diff --git a/.gitignore b/.gitignore index 089b0c31..2c9dd38b 100644 --- a/.gitignore +++ b/.gitignore @@ -63,8 +63,8 @@ instance/ .scrapy # Sphinx documentation -docs/_build/ -docs/autosummary/ +docs/build/ +docs/source/reference/ # PyBuilder target/ diff --git a/README.md b/README.md index fe9ae7fd..e58b5ba2 100644 --- a/README.md +++ b/README.md @@ -14,8 +14,8 @@ CodeEntropy CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.

- CodeEntropy logo - CodeEntropy logo + CodeEntropy logo + CodeEntropy logo

See [CodeEntropy’s documentation](https://codeentropy.readthedocs.io/en/latest/) for more information. diff --git a/docs/Makefile b/docs/Makefile index 1f4fb783..811d08b8 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -5,8 +5,8 @@ SPHINXOPTS = SPHINXBUILD = sphinx-build SPHINXPROJ = CodeEntropy -SOURCEDIR = . -BUILDDIR = _build +SOURCEDIR = source +BUILDDIR = build # Put it first so that "make" without argument is like "make help". help: diff --git a/docs/README.md b/docs/README.md deleted file mode 100644 index 79687e62..00000000 --- a/docs/README.md +++ /dev/null @@ -1,23 +0,0 @@ -# Compiling CodeEntropy's Documentation - -The docs for this project are built with [Sphinx](http://www.sphinx-doc.org/en/master/). -To compile the docs, first ensure that Sphinx and the ReadTheDocs theme are installed. - - -```bash -pip install sphinx sphinx_rtd_theme -``` - - -Once installed, you can use the `Makefile` in this directory to compile static HTML pages by -```bash -make html -``` - -The compiled docs will be in the `_build` directory and can be viewed by opening `index.html` (which may itself -be inside a directory called `html/` depending on what version of Sphinx is installed). - - -A configuration file for [Read The Docs](https://readthedocs.org/) (readthedocs.yaml) is included in the top level of the repository. To use Read the Docs to host your documentation, go to https://readthedocs.org/ and connect this repository. You may need to change your default branch to `main` under Advanced Settings for the project. - -If you would like to use Read The Docs with `autodoc` (included automatically) and your package has dependencies, you will need to include those dependencies in your documentation yaml file (`docs/requirements.yaml`). diff --git a/docs/_static/README.md b/docs/_static/README.md deleted file mode 100644 index 83281977..00000000 --- a/docs/_static/README.md +++ /dev/null @@ -1,16 +0,0 @@ -# Static Doc Directory - -Add any paths that contain custom static files (such as style sheets) here, -relative to the `conf.py` file's directory. -They are copied after the builtin static files, -so a file named "default.css" will overwrite the builtin "default.css". - -The path to this folder is set in the Sphinx `conf.py` file in the line: -```python -templates_path = ["_static"] -``` - -## Examples of file to add to this directory -* Custom Cascading Style Sheets -* Custom JavaScript code -* Static logo images diff --git a/docs/_templates/README.md b/docs/_templates/README.md deleted file mode 100644 index 2c20198e..00000000 --- a/docs/_templates/README.md +++ /dev/null @@ -1,14 +0,0 @@ -# Templates Doc Directory - -Add any paths that contain templates here, relative to -the `conf.py` file's directory. -They are copied after the builtin template files, -so a file named "page.html" will overwrite the builtin "page.html". - -The path to this folder is set in the Sphinx `conf.py` file in the line: -```python -html_static_path = ["_templates"] -``` - -## Examples of file to add to this directory -* HTML extensions of stock pages like `page.html` or `layout.html` diff --git a/docs/api/CodeEntropy.cli.rst b/docs/api/CodeEntropy.cli.rst deleted file mode 100644 index 8166c64f..00000000 --- a/docs/api/CodeEntropy.cli.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.cli module -====================== - -.. automodule:: CodeEntropy.cli - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.config.argparse.rst b/docs/api/CodeEntropy.config.argparse.rst deleted file mode 100644 index 5531f0f4..00000000 --- a/docs/api/CodeEntropy.config.argparse.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.config.argparse module -================================== - -.. automodule:: CodeEntropy.config.argparse - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.config.rst b/docs/api/CodeEntropy.config.rst deleted file mode 100644 index d7945e83..00000000 --- a/docs/api/CodeEntropy.config.rst +++ /dev/null @@ -1,19 +0,0 @@ -CodeEntropy.config package -========================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.config.argparse - CodeEntropy.config.runtime - -Module contents ---------------- - -.. automodule:: CodeEntropy.config - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.config.runtime.rst b/docs/api/CodeEntropy.config.runtime.rst deleted file mode 100644 index c942c9a0..00000000 --- a/docs/api/CodeEntropy.config.runtime.