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Merge pull request #5475 from lisajulia/move-documentation

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Move documentation
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Markus Blatt 2024-07-12 12:33:22 +02:00 committed by GitHub
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14 changed files with 62 additions and 1013 deletions
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29
.github/workflows/dispatch_opm_simulators.yml vendored Normal file
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name: Dispatch to opm-python-documentation
on:
push:
branches: master
paths:
- 'python/docstrings_simulators.json'
pull_request:
branches: master
paths:
- 'python/docstrings_simulators.json'
jobs:
dispatch:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Send dispatch to opm-simulators
env:
PERSONAL_ACCESS_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
run: |
curl -X POST \
-H "Accept: application/vnd.github+json" \
-H "Authorization: token ${{ secrets.PERSONAL_ACCESS_TOKEN }}" \
https://api.github.com/repos/${{ github.repository_owner }}/opm-python-documentation/dispatches \
-d '{"event_type":"docstrings_simulators_updated"}'

53
.github/workflows/python_sphinx_docs.yml vendored
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@ -1,53 +0,0 @@
name: Build Python Sphinx Docs and push to gh-pages
on:
push:
branches: main
paths:
- 'python/**'
- '.github/workflows/python_sphinx_docs.yml'
pull_request:
branches: main
paths:
- 'python/**'
- '.github/workflows/python_sphinx_docs.yml'
permissions:
contents: write
jobs:
build:
runs-on: ubuntu-latest
steps:
- name: checkout source code
uses: actions/checkout@v4
with:
fetch-depth: 0 # Fetch all history for all tags and branches
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11"
- name: Install poetry
uses: abatilo/actions-poetry@v2
- name: Install python dependencies
run: |
cd python/sphinx_docs
poetry install
- name: Build documentation
run: |
cd python
mkdir gh-pages
touch gh-pages/.nojekyll
cd sphinx_docs
# Currently we build only docs for the HEAD of the master branch
# Later we can add release tags to the list to get the docs for the releases
# For example: -b "main, release/2024.04/final" will build the docs for
# the main branch and the release/2024.04/final tag
poetry run sphinx-versioned -m master -b master --git-root ../../
- name: Copy documentation to gh-pages
run: |
cp -r python/sphinx_docs/docs/_build/* gh-pages/
- name: Deploy documentation
if: ${{ github.event_name == 'push' }}
uses: JamesIves/github-pages-deploy-action@v4
with:
branch: gh-pages
folder: python/gh-pages

