Add Python docs (#35)

* Add first version of python docs (local build)

* Try to reuse steps, test build docs

* Can't reuse job contant

* Add dummy step

* Make CI look organized

* Make mypy ignore docs

* Try publishing Python docs

* Can't deploy docs: interferes with julia docs

* Try again

* try something

* Change dir names

* Typo

* meh

* Ignore py docs build in main gitignore

* Get around gitignore

* Try this

* Push main docs to /python

* Correct docs CI url

.github/workflows/python.yml

@@ -17,6 +17,7 @@ on:
       - "python/pyproject.toml"
       - .github/workflows/python.yml
     types: [opened, synchronize, reopened]
+  workflow_call:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -33,7 +34,6 @@ jobs:
   lint-format:
     name: formatting and type checking 🔍️
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
@@ -119,3 +119,33 @@ jobs:
         run: pip install build
       - name: Build package
         run: python3 -m build
+  docs:
+    name: build docs 📖
+    runs-on: ubuntu-latest
+    env: 
+      BRANCH_NAME: ${{ github.head_ref || github.ref_name }}
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+          cache: "pip"
+      - name: Install docs requirements
+        run: pip install -r docs/requirements.txt
+      - name: Build docs
+        run: make -C docs/ html
+      - name: Move files
+        run: mv docs/_build/html pydocs
+      - name: Deploy docs
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: python/pydocs
+          destination_dir:
+            ${{ env.BRANCH_NAME == 'main' && 'python/' || format('python/branch/{0}', env.BRANCH_NAME) }}
+      - name: Display CI docs URL
+        run: echo https://www.ewatercycle.org/remotebmi/${{ env.BRANCH_NAME == 'main' && 'python/' || format('python/branch/{0}', env.BRANCH_NAME) }}

.gitignore

@@ -27,6 +27,7 @@ __pycache__
 /venv
 python/.venv/
 python/heat.toml
+python/docs/_build
 julia/example/Project.toml
 julia/example/heat.toml
 openapi-generator-cli.jar

