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‎.all-contributorsrc

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"test",
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"example"
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]
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},
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{
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"login": "priyanshuone6",
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"name": "Priyanshu Agarwal",
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"avatar_url": "https://avatars.githubusercontent.com/u/64051212?v=4",
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"profile": "https://github.com/priyanshuone6",
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"contributions": [
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"test"
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]
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},
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{
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"login": "DrSOKane",
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"name": "DrSOKane",
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"avatar_url": "https://avatars.githubusercontent.com/u/42972513?v=4",
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"profile": "https://github.com/DrSOKane",
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"contributions": [
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"code",
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"example",
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"doc",
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"test"
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]
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},
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{
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"login": "Saransh-cpp",
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"name": "Saransh Chopra",
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"avatar_url": "https://avatars.githubusercontent.com/u/74055102?v=4",
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"profile": "https://github.com/Saransh-cpp",
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"contributions": [
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"code",
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"test"
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]
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},
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{
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"login": "DavidMStraub",
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"name": "David Straub",
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"avatar_url": "https://avatars.githubusercontent.com/u/10965193?v=4",
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"profile": "https://github.com/DavidMStraub",
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"contributions": [
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"bug"
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]
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}
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],
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"contributorsPerLine": 7,

‎.github/workflows/benchmark_on_PR.yml

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@@ -0,0 +1,47 @@
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name: Run benchmarks on push
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on:
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push:
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jobs:
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benchmarks:
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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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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Install asv
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run: pip install -U pip virtualenv asv
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- name: Fetch base branch
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run: |
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git fetch origin $GITHUB_BASE_REF:$GITHUB_BASE_REF
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git fetch origin $GITHUB_HEAD_REF:$GITHUB_HEAD_REF
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- name: Run benchmarks
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run: |
22+
asv machine --machine "GitHubRunner"
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# Get IDs of branch and PR commits
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BASE_COMMIT=$(git rev-parse develop)
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HEAD_COMMIT=$(git rev-parse HEAD)
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echo $BASE_COMMIT | tee commits_to_compare.txt
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echo $HEAD_COMMIT | tee -a commits_to_compare.txt
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asv run HASHFILE:commits_to_compare.txt --m "GitHubRunner" --show-stderr
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- name: Compare commits' benchmark results
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run: |
31+
BASE_COMMIT=$(head -1 commits_to_compare.txt)
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HEAD_COMMIT=$(tail -1 commits_to_compare.txt)
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echo "SUMMARY OF CHANGES"
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echo "=================="
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asv compare $BASE_COMMIT $HEAD_COMMIT | tee compare_result.txt
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# Make sure grep returns error code 0 even if code 1 is
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# returned because no match is found
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REGRESSIONS=$({ grep "+" compare_result.txt || test $? = 1; })
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if [ ! -z "$REGRESSIONS" ]; \
40+
then \
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echo "REGRESSIONS FOUND"; \
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echo "================="; \
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echo "$REGRESSIONS"; \
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echo "================="; \
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printf "Found %d regression(s)\n" $(echo "$REGRESSIONS" | wc -l); \
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exit 1; \
47+
fi

‎.github/workflows/periodic_benchmarks.yml

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# This workflow periodically runs the benchmarks suite in benchmarks/
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# using asv and publish the results, effectively updating
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# the display website hosted in the pybamm-bench repo
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# Steps:
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# - Benchmark all commits since the last one that was benchmarked
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# - Push results to pybamm-bench repo
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# - Publish website
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name: Benchmarks
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on:
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# Everyday at 3 am UTC
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schedule:
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- cron: "0 3 * * *"
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jobs:
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benchmarks:
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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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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Install tox and asv
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run: pip install -U pip tox asv
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- name: Fetch develop branch
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# Not required when worklow trigerred
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# on develop, but useful when
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# experimenting/developing on another one.
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run: |
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git fetch origin develop:develop
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- name: Run benchmarks
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run: |
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asv machine --machine "GitHubRunner"
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asv run --machine "GitHubRunner" NEW
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- name: Upload results as artifact
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uses: actions/upload-artifact@v2
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with:
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name: asv_new_results
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path: results
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publish-results:
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name: Push and publish results
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needs: benchmarks
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runs-on: ubuntu-latest
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steps:
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Install asv
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run: pip install asv
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- name: Checkout pybamm-bench repo
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uses: actions/checkout@v2
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with:
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repository: pybamm-team/pybamm-bench
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token: ${{ secrets.BENCH_PAT }}
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- name: Download results artifact
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uses: actions/download-artifact@v2
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with:
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name: asv_new_results
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path: new_results
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- name: Copy new results and push to pybamm-bench repo
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run: |
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cp -vr new_results/* results
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git config --global user.email ${{ secrets.PUSH_BENCH_EMAIL }}
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git config --global user.name ${{ secrets.PUSH_BENCH_NAME }}
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git add results
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git commit -am "Add new results"
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git push
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- name: Publish results
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run:
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|
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asv publish
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git fetch origin gh-pages:gh-pages
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asv gh-pages

