Release/v1.3.0

.github/workflows/pytest.yml

@@ -28,15 +28,10 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip install -e .[test]  # coverage reports need -e to capture properly
-    - name: Lint with flake8
+    - name: Check with ruff
       run: |
-        pip install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
-    - name: Check with black
-      run: |
-        pip install black
-        black --check -S -l 100 pori_python tests
+        pip install ruff
+        ruff format --check pori_python tests
     - name: Full Tests with pytest
       run: |
         pip list
@@ -46,6 +41,7 @@ jobs:
         IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }}
         GRAPHKB_USER: ${{ secrets.GKB_TEST_USER }}
         GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }}
+        GRAPHKB_URL: ${{ secrets.GKB_TEST_URL }}
         # SDEV-3381 - Turn off integration tests temporarily, till efficiency is increased
         # turn on integration tests for one python version only
         EXCLUDE_INTEGRATION_TESTS: ${{ matrix.python-version != '3.11' }}

.github/workflows/quick-pytest.yml

@@ -25,22 +25,19 @@ jobs:
       run: |
         python -m pip install --upgrade pip setuptools
         pip install -e .[test]  # coverage reports need -e to capture properly
-    - name: Lint with flake8
+    - name: Check with ruff
       run: |
-        pip install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 pori_python --count --select=E9,F63,F7,F82 --show-source --statistics
-    - name: Check with black
-      run: |
-        pip install black
-        black --check -S -l 100 pori_python tests
+        pip install ruff
+        ruff format --check pori_python tests
     - name: Short Tests with pytest
       run: pytest --junitxml=junit/test-results-${{ matrix.python-version }}.xml --cov ipr --cov-report term --cov-report xml
       env:
         IPR_USER: ${{ secrets.IPR_TEST_USER }}
         IPR_PASS: ${{ secrets.IPR_TEST_PASSWORD }}
+        IPR_URL: ${{ secrets.IPR_TEST_URL }}
         GRAPHKB_USER: ${{ secrets.GKB_TEST_USER }}
         GRAPHKB_PASS: ${{ secrets.GKB_TEST_PASS }}
+        GRAPHKB_URL: ${{ secrets.GKB_TEST_URL }}
         EXCLUDE_INTEGRATION_TESTS: 1
         # EXCLUDE_INTEGRATION_TESTS: ${{ matrix.python-version != '3.11' }}
-      if: github.event_name != 'pull_request'
+      if: github.event_name != 'pull_request'

README.md

@@ -46,11 +46,9 @@ pip install -e .[dev]
 
 Run the tests:
 
-Export usernames, passwords, and set test options.
+Export usernames, passwords, and test options.
 
-Note that IPR tests will try to use the BCGSC production GraphKB API by default.
-If you want to test interaction with a different instance, you will need to
-set the GraphKB variables.
+IPR_URL and GRAPHKB_URL values must also be set.
 
 Set EXCLUDE vars to 1 if you don't want to run these tests.
 ONCOKB and BCGSC tests are enabled by default.
@@ -67,11 +65,12 @@ export EXCLUDE_ONCOKB_TESTS=1
 ```
 
 If you want to run tests that upload reports to a live IPR instance,
-specify the url of the IPR API you want to use and set the test var to 1.
+specify the url of the IPR API you want to use and set the test var
+INCLUDE_UPLOAD_TESTS to 1.
 These tests are disabled by default.
 
 The created reports are deleted by default. If you want to keep them,
-set DELETE_UPLOAD_TEST_REPORTS to 0 in the env.
+set DELETE_UPLOAD_TEST_REPORTS to 0.
 
 ```bash
 export IPR_TEST_URL='http://localhost:8081/api'
@@ -84,14 +83,16 @@ pytest tests
 ```
 
 ### JSON Validate and Upload to IPR
+An IPR_URL must be provided either as an environment variable or an arg.
+
 If you only want to validate the json content, use
 ```bash
-ipr --password $IPR_PASS -c 'path/to/content.json' --validate_json
+ipr --password $IPR_PASS -c 'path/to/content.json' --validate_json --ipr_url $IPR_URL
 ```
 
 If you only want to upload the json directly to ipr and skip all the preprocessing, use
 ```bash
-ipr --password $IPR_PASS -c 'path/to/content.json' --upload_json
+ipr --password $IPR_PASS -c 'path/to/content.json' --upload_json --ipr_url $IPR_URL
 ```
 
 ## Documentation

pori_python/graphkb/__init__.py

@@ -1,2 +1 @@
-from .constants import DEFAULT_URL  # noqa: F401
 from .util import GraphKBConnection, logger  # noqa: F401