Decoupler AUCell (#307)

* Initial AUCell commit * Passing python doctests * Galaxy wrapper and test data * Improvements for tests * More fixes * Additional testing fixes * Test 2 changes * Resolves issues with lists * More genes in test * Make conditional clear for older versions * Try newer galaxy * Make closer to IUC tools CI * More IUC * Fix lint version * Move to github * missing anndata option
ebi-gene-expression-group · Nov 9, 2023 · c8c39f1 · c8c39f1
1 parent 85a3118
commit c8c39f1
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Showing 5 changed files with 362 additions and 42 deletions.
diff --git a/.github/workflows/deploy.yaml b/.github/workflows/deploy.yaml
@@ -7,7 +7,7 @@ on:
 
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_21.01
+  GALAXY_BRANCH: release_23.1
   MAX_CHUNKS: 4
 
 jobs:
@@ -22,12 +22,12 @@ jobs:
   # which are needed in subsequent steps.
   setup:
     name: Setup cache and Planemo
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     outputs:
       galaxy_head_sha: ${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: ['3.7']
     steps:
     - name: Print github context properties
       run: |
@@ -38,20 +38,20 @@ jobs:
         echo 'base_ref: ${{ github.base_ref }}'
         echo 'event.before: ${{ github.event.before }}'
         echo 'event.after: ${{ github.event.after }}'
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "::set-output name=galaxy_head_sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy_head_sha }}
     - name: Cache .planemo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -62,7 +62,7 @@ jobs:
       run: pip install wheel
     - name: Install Planemo
       run: pip install planemo
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache
@@ -78,17 +78,17 @@ jobs:
   find_changed:
     name: Determine changed repositories
     needs: [setup]
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.8]
+        python-version: ['3.7']
     outputs:
       commit_range: ${{ steps.get-commit-range.outputs.commit_range }}
       nchunks: ${{ steps.get-chunks.outputs.nchunks }}
       chunk_list: ${{ steps.get-chunks.outputs.chunk_list }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     # The range of commits to check for changes is:
@@ -103,7 +103,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -114,7 +114,7 @@ jobs:
       run: planemo ci_find_repos --changed_in_commit_range $COMMIT_RANGE --exclude packages --exclude deprecated --output changed_repositories.list
     - name: Show repo list
       run: cat changed_repositories.list
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: Workflow artifacts
         path: changed_repositories.list
@@ -147,22 +147,22 @@ jobs:
     needs: [setup, find_changed]
     strategy:
       matrix:
-        python-version: [3.8]
-    runs-on: self-hosted
+        python-version: ['3.7']
+    runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/develop' && github.repository_owner == 'ebi-gene-expression-group'
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - uses: actions/download-artifact@v2
       with:
         name: Workflow artifacts
         path: ../workflow_artifacts/
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip

diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml
@@ -2,7 +2,7 @@ name: Galaxy Tool Linting and Tests for push and PR
 on: [pull_request]
 env:
   GALAXY_FORK: galaxyproject
-  GALAXY_BRANCH: release_21.01
+  GALAXY_BRANCH: release_23.1
   MAX_CHUNKS: 4
 jobs:
   # the setup job does two things:
@@ -14,7 +14,7 @@ jobs:
   # which are needed in subsequent steps.
   setup:
     name: Setup cache and determine changed repositories
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     outputs:
       galaxy-head-sha: ${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}
       repository-list: ${{ steps.discover.outputs.repository-list }}
@@ -23,7 +23,7 @@ jobs:
       chunk-list: ${{ steps.discover.outputs.chunk-list }}
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.7']
     steps:
     - name: Print github context properties
       run: |
@@ -37,17 +37,17 @@ jobs:
     - name: Determine latest commit in the Galaxy repo
       id: get-galaxy-sha
       run: echo "::set-output name=galaxy-head-sha::$(git ls-remote https://github.com/${{ env.GALAXY_FORK }}/galaxy refs/heads/${{ env.GALAXY_BRANCH }} | cut -f1)"
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ steps.get-galaxy-sha.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
     - name: Cache .planemo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -58,7 +58,7 @@ jobs:
       run: pip install wheel
     - name: Install jq
       run: sudo apt-get install -yq jq libjq1
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 0
     - name: Fake a Planemo run to update cache and determine commit range, repositories, and chunks
@@ -85,22 +85,22 @@ jobs:
     name: Lint tool-list
     needs: setup
     if: needs.setup.outputs.repository-list != ''
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.7']
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -120,14 +120,14 @@ jobs:
   test:
     name: Test tools
     # This job runs on Linux
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     needs: setup
     if: needs.setup.outputs.repository-list != ''
     strategy:
       fail-fast: false
       matrix:
         chunk: ${{ fromJson(needs.setup.outputs.chunk-list) }}
-        python-version: ['3.8']
+        python-version: ['3.7']
     services:
       postgres:
         image: postgres:11
@@ -140,20 +140,20 @@ jobs:
     steps:
     # checkout the repository
     # and use it as the current working directory
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
       with:
         fetch-depth: 1
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
         key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }}-${{ secrets.CACHE_VERSION }}
     - name: Cache .planemo
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-planemo
       with:
         path: ~/.planemo
@@ -182,7 +182,7 @@ jobs:
         chunk: ${{ matrix.chunk }}
         chunk-count: ${{ needs.setup.outputs.chunk-count }}
         html-report: true
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: 'Tool test output ${{ matrix.chunk }}'
         path: upload
@@ -197,18 +197,18 @@ jobs:
     needs: [setup, test]
     strategy:
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.7']
     # This job runs on Linux
-    runs-on: self-hosted
+    runs-on: ubuntu-latest
     steps:
-    - uses: actions/download-artifact@v2
+    - uses: actions/download-artifact@v3
       with:
         path: artifacts
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Cache .cache/pip
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-pip
       with:
         path: ~/.cache/pip
@@ -219,7 +219,7 @@ jobs:
       with:
         mode: combine
         html-report: true
-    - uses: actions/upload-artifact@v2
+    - uses: actions/upload-artifact@v3
       with:
         name: 'All tool test results'
         path: upload