merge 1 and 4

meom-group · Oct 25, 2023 · dd55c8f · dd55c8f
2 parents f90872d + 5fa68a5
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diff --git a/.github/workflows/python-documentation.yml b/.github/workflows/python-documentation.yml
@@ -0,0 +1,33 @@
+name: Build jaxparrow html documentation
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+permissions:
+  contents: write
+
+jobs:
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.9"
+      - name: Install dependencies
+        run: |
+          pip install sphinx sphinx_rtd_theme myst_parser
+      - name: Sphinx build
+        run: |
+          sphinx-build docs docs/_build
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/
+          force_orphan: true
diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -0,0 +1,42 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Build and test jaxparrow
+
+on:
+  push:
+    branches: [ "main" ]
+  pull_request:
+    branches: [ "main" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: "pip"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        # install the package locally
+        python -m pip install .
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest tests/test_velocities.py --doctest-modules --junitxml=junit/test-results.xml
diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -0,0 +1,33 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload jaxparrow to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.9"
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/README.md b/README.md
@@ -43,7 +43,7 @@ u_cyclo, v_cyclo = cyclogeostrophy(u_geos=u_geos, v_geos=v_geos,
 By default, the `cyclogeostrophy` function relies on our variational method.
 Its `method` argument provides the ability to use an iterative method instead, either the one described by [Penven *et al.*](https://doi.org/10.1016/j.dsr2.2013.10.015), or the one by [Ioannou *et al.*](https://doi.org/10.1029/2019JC015031).
 Additional arguments also give a finer control over the three approaches hyperparameters. \
-See [**jaxparrow** documentation](docs/_build/html/index.html) for more details.
+See [**jaxparrow** documentation](docs/_build/index.html) for more details.
 
 [Notebooks](notebooks/README.md) are available as step-by-step examples.
 

diff --git a/docs/_build/html/.buildinfo → docs/_build/.buildinfo b/docs/_build/html/.buildinfo → docs/_build/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: bd118657e0721db2929ba23353b9ee53
+config: 5ec2c7199585950b86ff044830b95058
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/.doctrees/environment.pickle b/docs/_build/.doctrees/environment.pickle
diff --git a/docs/_build/doctrees/index.doctree → docs/_build/.doctrees/index.doctree b/docs/_build/doctrees/index.doctree → docs/_build/.doctrees/index.doctree
diff --git a/...octrees/jaxparrow.cyclogeostrophy.doctree → ...octrees/jaxparrow.cyclogeostrophy.doctree b/...octrees/jaxparrow.cyclogeostrophy.doctree → ...octrees/jaxparrow.cyclogeostrophy.doctree
diff --git a/docs/_build/.doctrees/jaxparrow.doctree b/docs/_build/.doctrees/jaxparrow.doctree
diff --git a/...ild/doctrees/jaxparrow.geostrophy.doctree → ...ld/.doctrees/jaxparrow.geostrophy.doctree b/...ild/doctrees/jaxparrow.geostrophy.doctree → ...ld/.doctrees/jaxparrow.geostrophy.doctree
diff --git a/docs/_build/doctrees/jaxparrow.tools.doctree → .../_build/.doctrees/jaxparrow.tools.doctree b/docs/_build/doctrees/jaxparrow.tools.doctree → .../_build/.doctrees/jaxparrow.tools.doctree
diff --git a/...ld/doctrees/jaxparrow.tools.tools.doctree → ...d/.doctrees/jaxparrow.tools.tools.doctree b/...ld/doctrees/jaxparrow.tools.tools.doctree → ...d/.doctrees/jaxparrow.tools.tools.doctree
diff --git a/docs/_build/doctrees/modules.doctree → docs/_build/.doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree → docs/_build/.doctrees/modules.doctree
diff --git a/docs/_build/doctrees/usage.doctree → docs/_build/.doctrees/usage.doctree b/docs/_build/doctrees/usage.doctree → docs/_build/.doctrees/usage.doctree
diff --git a/docs/_build/html/_sources/index.rst.txt → docs/_build/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt → docs/_build/_sources/index.rst.txt
diff --git a/...sources/jaxparrow.cyclogeostrophy.rst.txt → ...sources/jaxparrow.cyclogeostrophy.rst.txt b/...sources/jaxparrow.cyclogeostrophy.rst.txt → ...sources/jaxparrow.cyclogeostrophy.rst.txt
diff --git a/...tml/_sources/jaxparrow.geostrophy.rst.txt → ...ild/_sources/jaxparrow.geostrophy.rst.txt b/...tml/_sources/jaxparrow.geostrophy.rst.txt → ...ild/_sources/jaxparrow.geostrophy.rst.txt
diff --git a/docs/_build/html/_sources/jaxparrow.rst.txt → docs/_build/_sources/jaxparrow.rst.txt b/docs/_build/html/_sources/jaxparrow.rst.txt → docs/_build/_sources/jaxparrow.rst.txt
@@ -7,7 +7,6 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
-   jaxparrow.grid
    jaxparrow.tools
 
