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fix: CI, tests & modpathfile (modflowpy#1495)
* fix ci.yml -> commit.yml * fix modflowpy#1491: workaround intermittent macos CI matplotlib failures * fix modflowpy#1479: sort in child's ctor instead of _ModpathSeries.get_data() * don't plt.show() in tests * add comments to conftest.py * give test_mt3d.py::test_mfnwt_CrnkNic more retries * skip ex-gwtgwt-mt3dms-p10 mf6 example (per MODFLOW-ORG/modflow6#1008) * rename release/ to scripts/ * move pull_request_prepare.py to scripts/ * add postprocess_benchmarks.py to scripts/ * separate CI workflows for benchmarks, examples and regression tests * name benchmark CI artifacts benchmarks-<system>-python version>-<run ID> * add CI job to post-process benchmarks (creates artifact benchmarks-<run ID>) * add cross-platform CI action to cache modflow exes & invalidate on new release * reenable PathlineFile.get_destination_pathline_data() benchmark * don't upload coverage after smoke tests, benchmarks, regression tests and example tests * upload coverage on PR as well as push (fix codecov bot comments) * decrease coverage precision to 1 decimal place (avoid small deltas) * update to codecov action v3
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‎.github/actions/cache_exes/action.yml‎

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name: Cache Modflow executables
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description: 'Cache MODFLOW executables from the MODFLOW-USGS/executables repository'
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inputs:
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path:
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description: 'The path to store the executables (e.g. a bin directory)'
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required: true
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default: 'bin'
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github_token:
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description: 'The GitHub API access token'
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required: true
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runs:
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using: "composite"
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steps:
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- name: Make bin directory
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if: runner.os != 'Windows'
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shell: bash
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run: |
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mkdir -p ${{ inputs.path }}
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- name: Make bin directory (Windows)
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if: runner.os == 'Windows'
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shell: pwsh
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run: |
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md -Force ${{ inputs.path }}
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- name: Check release
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if: runner.os != 'Windows'
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shell: bash
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run: |
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# get info for the executables repository's latest release
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release_json=$(gh api -X GET -H "Accept: application/vnd.github+json" /repos/MODFLOW-USGS/executables/releases/latest)
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# get asset ID of the release's metadata file, if one exists
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get_asset_id="
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import json
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import sys
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release = json.load(sys.stdin, strict=False)
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metadata = next(iter([a for a in release['assets'] if a['name'] == 'code.json']), None)
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print(dict(metadata)['id'] if metadata else '')
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"
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asset_id=$(echo "$release_json" | python -c "$get_asset_id")
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# asset_id is empty if metadata file asset wasn't found
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if [ ${#asset_id} -gt 0 ]; then
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gh api -H "Accept: application/octet-stream" "/repos/MODFLOW-USGS/executables/releases/assets/$asset_id" >> executables.json
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else
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# give hashFiles an empty file to hash
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touch executables.json
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fi
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env:
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GH_TOKEN: ${{ inputs.github_token }}
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- name: Check release (Windows)
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if: runner.os == 'Windows'
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shell: pwsh
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run: |
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# get info for the executables repository's latest release
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$release_json=(gh api -X GET -H "Accept: application/vnd.github+json" /repos/MODFLOW-USGS/executables/releases/latest)
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# get asset ID of the release's metadata file, if one exists
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$pattern="code.json"
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$release=(echo $release_json | ConvertFrom-Json)
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$asset_id=($release.assets | Where-Object {$_.name -match "$pattern"} | % {echo $_.id})
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# asset_id is empty if metadata file asset wasn't found
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if ($asset_id.Length -gt 0) {
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gh api -H "Accept: application/octet-stream" "/repos/MODFLOW-USGS/executables/releases/assets/$asset_id" >> executables.json
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} else {
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# give hashFiles an empty file to hash
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New-Item -Name "executables.json" -ItemType File
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}
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env:
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GH_TOKEN: ${{ inputs.github_token }}
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- name: Cache executables
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id: cache_executables
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uses: actions/cache@v3
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with:
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path: ${{ inputs.path }}
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key: modflow-exes-${{ runner.os }}-${{ hashFiles('executables.json') }}
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- name: Install executables
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if: runner.os != 'Windows' && steps.cache_executables.outputs.cache-hit != 'true'
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shell: bash
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run: |
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get-modflow ${{ inputs.path }}
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env:
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GITHUB_TOKEN: ${{ inputs.github_token }}
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- name: Install executables (Windows)
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if: runner.os == 'Windows' && steps.cache_executables.outputs.cache-hit != 'true'
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shell: pwsh
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run: |
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get-modflow ${{ inputs.path }}
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env:
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GITHUB_TOKEN: ${{ inputs.github_token }}
