BLD: update python versions for CI containers

.codecov.yml

@@ -0,0 +1,5 @@
+coverage:
+  status:
+    project:
+      default:
+        threshold: 0.1%

.github/workflows/basic-install.yml

@@ -22,7 +22,7 @@ jobs:
       matrix:
         # disable windows build test as bilby_cython is currently broken there
         os: [ubuntu-latest, macos-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
         with:

.github/workflows/build-containers.yml

@@ -5,56 +5,60 @@ on:
     - cron: "15 0 * * *" 
   workflow_dispatch:
 
-env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
-
 jobs:
   build-container:
     permissions:
-      contents: read
-      packages: write
       attestations: write
+      contents: read
       id-token: write
+      packages: write
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["310", "311", "312"]
+        python-version: ["11", "12", "13"]
+    env:
+      LABEL: ghcr.io/${{ github.repository }}-python3${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v4
-      - name: Setup dockerfile
+
+      - name: Remove unnecessary files
         run: |
-          cp containers/v3-dockerfile-test-suite-python${{ matrix.python-version }} Dockerfile
-          cp containers/env-template.yml .
+          df . -h
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+          df . -h
 
       - name: Login to the Container registry
-        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        uses: docker/login-action@v3
         with:
-          registry: ${{ env.REGISTRY }}
+          registry: ghcr.io
           username: ${{ github.actor }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Extract metadata (tags, labels) for Docker
-        id: meta
-        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
-        with:
-          tags: type=raw,value=latest
-          images: ghcr.io/${{ env.IMAGE_NAME }}-python${{ matrix.python-version }}
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
 
       - name: Build and push Docker image
         id: push
-        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        uses: docker/build-push-action@v6
         with:
           context: .
-          tags: ${{ steps.meta.outputs.tags }}
+          build-args: |
+            python_minor_version=${{ matrix.python-version }}
+            ENV_FILE=containers/environment.yml
           push: true
-          labels: ${{ steps.meta.outputs.labels }}
-
-      # FIXME: disabled as it is not working well but should probably be added in later
-      # https://docs.github.com/en/actions/security-for-github-actions/using-artifact-attestations/using-artifact-attestations-to-establish-provenance-for-builds
-      # - name: Generate artifact attestation
-      #   uses: actions/attest-build-provenance@v1
-      #   with:
-      #     subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
-      #     subject-digest: ${{ steps.push.outputs.digest }}
-      #     push-to-registry: true
+          file: containers/Dockerfile
+          tags: ${{ env.LABEL }}:latest
+          cache-from: type=registry,ref=${{ env.LABEL }}:buildcache
+          cache-to: type=registry,ref=${{ env.LABEL }}:buildcache,mode=max
+
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v3
+        with:
+          subject-name: ${{ env.LABEL }}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true

.github/workflows/pages.yml

@@ -23,7 +23,7 @@ concurrency:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: ghcr.io/bilby-dev/bilby-python311:latest
+    container: ghcr.io/bilby-dev/bilby-python312:latest
     steps:
       - name: Checkout
         uses: actions/checkout@v4

.github/workflows/unit-tests.yml

@@ -40,6 +40,9 @@ jobs:
           - name: Python 3.12
             version: 3.12
             short-version: 312
+          - name: Python 3.13
+            version: 3.13
+            short-version: 313
 
     steps:
     - uses: actions/checkout@v4

containers/Dockerfile

@@ -0,0 +1,52 @@
+#############################
+######## Setup base #########
+#############################
+
+FROM containers.ligo.org/docker/base:conda AS os-deps
+LABEL name="bilby CI testing" \
+maintainer="Gregory Ashton <gregory.ashton@ligo.org>, Colm Talbot <colm.talbot@ligo.org>"
+
+#############################
+##### Download ROQ data #####
+#############################
+
+FROM debian:bookworm-slim AS data
+WORKDIR /roq_basis
+RUN apt-get update && apt-get install -y --no-install-recommends ca-certificates wget \
+ && rm -rf /var/lib/apt/lists/*
+# Add the ROQ data to the image
+RUN  wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/B_linear.npy \
+    && wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/B_quadratic.npy \
+    && wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/fnodes_linear.npy \
+    && wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/fnodes_quadratic.npy \
+    && wget https://git.ligo.org/lscsoft/ROQ_data/raw/master/IMRPhenomPv2/4s/params.dat \
+    && wget https://git.ligo.org/soichiro.morisaki/roq_basis/raw/main/IMRPhenomD/16s_nospins/basis_addcal.hdf5 \
+    && wget https://git.ligo.org/soichiro.morisaki/roq_basis/raw/main/IMRPhenomD/16s_nospins/basis_multiband_addcal.hdf5
+
+#############################
+##### Build environment #####
+#############################
+
+FROM os-deps AS build-env
+ARG ENV_FILE=environment.yml
+COPY ${ENV_FILE} env.yml
+ARG python_major_version=3
+ARG python_minor_version=12
+
+RUN echo "  - python=${python_major_version}.${python_minor_version}" >> env.yml
+ENV conda_env=python${python_major_version}${python_minor_version}
+
+RUN mamba env create -f env.yml -n ${conda_env}
+RUN echo "source activate ${conda_env}" > ~/.bashrc
+ENV PATH=/opt/conda/envs/${conda_env}/bin:$PATH
+RUN /bin/bash -c "source activate ${conda_env}"
+RUN mamba clean --all
+
+#############################
+### Finalize environment ####
+#############################
+
+FROM build-env AS final
+COPY --from=data /roq_basis /roq_basis
+RUN mamba info
+RUN python --version

containers/env-template.yml → containers/environment.yml

@@ -2,19 +2,17 @@
 # The python version should be added before creating the env
 channels:
   - conda-forge
-  - defaults
   - pytorch
 dependencies:
   - pip
   - setuptools
   - setuptools_scm
   - matplotlib
-  - numpy<2.2  # dynesty<2.2 requires numpy<2.2
+  - numpy<2.4
   - scipy
   - pandas
   - astropy
   - flake8
-  - anaconda
   - coverage
   - configargparse
   - future
@@ -23,7 +21,7 @@ dependencies:
   - pytest-cov
   - pytest-requires
   - pytest-rerunfailures
-  - conda-forge::arviz
+  - arviz
   - parameterized
   - scikit-image
   - celerite
@@ -37,7 +35,7 @@ dependencies:
   - bilby.cython
   - pyseobnr
   - ligo-gracedb
-  - gwpy
+  - gwpy>=4.0.0
   - ligo.skymap
   - sphinx<9 # needed for sphinx_rtd_theme<3.1
   - numpydoc