fix: update Makefile, rename docs to doc, upgrade setup, clean

Author: duboise-cnes

.github/workflows/pandora_ci.yml

@@ -13,22 +13,31 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
+
     - name: Set up Python 3.x
       uses: actions/setup-python@v2
       with:
         python-version: '3.7'
+
     - name: Install Pandora with dependencies
       run: |
-        make install-github-ci
+        python -m pip install --upgrade pip
+        pip install codecov
+        pip install .[dev]
+
     - name: Test with pytest
       run: |
-        make test-github-ci
+        export NUMBA_DISABLE_JIT="1"
+        pytest -m "not notebook_tests" --junitxml=pytest-report.xml --cov-config=.coveragerc --cov-report xml --cov
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
+
     - name: Create source distribution
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
       run: |
-        make distribute-github-ci
+        python -m build --sdist
+
     - name: Publish package on pypi
       if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
       uses: pypa/gh-action-pypi-publish@release/v1

.gitignore

@@ -1,18 +1,97 @@
-# Python
+# Compiled python files
+*.py[cod]
+*$py.class
+*.pyc
+
+# C extensions
+*.so
+
+# Cache python
 __pycache__/
+
+# Python egg metadata, regenerated from source files by setuptools
+/*.egg-info
+/.eggs/
+develop-eggs/
+wheels/
+.installed.cfg
+*.egg
+
+# Setuptools build and distribution directories
+/dist/
+/build/
+sdist/
+
+# Virtualenv
+/venv/
+
+# Tox
+.tox
+
+# Pytest
+.pytest_cache/
+pytest-report.xml
+nosetests.xml
+
+# Python coverage output
 .coverage
+.coverage.*
 coverage.xml
-nosetests.xml
+/htmlcov/
+
+# pylint report
 pylint-report.txt
-*.egg-info/
 
-# Jupyter
-.ipynb_checkpoints/
-output/
+# Debug file logging
+debug.log
 
-# Virtualenv
-/venv/
+# Documentation build and API
+docs/build/
+docs/_build/
+docs/source/api_reference/
+docs/source/apidoc/
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+#  Code quality
+pylint-report.xml
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Jupyter Notebook
+.ipynb_checkpoints
+output
+
+# pyenv
+.python-version
+
+# dotenv
+.env
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+.idea/
 
-#doc sphinx
-doc/build/
-doc/sources/api_reference/
+# Swap file
+*.swp

.gitlab/merge_request_templates/MR.md

@@ -18,7 +18,7 @@ Si la Merge Request est en cours de développement, merci d'ajouter le mot clé
 
 Si la Merge Request est prête, merci de valider les étapes suivantes:
 - [ ] mise à jour de la documentation
-  - ajout de paramètres dans https://gitlab.cnes.fr/OutilsCommuns/CorrelateurChaine3D/pandora/-/blob/master/doc/sources/userguide/usage.rst
+  - ajout de paramètres dans https://gitlab.cnes.fr/OutilsCommuns/CorrelateurChaine3D/pandora/-/blob/master/docs/source/userguide/usage.rst
   - suppression des warnings éventuels lors de la génération de la doc
   - vérification visuelle des parties ajoutées dans la doc (cf. #138)
 - [ ]  mise à jour du changelog

.pre-commit-config.yaml

@@ -3,31 +3,38 @@ repos:
     hooks:
     - id: black
       name: black
-      entry: black --line-length=120
+      entry: black
       language: system
       files: \.py$
       stages: [commit]
       types: [python]
+
     - id: pylint
       name: PyLint
-      entry: python -m pylint --rcfile=.pylintrc
+      entry: pylint --rcfile=.pylintrc
       language: system
       files: \.py$
+      types: [python]
       stages: [commit]
+
     - id: mypy
       name: mypy
       entry: mypy
       language: system
       files: \.py$
       stages: [ commit ]
+
+    - id: jupyter-nb-clear-output
+      name: jupyter-nb-clear-output
+      files: \.ipynb$
+      stages: [commit]
+      language: system
+      entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+
     - id: sphinx-checking
       name: Checking Sphinx building
-      entry: python setup.py build_sphinx
+      entry: sphinx-build -M html docs/source/ docs/build -W --keep-going
       language: system
-      files: ^(doc/.*|pandora/.*)$
+      files: ^(docs/.*|pandora/.*)$
       pass_filenames: False
-      stages: [push]
-  - repo: https://github.com/kynan/nbstripout
-    rev: 0.6.0
-    hooks:
-      - id: nbstripout
+      stages: [push]

.readthedocs.yml

@@ -5,7 +5,7 @@ version: 2
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
-  configuration: doc/sources/conf.py
+  configuration: docs/source/conf.py
 
 python:
   version: 3.7

CONTRIBUTING.md

@@ -78,7 +78,7 @@ Here are some rules to apply when developing a new functionality:
 
 # Pre-commit validation
 
-Pre-commit hooks (black, pylint, mypy, sphinx-checking, nbstripout) for code analysis can be installed:
+Pre-commit hooks (black, pylint, mypy, sphinx-checking, jupyter-nb-clear-output) for code analysis can be installed:
 ```
 pre-commit install
 ```