From 17478350312ef8fdefa0bd960c448442c913df6d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:32:39 +0000 Subject: [PATCH 01/14] feat(docs): replace furo theme with custom ccpbiosim sphinx theme in `pyproject.toml` --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 0c165f1e..72438e20 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -75,7 +75,7 @@ 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", + "ccpbiosim-sphinx-theme>=1.0,<2.0", "markupsafe>=3.0,<4.0" ] From 636d4d384b6886a4aa6bf943851adbbf0bbc3169 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:44:35 +0000 Subject: [PATCH 02/14] chore(deps): replace `nbsphinx` and `sphinx_copybutton` with `sphinx-autoapi` --- pyproject.toml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 72438e20..8e2b9411 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,8 +73,7 @@ pre-commit = [ ] docs = [ "sphinx>=8.0.0,<10.0", - "nbsphinx>=0.9.3,<1.0", - "sphinx_copybutton>=0.5,<1.0", + "sphinx-autoapi>=3.8,<4.0", "ccpbiosim-sphinx-theme>=1.0,<2.0", "markupsafe>=3.0,<4.0" ] From 2a951cc175ae5416004d531c8beaceea0459cbb6 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:45:53 +0000 Subject: [PATCH 03/14] feat(docs): configure the ccpbiosim `sphinx` theme and `sphinx-autoapi` --- docs/{ => source}/conf.py | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) rename docs/{ => source}/conf.py (80%) diff --git a/docs/conf.py b/docs/source/conf.py similarity index 80% rename from docs/conf.py rename to docs/source/conf.py index 703b8bfa..ad80cb4b 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 ----------------------------------------------------- @@ -42,8 +41,7 @@ "sphinx.ext.napoleon", "sphinx.ext.intersphinx", "sphinx.ext.extlinks", - "nbsphinx", - "sphinx_copybutton", + "autoapi.extension", ] # Autosummary (API stubs) @@ -58,8 +56,22 @@ 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" +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 +84,8 @@ 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"] From 57703631252e3766708bae0daba30c227d742ee2 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:46:45 +0000 Subject: [PATCH 04/14] refactor(docs): remove the `sphinx-apidoc` files now the API reference is generated --- docs/api/CodeEntropy.cli.rst | 7 ---- docs/api/CodeEntropy.config.argparse.rst | 7 ---- docs/api/CodeEntropy.config.rst | 19 ----------- docs/api/CodeEntropy.config.runtime.rst | 7 ---- docs/api/CodeEntropy.core.dask_clusters.rst | 7 ---- docs/api/CodeEntropy.core.logging.rst | 7 ---- docs/api/CodeEntropy.core.rst | 19 ----------- .../CodeEntropy.entropy.configurational.rst | 7 ---- docs/api/CodeEntropy.entropy.graph.rst | 7 ---- .../CodeEntropy.entropy.nodes.aggregate.rst | 7 ---- ...eEntropy.entropy.nodes.configurational.rst | 7 ---- ...odeEntropy.entropy.nodes.orientational.rst | 7 ---- docs/api/CodeEntropy.entropy.nodes.rst | 21 ------------ .../CodeEntropy.entropy.nodes.vibrational.rst | 7 ---- .../api/CodeEntropy.entropy.orientational.rst | 7 ---- docs/api/CodeEntropy.entropy.rst | 31 ----------------- docs/api/CodeEntropy.entropy.vibrational.rst | 7 ---- docs/api/CodeEntropy.entropy.water.rst | 7 ---- docs/api/CodeEntropy.entropy.workflow.rst | 7 ---- docs/api/CodeEntropy.levels.axes.rst | 7 ---- ...py.levels.dihedrals.angle_observations.rst | 7 ---- ...dihedrals.conformational_state_builder.rst | 7 ---- .../CodeEntropy.levels.dihedrals.kernels.rst | 7 ---- ...ntropy.levels.dihedrals.peak_detection.rst | 7 ---- docs/api/CodeEntropy.levels.dihedrals.rst | 23 ------------- ...ropy.levels.dihedrals.state_assignment.rst | 7 ---- .../CodeEntropy.levels.dihedrals.topology.rst | 7 ---- .../CodeEntropy.levels.execution.chunks.rst | 7 ---- .../CodeEntropy.levels.execution.policy.rst | 7 ---- .../CodeEntropy.levels.execution.reducers.rst | 7 ---- docs/api/CodeEntropy.levels.execution.rst | 22 ------------ ...CodeEntropy.levels.execution.scheduler.rst | 7 ---- .../CodeEntropy.levels.execution.tasks.rst | 7 ---- docs/api/CodeEntropy.levels.forces.rst | 7 ---- ...eEntropy.levels.graph.conformation_dag.rst | 7 ---- .../CodeEntropy.levels.graph.frame_dag.rst | 7 ---- .../CodeEntropy.levels.graph.level_dag.rst | 7 ---- docs/api/CodeEntropy.levels.graph.rst | 20 ----------- docs/api/CodeEntropy.levels.hierarchy.rst | 7 ---- docs/api/CodeEntropy.levels.linalg.rst | 7 ---- docs/api/CodeEntropy.levels.neighbors.rst | 7 ---- .../CodeEntropy.levels.nodes.accumulators.rst | 7 ---- ...CodeEntropy.levels.nodes.axes_topology.rst | 7 ---- docs/api/CodeEntropy.levels.nodes.beads.rst | 7 ---- .../CodeEntropy.levels.nodes.covariance.rst | 7 ---- ...CodeEntropy.levels.nodes.detect_levels.rst | 7 ---- ...eEntropy.levels.nodes.detect_molecules.rst | 7 ---- docs/api/CodeEntropy.levels.nodes.rst | 23 ------------- docs/api/CodeEntropy.levels.rst | 34 ------------------- docs/api/CodeEntropy.levels.search.rst | 7 ---- docs/api/CodeEntropy.molecules.grouping.rst | 7 ---- docs/api/CodeEntropy.molecules.rst | 18 ---------- docs/api/CodeEntropy.results.reporter.rst | 7 ---- docs/api/CodeEntropy.results.rst | 18 ---------- docs/api/CodeEntropy.rst | 32 ----------------- docs/api/CodeEntropy.trajectory.frames.rst | 7 ---- docs/api/CodeEntropy.trajectory.mda.rst | 7 ---- docs/api/CodeEntropy.trajectory.rst | 20 ----------- docs/api/CodeEntropy.trajectory.source.rst | 7 ---- docs/api/modules.rst | 7 ---- 60 files changed, 629 deletions(-) delete mode 100644 docs/api/CodeEntropy.cli.rst delete mode 100644 docs/api/CodeEntropy.config.argparse.rst delete mode 100644 docs/api/CodeEntropy.config.rst delete mode 100644 docs/api/CodeEntropy.config.runtime.rst delete mode 100644 docs/api/CodeEntropy.core.dask_clusters.rst delete mode 100644 docs/api/CodeEntropy.core.logging.rst delete mode 100644 docs/api/CodeEntropy.core.rst delete mode 100644 docs/api/CodeEntropy.entropy.configurational.rst delete mode 100644 docs/api/CodeEntropy.entropy.graph.rst delete mode 100644 docs/api/CodeEntropy.entropy.nodes.aggregate.rst delete mode 100644 docs/api/CodeEntropy.entropy.nodes.configurational.rst delete mode 100644 docs/api/CodeEntropy.entropy.nodes.orientational.rst delete mode 100644 docs/api/CodeEntropy.entropy.nodes.rst delete mode 100644 docs/api/CodeEntropy.entropy.nodes.vibrational.rst delete mode 100644 docs/api/CodeEntropy.entropy.orientational.rst delete mode 100644 docs/api/CodeEntropy.entropy.rst delete mode 100644 docs/api/CodeEntropy.entropy.vibrational.rst delete mode 100644 docs/api/CodeEntropy.entropy.water.rst delete mode 100644 docs/api/CodeEntropy.entropy.workflow.rst delete mode 100644 docs/api/CodeEntropy.levels.axes.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.angle_observations.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.conformational_state_builder.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.kernels.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.peak_detection.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.state_assignment.rst delete mode 100644 docs/api/CodeEntropy.levels.dihedrals.topology.rst delete mode 100644 docs/api/CodeEntropy.levels.execution.chunks.rst delete mode 100644 docs/api/CodeEntropy.levels.execution.policy.rst delete mode 100644 docs/api/CodeEntropy.levels.execution.reducers.rst delete mode 100644 docs/api/CodeEntropy.levels.execution.rst delete mode 100644 docs/api/CodeEntropy.levels.execution.scheduler.rst delete mode 100644 docs/api/CodeEntropy.levels.execution.tasks.rst delete mode 100644 docs/api/CodeEntropy.levels.forces.rst delete mode 100644 docs/api/CodeEntropy.levels.graph.conformation_dag.rst delete mode 100644 docs/api/CodeEntropy.levels.graph.frame_dag.rst delete mode 100644 docs/api/CodeEntropy.levels.graph.level_dag.rst delete mode 100644 docs/api/CodeEntropy.levels.graph.rst delete mode 100644 docs/api/CodeEntropy.levels.hierarchy.rst delete mode 100644 docs/api/CodeEntropy.levels.linalg.rst delete mode 100644 docs/api/CodeEntropy.levels.neighbors.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.accumulators.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.axes_topology.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.beads.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.covariance.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.detect_levels.