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.config.runtime module -================================= - -.. automodule:: CodeEntropy.config.runtime - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.core.dask_clusters.rst b/docs/api/CodeEntropy.core.dask_clusters.rst deleted file mode 100644 index 6430e64c..00000000 --- a/docs/api/CodeEntropy.core.dask_clusters.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.core.dask\_clusters module -====================================== - -.. automodule:: CodeEntropy.core.dask_clusters - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.core.logging.rst b/docs/api/CodeEntropy.core.logging.rst deleted file mode 100644 index 2b61ad34..00000000 --- a/docs/api/CodeEntropy.core.logging.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.core.logging module -=============================== - -.. automodule:: CodeEntropy.core.logging - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.core.rst b/docs/api/CodeEntropy.core.rst deleted file mode 100644 index 86ebc99c..00000000 --- a/docs/api/CodeEntropy.core.rst +++ /dev/null @@ -1,19 +0,0 @@ -CodeEntropy.core package -======================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.core.dask_clusters - CodeEntropy.core.logging - -Module contents ---------------- - -.. automodule:: CodeEntropy.core - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.configurational.rst b/docs/api/CodeEntropy.entropy.configurational.rst deleted file mode 100644 index 3ab77362..00000000 --- a/docs/api/CodeEntropy.entropy.configurational.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.configurational module -========================================== - -.. automodule:: CodeEntropy.entropy.configurational - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.graph.rst b/docs/api/CodeEntropy.entropy.graph.rst deleted file mode 100644 index d6b23043..00000000 --- a/docs/api/CodeEntropy.entropy.graph.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.graph module -================================ - -.. automodule:: CodeEntropy.entropy.graph - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.nodes.aggregate.rst b/docs/api/CodeEntropy.entropy.nodes.aggregate.rst deleted file mode 100644 index b0bfe716..00000000 --- a/docs/api/CodeEntropy.entropy.nodes.aggregate.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.nodes.aggregate module -========================================== - -.. automodule:: CodeEntropy.entropy.nodes.aggregate - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.nodes.configurational.rst b/docs/api/CodeEntropy.entropy.nodes.configurational.rst deleted file mode 100644 index 93f66f70..00000000 --- a/docs/api/CodeEntropy.entropy.nodes.configurational.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.nodes.configurational module -================================================ - -.. automodule:: CodeEntropy.entropy.nodes.configurational - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.nodes.orientational.rst b/docs/api/CodeEntropy.entropy.nodes.orientational.rst deleted file mode 100644 index 21763359..00000000 --- a/docs/api/CodeEntropy.entropy.nodes.orientational.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.nodes.orientational module -============================================== - -.. automodule:: CodeEntropy.entropy.nodes.orientational - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.nodes.rst b/docs/api/CodeEntropy.entropy.nodes.rst deleted file mode 100644 index 4ff7516c..00000000 --- a/docs/api/CodeEntropy.entropy.nodes.rst +++ /dev/null @@ -1,21 +0,0 @@ -CodeEntropy.entropy.nodes package -================================= - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.entropy.nodes.aggregate - CodeEntropy.entropy.nodes.configurational - CodeEntropy.entropy.nodes.orientational - CodeEntropy.entropy.nodes.vibrational - -Module contents ---------------- - -.. automodule:: CodeEntropy.entropy.nodes - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.nodes.vibrational.rst b/docs/api/CodeEntropy.entropy.nodes.vibrational.rst deleted file mode 100644 index bf2183c4..00000000 --- a/docs/api/CodeEntropy.entropy.nodes.vibrational.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.nodes.vibrational module -============================================ - -.. automodule:: CodeEntropy.entropy.nodes.vibrational - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.orientational.rst b/docs/api/CodeEntropy.entropy.orientational.rst deleted file mode 100644 index 82214e8b..00000000 --- a/docs/api/CodeEntropy.entropy.orientational.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.orientational module -======================================== - -.. automodule:: CodeEntropy.entropy.orientational - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.rst b/docs/api/CodeEntropy.entropy.rst deleted file mode 100644 index f4322465..00000000 --- a/docs/api/CodeEntropy.entropy.rst +++ /dev/null @@ -1,31 +0,0 @@ -CodeEntropy.entropy package -=========================== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.entropy.nodes - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.entropy.configurational - CodeEntropy.entropy.graph - CodeEntropy.entropy.orientational - CodeEntropy.entropy.vibrational - CodeEntropy.entropy.water - CodeEntropy.entropy.workflow - -Module contents ---------------- - -.. automodule:: CodeEntropy.entropy - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.vibrational.rst b/docs/api/CodeEntropy.entropy.vibrational.rst deleted file mode 100644 index cd7dc90e..00000000 --- a/docs/api/CodeEntropy.entropy.vibrational.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.vibrational module -====================================== - -.. automodule:: CodeEntropy.entropy.vibrational - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.water.rst b/docs/api/CodeEntropy.entropy.water.rst deleted file mode 100644 index 7e4e807b..00000000 --- a/docs/api/CodeEntropy.entropy.water.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.water module -================================ - -.. automodule:: CodeEntropy.entropy.water - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.entropy.workflow.rst b/docs/api/CodeEntropy.entropy.workflow.rst deleted file mode 100644 index 0913a3e8..00000000 --- a/docs/api/CodeEntropy.entropy.workflow.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.entropy.workflow module -=================================== - -.. automodule:: CodeEntropy.entropy.workflow - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.axes.rst b/docs/api/CodeEntropy.levels.axes.rst deleted file mode 100644 index 82d2146e..00000000 --- a/docs/api/CodeEntropy.levels.axes.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.axes module -============================== - -.. automodule:: CodeEntropy.levels.axes - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.angle_observations.rst b/docs/api/CodeEntropy.levels.dihedrals.angle_observations.rst deleted file mode 100644 index 16bf9470..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.angle_observations.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.dihedrals.angle\_observations module -======================================================= - -.. automodule:: CodeEntropy.levels.dihedrals.angle_observations - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.conformational_state_builder.rst b/docs/api/CodeEntropy.levels.dihedrals.conformational_state_builder.rst deleted file mode 100644 index 449f21c8..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.conformational_state_builder.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.dihedrals.conformational\_state\_builder module -================================================================== - -.. automodule:: CodeEntropy.levels.dihedrals.conformational_state_builder - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.kernels.rst b/docs/api/CodeEntropy.levels.dihedrals.kernels.rst deleted file mode 100644 index 3e51f72a..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.kernels.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.dihedrals.kernels module -=========================================== - -.. automodule:: CodeEntropy.levels.dihedrals.kernels - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.peak_detection.rst b/docs/api/CodeEntropy.levels.dihedrals.peak_detection.rst deleted file mode 100644 index 11c89969..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.peak_detection.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.dihedrals.peak\_detection module -=================================================== - -.. automodule:: CodeEntropy.levels.dihedrals.peak_detection - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.rst b/docs/api/CodeEntropy.levels.dihedrals.rst deleted file mode 100644 index 30aa5a67..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.rst +++ /dev/null @@ -1,23 +0,0 @@ -CodeEntropy.levels.dihedrals package -==================================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.levels.dihedrals.angle_observations - CodeEntropy.levels.dihedrals.conformational_state_builder - CodeEntropy.levels.dihedrals.kernels - CodeEntropy.levels.dihedrals.peak_detection - CodeEntropy.levels.dihedrals.state_assignment - CodeEntropy.levels.dihedrals.topology - -Module contents ---------------- - -.. automodule:: CodeEntropy.levels.dihedrals - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.state_assignment.rst b/docs/api/CodeEntropy.levels.dihedrals.state_assignment.rst deleted file mode 100644 index aeed41ce..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.state_assignment.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.dihedrals.state\_assignment module -===================================================== - -.. automodule:: CodeEntropy.levels.dihedrals.state_assignment - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.dihedrals.topology.rst b/docs/api/CodeEntropy.levels.dihedrals.topology.rst deleted file mode 100644 index 30074514..00000000 --- a/docs/api/CodeEntropy.levels.dihedrals.topology.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.dihedrals.topology module -============================================ - -.. automodule:: CodeEntropy.levels.dihedrals.topology - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.execution.chunks.rst b/docs/api/CodeEntropy.levels.execution.chunks.rst deleted file mode 100644 index 6f7924f8..00000000 --- a/docs/api/CodeEntropy.levels.execution.chunks.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.execution.chunks module -========================================== - -.. automodule:: CodeEntropy.levels.execution.chunks - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.execution.policy.rst b/docs/api/CodeEntropy.levels.execution.policy.rst deleted file mode 100644 index 3dd1f5aa..00000000 --- a/docs/api/CodeEntropy.levels.execution.policy.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.execution.policy module -========================================== - -.. automodule:: CodeEntropy.levels.execution.policy - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.execution.reducers.rst b/docs/api/CodeEntropy.levels.execution.reducers.rst deleted file mode 100644 index 0beef239..00000000 --- a/docs/api/CodeEntropy.levels.execution.reducers.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.execution.reducers module -============================================ - -.. automodule:: CodeEntropy.levels.execution.reducers - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.execution.rst b/docs/api/CodeEntropy.levels.execution.rst deleted file mode 100644 index 2932017a..00000000 --- a/docs/api/CodeEntropy.levels.execution.rst +++ /dev/null @@ -1,22 +0,0 @@ -CodeEntropy.levels.execution package -==================================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.levels.execution.chunks - CodeEntropy.levels.execution.policy - CodeEntropy.levels.execution.reducers - CodeEntropy.levels.execution.scheduler - CodeEntropy.levels.execution.tasks - -Module contents ---------------- - -.. automodule:: CodeEntropy.levels.execution - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.execution.scheduler.rst b/docs/api/CodeEntropy.levels.execution.scheduler.rst deleted file mode 100644 index b8a95196..00000000 --- a/docs/api/CodeEntropy.levels.execution.scheduler.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.execution.scheduler module -============================================= - -.. automodule:: CodeEntropy.levels.execution.scheduler - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.execution.tasks.rst b/docs/api/CodeEntropy.levels.execution.tasks.rst deleted file mode 100644 index 9f2bda92..00000000 --- a/docs/api/CodeEntropy.levels.execution.tasks.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.execution.tasks module -========================================= - -.. automodule:: CodeEntropy.levels.execution.tasks - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.forces.rst b/docs/api/CodeEntropy.levels.forces.rst deleted file mode 100644 index a9297ffc..00000000 --- a/docs/api/CodeEntropy.levels.forces.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.forces module -================================ - -.. automodule:: CodeEntropy.levels.forces - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.graph.conformation_dag.rst b/docs/api/CodeEntropy.levels.graph.conformation_dag.rst deleted file mode 100644 index ee59e581..00000000 --- a/docs/api/CodeEntropy.levels.graph.conformation_dag.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.graph.conformation\_dag module -================================================= - -.. automodule:: CodeEntropy.levels.graph.conformation_dag - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.graph.frame_dag.rst b/docs/api/CodeEntropy.levels.graph.frame_dag.rst deleted file mode 100644 index 361e5502..00000000 --- a/docs/api/CodeEntropy.levels.graph.frame_dag.