45
python/docstrings.json → python/docstrings_simulators.json
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@ -1,78 +1,83 @@
{
"PyBlackOilSimulator":{
"type": "class",
"signature": "opm.simulators.BlackOilSimulator",
"doc": "The SummaryState class - this is where the current summary results of the simulator are stored.\nThe SummaryState class has methods to get hold of well, group and general variables."
},
"PyBlackOilSimulator_filename_constructor": {
"signature": "__init__(deck_filename: str) -> None",
"signature": "opm.simulators.BlackOilSimulator.__init__(deck_filename: str) -> None",
"doc": "Constructor using a deck file name.\n\n:param deck_filename: The file name of the deck to be used for the simulation.\n:type deck_filename: str"
},
"PyBlackOilSimulator_objects_constructor": {
"signature": "__init__(deck: Deck, state: EclipseState, schedule: Schedule, summary_config: SummaryConfig) -> None",
"signature": "opm.simulators.BlackOilSimulator.__init__(deck: Deck, state: EclipseState, schedule: Schedule, summary_config: SummaryConfig) -> None",
"doc": "Constructor using Deck, EclipseState, Schedule, and SummaryConfig objects.\n\n:param deck: Deck object.\n:type deck: Deck\n:param state: EclipseState object.\n:type state: EclipseState\n:param schedule: Schedule object.\n:type schedule: Schedule\n:param summary_config: SummaryConfig object.\n:type summary_config: SummaryConfig"
},
"advance": {
"signature": "advance(report_step: int) -> None",
"signature": "opm.simulators.BlackOilSimulator.advance(report_step: int) -> None",
"doc": "Advance the simulation to a specific report step.\n\n:param report_step: Target report step to advance to.\n:type report_step: int"
},
"checkSimulationFinished": {
"signature": "check_simulation_finished() -> bool",
"signature": "opm.simulators.BlackOilSimulator.check_simulation_finished() -> bool",
"doc": "Check if the simulation has finished.\n\n:return: True if the simulation is finished, False otherwise."
},
"currentStep": {
"signature": "current_step() -> int",
"signature": "opm.simulators.BlackOilSimulator.current_step() -> int",
"doc": "Get the current simulation step.\n\n:return: The current step number."
},
"getCellVolumes": {
"signature": "get_cell_volumes() -> NDArray[float]",
"signature": "opm.simulators.BlackOilSimulator.get_cell_volumes() -> NDArray[float]",
"doc": "Retrieve the cell volumes of the simulation grid.\n\n:return: An array of cell volumes.\n:type return: NDArray[float]"
},
"getDT": {
"signature": "get_dt() -> float",
"signature": "opm.simulators.BlackOilSimulator.get_dt() -> float",
"doc": "Get the timestep size of the last completed step.\n\n:return: Timestep size in days.\n:type return: float"
},
"getFluidStateVariable": {
"signature": "get_fluid_state_variable(name: str) -> NDArray[float]",
"signature": "opm.simulators.BlackOilSimulator.get_fluid_state_variable(name: str) -> NDArray[float]",
"doc": "Retrieve a fluid state variable for the simulation grid.\n\n:param name: The name of the variable. Valid names are 'pw' (pressure water), 'pg' (pressure gas), 'po' (pressure oil), 'rho_w' (density water), 'rho_g' (density gas), 'rho_o' (density oil)'Rs' (soultion gas-oil ratio), 'Rv' (volatile gas-oil ratio), 'Sw' (water saturation), 'Sg' (gas saturation), 'So' (oil saturation), and 'T' (temperature).\n:type name: str\n\n:return: An array of fluid state variables.\n:type return: NDArray[float]"
},
"getPorosity": {
"signature": "get_porosity() -> numpy.ndarray",
"signature": "opm.simulators.BlackOilSimulator.get_porosity() -> NDArray[float]",
"doc": "Retrieve the porosity values of the simulation grid.\n\n:return: An array of porosity values.\n:type return: numpy.ndarray"
},
"getPrimaryVarMeaning": {
"signature": "get_primary_var_meaning(variable: str) -> NDArray[int]",
"signature": "opm.simulators.BlackOilSimulator.get_primary_var_meaning(variable: str) -> NDArray[int]",
"doc": "Retrieve the primary variable meaning of the simulation grid.\n\n:param variable: The name of the variable. Valid names are 'pressure', 'water', 'gas', and 'brine'.\n:type variable: str\n\n:return: An array of primary variable meanings. See ``get_primary_variable_meaning_map()`` for more information.\n:type return: NDArray[int]"
},
"getPrimaryVarMeaningMap": {
"signature": "get_primary_var_meaning_map(variable: str) -> dict[str, int]",
"signature": "opm.simulators.BlackOilSimulator.get_primary_var_meaning_map(variable: str) -> dict[str, int]",
"doc": "Retrieve the primary variable meaning map for each primary variable.\n\n:param variable: The name of the variable. Valid names are 'pressure', 'water', 'gas', and 'brine'.\n:type variable: str\n\n:return: A dictionary of primary variable meanings. The keys are the primary variable meanings and the values are the corresponding integer codes. The integer codes are used to represent the primary variable meanings in the simulation grid. For variable name 'pressure', the valid keys are: 'Po', 'Pg', and 'Pw', for variable name 'water', the valid keys are: 'Sw', 'Rvw', 'Rsw', and 'Disabled', for variable name 'gas', the valid keys are: 'Sg', 'Rs', 'Rv', and 'Disabled', for variable name 'brine', the valid keys are: 'Cs', 'Sp', and 'Disabled'.\n:type return: dict[str, int]"
},
"getPrimaryVariable": {
"signature": "get_primary_variable(variable: str) -> NDArray[float]",
"signature": "opm.simulators.BlackOilSimulator.get_primary_variable(variable: str) -> NDArray[float]",
"doc": "Retrieve the primary variable's values for the simulation grid.\n\n:param variable: The name of the variable. Valid names are 'pressure', 'water', 'gas', and 'brine'.\n:type variable: str\n\n:return: An array of primary variable values. See ``get_primary_variable_meaning()`` for more information.\n:type return: NDArray[float]"
},
"run": {
"signature": "run() -> int",
"signature": "opm.simulators.BlackOilSimulator.run() -> int",
"doc": "Runs the simulation to completion with the provided deck file or previously set deck.\n\n:return: EXIT_SUCCESS if the simulation completes successfully."
},
"setPorosity": {
"signature": "set_porosity(array: NDArray[float]) -> None",
"signature": "opm.simulators.BlackOilSimulator.set_porosity(array: NDArray[float]) -> None",
"doc": "Set the porosity values for the simulation grid.\n\n:param array: An array of porosity values to be set.\n:type array: NDArray[float]"
},
"setPrimaryVariable": {
"signature": "set_primary_variable(variable: str, value: NDArray[float]) -> None",
"signature": "opm.simulators.BlackOilSimulator.set_primary_variable(variable: str, value: NDArray[float]) -> None",
"doc": "Set the primary variable's values for the simulation grid.\n\n:param variable: The name of the variable. Valid names are 'pressure', 'water', 'gas', and 'brine'.\n:type variable: str\n:param value: An array of primary variable values to be set. See ``get_primary_variable()`` for more information.\n:type value: NDArray[float]"
},
"setupMpi": {
"signature": "mpi_init(init: bool, finalize: bool) -> None",
"signature": "opm.simulators.BlackOilSimulator.mpi_init(init: bool, finalize: bool) -> None",
"doc": "Setup MPI for parallel simulation. This method should be called before any other method.\n:param init: Whether to call ``MPI_Init()`` or not.\n:param finalize:Whether to call ``MPI_Finalize()```when the simulator object goes out of scope.\n\n:return: None"
},
"step": {
"signature": "step() -> int",
"signature": "opm.simulators.BlackOilSimulator.step() -> int",
"doc": "Execute the next simulation report step.\n\n:return: Result of the simulation step."
},
"stepCleanup": {
"signature": "step_cleanup() -> int",
"signature": "opm.simulators.BlackOilSimulator.step_cleanup() -> int",
"doc": "Perform cleanup after the last simulation step.\n\n:return: EXIT_SUCCESS if cleanup is successful."
},
"stepInit": {
"signature": "step_init() -> int",
"signature": "opm.simulators.BlackOilSimulator.step_init() -> int",
"doc": "Initialize the simulation before taking the first report step. This method should be called before the first call to ``step()``\n\n:return: EXIT_SUCCESS if the initialization is successful."
}
}
}

