Packaging as namespace packages (#13)

Converting to python namespace packages

Author: Lionel Untereiner

.github/workflows/doc-test.yml

@@ -0,0 +1,13 @@
+name: "Pull Request Docs Check"
+on: 
+- pull_request
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - uses: ammaraskar/sphinx-action@dev
+      with:
+        docs-folder: "docs/"
+        build-command: "sphinx-build -b html . _build"

.github/workflows/python-package.yml

@@ -13,9 +13,10 @@ jobs:
     runs-on: ubuntu-22.04
     strategy:
       fail-fast: false
+      max-parallel: 3
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
-        package-name: ["geos_ats_package", "geosx_mesh_doctor", "geosx_mesh_tools_package", "geosx_xml_tools_package", "hdf5_wrapper_package", "pygeosx_tools_package", "timehistory_package"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        package-name: ["geos-ats", "geos-mesh", "geos-timehistory", "geos-xml-tools", "hdf5-wrapper", "pygeos-tools"]
 
     steps:
     - uses: actions/checkout@v3
@@ -24,16 +25,17 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
+        cache: 'pip'
     - name: Install package
-      working-directory: ./${{ matrix.package-name }}
+      # working-directory: ./${{ matrix.package-name }}
       run: |
         python -m pip install --upgrade pip
         python -m pip install pytest yapf toml
-        python -m pip install .
+        python -m pip install ${{ matrix.package-name }}/
     - name: Lint with yapf
-      working-directory: ./${{ matrix.package-name }}
+      # working-directory: ./${{ matrix.package-name }}
       run: |
-        yapf -r --diff . --style ../.style.yapf
+        yapf -r --diff ${{ matrix.package-name }} --style .style.yapf
     # - name: Test with pytest
     #   working-directory: ./${{ matrix.package-name }}
     #   run: |

.gitignore

@@ -1,16 +1,165 @@
+#MACOS
+DS_Store
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
 *.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
 *.exp
 *.lib
-*.obj
-*.pyc
-*.pyd.manifest
-*.pyo
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
 .cache
-.DS_Store
-.idea
-.project
-.pydevproject
-.settings
-build
-dist
-__pycache__
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.readthedocs.yml

@@ -4,7 +4,7 @@
 version: 2
 
 build:
-  os: "ubuntu-20.04"
+  os: ubuntu-22.04
   apt_packages:
   - npm
   - plantuml
@@ -18,9 +18,9 @@ build:
     - npm install -g @mermaid-js/[email protected]
 
 # Set requirements to build the docs
-python:
-  install:
-  - requirements: docs/requirements.txt
+# python:
+#   install:
+#   - requirements: docs/requirements.txt
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

docs/conf.py

@@ -18,10 +18,9 @@
 
 # Add python modules to be documented
 python_root = '..'
-python_modules = ( 'geosx_mesh_tools_package', 'geosx_xml_tools_package', 'geosx_mesh_doctor', 'geos_ats_package',
-                   'hdf5_wrapper_package', 'pygeosx_tools_package', 'timehistory_package' )
+python_modules = ( 'geos-xml-tools', 'geos-mesh', 'geos-ats', 'hdf5-wrapper', 'pygeos-tools', 'geos-timehistory' )
 for m in python_modules:
-    sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m ) ) )
+    sys.path.insert( 0, os.path.abspath( os.path.join( python_root, m, 'src' ) ) )
 
 # -- Project information -----------------------------------------------------
 

docs/geos_ats.rst docs/geos-ats.rstdocs/geos_ats.rst renamed to docs/geos-ats.rst

@@ -2,7 +2,7 @@
 GEOS ATS
 ==========
 
-The `geos_ats` python package includes tools for managing integrated tests for GEOS.
+The `geos-ats` python package includes tools for managing integrated tests for GEOS.
 It is built using the `Automated Test System <https://ats.readthedocs.io/en/latest/>`_ (ATS) package.
 The available console scripts for this package and its API are described below.
 
@@ -13,7 +13,7 @@ run_geos_ats
 Primary entry point for running integrated tests.
 
 .. argparse::
-   :module: geos_ats.command_line_parsers
+   :module: geos.ats.command_line_parsers
    :func: build_command_line_parser
    :prog: run_geos_ats
 
@@ -29,11 +29,11 @@ Primary entry point for running integrated tests.
 Debugging
 ------------------
 
-If for any reason you need to debug the geos_ats package, we recommend that you create a local copy of this entry point in the `build/integratedTests` directory: `geosPythonPackages/geos_ats_package/geos_ats/debug_geos_ats.py`.
+If for any reason you need to debug the geos-ats package, we recommend that you create a local copy of this entry point in the `build/integratedTests` directory: `geosPythonPackages/geos-ats_package/geos-ats/debug_geos-ats.py`.
 This script is designed as a debugger entry point, and will read the autogenerated run script that was built during setup.
-To use it, you must either have geos_ats installed in your target python environment, or a copy of geosPythonPackages in the expected location (`/usr/workspace/[username]/geosPythonPackages`).
+To use it, you must either have geos-ats installed in your target python environment, or a copy of geosPythonPackages in the expected location (`/usr/workspace/[username]/geosPythonPackages`).
 
-We recommend that you use VSCode with the Python extension to debug geos_ats.
+We recommend that you use VSCode with the Python extension to debug geos-ats.
 To begin the debugging session, you simply need to load the entry script, set any initial breakpoints you desire, then select the Debug run option.
 Note that this approach can only be used to debug the python code associated with tests, and not the underlying GEOS tests.
 
@@ -45,14 +45,14 @@ API
 Restart Check
 ^^^^^^^^^^^^^^^
 
-.. automodule:: geos_ats.helpers.restart_check
+.. automodule:: geos.ats.helpers.restart_check
     :members:
 
 
 Curve Check
 ^^^^^^^^^^^^^^^
 
-.. automodule:: geos_ats.helpers.curve_check
+.. automodule:: geos.ats.helpers.curve_check
     :members: