pin dependencies and check output

Author: Remi-Gau

.circleci/config.yml

@@ -57,35 +57,30 @@ jobs:
             -v /tmp/workspace/data/ds114_test1:/bids_dataset \
               bids/${CIRCLE_PROJECT_REPONAME,,} --version
 
-        # participant level tests for single session dataset
     - run:
+        name: participant level test
         command: |
           docker run -ti --rm --read-only \
             -v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
             -v ${HOME}/outputs<< parameters.dataset >>:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 01
-        no_output_timeout: 6h
-    - run:
-        command: |
-          docker run -ti --rm --read-only \
-            -v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
-            -v ${HOME}/outputs<< parameters.dataset >>:/outputs \
-              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant --participant_label 02
+              bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs participant
+          tree ${HOME}/outputs<< parameters.dataset >>
         no_output_timeout: 6h
 
     - run:
+        name: group level test
         command: |
           docker run -ti --rm --read-only \
             -v /tmp/workspace/data/ds114_test<< parameters.dataset >>:/bids_dataset \
-            -v ${HOME}/outputs1:/outputs \
+            -v ${HOME}/outputs<< parameters.dataset >>:/outputs \
               bids/${CIRCLE_PROJECT_REPONAME,,} /bids_dataset /outputs group
+          tree ${HOME}/outputs<< parameters.dataset >>
         no_output_timeout: 6h
 
     - store_artifacts:
         path: ~/output<< parameters.dataset >>
 
   deploy:
-
     machine:
       image: ubuntu-2204:2022.10.2
 

.pre-commit-config.yaml

@@ -14,14 +14,12 @@ repos:
   - id: check-case-conflict
   - id: check-merge-conflict
 
-
 - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt
   rev: 0.2.3
   hooks:
   - id: yamlfmt
     args: [--mapping, '2', --sequence, '2', --offset, '0']
 
-
 - repo: https://github.com/hadolint/hadolint
   rev: v2.13.0-beta
   hooks:
@@ -32,6 +30,11 @@ repos:
     types: [dockerfile]
     entry: ghcr.io/hadolint/hadolint hadolint
 
+- repo: https://github.com/pycqa/isort
+  rev: 5.13.2
+  hooks:
+  - id: isort
+
 # Aplly black formatting to python code
 # https://github.com/psf/black
 - repo: https://github.com/psf/black-pre-commit-mirror

Dockerfile

@@ -1,13 +1,14 @@
-FROM bids/base_fsl:6.0.1
+FROM bids/base_fsl:6.0.1@sha256:b92b9b4a0642dfbe011c3827384f781ba7d377686e82edaf14f406d3eb906783
 
 ARG DEBIAN_FRONTEND="noninteractive"
 
+COPY requirements.txt /requirements.txt
 
 RUN apt-get update -qq && \
     apt-get install -q -y --no-install-recommends \
         python3 \
         python3-pip && \
-    pip3 install nibabel==5.1.0 && \
+    pip3 install -r /requirements.txt && \
     apt-get remove -y python3-pip && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 

pyproject.toml

@@ -1,10 +1,7 @@
 [tool.black]
-# 'extend-exclude' excludes files or directories in addition to the defaults
 line-length = 79
 
-# [tool.codespell]
-# ignore-words = ".github/codespell_ignore_words.txt"
-# skip = ""
+[tool.codespell]
 
 [tool.isort]
 combine_as_imports = true

requirements.in

@@ -0,0 +1 @@
+nibabel

requirements.txt

@@ -0,0 +1,12 @@
+#
+# This file is autogenerated by pip-compile with Python 3.11
+# by the following command:
+#
+#    pip-compile --strip-extras requirements.in
+#
+nibabel==5.2.1
+    # via -r requirements.in
+numpy==1.26.4
+    # via nibabel
+packaging==24.0
+    # via nibabel

run.py

@@ -2,12 +2,13 @@
 import argparse
 import os
 import subprocess
-import nibabel
-import numpy
 import sys
 from glob import glob
 from pathlib import Path
 
+import nibabel
+import numpy
+
 __version__ = open(Path(__file__).parent / "version").read()
 
 
@@ -145,8 +146,10 @@ def main(argv=sys.argv):
             os.path.join(args.output_dir, "avg_brain_size.txt"), "w"
         ) as fp:
             fp.write(
-                "Average brain size is %g voxels"
-                % numpy.array(brain_sizes).mean()
+                f"Average brain size is {numpy.array(brain_sizes).mean()} voxels"
+            )
+            print(
+                f"Results were saved in {Path(args.output_dir) / 'avg_brain_size.txt'}"
             )
 
         exit(0)

tox.ini

@@ -0,0 +1,33 @@
+;  See https://tox.wiki/en
+[tox]
+requires =
+    tox>=4
+; run lint by default when just calling "tox"
+env_list = lint
+
+; ENVIRONMENTS
+; ------------
+[style]
+description = common environment for style checkers (rely on pre-commit hooks)
+skip_install = true
+deps =
+    pre-commit
+
+; COMMANDS
+; --------
+[testenv:lint]
+description = install pre-commit hooks and run all linters and formatters
+skip_install = true
+deps =
+    {[style]deps}
+commands =
+    pre-commit install
+	pre-commit run --all-files --show-diff-on-failure {posargs:}
+
+[testenv:update_dependencies]
+description = update requirements.txt
+skip_install = true
+deps =
+    pip-tools
+commands =
+    pip-compile --strip-extras requirements.in {posargs:}