chore: bump python floor to 3.14, modernize CI/build, ruff FURB sweep

.github/workflows/docker-publish.yml

@@ -0,0 +1,54 @@
+name: Build and Publish Docker image
+
+on:
+  push:
+    branches: ["main", "dev"]
+    tags: ["v*"]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v4.0.0
+
+      - name: Log in to GitHub Container Registry
+        uses: docker/login-action@v4.1.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata
+        id: meta
+        uses: docker/metadata-action@v6.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=ref,event=branch
+            type=ref,event=pr
+            type=semver,pattern={{version}}
+            type=semver,pattern={{major}}.{{minor}}
+            type=raw,value=latest,enable={{is_default_branch}}
+            type=raw,value=edge,enable=${{ github.ref == 'refs/heads/dev' }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v7.1.0
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/nextflow-ci.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v6.0.2
 
       - uses: actions/setup-java@v5.2.0
         with:
@@ -41,26 +41,13 @@ jobs:
           sudo chmod +x /usr/local/bin/nf-test
 
       - name: Lint Nextflow files
-        # `nextflow lint` does not load Groovy classes from `lib/`, so it
-        # falsely reports `Helpers` as undefined wherever the workflow calls
-        # `Helpers.X(...)`. We strip ANSI colour codes from the output, drop
-        # those known false-positives, and re-derive the exit status.
+        # Pass -project-dir so that nextflow lint (26.04+) can resolve Groovy
+        # classes from lib/ (e.g. Helpers). Each workflow lives in its own
+        # subdirectory, so lint is invoked once per workflow.
         run: |
-          tmp=$(mktemp)
-          nextflow lint \
-            workflows/preproc/preproc_rawtiles.nf \
-            workflows/reconst_3d/soct_3d_reconst.nf \
-            workflows/reconst_2.5d/soct_2.5d_reconst.nf \
-            > "$tmp" 2>&1 || true
-          sed 's/\x1b\[[0-9;]*[a-zA-Z]//g' "$tmp" \
-            | awk '/`Helpers` is not defined/ { skip = 3; next } skip > 0 { skip--; next } { print }' \
-            > "$tmp.filt"
-          cat "$tmp.filt"
-          if grep -qE '^Error ' "$tmp.filt"; then
-            echo "::error::nextflow lint reported errors (excluding Helpers false-positives)"
-            exit 1
-          fi
-          echo "Lint passed (Helpers false-positives ignored: lib/ classes are loaded at runtime but not by 'nextflow lint')."
+          nextflow lint -project-dir workflows/preproc workflows/preproc/preproc_rawtiles.nf
+          nextflow lint -project-dir workflows/reconst_3d workflows/reconst_3d/soct_3d_reconst.nf
+          nextflow lint -project-dir workflows/reconst_2.5d workflows/reconst_2.5d/soct_2.5d_reconst.nf
 
       - name: Validate Nextflow configs
         run: |

.github/workflows/publish.yaml

@@ -3,32 +3,28 @@ name: Build and Publish Toolkit
 on:
   push:
     tags:
-      - v1.*
-    workflow_dispatch:
+      - "v1.*"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
 jobs:
   build_and_publish:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@master
-      - name: Set up Python 3.10
-        uses: actions/setup-python@v3
-        with:
-          python-version: "3.10"
-      - name: Install pypa/build
-        run: >-
-          python -m
-          pip install
-          build
-          --user
-      - name: Build a binary wheel and a source tarball
-        run: >-
-          python -m
-          build
-          --sdist
-          --wheel
-          --outdir dist/
-          .
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
+
+      - name: Set up Python 3.14
+        run: uv python install 3.14
+
+      - name: Build sdist and wheel
+        run: uv build --sdist --wheel --out-dir dist/
+
       - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@v1.14.0
         with:
           password: ${{ secrets.PYPI_TOKEN }}

.github/workflows/python-app.yml

@@ -5,33 +5,39 @@ name: Python application
 
 on:
   push:
-    branches: [ "main" ]
+    branches: ["main", "dev"]
   pull_request:
-    branches: [ "main" ]
+    branches: ["main", "dev"]
 
 permissions:
   contents: read
 
 jobs:
   build:
-
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Install uv
-      uses: astral-sh/setup-uv@v5
-    - name: Set up Python 3.12
-      run: uv python install 3.12
-    - name: Install dependencies
-      run: uv sync
-    - name: Lint with ruff
-      run: |
-        uv run ruff check .
-        uv run ruff format --check .
-    - name: Type check with ty
-      continue-on-error: true
-      run: uv run ty check
-    - name: Test with pytest
-      run: |
-        uv run pytest
+      - uses: actions/checkout@v6.0.2
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v8.1.0
+        with:
+          enable-cache: true
+
+      - name: Set up Python 3.14
+        run: uv python install 3.14
+
+      - name: Install dependencies
+        run: uv sync
+
+      - name: Lint with ruff
+        run: |
+          uv run ruff check .
+          uv run ruff format --check .
+
+      - name: Type check with ty
+        continue-on-error: true
+        run: uv run ty check
+
+      - name: Test with pytest
+        run: uv run pytest

.gitignore

@@ -173,6 +173,10 @@ cython_debug/
 .nextflow/
 *.nextflow.log*
 
+# nf-test
+.nf-test/
+.nf-test.log
+
 # Standalone tools (separate git repos)
 tools/
 workflows/work/

.readthedocs.yaml

@@ -6,7 +6,7 @@ version: 2
 build:
   os: ubuntu-24.04
   tools:
-    python: "3.12"
+    python: "3.14"
   jobs:
     create_environment:
       - asdf plugin add uv

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12
+FROM python:3.14
 
 COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
@@ -19,5 +19,5 @@ RUN apt-get update && apt-get install -y \
 # Install with uv
 COPY linumpy ./linumpy
 COPY scripts ./scripts
-COPY pyproject.toml uv.lock README.md .python-version ./
+COPY pyproject.toml uv.lock README.md ./
 RUN uv sync --frozen --no-dev

README.md

@@ -7,7 +7,7 @@
 ## Installation
 *Although a version of the library is available on PyPI, it has not been updated in a while. We highly discourage its use.*
 
-The library is tested for python 3.12. To install the library, clone the repository, change directory to the repository root and then install it with the command below:
+The library is tested for python 3.14. To install the library, clone the repository, change directory to the repository root and then install it with the command below:
 ```
 pip install .
 ```

docs/NEXTFLOW_WORKFLOWS.md

@@ -935,7 +935,7 @@ rm -rf work/
 
 ```bash
 # Pull container manually
-apptainer pull linumpy.sif docker://ghcr.io/linum/linumpy:latest
+apptainer pull linumpy.sif docker://ghcr.io/linum-uqam/linumpy:latest
 
 # Run with explicit container
 nextflow run workflow.nf -with-apptainer linumpy.sif

docs/conf.py

@@ -2,8 +2,6 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 """Sphinx configuration for the linumpy documentation."""
 
-from __future__ import annotations
-
 import sys
 from datetime import datetime
 from pathlib import Path

linumpy/cli/args.py

@@ -1,7 +1,6 @@
 """Common argument-parsing helpers for linumpy CLI scripts."""
 
 import argparse
-import multiprocessing
 import os
 import shutil
 from pathlib import Path
@@ -19,7 +18,7 @@ def get_available_cpus() -> int:
     -------
         int: Number of available CPUs
     """
-    total_cpus = multiprocessing.cpu_count()
+    total_cpus = os.process_cpu_count() or os.cpu_count() or 1
 
     # Check for explicit max CPUs limit
     max_cpus = os.environ.get("LINUMPY_MAX_CPUS")