spatialdata 0.7.3a2__tar.gz → 0.9.0__tar.gz

spatialdata-0.9.0/.claude/skills/memray/SKILL.md

@@ -0,0 +1,37 @@
+---
+name: memray
+description: Profile the memory usage of a Python script using memray and visualize a temporal flamegraph in the browser. Use when the user wants to investigate memory consumption, find leaks, or understand allocation patterns.
+compatibility: Requires the pixi profiling environment (pixi run -e profiling). Supports Linux and macOS.
+allowed-tools: Bash(pixi run -e profiling memray-run:*) Bash(pixi run -e profiling memray-flame:*) Bash(open:*) Bash(xdg-open:*) Bash(python -m webbrowser:*)
+---
+
+## Steps
+
+1. Ask the user which script to profile (full or relative path).
+
+2. Run the script under memray:
+
+    ```bash
+    pixi run -e profiling memray-run script.py
+    ```
+
+    This produces a binary file named `memray-script.py.<pid>.bin` in the current directory.
+
+3. Generate the flamegraph HTML report from the `.bin` file:
+
+    ```bash
+    pixi run -e profiling memray-flame memray-script.py.<pid>.bin
+    ```
+
+    Replace `<pid>` with the actual PID shown in the filename. This writes `memray-flamegraph-script.py.<pid>.html`.
+
+4. Open the report in the browser:
+    - macOS: `open memray-flamegraph-script.py.<pid>.html`
+    - Linux: `xdg-open memray-flamegraph-script.py.<pid>.html`
+    - Either: `python -m webbrowser memray-flamegraph-script.py.<pid>.html`
+
+## Notes
+
+- The `--temporal` flag (included in `memray-flame`) shows memory over time, not just peak — use this to spot leaks and allocation bursts.
+- To find the `.bin` file if unsure of the name: `ls memray-*.bin`
+- To compare runs, save the previous report: `cp memray-flamegraph-script.py.<pid>.html memray-flamegraph-before.html`

spatialdata-0.9.0/.claude/skills/profimp/SKILL.md

@@ -0,0 +1,30 @@
+---
+name: profimp
+description: Profile Python import time using profimp and open a waterfall HTML report. Use when investigating slow startup or wanting to identify which imports are most expensive.
+compatibility: Requires profimp (available as a pixi dependency). macOS or Linux.
+allowed-tools: Bash(profimp:*) Bash(open:*) Bash(xdg-open:*) Bash(python -m webbrowser:*)
+---
+
+## Steps
+
+1. Ask what to profile. Suggest common patterns for this repo:
+    - `import spatialdata`
+    - `from spatialdata import SpatialData`
+    - `from spatialdata_io import xenium`
+
+2. Run:
+
+```bash
+profimp --html "<import_stmt>" > /tmp/profimp.html
+```
+
+3. Open the report:
+    - macOS: `open /tmp/profimp.html`
+    - Linux: `xdg-open /tmp/profimp.html`
+    - Either: `python -m webbrowser /tmp/profimp.html`
+
+## Notes
+
+- The report is a waterfall chart showing every sub-import and its timing.
+- To compare before/after: `cp /tmp/profimp.html /tmp/profimp-before.html` before re-running.
+- `pixi run python -m profimp` also works if `profimp` is not on PATH.