‎.github/workflows/run_benchmarks_over_history.yml

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# GitHub actions workflow that runs the benchmark suite in benchmarks/
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# from "commit_start" to "commit_end". It pushes the results to the
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# pybamm-bench repo and updates the display website.
4+
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# This workflow is meant to be triggered manually, see
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# https://docs.github.com/en/enterprise-server@3.0/actions/managing-workflow-runs/manually-running-a-workflow
7+
8+
name: Manual benchmarks
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on:
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workflow_dispatch:
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inputs:
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commit_start:
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description: 'Identifier of commit from which to start'
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default: 'v0.1.0'
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commit_end:
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description: 'Identifier of commit at which to end'
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default: 'develop'
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ncommits:
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description: 'Number of commits to benchmark between commit_start and commit_end'
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default: '100'
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jobs:
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benchmarks:
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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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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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with:
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python-version: 3.8
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- name: Install tox and asv
31+
run: pip install -U pip tox asv
32+
- name: Fetch develop branch
33+
# Not required when worklow trigerred
34+
# on develop, but useful when
35+
# experimenting/developing on another branch.
36+
run: |
37+
git fetch origin develop:develop
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- name: Run benchmarks
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run: |
40+
asv machine --machine "GitHubRunner"
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asv run -m "GitHubRunner" -s ${{ github.event.inputs.ncommits }} \
42+
${{ github.event.inputs.commit_start }}..${{ github.event.inputs.commit_end }}
43+
- name: Upload results as artifact
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uses: actions/upload-artifact@v2
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with:
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name: asv_new_results
47+
path: results
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49+
publish-results:
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name: Push and publish results
51+
needs: benchmarks
52+
runs-on: ubuntu-latest
53+
steps:
54+
- name: Set up Python 3.8
55+
uses: actions/setup-python@v2
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with:
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python-version: 3.8
58+
- name: Install asv
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run: pip install asv
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- name: Checkout pybamm-bench repo
61+
uses: actions/checkout@v2
62+
with:
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repository: tlestang/pybamm-bench
64+
token: ${{ secrets.BENCH_PAT }}
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- name: Download results artifact
66+
uses: actions/download-artifact@v2
67+
with:
68+
name: asv_new_results
69+
path: new_results
70+
- name: Copy new results and push to pybamm-bench repo
71+
run: |
72+
cp -vr new_results/* results
73+
git config --global user.email "thibault.lestang@cs.ox.ac.uk"
74+
git config --global user.name "Thibault Lestang"
75+
git add results
76+
git commit -am "Add new results"
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git push
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- name: Publish results
79+
run:
80+
|
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asv publish
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git fetch origin gh-pages:gh-pages
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asv gh-pages
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‎.github/workflows/test_on_push.yml

