for instructions.

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To install the latest Miniconda, type:

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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
-bash Miniconda3-latest-Linux-x86_64.sh
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Further details on Miniconda can be found on the Miniconda documentation page.

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2. Create the Conda Environment

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Create a conda environment proc-chain and install the requirements:

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conda env create --prefix $PROJECT/envs/proc-chain -f env/environment.yml
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To be able to activate your conda environment by simply using conda activate proc-chain instead of the full path, add the following to your .bashrc:

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export CONDA_ENVS_PATH=$PROJECT/envs
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Activate the environment (use “source activate” in case “conda activate” does not work):

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conda activate proc-chain
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If you already have the environment but want to update it:

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conda env update --file env/environment.yml --prune
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3. Store user-specific data

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To register your email address and standard project account, store them in these files within your home directory:

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echo <your_account_id> > ~/.acct
-echo <your_email_address> > ~/.forward
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-
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These settings are optional. The Processing Chain will first check the content of those files. If desired, the corresponding variables can be overridden by setting the compute_account and user_mail variables in the config.yaml file.

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- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/features.html b/pr-preview/pr-63/features.html deleted file mode 100644 index f4373e66..00000000 --- a/pr-preview/pr-63/features.html +++ /dev/null @@ -1,199 +0,0 @@ - - - - - - - Feature Overview — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - - - -
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Feature Overview

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  • Asynchronous submission of compute jobs to the HPC queue

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  • Intuitive definition of job dependencies

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  • Automatic cycling over time periods including folder structure creation

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  • Various jobs for pre- and post-processing steps

    • -

  • Using model built-in restarts or custom spinup

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  • Nested runs possible

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  • Easy creation of own cases and workflows

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  • Various examples for COSMO and ICON workflows available

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Jobs

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-jobs.biofluxes.main(cfg)[source]
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Prepare biofluxes files for COSMO simulations.

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Copies biofluxes files from the project folder (cfg.vprm['dir']) -to the int2lm input folder on scratch (cfg.int2lm_input/vprm).

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-
Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.check_output.main(cfg)[source]
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Check output variables for physical reasonability and create plots.

-

This function checks the output variables to ensure they are in a physically -reasonable range. It stores the time series of the minimum, maximum, mean, and -standard deviation of the variables as a pandas object into a pickle file.

-

It also creates per-variable plots from the stored time series data.

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-
Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.cosmo.main(cfg)[source]
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Setup the namelists for a COSMO run and submit the job to the queue.

-

Create necessary directory structure to run COSMO (run, output, and -restart directories, defined in cfg.cosmo_run, cfg.cosmo_output, -and cfg.cosmo_restart_out).

-

Copy the COSMO-executable from -cfg.cosmo['binary_file'] to cfg.cosmo_run/cfg.cosmo['execname'].

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Convert the tracer csv file to a COSMO namelist file.

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Format the COSMO namelist templates using the information in cfg.

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Format the runscript template and submit the job.

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Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.emissions.main(cfg)[source]
-

Copy emission files to the int2lm input directory.

-

Necessary for both COSMO and COSMOART simulations.

-

Copy emission files from project folder (cfg.emissions['dir']) to -int2lm input folder on scratch (cfg.int2lm_input/emissions).

-

For COSMO simulations, converts the netCDF-variable-names -from string to char (necessary for int2lm).

-

If there are multiple emission-datasets (cfg.emissions[‘dir’] is a list of -paths), they are copied as follows:

-
cfg.emissions['dir'][0]/cfg.emissions['gridname'][0]YYYYMMDD.nc -> int2lm_input/emissions/emis_YYYYMMDD.nc
-cfg.emissions['dir'][1]/cfg.emissions['gridname'][1]YYYYMMDD.nc -> int2lm_input/emissions2/emis_YYYYMMDD.nc
-cfg.emissions['dir'][2]/cfg.emissions['gridname'][2]YYYYMMDD.nc -> int2lm_input/emissions3/emis_YYYYMMDD.nc
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-
-
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Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.icon.main(cfg)[source]
-

Setup the namelists for an ICON run and submit the job to -the queue.

-

Copy the ICON-executable from -cfg.icon_binary_file to cfg.icon_work/icon.exe.

-

Format the ICON-namelist-templates: -icon_master.namelist.cfg, icon_NAMELIST_NWP.cfg, -using the information in cfg.

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Format the runscript-template and submit the job.

