Merge branch 'main' into fix/replace-print-with-logging-repo-load-controller

Author: ANJAN672

.github/workflows/functional_test.yml

@@ -0,0 +1,31 @@
+name: "Functional tests"
+# Runs automated test suites that ensure functionality is preserved. Any failures should prevent code from shipping.
+on:
+  pull_request:
+    branches: [main, release]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    name: test with ${{ matrix.env }} on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 15
+    strategy:
+      fail-fast: false
+      matrix:
+        env: ["3.10", "3.11"] #, "3.12", "3.13", "3.14"
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          enable-cache: true
+
+      - name: Run Tests
+        run: |
+          uv run --python ${{ matrix.env }} pytest \
+            tests/test_classes \
+            --color=yes

.pylintrc

@@ -142,7 +142,7 @@ confidence=HIGH,
 
 # Only enable specific messages
 disable=all
-enable=unused-import,redefined-outer-name,E1206,E1205,E0704,E0107,E4702,E1101,E0211,E0213,E0103,E1133,E1120,E3102,E0602,E1123,E0001,W0702,W1404,W0706,W0101,W0120,W0718,R1737,R1705,R1720,R1724,R1723,R0401,R1701,C1802,C0200,C0501,C0201,W1001,E1102,R0923
+enable=unused-import,redefined-outer-name,E1206,E1205,E0704,E0107,E4702,E1101,E0211,E0213,E0103,E1133,E1120,E3102,E0602,E1123,E0001,W0702,W1404,W0706,W0101,W0120,W0718,R1737,R1724,R1723,R0401,R1701,C1802,C0200,C0501,C0201,W1001,E1102,R0923
 
 
 [LOGGING]

augur/application/config.py

@@ -546,6 +546,8 @@ class JsonConfig(ConfigStore):
 
     def __init__(self, json_data, logger: logging.Logger):
         super().__init__(logger)
+        if not self.writable:
+            json_data = copy.deepcopy(json_data)
         self.json_data = json_data
 
     @property

pyproject.toml

@@ -187,6 +187,19 @@ legacy_tox_ini = """
     addopts = -ra -s
 """
 
+[tool.pytest.ini_options]
+addopts = "-ra -s"
+testpaths = [
+    "tests/test_classes",
+    # "tests/test_routes", # runs, but needs a fixture for connecting to the web interface of Augur
+    # "tests/test_metrics",
+    # "tests/test_tasks",
+    # "tests/test_application",
+    # "tests/test_workers",
+    # "tests/test_workers/worker_persistence/",
+    # "tests/test_routes/runner.py"
+]
+
 [tool.mypy]
 files = ['augur/application/db/*.py']
 ignore_missing_imports = true

scripts/control/refresh-matviews.sh

@@ -6,6 +6,5 @@ psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur
 psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur_data.augur_new_contributors with data;'
 psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur_data.explorer_contributor_actions with data;'
 psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur_data.explorer_libyear_all with data;'
-psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur_data.explorer_libyear_detail with data;'
 psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur_data.explorer_new_contributors with data;'
 psql -U augur -h localhost -p 5432 -d padres -c 'REFRESH MATERIALIZED VIEW augur_data.explorer_entry_list with data;'

tests/test_classes/test_config_stores.py

@@ -25,12 +25,31 @@ def test_jsonconfig_empty_true_false(mock_logger):
     assert JsonConfig({"A": {}}, mock_logger).empty is False
 
 
+def test_jsonconfig_write_protection(mock_logger):
+    # JsonConfig should be not writeable by default, so we should be unable to change
+    # its values, even by abusing references
+    
+    data = {"Alpha": {"a": 1, "b": "str"}, "Beta": {}}
+    cfg = JsonConfig(data, mock_logger)
+
+    # mutation via input
+    data["Alpha"]["a"] = 2
+
+    config_test = cfg.retrieve_dict() 
+    assert config_test != data # the data in the config should not change
+
+    # mutation via output
+    config_test["Alpha"]["a"] = 3
+    
+    config_test = cfg.retrieve_dict() 
+    assert config_test != data # the data in the config should not change
+
 def test_jsonconfig_retrieve_has_get(mock_logger):
     data = {"Alpha": {"a": 1, "b": "str"}, "Beta": {}}
     cfg = JsonConfig(data, mock_logger)
 
     # retrieve full dict
-    assert cfg.retrieve_dict() is data
+    assert cfg.retrieve_dict() == data
 
     # has/get section
     assert cfg.has_section("Alpha") is True