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@@ -47,17 +47,10 @@ jobs:
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sudo apt install gfortran gcc libopenblas-dev graphviz
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sudo apt install python${{ matrix.python-version }}.dev
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# Added fixes to homebrew installs:
51-
# rm -f /usr/local/bin/2to3
52-
# (see https://github.com/actions/virtual-environments/issues/2322)
53-
# brew unlink gcc@8 gcc@9
54-
# (see https://github.com/actions/virtual-environments/issues/2391)
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- name: Install MacOS system dependencies
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if: matrix.os == 'macos-latest'
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run: |
58-
rm -f /usr/local/bin/2to3
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brew update
60-
brew unlink gcc@8 gcc@9
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brew install graphviz
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brew install openblas
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@@ -71,23 +64,23 @@ jobs:
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python -m pip install tox
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- name: Install SuiteSparse and Sundials
74-
if: matrix.os != 'windows-latest'
67+
if: matrix.os == 'ubuntu-latest'
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run: tox -e pybamm-requires
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77-
- name: Run unit tests for GNU/Linux and MacOS
78-
if: matrix.os != 'windows-latest'
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- name: Run unit tests for GNU/Linux
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if: matrix.os == 'ubuntu-latest'
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run: python -m tox -e tests
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- name: Run unit tests for Windows
82-
if: matrix.os == 'windows-latest'
83-
run: python -m tox -e windows-tests
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- name: Run unit tests for Windows and MacOS
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if: matrix.os != 'ubuntu-latest'
76+
run: python -m tox -e mac-windows-tests
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- name: Install docs dependencies and run doctests
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if: matrix.os != 'windows-latest'
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if: matrix.os == 'ubuntu-latest'
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run: tox -e doctests
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- name: Install dev dependencies and run example tests
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if: matrix.os != 'windows-latest'
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if: matrix.os == 'ubuntu-latest'
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run: tox -e examples
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- name: Install and run coverage

‎.github/workflows/url_checker.yml

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name: Check URLs
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3+
on:
4+
push:
5+
schedule:
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# Run everyday at 3 am UTC
7+
- cron: 0 3 * * *
8+
9+
jobs:
10+
urlchecks:
11+
runs-on: ubuntu-latest
12+
steps:
13+
- name: Checkout
14+
uses: actions/checkout@v2
15+
- name: URLs-checker
16+
uses: urlstechie/urlchecker-action@master
17+
with:
18+
# A comma-separated list of file types to cover in the URL checks
19+
file_types: .rst,.md,.py,.ipynb
20+
21+
# Choose whether to include file with no URLs in the prints.
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print_all: false
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24+
# Timeout in 10 seconds if url is not reached
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timeout: 10
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27+
# How many times to retry a failed request (each is logged, defaults to 1)
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retry_count: 5
29+
30+
# A comma separated patterns to exclude during URL checks
31+
exclude_patterns: https://www.datacamp.com/community/tutorials/fuzzy-string-python,http://127.0.0.1
32+
33+
# A comma separated list of file patterns (direct paths work as well) to exclude
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exclude_files: CHANGELOG.md
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‎CHANGELOG.md

+6-1
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22

33
## Features
44

5+
- Added the electrolyte overpotential and Ohmic losses for full conductivity, including surface form ([#1350](https://github.com/pybamm-team/PyBaMM/pull/1350))
56
- Added functionality to `Citations` to print formatted citations ([#1340](https://github.com/pybamm-team/PyBaMM/pull/1340))
67
- Updated the way events are handled in `CasadiSolver` for more accurate event location ([#1328](https://github.com/pybamm-team/PyBaMM/pull/1328))
78
- Added error message if initial conditions are outside the bounds of a variable ([#1326](https://github.com/pybamm-team/PyBaMM/pull/1326))
89
- Added temperature dependence to density, heat capacity and thermal conductivity ([#1323](https://github.com/pybamm-team/PyBaMM/pull/1323))
9-
- Updated solvers' method `solve()` so it can take a list of inputs dictionaries as the `inputs` keyword argument. In this case the model is solved for each input set in the list, and a list of solutions mapping the set of inputs to the solutions is returned. Note that `solve()` can still take a single dictionary as the `inputs` keyword argument. In this case the behaviour is unchanged compared to previous versions.
1010
- Added temperature dependence to the transference number (`t_plus`) ([#1317](https://github.com/pybamm-team/PyBaMM/pull/1317))
1111
- Added new functionality for `Interpolant` ([#1312](https://github.com/pybamm-team/PyBaMM/pull/1312))
1212
- Added option to express experiments (and extract solutions) in terms of cycles of operating condition ([#1309](https://github.com/pybamm-team/PyBaMM/pull/1309))
1313
- The event time and state are now returned as part of `Solution.t` and `Solution.y` so that the event is accurately captured in the returned solution ([#1300](https://github.com/pybamm-team/PyBaMM/pull/1300))
14+
- Added reversible and irreversible lithium plating models ([#1287](https://github.com/pybamm-team/PyBaMM/pull/1287))
1415
- Reformatted the `BasicDFNHalfCell` to be consistent with the other models ([#1282](https://github.com/pybamm-team/PyBaMM/pull/1282))
1516
- Added option to make the total interfacial current density a state ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))
1617
- Added functionality to initialize a model using the solution from another model ([#1278](https://github.com/pybamm-team/PyBaMM/pull/1278))
1718
- Added submodels for active material ([#1262](https://github.com/pybamm-team/PyBaMM/pull/1262))
19+
- Updated solvers' method `solve()` so it can take a list of inputs dictionaries as the `inputs` keyword argument. In this case the model is solved for each input set in the list, and a list of solutions mapping the set of inputs to the solutions is returned. Note that `solve()` can still take a single dictionary as the `inputs` keyword argument. In this case the behaviour is unchanged compared to previous versions.([#1261](https://github.com/pybamm-team/PyBaMM/pull/1261))
1820
- Added composite surface form electrolyte models: `CompositeDifferential` and `CompositeAlgebraic` ([#1207](https://github.com/pybamm-team/PyBaMM/issues/1207))
1921