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-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.icontools.main(cfg)[source]
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    -

  • Add GEOSP to all meteo files

    • -

  • Submit the runscript for the DWD ICON tools to remap the meteorological files.

    • -

  • All runscripts specified in cfg.icontools_runjobs are submitted.

    • -

  • The meteorological files are read from the original input directory -(cfg.input_root_meteo), and the remapped meteorological files are saved -in the input folder on scratch (cfg.icon_input/icbc).

    • -
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- -
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-jobs.int2lm.main(cfg)[source]
-

Setup the namelist for int2lm and submit the job to the queue.

-

Necessary for both COSMO and COSMOART simulations.

-

Decide if the soil model should be TERRA or TERRA multi-layer depending on -startdate of the simulation.

-

Create necessary directory structure to run int2lm (run and output -directories, defined in cfg.int2lm and cfg.int2lm['output']).

-

Copy the int2lm-executable from cfg.int2lm['binary_file'] to -cfg.int2lm['work']/int2lm.

-

Copy the extpar-file cfg.int2lm['extpar_file'] to -cfg.int2lm_run/work.

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COSMOART: Copy the libgrib_api files to -cfg.int2lm['work']/libgrib_api.

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COSMO: Convert the tracer-csv-files into an int2lm-namelist file.

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Format the int2lm-namelist-template using the information in cfg.

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Format the runscript-template and submit the job.

-
-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.obs_nudging.main(cfg)[source]
-

Copy and rename the obs_nudging files to the COSMO input directory.

-

In the folder cfg.obs_nudging_dir, the files are saved in the format -{prefix}-YYYYMMDD000000-YYYYMMDD000000. COSMO expects files in the -format {prefix}x, where x is [nothing], .2, .3, .4, .... This -job handles this filename-change and copies them to the COSMO input -folder on scratch (cfg.cosmo_input/obs_nudging).

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Missing observation files are ignored.

-

Also copies the blacklist-file blklsttmp.

-
-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-
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- -
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-jobs.octe.main(cfg)[source]
-

Copy necessary input files for COSMO and perturb BG.

-

Copies the NetCDF-files found at cfg.octe_maps and cfg.octe_lambdas to -the COSMO input-directory.

-

Perturbs the background tracer field. To do that, it reads the lambda-value -from the cfg.octe_lambdas (last value along the nparam-dimension) and -scales the BG-field produced by int2lm, creating a new variable for each -ensemble.

-
-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-
-
- -
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-jobs.oem.main(cfg)[source]
-

Copy emission and profile files to the cosmo or icon input -directory.

-
-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

-
-
Raises:
-

RuntimeError – If an error occurs during the process.

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-
-
- -
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-jobs.online_vprm.main(cfg)[source]
-

Copy MODIS surface reflectance data and vegetation class fraction file -to the cosmo input directory.

-
-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-
-
- -
-
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-jobs.photo_rate.main(cfg)[source]
-

Copy photolysis-rate file to the COSMOART input directory.

-

Only necessary for COSMOART simulations.

-

Copy the photolysis-rate file from the project (cfg.photo_rate_file) to -the COSMOART input folder on scratch (cfg.cosmo_input/art_photolysis).

-
-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.post_cosmo.main(cfg)[source]
-

Copy the output of a COSMO-run to a user-defined position.

-

Write a runscript to copy all files (COSMO settings & output, -int2lm settings, logfiles) from cfg.cosmo_run, -cfg.cosmo_output, cfg.int2lm_run, cfg.log_finished_dir to -cfg.output_root/.... -If the job reduce_output has been run before post_cosmo, a -directory cfg.cosmo_output_reduced is created. In this case, -cfg.cosmo_output_reduced is copied instead of cfg.cosmo_output.

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Submit the job to the xfer-queue.

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-
Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.post_int2lm.main(cfg)[source]
-

Combine multiple int2lm tracer-output files into a single one for -COSMO.

-

Only necessary for COSMO simulations.

-

int2lm puts tracers into different netCDF files. Combine the files -specified in cfg.post_int2lm_species into a single netCDF file for -COSMO.

-

If cfg.spinup and cfg.post_int2lm_species_spinup are present, -also read in the specified variables and take them as an input for -COSMO.

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Parameters:
-

cfg (Config) – Object holding all user-configuration parameters as attributes.

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-jobs.prepare_cosmo.main(cfg)[source]
-

COSMO Data Preparation

-

This function prepares input data for COSMO simulations by creating necessary directories, -copying meteorological files, and handling specific data processing.

