Fix codecov CI and update template

.cruft.json

@@ -1,23 +1,23 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "57f6267716826dad73baba46dc3c00fe7262c459",
-    "checkout": "v0.2.0",
-    "context": {
-        "cookiecutter": {
-            "project_name": "scib-metrics",
-            "package_name": "scib_metrics",
-            "project_description": "Accelerated and Python-only scIB metrics",
-            "author_full_name": "Adam Gayoso",
-            "author_email": "adamgayoso@berkeley.edu",
-            "github_user": "adamgayoso",
-            "project_repo": "https://github.com/yoseflab/scib-metrics",
-            "license": "BSD 3-Clause License",
-            "_copy_without_render": [
-                ".github/workflows/**.yaml",
-                "docs/_templates/autosummary/**.rst"
-            ],
-            "_template": "https://github.com/scverse/cookiecutter-scverse"
-        }
-    },
-    "directory": null
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "c21b82bf134f3a0f13db7482d4fb04ca1f562d59",
+  "checkout": "main",
+  "context": {
+    "cookiecutter": {
+      "project_name": "scib-metrics",
+      "package_name": "scib_metrics",
+      "project_description": "Accelerated and Python-only scIB metrics",
+      "author_full_name": "Adam Gayoso",
+      "author_email": "adamgayoso@berkeley.edu",
+      "github_user": "adamgayoso",
+      "project_repo": "https://github.com/yoseflab/scib-metrics",
+      "license": "BSD 3-Clause License",
+      "_copy_without_render": [
+        ".github/workflows/**.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_template": "https://github.com/scverse/cookiecutter-scverse"
+    }
+  },
+  "directory": null
 }

.github/workflows/sync.yaml.rej

@@ -0,0 +1,7 @@
+diff a/.github/workflows/sync.yaml b/.github/workflows/sync.yaml	(rejected hunks)
+@@ -43,4 +43,4 @@ jobs:
+                       manually merge these changes.**
+
+                       For more information about the template sync, please refer to the
+-                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/developer_docs.html#automated-template-sync).
++                      [template documentation](https://cookiecutter-scverse-instance.readthedocs.io/en/latest/template_usage.html#automated-template-sync).

.github/workflows/test.yaml

@@ -6,6 +6,10 @@ on:
     pull_request:
         branches: [main]
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
 jobs:
     test:
         runs-on: ${{ matrix.os }}
@@ -24,27 +28,17 @@ jobs:
             PYTHON: ${{ matrix.python }}
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
             - name: Set up Python ${{ matrix.python }}
-              uses: actions/setup-python@v2
+              uses: actions/setup-python@v4
               with:
                   python-version: ${{ matrix.python }}
+                  cache: "pip"
+                  cache-dependency-path: "**/pyproject.toml"
 
-            - name: Get pip cache dir
-              id: pip-cache-dir
-              run: |
-                  echo "::set-output name=dir::$(pip cache dir)"
-            - name: Restore pip cache
-              uses: actions/cache@v2
-              with:
-                  path: ${{ steps.pip-cache-dir.outputs.dir }}
-                  key: pip-${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/pyproject.toml') }}
-                  restore-keys: |
-                      pip-${{ runner.os }}-${{ env.pythonLocation }}-
             - name: Install test dependencies
               run: |
                   python -m pip install --upgrade pip wheel
-                  pip install codecov
             - name: Install dependencies
               run: |
                   pip install ".[dev,test]"
@@ -56,7 +50,4 @@ jobs:
               run: |
                   pytest -v --cov --color=yes
             - name: Upload coverage
-              env:
-                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}
-              run: |
-                  codecov --required --flags=unittests
+              uses: codecov/codecov-action@v3