StochasticForceInference 2.0.0__tar.gz → 2.0.0.post1__tar.gz

{stochasticforceinference-2.0.0 → stochasticforceinference-2.0.0.post1}/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: StochasticForceInference
-Version: 2.0.0
+Version: 2.0.0.post1
 Summary: Stochastic Force Inference for Langevin SDEs
 Author-email: Pierre Ronceray <pierre.ronceray@univ-amu.fr>
 License: MIT
 Project-URL: Homepage, https://github.com/ronceray/StochasticForceInference
-Project-URL: Documentation, https://sfi.readthedocs.io
+Project-URL: Documentation, https://stochasticforceinference.readthedocs.io
 Project-URL: Repository, https://github.com/ronceray/StochasticForceInference
 Project-URL: Issues, https://github.com/ronceray/StochasticForceInference/issues
 Project-URL: Changelog, https://github.com/ronceray/StochasticForceInference/blob/main/CHANGELOG.md
@@ -54,6 +54,10 @@ Dynamic: license-file
 
 # Stochastic Force Inference (SFI)
 
+[![Documentation](https://readthedocs.org/projects/stochasticforceinference/badge/?version=latest)](https://stochasticforceinference.readthedocs.io/en/latest/)
+[![PyPI](https://img.shields.io/pypi/v/StochasticForceInference.svg)](https://pypi.org/project/StochasticForceInference/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/ronceray/StochasticForceInference/blob/main/LICENSE)
+
 **Infer force and diffusion fields from stochastic trajectory data.**
 
 SFI is a JAX-based Python package for learning the drift (force) and diffusion
@@ -165,14 +169,14 @@ inf.compare_to_exact(model_exact=proc)
 ## Documentation
 
 Full documentation is available at
-[sfi.readthedocs.io](https://sfi.readthedocs.io), including:
+[stochasticforceinference.readthedocs.io](https://stochasticforceinference.readthedocs.io), including:
 
-- **[Tutorial](https://sfi.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
-- **[Examples gallery](https://sfi.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
-- **[Model building](https://sfi.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
-- **[Trajectory handling](https://sfi.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
-- **[Running inference](https://sfi.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
-- **[API reference](https://sfi.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
+- **[Tutorial](https://stochasticforceinference.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
+- **[Examples gallery](https://stochasticforceinference.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
+- **[Model building](https://stochasticforceinference.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
+- **[Trajectory handling](https://stochasticforceinference.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
+- **[Running inference](https://stochasticforceinference.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
+- **[API reference](https://stochasticforceinference.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
 
 ## Package structure
 
@@ -192,11 +196,11 @@ guidance.
 
 ## Citation
 
-If you use SFI in your research, please cite:
-
-> Frishman, A. & Ronceray, P., *Learning force fields from stochastic
-> trajectories*, Physical Review X (2020).
-> [DOI: 10.1103/PhysRevX.10.021009](https://doi.org/10.1103/PhysRevX.10.021009)
+If you use SFI, please cite the software (see [`CITATION.cff`](CITATION.cff))
+together with the method paper(s) relevant to the features you use. See
+**[How to cite](https://stochasticforceinference.readthedocs.io/en/latest/#how-to-cite)** in the
+documentation for the full, feature-specific list (overdamped, underdamped/ULI,
+trapeze, and PASTIS references).
 
 ## License
 

{stochasticforceinference-2.0.0 → stochasticforceinference-2.0.0.post1}/README.md

@@ -1,5 +1,9 @@
 # Stochastic Force Inference (SFI)
 
+[![Documentation](https://readthedocs.org/projects/stochasticforceinference/badge/?version=latest)](https://stochasticforceinference.readthedocs.io/en/latest/)
+[![PyPI](https://img.shields.io/pypi/v/StochasticForceInference.svg)](https://pypi.org/project/StochasticForceInference/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/ronceray/StochasticForceInference/blob/main/LICENSE)
+
 **Infer force and diffusion fields from stochastic trajectory data.**
 