-
    -

  • Copy meteorological files to int2lm input.

    • -

  • Create the necessary directory cfg.int2lm_input/meteo.

    • -

  • Copy meteorological files from the project directory (cfg.meteo['dir']/cfg.meteo['prefix']YYYYMMDDHH) -to the int2lm input folder on scratch (cfg.int2lm_input/meteo).

    • -

  • For nested runs (meteorological files are COSMO output: cfg.meteo['prefix'] == 'lffd'), -also copy the *c.nc-file with constant parameters.

    • -
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-
Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes.

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-
Raises:
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RuntimeError – If any subprocess returns a non-zero exit code during execution.

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-jobs.prepare_icon.main(cfg)[source]
-

ICON Data Preparation

-

This function prepares input data for ICON simulations by creating necessary directories, -copying meteorological files, and handling specific data processing.

-
    -

  • Create working directories and copy input files

    • -
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Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes.

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Raises:
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RuntimeError – If any subprocess returns a non-zero exit code during execution.

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-jobs.reduce_output.main(cfg)[source]
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Calculates 2D column data and writes them into a new netCDF file. -Only a fixed number of levels from COSMO output are considered. -Those files are written into a new directory cosmo_output_reduced.

-

The number of levels is set by the configuration variable -cfg.reduce_output['output_levels'] (default = all levels).

-

Important: If several GRIBOUT sections are used to split the output -data, then this code only works in case of the following: -The tracers, for which the column-averaged dry-air (X) and -moist-air (Y) mole fractions are calculated, have to be

-
-
    -

  1. saved in a separate output file and

    2. -

  2. the output file appears alphabetically after the meteorological -variables.

    3. -
-
-

For example, use a GRIBOUT section suffix _met for standard COSMO -output, and _trc for tracers.

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Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes

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-jobs.verify_chain.main(cfg)[source]
-

Compare outputs of the chain to a reference.

-

Looks for the reference-file in cfg.verify_chain['reference_dir'].

-

Looks for the output file in cfg.verify_chain['output_dir'] (if not None), else it -goes to the output directory created by the COSMO-job.

-

In the dict cfg.verify_chain['values_to_check'], the user specifies the names of the -files to be compared as keys, and the variables to compare as a list.

-

To compare the temperatures of the last output of the example case, the -following variables should be added to the config.yaml file:

-
verify_chain['reference_dir'] = os.path.join(input_root, "reference_output")
-verify_chain['output_dir'] = None
-verify_chain['values_to_check'] = {("reference_lffd2015010200.nc","lffd2015010200.nc"):
-      ['T']}
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-
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Parameters:
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cfg (Config) – Object holding all user-configuration parameters as attributes

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Tools

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The tools are a collection of functions used by the jobs. Most of those -functions are well documented and listed here. For others, one may take -a look into jobs/tools directly.

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-jobs.tools.cams4int2cosmo.main(date, inpath, outpath, param)[source]
-

Prepare CAMS CO2, CO and NOx boundary conditions for -int2lm/int2cosmo for the project SMARTCARB.

-

The CAMS data consists of

- -

The data sets are retrieved as individual 3-hourly files from the MARS -archive at ECMWF with names:

-
cams_0001_2015010500.nc   # for NO and NO2
-sfc_0001_2015010500.nc    # for log of surface pressure
-cams_gf39_2015010500.nc   # for CO and CO2
-sfc_gf39_2015010500.nc    # for log of surface pressure
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-
-

The path to the directory of the CAMS data can optionally be supplied, -otherwise the script should be invoked in the directory of the CAMS data.

-

The script generates 8 individual 3-hourly IC/BC files:

-
cams_nox_yyyymmddhh.nc
-cams_co2_yyyymmddhh.nc
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-
-

Usage:

-
python cams4int2cosmo.py date [-i inpath -o outpath]
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-
-

Output:

-
-

cams_NOX_YYYYMMDD00.nc to cams_NOX_YYYYMMDD21.nc -cams_CO2_YYYYMMDD00.nc to cams_CO2_YYYYMMDD21.nc

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Parameters:
-
    -

  • date (str) – date in format YYYYMMDD

    • -

  • inpath (str) – path of original CAMS files (default is current path)

    • -

  • outpath (str) – path where output files should be generated (default is current path)

    • -

  • param (dict) –

    • -
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-jobs.tools.check_model.check_model(cfg, model='COSMO')[source]
-

Check that the model specified in cfg matched the prescribed model.

