🐛 Fix minified pipelines (#1801)

Author: shnizzedy

.github/workflows/check_updated_version.yml renamed to .github/workflows/check_updated_preconfigs.yml

@@ -1,19 +1,23 @@
-name: Check updated version
+name: Check updated preconfigs
 
 on:
   pull_request_target:
     types: [edited, opened, reopened, ready_for_review, synchronize]
   push:
 
 jobs:
-  check-updated-version:
-    name: Check if version updated
+  check-updated-preconfigs:
+    name: Check if preconfigs need updated
     runs-on: ubuntu-latest
     steps:
       - name: Check out C-PAC
         uses: actions/checkout@v2
         with:
           fetch-depth: 2
+      - uses: actions/setup-python@v4 
+        with:
+          python-version: '3.9'
+          cache: 'pip'
       - name: Check if version updated
         run: |
           git config --global user.email "[email protected]"
@@ -37,6 +41,14 @@ jobs:
             [skip ci]"
             git push origin HEAD:${GITHUB_BRANCH} || true
           fi
+          export PYTHONPATH=$PWD
+          pip install nipype numpy matplotlib pandas pathvalidate pytz pyyaml voluptuous yamlordereddictloader
+          python ./CPAC/utils/configuration/yaml_template.py
+          if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
+          then
+            git add CPAC/resources/configs
+            git commit -m ":bulb: Update comments based on default preconfig"
+          fi
           COMMIT_MESSAGE=$(git log -1 --pretty=%B)
           if [[ ! "$COMMIT_MESSAGE" == *"Update version to"* ]]
           then
@@ -48,14 +60,14 @@ jobs:
             git add version CPAC/resources/configs
             if [[ ! -z $(git diff origin/${GITHUB_BRANCH}) ]]
             then
-              git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)"
+              git commit -m ":bookmark: Update version to ${VERSION} ($COMMIT_MESSAGE)" || true
               git push origin HEAD:${GITHUB_BRANCH} || true
             fi
             cd ..
           fi
 
   trigger-next-workflow:
-    needs: check-updated-version
+    needs: check-updated-preconfigs
     runs-on: ubuntu-latest
     steps:
       - name: Set up check

CHANGELOG.md

@@ -34,8 +34,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added crash messages from during and before graph building to logs
 - Added data-config-specific hash string to C-PAC-generated config files
 - Updated `rbc-options` preconfig to use `fmriprep-options` preprocessing
+- Changed minimized pipeline base from `default` to `blank`
 
 ### Fixed
+- Fixed [a bug](https://github.com/FCP-INDI/C-PAC/issues/1779) in which generated pipeline configs were not 100% accurate. The only affected configurable option discovered in testing was seed-based correlation analysis always reverting to the default configuration.
 - Fixed [bug](https://github.com/FCP-INDI/C-PAC/issues/1795) that was causing `cpac run` to fail when passing a manual random seed via `--random_seed`.
 - Replaces ``DwellTime`` with ``EffectiveEchoSpacing`` for FSL usage of the term
 - Fixed an issue that was causing some epi field maps to not be ingressed if the BIDS tags were not in the correct order.

CPAC/pipeline/cpac_runner.py

@@ -26,7 +26,7 @@
 from CPAC.utils.monitoring import failed_to_start, log_nodes_cb
 from CPAC.longitudinal_pipeline.longitudinal_workflow import \
     anat_longitudinal_wf
-from CPAC.utils.yaml_template import upgrade_pipeline_to_1_8
+from CPAC.utils.configuration.yaml_template import upgrade_pipeline_to_1_8
 
 
 # Run condor jobs