update 1.2.2

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 1.2.1}
+\title{EUFAR, Olivier Henry}{}{EGADS Lineage Algorithm Handbook}{Version 1.2.2}
 %\author{}{}
 
 

Documentation/changelog.txt

@@ -10,6 +10,12 @@ To fix list:
 ------------
 
 
+February 25 2020, Release version 1.2.2
+=======================================
+  MODIFIED:
+    - the documentation has been updated for a possible conflict between NetCDF4 and H5Py for Python and for a possible solution.
+
+
 December 17 2019, Release version 1.2.1
 =======================================
   ADDED:

INSTALL.txt

@@ -62,6 +62,8 @@ To test the EGADS installation, from within Python, run the following commands:
 
   >>> import egads
   >>> egads.test()
+
+On Linux, if issues occure with NetCDF4 or H5py, please check the last section of this file for a possible solution.
 
 
 Uninstallation
@@ -71,3 +73,14 @@ Just run the following command from your terminal:
   pip uninstall egads-lineage
 or
   remove manually all folders in you Python site-packages folder containing egads name.
+
+
+Issues with NetCDF4 and/or H5py on a Linux distribution
+=======================================================
+If NetCDF4 and H5py libraries are installed through Pypi, a crash can occure when trying to read/write a netcdf or an hdf file. Here are the different steps to fix that particular issue:
+
+ 1. Uninstall entirely NetCDF4
+ 2. Download NetCDF4 sources corresponding to the same version
+ 3. Unzip the package, launch a terminal and build NetCDF4 module -> python setup.py build
+ 4. Finally install NetCDF4 moudle -> python setup.py install
+ 5. Check NetCDF4 integration into EGADS with EGADS test function

PKG-INFO

@@ -1,15 +1,13 @@
-Metadata-Version: 1.2
+Metadata-Version: 1.1
 Name: egads-lineage
-Version: 1.2.1
+Version: 0.9.3
 Summary: EGADS: EUFAR General Airborne Data-processing Software
-Home-page: https://github.com/EUFAR/egads/tree/Lineage
-Author: EUFAR, Olivier Henry
+Home-page: http://www.eufar.net
+Author: Olivier Henry
 Author-email: [email protected]
-Maintainer: Olivier Henry
-Maintainer-email: [email protected]
-License: GNU General Public License v3 (GPLv3)
+License: GPLv3
 Download-URL: https://github.com/EUFAR/egads/tree/Lineage
-Project-URL: Documentation, https://egads.readthedocs.io/en/lineage/
+Description-Content-Type: UNKNOWN
 Description: EGADS (EUFAR General Airborne Data-processing Software) is a Python-based
         toolbox for processing airborne atmospheric data. EGADS provides a framework
         for researchers to apply expert-contributed algorithms to data files, and acts
@@ -22,8 +20,17 @@ Keywords: airbornescience,netcdf,nasa-ames,eufar,science,microphysics,thermodyna
 Platform: Windows
 Platform: Linux
 Platform: MacOS
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Education
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python
+Classifier: Topic :: Scientific/Engineering :: Atmospheric Science
 Requires: numpy (>=1.14)
+Requires: scipy (>=1.00)
 Requires: netCDF4 (>=1.3.0)
 Requires: python_dateutil (>=2.6.1)
 Requires: quantities (>=0.12.1)
-Requires: h5py (>=2.10.0)

README.md

@@ -1,7 +1,7 @@
 Version:
 -------
 
-EGADS Lineage 1.2.1
+EGADS Lineage 1.2.2
 
 
 Developments:

doc/Makefile

@@ -0,0 +1,130 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = build
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
+
+.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  htmlhelp   to make HTML files and a HTML help project"
+	@echo "  qthelp     to make HTML files and a qthelp project"
+	@echo "  devhelp    to make HTML files and a Devhelp project"
+	@echo "  epub       to make an epub"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  man        to make manual pages"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+htmlhelp:
+	$(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
+	@echo
+	@echo "Build finished; now you can run HTML Help Workshop with the" \
+	      ".hhp project file in $(BUILDDIR)/htmlhelp."
+
+qthelp:
+	$(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
+	@echo
+	@echo "Build finished; now you can run "qcollectiongenerator" with the" \
+	      ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
+	@echo "# qcollectiongenerator $(BUILDDIR)/qthelp/EGADS.qhcp"
+	@echo "To view the help file:"
+	@echo "# assistant -collectionFile $(BUILDDIR)/qthelp/EGADS.qhc"
+
+devhelp:
+	$(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
+	@echo
+	@echo "Build finished."
+	@echo "To view the help file:"
+	@echo "# mkdir -p $$HOME/.local/share/devhelp/EGADS"
+	@echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/EGADS"
+	@echo "# devhelp"
+
+epub:
+	$(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
+	@echo
+	@echo "Build finished. The epub file is in $(BUILDDIR)/epub."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+man:
+	$(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
+	@echo
+	@echo "Build finished. The manual pages are in $(BUILDDIR)/man."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."

doc/source/conf.py

@@ -48,9 +48,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '1.2.1'
+version = '1.2.2'
 # The full version, including alpha/beta/rc tags.
-release = '1.2.1'
+release = '1.2.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/source/install.rst

@@ -30,6 +30,8 @@ To test EGADS after it is installed, from Python terminal, run the following com
    >>> import egads
    >>> egads.test()
 
+On Linux, if issues occure with NetCDF4 or H5py, please check the last section of this chapter for a possible solution.
+
 
 Options
 *******
@@ -79,7 +81,7 @@ Since version 0.8.6, EGADS can check for an update on GitHub. The check system i
 
    >>> import egads
    >>> egads.check_update()
-   EGADS Lineage vx.x.x is available on GitHub. You can update EGADS Lineage by using pip (pip install egads-lineage --upgrade)
+   EGADS Lineage vx.x.x is available on GitHub. You can update EGADS Lineage by using pip (``pip install egads-lineage --upgrade``)
    or by using the following link: https://github.com/eufarn7sp/egads/releases/download/x.x.x/egads-x.x.x.tar.gz
 
 If the ``check_update`` option is set on True in the egads.ini file, EGADS will check automatically for an update each time it is imported. By default, the option is set on False. The user can modify the option this way:
@@ -89,3 +91,14 @@ If the ``check_update`` option is set on True in the egads.ini file, EGADS will
    >>> exit()
 
 The module Requests is optional for EGADS but is mandatory to check for an update.
+
+
+Issues with NetCDF4 and/or H5py on a Linux distribution
+*******************************************************
+If NetCDF4 and H5py libraries are installed through Pypi, a crash can occure when trying to read/write a netcdf or an hdf file. Here are the different steps to fix that particular issue:
+
+#. Uninstall entirely NetCDF4
+#. Download NetCDF4 sources corresponding to the version installed with Pypi
+#. Unzip the package, launch a terminal and build NetCDF4 module -> ``python setup.py build``
+#. Finally install NetCDF4 moudle -> ``python setup.py install``
+#. Check NetCDF4 integration into EGADS with EGADS test function

egads_lineage.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.2
 Name: egads-lineage
-Version: 1.2.1
+Version: 1.2.2
 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 - v1.2.1.pdf
-Documentation/EGADS Lineage Documentation - v1.2.1.pdf
+Documentation/EGADS Lineage Algorithm Handbook - v1.2.2.pdf
+Documentation/EGADS Lineage Documentation - v1.2.2.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='1.2.1',
+      version='1.2.2',
       description=doclines[0],
       long_description='\n'.join(doclines[2:]),
       author='EUFAR, Olivier Henry',