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- name: Add executables to path
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if: runner.os != 'Windows'
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shell: bash
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run: |
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echo ${{ inputs.path }} >> $GITHUB_PATH
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- name: Add executables to path (Windows)
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if: runner.os == 'Windows'
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shell: pwsh
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run: |
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echo ${{ inputs.path }} | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append

‎.github/workflows/benchmark.yml‎

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name: FloPy benchmarks
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on:
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schedule:
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- cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
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jobs:
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benchmark:
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name: Benchmarks
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ ubuntu-latest, macos-latest ]
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python-version: [ 3.7, 3.8, 3.9, "3.10" ]
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exclude:
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# avoid shutil.copytree infinite recursion bug
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# https://github.com/python/cpython/pull/17098
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- python-version: '3.8.0'
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include:
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- os: ubuntu-latest
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path: ~/.cache/pip
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- os: macos-latest
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path: ~/Library/Caches/pip
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defaults:
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run:
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shell: bash
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timeout-minutes: 90
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steps:
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- name: Checkout repo
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uses: actions/checkout@v2.3.4
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- name: Cache Python
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uses: actions/cache@v3
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with:
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path: ${{ matrix.path }}
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key: ${{ matrix.os }}-${{ matrix.python-version }}-pip-${{ hashFiles('setup.cfg') }}
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restore-keys: |
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${{ matrix.os }}-${{ matrix.python-version }}-pip-
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Get branch name
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uses: nelonoel/branch-name@v1.0.1
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install .
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pip install ".[test, optional]"
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- name: Install Modflow executables
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uses: ./.github/actions/cache_exes
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with:
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path: ~/.local/bin
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github_token: ${{ secrets.GITHUB_TOKEN }}
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- name: Run benchmarks
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working-directory: ./autotest
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run: |
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mkdir -p .benchmarks
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pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ matrix.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Upload failed benchmark artifact
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uses: actions/upload-artifact@v2
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if: failure()
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with:
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name: failed-benchmark-${{ matrix.os }}-${{ matrix.python-version }}-${{ github.run_id }}
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path: |
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./autotest/.failed/**
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- name: Upload benchmark result artifact
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uses: actions/upload-artifact@v2
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with:
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name: benchmarks-${{ matrix.os }}-${{ matrix.python-version }}-${{ github.run_id }}
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path: |
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./autotest/.benchmarks/**/*.json
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benchmark_windows:
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name: Benchmarks (Windows)
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runs-on: windows-latest
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strategy:
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fail-fast: false
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matrix:
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python-version: [ 3.7, 3.8, 3.9, "3.10" ]
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exclude:
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# avoid shutil.copytree infinite recursion bug
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# https://github.com/python/cpython/pull/17098
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- python-version: '3.8.0'
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defaults:
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run:
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shell: pwsh
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timeout-minutes: 90
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steps:
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- name: Checkout repo
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uses: actions/checkout@v2.3.4
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- name: Get branch name
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uses: nelonoel/branch-name@v1.0.1
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- name: Cache Miniconda
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uses: actions/cache@v3
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.run-type }}-${{ hashFiles('etc/environment.yml') }}
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# Standard python fails on windows without GDAL installation
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# Using custom bash shell ("shell: bash -l {0}") with Miniconda
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- name: Setup Miniconda
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uses: conda-incubator/setup-miniconda@v2.1.1
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with:
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python-version: ${{ matrix.python-version }}
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channels: conda-forge
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auto-update-conda: true
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activate-environment: flopy
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use-only-tar-bz2: true
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- name: Install Python dependencies
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run: |
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conda env update --name flopy --file etc/environment.yml
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python -m pip install --upgrade pip
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pip install https://github.com/modflowpy/pymake/zipball/master
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pip install xmipy
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pip install .