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.graph.frame\_dag module -========================================== - -.. automodule:: CodeEntropy.levels.graph.frame_dag - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.graph.level_dag.rst b/docs/api/CodeEntropy.levels.graph.level_dag.rst deleted file mode 100644 index a00e69b5..00000000 --- a/docs/api/CodeEntropy.levels.graph.level_dag.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.graph.level\_dag module -========================================== - -.. automodule:: CodeEntropy.levels.graph.level_dag - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.graph.rst b/docs/api/CodeEntropy.levels.graph.rst deleted file mode 100644 index d4f75dbb..00000000 --- a/docs/api/CodeEntropy.levels.graph.rst +++ /dev/null @@ -1,20 +0,0 @@ -CodeEntropy.levels.graph package -================================ - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.levels.graph.conformation_dag - CodeEntropy.levels.graph.frame_dag - CodeEntropy.levels.graph.level_dag - -Module contents ---------------- - -.. automodule:: CodeEntropy.levels.graph - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.hierarchy.rst b/docs/api/CodeEntropy.levels.hierarchy.rst deleted file mode 100644 index c09c435e..00000000 --- a/docs/api/CodeEntropy.levels.hierarchy.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.hierarchy module -=================================== - -.. automodule:: CodeEntropy.levels.hierarchy - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.linalg.rst b/docs/api/CodeEntropy.levels.linalg.rst deleted file mode 100644 index b0adad18..00000000 --- a/docs/api/CodeEntropy.levels.linalg.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.linalg module -================================ - -.. automodule:: CodeEntropy.levels.linalg - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.neighbors.rst b/docs/api/CodeEntropy.levels.neighbors.rst deleted file mode 100644 index ef34b9f9..00000000 --- a/docs/api/CodeEntropy.levels.neighbors.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.neighbors module -=================================== - -.. automodule:: CodeEntropy.levels.neighbors - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.accumulators.rst b/docs/api/CodeEntropy.levels.nodes.accumulators.rst deleted file mode 100644 index dbe0ef2a..00000000 --- a/docs/api/CodeEntropy.levels.nodes.accumulators.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.nodes.accumulators module -============================================ - -.. automodule:: CodeEntropy.levels.nodes.accumulators - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.axes_topology.rst b/docs/api/CodeEntropy.levels.nodes.axes_topology.rst deleted file mode 100644 index af80bc9e..00000000 --- a/docs/api/CodeEntropy.levels.nodes.axes_topology.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.nodes.axes\_topology module -============================================== - -.. automodule:: CodeEntropy.levels.nodes.axes_topology - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.beads.rst b/docs/api/CodeEntropy.levels.nodes.beads.rst deleted file mode 100644 index 3a4b895f..00000000 --- a/docs/api/CodeEntropy.levels.nodes.beads.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.nodes.beads module -===================================== - -.. automodule:: CodeEntropy.levels.nodes.beads - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.covariance.rst b/docs/api/CodeEntropy.levels.nodes.covariance.rst deleted file mode 100644 index cee6c7da..00000000 --- a/docs/api/CodeEntropy.levels.nodes.covariance.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.nodes.covariance module -========================================== - -.. automodule:: CodeEntropy.levels.nodes.covariance - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.detect_levels.rst b/docs/api/CodeEntropy.levels.nodes.detect_levels.rst deleted file mode 100644 index 058073eb..00000000 --- a/docs/api/CodeEntropy.levels.nodes.detect_levels.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.nodes.detect\_levels module -============================================== - -.. automodule:: CodeEntropy.levels.nodes.detect_levels - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.detect_molecules.rst b/docs/api/CodeEntropy.levels.nodes.detect_molecules.rst deleted file mode 100644 index 14eb778c..00000000 --- a/docs/api/CodeEntropy.levels.nodes.detect_molecules.