-

Check that cfg.workflow_name == model. If not, raises a value-error. -Ignores capitalization of the strings

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Parameters:
-
    -

  • cfg (Config) – Object holding all user-configuration parameters as attributes.

    • -

  • model (str) – Prescribed model

    • -
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-jobs.tools.comp_nc.datasets_equal(dataset1, dataset2, variables, verbose=True)[source]
-

Compare the contents of dataset1 and dataset2

-

Compare with numpy.isclose whether the two datasets are equal. No check for -equality (of the values or bitwise of the files) is performed, as numerical -errors can produce slightly different files for essentially identical -computations. Rather, the values are compared to absolute and relative -tolerances, check np.isclose documentation for more detail.

-

If variables is not empty, only the provided variables are compared.

-
-
Parameters:
-
    -

  • dataset1 (netCDF4.Dataset) –

    • -

  • dataset2 (netCDF4.Dataset) –

    • -

  • variables (list of str) – List of the variables to be compared. If it is empty, all variables -are compared.

    • -

  • verbose (bool) – If True, results will be printed to stdout.

    • -
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Returns:
-

True if the datasets, or if provided the selected variables, are equal, -False otherwise.

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-
Return type:
-

bool

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-jobs.tools.ctnoaa4int2cosmo.main(date, indir, outdir, param)[source]
-

Process all CarbonTracker files of a single date to a format -compatible with int2lm

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-
Parameters:
-
    -

  • date (str) – date in format YYYYMMDD.

    • -

  • indir (str) – directory of original CarbonTracker files (default is current path).

    • -

  • outdir (str) – utput directory of processed files (default is indir/processed).

    • -

  • param (dict) – dictionary of the parameters

    • -
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-jobs.tools.mozart2int2lm.main(_, infile, outdir, params)[source]
-

Extract each timeslice from infile into seperate file in outdir.

-

Copies dimensions, renaming ‘lev’ -> ‘level’.

-

Copies, renames and combines variables (see source code for specifics).

-

Transforms ‘lon’ to [-180, 180) range.

-
-
Parameters:
-
    -

  • _ – Ignored

    • -

  • infile (str) – Path to file to extract from

    • -

  • outdir (str) – Path to the directory where the output files are written to

    • -

  • params (dict) – Only entry: ‘suffix’ -Processed files are stored as outdir/{suffix}_YYYYMMDDHH.nc

    • -
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-jobs.tools.reduce_output_start_end.main(indir, outdir, strdate_start, strdate_end, nout_levels, csvfile, convert_gas)[source]
-

Script to reduce output.

-

Output: TODO

-
-

Parameters (TODO)

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opathstr

Output path where the processed data is going to be written

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-jobs.tools.string2char.main(filename)[source]
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Convert the variable names of a netcdf-file from strings to a -np.array of chars.

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Parameters:
-

filename (str) – Path to the netcdf-file

-
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-jobs.tools.vprmsplit.main(year, ipath, opath)[source]
-

Script to extract VPRM emissions for a single day -and to convert the output into an int2lm compatible format.

-

Output: -The script generates individual 1-hour emission files for the specified -year:

-
gpp_yyyymmddhh.nc
-ra_yyyymmddhh.nc
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-
-
-
Parameters:
-
    -

  • year (str) – Year (YYYY) of data to be processed -The original VPRM input file (e.g., VPRM_ECMWF_*_2017.nc for 2017 -fluxes) needs to be present in the input directory ‘ipath’

    • -

  • ipath (str) – Input path where the VPRM input file is located

    • -

  • opath (str) – Output path where the processed data is going to be written

    • -
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-jobs.tools.write_cosmo_input_ghg.main(csv_filename, namelist_filename, cfg=None)[source]
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Convert a table (.csv file) to namelist file (INPUT_GHG) -read by COSMO.

-
-
Parameters:
-
    -

  • csv_filename (str) – Path to the source csv-file

    • -

  • namelist_filename (str) – Path to the namelist file that will be created

    • -

  • cfg (Config) – Object holding all user-configuration parameters as attributes.

