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Merge pull request #51 from ComputationalPhysiology/gotranx-support
Add support for gotranx and switch from setup.cfg to pyproject.toml
2 parents 209d401 + 617c079 commit 9f18de3

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‎.github/workflows/github-pages.yml‎

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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v5
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- name: Setup Python
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uses: actions/setup-python@v2
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uses: actions/setup-python@v6
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with:
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python-version: "3.9"
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python-version: "3.12"
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- name: Upgrade pip
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run: |
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make docs
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3
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uses: peaceiris/actions-gh-pages@v4
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs/build/html

‎.github/workflows/main.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10"]
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python-version: ["3.10", "3.13"]
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steps:
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- uses: actions/checkout@v4
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- uses: actions/checkout@v5
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install package

‎.gitignore‎

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.DS_Store
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docs/source/hodgkin_huxley_gotranx.md
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demo/*.png
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demo/*.dot
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docs/source/hodgkin_huxley.md

‎.pre-commit-config.yaml‎

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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v6.0.0
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hooks:
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- id: check-yaml
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- id: end-of-file-fixer
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-yaml
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- id: check-added-large-files
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- id: check-docstring-first
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- id: debug-statements
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- id: check-toml
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- repo: https://github.com/asottile/reorder-python-imports
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rev: v3.16.0
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hooks:
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- id: reorder-python-imports
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exclude: ^demo/
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- repo: https://github.com/psf/black-pre-commit-mirror
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rev: 25.9.0
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hooks:
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- id: black
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v2.0.0
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hooks:
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- id: flake8
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- repo: https://github.com/asottile/add-trailing-comma
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rev: v4.0.0
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hooks:
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- id: add-trailing-comma
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- repo: https://github.com/asottile/setup-cfg-fmt
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rev: v3.1.0
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- repo: https://github.com/astral-sh/ruff-pre-commit
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# Ruff version.
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rev: 'v0.14.1'
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hooks:
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- id: setup-cfg-fmt
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# Run the linter.
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- id: ruff-check
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args: [ --fix ]
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# Run the formatter.
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- id: ruff-format
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.18.2
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hooks:
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- id: mypy
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additional_dependencies: ["types-attrs"]
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files: ^src/|^tests/
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args: ["--config-file", "pyproject.toml"]

‎Makefile‎

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rm -f docs/source/modelgraph.rst´
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rm -f docs/source/modules.rst
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jupytext demo/hodgkin_huxley.py -o docs/source/hodgkin_huxley.md
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jupytext demo/hodgkin_huxley_gotranx.py -o docs/source/hodgkin_huxley_gotranx.md
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sphinx-apidoc -o docs/source src/modelgraph
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cd docs && make html
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‎demo/hodgkin_huxley.py‎

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# # Demo
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# # Demo gotran
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#
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# In this demo we will demonstrate how you can use the python API to visualize the dependencies in the Hodgkin Huxley model of the squid axon from 1952. This model is taken from <https://models.cellml.org/workspace/hodgkin_huxley_1952> and converted to a gotran `.ode` file using `gotran` and the `cellml2gotran` script
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# In this demo we will demonstrate how you can use the python API to visualize the dependencies
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# in the Hodgkin Huxley model of the squid axon from 1952. This model is taken
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# from <https://models.cellml.org/workspace/hodgkin_huxley_1952> and converted to a
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# gotran `.ode` file using `gotran` and the `cellml2gotran` script
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#
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# First we make the necessary imports
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‎demo/hodgkin_huxley_gotranx.py‎

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# # Demo gotranx
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#
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# In this demo we will demonstrate how you can use the python API to visualize the dependencies
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# in the Hodgkin Huxley model of the squid axon from 1952. This model is taken
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# from <https://models.cellml.org/workspace/hodgkin_huxley_1952> and converted to a
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# gotran `.ode` file using `gotran` and the `cellml2gotran` script
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#
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# First we make the necessary imports
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import gotranx
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import matplotlib.pyplot as plt
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import networkx as nx
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from modelgraph import DependencyGraph
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# and load the ode file
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ode = gotranx.load_ode("hodgkin_huxley_squid_axon_model_1952_original.ode")
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# Next we build the dependency graph
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graph = DependencyGraph(ode)
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# and get the graph of the expressions that depends on the parameter `g_Na`
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G_g_Na = graph.inv_dependency_graph("g_Na")
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# We plot this using `matplotlib`
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nx.draw(G_g_Na, with_labels=True, font_size=10, node_size=2000)
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plt.savefig("g_Na_mpl_gotranx.png")
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# ![_](_static/g_Na_mpl.png)
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#
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# and using `pydot`
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P_g_Na = nx.nx_pydot.to_pydot(G_g_Na)
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P_g_Na.write_png("g_Na_pydot_gotranx.png")
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# ![_](_static/g_Na_pydot.png)
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#
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# Finally we grab the graph of the dependencies of `dV_dt`
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# Visualize what dV_dt depdens on
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G_dV_dt = graph.dependency_graph("dV_dt")
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# and visualize this using `pydot`
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#
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P_dV_dt = nx.nx_pydot.to_pydot(G_dV_dt)
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P_dV_dt.write_png("dV_dt_pydot_gotranx.png")
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# ![_](_static/dV_dt_pydot.png)

