Adopt the scverse cookiecutter template

.codecov.yaml

@@ -0,0 +1,17 @@
+# Based on pydata/xarray
+codecov:
+  require_ci_to_pass: no
+
+coverage:
+  status:
+    project:
+      default:
+        # Require 1% coverage, i.e., always succeed
+        target: 1
+    patch: false
+    changes: false
+
+comment:
+  layout: diff, flags, files
+  behavior: once
+  require_base: no

.cruft.json

@@ -0,0 +1,44 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "eb4523fde2e18bcfc121ff2cd722c9037ff8b910",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "spatialdata",
+      "package_name": "spatialdata",
+      "project_description": "Spatial data format.",
+      "author_full_name": "scverse",
+      "author_email": "giov.pll@gmail.com",
+      "github_user": "scverse",
+      "github_repo": "spatialdata",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "issue_categorization": "labels",
+      "_copy_without_render": [
+        ".github/workflows/build.yaml",
+        ".github/workflows/test.yaml",
+        "docs/_templates/autosummary/**.rst"
+      ],
+      "_exclude_on_template_update": [
+        "CHANGELOG.md",
+        "LICENSE",
+        "README.md",
+        "docs/api.md",
+        "docs/index.md",
+        "docs/notebooks/example.ipynb",
+        "docs/references.bib",
+        "docs/references.md",
+        "src/**",
+        "tests/**"
+      ],
+      "_render_devdocs": false,
+      "_jinja2_env_vars": {
+        "lstrip_blocks": true,
+        "trim_blocks": true
+      },
+      "_template": "https://github.com/scverse/cookiecutter-scverse",
+      "_commit": "eb4523fde2e18bcfc121ff2cd722c9037ff8b910"
+    }
+  },
+  "directory": null
+}

.editorconfig

@@ -9,5 +9,8 @@ trim_trailing_whitespace = true
 insert_final_newline = true
 line_length = 120
 
+[{*.{yml,yaml,toml},.cruft.json}]
+indent_size = 2
+
 [Makefile]
 indent_style = tab

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,116 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Replicate problems on public datasets or share data subsets when full sharing isn't possible.
+
+        Generally, the easier it is for us to reproduce the issue, the faster we can work on it. If you can, please:
+
+        1. Reproduce using the [`blobs` dataset](https://spatialdata.scverse.org/en/stable/api/datasets.html#spatialdata.datasets.blobs):
+
+           ```python
+           from spatialdata.datasets import blobs
+
+           sdata = blobs()
+           ```
+
+           You can also use [`blobs_annotating_element`](https://spatialdata.scverse.org/en/stable/api/datasets.html#spatialdata.datasets.blobs_annotating_element) for more control:
+
+           ```python
+           from spatialdata.datasets import blobs_annotating_element
+
+           sdata = blobs_annotating_element("blobs_labels")
+           ```
+
+        2. If the above is not possible, reproduce using a public dataset and explain how we can download the data.
+        3. If the data is private, consider sharing an anonymized version/subset via a [Zulip private message](https://scverse.zulipchat.com/#user/480560), or provide screenshots/GIFs showing the behavior.
+
+        Please report only one bug per issue.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Versions
+      description: |
+        Which version of packages.
+
+        Please install `session-info2`, run the following command in a notebook,
+        click the “Copy as Markdown” button, then paste the results into the text box below.
+
+        ```python
+        In[1]: import session_info2; session_info2.session_info(dependencies=True)
+        ```
+
+        Alternatively, run this in a console:
+
+        ```python
+        >>> import session_info2; print(session_info2.session_info(dependencies=True)._repr_mimebundle_()["text/markdown"])
+        ```
+      render: python
+      placeholder: |
+        anndata	0.11.3
+        ----	----
+        charset-normalizer	3.4.1
+        coverage	7.7.0
+        psutil	7.0.0
+        dask	2024.7.1
+        jaraco.context	5.3.0
+        numcodecs	0.15.1
+        jaraco.functools	4.0.1
+        Jinja2	3.1.6
+        sphinxcontrib-jsmath	1.0.1
+        sphinxcontrib-htmlhelp	2.1.0
+        toolz	1.0.0
+        session-info2	0.1.2
+        PyYAML	6.0.2
+        llvmlite	0.44.0
+        scipy	1.15.2
+        pandas	2.2.3
+        sphinxcontrib-devhelp	2.0.0
+        h5py	3.13.0
+        tblib	3.0.0
+        setuptools-scm	8.2.0
+        more-itertools	10.3.0
+        msgpack	1.1.0
+        sparse	0.15.5
+        wrapt	1.17.2
+        jaraco.collections	5.1.0
+        numba	0.61.0
+        pyarrow	19.0.1
+        pytz	2025.1
+        MarkupSafe	3.0.2
+        crc32c	2.7.1
+        sphinxcontrib-qthelp	2.0.0
+        sphinxcontrib-serializinghtml	2.0.0
+        zarr	2.18.4
+        asciitree	0.3.3
+        six	1.17.0
+        sphinxcontrib-applehelp	2.0.0
+        numpy	2.1.3
+        cloudpickle	3.1.1
+        sphinxcontrib-bibtex	2.6.3
+        natsort	8.4.0
+        jaraco.text	3.12.1
+        setuptools	76.1.0
+        Deprecated	1.2.18
+        packaging	24.2
+        python-dateutil	2.9.0.post0
+        ----	----
+        Python	3.13.2 | packaged by conda-forge | (main, Feb 17 2025, 14:10:22) [GCC 13.3.0]
+        OS	Linux-6.11.0-109019-tuxedo-x86_64-with-glibc2.39
+        Updated	2025-03-18 15:47

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Scverse Community Forum
+    url: https://discourse.scverse.org/
+    about: If you have questions about “How to do X”, please ask them here.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for spatialdata
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: pre-commit
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      pre-commit:
+        patterns: ["*"]
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: weekly
+    cooldown:
+      default-days: 7
+    groups:
+      actions-deps:
+        patterns:
+          - "*"

.github/release.yml

@@ -1,29 +1,29 @@
 changelog:
-    exclude:
-        labels:
-            - release-ignore
-        authors:
-            - pre-commit-ci
-            - pre-commit-ci[bot]
-    categories:
-        - title: Added
-          labels:
-              - "release-added"
-        - title: Changed
-          labels:
-              - "release-changed"
-        - title: Deprecated
-          labels:
-              - "release-deprecated"
-        - title: Removed
-          labels:
-              - "release-removed"
-        - title: Fixed
-          labels:
-              - "release-fixed"
-        - title: Security
-          labels:
-              - "release-security"
-        - title: Other Changes
-          labels:
-              - "*"
+  exclude:
+    labels:
+      - release-ignore
+    authors:
+      - pre-commit-ci
+      - pre-commit-ci[bot]
+  categories:
+    - title: Added
+      labels:
+        - "release-added"
+    - title: Changed
+      labels:
+        - "release-changed"
+    - title: Deprecated
+      labels:
+        - "release-deprecated"
+    - title: Removed
+      labels:
+        - "release-removed"
+    - title: Fixed
+      labels:
+        - "release-fixed"
+    - title: Security
+      labels:
+        - "release-security"
+    - title: Other Changes
+      labels:
+        - "*"