spatialdata-io 0.7.1__tar.gz → 0.7.2__tar.gz

spatialdata_io-0.7.2/.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

spatialdata_io-0.7.2/.cruft.json

@@ -0,0 +1,44 @@
+{
+  "template": "https://github.com/scverse/cookiecutter-scverse",
+  "commit": "707f3faab836f9272912f92188b63b31da70c064",
+  "checkout": null,
+  "context": {
+    "cookiecutter": {
+      "project_name": "spatialdata-io",
+      "package_name": "spatialdata_io",
+      "project_description": "SpatialData IO for common techs",
+      "author_full_name": "scverse",
+      "author_email": "scverse@scverse.scverse",
+      "github_user": "scverse",
+      "github_repo": "spatialdata-io",
+      "license": "BSD 3-Clause License",
+      "ide_integration": false,
+      "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": "707f3faab836f9272912f92188b63b31da70c064"
+    }
+  },
+  "directory": null
+}

{spatialdata_io-0.7.1 → spatialdata_io-0.7.2}/.editorconfig

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

spatialdata_io-0.7.2/.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,93 @@
+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.
+
+  - 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_io-0.7.2/.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_io-0.7.2/.github/ISSUE_TEMPLATE/feature_request.yml

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

spatialdata_io-0.7.2/.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_io-0.7.2/.github/release.yml

@@ -0,0 +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:
+        - "*"

spatialdata_io-0.7.2/.github/workflows/autofix.yaml

@@ -0,0 +1,31 @@
+# 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
+      - 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_io-0.7.2/.github/workflows/build.yaml

@@ -0,0 +1,30 @@
+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@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
+      - name: Build package
+        run: uv build
+      - name: Check package
+        run: uvx twine check --strict dist/*.whl

spatialdata_io-0.7.2/.github/workflows/prepare_test_data.yaml

@@ -0,0 +1,107 @@
+name: Prepare test data
+
+on:
+  schedule:
+    - cron: "0 0 1 * *" # run once a month to prevent artifact expiration
+  workflow_dispatch:
+  # Uncomment and adjust the branch name if you need to add new datasets to the artifact.
+  # It needs to be a branch in the spatialdata-io origin repository, not from a fork.
+#  push:
+#    branches:
+#      - main
+
+permissions:
+  contents: read
+
+jobs:
+  prepare-data:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          persist-credentials: false
+
+      - name: Download test datasets
+        run: |
+          mkdir -p ./data
+          cd ./data
+
+          # -------
+          # the Xenium datasets are licensed as CC BY 4.0, as shown here
+          # https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/resources/xenium-example-data
+
+          # 10x Genomics Xenium 2.0.0
+          curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Breast_2fov/Xenium_V1_human_Breast_2fov_outs.zip
+          curl -O https://cf.10xgenomics.com/samples/xenium/2.0.0/Xenium_V1_human_Lung_2fov/Xenium_V1_human_Lung_2fov_outs.zip
+
+          # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, multimodal cell segmentation
+          # this file seems to be corrupted; skipping it for now
+          # curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny.zip
+
+          # 10x Genomics Xenium 3.0.0 (5K) Mouse ileum, nuclear expansion
+          curl -O https://cf.10xgenomics.com/samples/xenium/3.0.0/Xenium_Prime_Mouse_Ileum_tiny/Xenium_Prime_Mouse_Ileum_tiny_outs.zip
+
+          # 10x Genomics Xenium 4.0.0 (v1) Human ovary, nuclear expansion
+          curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Human_Ovary_tiny/Xenium_V1_Human_Ovary_tiny_outs.zip
+
+          # 10x Genomics Xenium 4.0.0 (v1) Human ovary, multimodal cell segmentation
+          curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_MultiCellSeg_Human_Ovary_tiny/Xenium_V1_MultiCellSeg_Human_Ovary_tiny_outs.zip
+
+          # 10x Genomics Xenium 4.0.0 (v1+Protein) Human kidney, multimodal cell segmentation
+          curl -O https://cf.10xgenomics.com/samples/xenium/4.0.0/Xenium_V1_Protein_Human_Kidney_tiny/Xenium_V1_Protein_Human_Kidney_tiny_outs.zip
+
+          # -------
+          # the Visium dataset is licensed as CC BY 4.0, as shown here
+          # https://www.10xgenomics.com/datasets/gene-and-protein-expression-library-of-human-breast-cancer-cytassist-ffpe-2-standard
+
+          # 10x Genomics Visium CytAssist Gene and Protein Expression Library of Human Breast Cancer, IF, 6.5mm (FFPE)
+          mkdir -p CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer
+          cd CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer
+          # The full-resolution tissue image is deliberately not downloaded (~2 GB): `fullres_image_file`
+          # is optional and the reader path it exercises is shared with the other readers.
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/2.1.0/CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer/CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer_filtered_feature_bc_matrix.h5
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/2.1.0/CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer/CytAssist_FFPE_Protein_Expression_Human_Breast_Cancer_spatial.tar.gz
+          cd ..
+
+          # -------
+          # the Visium HD dataset is licensed as CC BY 4.0, as shown here
+          # https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data
+
+          # 10x Genomics Visium HD 4.0.1 3' Mouse Brain Chunk
+          curl -O https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip
+
+          # -------
+          # we received written permission to make the following dataset public and integrate it in the CI system of spatialdata-io
+          # Spatial Genomics seqFISH v2
+          curl -O https://s3.embl.de/spatialdata/raw_data/seqfish-2-test-dataset.zip
+
+          # -------
+          # MACSima OMAP datasets are licensed as CC BY 4.0
+          # OMAP23 for format v1.x.x
+          curl -o OMAP23_small.zip "https://zenodo.org/api/records/18196452/files-archive"
+
+          # OMAP10 for format v0.x.x
+          curl -o OMAP10_small.zip "https://zenodo.org/api/records/18196366/files-archive"
+
+      - name: Unzip files
+        run: |
+          cd ./data
+          for file in *.zip; do
+              dir="${file%.zip}"
+              mkdir -p "$dir"
+              unzip "$file" -d "$dir"
+              rm "$file"
+          done
+          # the Visium archive contains a single `spatial/` directory, extracted next to the `.h5`
+          for file in */*.tar.gz; do
+              tar -xzf "$file" -C "$(dirname "$file")"
+              rm "$file"
+          done
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: data
+          path: ./data

