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| Original file line number | Diff line number | Diff line change |
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| name: Check docs build cleanly | ||
|
|
||
| on: | ||
| # Run on pushes to master | ||
| push: | ||
| branches: | ||
| - master | ||
| # And all pull requests | ||
| pull_request: | ||
|
|
||
| concurrency: | ||
| # Cancels jobs running if new commits are pushed | ||
| group: > | ||
| ${{ github.workflow }}- | ||
| ${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
|
|
||
| jobs: | ||
| build_docs: | ||
| name: Run doc build | ||
| # The type of runner that the job will run on | ||
| runs-on: ubuntu-latest | ||
| # The docker container to use. | ||
| container: | ||
| image: firedrakeproject/firedrake-docdeps:latest | ||
| options: --user root | ||
| volumes: | ||
| - ${{ github.workspace }}:/home/firedrake/output | ||
| # Steps represent a sequence of tasks that will be executed as | ||
| # part of the jobs | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Install checkedout Gusto | ||
| run: | | ||
| . /home/firedrake/firedrake/bin/activate | ||
| python -m pip install -e . | ||
| - name: Install Read the Docs theme | ||
| run: | | ||
| . /home/firedrake/firedrake/bin/activate | ||
| python -m pip install sphinx_rtd_theme | ||
| - name: Check documentation links | ||
| if: ${{ github.ref == 'refs/heads/master' }} | ||
| run: | | ||
| . /home/firedrake/firedrake/bin/activate | ||
| cd docs | ||
| make linkcheck | ||
| - name: Build docs | ||
| run: | | ||
| . /home/firedrake/firedrake/bin/activate | ||
| cd docs | ||
| make html | ||
| - name: Upload artifact | ||
| uses: actions/upload-pages-artifact@v1 | ||
| with: | ||
| name: github-pages | ||
| path: /__w/gusto/gusto/docs/build/html | ||
| retention-days: 1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| name: Run lint | ||
|
|
||
| on: | ||
| # Push to master or PR | ||
| push: | ||
| branches: | ||
| - master | ||
| pull_request: | ||
|
|
||
| jobs: | ||
| linter: | ||
| name: "Run linter" | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Setup python | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: 3.11 | ||
| - name: Setup flake8 annotations | ||
| uses: rbialon/flake8-annotations@v1 | ||
| - name: Install linter | ||
| run: | | ||
| pip install flake8 pylint | ||
| - name: Lint codebase | ||
| run: | | ||
| make lint GITHUB_ACTIONS_FORMATTING=1 | ||
| actionlint: | ||
| name: "Lint Github actions YAML files" | ||
| # There's a way to add error formatting so GH actions adds messages to code, | ||
| # but I can't work out the right number of quotes to get it to work | ||
| # https://github.com/rhysd/actionlint/blob/main/docs/usage.md | ||
| # #example-error-annotation-on-github-actions | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| - name: Check workflow files | ||
| uses: docker://rhysd/actionlint:latest | ||
| with: | ||
| args: -color |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| import numpy as np | ||
|
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||
|
|
||
| class NumericalIntegral(object): | ||
| """ | ||
| A class for numerically evaluating and tabulating some 1D integral. | ||
| Args: | ||
| lower_bound(float): lower bound of integral | ||
| upper_bound(float): upper bound of integral | ||
| num_points(float): number of points to tabulate integral at | ||
| """ | ||
| def __init__(self, lower_bound, upper_bound, num_points=500): | ||
|
|
||
| # if upper_bound <= lower_bound: | ||
| # raise ValueError('lower_bound must be lower than upper_bound') | ||
| self.x = np.linspace(lower_bound, upper_bound, num_points) | ||
| self.x_double = np.linspace(lower_bound, upper_bound, 2*num_points-1) | ||
| self.lower_bound = lower_bound | ||
| self.upper_bound = upper_bound | ||
| self.num_points = num_points | ||
| self.tabulated = False | ||
|
|
||
| def tabulate(self, expression): | ||
| """ | ||
| Tabulate some integral expression using Simpson's rule. | ||
| Args: | ||
| expression (func): a function representing the integrand to be | ||
| evaluated. should take a numpy array as an argument. | ||
| """ | ||
|
|
||
| self.cumulative = np.zeros_like(self.x) | ||
| self.interval_areas = np.zeros(len(self.x)-1) | ||
| # Evaluate expression in advance to make use of numpy optimisation | ||
| # We evaluate at the tabulation points and the midpoints of the intervals | ||
| f = expression(self.x_double) | ||
|
|
||
| # Just do Simpson's rule for evaluating area of each interval | ||
| self.interval_areas = ((self.x[1:] - self.x[:-1]) / 6.0 | ||
| * (f[2::2] + 4.0 * f[1::2] + f[:-1:2])) | ||
|
|
||
| # Add the interval areas together to create cumulative integral | ||
| for i in range(self.num_points - 1): | ||
| self.cumulative[i+1] = self.cumulative[i] + self.interval_areas[i] | ||
|
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| self.tabulated = True | ||
|
|
||
| def evaluate_at(self, points): | ||
| """ | ||
| Evaluates the integral at some point using linear interpolation. | ||
| Args: | ||
| points (float or iter) the point value, or array of point values to | ||
| evaluate the integral at. | ||
| Return: | ||
| returns the numerical approximation of the integral from lower | ||
| bound to point(s) | ||
| """ | ||
| # Do linear interpolation from tabulated values | ||
| if not self.tabulated: | ||
| raise RuntimeError( | ||
| 'Integral must be tabulated before we can evaluate it at a point') | ||
|
|
||
| return np.interp(points, self.x, self.cumulative) |
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