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- name: Install Modflow executables
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uses: ./.github/actions/cache_exes
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with:
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path: C:\Users\runneradmin\.local\bin
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github_token: ${{ secrets.GITHUB_TOKEN }}
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- name: Run benchmarks
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working-directory: ./autotest
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run: |
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md -Force .benchmarks
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pytest -v --durations=0 --benchmark-only --benchmark-json .benchmarks/${{ runner.os }}_python${{ matrix.python-version }}.json --keep-failed=.failed
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Upload failed benchmark artifact
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uses: actions/upload-artifact@v2
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if: failure()
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with:
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name: failed-benchmark-${{ runner.os }}-${{ matrix.python-version }}-${{ github.run_id }}
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path: |
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./autotest/.failed/**
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- name: Upload benchmark result artifact
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uses: actions/upload-artifact@v2
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with:
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name: benchmarks-${{ runner.os }}-${{ matrix.python-version }}-${{ github.run_id }}
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path: |
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./autotest/.benchmarks/**/*.json
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post_benchmark:
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needs:
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- benchmark
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- benchmark_windows
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name: Process benchmark results
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash
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timeout-minutes: 10
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steps:
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- name: Checkout repo
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uses: actions/checkout@v2.3.4
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- name: Cache Python
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uses: actions/cache@v3
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-3.7-pip-${{ hashFiles('setup.cfg') }}
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restore-keys: |
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${{ runner.os }}-3.7-pip-
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: 3.7
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- name: Install Python dependencies
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run: |
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python -m pip install --upgrade pip
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pip install numpy pandas matplotlib seaborn
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- name: Download all artifacts
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uses: actions/download-artifact@v3
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with:
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path: ./autotest/.benchmarks
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- name: Process benchmark results
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run: |
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artifact_json=$(gh api -X GET -H "Accept: application/vnd.github+json" /repos/modflowpy/flopy/actions/artifacts)
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get_artifact_ids="
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import json
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import sys
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from os import linesep
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artifacts = json.load(sys.stdin, strict=False)['artifacts']
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artifacts = [a for a in artifacts if a['name'].startswith('benchmarks-') and a['name'].split('-')[-1].isdigit()]
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print(linesep.join([str(a['id']) for a in artifacts]))
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"
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echo $artifact_json \
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| python -c "$get_artifact_ids" \
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| xargs -I@ bash -c "gh api -H 'Accept: application/vnd.github+json' /repos/modflowpy/flopy/actions/artifacts/@/zip >> ./autotest/.benchmarks/@.zip"
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zipfiles=( ./autotest/.benchmarks/*.zip )
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if (( ${#zipfiles[@]} )); then
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unzip -o './autotest/.benchmarks/*.zip' -d ./autotest/.benchmarks
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fi
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python ./scripts/process_benchmarks.py ./autotest/.benchmarks ./autotest/.benchmarks
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env:
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ARTIFACTS: ${{steps.run_tests.outputs.artifact_ids}}
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GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Upload benchmark results
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uses: actions/upload-artifact@v2
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with:
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name: benchmarks-${{ github.run_id }}
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path: |
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./autotest/.benchmarks/*.csv
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./autotest/.benchmarks/*.png

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