Merge pull request #35 from YosefLab/cookiecutter3

Refactor to cookiecutter template from scverse.

.github/workflows/build.yml

@@ -1,25 +1,25 @@
 name: Check Build
 
 on:
-    push:
-        branches: [main]
-    pull_request:
-        branches: [main]
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
 
 jobs:
-    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
+  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

.github/workflows/release.yml

@@ -1,32 +1,32 @@
 name: Release
 
 on:
-    push:
-        tags:
-            - "*.*.*"
+  push:
+    tags:
+      - "*.*.*"
 
 jobs:
-    release:
-        name: Release
-        runs-on: ubuntu-latest
-        steps:
-            # will use ref/SHA that triggered it
-            - name: Checkout code
-              uses: actions/checkout@v3
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      # will use ref/SHA that triggered it
+      - name: Checkout code
+        uses: actions/checkout@v3
 
-            - name: Set up Python 3.10
-              uses: actions/setup-python@v4
-              with:
-                  python-version: "3.10"
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
 
-            - name: Install hatch
-              run: |
-                  pip install hatch
+      - name: Install hatch
+        run: |
+          pip install hatch
 
-            - name: Build project for distribution
-              run: hatch build
+      - name: Build project for distribution
+        run: hatch build
 
-            - name: Publish a Python distribution to PyPI
-              uses: pypa/gh-action-pypi-publish@release/v1
-              with:
-                  password: ${{ secrets.PYPI_TOKEN }}
+      - name: Publish a Python distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/test.yml

@@ -4,57 +4,57 @@
 name: PopV
 
 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 }}
-        timeout-minutes: 40
-        defaults:
-            run:
-                shell: bash -e {0} # -e to fail on error
+  test:
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 40
+    defaults:
+      run:
+        shell: bash -e {0} # -e to fail on error
 
-        strategy:
-            fail-fast: false
-            matrix:
-                include:
-                    - os: ubuntu-latest
-                      python: "3.9"
-                    - os: ubuntu-latest
-                      python: "3.10"
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.9"
+          - os: ubuntu-latest
+            python: "3.10"
 
-        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"
-            - name: Install test dependencies
-              run: |
-                  python -m pip install --upgrade pip wheel
-            - name: Install dependencies
-              run: |
-                  pip install pytest-cov
-                  pip install ${{ matrix.pip-flags }} ".[dev]"
-            - name: Test
-              env:
-                  MPLBACKEND: agg
-                  PLATFORM: ${{ matrix.os }}
-                  DISPLAY: :42
-              run: |
-                  pytest -v --cov --color=yes
-            - name: Upload coverage
-              uses: codecov/codecov-action@v3
+    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
+      - name: Install dependencies
+        run: |
+          pip install pytest-cov
+          pip install ${{ matrix.pip-flags }} ".[dev]"
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          pytest -v --cov --color=yes
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3

codecov.yml

@@ -1,11 +1,11 @@
 # Run to check if valid
 # curl --data-binary @codecov.yml https://codecov.io/validate
 coverage:
-    status:
-        project:
-            default:
-                target: 85%
-                threshold: 1%
-        patch: off
+  status:
+    project:
+      default:
+        target: 85%
+        threshold: 1%
+    patch: off
 
 ignore:

docs/notebooks/tabula_sapiens_tutorial.ipynb

@@ -566,25 +566,15 @@
         "    ref_batch_key=ref_batch_key,\n",
         "    unknown_celltype_label=unknown_celltype_label,\n",
         "    save_path_trained_models=output_model_fn,\n",
-        "    cl_obo_folder=\"ontology/\",\n",
+        "    cl_obo_folder=\"./PopV/popv/ontology/\",\n",
         "    prediction_mode=\"inference\",  # 'fast' mode gives fast results (does not include BBKNN and Scanorama and makes more inaccurate predictions)\n",
         "    n_samples_per_label=n_samples_per_label,\n",
-        "    accelerator=\"cpu\",\n",
+        "    accelerator=\"cuda\",\n",
         "    compute_embedding=True,\n",
         "    hvg=None,\n",
         ").adata"
       ]
     },
-    {
-      "cell_type": "code",
-      "execution_count": 18,
-      "id": "f523194b",
-      "metadata": {},
-      "outputs": [],
-      "source": [
-        "adata.uns['_accelerator'] = 'cpu'"
-      ]
-    },
     {
       "cell_type": "code",
       "execution_count": 19,