Merge pull request #7 from umr-lops/package2

Package 3rd PR

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/publish.yml

@@ -0,0 +1,32 @@
+name: Upload package to PyPI
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.x'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip build twine
+      - name: Build
+        run: |
+          python -m build --sdist --wheel .
+      - name: Check the built archives
+        run: |
+          twine check dist/*
+          pip install dist/*.whl
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.pypi_token }}
+          repository_url: https://upload.pypi.org/legacy/
+          verify_metadata: true

.gitignore

@@ -1,9 +1,134 @@
-# Fichier .gitignore
+# 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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
 *.log
-*.csv
-*.dat
-*.out
-*.pid
-*.gz
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# celery beat schedule file
+celerybeat-schedule
+
+# 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/
+
+.settings/
+.project
+.pydevproject
+tmp/
+
+
+#.idea/
+/.idea/
+
+dask-worker-space/

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+ci:
+  autoupdate_schedule: weekly
+
+# https://pre-commit.com/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-docstring-first
+      - id: check-yaml
+      - id: check-toml
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+  - repo: https://github.com/keewis/blackdoc
+    rev: v0.3.8
+    hooks:
+      - id: blackdoc
+  - repo: https://github.com/pycqa/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.6.1
+    hooks:
+      - id: nbstripout
+        args: [--extra-keys=metadata.kernelspec metadata.language_info.version]
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v3.0.0-alpha.4
+    hooks:
+      - id: prettier

AUTHORS.rst

@@ -1,5 +1,5 @@
 =======
-Credits
+Authors
 =======
 
 Development Lead

README.rst

@@ -26,12 +26,13 @@ Package to perform Wind inversion from GRD Level-1 SAR images
 Features
 --------
 
-* TODO
+This Python library (based on `xarray`) allows to perform wind inversion from level-1 GRD (compressed magnitude image) or SLC (I and Q complexe image in slant range).
+
 
 Credits
 -------
 
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+This package was created with Cookiecutter_.
 
 .. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
+

ci/requirements/docs.yaml

@@ -0,0 +1,20 @@
+name: grdwindinversion-docs
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  - sphinx>=4
+  - sphinx-book-theme
+  - ipython
+  - myst-parser
+  - jinja2<=3.03
+  - pandoc
+  - numpydoc
+  - sphinx-rtd-theme
+  - nbsphinx
+  - jupyter-sphinx
+  - sphinxcontrib-programoutput
+  - aiohttp
+  - holoviews
+  - pip:
+    - -e ../..

ci/requirements/environment.yaml

@@ -0,0 +1,35 @@
+name: grdwindinversion-tests
+channels:
+  - conda-forge
+dependencies:
+  - python=3.10
+  # development
+  - ipython
+  - pre-commit
+  - jupyterlab
+  - jupyterlab_code_formatter
+  - isort
+  - black
+  - dask-labextension
+  # testing
+  - pytest
+  - pytest-reportlog
+  - hypothesis
+  - coverage
+  # I/O
+  - rioxarray
+  - h5netcdf
+  - zarr
+  - scipy
+  # data
+  - xarray
+  - xarray-datatree
+  - dask
+  - numpy
+  - pandas
+  - shapely
+  # processing
+  - more-itertools
+  - tqdm
+  - lxml
+  - importlib_resources

docs/Makefile

@@ -17,4 +17,5 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
+	pip install -r ../requirements_doc.txt
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/algorithm.rst

@@ -0,0 +1,4 @@
+Algorithm description
+=====================
+
+TODO

docs/conf.py

@@ -31,7 +31,36 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode']
+
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.doctest',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.autosectionlabel',
+    'sphinx_rtd_theme',
+    'sphinxcontrib.mermaid',
+    'nbsphinx',
+    'jupyter_sphinx',
+]
+# order by source
+autodoc_member_order = 'bysource'
+
+# Napoleon settings
+napoleon_google_docstring = False
+napoleon_numpy_docstring = True
+napoleon_include_init_with_doc = False
+napoleon_include_private_with_doc = False
+napoleon_include_special_with_doc = True
+napoleon_use_admonition_for_examples = False
+napoleon_use_admonition_for_notes = False
+napoleon_use_admonition_for_references = False
+napoleon_use_ivar = False
+napoleon_use_param = True
+napoleon_use_rtype = True
+napoleon_type_aliases = None
+
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -64,7 +93,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -84,6 +113,7 @@
 # a list of builtin themes.
 #
 html_theme = 'alabaster'
+#html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -95,7 +125,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ['_static']
-
+#html_style = 'css/grdwindinversion.css'
 
 # -- Options for HTMLHelp output ---------------------------------------