spatialdata-0.9.0/.claude/skills/pyspy/SKILL.md

@@ -0,0 +1,45 @@
+---
+name: pyspy
+description: Profile the execution time of a Python script using py-spy and visualize the result with speedscope. Use when the user wants to benchmark performance, find slow code paths, or profile CPU time.
+compatibility: Requires the pixi profiling environment (pixi run -e profiling). Speedscope must be installed separately (npm install -g speedscope). sudo is required on macOS.
+allowed-tools: Bash(pixi run -e profiling pyspy:*) Bash(pixi run -e profiling speedscope:*) Bash(sudo pixi run -e profiling pyspy:*)
+---
+
+## Steps
+
+1. Ask the user which script to profile (full or relative path).
+
+2. Run py-spy to record the profile. The output is always written to `profile.speedscope.json` in the current directory.
+
+    **Linux** (no sudo needed):
+
+    ```bash
+    pixi run -e profiling pyspy script.py
+    ```
+
+    **macOS** (sudo required — py-spy needs to attach to the process):
+
+    ```bash
+    sudo pixi run -e profiling pyspy script.py
+    ```
+
+    If sudo fails to find the pixi environment, use absolute paths:
+
+    ```bash
+    sudo /path/to/.pixi/envs/profiling/bin/py-spy record --gil \
+      -o profile.speedscope.json --format speedscope \
+      -- /path/to/.pixi/envs/profiling/bin/python script.py
+    ```
+
+3. Open the result in speedscope:
+    ```bash
+    pixi run -e profiling speedscope
+    ```
+    This opens `profile.speedscope.json` in the browser via the local speedscope CLI.
+
+## Notes
+
+- If the speedscope view is blank, switch threads using the thread selector in the top-right corner.
+- To save a profile before overwriting: `cp profile.speedscope.json profile-before.speedscope.json`
+- `--gil` records only time when the GIL is held (Python-level CPU time). Drop it to include C extension time.
+- speedscope must be installed globally: `npm install -g speedscope`

spatialdata-0.7.3a2/.github/codecov.yml → spatialdata-0.9.0/.codecov.yaml

@@ -1,6 +1,6 @@
 # Based on pydata/xarray
 codecov:
-    require_ci_to_pass: false
+    require_ci_to_pass: no
 
 coverage:
     status:
@@ -12,6 +12,6 @@ coverage:
         changes: false
 
 comment:
-    layout: "diff, flags, files"
+    layout: diff, flags, files
     behavior: once
-    require_base: false
+    require_base: no

spatialdata-0.9.0/.cruft.json

@@ -0,0 +1,44 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "eb4523fde2e18bcfc121ff2cd722c9037ff8b910",
+  "checkout": "main",
+  "context": {
+    "cookiecutter": {
+      "project_name": "spatialdata",
+      "package_name": "spatialdata",
+      "project_description": "Spatial data format.",
+      "author_full_name": "scverse",
+      "author_email": "luca.marconato@scverse.org",
+      "github_user": "scverse",
+      "github_repo": "spatialdata",
+      "license": "BSD 3-Clause License",
+      "ide_integration": true,
+      "issue_categorization": "issue types",
+      "_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
+}

{spatialdata-0.7.3a2 → spatialdata-0.9.0}/.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

spatialdata-0.9.0/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,116 @@
+name: Bug report
+description: Report something that is broken or incorrect
+type: 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

spatialdata-0.9.0/.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.

spatialdata-0.9.0/.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for spatialdata
+type: 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

spatialdata-0.9.0/.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:
+                  - "*"

spatialdata-0.9.0/.github/workflows/autofix.yaml

@@ -0,0 +1,32 @@
+# The workflow name is mandated by autofix.ci.
+# It needs to be a dedicated workflow, as autofix.ci times out on long runs.
+name: autofix.ci
+
+on:
+    pull_request:
+
+env:
+    FORCE_COLOR: "1"
+    UV_COMPILE_BYTECODE: "1"
+
+permissions:
+    contents: read
+
+jobs:
+    lint:
+        name: Pre-commit checks
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  fetch-depth: 0
+                  filter: blob:none
+                  persist-credentials: false
+            - uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+              with:
+                  enable-cache: true
+            - run: uv tool install hatch
+            - name: Run pre-commit hooks
+              run: uvx prek run --all-files --show-diff-on-failure --color=always
+            - uses: autofix-ci/action@c5b2d67aa2274e7b5a18224e8171550871fc7e4a # v1.3.4
+              if: ${{ !cancelled() }}

spatialdata-0.9.0/.github/workflows/build.yaml

@@ -0,0 +1,32 @@
+name: Check Build
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+permissions:
+    contents: read
+
+jobs:
+    package:
+        runs-on: ubuntu-latest
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - name: Install uv
+              uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+              with:
+                  enable-cache: false
+            - name: Build package
+              run: uv build
+            - name: Check package
+              run: uvx twine check --strict dist/*.whl