 Submodules

diff --git a/...ild/html/_sources/jaxparrow.tools.rst.txt → docs/_build/_sources/jaxparrow.tools.rst.txt b/...ild/html/_sources/jaxparrow.tools.rst.txt → docs/_build/_sources/jaxparrow.tools.rst.txt
diff --git a/...ml/_sources/jaxparrow.tools.tools.rst.txt → ...ld/_sources/jaxparrow.tools.tools.rst.txt b/...ml/_sources/jaxparrow.tools.tools.rst.txt → ...ld/_sources/jaxparrow.tools.tools.rst.txt
diff --git a/docs/_build/html/_sources/modules.rst.txt → docs/_build/_sources/modules.rst.txt b/docs/_build/html/_sources/modules.rst.txt → docs/_build/_sources/modules.rst.txt
diff --git a/docs/_build/html/_sources/usage.rst.txt → docs/_build/_sources/usage.rst.txt b/docs/_build/html/_sources/usage.rst.txt → docs/_build/_sources/usage.rst.txt
diff --git a/docs/_build/html/_static/alabaster.css → docs/_build/_static/alabaster.css b/docs/_build/html/_static/alabaster.css → docs/_build/_static/alabaster.css
diff --git a/docs/_build/html/_static/basic.css → docs/_build/_static/basic.css b/docs/_build/html/_static/basic.css → docs/_build/_static/basic.css
diff --git a/docs/_build/html/_static/custom.css → docs/_build/_static/custom.css b/docs/_build/html/_static/custom.css → docs/_build/_static/custom.css
diff --git a/docs/_build/html/_static/doctools.js → docs/_build/_static/doctools.js b/docs/_build/html/_static/doctools.js → docs/_build/_static/doctools.js
diff --git a/...ild/html/_static/documentation_options.js → docs/_build/_static/documentation_options.js b/...ild/html/_static/documentation_options.js → docs/_build/_static/documentation_options.js
diff --git a/docs/_build/html/_static/file.png → docs/_build/_static/file.png b/docs/_build/html/_static/file.png → docs/_build/_static/file.png
diff --git a/docs/_build/html/_static/language_data.js → docs/_build/_static/language_data.js b/docs/_build/html/_static/language_data.js → docs/_build/_static/language_data.js
diff --git a/docs/_build/html/_static/minus.png → docs/_build/_static/minus.png b/docs/_build/html/_static/minus.png → docs/_build/_static/minus.png
diff --git a/docs/_build/html/_static/plus.png → docs/_build/_static/plus.png b/docs/_build/html/_static/plus.png → docs/_build/_static/plus.png
diff --git a/docs/_build/html/_static/pygments.css → docs/_build/_static/pygments.css b/docs/_build/html/_static/pygments.css → docs/_build/_static/pygments.css
diff --git a/docs/_build/html/_static/searchtools.js → docs/_build/_static/searchtools.js b/docs/_build/html/_static/searchtools.js → docs/_build/_static/searchtools.js
diff --git a/docs/_build/html/_static/sphinx_highlight.js → docs/_build/_static/sphinx_highlight.js b/docs/_build/html/_static/sphinx_highlight.js → docs/_build/_static/sphinx_highlight.js
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/jaxparrow.doctree b/docs/_build/doctrees/jaxparrow.doctree
diff --git a/docs/_build/doctrees/jaxparrow.grid.cgrid.doctree b/docs/_build/doctrees/jaxparrow.grid.cgrid.doctree
diff --git a/docs/_build/doctrees/jaxparrow.grid.doctree b/docs/_build/doctrees/jaxparrow.grid.doctree
diff --git a/docs/_build/html/genindex.html → docs/_build/genindex.html b/docs/_build/html/genindex.html → docs/_build/genindex.html
@@ -39,36 +39,15 @@ <h1 id="index">Index</h1>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#N"><strong>N</strong></a>
  | <a href="#R"><strong>R</strong></a>
- | <a href="#S"><strong>S</strong></a>
 
 </div>
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid">CGrid (class in jaxparrow.grid)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid">(class in jaxparrow.grid.cgrid)</a>
-</li>
-      </ul></li>
       <li><a href="jaxparrow.tools.html#jaxparrow.tools.compute_coriolis_factor">compute_coriolis_factor() (in module jaxparrow.tools)</a>
 
