Merge branch 'main' into filter

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,53 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Recommendation: attach a minimal working example**
+Generally, the easier it is for us to reproduce the issue, the faster we can work on it. It is not required, but if you can, please:
+
+1. Reproduce using the [`blobs` dataset](https://spatialdata.scverse.org/en/latest/generated/spatialdata.datasets.blobs.html)
+
+    ```python
+    from spatialdata.datasets import blobs
+
+    sdata = blobs()
+    ```
+
+    You can also use [`blobs_annotating_element`](https://spatialdata.scverse.org/en/latest/generated/spatialdata.datasets.blobs_annotating_element.html) for more control:
+
+    ```
+    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.
+
+**Describe the bug**
+A clear and concise description of what the bug is; please report only one bug per issue.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (optional):**
+
+- OS: [e.g. macOS, Windows, Linux]
+- Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,19 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: ""
+assignees: ""
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/release.yml

@@ -0,0 +1,28 @@
+changelog:
+    exclude:
+        labels:
+            - release-ignore
+        authors:
+            - pre-commit-ci
+    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:
+              - "*"

.github/workflows/build_image.yml

@@ -0,0 +1,100 @@
+name: Build Docker image
+
+on:
+    workflow_dispatch:
+#    schedule:
+#        -   cron: '0 0 * * *'  # run daily at midnight UTC
+
+env:
+    REGISTRY: ghcr.io
+    IMAGE_NAME: ${{ github.repository }}
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+
+        defaults:
+            run:
+                shell: bash -e {0} # -e to fail on error
+
+        permissions:
+            contents: read
+            packages: write
+            attestations: write
+            id-token: write
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v4
+
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: "3.x"
+
+            - name: Upgrade pip
+              run: pip install pip
+
+            - name: Get latest versions
+              id: get_versions
+              run: |
+                  SPATIALDATA_VERSION=$(pip index versions spatialdata | grep "Available versions" | sed 's/Available versions: //' | awk -F', ' '{print $1}')
+                  SPATIALDATA_IO_VERSION=$(pip index versions spatialdata-io | grep "Available versions" | sed 's/Available versions: //' | awk -F', ' '{print $1}')
+                  SPATIALDATA_PLOT_VERSION=$(pip index versions spatialdata-plot | grep "Available versions" | sed 's/Available versions: //' | awk -F', ' '{print $1}')
+                  echo "SPATIALDATA_VERSION=${SPATIALDATA_VERSION}" >> $GITHUB_ENV
+                  echo "SPATIALDATA_IO_VERSION=${SPATIALDATA_IO_VERSION}" >> $GITHUB_ENV
+                  echo "SPATIALDATA_PLOT_VERSION=${SPATIALDATA_PLOT_VERSION}" >> $GITHUB_ENV
+
+            - name: Check if image tag exists
+              id: check_tag
+              env:
+                  IMAGE_TAG_SUFFIX: spatialdata${{ env.SPATIALDATA_VERSION }}_spatialdata-io${{ env.SPATIALDATA_IO_VERSION }}_spatialdata-plot${{ env.SPATIALDATA_PLOT_VERSION }}
+                  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+              run: |
+                  # Define the API URL
+                  API_URL="https://api.github.com/orgs/scverse/packages/container/spatialdata/versions"
+
+                  # Fetch all existing versions
+                  existing_tags=$(curl -s -H "Authorization: token $GITHUB_TOKEN" $API_URL | jq -r '.[].metadata.container.tags[]')
+
+                  # Debug: Output all existing tags
+                  echo "Existing tags:"
+                  echo "$existing_tags"
+
+                  # Check if the constructed tag exists
+                  if echo "$existing_tags" | grep -q "$IMAGE_TAG_SUFFIX"; then
+                    echo "Image tag $IMAGE_TAG_SUFFIX already exists. Skipping build."
+                    echo "skip_build=true" >> $GITHUB_ENV
+                  else
+                    echo "Image tag $IMAGE_TAG_SUFFIX does not exist. Proceeding with build."
+                    echo "skip_build=false" >> $GITHUB_ENV
+                    echo "IMAGE_TAG_SUFFIX=${IMAGE_TAG_SUFFIX}" >> $GITHUB_ENV
+                  fi
+
+            - name: Login to GitHub Container Registry
+              if: ${{ env.skip_build == 'false' }}
+              uses: docker/login-action@v3
+              with:
+                  registry: ${{ env.REGISTRY }}
+                  username: ${{ github.actor }}
+                  password: ${{ secrets.GITHUB_TOKEN }}
+
+            - uses: docker/build-push-action@v5
+              if: ${{ env.skip_build == 'false' }}
+              env:
+                  IMAGE_TAG: ${{ env.REGISTRY }}/scverse/spatialdata:${{ env.IMAGE_TAG_SUFFIX }}
+              with:
+                  context: .