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.detect_molecules.rst delete mode 100644 docs/api/CodeEntropy.levels.nodes.rst delete mode 100644 docs/api/CodeEntropy.levels.rst delete mode 100644 docs/api/CodeEntropy.levels.search.rst delete mode 100644 docs/api/CodeEntropy.molecules.grouping.rst delete mode 100644 docs/api/CodeEntropy.molecules.rst delete mode 100644 docs/api/CodeEntropy.results.reporter.rst delete mode 100644 docs/api/CodeEntropy.results.rst delete mode 100644 docs/api/CodeEntropy.rst delete mode 100644 docs/api/CodeEntropy.trajectory.frames.rst delete mode 100644 docs/api/CodeEntropy.trajectory.mda.rst delete mode 100644 docs/api/CodeEntropy.trajectory.rst delete mode 100644 docs/api/CodeEntropy.trajectory.source.rst delete mode 100644 docs/api/modules.rst 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 From 5dcdb04baadb23eb5db827d3aa76b64b3dabb7fa Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:47:48 +0000 Subject: [PATCH 05/14] feat(docs): add the banner, quick start and section cards to the home page --- docs/index.rst | 28 --------------- docs/source/index.rst | 83 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 83 insertions(+), 28 deletions(-) delete mode 100644 docs/index.rst create mode 100644 docs/source/index.rst 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/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..a82187a4 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,83 @@ +:html_theme.sidebar_secondary.remove: + +CodeEntropy +=========== + +.. ccpbiosim-hero:: + :logo: _static/logos/biosim-codeentropy_logo_light.png + :logo-alt: CodeEntropy logo + :tagline: Entropy of macromolecular systems from MD simulations + :button: getting_started | Get started + :github: CCPBioSim/CodeEntropy + +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 From 11d0c3c5c1cc7593cbdf113ab6db4455242c6ca8 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:48:43 +0000 Subject: [PATCH 06/14] chore(docs): remove leftover files to match Python template --- docs/README.md | 23 ----------------------- docs/_static/README.md | 16 ---------------- docs/_templates/README.md | 14 -------------- docs/config.yaml | 19 ------------------- docs/source/_templates/.gitkeep | 0 5 files changed, 72 deletions(-) delete mode 100644 docs/README.md delete mode 100644 docs/_static/README.md delete mode 100644 docs/_templates/README.md delete mode 100644 docs/config.yaml create mode 100644 docs/source/_templates/.gitkeep 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/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/source/_templates/.gitkeep b/docs/source/_templates/.gitkeep new file mode 100644 index 00000000..e69de29b From 5361bbbbeaadb6e0fa6cdbbe76f3f32cc52a9596 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 10:50:01 +0000 Subject: [PATCH 07/14] refactor(docs): move the documentation into `docs/source` --- .gitignore | 4 ++-- README.md | 4 ++-- docs/Makefile | 4 ++-- docs/{ => source}/_static/custom.css | 0 .../_static/logos/biosim-codeentropy_logo_dark.png | Bin .../_static/logos/biosim-codeentropy_logo_light.png | Bin docs/{ => source}/developer_guide.rst | 9 ++++----- docs/{ => source}/faq.rst | 0 docs/{ => source}/getting_started.rst | 0 docs/{ => source}/science.rst | 0 readthedocs.yml | 2 +- 11 files changed, 11 insertions(+), 12 deletions(-) rename docs/{ => source}/_static/custom.css (100%) rename docs/{ => source}/_static/logos/biosim-codeentropy_logo_dark.png (100%) rename docs/{ => source}/_static/logos/biosim-codeentropy_logo_light.png (100%) rename docs/{ => source}/developer_guide.rst (96%) rename docs/{ => source}/faq.rst (100%) rename docs/{ => source}/getting_started.rst (100%) rename docs/{ => source}/science.rst (100%) diff --git a/.gitignore b/.gitignore index 089b0c31..15ace2ed 100644 --- a/.gitignore +++ b/.gitignore @@ -63,8 +63,8 @@ instance/ .scrapy # Sphinx documentation -docs/_build/ -docs/autosummary/ +docs/build/ +docs/source/autosummary/ # 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/_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/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/science.rst b/docs/source/science.rst similarity index 100% rename from docs/science.rst rename to docs/source/science.rst 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 From 4684966410a8bca41429de0a2d3d6700ace1c0d2 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 11:26:15 +0000 Subject: [PATCH 08/14] chore(deps): update `ccpbiosim-sphinx-theme` to version 1.1.