 SFI is a JAX-based Python package for learning the drift (force) and diffusion
@@ -111,14 +115,14 @@ inf.compare_to_exact(model_exact=proc)
 ## Documentation
 
 Full documentation is available at
-[sfi.readthedocs.io](https://sfi.readthedocs.io), including:
+[stochasticforceinference.readthedocs.io](https://stochasticforceinference.readthedocs.io), including:
 
-- **[Tutorial](https://sfi.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
-- **[Examples gallery](https://sfi.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
-- **[Model building](https://sfi.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
-- **[Trajectory handling](https://sfi.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
-- **[Running inference](https://sfi.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
-- **[API reference](https://sfi.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
+- **[Tutorial](https://stochasticforceinference.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
+- **[Examples gallery](https://stochasticforceinference.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
+- **[Model building](https://stochasticforceinference.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
+- **[Trajectory handling](https://stochasticforceinference.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
+- **[Running inference](https://stochasticforceinference.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
+- **[API reference](https://stochasticforceinference.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
 
 ## Package structure
 
@@ -138,11 +142,11 @@ guidance.
 
 ## Citation
 
-If you use SFI in your research, please cite:
-
-> Frishman, A. & Ronceray, P., *Learning force fields from stochastic
-> trajectories*, Physical Review X (2020).
-> [DOI: 10.1103/PhysRevX.10.021009](https://doi.org/10.1103/PhysRevX.10.021009)
+If you use SFI, please cite the software (see [`CITATION.cff`](CITATION.cff))
+together with the method paper(s) relevant to the features you use. See
+**[How to cite](https://stochasticforceinference.readthedocs.io/en/latest/#how-to-cite)** in the
+documentation for the full, feature-specific list (overdamped, underdamped/ULI,
+trapeze, and PASTIS references).
 
 ## License
 

{stochasticforceinference-2.0.0 → stochasticforceinference-2.0.0.post1}/StochasticForceInference.egg-info/PKG-INFO

@@ -1,11 +1,11 @@
 Metadata-Version: 2.4
 Name: StochasticForceInference
-Version: 2.0.0
+Version: 2.0.0.post1
 Summary: Stochastic Force Inference for Langevin SDEs
 Author-email: Pierre Ronceray <pierre.ronceray@univ-amu.fr>
 License: MIT
 Project-URL: Homepage, https://github.com/ronceray/StochasticForceInference
-Project-URL: Documentation, https://sfi.readthedocs.io
+Project-URL: Documentation, https://stochasticforceinference.readthedocs.io
 Project-URL: Repository, https://github.com/ronceray/StochasticForceInference
 Project-URL: Issues, https://github.com/ronceray/StochasticForceInference/issues
 Project-URL: Changelog, https://github.com/ronceray/StochasticForceInference/blob/main/CHANGELOG.md
@@ -54,6 +54,10 @@ Dynamic: license-file
 
 # Stochastic Force Inference (SFI)
 
+[![Documentation](https://readthedocs.org/projects/stochasticforceinference/badge/?version=latest)](https://stochasticforceinference.readthedocs.io/en/latest/)
+[![PyPI](https://img.shields.io/pypi/v/StochasticForceInference.svg)](https://pypi.org/project/StochasticForceInference/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/ronceray/StochasticForceInference/blob/main/LICENSE)
+
 **Infer force and diffusion fields from stochastic trajectory data.**
 
 SFI is a JAX-based Python package for learning the drift (force) and diffusion
@@ -165,14 +169,14 @@ inf.compare_to_exact(model_exact=proc)
 ## Documentation
 
 Full documentation is available at
-[sfi.readthedocs.io](https://sfi.readthedocs.io), including:
+[stochasticforceinference.readthedocs.io](https://stochasticforceinference.readthedocs.io), including:
 
