Merge pull request #188 from LabForComputationalVision/github-actions…

…-fixes GitHub actions fixes
plenoptic-org · Jan 6, 2023 · 6c69ee9 · 6c69ee9
2 parents 5e4f209 + 90cfb8b
commit 6c69ee9
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Showing 3 changed files with 106 additions and 85 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -2,10 +2,10 @@ name: build
 on:
   workflow_dispatch:
   schedule:
-    - cron: "0 0 * * 0" # weekly
+  - cron: 0 0 * * 0     # weekly
   pull_request:
     branches:
-      - main
+    - main
 
 jobs:
   # based on https://slashgear.github.io/how-to-split-test-by-folder-with-github-action/
@@ -14,19 +14,23 @@ jobs:
     outputs:
       script: ${{ steps.get-scripts.outputs.script }}
     steps:
-      - uses: actions/checkout@v2
-      - id: get-scripts
-        # it's weird to me, but the quotes around \n should *not* be escaped or it breaks
-        run: echo "::set-output name=script::$(ls tests/test*py | jq -R -s -c 'split("\n")[:-1]')"
+    - uses: actions/checkout@v3
+    - id: get-scripts
+        # we cd into tests so that the output of this is just e.g.,
+        # "test_tools.py", not "tests/test_tools.py", because we want to run
+        # pytest from inside the tests/ dir for coverage to work properly (note
+        # this is different than for the notebooks)
+      run: "echo \"script=$(cd tests/ && ls test*py | jq -R -s -c 'split(\"\\n\")[:-1]')\"\
+        \ >> $GITHUB_OUTPUT\n"
   get_notebooks:
     runs-on: ubuntu-latest
     outputs:
       notebook: ${{ steps.get-notebooks.outputs.nb }}
     steps:
-      - uses: actions/checkout@v2
-      - id: get-notebooks
-        # it's weird to me, but the quotes around \n should *not* be escaped or it breaks
-        run: echo "::set-output name=nb::$(ls examples/*ipynb | jq -R -s -c 'split("\n")[:-1]')"
+    - uses: actions/checkout@v3
+    - id: get-notebooks
+      run: "echo \"nb=$(ls examples/*ipynb | jq -R -s -c 'split(\"\\n\")[:-1]')\"\
+        \ >> $GITHUB_OUTPUT\n"
   notebooks:
     runs-on: ubuntu-latest
     needs: [get_notebooks]
@@ -37,39 +41,39 @@ jobs:
       fail-fast: false
     name: Execute notebooks
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: setup.py
-      - name: Setup FFmpeg
-        uses: FedericoCarboni/setup-ffmpeg@v1
-      - name: Install dependencies
-        # nbclient 0.5.5 is the first version that includes jupyter execute
-        run: |
-          pip install --upgrade --upgrade-strategy eager .
-          pip install jupyter ipywidgets
-          pip install "nbclient>=0.5.5"
-      - name: Download TID2013 dataset
-        if: ${{ matrix.notebook == 'examples/04_Perceptual_distance.ipynb' }}
-        run: |
-          mkdir -p data
-          wget https://osf.io/7nfkz/download -O ./data/tid2013.rar
-          7z x ./data/tid2013.rar -o./data/tid2013/
-      - name: Run notebooks
-        if: ${{ matrix.notebook != 'examples/Demo_Eigendistortion.ipynb' }}
-        run: "jupyter execute ${{ matrix.notebook }}.ipynb --kernel_name=python3"
-      - name: Run notebooks
-        if: ${{ matrix.notebook == 'examples/Demo_Eigendistortion.ipynb' }}
-        # this notebook takes much longer than the rest (if run to completion,
-        # ~1hr on a laptop, more than 5 hours on the Github runners). We use
