Merge pull request #96 from labthings/ci-improvements

Use pinned dependencies for testing and update CI script.

Author: rwb27

.github/workflows/test.yml

@@ -25,7 +25,7 @@ jobs:
           mv coverage.lcov base-coverage.lcov
 
       - name: Upload code coverage for base branch
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: base-coverage.lcov
           path: ./base-coverage.lcov
@@ -34,7 +34,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python: ["3.9", "3.10", "3.11", "3.12"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - uses: actions/checkout@v3
@@ -45,7 +45,7 @@ jobs:
           python-version: ${{ matrix.python }}
 
       - name: Install Dependencies
-        run: pip install -e .[dev,server]
+        run: pip install -e . -r dev-requirements.txt
 
       - name: Lint with Ruff
         run: ruff check .
@@ -57,25 +57,57 @@ jobs:
         run: pytest --cov=src --cov-report=lcov
 
       - name: Upload code coverage
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: coverage.lcov
+          name: coverage-${{ matrix.python }}
           path: ./coverage.lcov
 
       - name: Analyse with MyPy
         run: mypy src
 
+  test-with-unpinned-deps:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python: ["3.10", "3.11", "3.12", "3.13"]
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python }}
+
+      - name: Install Dependencies
+        run: pip install -e .[dev,server]
+
+      - name: Lint with Ruff
+        run: ruff check .
+
+      - name: Format with Ruff
+        if: success() || failure()
+        run: ruff format --check .
+      
+      - name: Analyse with MyPy
+        if: success() || failure()
+        run: mypy src
+
+      - name: Test with pytest
+        if: success() || failure()
+        run: pytest --cov=src --cov-report=lcov
+
   coverage:
     runs-on: ubuntu-latest
     needs: [base_coverage, test]
     steps:
       - name: Download code coverage report
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: coverage.lcov
+          name: coverage-3.12
 
       - name: Download code coverage report for base branch
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: base-coverage.lcov
 

README.md

@@ -34,6 +34,14 @@ You can install this repository with `pip`, either clone it and run `pip install
 
 The code is linted with `ruff .`, type checked with `mypy src`, and tested with `pytest`. These all run in CI with GitHub Actions. The codebase is not even `v0.1` yet so it's still subject to summary rearrangement.
 
+Dependencies are defined in `pyproject.toml` and can be compiled to `dev-requirements.txt` with:
+```
+uv pip compile --extra dev --extra server pyproject.toml --output-file dev-requirements.txt
+```
+If you're not using `uv`, just regular `pip-compile` from `pip-tools` will do the same thing.
+
+All changes to the codebase should go via pull requests, and should only be merged once all the checks in the `test` job are passing. It is preferable to merge code where the `test-with-unpinned-dependencies` job fails, and deal with the dependency issues in another PR, particularly where the required changes are distinct from the code in the PR.
+
 ## Demo
 
 See the [examples folder](./examples/) for a runnable demo.

