Merge pull request #12 from piyueh/dev

The development iteration addresses the following issues

    Issue #7: fixed
    Issue #8: done
    Issue #9: done
    Issue #10: added two regression tests that also test basic usage and functionality. Regression 1 also tests the evaporation, and regression 2 also tests the in-land waterbodies.
    Issue #11: done

CMakeLists.txt

@@ -2,9 +2,11 @@
 cmake_minimum_required(VERSION 3.14)
 
 # cached variables
-set(CMAKE_BUILD_TYPE RELEASE CACHE STRING "Either DEBUG or RELEASE")
+set(CMAKE_BUILD_TYPE RELEASE CACHE STRING "Either DEBUG, Debug, RELEASE, or Release")
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "Compilation flags for release build.")
+set(CMAKE_Fortran_FLAGS_Release "-O3 -DNDEBUG" CACHE STRING "Compilation flags for release build.")
 set(CMAKE_Fortran_FLAGS_DEBUG "-g" CACHE STRING "Compilation flags for debug build.")
+set(CMAKE_Fortran_FLAGS_Debug "-g" CACHE STRING "Compilation flags for debug build.")
 
 # project initialization
 project(geoclaw-landspill Fortran)
@@ -45,7 +47,7 @@ endif()
 if(SKBUILD)
     message(STATUS "Built using scikit-build -- yes")
     find_package(PythonExtensions REQUIRED)  # scikit-build tries to set variables to this package?
-    set(DEST "geoclaw-landspill")
+    set(DEST "gclandspill")
 else()
     message(STATUS "Built using scikit-build -- no")
     set(DEST "${CMAKE_INSTALL_LIBDIR}/gclandspill")
@@ -56,7 +58,7 @@ message(STATUS "Python packages/modules will install to ${DEST}")
 add_subdirectory(third-party)
 
 # main program
-add_subdirectory(geoclaw-landspill)
+add_subdirectory(gclandspill)
 
 # print info
 message("")

MANIFEST.in

@@ -7,7 +7,7 @@ include pyproject.toml
 include CMakeLists.txt
 
 # main source files and cmake files
-graft geoclaw-landspill
+graft gclandspill
 include third-party/CMakeLists.txt
 
 # install amrclaw's Python module

geoclaw-landspill/CMakeLists.txt → gclandspill/CMakeLists.txt

@@ -1,5 +1,5 @@
 # use this variable to shorten the paths
-set(LANDSPILLLIB "${CMAKE_SOURCE_DIR}/geoclaw-landspill/src")
+set(LANDSPILLLIB "${CMAKE_CURRENT_SOURCE_DIR}/src")
 
 # geoclaw-landspill-bin
 add_executable(geoclaw-landspill-bin

geoclaw-landspill/__init__.py → gclandspill/__init__.py

@@ -18,5 +18,5 @@
 from . import data
 
 # meta
-__version__ = "1.0.dev1"
+__version__ = "1.0.dev2"
 __author__ = "Pi-Yueh Chuang <[email protected]>"

geoclaw-landspill/_misc.py → gclandspill/_misc.py

@@ -11,6 +11,7 @@
 import os
 import sys
 import pathlib
+import argparse
 import importlib.util
 
 try:
@@ -145,33 +146,88 @@ def process_path(path, parent, default):
     return pathlib.Path(parent).joinpath(path)
 
 
-def update_frame_range(frame_ed: int, rundata):
-    """Update the frame range in args.
+def extract_info_from_setrun(args: argparse.Namespace):
+    """Extract frequently used information from a setrun.py and write to a CMD argument object.
+
+    In post-processing functions, Some information is frequently requested from a setrun.py and set
+    into a argparse.Namespace object. This function does this job. Currently, the following values
+    are processed:
+
+    * args.level: maximum AMR level
+    * args.frame_ed: the end frame number
+    * args.dry_tol: dry tolerance
+    * args.topofiles: a list of topography file paths (abs paths)
+
+    If the provided `args` does not have these keys present, they will be ignore, except
+    `topofiles`. Currently, no subcommand set `topofiles` in `args` in geoclaw-landspill. So
+    `topofiles` will always be created in this function.
+
+    The provided `args` must have the key `case`. And it is assumed to be a pathlib.Path object.
 
     Arguments
     ---------
-    frame_ed : int
-        The original end frame number.
-    rundata : clawutil.ClawRunData
-        The configuration object of a simulation case.
+    args : argparse.Namespace
+        The CMD arguments parsed by the sub-parsers of subcommands.
 
     Returns
     -------
-    new_frame_ed : int
-        The updated value of end frame number.
+    The same `args` object with updated values.
     """
 
