Merge branch 'main' into re_iding

.coveragerc

@@ -1,7 +1,2 @@
 [run]
 branch = True
-omit =
-    nmdc_automation/workflow_automation/extract.py
-    nmdc_automation/workflow_automation/nmdcapi.py
-    nmdc_automation/workflow_automation/watch_nmdc.py
-    nmdc_automation/workflow_automation/generate_functional_agg.py	

.github/workflows/blt.yml

@@ -0,0 +1,34 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CI
+
+on:
+  push:
+
+permissions:
+  contents: read
+
+jobs:
+  build_lint_test:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: setup_mongodb
+      uses: supercharge/[email protected]
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v3
+      with:
+        python-version: "3.9"
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+    - name: Install dependencies
+      run: |
+        poetry install
+    - name: Lint with flake8
+      run: |
+        poetry run flake8 nmdc_automation --exit-zero --statistics --tee --output-file flake8stats.txt
+    - name: Test with pytest
+      run: |
+        poetry run pytest ./tests --junit-xml=pytest.xml --cov-report=term  \
+        --cov-report=xml --cov=nmdc_automation --local-badge-output-dir badges/

.gitignore

@@ -6,4 +6,4 @@ htmlcov/
 .coverage
 attic
 .idea/
-*.lock
+

Makefile

@@ -1,3 +1,3 @@
 
 test:
-	PYTHONPATH=$(shell pwd) pytest --cov-report term --cov-report html --cov=nmdc_automation ./tests
+	PYTHONPATH=$(shell pwd) pytest --cov-report term --cov=nmdc_automation ./tests

README.md

@@ -1,3 +1,11 @@
+[![CI](https://github.com/microbiomedata/nmdc_automation/actions/workflows/blt.yml/badge.svg)](https://github.com/microbiomedata/nmdc_automation/actions/workflows/blt.yml)
+![Tests](./badges/tests.svg)
+![Coverage](./badges/coverage.svg)
+
+
+<!-- Pytest Coverage Comment:Begin -->
+<!-- Pytest Coverage Comment:End -->
+
 # nmdc_automation
 
 ## Goal

configs/site_configuration.toml

@@ -14,15 +14,15 @@ site = "Processing Site"
 
 [nmdc]
 url_root = "https://data.microbiomedata.org/data/"
-api_url = "https://api.microbiomedata.org"
+api_url = "https://api.microbimedata.org"
 
 [state]
 watch_state = "State File"
 agent_state = "/tmp/agent.state"
 activity_id_state = "/Path/to/activity_id_state"
 
 [workflows]
-workflows_config = "/configs/workflows.yaml"
+workflows_config = "./configs/workflows.yaml"
 
 [credentials]
 client_id = "xxxxxx"