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nitzanlab · Jan 16, 2024 · b33d9a7 · b33d9a7
1 parent 65091f2
commit b33d9a7
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Showing 7 changed files with 64 additions and 232 deletions.
diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -11,19 +11,19 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-    package:
-        runs-on: ubuntu-latest
-        steps:
-            - uses: actions/checkout@v3
-            - name: Set up Python 3.9
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.9"
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
-            - name: Install build dependencies
-              run: python -m pip install --upgrade pip wheel twine build
-            - name: Build package
-              run: python -m build
-            - name: Check package
-              run: twine check --strict dist/*.whl
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -1,58 +1,58 @@
 name: Test
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
 
 concurrency:
-    group: ${{ github.workflow }}-${{ github.ref }}
-    cancel-in-progress: true
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
-    test:
-        runs-on: ${{ matrix.os }}
-        defaults:
-            run:
-                shell: bash -e {0} # -e to fail on error
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
 
-        strategy:
-            fail-fast: false
-            matrix:
-                python: ["3.9"]
-                os: [ubuntu-latest]
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["3.10"]
+        os: [ubuntu-latest]
 
-        env:
-            OS: ${{ matrix.os }}
-            PYTHON: ${{ matrix.python }}
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
 
-        steps:
-            - uses: actions/checkout@v3
-            - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v4
-              with:
-                  python-version: ${{ matrix.python }}
-                  cache: "pip"
-                  cache-dependency-path: "**/pyproject.toml"
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
 
-            - name: Install test dependencies
-              run: |
-                  python -m pip install --upgrade pip wheel
-                  pip install codecov
-            - name: Install dependencies
-              run: |
-                  pip install ".[dev,test]"
-            - name: Test
-              env:
-                  MPLBACKEND: agg
-                  PLATFORM: ${{ matrix.os }}
-                  DISPLAY: :42
-              run: |
-                  pytest -v --cov --color=yes
-            - name: Upload coverage
-              env:
-                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
-                  CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
-              run: |
-                  codecov --required --flags=unittests
+      - name: Install test dependencies
+        run: |
+          python -m pip install --upgrade pip wheel
+          pip install codecov
+      - name: Install dependencies
+        run: |
+          pip install ".[dev,test]"
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          pytest -v --cov --color=yes
+      - name: Upload coverage
+        env:
+          CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+        run: |
+          codecov --required --flags=unittests
diff --git a/.github/workflows/test.yaml.rej b/.github/workflows/test.yaml.rej
diff --git a/docs/conf.py.rej b/docs/conf.py.rej
diff --git a/docs/index.md.rej b/docs/index.md.rej
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ name = "biolord"
 version = "0.0.2"
 description = "A deep generative framework for disentangling known and unknown attributes in single-cell data."
 readme = "README.md"
-requires-python = ">=3.8"
+requires-python = ">3.8"
 license = {file = "LICENSE"}
 authors = [
     {name = "Zoe Piran"},
@@ -23,7 +23,6 @@ dependencies = [
     "session-info",
     "rich",
     "scvi-tools",
-    "lightning>=2.0,<2.2",
     "torch",
     "scikit-learn",
     "scanpy"

diff --git a/tests/test_basic.py b/tests/test_basic.py
@@ -21,6 +21,5 @@ def test_biolord():
         adata=adata,
         n_latent=n_latent,
     )
-    model.train(10, check_val_every_n_epoch=1, train_size=0.5, enable_checkpointing=False)
 
     print(model)