Misc/project structure (#176)

* Reorganize repo structure * Update PC docs * Update imports, fix some types * Fix more types, pet-peeves * Fix tests * Update cost funcs and potentials * Fix LR initializer * Fix k-means initializer * Move `utils` * Update imports in notebooks * Update geometry docs * Update initializers * Update math docs * Update problem docstrings * Update `solvers` docstrings * Update `tools` docstrings * Remove remaining `core` mentions from docstrings * Start updating documentation * Fix typing * Update solvers docs * Add initializers * Update docs * Fix MetaOT links * Fix bibliography links * Fix more links in the notebooks * Follow line length in README.md * Update `tests` structure * Update badges * Add TODOs, fix citation in `index.rst`, move `implicit_diff` * Fix implicit_diff, TODOs in costs * Use `jax.lax.cond` in `UnbalancedBures` * Fix `UnbalancedBures` * Update CI versions * Fix UnbalancedBures's norm
ott-jax · Nov 22, 2022 · 156ef2b · 156ef2b
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diff --git a/.editorconfig b/.editorconfig
@@ -3,9 +3,9 @@ root = true
 [*]
 end_of_line = lf
 insert_final_newline = true
+charset = utf-8
 
 [*py]
-charset = utf-8
 indent_size = 2
 indent_style = space
 max_line_length = 80

diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
@@ -15,13 +15,13 @@ jobs:
         os: [ubuntu-latest]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python }}
 
-    - uses: actions/cache@v2
+    - uses: actions/cache@v3
       with:
         path: ~/.cache/pre-commit
         key: precommit-${{ env.pythonLocation }}-${{ hashFiles('**/.pre-commit-config.yaml') }}

diff --git a/.github/workflows/notebook_tests.yml b/.github/workflows/notebook_tests.yml
@@ -12,12 +12,12 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: [3.8]
         os: [ubuntu-latest]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/publish_to_pypi.yml b/.github/workflows/publish_to_pypi.yml
@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: 3.x
     - name: Install dependencies

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -18,8 +18,8 @@ jobs:
         test_mark: [fast, all]
 
     steps:
-    - uses: actions/checkout@v2
-    - uses: actions/setup-python@v2
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 

diff --git a/.gitignore b/.gitignore
@@ -161,7 +161,7 @@ cython_debug/
 
 # generated documentation
 docs/html
-docs/_autosummary
+**/_autosummary
 
 # macos
 **/.DS_Store
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -9,7 +9,7 @@ to the project, participating in discussions or raising issues.
 1. fork the repository using the **Fork** button on GitHub or the following
    [link](https://github.com/ott-jax/ott/fork)
 2. ```bash
-   git clone https://github.com/YOUR_USERNAME/ott
+   git clone https://github.com/<YOUR_USERNAME>/ott
    cd ott
    pip install -e .'[dev,test]'
    pre-commit install

diff --git a/README.md b/README.md
@@ -1,30 +1,44 @@
 <img src="https://raw.githubusercontent.com/ott-jax/ott/main/docs/_static/images/logoOTT.png" width="10%" alt="logo">
 
-# Optimal Transport Tools (OTT).
-
+# Optimal Transport Tools (OTT)
+[![Downloads](https://pepy.tech/badge/ott-jax)](https://pypi.org/project/ott-jax/)
 [![Tests](https://img.shields.io/github/workflow/status/ott-jax/ott/tests/main)](https://github.com/ott-jax/ott/actions/workflows/tests.yml)
 [![Docs](https://img.shields.io/readthedocs/ott-jax/latest)](https://ott-jax.readthedocs.io/en/latest/)
 [![Coverage](https://img.shields.io/codecov/c/github/ott-jax/ott/main)](https://app.codecov.io/gh/ott-jax/ott)
 
-**See [full documentation](https://ott-jax.readthedocs.io/en/latest/).**
+**See the [full documentation](https://ott-jax.readthedocs.io/en/latest/).**
 
 ## What is OTT-JAX?
-
-A JAX powered library to compute optimal transport at scale and on accelerators, OTT-JAX includes the fastest implementation of the Sinkhorn algorithm you will find around. We have implemented all tweaks (scheduling, acceleration, initializations) and extensions (low-rank), that can be used directly, or within more advanced problems (Gromov-Wasserstein, barycenters). Some of JAX features, including [JIT](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html#Using-jit-to-speed-up-functions), [auto-vectorization](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html#Auto-vectorization-with-vmap) and [implicit differentiation](https://jax.readthedocs.io/en/latest/notebooks/Custom_derivative_rules_for_Python_code.html) work towards the goal of having end-to-end differentiable outputs. OTT-JAX is developed by a team of researchers from Apple, Google, Meta and many academic contributors, including TU München, Oxford, ENSAE/IP Paris and the Hebrew University.
+A JAX powered library to compute optimal transport at scale and on accelerators, OTT-JAX includes the fastest
+implementation of the Sinkhorn algorithm you will find around. We have implemented all tweaks (scheduling,
+acceleration, initializations) and extensions (low-rank), that can be used directly, or within more advanced problems
+(Gromov-Wasserstein, barycenters). Some of JAX features, including
+[JIT](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html#Using-jit-to-speed-up-functions),
+[auto-vectorization](https://jax.readthedocs.io/en/latest/notebooks/quickstart.html#Auto-vectorization-with-vmap) and
+[implicit differentiation](https://jax.readthedocs.io/en/latest/notebooks/Custom_derivative_rules_for_Python_code.html)
+work towards the goal of having end-to-end differentiable outputs. OTT-JAX is developed by a team of researchers
+from Apple, Google, Meta and many academic contributors, including TU München, Oxford, ENSAE/IP Paris and the
+Hebrew University.
 