41
python/generate_docstring_hpp.py
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@ -1,41 +0,0 @@
import json
import sys
def generate_hpp_from_json(json_path: str, output_hpp_path: str):
with open(json_path, 'r', encoding='utf-8') as file:
docstrings = json.load(file)
hpp_content = """\
#ifndef PYBLACKOILSIMULATORDOC_HPP
#define PYBLACKOILSIMULATORDOC_HPP
// Generated docstrings for PyBlackOilSimulator
namespace Opm::Pybind::DocStrings {
"""
for func_name, info in docstrings.items():
signature = info['signature']
doc = info['doc'].replace('\n', '\n ')
hpp_content += f"""
static constexpr char {func_name}_docstring[] = R\"doc(
{doc}
)doc\";\n"""
hpp_content += """\
} // namespace Opm::Pybind::DocStrings
#endif // PYBLACKOILSIMULATORDOC_HPP
"""
with open(output_hpp_path, 'w', encoding='utf-8') as file:
file.write(hpp_content)
if __name__ == "__main__":
# Check that exactly two command line arguments are provided
if len(sys.argv) != 3:
print("Usage: python generate_docstring_hpp.py <json_path> <output_hpp_path>")
sys.exit(1)
# Extract json_path and output_hpp_path from command line arguments
json_path = sys.argv[1]
output_hpp_path = sys.argv[2]
generate_hpp_from_json(json_path, output_hpp_path)