python/README.md

@@ -86,3 +86,8 @@ and the client can connect to it with the following code.
 > client.get_component_name()
 leakybucket
 ```
+
+## Documentation
+
+In a Python environment, go to the docs directory, do `pip install -r requirements.txt`
+and then `make html`.

python/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)

python/docs/conf.py

@@ -0,0 +1,197 @@
+# remotebmi documentation build configuration file
+#
+# This file is execfile()d with the current directory set to its
+# containing dir.
+#
+# Note that not all possible configuration values are present in this
+# autogenerated file.
+#
+# All configuration values have a default; values that are commented out
+# serve to show the default.
+from pathlib import Path
+
+import tomli
+
+# -- 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",
+    "myst_nb",
+    "sphinx.ext.intersphinx",
+    "sphinx_copybutton",
+    "autoapi.extension",
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+source_suffix = [".rst"]
+
+# The master toctree document.
+master_doc = "index"
+
+# General information about the project.
+project = "remotebmi"
+copyright = "2024, Netherlands eScience Center"  # noqa: A001
+author = "Stefan Verhoeven"
+
+
+# The version info for the project you're documenting, acts as replacement for
+# |version| and |release|, also used in various other places throughout the
+# built documents.
+#
+# The short X.Y version.
+# The full version, including alpha/beta/rc tags.
+def get_version():
+    """Get the version from pyproject.toml."""
+    # Not using importlib as we do not want to install
+    # package during readthdocs build, to keep build quick
+    project = Path(__file__).parent / "../pyproject.toml"
+    with project.open("rb") as f:
+        pyproject = tomli.load(f)
+        return pyproject["project"]["version"]
+
+
+version = get_version()
+release = version
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = "en"
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This patterns also effect to html_static_path and html_extra_path
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = "sphinx"
+
+# If true, `todo` and `todoList` produce output, else they produce nothing.
+todo_include_todos = False
+
+# -- 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 = "sphinx_rtd_theme"
+# TODO move logo to root of docs folder, also some notebooks will need to be updated
+html_logo = "examples/logo.png"
+
+# 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"]
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# This is required for the alabaster theme
+# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
+html_sidebars = {
+    "**": [
+        "relations.html",  # needs 'show_related': True theme option to display
+        "searchbox.html",
+    ]
+}
+
+
+# -- Options for HTMLHelp output ------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = "remotebmi_doc"
+
+
+# -- Options for LaTeX output ---------------------------------------------
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (
+        master_doc,
+        "remotebmi.tex",
+        "remotebmi Documentation",
+        "Stefan Verhoeven",
+        "manual",
+    ),
+]
+
+
+# -- Options for manual page output ---------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [(master_doc, "remotebmi", "remotebmi Documentation", [author], 1)]
+
+
+# -- Options for Texinfo output -------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (
+        master_doc,
+        "remotebmi",
+        "remotebmi Documentation",
+        author,
+        "remotebmi",
+        "Python utilities to gather input files for running a hydrology model",
+        "Miscellaneous",
+    ),
+]
+
+# Turned off nitpicky as not all warnings are fixable
+# To find reference target not found warnings turn this on
+nitpicky = False
+
+autodoc_mock_imports = [
+    "cf_units",  # Causes many errors in docs build.
+]
+# Prevent alphabetic sorting of (@data)class attributes/methods
+autodoc_member_order = "bysource"
+
+autoapi_dirs = ["../src"]
+autoapi_python_class_content = "both"
+autoapi_options = ["members", "undoc-members", "imported-members", "show-inheritance"]
+# If you get build errors pointing to audoapi/**/*.rst files,
+# to debug set `autoapi_keep_files` to True
+autoapi_keep_files = False
+
+myst_heading_anchors = 3
+nb_execution_mode = "off"
+nb_output_stderr = "remove"
+
+intersphinx_mapping = {
+    "cf_units": ("https://cf-units.readthedocs.io/en/latest/", None),
+    "esmvalcore": ("https://docs.esmvaltool.org/projects/ESMValCore/en/latest/", None),
+    "esmvaltool": ("https://docs.esmvaltool.org/en/latest/", None),
+    "grpc4bmi": ("https://grpc4bmi.readthedocs.io/en/latest/", None),
+    "iris": ("https://scitools-iris.readthedocs.io/en/latest/", None),
+    "lime": ("https://lime-ml.readthedocs.io/en/latest/", None),
+    "basic_modeling_interface": ("https://bmi.readthedocs.io/en/latest/", None),
+    "matplotlib": ("https://matplotlib.org/stable/", None),
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "pandas": ("https://pandas.pydata.org/pandas-docs/dev", None),
+    "python": ("https://docs.python.org/3/", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
+    "seaborn": ("https://seaborn.pydata.org/", None),
+    "sklearn": ("https://scikit-learn.org/stable", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+    "pydantic": ("https://docs.pydantic.dev/latest/", None),
+}
+
+# Dont copy line number, >>> and ... from code blocks
+copybutton_exclude = ".linenos, .gp"

python/docs/examples/.gitignore

@@ -0,0 +1,4 @@
+ewatercycle.yaml
+# Exclude intermediate Marrmot files
+BMI_testcase_m01_BuffaloRiver_TN_USA.mat
+marrmott_*_*

python/docs/index.rst

@@ -0,0 +1,108 @@
+################
+remotebmi Python
+################
+
+Welcome to ``remotebmi``'s python documentation!
+
+The `Basic Model Interface (BMI) <https://bmi.readthedocs.io/en/stable/>`_ 
+is a standard interface for models. 
+The interface is available in different languages and a 
+`language agnostic version in SIDL. <https://github.com/csdms/bmi/blob/stable/bmi.sidl>`_
+
+To have a consumer of the model and the provider of the model seperated you
+can use `grpc4bmi <https://grpc4bmi.readthedocs.io/>`_, but this only works on
+languages that have a grpc implementation.
+This repo replaced the gRPC protocol with an REST API.
+The `REST API specification <https://github.com/eWaterCycle/remotebmi/blob/main/openapi.yaml>`_
+is in the `OpenAPI <https://swagger.io/specification/>`_ format.
+
+Installation
+============
+
+.. code-block:: shell
+
+    pip install remotebmi
+
+How to use
+==========
+
+There are two parts to remotebmi: the server (which hosts the model) and the 
+consumer (who wants to interact with the model).
+
+The server is available for different languages (Julia, R, and Python). Any client
+can connect with any server.
+
+Python consumer
+---------------
+
+.. code-block:: python
+
+    from remotebmi.client.client import RemoteBmiClient
+
+    model = RemoteBmiClient('http://localhost:50051')
+    # Now you can use the BMI methods on model
+    # for example
+    model.initialize('config.file')
+    model.update()
+    model.get_value('var_name')
+
+A client can also start a `Apptainer <https://apptainer.org/>`_ container 
+containing the model and the server:
+
+.. code-block:: python
+
+    from remotebmi.client.apptainer import BmiClientApptainer
+
+    model = BmiClientApptainer('my_model.sif', work_dir='/tmp')
+
+The client picks a random port and expects the container to run the BMI web server
+on that port. The port is passed to the container using the ``BMI_PORT`` environment
+variable.
+A client can also start a `Docker <https://docs.docker.com/engine/>`_ container
+containing the model and the server.
+
+.. code-block:: python
+
+    from remotebmi.client.docker import BmiClientDocker
+
+    model = BmiClientDocker('ewatercycle/wflowjl:0.7.3', work_dir='/tmp')
+
+The BMI web server inside the Docker container should be running on port 50051.
+If the port is different, you can pass the port as the ``image_port`` argument 
+to the ``BmiClientDocker`` constructor.
+
+Python server
+-------------
+
+Given you have a model class called ``MyModel`` in a package ``mypackage``
+then the web service can be started with the following command.
+
+.. code-block:: shell
+
+    BMI_MODULE=mypackage BMI_CLASS=MyModel run-bmi-server
+
+For example `leakybucket <https://github.com/eWaterCycle/leakybucket-bmi>`_:
+
+.. code-block:: shell
+
+    pip install leakybucket
+    BMI_MODULE=leakybucket.leakybucket_bmi BMI_CLASS=LeakyBucketBmi run-bmi-server
+
+and the Python client can connect to it with the following code.
+
+.. code-block:: python
+
+    >>> from remotebmi.client.client import RemoteBmiClient
+    >>> client = RemoteBmiClient('http://localhost:50051')
+    >>> client.get_component_name()
+
+    leakybucket
+
+.. _Docker: https://docs.docker.com/engine/
+
+.. toctree::
+    :maxdepth: 3
+    :hidden:
+
+    self
+    autoapi/index