2022
## Optimizations
2123

24+
- Add URLs checker in workflows ([#1347](https://github.com/pybamm-team/PyBaMM/pull/1347))
2225
- The `Solution` class now only creates the concatenated `y` when the user asks for it. This is an optimization step as the concatenation can be slow, especially with larger experiments ([#1331](https://github.com/pybamm-team/PyBaMM/pull/1331))
2326
- If solver method `solve()` is passed a list of inputs as the `inputs` keyword argument, the resolution of the model for each input set is spread across several Python processes, usually running in parallel on different processors. The default number of processes is the number of processors available. `solve()` takes a new keyword argument `nproc` which can be used to set this number a manually.
2427
- Variables are now post-processed using CasADi ([#1316](https://github.com/pybamm-team/PyBaMM/pull/1316))
2528
- Operations such as `1*x` and `0+x` now directly return `x` ([#1252](https://github.com/pybamm-team/PyBaMM/pull/1252))
2629

2730
## Bug fixes
2831

32+
- Differentiation now works even when the differentiation variable is a constant ([#1294](https://github.com/pybamm-team/PyBaMM/pull/1294))
2933
- Fixed a bug where the event time and state were no longer returned as part of the solution ([#1344](https://github.com/pybamm-team/PyBaMM/pull/1344))
3034
- Fixed a bug in `CasadiSolver` safe mode which crashed when there were extrapolation events but no termination events ([#1321](https://github.com/pybamm-team/PyBaMM/pull/1321))
3135
- When an `Interpolant` is extrapolated an error is raised for `CasadiSolver` (and a warning is raised for the other solvers) ([#1315](https://github.com/pybamm-team/PyBaMM/pull/1315))
@@ -38,6 +42,7 @@
3842
- `Interpolant` now takes `x` and `y` instead of a single `data` entry ([#1312](https://github.com/pybamm-team/PyBaMM/pull/1312))
3943
- Boolean model options ('sei porosity change', 'convection') must now be given in string format ('true' or 'false' instead of True or False) ([#1280](https://github.com/pybamm-team/PyBaMM/pull/1280))
4044
- Operations such as `1*x` and `0+x` now directly return `x`. This can be bypassed by explicitly creating the binary operators, e.g. `pybamm.Multiplication(1, x)` ([#1252](https://github.com/pybamm-team/PyBaMM/pull/1252))
45+
- `'Cell capacity [A.h]'` has been renamed to `'Nominal cell capacity [A.h]'`. `'Cell capacity [A.h]'` will be deprecated in the next release. ([#1352](https://github.com/pybamm-team/PyBaMM/pull/1352))
4146

4247
# [v0.3.0](https://github.com/pybamm-team/PyBaMM) - 2020-11-22
4348

‎CMakeBuild.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -79,7 +79,7 @@ def run(self):
7979
"cmake configuration steps encountered errors, and the idaklu module"
8080
" could not be built. Make sure dependencies are correctly "
8181
"installed. See "
82-
"https://github.com/pybamm-team/PyBaMM/blob/develop/"
82+
"https://github.com/pybamm-team/PyBaMM/tree/develop"
8383
"INSTALL-LINUX-MAC.md"
8484
)
8585
raise RuntimeError(msg)

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