Merge pull request #1376 from Sage-Bionetworks/develop

Schematic `v24.2.1`

.github/workflows/test.yml

@@ -76,7 +76,7 @@ jobs:
       #    install your root project, if required
       #----------------------------------------------
       - name: Install library
-        run: poetry install --no-interaction
+        run: poetry install --no-interaction --all-extras
 
       #----------------------------------------------
       #             perform linting
@@ -96,7 +96,7 @@ jobs:
         run: |
           # ran only on certain files for now
           # add here when checked
-          poetry run black schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py --check
+          poetry run black schematic --check
 
       #----------------------------------------------
       #             type checking/enforcement
@@ -116,29 +116,23 @@ jobs:
         run: |
           # ran only on certain files for now
           # add here when checked
-          poetry run pylint schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
+          poetry run pylint schematic/visualization/* schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
+          # do all utils but schema_utils.py
+          poetry run pylint schematic/utils/cli_utils.py schematic/utils/curie_utils.py schematic/utils/df_utils.py
+          poetry run pylint schematic/utils/general.py schematic/utils/google_api_utils.py schematic/utils/io_utils.py
+          poetry run pylint schematic/utils/validate_rules_utils.py schematic/utils/validate_utils.py schematic/utils/viz_utils.py
 
       #----------------------------------------------
       #              run test suite
       #----------------------------------------------
-      - name: Run regular tests and rule combination tests
-        env:
-          SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
-        if: ${{ contains(github.event.head_commit.message, 'runcombos') }}
-        run: >
-          source .venv/bin/activate;
-          pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/
-          -m "not (google_credentials_needed or schematic_api or table_operations)" --reruns 2 -n auto
-
       - name: Run tests
         env:
           SYNAPSE_ACCESS_TOKEN: ${{ secrets.SYNAPSE_ACCESS_TOKEN }}
           SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
-        if: ${{ false == contains(github.event.head_commit.message, 'runcombos') }}
         run: >
           source .venv/bin/activate;
           pytest --durations=0 --cov-report=term --cov-report=html:htmlcov --cov=schematic/
-          -m "not (google_credentials_needed or rule_combos or schematic_api or table_operations)" --reruns 2  -n auto
+          -m "not (google_credentials_needed or schematic_api or table_operations)" --reruns 2 -n auto
 
       - name: Upload pytest test results
         uses: actions/upload-artifact@v2

.readthedocs.yml

@@ -12,7 +12,7 @@ build:
     python: "3.9"
   jobs:
     post_install:
-      - pip install poetry==1.2.0
+      - pip install poetry==1.3.0
       - poetry config virtualenvs.create false
       - poetry install --with doc
     #Poetry will install my dependencies into the virtualenv created by readthedocs if I set virtualenvs.create=false

README.md

@@ -71,6 +71,18 @@ poetry install
 ```
 This command will install the dependencies based on what we specify in poetry.lock. If this step is taking a long time, try to go back to step 2 and check your version of poetry. Alternatively, you could also 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)
 
+If you want to install the API you will need to install those dependencies as well:
+
+```
+poetry install --extras "api"
+```
+
+If you want to install the uwsgi:
+
+```
+poetry install --extras "api"
+```
+
 5. Fill in credential files: 
 *Note*: If you won't interact with Synapse, please ignore this section.
 

certificate.conf

@@ -7,6 +7,8 @@ server {
     proxy_read_timeout 300;
     proxy_connect_timeout 300;
     proxy_send_timeout 300;
+    send_timeout 300;
+    uwsgi_read_timeout 300;
     location / {
         try_files $uri @app;
     }