Fix codecov CI and update template

.cruft.json

@@ -1,23 +1,23 @@
 {
-    "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "57f6267716826dad73baba46dc3c00fe7262c459",
-    "checkout": "v0.1.4",
-    "context": {
-        "cookiecutter": {
-            "project_name": "spatialdata-plot",
-            "package_name": "spatialdata_plot",
-            "project_description": "A very interesting piece of code",
-            "author_full_name": "scverse",
-            "author_email": "scverse",
-            "github_user": "scverse",
-            "project_repo": "https://github.com/scverse/spatialdata-plot",
-            "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": "spatialdata-plot",
+      "package_name": "spatialdata_plot",
+      "project_description": "A very interesting piece of code",
+      "author_full_name": "scverse",
+      "author_email": "scverse",
+      "github_user": "scverse",
+      "project_repo": "https://github.com/scverse/spatialdata-plot",
+      "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/build.yaml

@@ -6,15 +6,21 @@ on:
     pull_request:
         branches: [main]
 
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
 jobs:
     package:
         runs-on: ubuntu-latest
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
             - name: Set up Python 3.10
-              uses: actions/setup-python@v2
+              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

.github/workflows/sync.yaml

@@ -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 }}

.github/workflows/test.yaml.rej

@@ -0,0 +1,42 @@
+diff a/.github/workflows/test.yaml b/.github/workflows/test.yaml	(rejected hunks)
+@@ -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

docs/conf.py

@@ -16,12 +16,15 @@
 
 # -- Project information -----------------------------------------------------
 
+# NOTE: If you installed your project in editable mode, this might be stale.
+#       If this is the case, reinstall it to refresh the metadata
 info = metadata("spatialdata-plot")
 project_name = info["Name"]
 author = info["Author"]
 copyright = f"{datetime.now():%Y}, {author}."
 version = info["Version"]
-repository_url = f"https://github.com/scverse/{project_name}"
+urls = dict(pu.split(", ") for pu in info.get_all("Project-URL"))
+repository_url = urls["Source"]
 
 # The full version, including alpha/beta/rc tags
 release = info["Version"]

docs/contributing.md

@@ -142,6 +142,7 @@ Please write documentation for new or changed features and use-cases. This proje
 -   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
 -   Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
 -   [Sphinx autodoc typehints][], to automatically reference annotated input and output types
+-   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
 on how to write documentation.

docs/references.bib

@@ -1,17 +1,10 @@
-@article{Wolf2018,
-  author   = {Wolf, F. Alexander
-              and Angerer, Philipp
-              and Theis, Fabian J.},
-  title    = {SCANPY: large-scale single-cell gene expression data analysis},
-  journal  = {Genome Biology},
-  year     = {2018},
-  month    = {Feb},
-  day      = {06},
-  volume   = {19},
-  number   = {1},
-  pages    = {15},
-  abstract = {Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks. Its Python-based implementation efficiently deals with data sets of more than one million cells (https://github.com/theislab/Scanpy). Along with Scanpy, we present AnnData, a generic class for handling annotated data matrices (https://github.com/theislab/anndata).},
-  issn     = {1474-760X},
-  doi      = {10.1186/s13059-017-1382-0},
-  url      = {https://doi.org/10.1186/s13059-017-1382-0}
+@article{Virshup_2023,
+	doi = {10.1038/s41587-023-01733-8},
+	url = {https://doi.org/10.1038%2Fs41587-023-01733-8},
+	year = 2023,
+	month = {apr},
+	publisher = {Springer Science and Business Media {LLC}},
+	author = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
+	title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
+	journal = {Nature Biotechnology}
 }

pyproject.toml.rej

@@ -0,0 +1,11 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -109,6 +109,9 @@ ignore = [
+     "D213",
+ ]
+
++[tool.ruff.pydocstyle]
++convention = "numpy"
++
+ [tool.ruff.per-file-ignores]
+ "docs/*" = ["I"]
+ "tests/*" = ["D"]

src/spatialdata_plot/pp/basic.py.rej

@@ -0,0 +1,10 @@
+diff a/src/spatialdata_plot/pp/basic.py b/src/spatialdata_plot/pp/basic.py	(rejected hunks)
+@@ -2,7 +2,7 @@ from anndata import AnnData
+
+
+ def basic_preproc(adata: AnnData) -> int:
+-    """Run a basic preprocessing on the AnnData :cite:p:`Wolf2018` object.
++    """Run a basic preprocessing on the AnnData object.
+
+     Parameters
+     ----------

tests/test_basic.py.rej

@@ -0,0 +1,10 @@
+diff a/tests/test_basic.py b/tests/test_basic.py	(rejected hunks)
+@@ -4,7 +4,7 @@ import spatialdata_plot
+
+
+ def test_package_has_version():
+-    spatialdata_plot.__version__
++    assert spatialdata_plot.__version__ is not None
+
+
+ @pytest.mark.skip(reason="This decorator should be removed when test passes.")