Restyle with ruff (#190)

Author: mattcieslak

.circleci/config.yml

@@ -4,35 +4,59 @@ version: 2.1
 
 .dockersetup: &dockersetup
   docker:
-    - image: pennlinc/babs_tests:datalad0.17.2_v5
-
-# TODO:
-# runinstall: &runinstall
-#     name: Install BABS
-# TODO: build; build_docs; see QSIPrep
-# TODO: add tests from flake8
+    - image: pennlinc/babs_testing:0.3
 
 jobs:
-  pytest:    # run pytest
+  download_test_data:
+    <<: *dockersetup
+    resource_class: medium
+    working_directory: /home/circleci/src/babs
+    steps:
+      - checkout:
+          path: /home/circleci/src/babs
+      - restore_cache:
+          keys:
+            - test-data-v1
+      - run:
+          name: Download test datasets
+          command: |
+            mkdir -p /home/circleci/test_data
+            cd /home/circleci/test_data
+            # Install datalad if not already in the image
+            pip install datalad-osf
+            # Download each dataset from origin_input_dataset.yaml
+            python3 /home/circleci/src/babs/tests/download_datasets.py
+            # Debug output
+            echo "Contents of test_data directory:"
+            ls -la /home/circleci/test_data/
+      - save_cache:
+          key: test-data-v1
+          paths:
+            - /home/circleci/test_data
+
+  pytest: # run pytest
     <<: *dockersetup
     resource_class: xlarge
     working_directory: /home/circleci/src/babs
     steps:
       - checkout:
           path: /home/circleci/src/babs
+      - restore_cache:
+          keys:
+            - test-data-v1
       - run:
           name: pytest of BABS
           no_output_timeout: 1h
           command: |
             pip install .[tests]
-            pytest -n 6 -sv
-  
-  deployable:  # checkpoint of deployable: requires all success
+            pytest -n 4 -sv --durations=0 --timeout=300 --log-cli-level=DEBUG
+
+  deployable: # checkpoint of deployable: requires all success
     <<: *dockersetup
     steps:
       - run: echo Deploying!
 
-  deploy_pypi:   # deploy to pypi
+  deploy_pypi: # deploy to pypi
     <<: *dockersetup
     working_directory: /tmp/src/babs
     steps:
@@ -49,31 +73,32 @@ jobs:
             python3 -m twine upload dist/*
         # NOTE: if want to test with test pypi, add `--repository testpypi` after `twine upload`
 
-
 workflows:
   # version: 2
   build_test_deploy:
     jobs:
-      # - build
-      # - build_docs
+      - download_test_data:
+          filters:
+            tags:
+              only: /.*/
       - pytest:
-          # requires:
-          #  - build
+          requires:
+            - download_test_data
           filters:
             tags:
-              only: /.*/    # i.e., all branches and tags
+              only: /.*/
       - deployable:
-          requires:    # should require all jobs' success before deploying
+          requires:
             - pytest
-          filters:    # run when main branch + any tags
+          filters:
             branches:
               only: main
             tags:
               only: /.*/
       - deploy_pypi:
           requires:
             - deployable
-          filters:   # runs for no branches but runs for any tags
+          filters:
             branches:
               ignore: /.*/
             tags:

.gitattributes

@@ -0,0 +1 @@
+babs/_version.py export-subst

.github/workflows/e2e-slurm.yml

@@ -1,7 +1,12 @@
 ---
 name: Slurm
 
-on: [push]
+# Temporarily disabled
+on:
+  push:
+    branches-ignore:
+      - '**'  # This prevents the workflow from running on any branch
+
 jobs:
     e2e-slurm:
       name: Test e2e with SLURM

.github/workflows/ruff.yml

@@ -0,0 +1,22 @@
+name: Ruff
+
+on: [push, pull_request]
+
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+          cache: 'pip'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ruff
+      - name: Run Ruff
+        run: |
+          ruff check .
+          ruff format --check .

.github/workflows/shellcheck.yml

@@ -16,7 +16,7 @@ jobs:
     - uses: actions/checkout@v4
     - name: Run shellcheck
       run: |
-        shellcheck \
+        shellcheck -x \
         tests/e2e-slurm/container/babs-user-script.sh \
         tests/e2e-slurm/container/ensure-env.sh \
         tests/e2e-slurm/container/walkthrough-tests.sh \

.gitignore

@@ -4,6 +4,103 @@ __pycache__/*
 BABS.egg-info/*
 babs.egg-info/*
 
+babs/_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+.pytest_cache/
+
+# C extensions
+*.so
+*.c
+
+# Distribution / packaging
+.Python
+env/
+# build/ # commented due to some strangeness with Docker/circle setup
+develop-eggs/
+dist/
+build/lib*
+build/temp*
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-wheel-metadata/
+
+# PyBuilder
+target/
+
+#Ipython Notebook
+.ipynb_checkpoints
+
+# pycharm project settings
+.idea
+
+# vscode project settings
+.vscode
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+auth/
+secrets.py
+local_settings.py
+
+*.swp
+
+*.DS_Store
+
+scratch/
+.Rproj.user
+
+ Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-wheel-metadata/
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+build/
+
 # Sphinx documentation
 docs/build
 docs/source/generated

.readthedocs.yaml

@@ -3,14 +3,14 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.10"
 
 sphinx:
-   configuration: docs/source/conf.py
+  configuration: docs/conf.py
 
 python:
   install:
     - method: pip
       path: .
       extra_requirements:
-        - doc
+        - doc

.vscode/launch.json

@@ -3,8 +3,21 @@
         "./babs"
     ],
     "python.linting.enabled": true,
-    "python.linting.flake8Enabled": true,
+    "python.linting.pylintEnabled": false,
+    "python.linting.flake8Enabled": false,
+    "python.linting.pycodestyleEnabled": false,
     "python.linting.lintOnSave": true,
     "python.analysis.autoImportCompletions": false,
-    "esbonio.sphinx.confDir": ""
+    "esbonio.sphinx.confDir": "",
+    "makefile.configureOnOpen": false,
+    "python.analysis.typeCheckingMode": "off",
+    "editor.formatOnSave": true,
+    "[python]": {
+        "editor.defaultFormatter": "charliermarsh.ruff",
+        "editor.formatOnSave": true,
+        "editor.codeActionsOnSave": {
+            "source.fixAll": "explicit",
+            "source.organizeImports": "explicit"
+        }
+    }
 }