Update changelog and add sphinx documentation (#83)

.github/actions/docs/action.yaml

@@ -0,0 +1,14 @@
+name: Run image
+description: Run private container from GitHub Packages Registry after Docker login
+inputs:
+  python_version:
+    description: 'Python version'
+    required: true
+runs:
+  using: 'docker'
+  image: docker.pkg.github.com/***REMOVED***/***REMOVED***:latest
+  args:
+   - /bin/bash
+   - "-l"
+   - "-c"
+   - "./.github/workflows/docs.sh ${{ inputs.python_version }}"

.github/workflows/ci.yml

@@ -49,8 +49,40 @@ jobs:
        uses: ./.github/actions/unittests
        with:
          python_version: ${{ matrix.PYTHON_VERSION }}
-     # - name: Publish Docs
-     #   run: cd docs/_build/html && gsutil -m cp -r * gs://***REMOVED***/${GITHUB_REPOSITORY}/${GITHUB_SHA}/
+  docs:
+    name: "Documentation"
+    runs-on: ubuntu-latest
+    env:
+      CI: True
+    strategy:
+      fail-fast: false
+      matrix:
+        PYTHON_VERSION: ['3.8']
+    steps:
+     - name: Docker login
+       run: docker login docker.pkg.github.com -u ${{ github.actor }} -p ${{ secrets.FQ_GH_TOKEN }}
+     - name: Pull image
+       run: docker pull docker.pkg.github.com/***REMOVED***/***REMOVED***:latest
+     - name: Checkout branch
+       uses: actions/[email protected]
+       with:
+         ref: ${{ github.head_ref }}
+     - uses: GoogleCloudPlatform/github-actions/setup-gcloud@master
+       with:
+         version: '290.0.1'
+         project_id: ${{ secrets.GCP_UPLOAD_PROJECT_ID }}
+         service_account_email: ${{ secrets.GCP_UPLOAD_SA_EMAIL }}
+         service_account_key: ${{ secrets.GCP_UPLOAD_SA_KEY }}
+         export_default_credentials: true
+     - name: Run CI inside of container
+       uses: ./.github/actions/docs
+       with:
+         python_version: ${{ matrix.PYTHON_VERSION }}
+     - name: Publish Docs
+       run: cd docs/_build/html && gsutil -m cp -r * gs://***REMOVED***/${GITHUB_REPOSITORY}/${GITHUB_SHA}/
+     - name: Publish Docs as latest
+       run: cd docs/_build/html && gsutil -m cp -r * gs://***REMOVED***/${GITHUB_REPOSITORY}/latest/
+       if: github.ref == 'refs/heads/master'
   linux-conda-build:
     name: "Linux - conda-build - Python ${{ matrix.CONDA_BUILD_YML }}"
     runs-on: ubuntu-latest

.github/workflows/docs.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+set -exo pipefail
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
+source ${SCRIPT_DIR}/base.sh $*
+
+yq -Y '. + {dependencies: [.dependencies[], "python=3.8"] }' environment.yml > /tmp/environment.yml
+mamba env create -f /tmp/environment.yml
+conda activate $(yq -r .name environment.yml)
+pip install --no-use-pep517 --no-deps --disable-pip-version-check -e .
+
+pushd $(pwd)/docs
+make html
+popd

CHANGELOG.rst

@@ -7,28 +7,24 @@
 Changelog
 =========
 
-2.0.1 - 2021-06-15
+2.0.0 - 2021-06-17
 ------------------
 
-**Other changes**:
-
-We removed the dependency on ``sparse_dot_mkl``. We now use ``scipy.sparse.csr_matvec`` instead of ``sparse_dot_mkl.dot_product_mkl`` on all platforms, because the former suffered from poor performance, especially on narrow problems.
+**Breaking changes**:
 
-2.0.0 - 2021-06-10
-------------------
+We renamed several public functions to make them private. These include functions in :mod:`quantcore.matrix.benchmark` that are unlikely to be used outside of this package as well as
 
-**Breaking change**:
+   - :func:`quantcore.matrix.dense_matrix._matvec_helper`
+   - :func:`quantcore.matrix.sparse_matrix._matvec_helper`.
+   - :func:`quantcore.matrix.split_matrix._prepare_out_array`.
 
-Renaming several public functions to make them private.
 
 **Other changes**:
 
-Updating linter
+- We removed the dependency on ``sparse_dot_mkl``. We now use :func:`scipy.sparse.csr_matvec` instead of :func:`sparse_dot_mkl.dot_product_mkl` on all platforms, because the former suffered from poor performance, especially on narrow problems. This also means that we removed the function :func:`quantcore.matrix.sparse_matrix._dot_product_maybe_mkl`.
+- We updated the pre-commit hooks and made sure the code is line with the new hooks.
 
 
-Changelog
-=========
-
 1.0.6 - 2020-04-26
 ------------------
 

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     = .
+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/changelog.rst

@@ -0,0 +1 @@
+../CHANGELOG.rst

docs/conf.py

@@ -0,0 +1,34 @@
+# 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('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "quantcore.matrix"
+copyright = "2021, QuantCo, Inc."
+author = "QuantCo, Inc."
+
+extensions = ["numpydoc", "sphinxcontrib.apidoc"]
+
+apidoc_module_dir = "../src/quantcore"
+apidoc_output_dir = "api"
+apidoc_separate_modules = True
+apidoc_extra_args = ["--implicit-namespaces"]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]

docs/index.rst

@@ -0,0 +1,18 @@
+Welcome to quantcore.matrix!
+==========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   API Reference <api/modules>
+   Changelog <changelog>
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

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=.
+set BUILDDIR=_build
+
+if "%1" == "" goto help
+
+%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.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

environment.yml

@@ -11,14 +11,19 @@ dependencies:
   - flake8
   - jemalloc
   - libblas>=0=*mkl
+  - make
   - mako
+  - matplotlib-base
   - mkl-include
+  - numpydoc
   - pandas
   - pip
   - pre-commit
   - pytest
   - pytest-xdist
+  - seaborn-base
   - setuptools_scm
+  - sphinx
+  - sphinx_rtd_theme
+  - sphinxcontrib-apidoc
   - xsimd
-  - matplotlib
-  - seaborn