nmdc-runtime 2.11.0__tar.gz → 2.11.1__tar.gz

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/.github/workflows/mkdocs.yml

@@ -43,4 +43,4 @@ jobs:
       #       file, or due to one of the dependencies becoming unavailable), which can prompt remedial action.
       #
       - name: Build MkDocs site
-        run: uv run mkdocs build -f docs/mkdocs.yml
+        run: uv run --no-sync mkdocs build -f docs/mkdocs.yml

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/Makefile

@@ -45,7 +45,7 @@ reset-db-test:
 run-test:
 	docker compose --file docker-compose.test.yml exec -it test \
 		./.docker/wait-for-it.sh fastapi:8000 --strict --timeout=300 -- \
-			uv run --active \
+			uv run --active --no-sync \
 				pytest --cov=nmdc_runtime \
 				       --doctest-modules \
 				       --ignore=util/load_testing \
@@ -60,16 +60,16 @@ test: down-test up-test run-test
 # Format Python code using `black`.
 # TODO: Migrate from `black` to `ruff`.
 black:
-	uv run --active black nmdc_runtime
+	uv run --active --no-sync black nmdc_runtime
 
 # Lint Python code using `flake8`.
 # TODO: Migrate from `flake8` to `ruff`.
 lint:
 	# Python syntax errors or undefined names
-	uv run --active flake8 --count --select=E9,F63,F7,F82 --show-source --statistics --extend-ignore=F722 \
+	uv run --active --no-sync flake8 --count --select=E9,F63,F7,F82 --show-source --statistics --extend-ignore=F722 \
 		./nmdc_runtime ./tests
 	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-	uv run --active flake8 --count --exit-zero --max-complexity=10 --max-line-length=127 \
+	uv run --active --no-sync flake8 --count --exit-zero --max-complexity=10 --max-line-length=127 \
 		--statistics --extend-exclude="./build/" --extend-ignore=F722 \
 		./nmdc_runtime ./tests
 
@@ -122,7 +122,7 @@ mongorestore-nmdc-db:
 		--drop --nsInclude='nmdc.*' --gzip --dir /tmp/remote-mongodump
 
 quick-blade:
-	uv run --active python -c "from nmdc_runtime.api.core.idgen import generate_id; print(f'nmdc:nt-11-{generate_id(length=8, split_every=0)}')"
+	uv run --active --no-sync python -c "from nmdc_runtime.api.core.idgen import generate_id; print(f'nmdc:nt-11-{generate_id(length=8, split_every=0)}')"
 
 # List of Make targets that do not represent files being created.
 # Note: I think _most_ of the targets in this Makefile meet that criterion,

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: nmdc-runtime
-Version: 2.11.0
+Version: 2.11.1
 Summary: A runtime system for NMDC data management and orchestration
 Project-URL: Changelog, https://github.com/microbiomedata/nmdc-runtime/releases
 Project-URL: Documentation, https://docs.microbiomedata.org/runtime

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/docker-compose.yml

@@ -96,7 +96,7 @@ services:
     #       oftentimes modify those files while doing load testing, and those files are
     #       not part of the FastAPI app.
     #       Docs: https://www.uvicorn.org/settings/?h=watch#reloading-with-watchfiles
-    command: ["uv", "run", "--active", "uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "8000", "--reload-exclude", "util/load_testing/*"]
+    command: ["uv", "run", "--active", "--no-sync", "uvicorn", "nmdc_runtime.api.main:app", "--reload", "--host", "0.0.0.0", "--port", "8000", "--reload-exclude", "util/load_testing/*"]
     env_file: .env
     # Note: Setting `tty: true` makes it so the console output is in color.
     #       Reference: https://docs.docker.com/reference/cli/docker/container/run/#tty

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/docs/content/contributing-docs.md

@@ -13,7 +13,7 @@ Reference for contributing to this documentation.
 2. Start the [MkDocs development server](https://www.mkdocs.org/user-guide/cli/#mkdocs-serve).
 
    ```shell
-   uv run mkdocs serve -f docs/mkdocs.yml
+   uv run --no-sync mkdocs serve -f docs/mkdocs.yml
    ```
 
    > The MkDocs development server will be accessible at: [`http://localhost:8000`](http://localhost:8000). It will have live reloading enabled. You can press `Ctrl+C` to terminate the server.
@@ -21,7 +21,7 @@ Reference for contributing to this documentation.
 3. (Optional) Build the MkDocs website.
 