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.nodes.detect\_molecules module -================================================= - -.. automodule:: CodeEntropy.levels.nodes.detect_molecules - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.nodes.rst b/docs/api/CodeEntropy.levels.nodes.rst deleted file mode 100644 index 048f7fcf..00000000 --- a/docs/api/CodeEntropy.levels.nodes.rst +++ /dev/null @@ -1,23 +0,0 @@ -CodeEntropy.levels.nodes package -================================ - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.levels.nodes.accumulators - CodeEntropy.levels.nodes.axes_topology - CodeEntropy.levels.nodes.beads - CodeEntropy.levels.nodes.covariance - CodeEntropy.levels.nodes.detect_levels - CodeEntropy.levels.nodes.detect_molecules - -Module contents ---------------- - -.. automodule:: CodeEntropy.levels.nodes - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.rst b/docs/api/CodeEntropy.levels.rst deleted file mode 100644 index 9438f461..00000000 --- a/docs/api/CodeEntropy.levels.rst +++ /dev/null @@ -1,34 +0,0 @@ -CodeEntropy.levels package -========================== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.levels.dihedrals - CodeEntropy.levels.execution - CodeEntropy.levels.graph - CodeEntropy.levels.nodes - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.levels.axes - CodeEntropy.levels.forces - CodeEntropy.levels.hierarchy - CodeEntropy.levels.linalg - CodeEntropy.levels.neighbors - CodeEntropy.levels.search - -Module contents ---------------- - -.. automodule:: CodeEntropy.levels - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.levels.search.rst b/docs/api/CodeEntropy.levels.search.rst deleted file mode 100644 index 5084eb75..00000000 --- a/docs/api/CodeEntropy.levels.search.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.levels.search module -================================ - -.. automodule:: CodeEntropy.levels.search - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.molecules.grouping.rst b/docs/api/CodeEntropy.molecules.grouping.rst deleted file mode 100644 index 4fd9ebf5..00000000 --- a/docs/api/CodeEntropy.molecules.grouping.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.molecules.grouping module -===================================== - -.. automodule:: CodeEntropy.molecules.grouping - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.molecules.rst b/docs/api/CodeEntropy.molecules.rst deleted file mode 100644 index 3dd473be..00000000 --- a/docs/api/CodeEntropy.molecules.rst +++ /dev/null @@ -1,18 +0,0 @@ -CodeEntropy.molecules package -============================= - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.molecules.grouping - -Module contents ---------------- - -.. automodule:: CodeEntropy.molecules - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.results.reporter.rst b/docs/api/CodeEntropy.results.reporter.rst deleted file mode 100644 index d8a56fd8..00000000 --- a/docs/api/CodeEntropy.results.reporter.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.results.reporter module -=================================== - -.. automodule:: CodeEntropy.results.reporter - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.results.rst b/docs/api/CodeEntropy.results.rst deleted file mode 100644 index 2606aaf4..00000000 --- a/docs/api/CodeEntropy.results.rst +++ /dev/null @@ -1,18 +0,0 @@ -CodeEntropy.results package -=========================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.results.reporter - -Module contents ---------------- - -.. automodule:: CodeEntropy.results - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.rst b/docs/api/CodeEntropy.rst deleted file mode 100644 index 2fb3c5bb..00000000 --- a/docs/api/CodeEntropy.rst +++ /dev/null @@ -1,32 +0,0 @@ -CodeEntropy package -=================== - -Subpackages ------------ - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.config - CodeEntropy.core - CodeEntropy.entropy - CodeEntropy.levels - CodeEntropy.molecules - CodeEntropy.results - CodeEntropy.trajectory - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.cli - -Module contents ---------------- - -.. automodule:: CodeEntropy - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.trajectory.frames.rst b/docs/api/CodeEntropy.trajectory.frames.rst deleted file mode 100644 index 6cf1a699..00000000 --- a/docs/api/CodeEntropy.trajectory.frames.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.trajectory.frames module -==================================== - -.. automodule:: CodeEntropy.trajectory.frames - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.trajectory.mda.rst b/docs/api/CodeEntropy.trajectory.mda.rst deleted file mode 100644 index b686c2a7..00000000 --- a/docs/api/CodeEntropy.trajectory.mda.