{spatialdata-0.7.3a2 → spatialdata-0.9.0}/.github/workflows/build_image.yml

@@ -2,8 +2,8 @@ name: Build Docker image
 
 on:
     workflow_dispatch:
-#    schedule:
-#        -   cron: '0 0 * * *'  # run daily at midnight UTC
+    #  schedule:
+    #    - cron: "0 0 * * *"  # run daily at midnight UTC
 
 env:
     REGISTRY: ghcr.io
@@ -13,6 +13,9 @@ concurrency:
     group: ${{ github.workflow }}-${{ github.ref }}
     cancel-in-progress: true
 
+permissions:
+    contents: read
+
 jobs:
     build:
         runs-on: ubuntu-latest
@@ -29,10 +32,13 @@ jobs:
 
         steps:
             - name: Checkout code
-              uses: actions/checkout@v4
+              uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  persist-credentials: false
 
             - name: Set up Python
-              uses: actions/setup-python@v4
+              uses: actions/setup-python@6d4fd22b20465ccc0f7354476588e8df7c9ca0e0 # v7.1.0
               with:
                   python-version: "3.x"
 
@@ -77,13 +83,13 @@ jobs:
 
             - name: Login to GitHub Container Registry
               if: ${{ env.skip_build == 'false' }}
-              uses: docker/login-action@v3
+              uses: docker/login-action@81c6f93d4bc991e510b342a00b419b3bb4efc5c6 # v4.7.0
               with:
                   registry: ${{ env.REGISTRY }}
                   username: ${{ github.actor }}
                   password: ${{ secrets.GITHUB_TOKEN }}
 
-            - uses: docker/build-push-action@v5
+            - uses: docker/build-push-action@c3c9e263c25d99ce0380d002d59b67737d91b0dc # v7.4.0
               if: ${{ env.skip_build == 'false' }}
               env:
                   IMAGE_TAG: ${{ env.REGISTRY }}/scverse/spatialdata:${{ env.IMAGE_TAG_SUFFIX }}

spatialdata-0.9.0/.github/workflows/release.yaml

@@ -0,0 +1,33 @@
+name: Release
+
+on:
+    release:
+        types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+permissions: {}
+
+jobs:
+    release:
+        name: Upload release to PyPI
+        runs-on: ubuntu-latest
+        environment:
+            name: pypi
+            url: https://pypi.org/p/spatialdata
+        permissions:
+            contents: read
+            id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+        steps:
+            - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - name: Install uv
+              uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+              with:
+                  enable-cache: false
+            - name: Build package
+              run: uv build
+            - name: Publish package distributions to PyPI
+              uses: pypa/gh-action-pypi-publish@7245906fb61fa33a13554f9d5fb856fe61758086 # v1.14.3