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 8e2b9411..50866a5b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -74,7 +74,7 @@ pre-commit = [ docs = [ "sphinx>=8.0.0,<10.0", "sphinx-autoapi>=3.8,<4.0", - "ccpbiosim-sphinx-theme>=1.0,<2.0", + "ccpbiosim-sphinx-theme>=1.1.0,<2.0", "markupsafe>=3.0,<4.0" ] From 9573e0c7e6343cece8f13bfb3c917b932a8e0d8d Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 11:50:21 +0000 Subject: [PATCH 09/14] chore(docs): ignore the temporary sphinx-autoapi files --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 15ace2ed..2c9dd38b 100644 --- a/.gitignore +++ b/.gitignore @@ -64,7 +64,7 @@ instance/ # Sphinx documentation docs/build/ -docs/source/autosummary/ +docs/source/reference/ # PyBuilder target/ From 5455566d8c72ea833f3b933f3748ddff9787efea Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 11:50:44 +0000 Subject: [PATCH 10/14] fix(docs): show constructor arguments and remove unused autodoc settings --- docs/source/conf.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/docs/source/conf.py b/docs/source/conf.py index ad80cb4b..6261b2db 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -34,8 +34,6 @@ # -- General configuration --------------------------------------------------- extensions = [ - "sphinx.ext.autosummary", - "sphinx.ext.autodoc", "sphinx.ext.mathjax", "sphinx.ext.viewcode", "sphinx.ext.napoleon", @@ -44,9 +42,6 @@ "autoapi.extension", ] -# Autosummary (API stubs) -autosummary_generate = True - # Napoleon: Google-style docstrings napoleon_google_docstring = True napoleon_numpy_docstring = False @@ -61,6 +56,8 @@ 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", From 542db824223e6b448b08869841356e6c1e8184e5 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 12:57:48 +0000 Subject: [PATCH 11/14] docs: show the project name under the logo on the home page --- docs/source/index.rst | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index a82187a4..a8d8f266 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -6,10 +6,12 @@ CodeEntropy .. ccpbiosim-hero:: :logo: _static/logos/biosim-codeentropy_logo_light.png :logo-alt: CodeEntropy logo - :tagline: Entropy of macromolecular systems from MD simulations + :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. From de9c057ce84290faefa48342875977bd2504beef Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 13:35:19 +0000 Subject: [PATCH 12/14] chore(deps): update `ccpbiosim-sphinx-theme` to version 1.2.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 50866a5b..cb73a2a7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -74,7 +74,7 @@ pre-commit = [ docs = [ "sphinx>=8.0.0,<10.0", "sphinx-autoapi>=3.8,<4.0", - "ccpbiosim-sphinx-theme>=1.1.0,<2.0", + "ccpbiosim-sphinx-theme>=1.2.0,<1.3.0", "markupsafe>=3.0,<4.0" ] From 59efe0098f945f3ab7dfdb9adbe62c0983bd44cf Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 14:17:18 +0000 Subject: [PATCH 13/14] chore(deps): update `ccpbiosim-sphinx-theme` to version 1.2.0 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index cb73a2a7..18d772ab 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -74,7 +74,7 @@ pre-commit = [ docs = [ "sphinx>=8.0.0,<10.0", "sphinx-autoapi>=3.8,<4.0", - "ccpbiosim-sphinx-theme>=1.2.0,<1.3.0", + "ccpbiosim-sphinx-theme>=1.3.0,<1.4.0", "markupsafe>=3.0,<4.0" ] From 2f9131b36b551b6acbe2e6b4871b05bd96c84184 Mon Sep 17 00:00:00 2001 From: harryswift01 Date: Fri, 30 Oct 2026 14:36:20 +0000 Subject: [PATCH 14/14] docs: use light and dark logos on the home page banner --- docs/source/index.rst | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/index.rst b/docs/source/index.rst index a8d8f266..1b115022 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -4,7 +4,8 @@ CodeEntropy =========== .. ccpbiosim-hero:: - :logo: _static/logos/biosim-codeentropy_logo_light.png + :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