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.trajectory.mda module -================================= - -.. automodule:: CodeEntropy.trajectory.mda - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.trajectory.rst b/docs/api/CodeEntropy.trajectory.rst deleted file mode 100644 index 2ac5a826..00000000 --- a/docs/api/CodeEntropy.trajectory.rst +++ /dev/null @@ -1,20 +0,0 @@ -CodeEntropy.trajectory package -============================== - -Submodules ----------- - -.. toctree:: - :maxdepth: 4 - - CodeEntropy.trajectory.frames - CodeEntropy.trajectory.mda - CodeEntropy.trajectory.source - -Module contents ---------------- - -.. automodule:: CodeEntropy.trajectory - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/CodeEntropy.trajectory.source.rst b/docs/api/CodeEntropy.trajectory.source.rst deleted file mode 100644 index 059201ff..00000000 --- a/docs/api/CodeEntropy.trajectory.source.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy.trajectory.source module -==================================== - -.. automodule:: CodeEntropy.trajectory.source - :members: - :show-inheritance: - :undoc-members: diff --git a/docs/api/modules.rst b/docs/api/modules.rst deleted file mode 100644 index 680d032d..00000000 --- a/docs/api/modules.rst +++ /dev/null @@ -1,7 +0,0 @@ -CodeEntropy -=========== - -.. toctree:: - :maxdepth: 4 - - CodeEntropy diff --git a/docs/config.yaml b/docs/config.yaml deleted file mode 100644 index 7de274a7..00000000 --- a/docs/config.yaml +++ /dev/null @@ -1,19 +0,0 @@ ---- - -run1: - top_traj_file: ["1AKI_prod.tpr", "1AKI_prod.trr"] - force_file: - file_format: - selection_string: 'all' - start: 0 - end: 500 - step: 1 - bin_width: 30 - temperature: 300 - verbose: True - force_partitioning: 0.5 - water_entropy: False - grouping: 'molecules' - customised_axes: True - combinded_forcetorque: False - search_type: 'RAD' diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 2e1bc5b4..00000000 --- a/docs/index.rst +++ /dev/null @@ -1,28 +0,0 @@ - -.. CodeEntropy documentation master file, created by - sphinx-quickstart on Thu Mar 15 13:55:56 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - - -Welcome to CodeEntropy's documentation! -========================================================= - -This code is a complete and generally applicable set of tools for computing entropy of macromolecular systems from the forces sampled in a MD simulation. - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - getting_started - api/modules - science - faq - developer_guide - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/_static/custom.css b/docs/source/_static/custom.css similarity index 100% rename from docs/_static/custom.css rename to docs/source/_static/custom.css diff --git a/docs/_static/logos/biosim-codeentropy_logo_dark.png b/docs/source/_static/logos/biosim-codeentropy_logo_dark.png similarity index 100% rename from docs/_static/logos/biosim-codeentropy_logo_dark.png rename to docs/source/_static/logos/biosim-codeentropy_logo_dark.png diff --git a/docs/_static/logos/biosim-codeentropy_logo_light.png b/docs/source/_static/logos/biosim-codeentropy_logo_light.png similarity index 100% rename from docs/_static/logos/biosim-codeentropy_logo_light.png rename to docs/source/_static/logos/biosim-codeentropy_logo_light.png diff --git a/docs/source/_templates/.gitkeep b/docs/source/_templates/.gitkeep new file mode 100644 index 00000000..e69de29b diff --git a/docs/conf.py b/docs/source/conf.py similarity index 76% rename from docs/conf.py rename to docs/source/conf.py index 703b8bfa..6261b2db 100644 --- a/docs/conf.py +++ b/docs/source/conf.py @@ -10,10 +10,9 @@ import sys import time -# Ensure the *repo root* is on sys.path so autodoc imports the local package. -# This works whether conf.py is in docs/ or docs/source/. +# Put the repo root on sys.path so the local package can be imported. DOCS_DIR = os.path.abspath(os.path.dirname(__file__)) -REPO_ROOT = os.path.abspath(os.path.join(DOCS_DIR, "..")) +REPO_ROOT = os.path.abspath(os.path.join(DOCS_DIR, "..", "..")) sys.path.insert(0, REPO_ROOT) # -- Project information ----------------------------------------------------- @@ -35,20 +34,14 @@ # -- General configuration --------------------------------------------------- extensions = [ - "sphinx.ext.autosummary", - "sphinx.ext.autodoc", "sphinx.ext.mathjax", "sphinx.ext.viewcode", "sphinx.ext.napoleon", "sphinx.ext.intersphinx", "sphinx.ext.extlinks", - "nbsphinx", - "sphinx_copybutton", + "autoapi.extension", ] -# Autosummary (API stubs) -autosummary_generate = True - # Napoleon: Google-style docstrings napoleon_google_docstring = True napoleon_numpy_docstring = False @@ -58,8 +51,24 @@ napoleon_use_rtype = True napoleon_use_ivar = True -# (Optional) If some modules have optional heavy deps, you can mock them here: -autodoc_mock_imports = ["MDAnalysis", "rdkit"] +# API reference generated from the source by sphinx-autoapi +autoapi_dirs = ["../../CodeEntropy"] +autoapi_root = "reference" +autoapi_add_toctree_entry = False +autoapi_member_order = "groupwise" +# Include the __init__ docstring, where the constructor arguments are documented +autoapi_python_class_content = "both" +autoapi_options = [ + "members", + "undoc-members", + "show-inheritance", + "show-module-summary", +] + +# Show type hints in the parameter list rather than the signature +autodoc_typehints = "description" +add_module_names = False +python_maximum_signature_line_length = 88 templates_path = ["_templates"] @@ -72,11 +81,8 @@ pygments_style = "default" # -- Options for HTML output ------------------------------------------------- -html_theme = "furo" -html_theme_options = { - "dark_logo": "logos/biosim-codeentropy_logo_light.png", - "light_logo": "logos/biosim-codeentropy_logo_dark.png", -} +html_theme = "ccpbiosim_sphinx_theme" +html_context = {"github_repo": "CodeEntropy"} html_static_path = ["_static"] diff --git a/docs/developer_guide.rst b/docs/source/developer_guide.rst similarity index 96% rename from docs/developer_guide.rst rename to docs/source/developer_guide.rst index 96589609..97568148 100644 --- a/docs/developer_guide.rst +++ b/docs/source/developer_guide.rst @@ -191,8 +191,9 @@ Run the same checks locally with `uv `_:: Building Documentation ---------------------- -Build documentation locally:: +Install the documentation dependencies and build the documentation locally:: + pip install -e ".[docs]" cd docs make html @@ -200,10 +201,8 @@ The generated HTML files will be in ``docs/build/html/``. Open ``index.html`` in your browser to preview. -Documentation sources are located in: - -- ``docs/user_guide/`` -- ``docs/developer_guide/`` +The documentation sources are in ``docs/source/``, and the API reference is generated +from the source code by sphinx-autoapi. Contributing Code ----------------- diff --git a/docs/faq.rst b/docs/source/faq.rst similarity index 100% rename from docs/faq.rst rename to docs/source/faq.rst diff --git a/docs/getting_started.rst b/docs/source/getting_started.rst similarity index 100% rename from docs/getting_started.rst rename to docs/source/getting_started.rst diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..1b115022 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,86 @@ +:html_theme.sidebar_secondary.remove: + +CodeEntropy +=========== + +.. ccpbiosim-hero:: + :logo-light: _static/logos/biosim-codeentropy_logo_dark.png + :logo-dark: _static/logos/biosim-codeentropy_logo_light.png + :logo-alt: CodeEntropy logo + :tagline: CodeEntropy + :button: getting_started | Get started + :github: CCPBioSim/CodeEntropy + + Entropy of macromolecular systems from MD simulations + +This code is a complete and generally applicable set of tools for computing +entropy of macromolecular systems from the forces sampled in a MD simulation. + +Quick start +----------- + +.. tab-set:: + + .. tab-item:: pip + + .. code-block:: bash + + pip install CodeEntropy + + .. tab-item:: Conda + + .. code-block:: bash + + conda install -c conda-forge -c ccpbiosim codeentropy + + .. tab-item:: Run + + .. code-block:: bash + + CodeEntropy --help + +Explore the documentation +------------------------- + +.. grid:: 1 2 2 3 + :gutter: 3 + + .. grid-item-card:: 🚀 Getting Started + :link: getting_started + :link-type: doc + + Install CodeEntropy and run the examples. + + .. grid-item-card:: 📖 API + :link: reference/CodeEntropy/index + :link-type: doc + + Reference for the CodeEntropy package. + + .. grid-item-card:: 🔬 Science + :link: science + :link-type: doc + + The Multiscale Cell Correlation theory behind the method. + + .. grid-item-card:: ❓ FAQ + :link: faq + :link-type: doc + + Answers to common warnings and questions. + + .. grid-item-card:: 👩‍💻 Developer Guide + :link: developer_guide + :link-type: doc + + Setting up a development environment and contributing. + +.. toctree:: + :maxdepth: 2 + :hidden: + + Getting Started + API + Science + FAQ + Developer Guide diff --git a/docs/science.rst b/docs/source/science.rst similarity index 100% rename from docs/science.rst rename to docs/source/science.rst diff --git a/pyproject.toml b/pyproject.toml index 0c165f1e..18d772ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,9 +73,8 @@ pre-commit = [ ] docs = [ "sphinx>=8.0.0,<10.0", - "nbsphinx>=0.9.3,<1.0", - "sphinx_copybutton>=0.5,<1.0", - "furo>=2025.12.19,<2026.0", + "sphinx-autoapi>=3.8,<4.0", + "ccpbiosim-sphinx-theme>=1.3.0,<1.4.0", "markupsafe>=3.0,<4.0" ] diff --git a/readthedocs.yml b/readthedocs.yml index b5efb63a..a3658ae2 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -16,4 +16,4 @@ python: sphinx: # Path to your Sphinx configuration file. - configuration: docs/conf.py + configuration: docs/source/conf.py