pyotc 0.2.2__py3-none-any.whl → 0.3.0__py3-none-any.whl

pyotc/__init__.py

@@ -2,4 +2,15 @@
 
 __author__ = """Jay Hineman"""
 __email__ = "jay.hineman@gmail.com"
-__version__ = "0.1.0"
+__version__ = "0.3.0"
+
+# Public API re-exports
+from .otc import entropic_otc, exact_otc
+
+__all__ = [
+    "exact_otc",
+    "entropic_otc",
+    "__author__",
+    "__email__",
+    "__version__",
+]

pyotc/otc.py

@@ -1,5 +1,53 @@
 """Main entry point for otc funcitonality"""
 
+from .otc_backend.policy_iteration.dense.exact import exact_otc as _exact_otc_dense
+from .otc_backend.policy_iteration.sparse.exact import exact_otc as _exact_otc_sparse
+from .otc_backend.policy_iteration.dense.entropic import entropic_otc as _entropic_otc
 
-def exact_OTC():
-    raise NotImplementedError
+
+def exact_otc(
+    P1,
+    P2,
+    c,
+    *,
+    stat_dist="best",
+    backend="dense",
+    max_iter=None,
+):
+    if backend == "dense":
+        return _exact_otc_dense(P1, P2, c, stat_dist=stat_dist)
+    elif backend == "sparse":
+        if max_iter is None:
+            return _exact_otc_sparse(P1, P2, c, stat_dist=stat_dist)
+        return _exact_otc_sparse(P1, P2, c, stat_dist=stat_dist, max_iter=max_iter)
+    else:
+        raise ValueError("Unknown backend: {backend}. Choose from {'dense', 'sparse'}.")
+
+
+def entropic_otc(
+    Px,
+    Py,
+    c,
+    *,
+    L=100,
+    T=100,
+    xi=0.1,
+    method="logsinkhorn",
+    sink_iter=100,
+    reg_num=None,
+    get_sd=False,
+    silent=True,
+):
+    return _entropic_otc(
+        Px,
+        Py,
+        c,
+        L=L,
+        T=T,
+        xi=xi,
+        method=method,
+        sink_iter=sink_iter,
+        reg_num=reg_num,
+        get_sd=get_sd,
+        silent=silent,
+    )

pyotc-0.3.0.dist-info/METADATA

@@ -0,0 +1,90 @@
+Metadata-Version: 2.4
+Name: pyotc
+Version: 0.3.0
+Summary: Perform optimal transition coupling (OTC) in python.
+Author: Jay Hineman, Yuning Pan, Bongsoo Yi
+License: MIT license
+License-File: AUTHORS.rst
+License-File: LICENSE
+Requires-Python: >=3.10
+Requires-Dist: matplotlib>=3.10.0
+Requires-Dist: networkx>=3.4.2
+Requires-Dist: numpy>=2.2.1
+Requires-Dist: pot>=0.9.5
+Description-Content-Type: text/markdown
+
+# pyotc
+[![codecov](https://codecov.io/github/pyotc/pyotc/graph/badge.svg?token=52QPNW0AP7)](https://codecov.io/github/pyotc/pyotc)
+
+A python implementations of optimal transport coupling algorithms.
+
+## Documentation
+Find sphinx documentation [here](https://pyotc.github.io/pyotc/).
+
+## Installation
+
+We expect `pyotc` to be pip-installable across all platforms. 
+
+
+### 1. Install from pypi (Recommended)
+
+```bash
+pip install pyotc
+```
+- Note: `pyotc` requires Python 3.10 or above.
+
+### 2. Install from github
+
+```bash
+pip install https://github.com/pyotc/pyotc.git
+```
+
+### 3. Install for Development
+We test in venvs provided by [uv](https://docs.astral.sh/uv/) via [nox](https://nox.thea.codes/en/stable/usage.html#changing-the-sessions-default-backend). It's helpful, but not strictly necessary to do the same.
+
+```bash
+git clone https://github.com/pyotc/pyotc.git
+cd pyotc
+pip install -e .
+```
+
+### `uv` workflow
+Install the [uv tool](https://docs.astral.sh/uv/getting-started/installation/). Then
+
+```bash
+git clone https://github.com/pyotc/pyotc.git
+cd pyotc
+uv sync
+uv pip install -e .
+```
+
+To verify your installation, run
+```bash
+uv run pytest
+```
+
+## Run Tests
+With a `uv` setup one can simply
+```bash
+uv run pytest
+```
+Otherwise, in `pip` installed context with deps met, `pytest` should behave as expected.
+
+## Contributing
+Guidelines for contribution to `pyotc` are provided in [CONTRIBUTING.md](./CONTRIBUTING.md).
+
+## Changelog
+A summary of changes and guide to versioning are recoreded in [CHANGELOG.md](./CHANGELOG.md).
+
+## Citing this Repository
+If you wish to cite our work, please use the following BibTeX code:
+```bibtex
+@article{yi2025alignment,
+  title={Alignment and comparison of directed networks via transition couplings of random walks},
+  author={Yi, Bongsoo and O'Connor, Kevin and McGoff, Kevin and Nobel, Andrew B},
+  journal={Journal of the Royal Statistical Society Series B: Statistical Methodology},
+  pages={qkae085},
+  year={2024},
+  doi = {10.1093/jrsssb/qkae085}
+}
+```

