docker onto python3.11-bookworm, mwalib, test shim, clippy CI

.dockerignore

@@ -6,3 +6,8 @@ doc
 img
 scripts
 target
+*.ms
+*.uvfits
+*.tar
+*.metafits
+*.fits

.github/workflows/clippy.yml

@@ -0,0 +1,31 @@
+on:
+  push:
+    tags-ignore:
+      - "**"
+    branches:
+      - "**"
+  pull_request:
+
+name: clippy
+
+jobs:
+  coverage:
+    runs-on: ubuntu-latest
+    container: mwatelescope/birli:latest
+    steps:
+      - name: Checkout sources
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          override: true
+          components: rustfmt, clippy
+      - name: Run cargo check, fmt, clippy
+        run: |
+          cargo check --all
+          cargo fmt --all -- --check
+          cargo clippy --all -- -D warnings

.github/workflows/docker_test.yml

@@ -16,45 +16,16 @@ jobs:
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
-      - name: Build and push
-        uses: docker/build-push-action@v6
-        with:
-          platforms: linux/amd64,linux/arm64
-          push: false
-          tags: mwatelescope/birli:latest
-          cache-from: type=gha
-          cache-to: type=gha,mode=max
-  check:
-    name: Docker Test and Release
-    needs: build
-    runs-on: ubuntu-latest
-    container: mwatelescope/birli:latest
-    steps:
       - name: Checkout sources
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
-      - run: /opt/cargo/bin/cargo check
-      - run: /opt/cargo/bin/cargo fmt --all -- --check
-      - run: /opt/cargo/bin/cargo clippy --all-targets --all-features -- -D warnings
-      - run: /opt/cargo/bin/cargo test --release
-      - run: /opt/cargo/bin/cargo test --no-default-features --release --features=cli
-  push:
-    needs: build # TODO: needs: check
-    runs-on: ubuntu-latest
-    steps:
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v3
-      - name: Login to Docker Hub
-        uses: docker/login-action@v3
-        with:
-          username: ${{ secrets.DOCKERHUB_USERNAME }}
-          password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Build and push
         uses: docker/build-push-action@v6
         with:
           platforms: linux/amd64,linux/arm64
           push: true
           tags: mwatelescope/birli:latest
           cache-from: type=gha
-          cache-to: type=gha,mode=max
+          cache-to: type=gha,mode=max
+          buildArgs: TEST_SHIM="cargo test --no-default-features; cargo test; cargo clean; rm -rf target"

Dockerfile

@@ -1,47 +1,101 @@
-FROM ubuntu:24.04
+FROM python:3.11-bookworm as base
 
-ENV DEBIAN_FRONTEND=noninteractive
+# suppress perl locale errors
 ENV LANG=en_US.UTF-8 LANGUAGE=en_US:en LC_ALL=en_US.UTF-8
-ARG DEBUG
+# suppress apt-get prompts
+ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update \
-    && apt-get install -y \
-    aoflagger-dev \
+    && apt-get install -y --no-install-recommends \
+    automake \
     build-essential \
+    casacore-data \
+    casacore-dev \
     clang \
+    cmake \
     curl \
-    git \
     jq \
     lcov \
+    libblas-dev \
+    libboost-date-time-dev \
+    libboost-system-dev \
     libcfitsio-dev \
     liberfa-dev \
+    libfftw3-dev \
+    libgsl-dev \
+    libgtkmm-3.0-dev \
+    libhdf5-serial-dev \
+    liblapack-dev \
+    liblua5.3-dev \
+    libpng-dev \
     libssl-dev \
+    libtool \
     pkg-config \
     unzip \
     zip \
-    automake \
-    libtool
+    2>&1 | tee /birli-apt.txt \
+    && \
+    apt-get clean all && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    apt-get -y autoremove
 
-RUN test -z "$DEBUG" || ( \
-    apt-get install -y vim gdb \
+# Get Rust
+ARG RUST_VERSION=stable
+ENV RUSTUP_HOME=/opt/rust CARGO_HOME=/opt/cargo
+ENV PATH="${CARGO_HOME}/bin:${PATH}"
+RUN mkdir -m755 $RUSTUP_HOME $CARGO_HOME && ( \
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | env RUSTUP_HOME=$RUSTUP_HOME CARGO_HOME=$CARGO_HOME sh -s -- -y \
+    --profile=minimal \
+    --component llvm-tools \
+    --default-toolchain=${RUST_VERSION} \
     )
-RUN apt-get clean \
-    && rm -rf /var/lib/apt/lists/*
+# # Get cargo make, llvm-cov
+RUN cargo install --force cargo-make cargo-llvm-cov && \
+    rm -rf ${CARGO_HOME}/registry
 
-# Get Rust
-RUN mkdir -m755 /opt/rust /opt/cargo
-ENV RUSTUP_HOME=/opt/rust CARGO_HOME=/opt/cargo PATH=/opt/cargo/bin:$PATH
-# install latest stable rust toolchian, with llvm-tools-preview (for coverage)
-ENV RUST_VERSION=stable
-RUN curl https://sh.rustup.rs -sSf | sh -s -- -y --default-toolchain=$RUST_VERSION
-RUN rustup toolchain install $RUST_VERSION --component llvm-tools-preview
-# Get cargo make, llvm-cov
-RUN /opt/cargo/bin/cargo install --force cargo-make cargo-llvm-cov
+RUN python -m pip install --no-cache-dir maturin[patchelf]==1.7.0
+
+ARG MWALIB_BRANCH=v1.5.0
+RUN git clone --depth 1 --branch=${MWALIB_BRANCH} https://github.com/MWATelescope/mwalib.git /mwalib && \
+    cd /mwalib && \
+    maturin build --release --features=python && \
+    python -m pip install $(ls -1 target/wheels/*.whl | tail -n 1) && \
+    cd / && \
+    rm -rf /mwalib ${CARGO_HOME}/registry
+
+# for example, CMAKE_ARGS="-D CMAKE_CXX_FLAGS='-march=native -mtune=native -O3 -fomit-frame-pointer'"
+ARG CMAKE_ARGS="-D PORTABLE=ON"
+
+ARG AOFLAGGER_BRANCH=v3.4.0
+RUN git clone --depth 1 --branch=${AOFLAGGER_BRANCH} --recurse-submodules https://gitlab.com/aroffringa/aoflagger.git /aoflagger && \
+    cd /aoflagger && \
+    mkdir build && \
+    cd build && \
+    cmake $CMAKE_ARGS \
+    -DENABLE_GUI=OFF \
+    .. && \
+    make install -j`nproc` && \
+    ldconfig && \
+    cd / && \
+    rm -rf /aoflagger
+# set up aoflagger python library
+ENV PYTHONPATH="/usr/local/lib/:$PYTHONPATH"
 
 ADD . /app
 WORKDIR /app
 
-RUN cargo clean \
-    && cargo install --path . --features aoflagger --locked $(test -z "$DEBUG" || echo "--debug") \
-    && cargo clean
+ARG DEBUG
+ARG BIRLI_FEATURES=cli,aoflagger
+RUN cargo install --path . --no-default-features --features=${BIRLI_FEATURES} --locked $(test -z "$DEBUG" || echo "--debug") && \
+    rm -rf /app/target ${CARGO_HOME}/registry
+
+RUN test -z "$DEBUG" || ( \
+    apt-get install -y vim gdb && \
+    apt-get clean all && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && \
+    apt-get -y autoremove \
+    )
+
+ARG TEST_SHIM
+RUN ${TEST_SHIM}
 
 ENTRYPOINT [ "/opt/cargo/bin/birli" ]