+                  file: ./Dockerfile
+                  push: true
+                  cache-from: type=registry,ref=${{ env.REGISTRY }}/scverse/spatialdata:buildcache
+                  cache-to: type=inline,ref=${{ env.REGISTRY }}/scverse/spatialdata:buildcache
+                  build-args: |
+                      SPATIALDATA_VERSION=${{ env.SPATIALDATA_VERSION }}
+                      SPATIALDATA_IO_VERSION=${{ env.SPATIALDATA_IO_VERSION }}
+                      SPATIALDATA_PLOT_VERSION=${{ env.SPATIALDATA_PLOT_VERSION }}
+                  tags: ${{ env.IMAGE_TAG }}

.github/workflows/release.yaml

@@ -5,26 +5,26 @@ on:
         types: [published]
 
 jobs:
-    release:
-        # requires that you have put your twine API key in your
-        # github secrets (see readme for details)
+    package_and_release:
         runs-on: ubuntu-latest
-        if: contains(github.ref, 'tags')
+        if: startsWith(github.ref, 'refs/tags/v')
         steps:
-            - name: Checkout code
-              uses: actions/checkout@v3
-
+            - uses: actions/checkout@v3
             - name: Set up Python 3.12
               uses: actions/setup-python@v4
               with:
                   python-version: "3.12"
-
+                  cache: pip
+            - name: Install build dependencies
+              run: python -m pip install --upgrade pip wheel twine build
+            - name: Build package
+              run: python -m build
+            - name: Check package
+              run: twine check --strict dist/*.whl
             - name: Install hatch
               run: pip install hatch
-
             - name: Build project for distribution
               run: hatch build
-
             - name: Publish a Python distribution to PyPI
               uses: pypa/gh-action-pypi-publish@release/v1
               with:

.github/workflows/test.yaml

@@ -18,11 +18,11 @@ jobs:
         strategy:
             fail-fast: false
             matrix:
-                python: ["3.9", "3.12"]
+                python: ["3.10", "3.12"]
                 os: [ubuntu-latest]
                 include:
                     - os: macos-latest
-                      python: "3.9"
+                      python: "3.10"
                     - os: macos-latest
                       python: "3.12"
                       pip-flags: "--pre"

.gitignore

@@ -17,7 +17,9 @@ __pycache__/
 /data/
 
 # docs
-/docs
+docs/_build
+!docs/api/.md
+docs/**/generated
 
 # IDEs
 /.idea/
@@ -29,8 +31,6 @@ __pycache__/
 # temp files
 temp/
 
-# rst generated from myst
-docs/generated
 
 # symlinks (luca) for extending the refactoring to satellite projects
 napari-spatialdata
@@ -47,3 +47,5 @@ _version.py
 
 # other
 node_modules/
+
+.asv/

.mypy.ini

@@ -1,5 +1,5 @@
 [mypy]
-python_version = 3.9
+python_version = 3.10
 plugins = numpy.typing.mypy_plugin
 
 ignore_errors = False

.pre-commit-config.yaml

@@ -2,32 +2,32 @@ fail_fast: false
 default_language_version:
     python: python3
 default_stages:
-    - commit
-    - push
+    - pre-commit
+    - pre-push
 minimum_pre_commit_version: 2.16.0
 ci:
     skip: []
 repos:
     - repo: https://github.com/psf/black
-      rev: 24.4.2
+      rev: 24.10.0
       hooks:
           - id: black
-    - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v4.0.0-alpha.8
+    - repo: https://github.com/rbubley/mirrors-prettier
+      rev: v3.4.2
       hooks:
           - id: prettier
     - repo: https://github.com/asottile/blacken-docs
-      rev: 1.18.0
+      rev: 1.19.1
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.10.1
+      rev: v1.14.1
       hooks:
           - id: mypy
             additional_dependencies: [numpy, types-requests]
             exclude: tests/|docs/
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.0
+      rev: v0.9.2
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

.readthedocs.yaml

@@ -13,6 +13,7 @@ python:
           path: .
           extra_requirements:
               - docs
+              - torch
 submodules:
     include:
         - "docs/tutorials/notebooks"