fixes to the utils file

Author: selmanozleyen

.github/workflows/benchmark.yml

@@ -1,62 +1,62 @@
 name: Benchmark
 
 on:
-  push:
-    branches: [main]
-  pull_request:
-    branches: [main]
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
 
 env:
-  FORCE_COLOR: "1"
+    FORCE_COLOR: "1"
 
 defaults:
-  run:
-    shell: bash -e {0} # -e to fail on error
+    run:
+        shell: bash -e {0} # -e to fail on error
 
 jobs:
-  benchmark:
-    runs-on: ${{ matrix.os }}
-
-    strategy:
-      fail-fast: false
-      matrix:
-        python: ["3.13"]
-        os: [ubuntu-latest]
-
-    env:
-      OS: ${{ matrix.os }}
-      PYTHON: ${{ matrix.python }}
-      ASV_DIR: "./benchmarks"
-
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Fetch main branch for `asv run`’s hash
-        run: git fetch origin main:main
-        if: ${{ github.ref_name != 'main' }}
-
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python }}
-          cache: 'pip'
-
-      - name: Cache datasets
-        uses: actions/cache@v4
-        with:
-          path: |
-            ~/.cache
-          key: benchmark-state-${{ hashFiles('benchmarks/**') }}
-
-      - name: Install dependencies
-        run: pip install 'asv>=0.6.4'
-
-      - name: Configure ASV
-        working-directory: ${{ env.ASV_DIR }}
-        run: asv machine --yes
-
-      - name: Quick benchmark run
-        working-directory: ${{ env.ASV_DIR }}
-        run: asv run --dry-run --quick --show-stderr --verbose HEAD^!
+    benchmark:
+        runs-on: ${{ matrix.os }}
+
+        strategy:
+            fail-fast: false
+            matrix:
+                python: ["3.13"]
+                os: [ubuntu-latest]
+
+        env:
+            OS: ${{ matrix.os }}
+            PYTHON: ${{ matrix.python }}
+            ASV_DIR: "./benchmarks"
+
+        steps:
+            - uses: actions/checkout@v4
+              with:
+                  fetch-depth: 0
+
+            - name: Fetch main branch for `asv run`’s hash
+              run: git fetch origin main:main
+              if: ${{ github.ref_name != 'main' }}
+
+            - name: Set up Python ${{ matrix.python }}
+              uses: actions/setup-python@v5
+              with:
+                  python-version: ${{ matrix.python }}
+                  cache: "pip"
+
+            - name: Cache datasets
+              uses: actions/cache@v4
+              with:
+                  path: |
+                      ~/.cache
+                  key: benchmark-state-${{ hashFiles('benchmarks/**') }}
+
+            - name: Install dependencies
+              run: pip install 'asv>=0.6.4'
+
+            - name: Configure ASV
+              working-directory: ${{ env.ASV_DIR }}
+              run: asv machine --yes
+
+            - name: Quick benchmark run
+              working-directory: ${{ env.ASV_DIR }}
+              run: asv run --dry-run --quick --show-stderr --verbose HEAD^!

benchmarks/asv.conf.json

@@ -25,7 +25,7 @@
     // "uninstall_command": ["return-code=any python -mpip uninstall -y {project}"],
     "build_command": [
         "python -m pip install build",
-        "python -m build --wheel -o {build_cache_dir} {build_dir}",
+        "python -m build --wheel -o {build_cache_dir} {build_dir}"
     ],
 
     // List of branches to benchmark. If not provided, defaults to "master"
@@ -73,7 +73,7 @@
     "matrix": {
         "numpy": [""],
         "scipy": [""],
-        "squidpy": [""],
+        "squidpy": [""]
     },
 
     // Combinations of libraries/python versions can be excluded/included
@@ -123,7 +123,7 @@
 
     // The directory (relative to the current directory) that the html tree
     // should be written to.  If not provided, defaults to "html".
-    "html_dir": ".asv/html",
+    "html_dir": ".asv/html"
 
     // The number of characters to retain in the commit hashes.
     // "hash_length": 8,

benchmarks/benchmarks/_utils.py

@@ -69,16 +69,6 @@ def get_dataset(dataset: Dataset, *, layer: KeyX = None) -> tuple[AnnData, str |
     return adata, batch_key
 
 
-def get_count_dataset(dataset: Dataset, *, layer: KeyCount = "counts") -> tuple[AnnData, str | None]:
-    adata, batch_key = _get_dataset_raw(dataset)
-
-    adata.X = adata.layers.pop(layer)
-    # remove indicators that X was transformed
-    adata.uns.pop("log1p", None)
-
-    return adata, batch_key
-
-
 def param_skipper(param_names: Sequence[str], params: tuple[Sequence[object], ...]) -> ParamSkipper:
     """Create a decorator that will skip all combinations that contain any of the given parameters.