    • -
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-jobs.tools.write_int2lm_input_art.main(trcr_filename, set_filename, nml_filename, hstart=0)[source]
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Write the INPUT_ART namelist file for int2lm from .csv files

-
-
Parameters:
-
    -

  • trcr_filename (str) – csv file with tracer definitions

    • -

  • set_filename (str) – csv file with tracer datasets

    • -

  • nml_filename (str) – output filename (INPUT_ART)

    • -

  • hstart (int) – meteorology spin up in hours

    • -
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- - - - \ No newline at end of file diff --git a/pr-preview/pr-63/genindex.html b/pr-preview/pr-63/genindex.html deleted file mode 100644 index fa16c53f..00000000 --- a/pr-preview/pr-63/genindex.html +++ /dev/null @@ -1,277 +0,0 @@ - - - - - - Index — Processing Chain v3.1 documentation - - - - - - - - - - - - - - - - - - - - - - -
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Index

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How to Run

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The Python file run_chain.py in the root directory is the main script of the -Processing Chain. -It reads the user’s input from the command line and from the config.yaml file of the -respective case. -Then it will start the Processing Chain.

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Starting the Chain

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The chain has to be run with the following command:

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$ ./run_chain.py <casename>
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Here, <casename> is the name of a directory in the cases/-directory where -there is a config.yaml-file specifying the configuration, as well as templates -for the necessary namelist files for int2lm, COSMO or ICON. It may also -contain additional runscripts to be submitted via sbatch.

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Hint

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Technically, you can run several cases (instead of a single case) in one command, -which is useful for nested runs, for example. This can be achieved by running -./run_chain.py <case1> <case2>. With that, the full chain is executed for -case1 first, and afterwards for case2.

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There are several optional arguments available to change the behavior of the chain:

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$ ./run_chain.py -h
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    -h, --help

    Show this help message and exit.

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    -j [JOB_LIST ...], --jobs [JOB_LIST ...]

    List of job names to be executed. -A job is a .py file in i``jobs/`` with a main() function, which -handles one aspect of the Processing Chain, for -example copying meteo input data or launching a -job for int2lm. Jobs are executed in the order -in which they are given here. If no jobs are -given, default jobs will be executed as defined -in config/models.yaml.

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    -f, --force

    Force the Processing Chain to redo all specified -jobs, even if they have been started already or -were finished previously. WARNING: Only logfiles -get deleted, other effects of a given job -(copied files etc.) are simply overwritten. This -may cause errors or unexpected behavior.

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    -r, --resume

    Resume the Processing Chain by restarting the -last unfinished job. WARNING: Only the logfile -gets deleted, other effects of a given job -(copied files etc.) are simply overwritten. This -may cause errors or unexpected behavior.

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What it Does

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The script run_chain.py reads the command line arguments and the config file -from the specified case. -It then calls the function run_chain.restart_runs(), which divides the -simulation time according to the specified restart steps. Then it calls -run_chain.run_chunk() for each part (chunk) of the simulation workflow. -This function sets up the directory structure of the chain and then submits the -specified jobs via sbatch to the Slurm workload manager, -taking job dependencies into account.

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Test Cases

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The following test cases are available:

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  • cosmo-ghg-spinup-test

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  • cosmo-ghg-test

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  • icon-test

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  • icon-art-oem-test

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  • icon-art-global-test

    • -
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To be able to run these test cases, it is necessary to provide the input data, -to setup spack and to compile the models and tools. All this is automized via -the script:

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$ ./jenkins/scripts/jenkins.sh
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This will run all the individual scripts in jenkins/scripts/, which -can also be launched separately if desired.

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These cases undergo regulary testing to ensure that the Processing Chain runs -correctly. A corresponding Jenkins plan is launched on a weekly basis and -when triggered within a GitHub pull request.

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Directory Structure

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The directory structure generated by the Processing Chain for a cosmo-ghg -run looks like this:

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cfg.work_root/cfg.casename/
-└── cfg.chain_root/
-    ├── checkpoints/
-    │   ├── cfg.log_working_dir/
-    │   ├── cfg.log_finished_dir/
-    ├── cfg.cosmo_base/
-    │   ├── cfg.cosmo_work/
-    │   ├── cfg.cosmo_output/
-    │   ├── cfg.cosmo_restart_out/
-    └── cfg.int2lm_base/
-        ├── cfg.int2lm_input/
-        ├── cfg.int2lm_work/
-        └── cfg.int2lm_output/
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As one can see, it creates working directories for both the int2lm preprocessor -and cosmo. Additionally, and this is always the case, the checkpoints -directory holds all the job logfiles. Whenever a job has successfully finished, -the logfile is copied from the working to the finished sub-directory.