dev-requirements.txt

@@ -0,0 +1,166 @@
+# This file was autogenerated by uv via the following command:
+#    uv pip compile --extra dev --extra server pyproject.toml --output-file dev-requirements.txt
+annotated-types==0.7.0
+    # via pydantic
+anyio==4.8.0
+    # via
+    #   labthings-fastapi (pyproject.toml)
+    #   httpx
+    #   starlette
+    #   watchfiles
+attrs==25.1.0
+    # via
+    #   jsonschema
+    #   referencing
+certifi==2025.1.31
+    # via
+    #   httpcore
+    #   httpx
+click==8.1.8
+    # via
+    #   rich-toolkit
+    #   typer
+    #   uvicorn
+colorama==0.4.6
+    # via
+    #   click
+    #   pytest
+    #   uvicorn
+coverage==7.6.12
+    # via pytest-cov
+dnspython==2.7.0
+    # via email-validator
+email-validator==2.2.0
+    # via fastapi
+fastapi==0.115.11
+    # via labthings-fastapi (pyproject.toml)
+fastapi-cli==0.0.7
+    # via fastapi
+h11==0.14.0
+    # via
+    #   httpcore
+    #   uvicorn
+httpcore==1.0.7
+    # via httpx
+httptools==0.6.4
+    # via uvicorn
+httpx==0.28.1
+    # via
+    #   labthings-fastapi (pyproject.toml)
+    #   fastapi
+idna==3.10
+    # via
+    #   anyio
+    #   email-validator
+    #   httpx
+ifaddr==0.2.0
+    # via zeroconf
+iniconfig==2.0.0
+    # via pytest
+itsdangerous==2.2.0
+    # via fastapi
+jinja2==3.1.6
+    # via fastapi
+jsonschema==4.23.0
+    # via labthings-fastapi (pyproject.toml)
+jsonschema-specifications==2024.10.1
+    # via jsonschema
+markdown-it-py==3.0.0
+    # via rich
+markupsafe==3.0.2
+    # via jinja2
+mdurl==0.1.2
+    # via markdown-it-py
+mypy==1.15.0
+    # via labthings-fastapi (pyproject.toml)
+mypy-extensions==1.0.0
+    # via mypy
+numpy==2.2.3
+    # via labthings-fastapi (pyproject.toml)
+orjson==3.10.15
+    # via fastapi
+packaging==24.2
+    # via pytest
+pluggy==1.5.0
+    # via pytest
+pydantic==2.10.6
+    # via
+    #   labthings-fastapi (pyproject.toml)
+    #   fastapi
+    #   pydantic-extra-types
+    #   pydantic-settings
+pydantic-core==2.27.2
+    # via pydantic
+pydantic-extra-types==2.10.2
+    # via fastapi
+pydantic-settings==2.8.1
+    # via fastapi
+pygments==2.19.1
+    # via rich
+pytest==7.4.4
+    # via
+    #   labthings-fastapi (pyproject.toml)
+    #   pytest-cov
+pytest-cov==6.0.0
+    # via labthings-fastapi (pyproject.toml)
+python-dotenv==1.0.1
+    # via
+    #   pydantic-settings
+    #   uvicorn
+python-multipart==0.0.20
+    # via fastapi
+pyyaml==6.0.2
+    # via
+    #   fastapi
+    #   uvicorn
+referencing==0.36.2
+    # via
+    #   jsonschema
+    #   jsonschema-specifications
+    #   types-jsonschema
+rich==13.9.4
+    # via
+    #   rich-toolkit
+    #   typer
+rich-toolkit==0.13.2
+    # via fastapi-cli
+rpds-py==0.23.1
+    # via
+    #   jsonschema
+    #   referencing
+ruff==0.9.10
+    # via labthings-fastapi (pyproject.toml)
+shellingham==1.5.4
+    # via typer
+sniffio==1.3.1
+    # via anyio
+starlette==0.46.0
+    # via fastapi
+typer==0.15.2
+    # via fastapi-cli
+types-jsonschema==4.23.0.20241208
+    # via labthings-fastapi (pyproject.toml)
+typing-extensions==4.12.2
+    # via
+    #   labthings-fastapi (pyproject.toml)
+    #   anyio
+    #   fastapi
+    #   mypy
+    #   pydantic
+    #   pydantic-core
+    #   pydantic-extra-types
+    #   referencing
+    #   rich-toolkit
+    #   typer
+ujson==5.10.0
+    # via fastapi
+uvicorn==0.34.0
+    # via
+    #   fastapi
+    #   fastapi-cli
+watchfiles==1.0.4
+    # via uvicorn
+websockets==15.0.1
+    # via uvicorn
+zeroconf==0.146.1
+    # via labthings-fastapi (pyproject.toml)

pyproject.toml

@@ -6,7 +6,7 @@ authors = [
 ]
 description = "A test implementation of LabThings using FastAPI"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 classifiers = [
   "Programming Language :: Python :: 3",
   "License :: OSI Approved :: MIT License",

requirements.txt

@@ -43,9 +43,7 @@ def generate_message(cls, data: Any):
                     # it will cause 500 errors when retrieving
                     # the invocation.
                     # This way, you can find and fix the source.
-                    data.message = (
-                        f"Error constructing message ({e}) " f"from {data!r}."
-                    )
+                    data.message = f"Error constructing message ({e}) from {data!r}."
         return data
 
 

src/labthings_fastapi/actions/invocation_model.py

@@ -27,7 +27,7 @@ def validate_thing_description(td: dict) -> None:
     jsonschema.validate(instance=td, schema=schema)
     validated_td = time.time()
     logging.info(
-        f"Thing Description validated OK (schema load: {loaded_schema-start:.1f}s, "
-        f"schema validation: {validated_schema-loaded_schema:.1f}s, TD validation: "
-        f"{validated_td-validated_schema:.1f}s)"
+        f"Thing Description validated OK (schema load: {loaded_schema - start:.1f}s, "
+        f"schema validation: {validated_schema - loaded_schema:.1f}s, TD validation: "
+        f"{validated_td - validated_schema:.1f}s)"
     )

src/labthings_fastapi/thing_description/validation.py

@@ -60,7 +60,7 @@ def np_to_listoflists(arr: np.ndarray) -> NestedListOfNumbers:
     NB this will not be quick! Large arrays will be much better
     serialised by dumping to base64 encoding or similar.
     """
-    return arr.tolist()
+    return arr.tolist()  # type: ignore[return-value]
 
 
 def listoflists_to_np(lol: Union[NestedListOfNumbers, np.ndarray]) -> np.ndarray: