Merge branch 'master' into ci/add-python-3-12-to-testing

Author: rflamary

.circleci/config.yml

@@ -46,7 +46,7 @@ jobs:
             command: |
               python -m pip install --user --upgrade --progress-bar off pip
               python -m pip install --user -e .
-              python -m pip install --user --upgrade --no-cache-dir --progress-bar off -r requirements.txt 
+              python -m pip install --user --upgrade --no-cache-dir --progress-bar off -r requirements_all.txt 
               python -m pip install --user --upgrade --progress-bar off -r docs/requirements.txt
               python -m pip install --user --upgrade --progress-bar off ipython sphinx-gallery memory_profiler              
           # python -m pip install --user --upgrade --progress-bar off ipython "https://api.github.com/repos/sphinx-gallery/sphinx-gallery/zipball/master" memory_profiler

.github/workflows/build_doc.yml

@@ -24,7 +24,7 @@ jobs:
     - 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 requirements_all.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 .

.github/workflows/build_tests.yml

@@ -35,8 +35,8 @@ jobs:
         pip install -e .
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
+        python -m pip install --upgrade pip setuptools
+        pip install -r requirements_all.txt
         pip install pytest pytest-cov
     - name: Run tests
       run: |
@@ -55,8 +55,8 @@ jobs:
         python-version: "3.x"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install flake8
+        python -m pip install --upgrade pip setuptools
+        pip install flake8 
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -76,7 +76,7 @@ jobs:
         python-version: "3.12"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools
         pip install pytest pytest-cov
     - name: Install POT
       run: |
@@ -106,9 +106,9 @@ jobs:
          pip install -e .
      - name: Install dependencies
        run: |
-         python -m pip install --upgrade pip
-         pip install -r requirements.txt
-         pip install pytest
+         python -m pip install --upgrade pip setuptools
+         pip install -r requirements_all.txt
+         pip install pytest 
      - name: Run tests
        run: |
          python -m pytest --durations=20  -v test/ ot/ --color=yes

.github/workflows/build_tests_cuda.yml

@@ -15,7 +15,8 @@ jobs:
     - uses: actions/checkout@v4
     - name: Install POT
       run: |
-        python3.10 -m pip install  --ignore-installed -e .
+        python3.10 -m pip install --upgrade pip setuptools
+        python3.10 -m pip install --ignore-installed -e .
     - name: Run tests
       run: |
         python3.10 -m pytest --durations=20 -v test/ ot/ --doctest-modules --color=yes --ignore=test/test_dr.py --ignore=ot.dr --ignore=ot.plot

.github/workflows/build_wheels.yml

@@ -26,7 +26,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools
 
     - name: Install cibuildwheel
       run: |
@@ -61,7 +61,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools
 
     - name: Install cibuildwheel
       run: |

.github/workflows/build_wheels_weekly.yml

@@ -25,7 +25,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
+        python -m pip install --upgrade pip setuptools
 
