Merge branch 'master' into add-datatypes

Author: awarkow

.circleci/config.yml

@@ -0,0 +1,70 @@
+name: ✅ CI
+
+on:
+  pull_request:
+    types: [opened, reopened, synchronize, closed]
+
+concurrency:
+  group: ci-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: 🚨 Lint code
+    runs-on: ubuntu-22.04
+    timeout-minutes: 10
+    steps:
+      - name: 👩‍💻 Checkout code
+        uses: actions/checkout@v3
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.7"
+
+      - name: 📦 Install deps
+        run: |
+          pip install black==23.3.0
+
+      - name: 🚨 Lint code
+        run: |
+          black --check --line-length 80 tests kf_lib_data_ingest
+
+  test:
+    name: ✅ Unit test
+    runs-on: ubuntu-22.04
+    timeout-minutes: 10
+    strategy:
+      matrix:
+        python-version: [3.7]
+    steps:
+      - name: 👩‍💻 Checkout code
+        uses: actions/checkout@v3
+
+      - name: 🐍 Setup Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v3
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: 🔐 Setup SSH Key
+        run: |
+          mkdir -p ~/.ssh
+          echo "${{ secrets.GH_SSH_PRIVATE_KEY }}" > ~/.ssh/id_rsa
+          chmod 600 ~/.ssh/id_rsa
+          ssh-keyscan github.com >> ~/.ssh/known_hosts
+
+      - name: 📦 Install deps
+        run: |
+          pip install --upgrade virtualenv
+          virtualenv -p python3 venv
+          source venv/bin/activate
+          pip uninstall -y setuptools
+          pip install setuptools>61
+          pip install -e .
+          pip install -r dev-requirements.txt 
+
+      - name: ✅ Unit Test
+        run: |
+          source venv/bin/activate
+          pytest  ./tests
+

.github/workflows/ci.yaml

@@ -0,0 +1,46 @@
+name: 🛠️ Doc site
+
+on:
+  push:
+    branches: 
+      - master
+
+concurrency:
+  group: docs-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  docs:
+    name: 📝 Build docs site
+    runs-on: ubuntu-22.04
+    timeout-minutes: 10
+    steps:
+      - name: 👩‍💻 Checkout code
+        uses: actions/checkout@v3
+
+      - name: 🐍 Setup Python
+        uses: actions/setup-python@v3
+        with:
+          python-version: "3.7"
+
+      - name: 📦 Install deps
+        run: |
+          cd kf-lib-data-ingest
+          pip install --upgrade virtualenv
+          virtualenv -p python3 venv
+          source venv/bin/activate
+          pip uninstall -y setuptools
+          pip install setuptools>61
+          pip install -r doc-requirements.txt 
+
+      - name: 👷 Build site
+        run: |
+          source venv/bin/activate
+          doc8 docs/source
+          make -C docs html
+
+      - name: 🚀 Deploy to github pages
+        run: |
+          source venv/bin/activate
+          ./scripts/deploy-ghpages.sh
+

.github/workflows/docs.yaml

@@ -83,5 +83,7 @@ test_graph.gml
 # dot files and folders
 .*
 
+!.github/
+
 # validation results
 validation_results/

.github/workflows/test.yml

@@ -4,6 +4,6 @@ codacy-coverage==1.3.11
 moto==2.0.7
 requests-mock==1.8.0
 flake8
-black
+black==23.3.0
 deepdiff
 -r requirements.txt

.gitignore

@@ -190,7 +190,6 @@ class VOLUME(QuantityMixin):
         EXTERNAL_COLLECTION_ID = None
 
     class BIOSPECIMEN(SAMPLE):
-
         class CONCENTRATION(QuantityMixin):
             pass
 

dev-requirements.txt

@@ -230,10 +230,6 @@ def _postrun_validation(self, validation_mode=None, report_kwargs={}):
             report_kwargs=report_kwargs,
         )
         if self.validation_success:
-            self.logger.info(
-                f"✅ {self.stage_type.__name__} passed validation!"
-            )
+            self.logger.info(f"✅ {self.stage_type.__name__} passed validation!")
         else:
-            self.logger.info(
-                f"❌ {self.stage_type.__name__} failed validation!"
-            )
+            self.logger.info(f"❌ {self.stage_type.__name__} failed validation!")

kf_lib_data_ingest/common/concept_schema.py

@@ -18,9 +18,9 @@
 }
 
 VERBOTEN_PATTERNS['"access_token":".+"'] = '"access_token":"<ACCESS_TOKEN>"'
-VERBOTEN_PATTERNS["'Authorization': '.+'"] = (
-    "'Authorization': '<AUTHORIZATION>'"
-)
+VERBOTEN_PATTERNS[
+    "'Authorization': '.+'"
+] = "'Authorization': '<AUTHORIZATION>'"
 
 
 class NoTokenFormatter(logging.Formatter):