Merge pull request #8 from ESMG/dev

Release 0.2.0

.github/workflows/base.yml

@@ -8,7 +8,10 @@ on:
   push:
     branches: [ exp/** ]
   pull_request:
-    branches: [ exp/** ]
+    branches:
+      - 'exp/**'
+      - 'dev'
+      - 'main'
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
@@ -43,21 +46,23 @@ jobs:
           echo "💡 The ${{ github.repository }} repository has been cloned to the runner."
           echo "🖥️ The workflow is now ready to test your code on the runner."
           uname -a
+          pwd
+          df -h
           printenv
 
       # The worker drops you in the middle of your checked out repository
       - name: Install
         run: |
-          conda env create -f=conda/gridTools_export.yml
+          conda env create -q -f conda/gridTools_export.yml
           conda activate gridTools
-          python -m pip install .
+          python -m pip install -q -e .
 
       # Run tests
       - name: Tests
         run: |
           cd ${{ github.workspace }}
           conda activate gridTools
           cd tests
-          pytest
+          pytest -rA
 
 

.readthedocs.yaml

@@ -0,0 +1,13 @@
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: source/conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+conda:
+  environment: binder/environment.yml

LICENSE.md

@@ -0,0 +1,173 @@
+This file is part of the gridtools python library, referred to as
+gridtools, which is made available under version 3 of the Gnu Lesser
+General Public License, which is provided below.
+
+The intent of this license is to ensure free and unrestricted access to
+the gridtools python library software, and to pass on those rights to
+modified versions this software.
+
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
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+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
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+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
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+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

README.md

@@ -115,7 +115,7 @@ or [clone](https://github.com/ESMG/gridtools.git) the
 [ESMG/gridtools](https://github.com/ESMG/gridtools) repository.
 
 The `python setup.py install` method is now considered a legacy installation
-method.  Please use the `python -m pip install` method.
+method.  Please use the `python -m pip install .` method.
 
 ### pip
 
@@ -124,31 +124,16 @@ $ cd gridtools
 $ python -m pip install .
 ```
 
+If using **conda**, only minimal changes will be noted.
+
 # Workarounds
 
 These are the current workarounds that are required for the grid
 toolset package.  You may need to perform these steps once if you
 plan to install a copy of the grid generation software.
 
 NOTE: These workarounds should be automatically installed with
-an installation of gridtools.
-
-## datashader
-
-The lastest version from github is required for proper operation of
-bokeh, holoviews and panel which are used by the interactive portions
-of the grid generation library.
-
-[REPO](https://github.com/holoviz/datashader)
-
-Installation:
-  * Download or clone this repository.
-  * Change directory to the datashader directory.
-  * Make sure your conda enviroment is active.
-  * `pip install -e .`
-
-NOTE: The datashader library should be automatically installed as a
-dependency of gridtools.
+an installation of gridtools in step 2 using pip.
 
 ## numpypi
 
@@ -157,6 +142,15 @@ For bitwise-the-same reproducable results, a numpy subset of computational funct
 provided.  These routines are slower than the numpy native routines.
 A repackaged installable [REPO](https://github.com/jr3cermak/numpypi/tree/dev) of the library.
 
+## xesmf
+
+A slight modification to xesmf is required to fix a periodic boundary
+problem when regridding.  Note that conda loads an older version of
+xesmf and then pip replaces it with a fixed copy.
+
+Users using **venv**, a working compiled copy of ESMF and ESMPy need to
+be installed prior to installing gridutils via pip.
+
 # Code contributions
 
 ## Lambert Conformal Conic Grid Generation
@@ -176,7 +170,7 @@ Authors: Mehmet Ilicak; Alistair Adcroft [REPO](https://github.com/ESMG/pyroms)
 Until we can activate Sphinx to create our body of documentation we will have to resort
 to upkeep of a manual index.
 
-[Documentation](docs/Documentation.md)
+[Documentation](docs/development/Documentation.md)
   * [conda](docs/conda/README.md)
   * [development](docs/development)
     * [CHANGELOG](docs/development/CHANGELOG.md): Development log of changes
@@ -207,4 +201,5 @@ to upkeep of a manual index.
 This project is soliciting help in development.  Please contribute
 ideas or bug requests using the issues tab.  Code contributions can
 be sent via github's pull request process.  Code adoption will follow
-the [contribution](CONTRIBUTING.md) process.
+the [contribution](CONTRIBUTING.md) process.  Development can be
+discussed in the [MOM6 forum](https://bb.cgd.ucar.edu/cesm/forums/mom6.148/).