spatialdata_io-0.7.2/.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_io
+    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@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
+        with:
+          enable-cache: false
+      - name: Build package
+        run: uv build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

spatialdata_io-0.7.2/.github/workflows/test.yaml

@@ -0,0 +1,114 @@
+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:
+  # Get the test environment from hatch as defined in pyproject.toml.
+  # This ensures that the pyproject.toml is the single point of truth for test definitions and the same tests are
+  # run locally and on continuous integration.
+  # Check [[tool.hatch.envs.hatch-test.matrix]] in pyproject.toml and https://hatch.pypa.io/latest/environment/ for
+  # more details.
+  get-environments:
+    runs-on: ubuntu-slim
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - &clone
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          filter: blob:none
+          fetch-depth: 0
+          persist-credentials: false
+      - &setup-uv
+        uses: astral-sh/setup-uv@bec219d24cd3e171d82865faccec33120bb574f4 # v10.1.0
+      - name: Get test environments
+        id: get-envs
+        run: |
+          ENVS_JSON=$(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
+
+  # Run tests through hatch. Spawns a separate runner for each environment defined in the hatch matrix obtained above.
+  test:
+    needs: get-environments
+    permissions:
+      id-token: write # for codecov OIDC
+      contents: read
+      actions: read # to download the test data artifact
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        env: ${{ fromJSON(needs.get-environments.outputs.envs) }}
+
+    name: ${{ matrix.env.label }}
+    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: Download artifact of test data
+        uses: dawidd6/action-download-artifact@d63b86af1b34672e53c440b1b83979861906bad7 # v24
+        with:
+          workflow: prepare_test_data.yaml
+          name: data
+          path: ./data
+      - 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
+      - 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@0b35c9ecc4f0529d0eb674914510c22f85b196b4 # v7.1.0
+        with:
+          fail_ci_if_error: true
+          use_oidc: true
+
+  # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
+  # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.
+  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_io-0.7.1 → spatialdata_io-0.7.2}/.gitignore

@@ -1,51 +1,36 @@
 # Temp files
 .DS_Store
 *~
-*.tmp
-temp/
+buck-out/
+
+# IDEs
+/.idea/
+/.vscode/
+/.spyproject/
+*.code-workspace
 
 # Compiled files
+.venv/
 __pycache__/
+.*cache/
 .ipynb_checkpoints/
 
 # Distribution / packaging
-/build/
 /dist/
-/*.egg-info/
+_version.py
+uv.lock
 
 # Tests and coverage
-/.pytest_cache/
-/.cache/
 /data/
+/node_modules/
+/.coverage*
+/tests/data/
 
 # docs
 /docs/generated/
 /docs/_build/
 
-# IDEs
-/.idea/
-/.vscode/
-/.spyproject/
-
-# docs
-/docs/generated/
-/docs/_build/
-
-# other
-_version.py
-node_modules/
-.code-workspace
-.asv/
-uv.lock
-
-# memray report
+# benchmarks
+/.asv/
 *.bin
-
-# speedscope report
 profile.speedscope.json
-
-# test datasets (e.g. Xenium ones)
-# data folder
-data/
-tests/data
-.venv

spatialdata_io-0.7.2/.panache.toml

@@ -0,0 +1,14 @@
+#:schema https://panache.bz/panache.schema.json
+flavor = "myst"
+
+[format]
+wrap = "preserve"
+smart-punctuation = "unicode"
+tab-stops = "preserve"
+
+# MyST syntax extensions from `scverse_doc.config.MYST_ENABLE_EXTENSIONS`
+[extensions]
+myst-colon-fence = true  # colon_fence
+definition-lists = true  # deflist
+tex-math-dollars = true  # dollarmath, amsmath
+raw-html = true          # html_image, html_admonition