From 981fbe3873d7c1c121499bf83557f6d72425bf69 Mon Sep 17 00:00:00 2001 From: Rémi Flamary Date: Fri, 24 Mar 2023 10:13:59 +0100 Subject: [WIP] Build donc in GH Action and report warnings + move contributing and code of conduct in documentation (#441) * use action for doc with wraning visible * remove space * remove space again * test pre commands * install pot properly * install compiler... * try composite action * remoe warning in sliced exmaple * pep8 * move contributing and code of conduct * cleanup * underline too short * update quickstart * replace version selector by static list to avoid jsQuery bug --- .github/CONTRIBUTING.md | 1 - .github/workflows/build_doc.yml | 44 +++++++++++++++ README.md | 2 +- docs/source/.github/CODE_OF_CONDUCT.rst | 6 --- docs/source/.github/CONTRIBUTING.rst | 6 --- docs/source/_templates/versions.html | 69 ++++++++++++------------ docs/source/all.rst | 2 +- docs/source/code_of_conduct.rst | 6 +++ docs/source/contributing.rst | 6 +++ docs/source/index.rst | 4 +- docs/source/quickstart.rst | 92 ++++++++++++++++---------------- examples/backends/plot_ssw_unif_torch.py | 2 +- 12 files changed, 142 insertions(+), 98 deletions(-) create mode 100644 .github/workflows/build_doc.yml delete mode 100644 docs/source/.github/CODE_OF_CONDUCT.rst delete mode 100644 docs/source/.github/CONTRIBUTING.rst create mode 100644 docs/source/code_of_conduct.rst create mode 100644 docs/source/contributing.rst diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 9bc8e87..168ffb3 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,4 +1,3 @@ - Contributing to POT =================== diff --git a/.github/workflows/build_doc.yml b/.github/workflows/build_doc.yml new file mode 100644 index 0000000..93bd113 --- /dev/null +++ b/.github/workflows/build_doc.yml @@ -0,0 +1,44 @@ +name: Build doc + +on: + workflow_dispatch: + pull_request: + push: + branches: + - 'master' + +jobs: + build: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v1 + # Standard drop-in approach that should work for most people. + + - name: Set up Python 3.8 + uses: actions/setup-python@v1 + with: + python-version: 3.8 + + - name: Get Python running + run: | + python -m pip install --user --upgrade --progress-bar off pip + python -m pip install --user --upgrade --progress-bar off -r requirements.txt + python -m pip install --user --upgrade --progress-bar off -r docs/requirements.txt + python -m pip install --user --upgrade --progress-bar off ipython "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler + python -m pip install --user -e . + # Look at what we have and fail early if there is some library conflict + - name: Check installation + run: | + which python + python -c "import ot" + # Build docs + - name: Generate HTML docs + uses: rickstaa/sphinx-action@master + with: + docs-folder: "docs/" + - uses: actions/upload-artifact@v1 + with: + name: Documentation + path: docs/build/html/ \ No newline at end of file diff --git a/README.md b/README.md index 9c5e07e..2a81e95 100644 --- a/README.md +++ b/README.md @@ -192,7 +192,7 @@ POT has benefited from the financing or manpower from the following partners: ## Contributions and code of conduct -Every contribution is welcome and should respect the [contribution guidelines](.github/CONTRIBUTING.md). Each member of the project is expected to follow the [code of conduct](.github/CODE_OF_CONDUCT.md). +Every contribution is welcome and should respect the [contribution guidelines](https://pythonot.github.io/master/contributing.html). Each member of the project is expected to follow the [code of conduct](https://pythonot.github.io/master/code_of_conduct.html). ## Support diff --git a/docs/source/.github/CODE_OF_CONDUCT.rst b/docs/source/.github/CODE_OF_CONDUCT.rst