11
python/simulators/CMakeLists.txt
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@ -1,17 +1,22 @@
set(PYTHON_OPM_SIMULATORS_PACKAGE_PATH ${PROJECT_BINARY_DIR}/python/opm/simulators)
# Set the path to the input docstrings.json file and the output .hpp file
set(PYTHON_DOCSTRINGS_FILE "${PROJECT_SOURCE_DIR}/python/docstrings.json")
set(PYTHON_DOCSTRINGS_FILE "${PROJECT_SOURCE_DIR}/python/docstrings_simulators.json")
set(PYTHON_DOCSTRINGS_GENERATED_HPP "${PROJECT_BINARY_DIR}/python/PyBlackOilSimulatorDoc.hpp")
# Note: If the new find_package(Python3) is used in the top level CMakeLists.txt, the variable
# ${PYTHON_EXECUTABLE} is set there to ${Python3_EXECUTABLE}
#
# Command to run the Python script
find_file(PYTHON_GENERATE_DOCSTRINGS_PY generate_docstring_hpp.py
PATHS ${opm-common_DIR} ${opm-common_PYTHON_COMMON_DIR}
PATH_SUFFIXES python NO_DEFAULT_PATH REQUIRED)
add_custom_command(
OUTPUT ${PYTHON_DOCSTRINGS_GENERATED_HPP}
COMMAND ${CMAKE_COMMAND} -E env PYTHONPATH=${CMAKE_SOURCE_DIR}
${PYTHON_EXECUTABLE} ${PROJECT_SOURCE_DIR}/python/generate_docstring_hpp.py
${PYTHON_DOCSTRINGS_FILE} ${PYTHON_DOCSTRINGS_GENERATED_HPP}
${PYTHON_EXECUTABLE} ${PYTHON_GENERATE_DOCSTRINGS_PY}
${PYTHON_DOCSTRINGS_FILE} ${PYTHON_DOCSTRINGS_GENERATED_HPP} PYBLACKOILSIMULATORDOC_HPP "Opm::Pybind::DocStrings"
DEPENDS ${PYTHON_DOCSTRINGS_FILE}
COMMENT "Generating PyBlackOilSimulatorDoc.hpp from JSON file"
)

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python/sphinx_docs/Makefile
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.PHONY: docs
# Build the documentation locally for the current branch
# NOTE: You need to commit your changes before running this command
docs:
@CURRENT_BRANCH=$(shell git rev-parse --abbrev-ref HEAD)
sphinx-versioned -m $$CURRENT_BRANCH -b $$CURRENT_BRANCH --git-root ../../

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python/sphinx_docs/README.md
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# Python scripts for building opm-simulators sphinx documentation
## Installation of the python scripts
- Requires python3 >= 3.10
### Using poetry
For development it is recommended to use poetry:
- Install [poetry](https://python-poetry.org/docs/)
- Then run:
```
$ poetry install
$ poetry shell
```
### Installation into virtual environment
If you do not plan to change the code, you can do a regular installation into a VENV:
```
$ python -m venv .venv
$ source .venv/bin/activate
$ pip install .
```

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python/sphinx_docs/docs/conf.py
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# Configuration file for the Sphinx documentation builder.
project = "opm.simulators"
copyright = "2024 Equinor ASA"
author = "Håkon Hægland"
# Function to extract release version from dune.module file
def extract_opm_simulators_release():
version_file_path = '../../../dune.module'
with open(version_file_path, 'r') as file:
for line in file:
if line.startswith('Version:'):
version_string = line.split(':')[1].strip()
return version_string
return "unknown" # Fallback version
release = extract_opm_simulators_release()
# -- General configuration ---------------------------------------------------
import os
import sys
# For regular Python packages, the path to the package is usually added to sys.path
# here such that autodoc can find the modules. However, our Python module
# opm.simulators.BlackOilSimulator is not generated yet. Since it is a pybind11
# extension module, it needs to be compiled as part of the opm-simulators build
# process (which requires building opm-common first and so on). The full compilation
# of opm-simulators requres time and storage resources, so we do not want to
# do this as part of the documentation build. Instead, we will use a sphinx extension
# (Python script) to generate documentation from a JSON input file. (This JSON file
# is also is also used to generate a C++ header file with docstrings. The header file
# is generated when opm-simulators is built and is then included
# in the pybind11 binding code for the BlackOilSimulator class. In this way, the
# opm.simulators.BlackOilSimulator Python module will also have access to the docstrings.)
sys.path.insert(0, os.path.abspath("../src"))
# Our sphinx extension that will use the docstrings.json file to generate documentation
extensions = ["opm_simulators_docs.sphinx_ext_docstrings"]
# Path to docstrings.json
opm_simulators_docstrings_path = os.path.abspath('../../docstrings.json')
templates_path = ["_templates"]
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
# -- Options for HTML output -------------------------------------------------
# See: https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
html_theme = "sphinx_rtd_theme"
html_static_path = ["_static"]
html_context = {
"display_github": True,
"github_user": "OPM",
"github_repo": "opm-simulators",
"github_version": "master",
"conf_py_path": "/python/docs/",
}

