Merge branch 'develop' into fds-2525-authenticated-exports

.github/workflows/test.yml

@@ -134,7 +134,16 @@ jobs:
           SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
         run: >
           poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/
-          -m "not (rule_benchmark)" --reruns 4 -n 8 --ignore=tests/unit
+          -m "not (rule_benchmark or single_process_execution)" --reruns 4 -n 8 --ignore=tests/unit
+
+      - name: Run integration tests single process
+        if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) }}
+        env:
+          SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
+          SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
+        run: >
+          poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/
+          -m "single_process_execution" --reruns 4 --ignore=tests/unit
 
 
       - name: Upload pytest test results

.readthedocs.yml

@@ -7,14 +7,15 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.9"
   jobs:
     post_install:
       - pip install poetry==1.3.0
       - poetry config virtualenvs.create false
-      - poetry install --with doc
+      - poetry install --all-extras
+      - pip install typing-extensions==4.12.2
     #Poetry will install my dependencies into the virtualenv created by readthedocs if I set virtualenvs.create=false
     # You can also specify other tool versions:
     # nodejs: "16"

CONTRIBUTION.md

@@ -49,7 +49,7 @@ For new features, bugs, enhancements:
 #### 4. Pull Request and Review
 * Create a PR from `develop-<feature/fix-name>` into the develop branch of the upstream repo
 * Request a code review on the PR
-* Once code is approved merge in the develop branch. We suggest creating a merge commit for a cleaner commit history on the `develop` branch.
+* Once code is approved merge in the develop branch. The **"Squash and merge"** strategy should be used for a cleaner commit history on the `develop` branch. The description of the squash commit should include enough information to understand the context of the changes that were made.
 * Once the actions pass on the main branch, delete the `develop-<feature/fix-name>` branch
 
 ### Updating readthedocs documentation

README.md

@@ -273,12 +273,17 @@ poetry debug info
 
 Before you begin, make sure you are in the latest `develop` of the repository.
 
-The following command will install the dependencies based on what we specify in the `poetry.lock` file of this repository. If this step is taking a long time, try to go back to Step 2 and check your version of `poetry`. Alternatively, you can try deleting the lock file and regenerate it by doing `poetry install` (Please note this method should be used as a last resort because this would force other developers to change their development environment)
+The following command will install the dependencies based on what we specify in the `poetry.lock` file of this repository (which is generated from the libraries listed in the `pyproject.toml` file). If this step is taking a long time, try to go back to Step 2 and check your version of `poetry`. Alternatively, you can try deleting the lock file and regenerate it by doing `poetry lock` (Please note this method should be used as a last resort because this would force other developers to change their development environment).
 
 ```
-poetry install --all-extras
+poetry install --with dev,doc
 ```
 
+This command will install:
+* The main dependencies required for running the package.
+* Development dependencies for testing, linting, and code formatting.
+* Documentation dependencies such as `sphinx` for building and maintaining documentation.
+
 ### 5. Set up configuration files
 
 The following section will walk through setting up your configuration files with your credentials to allow for communication between `schematic` and the Synapse API.

env.example

@@ -21,3 +21,21 @@ SERVICE_ACCOUNT_CREDS='Provide service account creds'
 # TELEMETRY_EXPORTER_CLIENT_AUDIENCE=...
 ## Alternative Opentelemetry authentication: Sets a static Authorization header to use for all requests. Used when developing locally
 # OTEL_EXPORTER_OTLP_HEADERS=Authorization=Bearer ey...
+
+
+# Used during integration test run to determine if files will be output for manual
+# inspection. These tests cannot fully finish all validation via code. All of these
+# tests will be marked by pytest "manual_verification_required"
+# More information: https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3055779846/Schematic+API+test+plan 
+MANUAL_TEST_VERIFICATION=false
+
+# Used to determine if a local flask instance is created during integration testing. If
+# this is true schematic tests will use a schematic API server running outside of the
+# context of the integration test. The url used is defined below.
+USE_DEPLOYED_SCHEMATIC_API_SERVER=false
+
+# The URL used to execute integration tests for schematic API. Defaults to localhost.
+# dev: https://schematic-dev.api.sagebionetworks.org
+# staging: https://schematic-staging.api.sagebionetworks.org
+# prod: https://schematic.api.sagebionetworks.org
+SCHEMATIC_API_SERVER_URL=http://localhost:3001