    ```shell
-   uv run mkdocs build -f docs/mkdocs.yml
+   uv run --no-sync mkdocs build -f docs/mkdocs.yml
    ```
 
 ## File tree

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/nmdc_runtime/Dockerfile

@@ -85,13 +85,17 @@ ENV PATH="/root/.local/bin/:$PATH"
 #       instead of when the container is running. By default, `uv` defers this compilation
 #       to "import time," whereas `pip` (by default) performs it at "install time" (like this).
 #
+# Note: We use `--locked` so that `uv sync` exits with an error if the `uv.lock` file isn't _already_
+#       up to date. By default, `uv sync` would automatically update the lock file if necessary.
+#       Reference: https://docs.astral.sh/uv/reference/cli/#uv-sync--locked
+#
 ENV VIRTUAL_ENV="/venv"
 RUN mkdir -p "${VIRTUAL_ENV}"
 COPY ./pyproject.toml /code/pyproject.toml
 COPY ./uv.lock        /code/uv.lock
 RUN --mount=type=cache,target=/root/.cache/uv \
     cd /code && \
-    UV_LINK_MODE=copy uv sync --active --no-dev --no-install-project --compile-bytecode
+    UV_LINK_MODE=copy uv sync --active --no-dev --no-install-project --compile-bytecode --locked
 
 # ────────────────────────────────────────────────────────────────────────────┐
 FROM base AS fastapi
@@ -103,12 +107,18 @@ COPY . /code
 # Install the project in editable mode.
 RUN --mount=type=cache,target=/root/.cache/uv \
     cd /code && \
-    uv sync --active --no-dev
+    uv sync --active --no-dev --compile-bytecode --locked
 
 # Use Uvicorn to serve the FastAPI app on port 8000.
+#
+# Note: We include the `--no-sync` option to prevent `uv run` from automatically syncing dependencies.
+#       If it were to sync dependencies at this point, it would install development dependencies, since
+#       we exclude them above, but they are listed in uv's `default-groups` configuration by default.
+#       This is explained at: https://github.com/astral-sh/uv/issues/12558#issuecomment-2764611918
+#
 EXPOSE 8000
 WORKDIR /code
-CMD ["uv", "run", "--active", "uvicorn", "nmdc_runtime.api.main:app", "--proxy-headers", "--host", "0.0.0.0", "--port", "8000"]
+CMD ["uv", "run", "--active", "--no-sync", "uvicorn", "nmdc_runtime.api.main:app", "--proxy-headers", "--host", "0.0.0.0", "--port", "8000"]
 
 # ────────────────────────────────────────────────────────────────────────────┐
 FROM base AS dagster
@@ -124,7 +134,7 @@ COPY . /opt/dagster/lib
 # Install the project in editable mode.
 RUN --mount=type=cache,target=/root/.cache/uv \
     cd /opt/dagster/lib && \
-    uv sync --active --no-dev
+    uv sync --active --no-dev --compile-bytecode --locked
 
 # Move Dagster configuration files to the place Dagster expects.
 ENV DAGSTER_HOME="/opt/dagster/dagster_home/"
@@ -154,7 +164,7 @@ COPY . /code
 # Install the project in editable mode, and install development dependencies.
 RUN --mount=type=cache,target=/root/.cache/uv \
     cd /code && \
-    uv sync --active
+    uv sync --active --compile-bytecode --locked
 
 # Make `wait-for-it.sh` executable.
 RUN chmod +x /code/.docker/wait-for-it.sh

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/nmdc_runtime/site/entrypoint-daemon.sh

@@ -23,4 +23,4 @@ file_env() {
 file_env "MONGO_PASSWORD"
 file_env "DAGSTER_POSTGRES_PASSWORD"
 
-exec uv run --active dagster-daemon run
+exec uv run --active --no-sync dagster-daemon run

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/nmdc_runtime/site/entrypoint-dagit-readonly.sh

@@ -23,4 +23,4 @@ file_env() {
 file_env "MONGO_PASSWORD"
 file_env "DAGSTER_POSTGRES_PASSWORD"
 
-exec uv run --active dagit -h 0.0.0.0 -p 3000 -w workspace.yaml --read-only
+exec uv run --active --no-sync dagit -h 0.0.0.0 -p 3000 -w workspace.yaml --read-only

{nmdc_runtime-2.11.0 → nmdc_runtime-2.11.1}/nmdc_runtime/site/entrypoint-dagit.sh

@@ -23,4 +23,4 @@ file_env() {
 file_env "MONGO_PASSWORD"
 file_env "DAGSTER_POSTGRES_PASSWORD"
 
-exec uv run --active dagit -h 0.0.0.0 -p 3000 -w workspace.yaml
+exec uv run --active --no-sync dagit -h 0.0.0.0 -p 3000 -w workspace.yaml