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python/sphinx_docs/docs/index.rst
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Welcome to the Python documentation for opm-simulators!
=======================================================
.. toctree::
:maxdepth: 1
:caption: Contents:
introduction
python
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

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python/sphinx_docs/docs/introduction.rst
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Introduction
============
Documentation for the ``opm.simulators`` Python module.

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python/sphinx_docs/docs/python.rst
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Python Module Documentation
===========================
.. opm_simulators_docstrings::

720
python/sphinx_docs/poetry.lock generated
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# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
[[package]]
name = "alabaster"
version = "0.7.16"
description = "A light, configurable Sphinx theme"
optional = false
python-versions = ">=3.9"
files = [
{file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
{file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
]
[[package]]
name = "babel"
version = "2.14.0"
description = "Internationalization utilities"
optional = false
python-versions = ">=3.7"
files = [
{file = "Babel-2.14.0-py3-none-any.whl", hash = "sha256:efb1a25b7118e67ce3a259bed20545c29cb68be8ad2c784c83689981b7a57287"},
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]
[package.extras]
dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
[[package]]
name = "certifi"
version = "2024.2.2"
description = "Python package for providing Mozilla's CA Bundle."
optional = false
python-versions = ">=3.6"
files = [
{file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
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]
[[package]]
name = "charset-normalizer"
version = "3.3.2"
description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
optional = false
python-versions = ">=3.7.0"
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21
python/sphinx_docs/pyproject.toml
View File

@ -1,21 +0,0 @@
[tool.poetry]
name = "opm-simulators-docs"
version = "0.1.0"
description = """Helper scripts for generating sphinx documentation for the \
opm-simulators Python bindings"""
authors = ["Håkon Hægland <hakon.hagland@gmail.com>"]
readme = "README.md"
packages = [{ include = "opm_simulators_docs", from = "src"}]
license = "GPL3"
repository = "https://github.com/OPM/opm-simulators"
[tool.poetry.dependencies]
python = "^3.10"
sphinx = "^7.2.5"
sphinx-rtd-theme = "^1.3.0"
click = "^8.1.7"
sphinx-versioned-docs = "^1.3.1"
[build-system]
requires = ["poetry-core"]
build-backend = "poetry.core.masonry.api"

46
python/sphinx_docs/src/opm_simulators_docs/sphinx_ext_docstrings.py
View File

@ -1,46 +0,0 @@
import json
from sphinx.util.nodes import nested_parse_with_titles
from docutils.statemachine import ViewList
from sphinx.util.docutils import SphinxDirective
from docutils import nodes
class PybindDocstringsDirective(SphinxDirective):
required_arguments = 0
optional_arguments = 0
final_argument_whitespace = False
option_spec = {}
def run(self):
env = self.state.document.settings.env
docstrings_path = env.app.config.opm_simulators_docstrings_path
with open(docstrings_path, 'r') as file:
docstrings = json.load(file)
result = []
for func_name, doc_info in docstrings.items():
signature = doc_info.get('signature', '')
docstring = doc_info.get('doc', '')
# Create a ViewList instance for the function signature and docstring
rst = ViewList()
# Check if signature exists and prepend it to the docstring
signature_line = f".. py:function:: {signature}" if signature else f".. py:function:: {func_name}()"
rst.append(signature_line, source="")
rst.append("", source="")
# Add the docstring text if it exists
if docstring:
for line in docstring.split('\n'):
rst.append(f" {line}", source="")
# Create a node that will be populated by nested_parse_with_titles
node = nodes.section()
node.document = self.state.document
# Parse the rst content
nested_parse_with_titles(self.state, rst, node)
result.extend(node.children)
return result
def setup(app):
app.add_config_value('opm_simulators_docstrings_path', None, 'env')
app.add_directive("opm_simulators_docstrings", PybindDocstringsDirective)