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Merge pull request #1 from MindTheGap-ERC/Add_improve_and_generate_documentation
Add improve and generate documentation
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‎.github/workflows/docs.yml

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name: website
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# build the documentation whenever there are new commits on main
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on:
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push:
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branches:
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- main
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# Alternative: only build for tags.
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# tags:
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# - '*'
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# security: restrict permissions for CI jobs.
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permissions:
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contents: read
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jobs:
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# Build the documentation and upload the static HTML files as an artifact.
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: actions/setup-python@v5
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with:
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python-version: '3.12'
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# install all dependencies (including pdoc)
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- run: pip install pipenv
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- run: pipenv install
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- run: pipenv shell
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# build your documentation into docs/.
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- run: pdoc marlpde/*.py -o ./docs/
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- uses: actions/upload-pages-artifact@v3
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with:
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path: docs/
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# Deploy the artifact to GitHub pages.
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# This is a separate job so that only actions/deploy-pages has the necessary permissions.
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deploy:
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needs: build
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runs-on: ubuntu-latest
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permissions:
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pages: write
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id-token: write
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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steps:
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- id: deployment
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uses: actions/deploy-pages@v4

‎docs/index.html

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<!doctype html>
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<html>
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<head>
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<meta charset="utf-8">
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<meta http-equiv="refresh" content="0; url=./marlpde.html"/>
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</head>
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</html>

‎docs/marlpde.html

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‎docs/marlpde/Evolve_scenario.html

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‎docs/marlpde/LHeureux_model.html

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‎docs/marlpde/parameters.html

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‎docs/search.js

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‎marlpde/Evolve_scenario.py

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matplotlib.use("AGG")
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def integrate_equations(solver_parms, tracker_parms, pde_parms):
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'''
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'''Perform the integration and display and store the results.
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This function retrieves the parameters of the Scenario to be simulated and
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the solution parameters for the integration. It then integrates the five
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partial differential equations from L'Heureux, stores and returns the
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solution, to be used for plotting.
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solution, to be used for plotting. Its inputs come from the parameters
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module, which has dataclasses governing the solver, storage and model specs,
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through the solver_parms, tracker_parms and pde_parms dicts, respectively.
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A progress bar shows how long the (remaining) integration will take.
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Parameters:
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-----------
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solver_parms: dict
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Parameters about solver settings.
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tracker_parms: dict
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Parameters about the progress bar and time interval for storage
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pde_parms: dict
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Model parameters, which govern e.g. the physical processes, but
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also the discretization, such as the number of grid cells.
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Returns:
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--------
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field_solutions: ndarray
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This is the "y" attribute of "sol" i.e. the solution derived by
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solve_ivp. See the scipy.integrate.solve_ivp documentation for
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some background. A reshape has been applied to arrive at one row per
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field. The solutions as a function of time have been removed such that
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only the solution for the last time is returned.
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covered_time: float
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This is the time interval of integration in years, from the start time
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(probably 0) until the requested final time. When the integration halted
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unexpectedly, the covered_time corresponds to the time covered until the
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integration halted.
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depths: pde.CartesianGrid
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These are the centers of the grid cells that together constitute the
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grid.
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Xstar: float
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Scaling factor between physical depths and dimensionless depths as used
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in the differential equations.
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Store_folder: str
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Could be a relative path, i.e. a path relative to the root of this
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repository, to a folder where solutions of the integration should be
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stored. Could also be an absolute path, though.
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'''
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Xstar = pde_parms["Xstar"]
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slices_all_fields = [slice(i * Number_of_depths, (i+1) * Number_of_depths) \
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for i in range(5)]
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eq = LMAHeureuxPorosityDiff(depths, slices_all_fields, not_too_shallow,
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not_too_deep, **filtered_pde_parms)
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f"{end_computing - start_computing:.2e}s. \n"))
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if sol.status == 0:
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covered_time = Tstar * end_time
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covered_time = Tstar * (end_time - t0)
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else:
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covered_time = pbar.n * Tstar * end_time / no_progress_updates
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covered_time = pbar.n * Tstar * (end_time - t0) / no_progress_updates
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# Store your results somewhere in a subdirectory of a parent directory.
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store_folder = "../Results/" + \

‎pyproject.toml

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license = "Apache-2"
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[tool.poetry.dependencies]
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python = ">=3.10,<3.12"
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python = ">=3.10,<=3.12"
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py-pde = "^0.32.0"
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tqdm = "^4.64.1"
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numpy = "^1.23.5"

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