Pixi package migration

.github/workflows/test_and_deploy.yml

@@ -0,0 +1,188 @@
+name: Tests, Package, and Deployment
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches: [next]
+    tags: ['v*']
+
+env:
+  PKG_NAME: shiver
+
+jobs:
+  tests:
+    name: Testing Suite
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+
+    - name: Setup Pixi
+      uses: prefix-dev/setup-pixi@v0.8.10
+      with:
+        pixi-version: v0.48.2
+
+    - name: pylint
+      run: pixi run pre-commit run -a pylint
+
+    - name: Install shiver
+      run: pixi run python -m pip install -e .
+
+    - name: Run tests
+      run: pixi run xvfb-run --server-args="-screen 0 1920x1080x24" -a python -m pytest --cov=src --cov-report=xml --cov-report=term
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+
+  build:
+    name: Conda build with Pixi
+    runs-on: ubuntu-24.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
+          fetch-tags: true
+          ref: ${{ github.ref }}
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          pixi-version: v0.48.2
+
+      - name: Build Conda package
+        run: pixi run conda-build
+
+      - name: upload conda package as artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: artifact-conda-package
+          path: ${{ env.PKG_NAME }}-*.conda
+
+  conda-verify:
+    name: Conda Verify
+    needs: build
+    runs-on: ubuntu-24.04
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          fetch-tags: true
+          ref: ${{ github.ref }}
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v2
+        with:
+          environment-name: test
+          init-shell: bash
+          create-args: >-
+            python=3.10
+
+      - name: Download conda package artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: artifact-conda-package
+          path: /tmp/local-channel/linux-64
+
+      - name: Install the package
+        run: |
+          micromamba install --yes -c conda-forge conda-build conda-index
+          python -m conda_index /tmp/local-channel
+          micromamba install -c /tmp/local-channel -c conda-forge -c mantid-ornl -c mantid -c neutrons -c oncat ${{ env.PKG_NAME }}
+
+      - name: Verify the installation
+        env:
+          MPLBACKEND: Agg
+        run: |
+          conda_version=$(micromamba list "${{ env.PKG_NAME }}" | awk -v pkg="${{ env.PKG_NAME }}" '$1 == pkg { print $2 }')
+          echo "Conda version: $conda_version"
+          python_version=$(python -c "import ${{ env.PKG_NAME }}; print(${{ env.PKG_NAME }}.__version__)")
+          echo "Python version: $python_version"
+          if [ "$conda_version" != "$python_version" ]; then
+            echo "Version mismatch!"
+            exit 1
+          else
+            echo "Versions match."
+          fi
+
+  publish:
+    name: Publish
+    runs-on: ubuntu-24.04
+    needs: [tests, conda-verify]
+    if: startsWith(github.ref, 'refs/tags/v')
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 100
+          fetch-tags: true
+          ref: ${{ github.ref }}
+
+      - name: Setup Pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          pixi-version: v0.48.2
+
+      - name: Download previous conda package artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: artifact-conda-package
+
+      - name: Get artifact conda package filename
+        run: |
+          echo "Files downloaded:"
+          ls
+          # Get the first file
+          FILE_NAME=$(ls ./shiver-*.conda)
+          echo "Conda package file to publish: $FILE_NAME"
+
+      - name: Upload package to anaconda
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+          IS_RC: ${{ contains(github.ref, 'rc') }}
+        run: |
+          # label is main or rc depending on the tag-name
+          CONDA_LABEL="main"
+          if [ "${IS_RC}" = "true" ]; then CONDA_LABEL="rc"; fi
+          echo pushing ${{ github.ref }} with label $CONDA_LABEL
+          pixi run anaconda upload --label $CONDA_LABEL --user neutrons ${{ env.PKG_NAME }}-*.conda
+
+  # trigger-deploy:
+  #   runs-on: ubuntu-22.04
+  #   needs: [tests, conda-build]
+  #   # only trigger deploys from protected branches and tags
+  #   if: ${{ github.ref_protected || github.ref_type == 'tag' }}
+  #   steps:
+  #     - name: Determine Environment
+  #       uses: neutrons/branch-mapper@v2
+  #       id: conda_env_name
+  #       with:
+  #         prefix: shiver
+
+  #     - name: Trigger deploy
+  #       id: trigger
+  #       uses: eic/trigger-gitlab-ci@v2
+  #       with:
+  #         url: https://code.ornl.gov
+  #         token: ${{ secrets.GITLAB_TRIGGER_TOKEN }}
+  #         project_id: 7835
+  #         ref_name: main
+  #         variables: |
+  #           PLAY="update"
+  #           CONDA_ENV="${{ steps.conda_env_name.outputs.name }}"
+
+  #     - name: Annotate commit
+  #       uses: peter-evans/commit-comment@v2
+  #       with:
+  #         body: |
+  #           GitLab pipeline for ${{ steps.conda_env_name.outputs.name }} has been submitted for this commit: ${{ steps.trigger.outputs.web_url }}

.github/workflows/update-lockfiles.yml

@@ -0,0 +1,36 @@
+name: Update lockfiles
+
+permissions:
+  contents: write
+  pull-requests: write
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: 0 5 1 * *
+
+jobs:
+  pixi-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4.2.2
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.10
+        with:
+          run-install: false
+      - name: Update lockfiles
+        run: |
+          set -o pipefail
+          pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: Update pixi lockfile
+          title: Update pixi lockfile
+          body-path: diff.md
+          branch: update-pixi
+          base: next  # change this to the default branch of your repository
+          labels: pixi
+          delete-branch: true
+          add-paths: pixi.lock

.gitignore

@@ -130,3 +130,5 @@ dmypy.json
 
 src/shiver/_version.py
 .vscode/launch.json
+# pixi environments
+.pixi

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: "DGS_SC_scripts/.*|.*\\.mat$"
 
 ci:
-    skip: [pylint]
+    skip: [pylint, pixi-lock-check]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -25,6 +25,7 @@ repos:
     rev: v2.4.1
     hooks:
     - id: codespell
+      exclude: pixi.lock
   - repo: local
     hooks:
     - id: pylint
@@ -37,3 +38,8 @@ repos:
           "-rn", # Only display messages
           "-sn", # Don't display the score
         ]
+    - id: pixi-lock-check
+      name: pixi-lock-check
+      entry: bash -c "pixi lock --check"
+      stage: pre-push
+      language: system

.readthedocs.yaml

@@ -1,19 +1,16 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-4.10"
-
-python:
-  install:
-    - method: pip
-      path: .
-
-sphinx:
-  builder: html
-  configuration: docs/source/conf.py
-  fail_on_warning: true
-
-conda:
-  environment: environment.yml
+    python: "3.11"
+  jobs:
+    create_environment:
+      - asdf plugin add pixi
+      - asdf install pixi latest
+      - asdf global pixi latest
+    install:
+      - pixi install
+    build:
+      html:
+        - pixi run sphinx-build -T -b html docs/source $READTHEDOCS_OUTPUT/html