       <ul>
         <li><a href="jaxparrow.tools.tools.html#jaxparrow.tools.tools.compute_coriolis_factor">(in module jaxparrow.tools.tools)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.compute_cyclogeostrophy">compute_cyclogeostrophy() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.compute_cyclogeostrophy">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.compute_geostrophy">compute_geostrophy() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.compute_geostrophy">(jaxparrow.grid.cgrid.CGrid method)</a>
 </li>
       </ul></li>
       <li><a href="jaxparrow.tools.html#jaxparrow.tools.compute_spatial_step">compute_spatial_step() (in module jaxparrow.tools)</a>
@@ -77,6 +56,8 @@ <h2 id="C">C</h2>
         <li><a href="jaxparrow.tools.tools.html#jaxparrow.tools.tools.compute_spatial_step">(in module jaxparrow.tools.tools)</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="jaxparrow.html#jaxparrow.cyclogeostrophy">cyclogeostrophy() (in module jaxparrow)</a>
 
       <ul>
@@ -93,50 +74,6 @@ <h2 id="G">G</h2>
 
       <ul>
         <li><a href="jaxparrow.geostrophy.html#jaxparrow.geostrophy.geostrophy">(in module jaxparrow.geostrophy)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_ssh">get_ssh() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_ssh">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_u">get_u() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_u">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_u_cyclo">get_u_cyclo() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_u_cyclo">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_u_geos">get_u_geos() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_u_geos">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_v">get_v() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_v">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_v_cyclo">get_v_cyclo() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_v_cyclo">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.get_v_geos">get_v_geos() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.get_v_geos">(jaxparrow.grid.cgrid.CGrid method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -164,25 +101,11 @@ <h2 id="J">J</h2>
 
       <ul>
         <li><a href="jaxparrow.geostrophy.html#module-jaxparrow.geostrophy">module</a>
-</li>
-      </ul></li>
-      <li>
-    jaxparrow.grid
-
-      <ul>
-        <li><a href="jaxparrow.grid.html#module-jaxparrow.grid">module</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
-    jaxparrow.grid.cgrid
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#module-jaxparrow.grid.cgrid">module</a>
-</li>
-      </ul></li>
-      <li>
     jaxparrow.tools
 
       <ul>
@@ -219,10 +142,6 @@ <h2 id="M">M</h2>
         <li><a href="jaxparrow.cyclogeostrophy.html#module-jaxparrow.cyclogeostrophy">jaxparrow.cyclogeostrophy</a>
 </li>
         <li><a href="jaxparrow.geostrophy.html#module-jaxparrow.geostrophy">jaxparrow.geostrophy</a>
-</li>
-        <li><a href="jaxparrow.grid.html#module-jaxparrow.grid">jaxparrow.grid</a>
-</li>
-        <li><a href="jaxparrow.grid.cgrid.html#module-jaxparrow.grid.cgrid">jaxparrow.grid.cgrid</a>
 </li>
         <li><a href="jaxparrow.tools.html#module-jaxparrow.tools">jaxparrow.tools</a>
 </li>
@@ -258,56 +177,6 @@ <h2 id="R">R</h2>
   </ul></td>
 </tr></table>
 
-<h2 id="S">S</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_ssh">set_ssh() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_ssh">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_u">set_u() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_u">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_u_cyclo">set_u_cyclo() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_u_cyclo">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_u_geos">set_u_geos() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_u_geos">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_v">set_v() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_v">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_v_cyclo">set_v_cyclo() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_v_cyclo">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-      <li><a href="jaxparrow.grid.html#jaxparrow.grid.CGrid.set_v_geos">set_v_geos() (jaxparrow.grid.CGrid method)</a>
-
-      <ul>
-        <li><a href="jaxparrow.grid.cgrid.html#jaxparrow.grid.cgrid.CGrid.set_v_geos">(jaxparrow.grid.cgrid.CGrid method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-</tr></table>
-
 
 
           </div>
@@ -361,7 +230,7 @@ <h3 id="searchlabel">Quick search</h3>
       <div class="clearer"></div>
     </div>
     <div class="footer">
-      &copy;2023, Victor Zaia, Vadim Bertrand.
+      &copy;2023, Victor Zaia, Vadim Bertrand, Emmanuel Cosme, Julien Le Sommer.
 
       |
       Powered by <a href="http://sphinx-doc.org/">Sphinx 7.2.6</a>

diff --git a/docs/_build/html/_sources/jaxparrow.grid.cgrid.rst.txt b/docs/_build/html/_sources/jaxparrow.grid.cgrid.rst.txt
diff --git a/docs/_build/html/_sources/jaxparrow.grid.rst.txt b/docs/_build/html/_sources/jaxparrow.grid.rst.txt