refactor: migrate GitHub Actions from conda to pixi (#75)

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: jayhesselberth

.github/workflows/ci.yml

@@ -2,7 +2,7 @@ name: CI
 
 on:
   push:
-    branches: [main, master, develop, claude/**]
+    branches: [main, master, develop, claude/**, refactor/**]
   pull_request:
     branches: [main, master, develop]
   workflow_dispatch:
@@ -15,36 +15,17 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Miniforge
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          activate-environment: aatrnaseqpipe
-          use-mamba: true
-
-      - name: Cache conda environment
-        uses: actions/cache@v3
-        with:
-          path: /usr/share/miniconda3/envs/aatrnaseqpipe
-          key: conda-${{ runner.os }}-${{ hashFiles('workflow/envs/aatrnaseqpipe-env.yml') }}
-
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: |
-          mamba env update -n aatrnaseqpipe -f workflow/envs/aatrnaseqpipe-env.yml
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
 
       - name: Verify Snakemake installation
-        shell: bash -l {0}
-        run: |
-          conda activate aatrnaseqpipe
-          snakemake --version
+        run: pixi run snakemake --version
+
+      - name: Download test data
+        run: pixi run dl-test-data
 
       - name: Snakemake dry-run (syntax check)
-        shell: bash -l {0}
-        run: |
-          conda activate aatrnaseqpipe
-          snakemake -n --configfile=config/config-test.yml
+        run: pixi run dry-run
 
   pipeline-test:
     name: Pipeline Integration Test
@@ -54,57 +35,18 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Miniforge
-        uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          activate-environment: aatrnaseqpipe
-          use-mamba: true
-
-      - name: Cache conda environment
-        uses: actions/cache@v3
-        with:
-          path: /usr/share/miniconda3/envs/aatrnaseqpipe
-          key: conda-${{ runner.os }}-${{ hashFiles('workflow/envs/aatrnaseqpipe-env.yml') }}
-
-      - name: Install dependencies
-        shell: bash -l {0}
-        run: |
-          mamba env update -n aatrnaseqpipe -f workflow/envs/aatrnaseqpipe-env.yml
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
 
       - name: Download test data
-        shell: bash -l {0}
-        run: |
-          bash .tests/dl_test_data.sh
-
-      - name: Setup dorado
-        shell: bash -l {0}
-        run: |
-          conda activate aatrnaseqpipe
-          snakemake setup_dorado --cores 1 --configfile=config/config-test.yml
-
-      - name: Download dorado model
-        shell: bash -l {0}
-        run: |
-          conda activate aatrnaseqpipe
-          snakemake dorado_model --cores 1 --configfile=config/config-test.yml
-
-      - name: Setup modkit
-        shell: bash -l {0}
-        run: |
-          conda activate aatrnaseqpipe
-          snakemake setup_modkit --cores 1 --configfile=config/config-test.yml
+        run: pixi run dl-test-data
 
       - name: Run pipeline test (non-GPU rules only)
-        shell: bash -l {0}
         run: |
-          conda activate aatrnaseqpipe
           # Run merge_pods rule as a basic test (doesn't require GPU)
-          snakemake merge_pods --cores 2 --configfile=config/config-test.yml
+          pixi run snakemake .tests/outputs/pod5/sample1/sample1.pod5 --cores 2 --configfile=config/config-test.yml
 
       - name: Validate outputs
-        shell: bash -l {0}
         run: |
           # Check that expected output files were created
           if [ ! -d ".tests/outputs" ]; then
@@ -120,12 +62,15 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
+
       - name: Check config files syntax
         run: |
           # Validate YAML syntax
-          python3 -c "import yaml; yaml.safe_load(open('config/config-base.yml'))"
-          python3 -c "import yaml; yaml.safe_load(open('config/config-test.yml'))"
-          python3 -c "import yaml; yaml.safe_load(open('config/config-preprint.yml'))"
+          pixi run python -c "import yaml; yaml.safe_load(open('config/config-base.yml'))"
+          pixi run python -c "import yaml; yaml.safe_load(open('config/config-test.yml'))"
+          pixi run python -c "import yaml; yaml.safe_load(open('config/config-preprint.yml'))"
           echo "All config files are valid YAML"
 
       - name: Check samples files

.github/workflows/lint.yml

@@ -2,7 +2,7 @@ name: Lint
 
 on:
   push:
-    branches: [main, master, develop, claude/**]
+    branches: [main, master, develop, claude/**, refactor/**]
   pull_request:
     branches: [main, master, develop]
   workflow_dispatch:
@@ -15,18 +15,11 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-
-      - name: Install Snakemake
-        run: |
-          pip install snakemake snakefmt
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
 
