update dev branch

.github/actions/setup-pysits/action.yml

@@ -0,0 +1,43 @@
+name: Set up pysits
+description: R with the sits stack, and uv-managed Python
+
+inputs:
+  python-version:
+    description: Python version to run pysits on
+    required: true
+
+runs:
+  using: composite
+
+  steps:
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        Ncpus: '4'
+
+    # R is installed under `/opt/R`, which the dynamic loader does not search.
+    # `rpy2` links against `libR.so` at import, so without this it falls back
+    # to ABI mode and then fails to load R's own base packages
+    - name: Put libR on the loader path
+      shell: bash
+      run: |
+        echo "LD_LIBRARY_PATH=$(R RHOME)/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}" >> "$GITHUB_ENV"
+
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        packages: |
+          github::e-sensing/sits@dev
+          any::arrow
+          any::earthdatalogin
+
+    # The `torch` R package ships without libtorch, and pysits disables the
+    # implicit download (`TORCH_INSTALL=0`), so without this operation
+    # the deep learning models would fail only once a test train one
+    - name: Install libtorch
+      shell: bash
+      run: Rscript -e 'torch::install_torch()'
+
+    # After R: `rpy2` has no Linux wheel and is compiled against it
+    - uses: astral-sh/setup-uv@v9.0.0
+      with:
+        python-version: ${{ inputs.python-version }}
+        enable-cache: true

.github/workflows/ruff.yaml

@@ -6,37 +6,27 @@ on:
   pull_request:
     branches: [main]
 
-  # Run every Saturday at 3:00 AM
-  schedule:
-    # * is a special character in YAML so you have to quote this string
-    - cron:  '0 3 * * 6'
-
   workflow_dispatch:
     inputs:
       reason:
         required: false
         description: 'Reason'
         default: 'Manual trigger'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+permissions:
+  contents: read
+
 jobs:
   lint:
     name: Run ruff
     runs-on: ubuntu-latest
 
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-
-      - name: Set up Python (Dev version)
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v7
+      - uses: astral-sh/ruff-action@v4.1.0
         with:
-          python-version: '3.11-dev'
-
-      - name: Install dependencies
-        run: pip install .[dev]
-
-      - name: Check
-        run: ruff check .
+          version-file: uv.lock

.github/workflows/tests.yaml

@@ -1,96 +1,80 @@
 name: Tests
 
 on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+  # Run every Saturday at 3:00 AM
+  schedule:
+    # * is a special character in YAML so you have to quote this string
+    - cron:  '0 3 * * 6'
+
   workflow_dispatch:
     inputs:
       reason:
         required: false
         description: 'Reason'
         default: 'Manual trigger'
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.event_name == 'pull_request' }}
+
+permissions:
+  contents: read
+
+env:
+  # pak resolves `sits` from GitHub; without a token it shares the anonymous
+  # rate limit with every other runner
+  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
 jobs:
   test:
     name: Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
+    timeout-minutes: 120
 
     strategy:
-      # Report every version, so a single break does not hide the others.
+      # Report every version, so a single break does not hide the others
       fail-fast: false
       matrix:
-        python-version: ['3.10', '3.11', '3.12', '3.13', '3.14']
-
-    env:
-      # Fail the build on R warnings that would otherwise pass unnoticed
-      R_KEEP_PKG_SOURCE: yes
+        # The suite trains various models on CPU. To reduce execution time,
+        # a change is only checked against floor and ceiling versions.
+        # The weekly test covers all other versions
+        python-version: ${{ fromJSON((github.event_name == 'push' || github.event_name == 'pull_request') && '["3.10", "3.14"]' || '["3.10", "3.11", "3.12", "3.13", "3.14"]') }}
 
     steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-
-      - name: Set up R
-        uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - uses: actions/checkout@v7
 
-      - name: Install R dependencies
-        uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          # `arrow` and `kohonen` are required by pysits but are not part of a
-          # default `install.packages("sits")`, so they are listed explicitly.
-          packages: |
-            any::sits
-            any::arrow
-            any::kohonen
-            any::jsonlite
-
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: ./.github/actions/setup-pysits
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Create a clean virtual environment
-        # Mirrors how users install pysits, so a broken dependency resolution
-        # is caught here rather than by them.
-        run: python -m venv .venv
-
       - name: Install pysits
-        # `--only-binary` makes pip fail instead of falling back to a source
-        # build when no wheel matches this interpreter. Those builds have
-        # shipped binaries that segfault. Only pysits itself is built here.
-        run: |
-          .venv/bin/python -m pip install --upgrade pip
-          .venv/bin/python -m pip install \
-            --only-binary=:all: --no-binary pysits \
-            ".[dev]"
-
-      - name: Report resolved dependency versions
-        run: .venv/bin/python -m pip list
-
-      - name: Verify Arrow interoperability between R and Python
-        # pyarrow and R arrow package each bundle libarrow. If they stop
-        # sharing an allocator, transfers are silently corrupted rather than
-        # failing, so this asserts a known value survives a round-trip.
-        run: |
-          .venv/bin/python - <<'EOF'
-          import pyarrow as pa
-
-          import pysits
-          from pysits.conversions.tibble import (
-              pandas_sits_to_tibble,
-              tibble_sits_to_pandas,
-          )
-
-          probe = [0.5, 1.5, 2.5]
-          assert pa.array(probe).to_pylist() == probe, "pyarrow returns corrupted data"
-
-          samples = pysits.samples_modis_ndvi
-          expected = samples["time_series"][0]["NDVI"].tolist()
-          actual = tibble_sits_to_pandas(pandas_sits_to_tibble(samples.head(1)))
-          actual = actual["time_series"][0]["NDVI"].tolist()
-
-          assert actual == expected, f"round-trip corrupted data: {actual} != {expected}"
-          print("Arrow round-trip is lossless.")
-          EOF
+        run: uv sync --locked --extra dev
+
+      - name: Run tests
+        run: uv run pytest
+
+  latest-dependencies:
+    name: Latest dependencies
+    # `uv.lock` pins what `test` runs against, so a release that breaks pysits
+    # stays invisible there until someone relocks. This resolves from scratch.
+    if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: ./.github/actions/setup-pysits
+        with:
+          python-version: '3.14'
+
+      - name: Install pysits, ignoring the lockfile
+        run: uv sync --upgrade --extra dev
 
       - name: Run tests
-        run: .venv/bin/python -m pytest
+        run: uv run pytest

pyproject.toml

@@ -17,7 +17,7 @@
 
 [project]
 name = "pysits"
-version = "2.0.0.dev2"
+version = "2.0.0.dev3"
 description = "Python wrapper for the sits R package"
 readme = "README.md"
 requires-python = ">=3.10,<4"