-        # papermill's parameters to reduce the max number of steps for
-        # eigendistortion synthesis here (we want to test that each cell runs,
-        # but we don't need synthesis to go to completion)
-        run: |
-          pip install --upgrade --upgrade-strategy eager papermill
-          papermill ${{ matrix.notebook }} examples/Demo_Eigendistortion_output.ipynb -p max_steps_frontend 10 -p max_steps_vgg 10 -k python3 --cwd examples/
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: setup.py
+    - name: Setup FFmpeg
+      uses: FedericoCarboni/setup-ffmpeg@v2
+    - name: Install dependencies
+      # nbclient 0.5.5 is the first version that includes jupyter execute
+      run: |
+        pip install --upgrade --upgrade-strategy eager .
+        pip install jupyter ipywidgets
+        pip install "nbclient>=0.5.5"
+    - name: Download TID2013 dataset
+      if: ${{ matrix.notebook == 'examples/04_Perceptual_distance.ipynb' }}
+      run: |
+        mkdir -p data
+        wget https://osf.io/7nfkz/download -O ./data/tid2013.rar
+        7z x ./data/tid2013.rar -o./data/tid2013/
+    - name: Run notebooks
+      if: ${{ matrix.notebook != 'examples/Demo_Eigendistortion.ipynb' }}
+      run: jupyter execute ${{ matrix.notebook }}.ipynb --kernel_name=python3
+    - name: Run notebooks
+      if: ${{ matrix.notebook == 'examples/Demo_Eigendistortion.ipynb' }}
+      # this notebook takes much longer than the rest (if run to completion,
+      # ~1hr on a laptop, more than 5 hours on the Github runners). We use
+      # papermill's parameters to reduce the max number of steps for
+      # eigendistortion synthesis here (we want to test that each cell runs,
+      # but we don't need synthesis to go to completion)
+      run: |
+        pip install --upgrade --upgrade-strategy eager papermill
+        papermill ${{ matrix.notebook }} examples/Demo_Eigendistortion_output.ipynb -p max_steps_frontend 10 -p max_steps_vgg 10 -k python3 --cwd examples/
   tests:
     runs-on: ubuntu-latest
     needs: [get_test_scripts]
@@ -80,35 +84,46 @@ jobs:
       fail-fast: false
     name: Run pytest scripts
     steps:
-      - uses: actions/checkout@v2
-      - name: Install Python 3
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-          cache: pip
-          cache-dependency-path: setup.py
-      - name: Install dependencies
-        run: |
-          # using the --upgrade and --upgrade-strategy eager flags ensures that
-          # pip will always install the latest allowed version of all
-          # dependencies, to make sure the cache doesn't go stale
-          pip install --upgrade --upgrade-strategy eager .
-          pip install --upgrade --upgrade-strategy eager pytest-cov
+    - uses: actions/checkout@v3
+    - name: Install Python 3
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: setup.py
+    - name: Install dependencies
+      run: |
+        # using the --upgrade and --upgrade-strategy eager flags ensures that
+        # pip will always install the latest allowed version of all
+        # dependencies, to make sure the cache doesn't go stale
+        pip install --upgrade --upgrade-strategy eager .
+        pip install --upgrade --upgrade-strategy eager pytest-cov
 