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Running the cosmo-ghg-test case therefore produces the following -directories and files (showing four levels of directories deep):

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work/cosmo-ghg-test
-├── 2015010100_2015010106/
-│   ├── checkpoints/
-│   │   ├── finished/
-│   │   │   ├── biofluxes
-│   │   │   ├── cosmo
-│   │   │   ├── emissions
-│   │   │   ├── int2lm
-│   │   │   ├── oem
-│   │   │   ├── online_vprm
-│   │   │   ├── post_cosmo
-│   │   │   ├── post_int2lm
-│   │   │   └── prepare_cosmo
-│   │   └── working/
-│   │       ├── biofluxes
-│   │       ├── cosmo
-│   │       ├── emissions
-│   │       ├── int2lm
-│   │       ├── oem
-│   │       ├── online_vprm
-│   │       ├── post_cosmo
-│   │       ├── post_int2lm
-│   │       └── prepare_cosmo
-│   ├── cosmo/
-│   │   ├── input/
-│   │   │   ├── oem/
-│   │   │   └── vprm/
-│   │   ├── output/
-│   │   │   └── lffd*.nc
-│   │   ├── restart/
-│   │   │   └── lrff00060000o.nc
-│   │   └── run/
-│   │       ├── cosmo-ghg
-│   │       ├── INPUT_*
-│   │       ├── post_cosmo.job
-│   │       ├── run.job
-│   │       └── YU*
-│   └── int2lm/
-│       ├── input/
-│       │   ├── emissions
-│       │   ├── extpar
-│       │   ├── icbc
-│       │   ├── meteo
-│       │   └── vprm
-│       ├── output/
-│       │   ├── laf*.nc
-│       │   └── lbfd*.nc
-│       └── run/
-│           ├── INPUT
-│           ├── INPUT_ART
-│           ├── int2lm
-│           ├── OUTPUT
-│           ├── run.job
-│           └── YU*
-└── 2015010106_2015010112/
-        ├── checkpoints/
-        │   ├── finished/
-        │   │   ├── biofluxes
-        │   │   ├── cosmo
-        │   │   ├── emissions
-        │   │   ├── int2lm
-        │   │   ├── oem
-        │   │   ├── online_vprm
-        │   │   ├── post_cosmo
-        │   │   ├── post_int2lm
-        │   │   └── prepare_cosmo
-        │   └── working/
-        │       ├── biofluxes
-        │       ├── cosmo
-        │       ├── emissions
-        │       ├── int2lm
-        │       ├── oem
-        │       ├── online_vprm
-        │       ├── post_cosmo
-        │       ├── post_int2lm
-        │       └── prepare_cosmo
-        ├── cosmo/
-        │   ├── input/
-        │   │   ├── oem
-        │   │   └── vprm
-        │   ├── output/
-        │   │   └── lffd*.nc
-        │   ├── restart/
-        │   │   └── lrff00060000o.nc
-        │   └── run/
-        │       ├── cosmo-ghg
-        │       ├── INPUT_*
-        │       ├── post_cosmo.job
-        │       ├── run.job
-        │       └── YU*
-        └── int2lm/
-                ├── input/
-                │   ├── emissions
-                │   ├── extpar
-                │   ├── icbc
-                │   ├── meteo
-                │   └── vprm
-                ├── output/
-                │   ├── laf*.nc
-                │   └── lbfd*.nc
-                └── run/
-                        ├── INPUT
-                        ├── INPUT_ART
-                        ├── int2lm
-                        ├── OUTPUT
-                        ├── run.job
-                        └── YU*
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-run_chain.run_chunk(cfg, force, resume)[source]
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Run a chunk of the processing chain, managing job execution and logging.

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This function sets up and manages the execution of a Processing Chain, handling -job execution, logging, and various configuration settings.

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Parameters:
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  • cfg (Config) – Object holding user-defined configuration parameters as attributes.

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  • force (bool) – If True, it will force the execution of jobs regardless of their completion status.

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  • resume (bool) – If True, it will resume the last unfinished job.

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Raises:
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RuntimeError – If an error or timeout occurs during job execution.

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Notes

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  • This function sets various configuration values based on the provided parameters.

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  • It checks for job completion status and resumes or forces execution accordingly.

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  • Job log files are managed, and errors or timeouts are handled with notifications.

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-run_chain.restart_runs(cfg, force, resume)[source]
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Start subchains in specified intervals and manage restarts.

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This function slices the total runtime of the processing chain according to the -cfg.restart_step_hours configuration. It calls run_chunk() for each -specified interval.

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Parameters:
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  • cfg (Config) – Object holding all user-configuration parameters as attributes.

