update 1.1.0

Documentation/EGADS Algorithm Handbook - LATEX/cover/alg_cover.tex

@@ -24,7 +24,7 @@
 \setlength{\voffset}{.0cm}
 
 \logoeufar
-\title{EUFAR, Olivier Henry}{}{EGADS Lineage Algorithm Handbook}{Version 1.0.3}
+\title{EUFAR, Olivier Henry}{}{EGADS Lineage Algorithm Handbook}{Version 1.1.0}
 %\author{}{}
 
 

Documentation/changelog.txt

@@ -10,6 +10,11 @@ To fix list:
 ------------
 
 
+September 4 2019, Release version 1.1.0
+=======================================
+The configuration file and user algorithm structure have been moved to a dedicated directory in the $HOME folder (Windows, Linux and MacOS), to avoid issues when Python is installed in a system folder. Read the documentation for more details.
+
+
 August 14 2019, Release version 1.0.3
 =====================================
   FIXED:

PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.2
 Name: egads-lineage
-Version: 1.0.3
+Version: 1.1.0
 Summary: EGADS: EUFAR General Airborne Data-processing Software
 Home-page: https://github.com/EUFAR/egads/tree/Lineage
 Author: EUFAR, Olivier Henry

README.md

@@ -1,7 +1,7 @@
 Version:
 -------
 
-EGADS Lineage 1.0.3
+EGADS Lineage 1.1.0
 
 
 Developments:

doc/source/alg_development.rst

@@ -77,9 +77,9 @@ Within the file itself, there are one rule to respect and several elements in th
     The algorithm itself gets written in the _algorithm method and uses variables passed in by the user. The variables which arrive here are simply scalar or arrays, and if the source is an instance of EgadsData, the variables will be converted to the units you specified in the InputUnits of the algorithm metadata.
 
 7. Integration of the algorithm in EGADS
-    Once the algorithm file is ready, the user has to move it in the appropriate directory in the ``./egads/algorithms/user`` directory. Once it has been done, the ``__init__.py`` file has to be modified to declare the new algorithm. The following line can be added to the ``__init__.py`` file: ``from the_name_of_the_file import *``.
+    Once the algorithm file is ready, the user has to move it in the appropriate directory in the ``$HOME/.egads_lineage/user_algorithms`` directory. Once it has been done, the ``__init__.py`` file has to be modified to declare the new algorithm. The following line can be added to the ``__init__.py`` file: ``from the_name_of_the_file import *``.
 
-    If the algorithm requires a new directory, the user has to create it in the ``user`` directory, move the file inside and create a ``__init__.py`` file to declare the new directory and the algoritm to EGADS. A template can be found in ``./egads/algorithms/user/file_templates/init_template.py`` and is shown below:
+    If the algorithm requires a new directory, the user has to create it in the ``user`` directory, move the file inside and create a ``__init__.py`` file to declare the new directory and the algoritm to EGADS. A template can be found in ``doc/source/example_files/init_template.py`` and is shown below:
 
     .. literalinclude:: example_files/init_template.py
 

doc/source/conf.py

@@ -48,9 +48,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.0.3'
+version = '1.1.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.0.3'
+release = '1.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/tutorial.rst

@@ -1022,7 +1022,7 @@ This file has been created with the following commands:
 Working with algorithms
 ************************
 
-Algorithms in EGADS are stored in the :mod:`egads.algorithms` module, and separated into sub-modules by category (microphysics, thermodynamics, radiation, etc). Each algorithm follows a standard naming scheme, using the algorithm's purpose and source:
+Algorithms in EGADS are stored in the :mod:`egads.algorithms` module for embedded algorithms and in :mod:`egads.user_algorithms` module for user-defined algorithms. They are separated into sub-modules by category (microphysics, thermodynamics, radiation, etc). Each algorithm follows a standard naming scheme, using the algorithm's purpose and source:
 
 ``{CalculatedParameter}{Detail}{Source}``
 
@@ -1082,13 +1082,18 @@ Algorithms in EGADS generally accept and return arguments of :class:`~.EgadsData
 To call an algorithm, simply pass in the required arguments, in the order they are described in the algorithm help function. An algorithm call, using the ``VelocityTasCnrm`` in the previous section as an example, would therefore be the following:
 
     >>> V_p = egads.algorithms.thermodynamics.VelocityTasCnrm().run(T_s, P_s, dP, 
-        cpa, Racpa)	
+        cpa, Racpa)
 
 where the arguments ``T_s``, ``P_s``, ``dP``, etc are all assumed to be previously defined in the program scope. In this instance, the algorithm returns an :class:`~.EgadsData` instance to ``V_p``. To run the algorithm, but return a standard data type (scalar or array of doubles), set the ``return_Egads`` flag to ``false``.
 
