Merge pull request #2 from FCP-INDI/engine/(th)re(e)sources

♻️ Split `ResourcePool` into three classes

Author: sgiavasis

.circleci/main.yml

@@ -68,7 +68,9 @@ commands:
     steps:
       - run:
           name: Getting Sample BIDS Data
-          command: git clone https://github.com/bids-standard/bids-examples.git
+          command: |
+            mkdir -p /home/circleci/project/dev/circleci_data/.pytest_cache/d/bids-examples
+            git clone https://github.com/bids-standard/bids-examples.git /home/circleci/project/dev/circleci_data/.pytest_cache/d/bids-examples
   get-singularity:
     parameters:
       version:
@@ -156,7 +158,7 @@ commands:
             then
               TAG=nightly
             else
-              TAG="${CIRCLE_BRANCH//\//_}"
+              TAG=`echo ${CIRCLE_BRANCH} | sed 's/[^a-zA-Z0-9._]/-/g'`
             fi
             DOCKER_TAG="ghcr.io/${CIRCLE_PROJECT_USERNAME,,}/${CIRCLE_PROJECT_REPONAME,,}:${TAG,,}"
             if [[ -n "<< parameters.variant >>" ]]
@@ -172,7 +174,7 @@ commands:
           name: Testing Singularity installation
           command: |
             pip install -r dev/circleci_data/requirements.txt
-            coverage run -m pytest --junitxml=test-results/junit.xml --continue-on-collection-errors dev/circleci_data/test_install.py
+            coverage run -m pytest --capture=no --junitxml=test-results/junit.xml --continue-on-collection-errors dev/circleci_data/test_install.py
 
 jobs:
   combine-coverage:

.github/workflows/build_C-PAC.yml

@@ -42,7 +42,7 @@ jobs:
           GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
           if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
           then
-            TAG=${GITHUB_BRANCH//\//_}
+            TAG=`echo ${GITHUB_BRANCH} | sed 's/[^a-zA-Z0-9._]/-/g'`
             DOCKERFILE=.github/Dockerfiles/C-PAC.develop$VARIANT-$OS.Dockerfile
           elif [[ $GITHUB_BRANCH == 'develop' ]]
           then

.github/workflows/regression_test_full.yml

@@ -13,7 +13,7 @@ jobs:
           GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
           if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
           then
-            TAG=${GITHUB_BRANCH//\//_}
+            TAG=`echo ${GITHUB_BRANCH} | sed 's/[^a-zA-Z0-9._]/-/g'`
           elif [[ $GITHUB_BRANCH == 'develop' ]]
           then
             TAG=nightly

.github/workflows/regression_test_lite.yml

@@ -37,7 +37,7 @@ jobs:
         run: |
           if [[ ! $GITHUB_REF_NAME == 'main' ]] && [[ ! $GITHUB_REF_NAME == 'develop' ]]
           then
-            TAG=${GITHUB_REF_NAME//\//_}
+            TAG=`echo ${GITHUB_REF_NAME} | sed 's/[^a-zA-Z0-9._]/-/g'`
           elif [[ $GITHUB_REF_NAME == 'develop' ]]
           then
             TAG=nightly

.github/workflows/smoke_test_participant.yml

@@ -68,7 +68,7 @@ jobs:
           GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
           if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
           then
-            TAG=${GITHUB_BRANCH//\//_}
+            TAG=`echo ${GITHUB_BRANCH} | sed 's/[^a-zA-Z0-9._]/-/g'`
           elif [[ $GITHUB_BRANCH == 'develop' ]]
           then
             TAG=nightly
@@ -133,7 +133,7 @@ jobs:
           GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
           if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
           then
-            TAG=${GITHUB_BRANCH//\//_}
+            TAG=`echo ${GITHUB_BRANCH} | sed 's/[^a-zA-Z0-9._]/-/g'`
           elif [[ $GITHUB_BRANCH == 'develop' ]]
           then
             TAG=nightly
@@ -192,7 +192,7 @@ jobs:
           GITHUB_BRANCH=$(echo ${GITHUB_REF} | cut -d '/' -f 3-)
           if [[ ! $GITHUB_BRANCH == 'main' ]] && [[ ! $GITHUB_BRANCH == 'develop' ]]
           then
-            TAG=${GITHUB_BRANCH//\//_}
+            TAG=`echo ${GITHUB_BRANCH} | sed 's/[^a-zA-Z0-9._]/-/g'`
           elif [[ $GITHUB_BRANCH == 'develop' ]]
           then
             TAG=nightly

.ruff.toml

@@ -13,6 +13,7 @@ external = ["T20"]  # Don't autoremove 'noqa` comments for these rules
 "CPAC/utils/sklearn.py" = ["RUF003"]
 "CPAC/utils/tests/old_functions.py" = ["C", "D", "E", "EM", "PLW", "RET"]
 "CPAC/utils/utils.py" = ["T201"]  # until `repickle` is removed
+"dev/circleci_data/conftest.py" = ["F401"]
 "setup.py" = ["D1"]
 
 [lint.flake8-import-conventions.extend-aliases]

CHANGELOG.md

@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Changed
 
 - Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
+- Split `ResourcePool` into three classes: `Resource`, `ResourcePool`, and `StratPool`.
 
 ### Fixed
 

CPAC/alff/alff.py

@@ -22,7 +22,7 @@
 
 from CPAC.alff.utils import get_opt_string
 from CPAC.pipeline import nipype_pipeline_engine as pe
-from CPAC.pipeline.nodeblock import nodeblock
+from CPAC.pipeline.engine.nodeblock import nodeblock
 from CPAC.registration.registration import apply_transform
 from CPAC.utils.interfaces import Function
 from CPAC.utils.utils import check_prov_for_regtool

CPAC/anat_preproc/anat_preproc.py

@@ -34,7 +34,7 @@
     wb_command,
 )
 from CPAC.pipeline import nipype_pipeline_engine as pe
-from CPAC.pipeline.nodeblock import nodeblock
+from CPAC.pipeline.engine.nodeblock import nodeblock
 from CPAC.utils.interfaces import Function
 from CPAC.utils.interfaces.fsl import Merge as fslMerge
 

CPAC/conftest.py

@@ -0,0 +1,32 @@
+# Copyright (C) 2024  C-PAC Developers
+
+# This file is part of C-PAC.
+
+# C-PAC is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+
+# C-PAC is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public
+# License for more details.
+
+# You should have received a copy of the GNU Lesser General Public
+# License along with C-PAC. If not, see <https://www.gnu.org/licenses/>.
+"""Global pytest configuration."""
+
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def bids_examples(cache: pytest.Cache) -> Path:
+    """Get cached example BIDS directories."""
+    bids_dir = cache.mkdir("bids-examples").absolute()
+    if not (bids_dir.exists() and list(bids_dir.iterdir())):
+        from git import Repo
+
+        Repo.clone_from("https://github.com/bids-standard/bids-examples.git", bids_dir)
+    return bids_dir