spatialdata-0.9.0/.github/workflows/test.yaml

@@ -0,0 +1,103 @@
+name: Test
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+    schedule:
+        - cron: "0 5 1,15 * *"
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+permissions:
+    contents: read
+
+jobs:
+    # [tool.hatch.envs.hatch-test.matrix] in pyproject.toml is the single source of truth: the same environments run here and locally.
+    get-environments:
+        runs-on: ubuntu-slim
+        outputs:
+            envs: ${{ steps.get-envs.outputs.envs }}
+        steps:
+            - &clone
+              uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+              with:
+                  filter: blob:none
+                  fetch-depth: 0
+                  persist-credentials: false
+            - &setup-uv
+              uses: astral-sh/setup-uv@68559e99cc807c1eb7e9238fd43a15bba460eec2 # v10.3.3
+              with:
+                  prune-cache: true
+            - name: Get test environments
+              id: get-envs
+              run: |
+                  ENVS_JSON=$(uvx hatch env show --json | jq -c 'to_entries
+                    | map(
+                        select(.key | startswith("hatch-test"))
+                        | {
+                            name: .key,
+                            label: (if (.key | contains("pre")) then .key + " (PRE-RELEASE DEPENDENCIES)" else .key end),
+                            python: .value.python
+                          }
+                      )')
+                  echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+
+    test:
+        needs: get-environments
+        permissions:
+            id-token: write # for codecov OIDC
+            contents: read
+
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest, macos-latest, windows-latest]
+                env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+        name: ${{ matrix.env.label }} (${{ matrix.os }})
+        runs-on: ${{ matrix.os }}
+        continue-on-error: ${{ contains(matrix.env.name, 'pre') }} # make "all-green" pass even if pre-release job fails
+        env:
+            UV_PYTHON: ${{ matrix.env.python }}
+
+        steps:
+            - *clone
+            - *setup-uv
+            - name: create hatch environment
+              run: uvx hatch env create ${{ matrix.env.name }}
+            - name: list all all installed package versions
+              run: uvx hatch run ${{ matrix.env.name }}:uv pip list
+            - name: run tests using hatch
+              env:
+                  MPLBACKEND: agg
+                  PLATFORM: ${{ matrix.os }}
+                  DISPLAY: :42
+              run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto --dist worksteal --run-network
+            - name: generate coverage report
+              run: |
+                  # See https://coverage.readthedocs.io/page/config.html#run-patch
+                  test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+                  uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+                  uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
+            - name: Upload coverage
+              uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
+              with:
+                  fail_ci_if_error: true
+                  use_oidc: true
+
+    # One required check for branch protection, so it does not need updating whenever the matrix changes.
+    check:
+        name: Tests pass in all hatch environments
+        if: always()
+        needs:
+            - get-environments
+            - test
+        runs-on: ubuntu-latest
+        steps:
+            - uses: re-actors/alls-green@b5b5b37504aa4183270bd3d855c52a67f212be35 # v1.3.0
+              with:
+                  jobs: ${{ toJSON(needs) }}

{spatialdata-0.7.3a2 → spatialdata-0.9.0}/.gitignore

@@ -1,10 +1,16 @@
 # Temp files
 .DS_Store
 *~
+buck-out/
 .dmypy.json
+temp/
 
 # Compiled files
+.venv/
+uv.lock
+pixi.lock
 __pycache__/
+.*cache/
 
 # Distribution / packaging
 /build/
@@ -12,27 +18,23 @@ __pycache__/
 /*.egg-info/
 
 # Tests and coverage
-/.pytest_cache/
-/.cache/
 /data/
+/node_modules/
+/.coverage*
+/coverage.xml
 
 # docs
-docs/_build
-!docs/api/.md
-docs/**/generated
+/docs/generated/
+/docs/_build/
+docs/**/generated/
 docs/_static/datasets_data.js
 
 # IDEs
 /.idea/
-.vscode
 
 # data
 *.zarr/
 
-# temp files
-temp/
-
-
 # symlinks (luca) for extending the refactoring to satellite projects
 napari-spatialdata
 spatialdata-io
@@ -46,11 +48,9 @@ spatialdata-sandbox
 # version file
 _version.py
 
-# other
-node_modules/
+# agents configurations
+.claude/settings.local.json
 
+# benchmarking and profiling
 .asv/
-
-.mypy_cache
-.ruff_cache
-uv.lock
+profile.speedscope.json

{spatialdata-0.7.3a2 → spatialdata-0.9.0}/.gitmodules

@@ -1,3 +1,3 @@
 [submodule "docs/tutorials/notebooks"]
 	path = docs/tutorials/notebooks
-	url = https://github.com/scverse/spatialdata-notebooks
+	url = https://github.com/scverse/spatialdata-tutorials