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Auto initialize algorithms in DB #89

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merged 59 commits into from
Oct 21, 2024
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267a629
installing recordlinker code into .venv and making it editable
ericbuckley Oct 5, 2024
b260188
creating the skeleton of a configure script
ericbuckley Oct 5, 2024
ebd499e
making recordlinker.schemas to store pydantic classes
ericbuckley Oct 6, 2024
49eb817
fixing matcher signatures
ericbuckley Oct 7, 2024
619328a
schemas can depend on models but not the other way around
ericbuckley Oct 7, 2024
a7af04e
removing algorithm_config for now
ericbuckley Oct 7, 2024
7ba1b83
updating cascades
ericbuckley Oct 7, 2024
571eadf
removing dated FIXME
ericbuckley Oct 7, 2024
8e5372d
removing schema/algorithm reference for now
ericbuckley Oct 7, 2024
4a1c030
adding src back to pythonpath
ericbuckley Oct 7, 2024
7874d34
expanding algorithm_service for more database operations
ericbuckley Oct 7, 2024
0736912
renaming Feature.ZIPCODE to Feature.ZIP
ericbuckley Oct 7, 2024
a69e185
updating algorithm_service test cases
ericbuckley Oct 7, 2024
09722a2
adding schemas.algorithms
ericbuckley Oct 7, 2024
702159b
adding utils.check_signature
ericbuckley Oct 8, 2024
1e88cbc
updating matcher signatures to adhere to correct signatures
ericbuckley Oct 8, 2024
2e8c41b
remove unused import
ericbuckley Oct 8, 2024
b258c09
adding configuration script
ericbuckley Oct 8, 2024
fb97a15
Merge branch 'main' into feature/65-project-structure-cleanup
ericbuckley Oct 8, 2024
4bb6d00
Merge branch 'main' into feature/65-project-structure-cleanup
ericbuckley Oct 9, 2024
4936a10
tests no longer need postgres as an external service
ericbuckley Oct 9, 2024
295d6d5
Merge branch 'feature/65-project-structure-cleanup' into feature/65-a…
ericbuckley Oct 9, 2024
2b80e3b
Merge branch 'main' into feature/65-algorithm-config
ericbuckley Oct 11, 2024
d5324b3
fixing type checks
ericbuckley Oct 11, 2024
2cde5f9
Merge branch 'main' into feature/65-project-structure-cleanup
ericbuckley Oct 11, 2024
43e902f
ignoring matching function typing calls for now
ericbuckley Oct 11, 2024
12af3b7
adding more pii tests
ericbuckley Oct 14, 2024
015a16c
Merge branch 'feature/65-project-structure-cleanup' into feature/65-a…
ericbuckley Oct 14, 2024
e1f279e
Merge branch 'main' into feature/65-project-structure-cleanup
ericbuckley Oct 15, 2024
a71fcef
Merge branch 'main' into feature/65-project-structure-cleanup
ericbuckley Oct 16, 2024
59ed871
Merge branch 'feature/65-project-structure-cleanup' into feature/65-a…
ericbuckley Oct 16, 2024
41ad352
Merge branch 'main' into feature/65-algorithm-config
ericbuckley Oct 16, 2024
5fa6aca
moving algorithm endpoints to its own router
ericbuckley Oct 16, 2024
cf0db41
updating config script to load json
ericbuckley Oct 17, 2024
640b25f
tests for the algorithm router
ericbuckley Oct 17, 2024
00438fa
Merge branch 'main' into feature/65-algorithm-config
ericbuckley Oct 17, 2024
5767a50
removing explicit pyyaml dep
ericbuckley Oct 17, 2024
cb4e8cf
"or {}" isnt necessary
ericbuckley Oct 17, 2024
e97f6bb
removing extra commas
ericbuckley Oct 17, 2024
74ac447
adding them back because of ruff
ericbuckley Oct 17, 2024
488ab04
addressing mypy warning with an ignore
ericbuckley Oct 17, 2024
2e0f559
fixing query for other databases
ericbuckley Oct 17, 2024
552f639
adding more test cases
ericbuckley Oct 17, 2024
68c2ce4
adding another test case for signature check
ericbuckley Oct 17, 2024
49dcd42
awareness is automatic with GH/Slack notifications
ericbuckley Oct 17, 2024
4352431
removing alembic from project
ericbuckley Oct 17, 2024
e6526aa
removing redundancy in testing assets
ericbuckley Oct 17, 2024
c19b4f5
using capital names for Features
ericbuckley Oct 17, 2024
fc1bdb4
adding default algorithms asset
ericbuckley Oct 17, 2024
f37e40e
drying up default algorithms in tests
ericbuckley Oct 17, 2024
71f1af4
adding initial_algorithms.json file
ericbuckley Oct 17, 2024
7a84ee5
small changes to hot reloading and logging
ericbuckley Oct 17, 2024
3bfbe1d
override initial_algorithms setting for tests in pyproject.toml
ericbuckley Oct 17, 2024
c4e2e49
adding create_initial_algorithms to create initial algorithms on sche…
ericbuckley Oct 17, 2024
d95ea06
updating descirptions of intial algorithms
ericbuckley Oct 17, 2024
13938da
Merge branch 'main' into feature/57-auto-init-db
ericbuckley Oct 18, 2024
1e040a4
fixing typing issues
ericbuckley Oct 18, 2024
7157ec1
adding more tests
ericbuckley Oct 18, 2024
c0c55ea
Update assets/initial_algorithms.json
ericbuckley Oct 21, 2024
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override initial_algorithms setting for tests in pyproject.toml
ericbuckley committed Oct 17, 2024
commit 3bfbe1d35137fa245f34a064d53eb315d65365d6
1 change: 0 additions & 1 deletion .github/workflows/check_unit_tests.yml
Original file line number Diff line number Diff line change
@@ -40,7 +40,6 @@ jobs:
- name: Run unit tests
env:
TEST_DB_URI: "postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
INITIAL_ALGORITHMS: ""
run: |
pytest --cov=recordlinker --cov-report=xml tests/unit
- name: Upload test results to Codecov
4 changes: 4 additions & 0 deletions pyproject.toml
Original file line number Diff line number Diff line change
@@ -39,6 +39,7 @@ dev = [
"fastapi[standard]",
"pytest>=8.3",
"pytest-cov",
"pytest-env",
"ruff",
"mypy",
"types-python-dateutil"
@@ -85,6 +86,9 @@ pythonpath = ["src", "tests/unit"]
filterwarnings = [
"ignore:typing.io is deprecated, import directly from typing instead:DeprecationWarning"
]
env = [
"INITIAL_ALGORITHMS=",
]

[tool.mypy]
mypy_path = ["src"]
2 changes: 1 addition & 1 deletion scripts/test_unit.sh
Original file line number Diff line number Diff line change
@@ -14,4 +14,4 @@ cd "$(dirname "$0")/.."
TESTS=${1:-tests/unit/}

# Run the tests
INITIAL_ALGORITHMS="" pytest ${TESTS}
pytest ${TESTS}