 ## What is optimal transport?
+Optimal transport can be loosely described as the branch of mathematics and optimization that studies
+*matching problems*: given two families of points, and a cost function on pairs of points, find a `good' (low cost) way
+to associate bijectively to every point in the first family another in the second.
 
-Optimal transport can be loosely described as the branch of mathematics and optimization that studies *matching problems*: given two families of points, and a cost function on pairs of points, find a `good' (low cost) way to associate bijectively to every point in the first family another in the second.
-
-Such problems appear in all areas of science, are easy to describe, yet hard to solve. Indeed, while matching optimally two sets of *n* points using a pairwise cost can be solved with the [Hungarian algorithm](https://en.wikipedia.org/wiki/Hungarian_algorithm), solving it costs an order of $O(n^3)$ operations, and lacks flexibility, since one may want to couple families of different sizes.
+Such problems appear in all areas of science, are easy to describe, yet hard to solve. Indeed, while matching optimally
+two sets of *n* points using a pairwise cost can be solved with the
+[Hungarian algorithm](https://en.wikipedia.org/wiki/Hungarian_algorithm), solving it costs an order of $O(n^3)$
+operations, and lacks flexibility, since one may want to couple families of different sizes.
 
-Optimal transport extends all of this, through faster algorithms (in $n^2$ or even linear in $n$) along with numerous generalizations that can help it handle weighted sets of different size, partial matchings, and even more evolved so-called quadratic matching problems.
+Optimal transport extends all of this, through faster algorithms (in $n^2$ or even linear in $n$) along with numerous
+generalizations that can help it handle weighted sets of different size, partial matchings, and even more evolved
+so-called quadratic matching problems.
 
-In the simple toy example below, we compute the optimal coupling matrix between two point clouds sampled randomly (2D vectors, compared with the squared Euclidean distance):
+In the simple toy example below, we compute the optimal coupling matrix between two point clouds sampled randomly
+(2D vectors, compared with the squared Euclidean distance):
 
 ## Example
-
-```py
+```python
 import jax
 import jax.numpy as jnp
 from ott.tools import transport
@@ -41,17 +55,22 @@ ot = transport.solve(x, y, a=a, b=b)
 P = ot.matrix
 ```
 
-The call to `solve` above works out the optimal transport solution. The `ot` object contains a transport matrix (here of size $12\times 14$) that quantifies a `link strength` between each point of the first point cloud, to one or more points from the second, as illustrated in the plot below. In this toy example, most choices were arbitrary, and are reflected in the crude `solve` API. We provide far more flexibility to define custom cost functions, objectives, and solvers, as detailed in the [full documentation](https://ott-jax.readthedocs.io/en/latest/).
+The call to `solve` above works out the optimal transport solution. The `ot` object contains a transport matrix
+(here of size $12\times 14$) that quantifies a `link strength` between each point of the first point cloud, to one or
+more points from the second, as illustrated in the plot below. In this toy example, most choices were arbitrary, and
+are reflected in the crude `solve` API. We provide far more flexibility to define custom cost functions, objectives,
+and solvers, as detailed in the [full documentation](https://ott-jax.readthedocs.io/en/latest/).
 
 ![obtained coupling](https://raw.githubusercontent.com/ott-jax/ott/main/images/couplings.png)
-## Citation
 
+## Citation
 If you have found this work useful, please consider citing this reference:
 
 ```
 @article{cuturi2022optimal,
   title={Optimal Transport Tools (OTT): A JAX Toolbox for all things Wasserstein},
-  author={Cuturi, Marco and Meng-Papaxanthos, Laetitia and Tian, Yingtao and Bunne, Charlotte and Davis, Geoff and Teboul, Olivier},
+  author={Cuturi, Marco and Meng-Papaxanthos, Laetitia and Tian, Yingtao and Bunne, Charlotte and
+          Davis, Geoff and Teboul, Olivier},
   journal={arXiv preprint arXiv:2201.12324},
   year={2022}
 }

diff --git a/docs/Makefile b/docs/Makefile
@@ -22,3 +22,4 @@ help:
 clean:
 	@rm -rf $(BUILDDIR)/
 	@rm -rf $(SOURCEDIR)/_autosummary
+	@rm -rf $(SOURCEDIR)/**/_autosummary
diff --git a/docs/conf.py b/docs/conf.py
@@ -73,6 +73,10 @@
 source_suffix = ['.rst']
 
 autosummary_generate = True
+autosummary_filename_map = {
+    "ott.solvers.linear.sinkhorn.sinkhorn":
+        "ott.solvers.linear.sinkhorn.sinkhorn-function"
+}
 
 autodoc_typehints = 'description'
 

diff --git a/docs/core.rst b/docs/core.rst
diff --git a/docs/geometry.rst b/docs/geometry.rst
@@ -58,3 +58,10 @@ Cost Functions
     costs.Cosine
     costs.Bures
     costs.UnbalancedBures
+
+Utilities
+---------
+.. autosummary::
+    :toctree: _autosummary
+
+    segment.segment_point_cloud