Merge pull request #173 from Genentech/update-runner

Update GitHub runner to Linux-x64

Author: avantikalal

.github/workflows/pypi-publish.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   docs:
     name: Push Sphinx Pages
-    runs-on: ubuntu-latest
+    runs-on: Linux-x64
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v3

.github/workflows/pypi-test.yml

@@ -1,40 +1,74 @@
-# This workflow will install Python dependencies, run tests and lint with a single version of Python
-# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Test the library
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - master # for legacy repos
+      - main
   pull_request:
-    branches: [ main ]
+    branches:
+      - master # for legacy repos
+      - main
+  workflow_dispatch: # Allow manually triggering the workflow
+  schedule:
+    # Run roughly every 15 days at 00:00 UTC
+    # (useful to check if updates on dependencies break the package)
+    - cron: "0 0 1,16 * *"
 
-jobs:
-  build:
+permissions:
+  contents: read
+
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.ref_type }}-
+    ${{ github.event.pull_request.number || github.sha }}
+  cancel-in-progress: true
 
-    runs-on: ubuntu-latest
+jobs:
+  test:
     strategy:
       matrix:
-        python-version: [ '3.10' ]
-
-    name: Python ${{ matrix.python-version }}
+        python: ["3.10"] # , "3.11", "3.12", "3.13", "3.14"
+        platform:
+          - Linux-x64
+          # - ubuntu-latest
+          # - macos-latest
+          # - windows-latest
+    runs-on: ${{ matrix.platform }}
+    name: Python ${{ matrix.python }}, ${{ matrix.platform }}
     steps:
-    - uses: actions/checkout@v3
-    - name: Setup Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: ${{ matrix.python-version }}
-        cache: 'pip'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flake8 pytest tox
-    # - name: Lint with flake8
-    #   run: |
-    #     # stop the build if there are Python syntax errors or undefined names
-    #     flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-    #     # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-    #     # flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-    - name: Test with tox
-      run: |
-        tox
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        id: setup-python
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox coverage
+
+      - name: Run tests
+        run: >-
+          pipx run --python '${{ steps.setup-python.outputs.python-path }}'
+          tox
+          -- -rFEx --durations 10 --color yes --cov --cov-branch --cov-report=xml  # pytest args
+
+      - name: Check for codecov token availability
+        id: codecov-check
+        shell: bash
+        run: |
+          if [ ${{ secrets.CODECOV_TOKEN }} != '' ]; then
+            echo "codecov=true" >> $GITHUB_OUTPUT;
+          else
+            echo "codecov=false" >> $GITHUB_OUTPUT;
+          fi
+
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v5
+        if: ${{ steps.codecov-check.outputs.codecov == 'true' }}
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          slug: ${{ github.repository }}
+          flags: ${{ matrix.platform }} - py${{ matrix.python }}

tests/test_interpret.py

@@ -231,7 +231,7 @@ def test_scan_sequences():
      'fimo_p-value': [0.000244140625, 0.000244140625],
      'matched_seq': ['CACGTG', 'TGCGTG']
     })
-    assert out.equals(expected)
+    pd.testing.assert_frame_equal(out, expected, atol=1e-3)
 
     # Allow reverse complement
     out = scan_sequences(seqs, motifs=meme_file, rc=True, pthresh=1e-3)
@@ -248,7 +248,7 @@ def test_scan_sequences():
      'matched_seq': ['CACGTG', 'CACGTG', 'CACGCA', 'TGCGTG']
     })
 
-    assert out.equals(expected)
+    pd.testing.assert_frame_equal(out, expected, atol=1e-3)
 
     # Reverse complement with attributions
     attrs = get_attributions(model, seqs, method="inputxgradient")
@@ -266,7 +266,7 @@ def test_scan_sequences():
      'site_attr_score': np.float32([0.0, 0.0, 0.009259258396923542, -0.009259259328246117]),
      'motif_attr_score': [0.003703703731298441, 0.0, 0.0, -0.03549381507926434]
     })
-    assert out.equals(expected)
+    pd.testing.assert_frame_equal(out, expected, atol=1e-3)
 
 
 def test_compare_motifs():
@@ -288,7 +288,7 @@ def test_compare_motifs():
         'fimo_score_ref': [11.60498046875, -2.9944558143615723],
         'fimo_score_diff': [-26.253820657730103, 13.22646164894104]
     })
-    assert out.equals(expected)
+    pd.testing.assert_frame_equal(out, expected, atol=1e-3)
 
 
 def test_run_tomtom():

tox.ini

@@ -13,6 +13,8 @@ description = Invoke pytest to run automated tests
 setenv =
     TOXINIDIR = {toxinidir}
     CONDA_EXE = mamba
+    WANDB_MODE = disabled
+    WANDB_API_KEY = dummy
 passenv =
     HOME
     SETUPTOOLS_*