-      - name: Run tests with pytest
-        if: ${{ matrix.test_script == 'tests/test_display.py' }}
+    - name: Run tests with pytest
+      if: ${{ matrix.test_script == 'test_display.py' }}
         # we have two cores on the linux github action runners:
         # https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners
-        run: |
-          pip install --upgrade --upgrade-strategy eager pytest-xdist
-          pytest -n 2 --cov=plenoptic ${{ matrix.test_script }}
-      - name: Run tests with pytest
-        if: ${{ matrix.test_script != 'tests/test_display.py' }}
+      run: |
+        pip install --upgrade --upgrade-strategy eager pytest-xdist
+        # for some reason, need to run this in the tests/ dir in order to get
+        # coverage to work (I couldn't get an analogous .coveragerc working in
+        # the root directory)
+        cd tests/ && pytest -n 2 --cov=plenoptic ${{ matrix.test_script }}
+        # generate the xml file and move it to root dir for codecov
+        coverage xml -o ../coverage.xml
+    - name: Run tests with pytest
+      if: ${{ matrix.test_script != 'test_display.py' }}
         # only test_display should parallelize across the cores, the others get
         # slowed down by it
-        run: 'pytest --cov=plenoptic ${{ matrix.test_script }}'
-      - name: Upload to codecov
-        run: 'bash <(curl -s https://codecov.io/bash)'
+      run: |
+        # for some reason, need to run this in the tests/ dir in order to get
+        # coverage to work (I couldn't get an analogous .coveragerc working in
+        # the root directory)
+        cd tests/ && pytest --cov=plenoptic ${{ matrix.test_script }}
+        # generate the xml file and move it to root dir for codecov
+        coverage xml -o ../coverage.xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@858dd794fbb81941b6d60b0dca860878cba60fa9 # v3.1.1
   all_tutorials_in_docs:
     runs-on: ubuntu-latest
     name: Check that all tutorial notebooks are included in docs
@@ -117,30 +132,31 @@ jobs:
       matrix:
         notebook: ${{fromJson(needs.get_notebooks.outputs.notebook)}}
     steps:
-      - uses: actions/checkout@v2
-      - name: Check for file
-        shell: bash
-        run: if [[ -z "$(grep ${{ matrix.notebook }} docs/tutorials/*nblink)" ]] ; then exit 1; fi
+    - uses: actions/checkout@v3
+    - name: Check for file
+      shell: bash
+      run: if [[ -z "$(grep ${{ matrix.notebook }} docs/tutorials/*nblink)" ]] ; then
+        exit 1; fi
   no_extra_nblinks:
     runs-on: ubuntu-latest
     name: Check that we don't have any extra nblink files
     steps:
-      - uses: actions/checkout@v2
-      - name: Check same number of nblink and notebooks
-        shell: bash
-        run: |
-          n_nblink=0; for file in docs/tutorials/*nblink; do let "n_nblink+=1"; done;
-          n_ipynb=0; for file in examples/*ipynb; do let "n_ipynb+=1"; done;
-          if [[ $n_nblink != $n_ipynb ]]; then exit 1; fi;
+    - uses: actions/checkout@v3
+    - name: Check same number of nblink and notebooks
+      shell: bash
+      run: |
+        n_nblink=0; for file in docs/tutorials/*nblink; do let "n_nblink+=1"; done;
+        n_ipynb=0; for file in examples/*ipynb; do let "n_ipynb+=1"; done;
+        if [[ $n_nblink != $n_ipynb ]]; then exit 1; fi;
 
   check:
     if: always()
     needs:
-      - notebooks
-      - tests
+    - notebooks
+    - tests
     runs-on: ubuntu-latest
     steps:
-      - name: Decide whether all tests and notebooks succeeded
-        uses: re-actors/alls-green@release/v1
-        with:
-          jobs: ${{ toJSON(needs) }}
+    - name: Decide whether all tests and notebooks succeeded
+      uses: re-actors/alls-green@afee1c1eac2a506084c274e9c02c8e0687b48d9e # v1.2.2
+      with:
+        jobs: ${{ toJSON(needs) }}
diff --git a/jenkins/requirements.txt b/jenkins/requirements.txt
@@ -1,6 +1,6 @@
 numpy>=1.1
 torch>=1.8,!=1.12.0
-pyrtools>=1.0.0
+pyrtools>=1.0.1
 scipy>=1.0
 matplotlib>=3.1
 torchvision>=0.3

diff --git a/.coveragerc → tests/.coveragerc b/.coveragerc → tests/.coveragerc
@@ -1,3 +1,8 @@
+[paths]
+source =
+    ../plenoptic
+    */site-packages/plenoptic
+
 [run]
 branch = True
 source = plenoptic