Merge branch 'main' into pre-comp-signature-passing

datasig-ac-uk · Oct 12, 2023 · a24bfbf · a24bfbf
2 parents 1d2ad4c + 53a1a5e
commit a24bfbf
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diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -55,6 +55,6 @@ jobs:
       - uses: pypa/gh-action-pypi-publish@release/v1
         if: github.event_name == 'release' && github.event.action == 'published'
         with:
-          # Remember to tell (test-)pypi about this repo before publishing
-          # Remove this line to publish to PyPI
-          repository-url: https://test.pypi.org/legacy/
+          # Remember to generate this and set it in "GitHub Secrets"
+          user: __token__
+          password: ${{ secrets.PYPI_API_TOKEN }}
diff --git a/docs/authors.rst b/docs/authors.rst
@@ -0,0 +1,6 @@
+Authors / collaborators
+=======================
+
+``signature_mahalanobis_knn`` is a `DataSig <https://datasig.ac.uk/>`_ project and originally written by `Zhen Shao <https://github.com/sz85512678>`_ and `Ryan Chan <https://github.com/rchan26>`_.
+
+For an up-to-date list of collaborators, please see the `GitHub repo <https://github.com/datasig-ac-uk/signature_mahalanobis_knn>`_ for this package.
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,12 +1,28 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
 from __future__ import annotations
 
 import importlib.metadata
 
+# Warning: do not change the path here. To use autodoc, you need to install the
+# package first.
+
+# -- Project information -----------------------------------------------------
+
 project = "signature_mahalanobis_knn"
-copyright = "2023, Ryan Chan"
-author = "Ryan Chan"
+copyright = "2023, DataSig"
+author = "DataSig"
 version = release = importlib.metadata.version("signature_mahalanobis_knn")
 
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
 extensions = [
     "myst_parser",
     "sphinx.ext.autodoc",
@@ -17,29 +33,33 @@
     "sphinx_copybutton",
 ]
 
+# Add any paths that contain templates here, relative to this directory.
+templates_path = []
+
+# Include both markdown and rst files
 source_suffix = [".rst", ".md"]
-exclude_patterns = [
-    "_build",
-    "**.ipynb_checkpoints",
-    "Thumbs.db",
-    ".DS_Store",
-    ".env",
-    ".venv",
-]
 
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["_build", "**.ipynb_checkpoints", "Thumbs.db", ".DS_Store", ".env"]
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
 html_theme = "furo"
 
-myst_enable_extensions = [
-    "colon_fence",
-]
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path: list[str] = []
 
-intersphinx_mapping = {
-    "python": ("https://docs.python.org/3", None),
-}
 
-nitpick_ignore = [
-    ("py:class", "_io.StringIO"),
-    ("py:class", "_io.BytesIO"),
+# -- Extension configuration -------------------------------------------------
+myst_enable_extensions = [
+    "colon_fence",
+    "deflist",
 ]
-
-always_document_param_types = True
diff --git a/docs/index.md b/docs/index.md
diff --git a/docs/index.rst b/docs/index.rst
@@ -0,0 +1,32 @@
+
+The ``signature_mahalanobis_knn`` Python package
+================================================
+
+``signature_mahalanobis_knn``
+-----------------------------
+
+.. toctree::
+   :maxdepth: 2
+   :titlesonly:
+   :caption: API
+   :glob:
+
+   mahal_distance.rst
+   sig_mahal_knn.rst
+
+.. toctree::
+   :maxdepth: 2
+   :titlesonly:
+   :caption: About
+   :glob:
+
+   authors.rst
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/mahal_distance.rst b/docs/mahal_distance.rst
@@ -0,0 +1,7 @@
+Mahalanobis distance
+====================
+
+.. automodule:: signature_mahalanobis_knn.Mahalanobis
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/sig_mahal_knn.rst b/docs/sig_mahal_knn.rst
@@ -0,0 +1,7 @@
+Signature Mahalanobis KNN method for anomaly detection
+======================================================
+
+.. automodule:: signature_mahalanobis_knn.SignatureMahalanobisKNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/pyproject.toml b/pyproject.toml
@@ -29,7 +29,8 @@ classifiers = [
 ]
 dynamic = ["version"]
 dependencies = [
-  "sktime@git+https://github.com/sz85512678/sktime",
+  # "sktime@git+https://github.com/sz85512678/sktime",
+  "sktime",
   "numpy",
   "scikit-learn",
   "matplotlib",