     >>> V_p = egads.algorithms.thermodynamics.VelocityTasCnrm(return_Egads=False).
         run(T_s, P_s, dP, cpa, Racpa)
 
+If an algorithm has been created by a user and is not embedded by default in EGADS, it should be called like this:
+
+    >>> V_p = egads.user_algorithms.thermodynamics.VelocityTasCnrm().run(T_s, P_s, dP, 
+        cpa, Racpa)
+
 .. NOTE::
   When injecting a variable in an EgadsAlgorithm, the format of the variable should follow closely the documentation of the algorithm. If the variable is a scalar, and the algorithm needs a vector, the scalar should be surrounded by brackets: 52.123 -> [52.123].
 

egads/__init__.py

@@ -1,6 +1,6 @@
 __author__ = "ohenry"
 __date__ = "2018-03-05 10:59"
-__version__ = "1.4"
+__version__ = "1.5"
 
 
 import logging
@@ -9,6 +9,7 @@
 import quantities
 import configparser
 import sys
+import pathlib
 from ._version import __version__
 from ._version import __branch__
 from .utils.egads_utils import _create_user_algorithms_structure
@@ -28,11 +29,12 @@
 else:
     frozen = False
 
-path = os.path.abspath(os.path.dirname(__file__))
-_create_option_dictionary(path)
+
+user_path = str(pathlib.Path.home().joinpath('.egads_lineage'))
+_create_option_dictionary(user_path)
 config_dict = configparser.ConfigParser()
-config_dict.read(os.path.join(path, 'egads.ini'))
-_create_log_system(config_dict, path)
+config_dict.read(os.path.join(user_path, 'egads.ini'))
+_create_log_system(config_dict, user_path)
 logging.info('*****************************************')
 logging.info('EGADS ' + __version__ + ' is starting ...')
 logging.info('*****************************************')
@@ -48,8 +50,10 @@
 
 import egads.core
 import egads.core.metadata
-_create_user_algorithms_structure(path)
+_create_user_algorithms_structure(user_path)
+sys.path.append(user_path)
 import egads.algorithms
+import user_algorithms
 from .input import get_file_list
 from .core.egads_core import *
 from .tests.test_all import test
@@ -77,7 +81,7 @@ def set_options(log_level=None, log_path=None, check_update=None):
     if check_update is not None:
         config_dict.set('OPTIONS', 'check_update', str(check_update))
     if log_level or log_path or check_update:
-        set_options_file = open(os.path.join(path, 'egads.ini'), 'w')
+        set_options_file = open(os.path.join(user_path, 'egads.ini'), 'w')
         config_dict.write(set_options_file)
         set_options_file.close()
 

egads/_version.py

@@ -1,2 +1,2 @@
-__version__ = '1.0.3'
+__version__ = '1.1.0'
 __branch__ = 'Lineage'

egads/algorithms/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = "ohenry"
 __date__ = "2018-03-05 11:13"
-__version__ = "1.1"
+__version__ = "1.2"
 
 import egads.algorithms.comparisons
 import egads.algorithms.corrections
@@ -13,4 +13,3 @@
 import egads.algorithms.thermodynamics
 import egads.algorithms.transforms
 import egads.algorithms.radiation
-import egads.algorithms.user

egads/utils/egads_utils.py

@@ -9,14 +9,16 @@
 import pathlib
 
 
-def _create_option_dictionary(main_path):
+def _create_option_dictionary(user_path):
     config_dict = configparser.ConfigParser()
-    if not os.path.exists(os.path.join(main_path, 'egads.ini')):
-        ini_file = open(os.path.join(main_path, 'egads.ini'), 'w')
+    if not pathlib.Path(pathlib.Path(user_path).joinpath('egads.ini')).is_file():
+        if not pathlib.Path(user_path).is_dir():
+            pathlib.Path(user_path).mkdir()
+        ini_file = open(os.path.join(user_path, 'egads.ini'), 'w')
         config_dict.add_section('LOG')
         config_dict.add_section('OPTIONS')
-        config_dict.set('LOG', 'level', 'INFO')
-        config_dict.set('LOG', 'path', main_path)
+        config_dict.set('LOG', 'level', 'DEBUG')
+        config_dict.set('LOG', 'path', user_path)
         config_dict.set('OPTIONS', 'check_update', 'False')
         config_dict.write(ini_file)
         ini_file.close()
@@ -43,42 +45,42 @@ def _create_log_system(config_dict, default_path):
         logging.error('egads - logging system - path from ini file not found, using default path')
 
