Merge branch 'master' into refactor-simplex-storage

Author: rflamary

.circleci/config.yml

@@ -4,8 +4,8 @@ version: 2
 jobs:
     build_docs:
       docker:
-        - image: cimg/python:3.10
-      resource_class: medium
+        - image: cimg/python:3.12
+      resource_class: large
       steps:
         - checkout
         - run:
@@ -27,6 +27,7 @@ jobs:
                 git remote add upstream https://github.com/PythonOT/POT.git;
                 git pull --ff-only upstream "refs/pull/$(cat merge.txt)/merge";
                 git fetch upstream master;
+                git submodule update --init --recursive
               fi
 
         # Load our data

.github/workflows/build_doc.yml

@@ -14,6 +14,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
     # Standard drop-in approach that should work for most people.
     - name: Free Disk Space (Ubuntu)
       uses: insightsengineering/disk-space-reclaimer@v1
@@ -32,7 +34,7 @@ jobs:
         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 sphinx-gallery memory_profiler
-        python -m pip install --user -e .
+        python -m pip install -v --user -e .
     # Look at what we have and fail early if there is some library conflict
     - name: Check installation
       run: |

.github/workflows/build_tests.yml

@@ -28,6 +28,8 @@ jobs:
 
     - name: Checking Out Repository
       uses: actions/checkout@v4
+      with:
+        submodules: true
     # Install Python & Packages
     - uses: actions/setup-python@v4
       with:
@@ -43,6 +45,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -70,6 +75,9 @@ jobs:
         android: true
         dotnet: true
     - uses: actions/checkout@v4
+      with:
+        submodules: true
+
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
@@ -98,6 +106,9 @@ jobs:
     if: "!contains(github.event.head_commit.message, 'no ci')"
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
+
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
@@ -125,6 +136,8 @@ jobs:
 
      steps:
      - uses: actions/checkout@v4
+       with:
+        submodules: true
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
@@ -153,6 +166,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:

.github/workflows/build_wheels.yml

@@ -19,6 +19,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
     - name: Set up Python 3.10
       uses: actions/setup-python@v5
       with:
@@ -54,6 +56,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
     - name: Set up Python 3.10
       uses: actions/setup-python@v5
       with:

.github/workflows/build_wheels_weekly.yml

@@ -18,6 +18,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        submodules: true
     - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:

.gitignore

@@ -16,6 +16,7 @@ docs/modules/
 # Cython output
 ot/lp/emd_wrap.cpp
 ot/partial/partial_cython.cpp
+ot/bsp/bsp_wrap.cpp
 
 # Distribution / packaging
 .Python

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "deps/eigen"]
+	path = deps/eigen
+	url = https://gitlab.com/libeigen/eigen.git
+	branch = 3.4

CITATION.cff

@@ -75,6 +75,13 @@ authors:
   - given-names: Nathan
     family-names: Neike
     affiliation: Hi! PARIS
+  - given-names: Baptiste
+    family-names: Genest
+    affiliation: CNRS, LIRIS
+  - given-names: David
+    family-names: Coeurjolly
+    affiliation: CNRS, LIRIS
+
 identifiers:
   - type: url
     value: 'https://github.com/PythonOT/POT'

MANIFEST.in

@@ -12,3 +12,8 @@ include ot/lp/network_simplex_simple.h
 include ot/lp/network_simplex_simple_omp.h
 include ot/lp/sparse_bipartitegraph.h
 include ot/partial/partial_cython.pyx
+include ot/bsp/BSP-OT_header_only.h
+include ot/bsp/bsp_wrapper.cpp
+include ot/bsp/bsp_wrapper.h
+include ot/bsp/bsp_wrap.pyx
+graft deps/eigen/Eigen

README.md

@@ -73,6 +73,7 @@ POT provides the following generic OT solvers:
 * Fused unbalanced Gromov-Wasserstein [70].
 * [Optimal Transport Barycenters for Generic Costs](https://pythonot.github.io/auto_examples/barycenters/plot_free_support_barycenter_generic_cost.html) [77]
 * [Barycenters between Gaussian Mixture Models](https://pythonot.github.io/auto_examples/barycenters/plot_gmm_barycenter.html) [69, 77]
+* [Fast and accurate transport bijections using BSP-OT](https://pythonot.github.io/auto_examples/plot_bsp_ot.html) [84]
 
 POT provides the following Machine Learning related solvers:
 
@@ -139,7 +140,7 @@ pip install POT
 or get the very latest version by running:
 
 ```console
-pip install -U https://github.com/PythonOT/POT/archive/master.zip # with --user for user install (no root)
+pip install -U git+https://github.com/PythonOT/POT.git # with --user for user install (no root)
 ```
 
 Optional dependencies may be installed with
@@ -452,4 +453,6 @@ Artificial Intelligence.
 
 [82] Bonet, C., Nadjahi, K., Séjourné, T., Fatras, K., & Courty, N. (2024). [Slicing Unbalanced Optimal Transport](https://openreview.net/forum?id=AjJTg5M0r8). Transactions on Machine Learning Research.
 
-[83] Germain, T., Flamary, R., Kostic, V. R., & Lounici, K. (2025). [A Spectral-Grassmann Wasserstein Metric for Operator Representations of Dynamical Systems](https://arxiv.org/abs/2509.24920).
+[83] Germain, T., Flamary, R., Kostic, V. R., & Lounici, K. (2025). [A Spectral-Grassmann Wasserstein Metric for Operator Representations of Dynamical Systems](https://arxiv.org/abs/2509.24920).
+
+[84] Genest, B., Bonneel, N., Nivoliers, V., & Coeurjolly, D. (2025). [BSP-OT: Sparse transport plans between discrete measures in loglinear time.](https://dl.acm.org/doi/10.1145/3763281) ACM Transactions on Graphics (TOG), 44(6), 1-15.