deleted file mode 100644 index d4c5cec..0000000 --- a/docs/source/.github/CODE_OF_CONDUCT.rst +++ /dev/null @@ -1,6 +0,0 @@ -Code of Conduct -=============== - -.. include:: ../../../.github/CODE_OF_CONDUCT.md - :parser: myst_parser.sphinx_ - :start-line: 2 diff --git a/docs/source/.github/CONTRIBUTING.rst b/docs/source/.github/CONTRIBUTING.rst deleted file mode 100644 index aef24e9..0000000 --- a/docs/source/.github/CONTRIBUTING.rst +++ /dev/null @@ -1,6 +0,0 @@ -Contributing to POT -=================== - -.. include:: ../../../.github/CONTRIBUTING.md - :parser: myst_parser.sphinx_ - :start-line: 3 diff --git a/docs/source/_templates/versions.html b/docs/source/_templates/versions.html index f48ab86..5b1021a 100644 --- a/docs/source/_templates/versions.html +++ b/docs/source/_templates/versions.html @@ -1,47 +1,50 @@
- - + + Python Optimal Transport - versions - +
+ + + Versions: + Release + Development + Code + + + + -
+ +
\ No newline at end of file diff --git a/docs/source/all.rst b/docs/source/all.rst index 1b8d13c..a9d7fe2 100644 --- a/docs/source/all.rst +++ b/docs/source/all.rst @@ -37,7 +37,7 @@ API and modules Main :py:mod:`ot` functions --------------- +--------------------------- .. automodule:: ot :members: diff --git a/docs/source/code_of_conduct.rst b/docs/source/code_of_conduct.rst new file mode 100644 index 0000000..40b432e --- /dev/null +++ b/docs/source/code_of_conduct.rst @@ -0,0 +1,6 @@ +Code of conduct +=============== + +.. include:: ../../.github/CODE_OF_CONDUCT.md + :parser: myst_parser.sphinx_ + :start-line: 2 diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst new file mode 100644 index 0000000..8dec19a --- /dev/null +++ b/docs/source/contributing.rst @@ -0,0 +1,6 @@ +Contributing to POT +=================== + +.. include:: ../../.github/CONTRIBUTING.md + :parser: myst_parser.sphinx_ + :start-line: 2 diff --git a/docs/source/index.rst b/docs/source/index.rst index 3d53ef4..0f04738 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -21,9 +21,9 @@ Contents all auto_examples/index releases - .github/CONTRIBUTING contributors - .github/CODE_OF_CONDUCT + contributing + code_of_conduct .. include:: ../../README.md diff --git a/docs/source/quickstart.rst b/docs/source/quickstart.rst index c8eac30..1dc9f71 100644 --- a/docs/source/quickstart.rst +++ b/docs/source/quickstart.rst @@ -127,14 +127,6 @@ been used to solve both graph Laplacian regularization OT and Gromov Wasserstein [30]_. -.. note:: - - POT is originally designed to solve OT problems with Numpy interface and - is not yet compatible with Pytorch API. We are currently working on a torch - submodule that will provide OT solvers and losses for the most common deep - learning configurations. - - When not to use POT """"""""""""""""""" @@ -692,42 +684,8 @@ A list of the provided implementation is given in the following note. :heading-level: " -Other applications ------------------- - -We discuss in the following several OT related problems and tools that has been -proposed in the OT and machine learning community. - -Wasserstein Discriminant Analysis -^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ - -Wasserstein Discriminant Analysis [11]_ is a generalization of `Fisher Linear Discriminant -Analysis `__ that -allows discrimination between classes that are not linearly separable. It -consists in finding a linear projector optimizing the following criterion - -.. math:: - P = \text{arg}\min_P \frac{\sum_i OT_e(\mu_i\#P,\mu_i\#P)}{\sum_{i,j\neq i} - OT_e(\mu_i\#P,\mu_j\#P)} - -where :math:`\#` is the push-forward operator, :math:`OT_e` is the entropic OT -loss and :math:`\mu_i` is the -distribution of samples from class :math:`i`. :math:`P` is also constrained