       - name: Run snakefmt check
-        run: |
-          snakefmt --check workflow/
+        run: pixi run lint-snakefmt
 
   python-lint:
     name: Python Linting
@@ -35,45 +28,12 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-
-      - name: Install linting tools
-        run: |
-          pip install black flake8 pylint
-
-      - name: Run black check
-        continue-on-error: true
-        run: |
-          black --check workflow/scripts/ || echo "Black formatting issues found (non-blocking)"
-
-      - name: Run flake8
-        continue-on-error: true
-        run: |
-          flake8 workflow/scripts/ --max-line-length=100 --ignore=E203,W503 || echo "Flake8 issues found (non-blocking)"
-
-  markdown-lint:
-    name: Markdown Linting
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Setup Node.js
-        uses: actions/setup-node@v4
-        with:
-          node-version: '18'
-
-      - name: Install markdownlint
-        run: |
-          npm install -g markdownlint-cli
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
 
-      - name: Run markdownlint
+      - name: Run ruff check and format
         continue-on-error: true
-        run: |
-          markdownlint '**/*.md' --ignore node_modules || echo "Markdown linting issues found (non-blocking)"
+        run: pixi run lint-python || echo "Python linting issues found (non-blocking)"
 
   yaml-lint:
     name: YAML Linting
@@ -82,16 +42,9 @@ jobs:
       - name: Checkout repository
         uses: actions/checkout@v4
 
-      - name: Setup Python
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.11'
-
-      - name: Install yamllint
-        run: |
-          pip install yamllint
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.9.3
 
       - name: Run yamllint
         continue-on-error: true
-        run: |
-          yamllint -d "{extends: default, rules: {line-length: {max: 120}, document-start: disable}}" config/ .github/ || echo "YAML linting issues found (non-blocking)"
+        run: pixi run lint-yaml || echo "YAML linting issues found (non-blocking)"

pixi.lock

@@ -27,6 +27,9 @@ snakemake-executor-plugin-cluster-generic = "*"
 # ONT tools
 pod5 = "*"
 ont-modkit = "*"
+# Linting tools
+ruff = "*"
+yamllint = "*"
 
 [activation]
 scripts = ["scripts/setup-env.sh"]
@@ -41,6 +44,10 @@ run-preprint = { cmd = "snakemake --configfile=config/config-preprint.yml --prof
 # Development
 fmt = { cmd = "snakefmt workflow/Snakefile workflow/rules/*.smk", description = "Format Snakemake files" }
 dag = { cmd = "snakemake --configfile=config/config-test.yml --dag | dot -Tpng > workflow/workflow_dag.png", description = "Generate workflow DAG image" }
+# Linting
+lint-snakefmt = { cmd = "snakefmt --check workflow/", description = "Check Snakemake formatting" }
+lint-python = { cmd = "ruff check workflow/scripts/ && ruff format --check workflow/scripts/", description = "Lint and check Python formatting" }
+lint-yaml = { cmd = "yamllint -d \"{extends: default, rules: {line-length: {max: 120}, document-start: disable}}\" config/ .github/", description = "Lint YAML files" }
 
 # WarpDemuX demultiplexing feature
 [feature.demux]
@@ -66,7 +73,7 @@ ruptures = "*"
 catboost = "*"
 
 [feature.demux.tasks]
-install-warpdemux = { cmd = "[ -d resources/WarpDemuX ] || git clone --recursive https://github.com/KleistLab/WarpDemuX.git resources/WarpDemuX && uv pip install -e resources/WarpDemuX", description = "Clone and install WarpDemuX" }
+install-warpdemux = { cmd = "[ -d resources/tools/WarpDemuX ] || git clone --recursive https://github.com/KleistLab/WarpDemuX.git resources/tools/WarpDemuX && uv pip install -e resources/tools/WarpDemuX", description = "Clone and install WarpDemuX" }
 warpdemux = { cmd = "warpdemux $@", env = { LD_LIBRARY_PATH = "$CONDA_PREFIX/lib:$LD_LIBRARY_PATH" } }
 dry-run-demux = { cmd = "snakemake -n --configfile=config/config-demux-test.yml", description = "Dry run demux test" }
 

pixi.toml

@@ -68,7 +68,9 @@ def parse_samples_yaml(fl):
         run_path = run["path"]
         # Create a unique run_id from the path (last directory component)
         run_id = os.path.basename(run_path.rstrip("/"))
-        barcode_kit = run.get("barcode_kit", config.get("warpdemux", {}).get("barcode_kit"))
+        barcode_kit = run.get(
+            "barcode_kit", config.get("warpdemux", {}).get("barcode_kit")
+        )
 
         for sample_name, barcode in run["samples"].items():
             if sample_name in samples:
@@ -284,4 +286,6 @@ def get_sample_pod5(wildcards):
     if sample_needs_demux(wildcards.sample):
         return os.path.join(outdir, "demux", "pod5", f"{wildcards.sample}.pod5")
     else:
-        return os.path.join(outdir, "pod5", wildcards.sample, f"{wildcards.sample}.pod5")
+        return os.path.join(
+            outdir, "pod5", wildcards.sample, f"{wildcards.sample}.pod5"
+        )