Automated publishing workflows

.github/workflows/python-publish.yml

@@ -0,0 +1,107 @@
+name: publish-caked-to-pypi
+
+on: push
+
+jobs:
+  build:
+    name: build-dist
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: setup-python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10.4"
+      - name: install-pypa/build
+        run: >-
+          python3 -m pip install build --user
+      - name: build-bin-whl
+        run: python3 -m build
+      - name: grab-build
+        uses: actions/upload-artifact@v4
+        with:
+          name: pkg-dist
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      publish-to-pypi
+    if: startsWith(github.ref, 'refs/tags/')
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    environment:
+      name: production
+      url: https://pypi.org/p/caked
+    permissions:
+      id-token: write
+
+    steps:
+      - name: download-dists
+        uses: actions/download-artifact@v4
+        with:
+          name: pkg-dist
+          path: dist/
+      - name: publish-dist-to-pypi
+        uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      sign-dist-via-sigstore-and-upload-to-github-release
+    needs:
+      - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write
+      id-token: write
+
+    steps:
+      - name: download-dists
+        uses: actions/download-artifact@v4
+        with:
+          name: pkg-dist
+          path: dist/
+      - name: sign-dists
+        uses: sigstore/gh-action-sigstore-python@v1.2.3
+        with:
+          inputs: >-
+            ./dist/*.tar.gz ./dist/*.whl
+      - name: create-github-release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create '${{ github.ref_name }}' --repo '${{
+          github.repository }}' --notes ""
+      - name: upload-artifact-signature-to-github-release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release upload '${{ github.ref_name }}' dist/** --repo '${{
+          github.repository }}'
+
+  publish-to-test-pypi:
+    name: publish-to-test-pypi
+    if: startsWith(github.ref, 'refs/heads/development')
+    needs:
+      - build
+    runs-on: ubuntu-latest
+
+    environment:
+      name: testing
+      url: https://test.pypi.org/p/caked
+
+    permissions:
+      id-token: write
+
+    steps:
+      - name: download-dists
+        uses: actions/download-artifact@v4
+        with:
+          name: pkg-dist
+          path: dist/
+      - name: publish-dist-to-test-pypi
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.pre-commit-config.yaml

@@ -49,3 +49,14 @@ repos:
     rev: "v0.9.0.5"
     hooks:
       - id: shellcheck
+
+  - repo: local
+    hooks:
+      - id: pytest
+        stages: [commit, push]
+        types: [python]
+        name: pytest
+        entry: pytest
+        pass_filenames: false
+        language: system
+        always_run: true

.readthedocs.yaml

@@ -0,0 +1,20 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+sphinx:
+  configuration: docs/source/conf.py
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - doc

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,51 @@
+# 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
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+from __future__ import annotations
+
+# -- Project information -----------------------------------------------------
+
+project = "CAKED"
+copyright = "MIT License"
+author = "mooniean, jolaem, crangelsmith"
+
+
+# -- 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 = ["sphinx.ext.autodoc", "sphinx.ext.napoleon"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# 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: list[str] = []
+
+
+# -- 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 = "pydata_sphinx_theme"
+
+# 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 = ["_static"]

docs/source/index.rst

@@ -0,0 +1,34 @@
+.. CAKED documentation master file, edited copy of file created by
+   sphinx-quickstart
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to CAKED documentation!
+==========================
+
+Provide an overview of the CAKED project here
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   installation
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+
+CAKED details
+===================================
+
+
+Example heading
+----------------
+Example text
+
+Example code formatting: ```caked```

docs/source/installation.rst

@@ -0,0 +1,15 @@
+.. _installation-instructions:
+
+Installation instructions
+=========================
+
+Installing CAKED from PyPI
+---------------------------------
+
+This is recommended for most users.
+
+.. code:: bash
+
+   pip install caked
+
+If you want to install the latest version, use:

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["setuptools>=61"]
 build-backend = "setuptools.build_meta"
 [project]
 name = "CAKED"
-version = "0.1.0"  # need to also update version in src/caked/__init__.py
+version = "0.1.6"  # need to also update version in src/caked/__init__.py
 authors = [
   { name = "Bea Costa Gomes", email = "bcostagomes@turing.ac.uk" },
 ]
@@ -40,6 +40,10 @@ dev = [
   "pytest >=6",
   "pytest-cov >=3",
 ]
+doc = [
+  "sphinx >=5.0.0",
+  "pydata-sphinx-theme >=0.7",
+]
 
 [project.urls]
 Homepage = "https://github.com/alan-turing-institute/CAKED"

src/caked/__init__.py

@@ -4,4 +4,4 @@
 from __future__ import annotations
 
 __all__ = ("__version__",)
-__version__ = "0.1.0"
+__version__ = "0.1.6"

tests/test_disk_io.py

@@ -5,9 +5,9 @@
 import numpy as np
 import pytest
 import torch
-from tests import testdata_mrc, testdata_npy
 
 from caked.dataloader import DiskDataLoader, DiskDataset
+from tests import testdata_mrc, testdata_npy
 
 ORIG_DIR = Path.cwd()
 TEST_DATA_MRC = Path(testdata_mrc.__file__).parent