    • -

  • force (bool) – If True, it will force the execution of jobs regardless of their completion status.

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  • resume (bool) – If True, it will resume the last unfinished job.

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Notes

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  • The function iterates over specified intervals, calling run_chunk() for each.

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  • It manages restart settings and logging for each subchain.

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Processing Chain

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The Processing Chain is a Python-based workflow tool designed to streamline -weather and climate simulations. -It facilitates the preparation of essential input data, submission of compute -jobs to the queue on CSCS HPC systems, and the implementation of post-processing -steps. -In addition to supporting standard versions of the COSMO and ICON models, -it is equipped to handle various model variants, notably COSMO-GHG -(Greenhouse Gas Extension) and ICON-ART (Aerosols and Reactive Trace Gases)

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The Processing Chain can be easily customized to meet your specific requirements. -This includes defining custom workflows, creating your own simulation cases, -and integrating new jobs and auxiliary scripts.

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Getting Started

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Configuration

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Jobs & Workflows

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API

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Overview

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Jobs have to be part of the respective workflow. They are submitted via sbatch -to the Slurm workload manager.

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The order of job submission is based on the list given in workflows.yaml -(or in config.yaml in case a custom, user-defined workflow is used.)

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Let’s have a look at the icon-art example:

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icon-art:
-   features:
-      - restart
-   jobs:
-      - prepare_icon
-      - icontools
-      - prepare_art
-      - icon
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This workflow consists of four jobs: prepare_icon, icontools, -prepare_art and icon.

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These jobs will be submitted, however, they are not starting at the same time, -because some of them depend on others:

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dependencies:
-   icontools:
-      current:
-        - prepare_icon
-   prepare_art:
-      current:
-        - icontools
-   icon:
-      current:
-        - prepare_icon
-        - icontools
-        - prepare_art
-      previous:
-        - icon
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Since icontools depends on prepare_icon, and prepare_art depends -on icontools, the order of execution is prepare_icon –> icontools -–> prepare_art. Note that if we had another job in there without dependencies, -it would run in parallel to the others.

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Since icon depends on all other jobs, it will be executed last. Note that -these dependencies are all listed under the current keyword, targeting -the current chunk. For icon, there is an additional previous keyword. -This means that an icon simulation will always wait until the simulation -from the last chunk is finished (because the restart file has to be available).

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Another effect of this workflow definition is that the prepare_icon, -icontools and prepare_art jobs will also be launched for the next chunk, -as they are not dependent on their previous ones.

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-Flowchart for the ``icon-art`` workflow. -
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Flowchart for the icon-art workflow.

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Adding New Jobs

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Adding a new job to the chain is simple:

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  1. In the directory jobs/, create a file called <jobname>.py containing -a function called main which takes the same arguments as every other job. -Make sure the function is documented with a docstring.

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  2. Import it in jobs/__init__.py to make it accessible to run_chain.py.

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  3. Add the job to your workflow.

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Namelist and Runscript Templates

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The namelists and run jobs for int2lm and COSMO, as well as for icontools and ICON are dynamically generated -using templates located in the cases/<casename> directory. These templates are essentially -text files containing “normal” namelist parameters alongside Python variables enclosed in curly braces.

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During runtime, these template files are read by their respective jobs. -The resulting strings are formatted through Python’s .format() function, facilitating the -substitution of Python variables with their corresponding value. -Subsequently, the formatted strings are then saved as the actual namelist and run scripts in the -run directory of their respective jobs.

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cases/example/example_namelist.cfg -> [read file] ->
-"namelist_var = '{cfg.prefix}{cfg.suffix}'" -> ["".format(cfg)] ->
-"namelist_var = 'pref_suff.nc'" -> [write to disk] ->
-int2lm/run/example_namelist
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A special case is INPUT_ART for int2lm and INPUT_GHG for COSMO . These namelists are -generated by jobs.tools.write_int2lm_input_art.main() and jobs.tools.write_cosmo_input_ghg.main() -from .csv-files containing all necessary information.

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-jobs.tools.write_int2lm_input_art.main(trcr_filename, set_filename, nml_filename, hstart=0)[source]
-

Write the INPUT_ART namelist file for int2lm from .csv files

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  • trcr_filename (str) – csv file with tracer definitions

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  • set_filename (str) – csv file with tracer datasets

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  • nml_filename (str) – output filename (INPUT_ART)

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  • hstart (int) – meteorology spin up in hours

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-jobs.tools.write_cosmo_input_ghg.main(csv_filename, namelist_filename, cfg=None)[source]
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Convert a table (.csv file) to namelist file (INPUT_GHG) -read by COSMO.

