DM-45314: add workflow for pytest

.github/workflows/pytest.yaml

@@ -0,0 +1,41 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: Run PyTest
+
+on: [push, pull_request]
+
+jobs:
+  run_pytest:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+        cache: "pip"
+
+    - name: Editable mode install
+      run: |
+        python -m pip install uv
+        uv pip install --system pytest pytest-cov pytest-html
+        uv pip install --system -e .
+    - name: Test with pytest
+      run: |
+        pytest --cov=./ --cov-report=html --html=pytest_report.html --self-contained-html
+
+    - name: Upload test report
+      uses: actions/upload-artifact@v4
+      with:
+        name: pytest_report
+        path: pytest_report.html
+
+    - name: Upload coverage report
+      uses: actions/upload-artifact@v4
+      with:
+        name: coverage_report
+        path: htmlcov
+

.gitignore

@@ -8,6 +8,7 @@ config.log
 *.pyc
 *_wrap.cc
 *Lib.py
+*.egg-info
 
 # Built by sconsUtils
 version.py
@@ -16,10 +17,16 @@ bin/
 # Pytest
 tests/.tests
 pytest_session.txt
+pytest_report.html
+htmlcov
 .cache/
 .pytest_cache
 .coverage
 .pre-commit-config.yaml
 .flake8
 .isort.cfg
 .mypy.ini
+
+# environment
+.venv
+.vscode

Dockerfile.pqserver

@@ -1,12 +1,12 @@
 FROM python:3.11
 RUN pip install flask gunicorn sqlalchemy psycopg2
-WORKDIR /consdb-pq
-COPY python/lsst/consdb/pqserver.py python/lsst/consdb/utils.py /consdb-pq/
+WORKDIR /
+COPY python/lsst/consdb/__init__.py python/lsst/consdb/pqserver.py python/lsst/consdb/utils.py /consdb-pq/
 # Environment variables that must be set:
 # DB_HOST DB_PASS DB_USER DB_NAME or POSTGRES_URL
 
 # Expose the port.
 EXPOSE 8080
 
-ENTRYPOINT [ "gunicorn", "-b", "0.0.0.0:8080", "-w", "2", "pqserver:app" ]
+ENTRYPOINT [ "gunicorn", "-b", "0.0.0.0:8080", "-w", "2", "consdb-pq.pqserver:app" ]
 

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "consdb"
 description = "consdb provides support for the Consolidated Database for the `Vera C. Rubin Observatory <https://lsst.org>`_."
 license = { text = "GPL" }
-dependencies = ["flask", "requests"]
+dependencies = ["flask", "requests", "sqlalchemy"]
 readme = "README.rst"
 urls = { documentation = "https://consdb.lsst.io", source_code = "https://github.com/lsst-dm/consdb"}
 dynamic = ["version"]

python/lsst/consdb/pqserver.py

@@ -24,7 +24,7 @@
 import sqlalchemy
 import sqlalchemy.dialects.postgresql
 from flask import Flask, request
-from utils import setup_logging, setup_postgres
+from .utils import setup_logging, setup_postgres
 
 OBS_TYPE_LIST = ["exposure", "visit1", "ccdexposure", "ccdvisit1"]
 DTYPE_LIST = ["bool", "int", "float", "str"]

tests/test_pqserver.py

@@ -52,7 +52,7 @@ def db(tmpdir, scope="module"):
 @pytest.fixture
 def app(db, scope="module"):
     os.environ["POSTGRES_URL"] = f"sqlite:///{db}"
-    import pqserver
+    from lsst.consdb import pqserver
 
     return pqserver.app
 
@@ -198,16 +198,14 @@ def test_flexible_metadata(client):
     assert result["required_keys"] == ["values"]
 
     response = client.post(
-        "/consdb/insert/latiss",
+        "/consdb/insert/latiss/exposure/obs/2024032100003",
         json={
-            "table": "exposure",
             "values": {
                 "exposure_name": "AT_O_20240327_000002",
                 "controller": "O",
                 "day_obs": 20240327,
                 "seq_num": 2,
             },
-            "obs_id": 2024032700002,
         },
     )
     _assert_http_status(response, 200)
@@ -216,6 +214,7 @@ def test_flexible_metadata(client):
         "message": "Data inserted",
         "table": "cdb_latiss.exposure",
         "instrument": "latiss",
+        "obs_id": 2024032100003,
     }
 
     response = client.post("/consdb/query", json={"query": "SELECT * FROM exposure ORDER BY day_obs;"})