develop => main

.dockerignore

@@ -0,0 +1,11 @@
+.git
+.github
+.ipython
+.jupyter
+.pytest_cache
+.venv
+.vscode
+CODE_OF_CONDUCT.md
+CONTRIBUTING.md
+Dockerfile
+LICENSE

.github/workflows/tests.yml

@@ -103,7 +103,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
-        run: uv sync --dev --group local
+        run: uv sync --dev
 
       - name: Run local tests
         shell: bash

Dockerfile

@@ -1,8 +1,16 @@
+# Dockerfile for running dlt pipelines
+
+# Dockerfile is based heavily on the example uv dockerfile:
+# https://github.com/astral-sh/uv-docker-example
+
 # Use a Python image with uv pre-installed
-FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim
+FROM ghcr.io/astral-sh/uv:python3.13-trixie-slim
 
-# Install the project into `/app`
-WORKDIR /app
+# Set environment variable to noninteractive to prevent prompts during apt operations
+ENV DEBIAN_FRONTEND=noninteractive
+
+# add tini
+RUN apt-get update -y && apt-get install -y --no-install-recommends tini git
 
 # Enable bytecode compilation
 ENV UV_COMPILE_BYTECODE=1
@@ -16,6 +24,9 @@ ENV UV_NO_DEV=1
 # Ensure installed tools can be executed out of the box
 ENV UV_TOOL_BIN_DIR=/usr/local/bin
 
+# Install the project into `/app`
+WORKDIR /app
+
 # Install the project's dependencies using the lockfile and settings
 RUN --mount=type=cache,target=/root/.cache/uv \
     --mount=type=bind,source=uv.lock,target=uv.lock \
@@ -35,10 +46,7 @@ ENV PATH="/app/.venv/bin:$PATH"
 RUN groupadd --system --gid 999 nonroot \
  && useradd --system --gid 999 --uid 999 --create-home nonroot
 
+COPY --chmod=+x ./scripts/entrypoint.sh /app/
 # Use the non-root user to run our application
 USER nonroot
-
-# Reset the entrypoint, don't invoke `uv`
-ENTRYPOINT []
-
-# CMD ["uv", "run", "python", "--version"]
+ENTRYPOINT ["./entrypoint.sh"]

pyproject.toml

@@ -9,13 +9,11 @@ authors = [
 ]
 
 dependencies = [
-    "biopython>=1.86",
     "click>=8.3.1",
     "dlt[deltalake,filesystem,parquet]>=1.21.0",
     "lxml>=6.0.2",
     "pydantic>=2.12.5",
     "pydantic-settings>=2.12.0",
-    "ruff>=0.14.14",
 ]
 
 [project.scripts]
@@ -25,35 +23,40 @@ uniref_pipeline = "cdm_data_loader_utils.pipelines.uniref_pipeline:cli"
 
 [dependency-groups]
 dev = [
+    "berdl-notebook-utils>=0.0.1",
+    "biopython>=1.86",
     "pytest>=9.0.2",
     "pytest-asyncio>=1.3.0",
     "pytest-cov>=7.0.0",
     "pytest-env>=1.2.0",
+    "ruff>=0.14.14",
 ]
 experimental = [
     "mutmut>=3.4.0",
 ]
-local = [
-    "berdl-notebook-utils>=0.0.1",
-]
-minio = [
-    "boto3[crt]>=1.42.0",
-    "tqdm>=4.67.3",
-]
 models = [
     "genson>=1.3.0",
     "json2python-models>=0.3.1",
 ]
-pipeline = []
 xml = [
     "xmlschema>=4.3.1",
     "xsdata[cli,lxml]>=26.1",
 ]
 
+[project.optional-dependencies]
+# for minio interactions -- see utils/minio.py for more details
+minio = [
+    "boto3[crt]>=1.42.0",
+    "tqdm>=4.67.3",
+]
+
+biopython = [
+    "biopython>=1.86",
+]
+
 [tool.ruff]
 line-length = 120
 target-version = "py313"
-
 # Exclude a variety of commonly ignored directories.
 exclude = [
     "__pypackages__",
@@ -127,7 +130,7 @@ select = [
     "SLOT", # flake8-slots
     "SIM", # flake8-simplify
     "TID", # flake8-tidy-imports
-    "TCH", # flake8-type-checking
+    "TC", # flake8-type-checking
     "INT", # flake8-gettext
     "ARG", # flake8-unused-arguments
     "PTH", # flake8-use-pathlib
@@ -149,7 +152,6 @@ select = [
 
 # Allow autofix for all enabled rules (when `--fix`) is provided.
 fixable = ["ALL"]
-unfixable = []
 
 ignore = [
     # D200: unnecessary-multiline-docstring

scripts/entrypoint.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Ensure at least one argument is provided
+if [ "$#" -eq 0 ]; then
+  echo "Usage: $0 {uniref|uniprot} [args...]"
+  exit 1
+fi
+
+cmd="$1"
+shift
+
+case "$cmd" in
+  uniref)
+    # Run the uniref pipeline with any additional arguments via tini
+    exec /usr/bin/tini -- uv run uniref_pipeline "$@"
+    ;;
+  uniprot)
+    # Run the uniprot pipeline with any additional arguments via tini
+    exec /usr/bin/tini -- uv run uniprot_pipeline "$@"
+    ;;
+  *)
+    echo "Error: unknown command '$cmd'; valid commands are 'uniref' or 'uniprot'." >&2
+    exit 1
+    ;;
+esac