Switch from poetry to pixi

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

@@ -10,40 +10,42 @@ jobs:
     name: Lint code
     runs-on: ubuntu-latest
     steps:
+      - name: Clone repo
+        uses: actions/checkout@v4
+
       - name: Install non-python dependencies
         run: |
           sudo apt-get install -y graphviz-dev
+
       - 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 -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

.github/workflows/push_conda.yml

@@ -74,4 +74,4 @@ jobs:
             --user khanlab \
             --label main \
             --force \
-            "$PACKAGE_PATH"
+            "$PACKAGE_PATH"

.github/workflows/wetrun-testing.yml

@@ -15,25 +15,10 @@ 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
-      - 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-
+          activate-environment: true
       - name: Restore cached CNN model
         uses: actions/cache@v4
         with:
@@ -45,19 +30,16 @@ jobs:
       - 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
 
@@ -30,6 +28,7 @@
 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

autoafids/workflow/Snakefile

@@ -129,7 +129,7 @@ if config["modality"] != "T1w":
             bids(
                 root="logs",
                 suffix="synthsr_output.txt",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             ),
         resources:
             mem_mb=10000,
@@ -147,27 +147,29 @@ if "n4_bias_correction" in profile_settings and config["modality"] == "T1w":
 
     rule n4_bias_correction:
         input:
-            im=bids(
-                root=str(Path(config["bids_dir"])),
-                datatype="anat",
-                suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards,
-            )
-            if config["modality"] == "T1w"
-            else bids(
-                root=work,
-                datatype="SynthSR",
-                desc=f"{config['modality']}-SynthSR",
-                suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards,
+            im=(
+                bids(
+                    root=str(Path(config["bids_dir"])),
+                    datatype="anat",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+                if config["modality"] == "T1w"
+                else bids(
+                    root=work,
+                    datatype="SynthSR",
+                    desc=f"{config['modality']}-SynthSR",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
             ),
         output:
             corrected_im=bids(
                 root=work,
                 datatype="n4biascorr",
                 desc="n4corrected",
                 suffix="T1w.nii.gz",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             ),
         conda:
             "envs/ants.yaml"
@@ -177,36 +179,42 @@ if "n4_bias_correction" in profile_settings and config["modality"] == "T1w":
 
 rule norm_im:
     input:
-        im_raw=lambda wildcards: bids(
-            root=work,
-            datatype="synthstrip",
-            desc="synthstrip",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if "skull_strip" in profile_settings
-        else bids(
-            root=work,
-            datatype="n4biascorr",
-            desc="n4corrected",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if "n4_bias_correction" in profile_settings
-        and config["modality"] == "T1w"
-        else bids(
-            root=str(Path(config["bids_dir"])),
-            datatype="anat",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if config["modality"] == "T1w"
-        else bids(
-            root=work,
-            datatype="SynthSR",
-            desc=f"{config['modality']}-SynthSR",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
+        im_raw=lambda wildcards: (
+            bids(
+                root=work,
+                datatype="synthstrip",
+                desc="synthstrip",
+                suffix="T1w.nii.gz",
+                **inputs[config["modality"]].wildcards,
+            )
+            if "skull_strip" in profile_settings
+            else (
+                bids(
+                    root=work,
+                    datatype="n4biascorr",
+                    desc="n4corrected",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+                if "n4_bias_correction" in profile_settings
+                and config["modality"] == "T1w"
+                else (
+                    bids(
+                        root=str(Path(config["bids_dir"])),
+                        datatype="anat",
+                        suffix="T1w.nii.gz",
+                        **inputs[config["modality"]].wildcards,
+                    )
+                    if config["modality"] == "T1w"
+                    else bids(
+                        root=work,
+                        datatype="SynthSR",
+                        desc=f"{config['modality']}-SynthSR",
+                        suffix="T1w.nii.gz",
+                        **inputs[config["modality"]].wildcards,
+                    )
+                )
+            )
         ),
     output:
         im_norm=bids(
@@ -254,28 +262,32 @@ if "resample_im" in profile_settings and config["modality"] == "T1w":
 
 rule regmni2sub:
     input:
-        im_resamp=bids(
-            root=work,
-            datatype="n4biascorr",
-            desc="n4corrected",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if "n4_bias_correction" in profile_settings
-        and config["modality"] == "T1w"
-        else bids(
-            root=str(Path(config["bids_dir"])),
-            datatype="anat",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
-        )
-        if config["modality"] == "T1w"
-        else bids(
-            root=work,
-            datatype="SynthSR",
-            desc=f"{config['modality']}-SynthSR",
-            suffix="T1w.nii.gz",
-            **inputs[config["modality"]].wildcards,
+        im_resamp=(
+            bids(
+                root=work,
+                datatype="n4biascorr",
+                desc="n4corrected",
+                suffix="T1w.nii.gz",
+                **inputs[config["modality"]].wildcards,
+            )
+            if "n4_bias_correction" in profile_settings
+            and config["modality"] == "T1w"
+            else (
+                bids(
+                    root=str(Path(config["bids_dir"])),
+                    datatype="anat",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+                if config["modality"] == "T1w"
+                else bids(
+                    root=work,
+                    datatype="SynthSR",
+                    desc=f"{config['modality']}-SynthSR",
+                    suffix="T1w.nii.gz",
+                    **inputs[config["modality"]].wildcards,
+                )
+            )
         ),
     output:
         xfm_slicer=bids(
@@ -351,29 +363,33 @@ rule all:
                 datatype="afids-cnn",
                 desc="afidscnn",
                 suffix="afids.fcsv",
-                **inputs[config["modality"]].wildcards
+                **inputs[config["modality"]].wildcards,
             ),
         ),
-        fidqc=inputs[config["modality"]].expand(
-            bids(
-                root=root,
-                datatype="fidqc",
-                desc="fidqc",
-                suffix="afids.html",
-                **inputs[config["modality"]].wildcards
+        fidqc=(
+            inputs[config["modality"]].expand(
+                bids(
+                    root=root,
+                    datatype="fidqc",
+                    desc="fidqc",
+                    suffix="afids.html",
+                    **inputs[config["modality"]].wildcards,
+                )
             )
-        )
-        if config["fidqc"]
-        else [],
-        afidspred=inputs[config["modality"]].expand(
-            bids(
-                root=root,
-                datatype="stereotaxy",
-                desc=stereotaxy_target,
-                suffix="native.fcsv",
-                **inputs[config["modality"]].wildcards
+            if config["fidqc"]
+            else []
+        ),
+        afidspred=(
+            inputs[config["modality"]].expand(
+                bids(
+                    root=root,
+                    datatype="stereotaxy",
+                    desc=stereotaxy_target,
+                    suffix="native.fcsv",
+                    **inputs[config["modality"]].wildcards,
+                )
             )
-        )
-        if config["stereotaxy"]
-        else [],
+            if config["stereotaxy"]
+            else []
+        ),
     default_target: True