‎docs/source/index.rst‎

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|codecov| |CI| |github pages| |pre-commit.ci status|
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|CI| |github pages| |pre-commit.ci status|
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modelgraph
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==========
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.. code:: python
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from modelgraph import DependencyGraph
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import gotran
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import gotranx
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# Load ode using gotran
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ode = gotran.load_ode("hodgkin_huxley_squid_axon_model_1952_original.ode")
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ode = gotranx.load_ode("hodgkin_huxley_squid_axon_model_1952_original.ode")
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# Build dependency graph
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graph = DependencyGraph(ode)
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# Get the components that depends on g_Na (we call this inverse dependents)
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MIT
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.. |codecov| image:: https://codecov.io/gh/ComputationalPhysiology/modelgraph/branch/main/graph/badge.svg?token=C4YKKMJ4H8
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:target: https://codecov.io/gh/ComputationalPhysiology/modelgraph
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.. |CI| image:: https://github.com/ComputationalPhysiology/modelgraph/actions/workflows/main.yml/badge.svg
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:target: https://github.com/ComputationalPhysiology/modelgraph/actions/workflows/main.yml
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.. |github pages| image:: https://github.com/ComputationalPhysiology/modelgraph/actions/workflows/github-pages.yml/badge.svg
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:caption: Contents:
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hodgkin_huxley
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hodgkin_huxley_gotranx
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modules
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‎pyproject.toml‎

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[build-system]
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requires = ["setuptools>=61.2"]
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build-backend = "setuptools.build_meta"
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[project]
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name = "modelgraph"
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version = "1.0.1"
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description = "Tool for extracting dependency graphs from gotran ODE models"
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authors = [{name = "Henrik Finsberg", email = "henriknf@simula.no"}]
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license = {text = "MIT"}
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classifiers = [
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"License :: OSI Approved :: MIT License",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3 :: Only",
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]
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keywords = ["ODE", "models", "graphs", "dependencies"]
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requires-python = ">=3.8"
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dependencies = [
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"click",
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"networkx",
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"pydot",
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"importlib-metadata;python_version<'3.8'",
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]
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[project.readme]
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file = "README.md"
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content-type = "text/markdown"
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[project.urls]
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Homepage = "https://github.com/ComputationalPhysiology/modelgraph"
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[project.optional-dependencies]
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dev = [
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"Sphinx",
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"black",
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"build",
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"bump2version",
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"flake8",
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"ipython",
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"isort",
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"mypy",
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"pdbpp",
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"pip",
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"pre-commit",
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"sphinx",
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"twine",
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"wheel",
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]
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docs = [
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"Sphinx",
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"jupytext",
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"myst-parser",
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"gotran",
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"gotranx",
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"sphinx-press-theme",
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]
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gui = ["streamlit"]
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plot = [
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"matplotlib",
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"pydot",
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]
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test = [
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"gotran",
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"gotranx",
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"pytest",
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"pytest-cov",
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]
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[tool.setuptools]
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package-dir = {"" = "src"}
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zip-safe = false
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license-files = ["LICENSE"]
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include-package-data = false
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[tool.setuptools.packages.find]
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where = ["src"]
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namespaces = false
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[tool.flake8]
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exclude = "docs"
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ignore = "E203, E266, E501, W503, E731"
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max-line-length = "88"
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max-complexity = "18"
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select = "B,C,E,F,W,T4"
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[tool.aliases]
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test = "pytest"
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[tool.pytest.ini_options]
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addopts = "--cov=src/modelgraph --cov-report html --cov-report xml --cov-report term-missing -v"
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testpaths = ["tests"]
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[tool.mypy]
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files = ["src/modelgraph", "tests"]
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ignore_missing_imports = true
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exclude = "docs"
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[tool.coverage.run]
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omit = [
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"src/modelgraph/gui.py",
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"src/modelgraph/cli.py",
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"src/modelgraph/__main__.py",
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]
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[tool.ruff]
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# Exclude a variety of commonly ignored directories.
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exclude = [
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"examples",
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".bzr",
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".direnv",
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".eggs",
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".git",
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".hg",
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".mypy_cache",
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".nox",
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".pants.d",
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".pytype",
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".ruff_cache",
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".svn",
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".tox",
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".venv",
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"__pypackages__",
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"_build",
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"buck-out",
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"build",
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"dist",
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"node_modules",
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"venv",
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"submit.py"
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]
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# Same as Black.
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line-length = 110
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# Assume Python 3.10.
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target-version = "py310"
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[tool.ruff.lint]
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# Enable pycodestyle (`E`) and Pyflakes (`F`) codes by default.
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select = ["E", "F"]
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ignore = ["E402", "E741", "E743", "E731"]
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# Allow autofix for all enabled rules (when `--fix`) is provided.
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fixable = ["A", "B", "C", "D", "E", "F"]
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unfixable = []
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# Allow unused variables when underscore-prefixed.
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dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"
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[tool.ruff.lint.mccabe]
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# Unlike Flake8, default to a complexity level of 10.
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max-complexity = 10

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