Setup Sphinx and ReadTheDocs (#176)

.gitignore

@@ -15,3 +15,5 @@ speedscope.json
 *.pkl
 .venv/
 benchmarks/
+docs/_build/
+docs/api/

.readthedocs.yaml

@@ -0,0 +1,34 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats:
+  - pdf
+  # - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+    - requirements: docs/requirements.txt
+    # Install our python package before building the docs
+    - method: pip
+      path: .

README.md

@@ -26,7 +26,19 @@ After installation, run the following command to see the basic usage and availab
 xl2times --help
 ```
 
-## Development Setup
+## Documentation
+
+The tool's documentation is at http://xl2times.readthedocs.io/ and the source is in the [`docs/`](docs/) directory.
+
+The documentation is generated by Sphinx and hosted on ReadTheDocs. We use the following extensions:
+- `myst-parser`: to be able to write documentation in markdown
+- `sphinx-book-theme`: the theme
+- `sphinx-copybutton`: to add copy buttons to code blocks
+- `sphinxcontrib-apidoc`: to automatically generate API documentation from the Python package
+
+## Development
+
+### Setup
 
 We recommend installing the tool in editable mode (`-e`) in a Python virtual environment:
 ```bash
@@ -53,18 +65,11 @@ If you want to skip these pre-commit steps for a particular commit, if for insta
 git commit --no-verify
 ```
 
-### Publishing the Tool
+### Running Benchmarks
 
-To publish a new version of the tool on PyPI, update the version number in `pyproject.toml`, and then run:
-```bash
-python -m pip install --upgrade build
-python -m pip install --upgrade twine
-rm -rf dist
-python -m build
-python -m twine upload dist/*
-```
+See our GitHub Actions CI `.github/workflows/ci.yml` and the utility script `utils/run_benchmarks.py` to see how to run the tool on the DemoS models.
 
-## Debugging Regressions
+### Debugging Regressions
 
 If your change is causing regressions on one of the benchmarks, a useful way to debug and find the difference is to run the tool in verbose mode and compare the intermediate tables. For example, if your branch has regressions on Demo 1:
 ```bash
@@ -78,9 +83,16 @@ code -d before after
 ```
 VS Code will highlight the changes in the two files, which should correspond to any differences in the intermediate tables.
 
-## Running Benchmarks
+### Publishing the Tool
 
-See our GitHub Actions CI `.github/workflows/ci.yml` and the utility script `utils/run_benchmarks.py` to see how to run the tool on the DemoS models.
+To publish a new version of the tool on PyPI, update the version number in `pyproject.toml`, and then run:
+```bash
+python -m pip install --upgrade build
+python -m pip install --upgrade twine
+rm -rf dist
+python -m build
+python -m twine upload dist/*
+```
 
 ## Contributing
 

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/conf.py

@@ -0,0 +1,57 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "xl2times"
+copyright = "2024, xl2times authors"
+author = "xl2times authors"
+# TODO version = xl2times.__version__ ?
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "myst_parser",
+    "sphinx.ext.duration",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx_copybutton",
+    "sphinxcontrib.apidoc",
+]
+
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "_old"]
+
+apidoc_module_dir = "../xl2times"
+apidoc_output_dir = "api"
+# apidoc_excluded_paths = ['tests']
+# apidoc_separate_modules = True
+
+# -- Options for autodoc ----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html#configuration
+
+# Automatically extract typehints when specified and place them in
+# descriptions of the relevant function/method.
+autodoc_typehints = "description"
+
+# Don't show class signature with the class' name.
+autodoc_class_signature = "separated"
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_book_theme"
+html_static_path = ["_static"]
+
+html_theme_options = {
+    "repository_url": "https://github.com/etsap-TIMES/xl2times",
+    "use_repository_button": True,
+    "path_to_docs": "docs",
+    "use_edit_page_button": True,
+    "home_page_in_toc": True,
+}

docs/index.rst

@@ -0,0 +1,21 @@
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   API Documentation <api/modules.rst>
+
+..
+   Include the README as the index page of the docs to avoid duplication of essential information
+   https://stackoverflow.com/a/69134918/3189420
+
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
+
+
+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
+
+%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/requirements.txt

@@ -0,0 +1,4 @@
+myst-parser >= 2.0
+sphinx-book-theme >= 1.1
+sphinx-copybutton >= 0.5
+sphinxcontrib-apidoc >= 0.5

xl2times/excel.py

@@ -73,24 +73,29 @@ def extract_table(
     sheetname: str,
     filename: str,
 ) -> datatypes.EmbeddedXlTable:
-    """
-    For each individual table tag found in a worksheet, this function aims to extract
-    the associated table. We recognise several types of tables:
-    - Single cell tables:   Tables with only one value, either below or to the right of
-                            the table tag. We interpret these as a single data item with
-                            a column name VALUE.
-    - Multiple cell tables: Tables with multiple values, possibly extending accross
-                            several rows and columns. We delimitate them using empty
-                            spaces around them and the column names are determined by the
-                            values in the row immediately below the table tag
+    """For each individual table tag found in a worksheet, this function aims to extract
+    the associated table.
 
-    :param tag_row:         Row number for the tag designating the table to be extracted
-    :param tag_col:         Column number for the tag designating the table to be extracted
-    :param uc_sets:         Sets (regions and timeslices) for user constraints
-    :param df:              Dataframe object containing all values for the worksheet being evaluated
-    :param sheetname:       Name of the worksheet being evaluated
-    :param filename:        Path to the excel file being evaluated.
-    :return:                Table object in the EmbeddedXlTable format.
+    We recognise several types of tables:
+
+    - Single cell tables: Tables with only one value, either below or to the right of
+      the table tag. We interpret these as a single data item with
+      a column name VALUE.
+    - Multiple cell tables: Tables with multiple values, possibly extending accross
+      several rows and columns. We delimitate them using empty
+      spaces around them and the column names are determined by the
+      values in the row immediately below the table tag
+
+    Args:
+        tag_row:         Row number for the tag designating the table to be extracted
+        tag_col:         Column number for the tag designating the table to be extracted
+        uc_sets:         Sets (regions and timeslices) for user constraints
+        df:              Dataframe object containing all values for the worksheet being evaluated
+        sheetname:       Name of the worksheet being evaluated
+        filename:        Path to the excel file being evaluated.
+
+    Returns:
+       Table object in the EmbeddedXlTable format.
     """
     # If the cell to the right is not empty then we read a scalar from it
     # Otherwise the row below is the header