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  • csv_filename (str) – Path to the source csv-file

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  • namelist_filename (str) – Path to the namelist file that will be created

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  • cfg (Config) – Object holding all user-configuration parameters as attributes.

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Store user-specific data": [[2, "store-user-specific-data"]], "Feature Overview": [[3, "feature-overview"]], "Jobs": [[4, "jobs"]], "Tools": [[4, "tools"]], "Parameters (TODO)": [[4, "parameters-todo"]], "How to Run": [[5, "how-to-run"]], "Starting the Chain": [[5, "starting-the-chain"]], "What it Does": [[5, "what-it-does"]], "Test Cases": [[5, "test-cases"]], "Directory Structure": [[5, "directory-structure"]], "Processing Chain": [[6, "processing-chain"]], "Getting Started": [[6, null]], "Configuration": [[6, null]], "Jobs & Workflows": [[6, null]], "API": [[6, null]], "Overview": [[7, "overview"]], "Adding New Jobs": [[7, "adding-new-jobs"]], "Namelist and Runscript Templates": [[8, "namelist-and-runscript-templates"]]}, "indexentries": {"check_model() (in module jobs.tools.check_model)": [[4, "jobs.tools.check_model.check_model"]], "datasets_equal() (in module jobs.tools.comp_nc)": [[4, "jobs.tools.comp_nc.datasets_equal"]], "main() (in module jobs.biofluxes)": [[4, "jobs.biofluxes.main"]], "main() (in module jobs.check_output)": [[4, "jobs.check_output.main"]], "main() (in module jobs.cosmo)": [[4, "jobs.cosmo.main"]], "main() (in module jobs.emissions)": [[4, "jobs.emissions.main"]], "main() (in module jobs.icon)": [[4, "jobs.icon.main"]], "main() (in module jobs.icontools)": [[4, "jobs.icontools.main"]], "main() (in module jobs.int2lm)": [[4, "jobs.int2lm.main"]], "main() (in module jobs.obs_nudging)": [[4, "jobs.obs_nudging.main"]], "main() (in module jobs.octe)": [[4, "jobs.octe.main"]], "main() (in module jobs.oem)": [[4, "jobs.oem.main"]], "main() (in module jobs.online_vprm)": [[4, "jobs.online_vprm.main"]], "main() (in module jobs.photo_rate)": [[4, "jobs.photo_rate.main"]], "main() (in module jobs.post_cosmo)": [[4, "jobs.post_cosmo.main"]], "main() (in module jobs.post_int2lm)": [[4, "jobs.post_int2lm.main"]], "main() (in module jobs.prepare_cosmo)": [[4, "jobs.prepare_cosmo.main"]], "main() (in module jobs.prepare_icon)": [[4, "jobs.prepare_icon.main"]], "main() (in module jobs.reduce_output)": [[4, "jobs.reduce_output.main"]], "main() (in module jobs.tools.cams4int2cosmo)": [[4, "jobs.tools.cams4int2cosmo.main"]], "main() (in module jobs.tools.ctnoaa4int2cosmo)": [[4, "jobs.tools.ctnoaa4int2cosmo.main"]], "main() (in module jobs.tools.mozart2int2lm)": [[4, "jobs.tools.mozart2int2lm.main"]], "main() (in module jobs.tools.reduce_output_start_end)": [[4, "jobs.tools.reduce_output_start_end.main"]], "main() (in module jobs.tools.string2char)": [[4, "jobs.tools.string2char.main"]], "main() (in module jobs.tools.vprmsplit)": [[4, "jobs.tools.vprmsplit.main"]], "main() (in module jobs.tools.write_cosmo_input_ghg)": [[4, "jobs.tools.write_cosmo_input_ghg.main"], [8, "jobs.tools.write_cosmo_input_ghg.main"]], "main() (in module jobs.tools.write_int2lm_input_art)": [[4, "jobs.tools.write_int2lm_input_art.main"], [8, "jobs.tools.write_int2lm_input_art.main"]], "main() (in module jobs.verify_chain)": [[4, "jobs.verify_chain.main"]], "restart_runs() (in module run_chain)": [[5, "run_chain.restart_runs"]], "run_chunk() (in module run_chain)": [[5, "run_chain.run_chunk"]]}}) \ No newline at end of file