     - name: Install cibuildwheel
       run: |

README.md

@@ -113,6 +113,12 @@ or get the very latest version by running:
 pip install -U https://github.com/PythonOT/POT/archive/master.zip # with --user for user install (no root)
 ```
 
+Optional dependencies may be installed with
+```console
+pip install POT[all]
+```
+Note that this installs `cvxopt`, which is licensed under GPL 3.0. Alternatively, if you cannot use GPL-licensed software, the specific optional dependencies may be installed individually, or per-submodule. The available optional installations are `backend-jax, backend-tf, backend-torch, cvxopt, dr, gnn, all`.
+
 #### Anaconda installation with conda-forge
 
 If you use the Anaconda python distribution, POT is available in [conda-forge](https://conda-forge.org). To install it and the required dependencies:

RELEASES.md

@@ -10,6 +10,7 @@
 + New general unbalanced solvers for `ot.solve` and BFGS solver and illustrative example (PR #620)
 + Add gradient computation with envelope theorem to sinkhorn solver of `ot.solve` with `grad='envelope'` (PR #605).
 + Added support for [Low rank Gromov-Wasserstein](https://proceedings.mlr.press/v162/scetbon22b/scetbon22b.pdf) with `ot.gromov.lowrank_gromov_wasserstein_samples` (PR #614)
++ Optional dependencies may now be installed with `pip install POT[all]` The specific backends or submodules' dependencies may also be installed individually. The pip options are: `backend-jax, backend-tf, backend-torch, cvxopt, dr, gnn, all`. The installation of the `cupy` backend should be done with conda.
 
 #### Closed issues
 - Fix gpu compatibility of sr(F)GW solvers when `G0 is not None`(PR #596)

ot/da.py

@@ -376,8 +376,10 @@ def emd_laplace(a, b, xs, xt, M, sim='knn', sim_param=None, reg='pos', eta=1, al
     elif sim == 'knn':
         if sim_param is None:
             sim_param = 3
-
-        from sklearn.neighbors import kneighbors_graph
+        try:
+            from sklearn.neighbors import kneighbors_graph
+        except ImportError:
+            raise ValueError('scikit-learn must be installed to use knn similarity. Install with `$pip install scikit-learn`.')
 
         sS = nx.from_numpy(kneighbors_graph(
             X=nx.to_numpy(xs), n_neighbors=int(sim_param)

ot/dr.py

@@ -17,12 +17,15 @@
 # License: MIT License
 
 from scipy import linalg
-import autograd.numpy as np
-from sklearn.decomposition import PCA
-
-import pymanopt
-import pymanopt.manifolds
-import pymanopt.optimizers
+try:
+    import autograd.numpy as np
+    from sklearn.decomposition import PCA
+
+    import pymanopt
+    import pymanopt.manifolds
+    import pymanopt.optimizers
+except ImportError:
+    raise ImportError("Missing dependency for ot.dr. Requires autograd, pymanopt, scikit-learn. You can install with install with 'pip install POT[dr]', or 'conda install autograd pymanopt scikit-learn'")
 
 from .bregman import sinkhorn as sinkhorn_bregman
 from .utils import dist as dist_utils, check_random_state

ot/gromov/_gw.py

@@ -43,11 +43,11 @@ def gromov_wasserstein(C1, C2, p=None, q=None, loss_fun='square_loss', symmetric
 
     Where :
 
-    - :math:`\mathbf{C_1}`: Metric cost matrix in the source space
-    - :math:`\mathbf{C_2}`: Metric cost matrix in the target space
-    - :math:`\mathbf{p}`: distribution in the source space
-    - :math:`\mathbf{q}`: distribution in the target space
-    - `L`: loss function to account for the misfit between the similarity matrices
+    - :math:`\mathbf{C_1}`: Metric cost matrix in the source space.
+    - :math:`\mathbf{C_2}`: Metric cost matrix in the target space.
+    - :math:`\mathbf{p}`: Distribution in the source space.
+    - :math:`\mathbf{q}`: Distribution in the target space.
+    - `L`: Loss function to account for the misfit between the similarity matrices.
 
     .. note:: This function is backend-compatible and will work on arrays
         from all compatible backends. But the algorithm uses the C++ CPU backend
@@ -62,39 +62,39 @@ def gromov_wasserstein(C1, C2, p=None, q=None, loss_fun='square_loss', symmetric
     Parameters
     ----------
     C1 : array-like, shape (ns, ns)
-        Metric cost matrix in the source space
+        Metric cost matrix in the source space.
     C2 : array-like, shape (nt, nt)
-        Metric cost matrix in the target space
+        Metric cost matrix in the target space.
     p : array-like, shape (ns,), optional
         Distribution in the source space.
         If let to its default value None, uniform distribution is taken.
     q : array-like, shape (nt,), optional
         Distribution in the target space.
         If let to its default value None, uniform distribution is taken.
     loss_fun : str, optional
-        loss function used for the solver either 'square_loss' or 'kl_loss'
+        Loss function used for the solver either 'square_loss' or 'kl_loss'.
     symmetric : bool, optional
         Either C1 and C2 are to be assumed symmetric or not.
         If let to its default None value, a symmetry test will be conducted.
         Else if set to True (resp. False), C1 and C2 will be assumed symmetric (resp. asymmetric).
     verbose : bool, optional
-        Print information along iterations
+        Print information along iterations.
     log : bool, optional
-        record log if True
+        Record log if True.
     armijo : bool, optional
-        If True the step of the line-search is found via an armijo research. Else closed form is used.
-        If there are convergence issues use False.
+        If True, the step of the line-search is found via an armijo search. Else closed form is used.
+        If there are convergence issues, use False.
     G0: array-like, shape (ns,nt), optional
-        If None the initial transport plan of the solver is pq^T.
+        If None, the initial transport plan of the solver is pq^T.
         Otherwise G0 must satisfy marginal constraints and will be used as initial transport of the solver.
     max_iter : int, optional
-        Max number of iterations
+        Max number of iterations.
     tol_rel : float, optional
-        Stop threshold on relative error (>0)
+        Stop threshold on relative error (>0).
     tol_abs : float, optional
-        Stop threshold on absolute error (>0)
+        Stop threshold on absolute error (>0).
     **kwargs : dict
-        parameters can be directly passed to the ot.optim.cg solver
+        Parameters can be directly passed to the ot.optim.cg solver.
 
     Returns
     -------
@@ -175,7 +175,7 @@ def line_search(cost, G, deltaG, Mi, cost_G, **kwargs):
 
     if not nx.is_floating_point(C10):
         warnings.warn(
-            "Input structure matrix consists of integer. The transport plan will be "
+            "Input structure matrix consists of integers. The transport plan will be "
             "casted accordingly, possibly resulting in a loss of precision. "
             "If this behaviour is unwanted, please make sure your input "
             "structure matrix consists of floating point elements.",

ot/helpers/openmp_helpers.py

@@ -9,7 +9,7 @@
 import textwrap
 import subprocess
 
-from distutils.errors import CompileError, LinkError
+from setuptools.errors import CompileError, LinkError
 
 from pre_build_helpers import compile_test_program
 

requirements.txt renamed to requirements_all.txt

@@ -46,6 +46,9 @@
     sdk_path = subprocess.check_output(['xcrun', '--show-sdk-path'])
     os.environ['CFLAGS'] = '-isysroot "{}"'.format(sdk_path.rstrip().decode("utf-8"))
 
+with open('requirements_all.txt') as f:
+    optional_requirements = f.read().splitlines()
+
 setup(
     name='POT',
     version=__version__,
@@ -70,6 +73,17 @@
     scripts=[],
     data_files=[],
     install_requires=["numpy>=1.16", "scipy>=1.6"],
+    extras_require={
+        'backend-numpy': [], # in requirements.
+        'backend-jax': ['jax<=0.4.24', 'jaxlib<=0.4.24'],
+        'backend-cupy': [], # should be installed with conda, not pip, or figure out what CUDA version above.
+        'backend-tf': ['tensorflow'],
+        'backend-torch': ['torch'],
+        'cvxopt': ['cvxopt'], # on it's own to prevent accidental GPL violations
+        'dr': ['scikit-learn', 'pymanopt', 'autograd'],
+        'gnn': ['torch', 'torch_geometric'],
+        'all': optional_requirements
+    },
     python_requires=">=3.7",
     classifiers=[
         'Development Status :: 5 - Production/Stable',