-    if frame_ed is not None:
-        new_frame_ed = frame_ed + 1  # plus 1 so can be used as the `end` in the `range` function
-    elif rundata.clawdata.output_style == 1:  # if it's None, and the style is 1
-        new_frame_ed = rundata.clawdata.num_output_times
-        if rundata.clawdata.output_t0:
-            new_frame_ed += 1
-    elif rundata.clawdata.output_style == 2:  # if it's None, and the style is 2
-        new_frame_ed = len(rundata.clawdata.output_times)
-    elif rundata.clawdata.output_style == 3:  # if it's None, and the style is 3
-        new_frame_ed = int(rundata.clawdata.total_steps / rundata.clawdata.output_step_interval)
-        if rundata.clawdata.output_t0:
-            new_frame_ed += 1
-
-    return new_frame_ed
+    def test_and_set_amr_level():
+        """Local function to avoid pylint's complaint: test and set AMR maximum level."""
+        try:
+            if args.level is None:
+                args.level = rundata.amrdata.amr_levels_max
+        except AttributeError as err:
+            if str(err).startswith("'Namespace' object"):
+                pass
+
+    def test_and_set_frame_ed():
+        """Local function to avoid pylint's complaint: test and set end frame number."""
+        try:
+            if args.frame_ed is not None:
+                args.frame_ed += 1  # plus 1 so it can be used as the `end` in the `range` function
+            elif rundata.clawdata.output_style == 1:  # if it's None, and the style is 1
+                args.frame_ed = rundata.clawdata.num_output_times
+                if rundata.clawdata.output_t0:
+                    args.frame_ed += 1
+            elif rundata.clawdata.output_style == 2:  # if it's None, and the style is 2
+                args.frame_ed = len(rundata.clawdata.output_times)
+            elif rundata.clawdata.output_style == 3:  # if it's None, and the style is 3
+                args.frame_ed = rundata.clawdata.total_steps // rundata.clawdata.output_step_interval
+                if rundata.clawdata.output_t0:
+                    args.frame_ed += 1
+        except AttributeError as err:
+            if str(err).startswith("'Namespace' object"):
+                pass
+
+    def test_and_set_dry_tol():
+        """Local function to avoid pylint's complaint: test and set dry tolerance."""
+        try:
+            if args.dry_tol is None:
+                args.dry_tol = rundata.geo_data.dry_tolerance
+        except AttributeError as err:
+            if str(err).startswith("'Namespace' object"):
+                pass
+
+    # get the case's setrun data
+    rundata = import_setrun(args.case).setrun()
+
+    test_and_set_amr_level()
+    test_and_set_frame_ed()
+    test_and_set_dry_tol()
+
+    # always create topofiles
+    args.topofiles = []
+    for topo in rundata.topo_data.topofiles:
+        if topo[0] != 3:
+            raise WrongTopoFileError("Only accept type-3 topography: {} at {}".format(*topo))
+
+        topo[-1] = pathlib.Path(topo[-1])
+        if not topo[-1].is_absolute():
+            topo[-1] = args.case.joinpath(topo[-1]).resolve()
+
+        args.topofiles.append(topo[-1])
+
+    return args

geoclaw-landspill/_postprocessing/calc.py → gclandspill/_postprocessing/calc.py

@@ -254,12 +254,12 @@ def get_topo_max(soln_dir: os.PathLike, frame_bg: int, frame_ed: int, level: int
     return vmax
 
 
-def get_topo_lims(topo_files: Sequence[Tuple[int, os.PathLike]], **kwargs):
+def get_topo_lims(topo_files: Sequence[os.PathLike], **kwargs):
     """Get the min and max elevation from a set of topography files.
 
     Arguments
     ---------
-    topo_files : tuple/lsit of sub-tuples/lists of [int, pathlike]
+    topo_files : tuple/lsit of pathlike.PathLike
         A list of list following the topography files specification in GeoClaw's settings.
     **kwargs :
         Available keyword arguments are:
@@ -275,11 +275,7 @@ def get_topo_lims(topo_files: Sequence[Tuple[int, os.PathLike]], **kwargs):
     extent = None if "extent" not in kwargs else kwargs["extent"]
 
     # use mosaic raster to obtain interpolated terrain
-    rasters = []
-    for topo in topo_files:
-        if topo[0] != 3:
-            raise _misc.WrongTopoFileError("Only accept type 3 topography file: {}".format(topo[0]))
-        rasters.append(rasterio.open(topo[-1], "r"))
+    rasters = [rasterio.open(topo, "r") for topo in topo_files]
 
     # merge and interplate
     dst, _ = rasterio.merge.merge(rasters, extent)

geoclaw-landspill/_postprocessing/netcdf.py → gclandspill/_postprocessing/netcdf.py

@@ -237,26 +237,8 @@ def convert_to_netcdf(args: argparse.Namespace):
     args.case = pathlib.Path(args.case).expanduser().resolve()
     _misc.check_folder(args.case)
 
-    # case's setrun data
-    rundata = _misc.import_setrun(args.case).setrun()
-
-    # process target AMR level
-    if args.level is None:
-        args.level = rundata.amrdata.amr_levels_max
-
-    # process args.frame_ed
-    if args.frame_ed is not None:
-        args.frame_ed += 1  # plus 1 so can be used as the `end` in the `range` function
-    elif rundata.clawdata.output_style == 1:  # if it's None, and the style is 1
-        args.frame_ed = rundata.clawdata.num_output_times
-        if rundata.clawdata.output_t0:
-            args.frame_ed += 1
-    elif rundata.clawdata.output_style == 2:  # if it's None, and the style is 2
-        args.frame_ed = len(rundata.clawdata.output_times)
-    elif rundata.clawdata.output_style == 3:  # if it's None, and the style is 3
-        args.frame_ed = int(rundata.clawdata.total_steps / rundata.clawdata.output_step_interval)
-        if rundata.clawdata.output_t0:
-            args.frame_ed += 1
+    # process level, frame_ed, dry_tol, and topofiles
+    args = _misc.extract_info_from_setrun(args)
 
     # process args.soln_dir
     args.soln_dir = _misc.process_path(args.soln_dir, args.case, "_output")
@@ -281,10 +263,6 @@ def convert_to_netcdf(args: argparse.Namespace):
         args.res = min(_postprocessing.calc.get_soln_res(
             args.soln_dir, args.frame_bg, args.frame_ed, args.level))
 
-    # process args.dry_rol
-    if args.dry_tol is None:  # get the dry tolerance from setrun.py
-        args.dry_tol = rundata.geo_data.dry_tolerance
-
     # process args.use_case_settings and timestamp information
     case_settings_file = args.case.joinpath("case_settings.txt")