{pyotc-0.2.2.dist-info → pyotc-0.3.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
-pyotc/__init__.py,sha256=Od-nJxr4TP_mgmXMxpwaItNDISKzR0V6X8QakVNTmr8,125
-pyotc/otc.py,sha256=_we15B7Gw-IgxVlXnXbWS_8d0LGwHbaZiSrHwBSGbM0,94
+pyotc/__init__.py,sha256=xeEd5NMPTp_zvS0KFWDUJJxDQWy89IhMybeSfeExAl8,297
+pyotc/otc.py,sha256=ViNIL9bqdYUQj_5HDkVyfVVVIyNfbvNql8_wpxhmc_M,1233
 pyotc/examples/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyotc/examples/edge_awareness.py,sha256=k4pAs_UkDC2ZzgvkQZD9aY-gemjd8I9UAzWA1x8Z_3E,2513
 pyotc/examples/lollipops.py,sha256=fmvPkdSL9T5ZjQU8SpFnIox5DDuiVVwikjt7w3ukxLc,1589
@@ -27,8 +27,8 @@ pyotc/otc_backend/policy_iteration/sparse/__init__.py,sha256=47DEQpj8HBSa-_TImW-
 pyotc/otc_backend/policy_iteration/sparse/exact.py,sha256=2VskHrp1nDGPV2yEsD5MBagrZHkUDCdChMZ28WOb0uk,4400
 pyotc/otc_backend/policy_iteration/sparse/exact_tce.py,sha256=oSymhuok3logzt0wYSYJeMkTls0zzC0kRiQw2nHXk7c,3626
 pyotc/otc_backend/policy_iteration/sparse/exact_tci.py,sha256=mW90o-2ZVd9fjgKFDlJhR223G5JYxBSzsHBr7NdK6eg,3446
-pyotc-0.2.2.dist-info/METADATA,sha256=yTtg2-uCXeJCSpSeh-NUWJ_i2NnxLzLjFuLcO46mexY,1122
-pyotc-0.2.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-pyotc-0.2.2.dist-info/licenses/AUTHORS.rst,sha256=FtGxBvQjLU6Vdej_-zcsdWxTwnInCsjqejFRmaeC7TU,136
-pyotc-0.2.2.dist-info/licenses/LICENSE,sha256=DfWCeVpuOnLG1KJZfBO24ry8u90eeQi7mTdjoo5pt8M,1070
-pyotc-0.2.2.dist-info/RECORD,,
+pyotc-0.3.0.dist-info/METADATA,sha256=tmOqDSpLPDu6nJ2AoxNmCtyKeq3tFvDjyBOHaQVHwjY,2419
+pyotc-0.3.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+pyotc-0.3.0.dist-info/licenses/AUTHORS.rst,sha256=FtGxBvQjLU6Vdej_-zcsdWxTwnInCsjqejFRmaeC7TU,136
+pyotc-0.3.0.dist-info/licenses/LICENSE,sha256=DfWCeVpuOnLG1KJZfBO24ry8u90eeQi7mTdjoo5pt8M,1070
+pyotc-0.3.0.dist-info/RECORD,,

{pyotc-0.2.2.dist-info → pyotc-0.3.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pyotc-0.2.2.dist-info/METADATA

@@ -1,38 +0,0 @@
-Metadata-Version: 2.4
-Name: pyotc
-Version: 0.2.2
-Summary: Perform optimal transition coupling (OTC) in python.
-Author: Jay Hineman, Yuning Pan, Bongsoo Yi
-License: MIT license
-License-File: AUTHORS.rst
-License-File: LICENSE
-Requires-Python: >=3.10
-Requires-Dist: matplotlib>=3.10.0
-Requires-Dist: networkx>=3.4.2
-Requires-Dist: numpy>=2.2.1
-Requires-Dist: pot>=0.9.5
-Description-Content-Type: text/markdown
-
-# pyotc
-[![codecov](https://codecov.io/github/pyotc/pyotc/graph/badge.svg?token=52QPNW0AP7)](https://codecov.io/github/pyotc/pyotc)
-
-A python implementations of optimal transport coupling algorithms.
-
-## Documentation
-Find sphinx documentation [here](https://pyotc.github.io/pyotc/).
-
-## Install
-See [install instructions](INSTALL.md)
-
-## Run Tests
-With a `uv` setup one can simply
-```bash
-uv run pytest
-```
-Otherwise, in `pip` installed context with deps met, `pytest` should behave as expected.
-
-## Contributing
-Guidelines for contribution to `pyotc` are provided in [CONTRIBUTING.md](./CONTRIBUTING.md).
-
-## Changelog
-A summary of changes and guide to versioning are recoreded in [CHANGELOG.md](./CHANGELOG.md).