 
-def _create_user_algorithms_structure(main_path):
-    logging.debug('egads - egads_utils.py - create_user_algorithms_structure - main_path ' + str(main_path))
-    user_path = os.path.join(main_path, 'algorithms/user/')
-    if not os.path.isdir(user_path):
+def _create_user_algorithms_structure(user_path):
+    logging.debug('egads - egads_utils.py - create_user_algorithms_structure - user_path ' + str(user_path))
+    algo_path = str(pathlib.Path(user_path).joinpath('user_algorithms'))
+    if not pathlib.Path(algo_path).is_dir():
         logging.debug('egads - egads_utils.py - create_user_algorithms_structure - no user folder detected, '
                       'creating user structure')
-        os.makedirs(user_path)
+        pathlib.Path(algo_path).mkdir()
         init_string = ('__author__ = "Olivier Henry"\n'
                        + '__date__ = "2019/05/06 11:45"\n'
                        + '__version__ = "1.0"\n\n'
-                       + 'import egads.algorithms.user.comparisons\n'
-                       + 'import egads.algorithms.user.corrections\n'
-                       + 'import egads.algorithms.user.mathematics\n'
-                       + 'import egads.algorithms.user.microphysics\n'
-                       + 'import egads.algorithms.user.thermodynamics\n'
-                       + 'import egads.algorithms.user.transforms\n'
-                       + 'import egads.algorithms.user.radiation\n')
-        init_file = open(user_path + '__init__.py', 'w')
+                       + 'import user_algorithms.comparisons\n'
+                       + 'import user_algorithms.corrections\n'
+                       + 'import user_algorithms.mathematics\n'
+                       + 'import user_algorithms.microphysics\n'
+                       + 'import user_algorithms.thermodynamics\n'
+                       + 'import user_algorithms.transforms\n'
+                       + 'import user_algorithms.radiation\n')
+        init_file = open(algo_path + '/__init__.py', 'w')
         init_file.write(init_string)
         init_file.close()
         user_folder = ['comparisons', 'corrections', 'mathematics', 'microphysics', 'thermodynamics', 'transforms',
                        'radiation']
         for folder in user_folder:
-            logging.debug('egads - egads_utils.py - create_user_algorithms_structure - creating [user/' + folder + '] '
-                          + 'folder')
-            os.makedirs(os.path.join(user_path, folder))
+            logging.debug('egads - egads_utils.py - create_user_algorithms_structure - creating [user_algorithms/'
+                          + folder + '] folder')
+            pathlib.Path(pathlib.Path(algo_path).joinpath(folder)).mkdir()
             init_string = ('__author__ = "Olivier Henry"\n'
                            + '__date__ = "2019/05/06 11:45"\n'
                            + '__version__ = "1.0"\n\n'
                            + 'import logging\n\n'
                            + 'try:\n'
-                           + "    logging.info('egads [user/" + folder + "] algorithms have been loaded')\n"
+                           + "    logging.info('egads [user_algorithms/" + folder + "] algorithms have been loaded')\n"
                            + 'except Exception as e:\n'
-                           + "    logging.error('an error occured during the loading of a [user/" + folder
+                           + "    logging.error('an error occured during the loading of a [user_algorithms/" + folder
                            + "] algorithm: ' + str(e))\n")
-            init_file = open(os.path.join(user_path, folder) + '/__init__.py', 'w')
+            init_file = open(str(pathlib.Path(algo_path).joinpath(folder)) + '/__init__.py', 'w')
             init_file.write(init_string)
             init_file.close()
     else:

egads_lineage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.2
 Name: egads-lineage
-Version: 1.0.3
+Version: 1.1.0
 Summary: EGADS: EUFAR General Airborne Data-processing Software
 Home-page: https://github.com/EUFAR/egads/tree/Lineage
 Author: EUFAR, Olivier Henry

egads_lineage.egg-info/SOURCES.txt

@@ -3,8 +3,8 @@ MANIFEST.in
 README.md
 setup.cfg
 setup.py
-Documentation/EGADS Lineage Algorithm Handbook - v1.0.3.pdf
-Documentation/EGADS Lineage Documentation - v1.0.3.pdf
+Documentation/EGADS Lineage Algorithm Handbook - v1.1.0.pdf
+Documentation/EGADS Lineage Documentation - v1.1.0.pdf
 Documentation/changelog.txt
 Documentation/EGADS Algorithm Handbook - LATEX/EGADS_alg_doc.tex
 Documentation/EGADS Algorithm Handbook - LATEX/example.py

setup.py

@@ -30,7 +30,7 @@
 doclines = __doc__.split('\n')
 
 setup(name='egads-lineage',
-      version='1.0.3',
+      version='1.1.0',
       description=doclines[0],
       long_description='\n'.join(doclines[2:]),
       author='EUFAR, Olivier Henry',