Update our docker image, linting, and GH actions

.github/workflows/docker.yml

@@ -16,20 +16,6 @@ jobs:
     steps:
     - uses: actions/checkout@v3
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.10'
-
-    - name: Install build dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel build
-
-    - name: Build and publish
-      run: |
-        python -m build --wheel .
-
     - name: Set up QEMU
       uses: docker/setup-qemu-action@v2
 

.github/workflows/lint.yml

@@ -21,9 +21,10 @@ jobs:
           python -m pip install --upgrade pip
           pip install ruff
 
-      - name: Run black
-        uses: psf/black@stable
-
       - name: Lint with Ruff
         run: |
           ruff check . --output-format=github
+
+      - name: Check formatting with Ruff
+        run: |
+          ruff format --check .

.pre-commit-config.yaml

@@ -1,19 +1,19 @@
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v4.4.0
+  rev: v4.6.0
   hooks:
   - id: check-toml
   - id: check-yaml
   - id: end-of-file-fixer
   - id: trailing-whitespace
   - id: detect-private-key
-- repo: https://github.com/psf/black
-  rev: 23.3.0
-  hooks:
-    - id: black
-      language_version: python3.10
 - repo: https://github.com/charliermarsh/ruff-pre-commit
-  rev: v0.0.264
+  rev: v0.4.10
   hooks:
+    # Run the linter.
     - id: ruff
-      args: ['--fix']
+      types_or: [ python, pyi, jupyter ]
+      args: [ --fix, --show-fixes ]
+    # Run the formatter.
+    - id: ruff-format
+      types_or: [ python, pyi, jupyter ]

Dockerfile

@@ -1,14 +1,22 @@
-FROM mambaorg/micromamba:latest
-MAINTAINER William E Fondrie <wfondrie@talus.bio>
-COPY --chown=$MAMBA_USER:$MAMBA_USER environment.yml /tmp/environment.yml
-COPY --chown=$MAMBA_USER:$MAMBA_USER dist/*.whl /tmp/
+# Base image for building
+FROM python:3.11 as build
 
-WORKDIR /app
+# Install essentials:
+RUN apt-get update && apt-get install -y build-essential libhdf5-dev
 
-RUN micromamba install -y -n base -f /tmp/environment.yml && \
-    micromamba clean --all --yes
+# Install uv:
+ADD https://astral.sh/uv/install.sh /install.sh
+RUN chmod -R 655 /install.sh  && /install.sh && rm /install.sh
 
-ARG MAMBA_DOCKERFILE_ACTIVATE=1
-RUN WHEEL=$(ls /tmp/*.whl) && pip install ${WHEEL}
+# Install our package:
+ENV VIRTUAL_ENV=/opt/venv \
+    PATH="/opt/venv/bin:$PATH"
 
-RUN pip install petasus
+ADD . /src
+RUN /root/.cargo/bin/uv venv --no-cache /opt/venv && \
+    /root/.cargo/bin/uv pip install --no-cache /src
+
+# The app stage (slim debian build):
+FROM python:3.11-slim-bookworm
+COPY --from=build /opt/venv /opt/venv
+ENV PATH="/opt/venv/bin:$PATH"

petasus/mzml.py

@@ -8,7 +8,8 @@
 def read(mzml_file: str) -> dict[tuple[np.ndarray, np.ndarray]]:
     """Parse the mzML file
 
-    This parser is much faster than Pyteomics, but doesn't do any error checking.
+    This parser is much faster than Pyteomics, but doesn't do any error
+    checking.
 
     Parameters
     ----------

pyproject.toml

@@ -28,7 +28,7 @@ dependencies = [
     "numba",
     "pyarrow",
     "hdf5plugin>=3.10.0",
-    "ms2ml @ git+https://github.com/wfondrie/ms2ml.git@encyclopedia-update"
+    "ms2ml",
 ]
 dynamic = ["version"]
 
@@ -56,31 +56,11 @@ find = {namespaces = false}
 [tool.setuptools_scm]
 
 [tool.ruff]
+line-length = 79
+target-version = "py310"
+
+[tool.ruff.lint]
 select = ["E", "F", "T20"]  # T20 is for print() statements.
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F401"]
-
-[tool.black]
-line-length = 79
-target-version = ['py310']
-include = '\.pyi?$'
-exclude = '''
-
-(
-  /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
-    | \.venv
-    | _build
-    | buck-out
-    | build
-    | dist
-  )/
-  | foo.py           # also separately exclude a file named foo.py in
-                     # the root of the project
-)
-'''