Remove poetry for pixi

.github/workflows/lint-and-dryrun-testing.yml → .github/workflows/python-testing.yml

@@ -10,58 +10,63 @@ jobs:
     name: Lint code
     runs-on: ubuntu-latest
     steps:
-      - name: Install non-python dependencies
-        run: |
-          sudo apt-get install -y graphviz-dev
+      - name: Clone repo
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha || github.base_ref }}
+
       - name: Setup Python environment
-        uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.3.6
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          python-version: '3.10'
-      - name: yamlfix
-        run: poetry run poe yamlfix-check
-      - name: ruff
-        run: poetry run poe ruff-lint-check
+          environments: >-
+            dev-only
+          activate-environment: dev-only
+
+      - name: isort
+        run: isort autoafids/*.py -c
+
+      - name: Black
+        run: black autoafids --check
+
       - name: snakefmt
-        run: poetry run poe snakefmt-check
+        run: snakefmt autoafids --check
   test:
     runs-on: ubuntu-latest
     needs: [quality]
-    defaults:
-      run:
-        shell: bash -l {0}
+
     steps:
       - name: checkout repository
         uses: actions/checkout@v4
-      - name: Setup Miniforge and mamba
-        uses: conda-incubator/setup-miniconda@v3
+
+      - name: Setup Pixi environment
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          mamba-version: '*'
-          use-mamba: true
-          conda-solver: libmamba
-          auto-activate-base: true
-      - name: Install snakebids
-        run: |
-          mamba install snakebids appdirs -c bioconda -c conda-forge -y
+          activate-environment: true
+
       - name: Setup env for autoafids
         run: |
           echo "AUTOAFIDS_CACHE_DIR=`pwd`/test_data/autoafids_cache_dir" >> $GITHUB_ENV
+
       - name: Test T1w modality
         run: |
           ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 -np
+
       - name: Test T2w modality
         run: |
           ./autoafids/run.py test_data/bids_T2w test_out participant --modality T2w -np -c1
+
       - name: Test CT modality
         run: |
           ./autoafids/run.py test_data/bids_ct test_out participant --modality ct -np -c1
+
       - name: Test stereotaxy feature with T1w modality
         run: |
           ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --stereotaxy STN -np
+
       - name: Test stereotaxy feature with T2w modality
         run: |
           ./autoafids/run.py test_data/bids_T2w test_out participant --stereotaxy STN --modality T2w -np -c1
+
       - name: Test fidqc feature
         run: |-
           ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 002 --fidqc -np

.github/workflows/wetrun-testing.yml

@@ -16,49 +16,46 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-      - name: Setup Miniforge and mamba
-        uses: conda-incubator/setup-miniconda@v3
+
+
+      - name: Setup Pixi environment
+        uses: prefix-dev/setup-pixi@v0.8.14
         with:
-          miniforge-variant: Miniforge3
-          miniforge-version: latest
-          mamba-version: '*'
-          use-mamba: true
-          conda-solver: libmamba
-          auto-activate-base: true
-      - name: Create environment with snakebids
-        run: |
-          mamba create -n snakebids-env snakebids scikit-learn pandas -c bioconda -c conda-forge -y
+          activate-environment: true
+
       - name: Cache Snakemake Conda environments
         uses: actions/cache@v4
         with:
           path: test_data/autoafids_cache_dir/conda
           key: conda-env-${{ hashFiles('autoafids/workflow/envs/*.yaml') }}
           restore-keys: |
             conda-env-
+
       - name: Restore cached CNN model
         uses: actions/cache@v4
         with:
           path: test_data/autoafids_cache_dir/models
           key: static-model-cache-v1
+
       - name: Set AUTOAFIDS_CACHE_DIR
         run: |
           echo "AUTOAFIDS_CACHE_DIR=`pwd`/test_data/autoafids_cache_dir" >> $GITHUB_ENV
+
       - name: Run wet-run test for T1w modality
         shell: bash -l {0}
         run: |
-          conda activate snakebids-env
           ./autoafids/run.py test_data/bids_wetrun_testing/bids_T1w test_out participant \
             --cores all --force-output --stereotaxy STN --fidqc --conda-frontend mamba | tee autoafids_output.log
+
       - name: Model accuracy check
         shell: bash -l {0}
         run: |
-          conda activate snakebids-env
           python ./tests/test_fcsv_output.py \
             --autoafids_fcsv ./test_out/sub-001/afids-cnn/*.fcsv \
             --baseline_fcsv ./test_data/bids_wetrun_testing/bids_T1w/sub-001/anat/sub-001*.fcsv | tee test_fcsv_output.log
+
       - name: Run wet-run test for T2w modality
         shell: bash -l {0}
         run: |-
-          conda activate snakebids-env
           ./autoafids/run.py test_data/bids_wetrun_testing/bids_T2w test_out participant \
             --modality T2w --cores all --force-output --conda-frontend mamba

.readthedocs.yaml

@@ -17,7 +17,7 @@ formats: [pdf]
 build:
   os: ubuntu-20.04
   tools:
-    python: '3.10'
+    python: '3.11'
 python:
   install:
     - requirements: docs/requirements.txt

autoafids/run.py

@@ -5,9 +5,7 @@
 from snakebids import bidsapp, plugins
 
 try:
-    from autoafids.workflow.lib import (
-        utils as utils,  # Works when run as a package
-    )
+    from autoafids.workflow.lib import utils as utils  # Works when run as a package
 except ImportError:
     from workflow.lib import utils as utils  # Works when run directly
 
@@ -27,14 +25,13 @@
 conda_prefix = Path(utils.get_download_dir()) / "conda"
 
 # Set templateflow directory
-os.environ['TEMPLATEFLOW_HOME'] = str(
-    Path(utils.get_download_dir()) / "templateflow"
-    )
+os.environ["TEMPLATEFLOW_HOME"] = str(Path(utils.get_download_dir()) / "templateflow")
 
 # Set the environment variable SNAKEMAKE_CONDA_PREFIX if not already set
 if "SNAKEMAKE_CONDA_PREFIX" not in os.environ:
     os.environ["SNAKEMAKE_CONDA_PREFIX"] = str(conda_prefix)
 
+
 def get_parser():
     """Exposes parser for sphinx doc generation, cwd is the docs dir"""
     return app.build_parser().parser