-- **[Tutorial](https://sfi.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
-- **[Examples gallery](https://sfi.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
-- **[Model building](https://sfi.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
-- **[Trajectory handling](https://sfi.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
-- **[Running inference](https://sfi.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
-- **[API reference](https://sfi.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
+- **[Tutorial](https://stochasticforceinference.readthedocs.io/en/latest/gallery/ou_demo.html)** — end-to-end walkthrough
+- **[Examples gallery](https://stochasticforceinference.readthedocs.io/en/latest/gallery/index.html)** — worked examples covering sparsity, multi-particle, and SPDE inference
+- **[Model building](https://stochasticforceinference.readthedocs.io/en/latest/statefunc/user_guide.html)** — composable state functions
+- **[Trajectory handling](https://stochasticforceinference.readthedocs.io/en/latest/trajectory/user_guide.html)** — data ingestion, masking, degradation
+- **[Running inference](https://stochasticforceinference.readthedocs.io/en/latest/inference/user_guide.html)** — estimator choice, overdamped/underdamped engines
+- **[API reference](https://stochasticforceinference.readthedocs.io/en/latest/api_frontend.html)** — full autodoc
 
 ## Package structure
 
@@ -192,11 +196,11 @@ guidance.
 
 ## Citation
 
-If you use SFI in your research, please cite:
-
-> Frishman, A. & Ronceray, P., *Learning force fields from stochastic
-> trajectories*, Physical Review X (2020).
-> [DOI: 10.1103/PhysRevX.10.021009](https://doi.org/10.1103/PhysRevX.10.021009)
+If you use SFI, please cite the software (see [`CITATION.cff`](CITATION.cff))
+together with the method paper(s) relevant to the features you use. See
+**[How to cite](https://stochasticforceinference.readthedocs.io/en/latest/#how-to-cite)** in the
+documentation for the full, feature-specific list (overdamped, underdamped/ULI,
+trapeze, and PASTIS references).
 
 ## License
 

{stochasticforceinference-2.0.0 → stochasticforceinference-2.0.0.post1}/examples/gallery/multiplicative_diffusion_demo.py

@@ -15,7 +15,7 @@ synthetic · overdamped · multiplicative-noise · diffusion-field · 1D
 """
 
 # sphinx_gallery_tags = ["synthetic", "overdamped", "multiplicative-noise", "diffusion-field", "1D"]
-# sphinx_gallery_thumbnail_number = 5
+# sphinx_gallery_thumbnail_number = 4
 
 # sphinx_gallery_start_ignore
 from __future__ import annotations

{stochasticforceinference-2.0.0 → stochasticforceinference-2.0.0.post1}/examples/gallery/velocity_dependent_noise_demo.py

@@ -16,7 +16,7 @@ synthetic · underdamped · multiplicative-noise · diffusion-field · 1D
 """
 
 # sphinx_gallery_tags = ["synthetic", "underdamped", "multiplicative-noise", "diffusion-field", "1D"]
-# sphinx_gallery_thumbnail_number = 4
+# sphinx_gallery_thumbnail_number = 3
 
 # sphinx_gallery_start_ignore
 from __future__ import annotations

{stochasticforceinference-2.0.0 → stochasticforceinference-2.0.0.post1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "StochasticForceInference"
-version = "2.0.0"
+version = "2.0.0.post1"
 description = "Stochastic Force Inference for Langevin SDEs"
 authors = [{name = "Pierre Ronceray", email = "pierre.ronceray@univ-amu.fr"}]
 readme = "README.md"
@@ -47,7 +47,7 @@ io = ["pyarrow>=14", "h5py>=3.9", "pandas>=2.0", "PyYAML>=6.0"]
 
 [project.urls]
 Homepage = "https://github.com/ronceray/StochasticForceInference"
-Documentation = "https://sfi.readthedocs.io"
+Documentation = "https://stochasticforceinference.readthedocs.io"
 Repository = "https://github.com/ronceray/StochasticForceInference"
 Issues = "https://github.com/ronceray/StochasticForceInference/issues"
 Changelog = "https://github.com/ronceray/StochasticForceInference/blob/main/CHANGELOG.md"