Use jinja templates for creating scripts/yamls (#231)

Co-authored-by: Parker Singleton <[email protected]>
Co-authored-by: Taylor Salo <[email protected]>
Co-authored-by: Steven Meisler <[email protected]>
Co-authored-by: Tien Tong <[email protected]>

Author: 5 people

.circleci/config.yml

@@ -71,13 +71,36 @@ jobs:
             -t pennlinc/slurm-docker-ci:unstable \
             -f Dockerfile_testing .
 
+            # Make a directory that will hold the test artifacts
+            mkdir -p /home/circleci/testing
             docker run -it \
                 -v ${PWD}:/tests \
+                -v /home/circleci/testing:/test-temp:rw \
                 -h slurmctl --cap-add sys_admin \
                 --privileged \
                 pennlinc/slurm-docker-ci:unstable \
                 /tests/tests/e2e-slurm/container/walkthrough-tests.sh
 
+      - run:
+          name: clean up test artifacts
+          when: always
+          command: |
+            TEST_ARTIFACTS_DIR=/home/circleci/testing/test_project/analysis
+            sudo chmod -R 777 $TEST_ARTIFACTS_DIR
+            # Find and remove all .git directories recursively
+            sudo find $TEST_ARTIFACTS_DIR -type d -name ".git" -exec rm -rf {} +
+            # Also remove any .git files
+            sudo find $TEST_ARTIFACTS_DIR -type f -name ".git" -exec rm -f {} +
+            # Remove any .gitignore files
+            sudo find $TEST_ARTIFACTS_DIR -type f -name ".gitignore" -exec rm -f {} +
+            # Remove any .gitattributes files
+            sudo find $TEST_ARTIFACTS_DIR -type f -name ".gitattributes" -exec rm -f {} +
+            sudo find $TEST_ARTIFACTS_DIR/inputs/data -type d -name "sub-*" -exec rm -rf {} +
+
+      - store_artifacts:
+          path: /home/circleci/testing/test_project/analysis
+          destination: test-artifacts
+
   deployable: # checkpoint of deployable: requires all success
     <<: *dockersetup
     steps:

.vscode/settings.json

@@ -19,5 +19,13 @@
             "source.fixAll": "explicit",
             "source.organizeImports": "explicit"
         }
+    },
+    "[jinja]": {
+        "editor.formatOnSave": false,
+        "editor.wordWrap": "off"
+    },
+    "[jinja-html]": {
+        "editor.formatOnSave": false,
+        "editor.wordWrap": "off"
     }
 }

MANIFEST.in

@@ -5,6 +5,7 @@ include LICENSE
 # necessary files in babs/:
 #   by default it only includes *.py
 recursive-include babs *.yaml
+recursive-include babs/templates *.jinja2
 
 # versioneer
 include babs/_version.py