to -be in the Stiefel manifold. WDA can be solved in POT using function -:any:`ot.dr.wda`. It requires to have installed :code:`pymanopt` and -:code:`autograd` for manifold optimization and automatic differentiation -respectively. Note that we also provide the Fisher discriminant estimator in -:any:`ot.dr.fda` for easy comparison. - -.. warning:: - - Note that due to the hard dependency on :code:`pymanopt` and - :code:`autograd`, :any:`ot.dr` is not imported by default. If you want to - use it you have to specifically import it with :code:`import ot.dr` . - -.. minigallery:: ot.dr.wda - :add-heading: Examples of the use of WDA - :heading-level: " +Unbalanced and partial OT +------------------------- @@ -845,10 +803,11 @@ regularization of the problem. :heading-level: " +Gromov Wasserstein and extensions +--------------------------------- - -Gromov-Wasserstein -^^^^^^^^^^^^^^^^^^ +Gromov Wasserstein(GW) +^^^^^^^^^^^^^^^^^^^^^^ Gromov Wasserstein (GW) is a generalization of OT to distributions that do not lie in the same space [13]_. In this case one cannot compute distance between samples @@ -877,6 +836,8 @@ There also exists an entropic regularized variant of GW that has been proposed i :add-heading: Examples of computation of GW, regularized G and FGW :heading-level: " +Gromov Wasserstein barycenters +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Note that similarly to Wasserstein distance GW allows for the definition of GW barycenters that can be expressed as @@ -905,6 +866,43 @@ The implementations of FGW and FGW barycenter is provided in functions :heading-level: " +Other applications +------------------ + +We discuss in the following several OT related problems and tools that has been +proposed in the OT and machine learning community. + +Wasserstein Discriminant Analysis +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +Wasserstein Discriminant Analysis [11]_ is a generalization of `Fisher Linear Discriminant +Analysis `__ that +allows discrimination between classes that are not linearly separable. It +consists in finding a linear projector optimizing the following criterion + +.. math:: + P = \text{arg}\min_P \frac{\sum_i OT_e(\mu_i\#P,\mu_i\#P)}{\sum_{i,j\neq i} + OT_e(\mu_i\#P,\mu_j\#P)} + +where :math:`\#` is the push-forward operator, :math:`OT_e` is the entropic OT +loss and :math:`\mu_i` is the +distribution of samples from class :math:`i`. :math:`P` is also constrained to +be in the Stiefel manifold. WDA can be solved in POT using function +:any:`ot.dr.wda`. It requires to have installed :code:`pymanopt` and +:code:`autograd` for manifold optimization and automatic differentiation +respectively. Note that we also provide the Fisher discriminant estimator in +:any:`ot.dr.fda` for easy comparison. + +.. warning:: + + Note that due to the hard dependency on :code:`pymanopt` and + :code:`autograd`, :any:`ot.dr` is not imported by default. If you want to + use it you have to specifically import it with :code:`import ot.dr` . + +.. minigallery:: ot.dr.wda + :add-heading: Examples of the use of WDA + :heading-level: " + Solving OT with Multiple backends on CPU/GPU -------------------------------------------- diff --git a/examples/backends/plot_ssw_unif_torch.py b/examples/backends/plot_ssw_unif_torch.py index d1de5a9..7ccc2af 100644 --- a/examples/backends/plot_ssw_unif_torch.py +++ b/examples/backends/plot_ssw_unif_torch.py @@ -50,7 +50,7 @@ def plot_sphere(ax): r = np.linspace(1.0, 1.0, 50) X, Y = np.meshgrid(xlist, ylist) - Z = np.sqrt(r**2 - X**2 - Y**2) + Z = np.sqrt(np.maximum(r**2 - X**2 - Y**2, 0)) ax.plot_wireframe(X, Y, Z, color="gray", alpha=.3) ax.plot_wireframe(X, Y, -Z, color="gray", alpha=.3) # Now plot the bottom half -- cgit v1.2.3