Add sentence to readme about desc in input file issue

.github/auto_assign.yml

@@ -23,4 +23,4 @@ numberOfReviewers: 0
 
 # A list of keywords to be skipped the process that add reviewers if pull requests include it
 # skipKeywords:
-#   - wip
+#   - wip

.github/workflows/auto_assign_reviewers.yml

@@ -1,12 +1,10 @@
+---
 name: Auto Assign Reviewers
-
 on:
   pull_request:
     types: [opened, ready_for_review]
   pull_request_target:
     types: [opened, ready_for_review]
-
 jobs:
   assign-reviewer:
     uses: khanlab/actions/.github/workflows/workflow-pr_task-assignReviewer.yml@v0.3.4
-

.github/workflows/build_docker.yml

@@ -1,27 +1,21 @@
+---
 name: Build and Push Docker Image
-
 on:
   push:
-    branches:
-      - main
+    branches: [main]
   workflow_dispatch:
-
 jobs:
   build-and-push:
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout repo
         uses: actions/checkout@v3
-
       - name: Log in to Docker Hub
         uses: docker/login-action@v2
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
           password: ${{ secrets.DOCKER_PASSWORD }}
-
       - name: Build Docker image
         run: docker build -t jclauneurolab/autoafids:latest .
-
       - name: Push Docker image
-        run: docker push jclauneurolab/autoafids:latest
+        run: docker push jclauneurolab/autoafids:latest

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

@@ -1,85 +1,67 @@
 ---
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
-
 name: Lint and test workflow
 on:
   push:
   workflow_dispatch:
-
 jobs:
   quality:
     name: Lint code
     runs-on: ubuntu-latest
-
     steps:
       - 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
         with:
-          python-version: "3.10"
-
+          python-version: '3.10'
       - name: yamlfix
         run: poetry run poe yamlfix-check
-
       - name: ruff
         run: poetry run poe ruff-lint-check
-
       - name: snakefmt
         run: poetry run poe snakefmt-check
-
   test:
     runs-on: ubuntu-latest
-    needs: ["quality"]
+    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
         with:
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          mamba-version: "*"
+          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
-
       - 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 001 -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 001 --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: |
+        run: |-
           ./autoafids/run.py test_data/bids_T1w test_out participant --participant-label 001 --fidqc -np

.github/workflows/push_conda.yml

@@ -1,50 +1,41 @@
+---
 # .github/workflows/build-conda.yml
-
 name: Build and Upload Conda Package
-
 on:
   push:
-    branches:
-      - main
+    branches: [main]
   workflow_dispatch:
-
 jobs:
   build-and-upload:
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-
       - name: Cache conda build cache
         uses: actions/cache@v3
         with:
           path: /home/runner/miniconda3/conda-bld
           key: ${{ runner.os }}-conda-bld-${{ hashFiles('recipe/meta.yaml') }}
           restore-keys: |
             ${{ runner.os }}-conda-bld-
-
       - name: Setup Miniforge and mamba
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          mamba-version: "*"
+          mamba-version: '*'
           use-mamba: true
           conda-solver: libmamba
           auto-activate-base: true
-
       - name: Install dependencies
         run: |
           mamba install -y -c conda-forge conda-build anaconda-client boa
-
       - name: Get latest commit SHA from main
         id: get_sha
         run: |
           echo "Fetching latest commit on main branch..."
           COMMIT_SHA=$(git ls-remote origin refs/heads/main | cut -f1)
           echo "COMMIT_SHA=$COMMIT_SHA" >> $GITHUB_ENV
-
       - name: Update meta.yaml with latest ref and sha256
         run: |
           echo "Updating meta.yaml with commit: $COMMIT_SHA"
@@ -60,22 +51,20 @@ jobs:
 
           # 3) Replace the literal 'sha256:' line under source:
           sed -i "s|^\(\s*sha256:\s*\).*|\1$SHA256_SUM|" ./recipe/meta.yaml
-
       - name: Build & capture path
         id: build
         run: |
           cd recipe
           OUT=$(conda build . -c conda-forge -c bioconda --output 2>/dev/null)
           echo "PACKAGE_PATH=$OUT" >> $GITHUB_ENV
           conda mambabuild . -c conda-forge -c bioconda
-
       - name: Upload package to Khanlab channel
         shell: bash -l {0}
-        run: |
+        run: |-
           conda activate base
           anaconda login \
             --username ${{ secrets.ANACONDA_USERNAME }} \
             --password ${{ secrets.ANACONDA_PASSWORD }}
           anaconda upload "$PACKAGE_PATH" \
             --label main \
-            --force \
+            --force \

.github/workflows/wetrun-testing.yml

@@ -1,66 +1,57 @@
-name: test workflow with wet run 
+---
+name: test workflow with wet run
 on:
   pull_request:
   workflow_dispatch:
-
 jobs:
   wetrun_test:
     runs-on: ubuntu-latest
-
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
-
       - name: Setup Miniforge and mamba
         uses: conda-incubator/setup-miniconda@v3
         with:
           miniforge-variant: Miniforge3
           miniforge-version: latest
-          mamba-version: "*"
+          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-
-
       - 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 
+      - 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: |
+        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

@@ -22,4 +22,4 @@ python:
   install:
     - requirements: docs/requirements.txt
     - method: pip
-      path: .
+      path: .

README.md

@@ -54,6 +54,7 @@ Below is a high-level summary of the AutoAFIDs processing pipeline:
 
 - `gen_fcsv` rule is currently sequential and may benefit from AFID-level parallelization
 - T1w-like scan synthesis is available (via SynthSR [Iglesias et al., 2023](https://www-science-org.proxy1.lib.uwo.ca/doi/10.1126/sciadv.add3607)) but requires millimetric validation and may not work for all operating systems
+- AutoAFIDs does not currently filter for the `desc` entity in BIDS input files, since it outputs files with a fixed, custom `desc` value. Therefore, BIDS input filenames must not include a `desc` field, or the pipeline may fail to resolve inputs correctly.
 
 ---
 

autoafids-dev.yml

@@ -1,8 +1,6 @@
+---
 name: autoafids-dev
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
+channels: [conda-forge, bioconda, defaults]
 dependencies:
   - python=3.10
   - snakebids=0.14.0
@@ -13,4 +11,4 @@ dependencies:
   - snakefmt >=0.8.4,<0.9.0
   - yamlfix >=1.11.0,<2.0.0
   - pygraphviz ==1.7
-  - jinja2 >=3.0.3,<4.0.0
+  - jinja2 >=3.0.3,<4.0.0

autoafids/workflow/envs/synthsr.yaml

@@ -1,6 +1,4 @@
 ---
 name: synthsr
 channels: [khanlab, anaconda, conda-forge, defaults]
-dependencies:
-  - python=3.8
-  - synthsr
+dependencies: [python=3.8, synthsr]

autoafids/workflow/profiles/default/config.yaml

@@ -1,2 +1,3 @@
-use-conda: True
-conda-frontend: conda
+---
+use-conda: true
+conda-frontend: conda

autoafids/workflow/profiles/docker-conda/config.yaml

@@ -1,2 +1,3 @@
-use-conda: True
-conda-prefix: /src/conda-envs
+---
+use-conda: true
+conda-prefix: /src/conda-envs