Merge branch 'master' into feat/populate-guids

.github/workflows/ci.yaml

@@ -0,0 +1,20 @@
+name: CI
+
+on:
+  # run on pushed commits to master and on new commits on pull requests
+  push:
+  pull_request:
+    types: [opened, synchronize]
+
+jobs:
+  Security:
+    name: Security Pipeline
+    uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
+    with:
+       python-poetry: 'false'
+    secrets: inherit  # pragma: allowlist secret
+  UnitTest:
+    name: Python Unit Test
+    uses: uc-cdis/.github/.github/workflows/python_unit_test.yaml@master
+    with:
+        python-version: '3.9'

.github/workflows/docs.yml → .github/workflows/docs.yaml

@@ -1,8 +1,9 @@
-name: Build docs
+name: Docs
 
 on:
+  # DON'T run on pushed commits to master, ONLY on new commits on pull requests
   pull_request:
-    branches: [ master ]
+    types: [opened, synchronize]
 
 jobs:
   build_docs:
@@ -11,7 +12,8 @@ jobs:
     steps:
     - uses: actions/checkout@v2
       with:
-        ref: ${{ github.head_ref }}
+        ref: ${{github.event.pull_request.head.ref}}
+        repository: ${{github.event.pull_request.head.repo.full_name}}
     - name: Set up Python 3.9
       uses: actions/setup-python@v1
       with:
@@ -24,19 +26,20 @@ jobs:
           ${{ runner.os }}-poetry-
     - name: Install dependencies
       run: |
-        curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python -
-        source $HOME/.poetry/env
+        pip install poetry
         poetry config virtualenvs.create false
-        poetry install -vv
+        poetry install -vv --all-extras --no-interaction
+        poetry show -vv
+
         # install sphinx from PyPI (as of 03/16/21 python3-sphinx is broken)
         # sudo apt-get install python3-sphinx
         pip install sphinx
         pip uninstall -y asyncio
+        pip list
         cd
     - name: Build docs
       run: |
         sphinx-build --version
-        source $HOME/.poetry/env
         export PYTHONPATH="${PYTHONPATH}:${{ env.pythonLocation }}/lib/python3.9/site-packages"
         cd docs
         poetry run make html

.github/workflows/main.yml → .github/workflows/lint.yaml

@@ -1,5 +1,6 @@
 on:
   pull_request:
+    types: [opened, synchronize]
   issue_comment:
     types: [created, edited]
 
@@ -11,7 +12,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@master
-
     - uses: uc-cdis/wool@master
       env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -115,3 +115,11 @@ indexing-output-manifest.csv
 object-manifest.csv
 output_manifest.csv
 
+.dccache
+.idea
+# Files generated during pytest
+input.csv
+test_combined_discovery_metadata.tsv
+test_combined_discovery_metadata_exact_match.tsv
+tmp_output_file.csv
+tmp_output_file_info.csv

.pre-commit-config.yaml

@@ -1,17 +1,17 @@
 repos:
 -   repo: [email protected]:Yelp/detect-secrets
-    rev: v0.13.1
+    rev: v1.4.0
     hooks:
     -   id: detect-secrets
         args: ['--baseline', '.secrets.baseline']
         exclude: '(docs\/_build|poetry.lock)'
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.5.0
+    rev: v4.4.0
     hooks:
     -   id: no-commit-to-branch
         args: [--branch, develop, --branch, master, --pattern, release/.*]
 -   repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
     -   id: black
         additional_dependencies: ['click==8.0.4']