Merge branch 'master' into feature/lims-1669/parent-child

Author: gfrn

.github/actions/install_requirements/action.yml

@@ -0,0 +1,34 @@
+name: Install requirements
+description: Install a version of python then call pip install and report what was installed
+inputs:
+  python-version:
+    description: Python version to install, default is from Dockerfile
+    default: "dev"
+  pip-install:
+    description: Parameters to pass to pip install
+    default: "$([ -f dev-requirements.txt ] && echo '-c dev-requirements.txt') -e .[dev]"
+
+runs:
+  using: composite
+  steps:
+    - name: Get version of python
+      run: |
+        PYTHON_VERSION="${{ inputs.python-version }}"
+        if [ $PYTHON_VERSION == "dev" ]; then
+          PYTHON_VERSION=$(sed -n "s/ARG PYTHON_VERSION=//p" Dockerfile)
+        fi
+        echo "PYTHON_VERSION=$PYTHON_VERSION" >> "$GITHUB_ENV"
+      shell: bash
+
+    - name: Setup python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ env.PYTHON_VERSION }}
+
+    - name: Install packages
+      run: pip install ${{ inputs.pip-install }}
+      shell: bash
+
+    - name: Report what was installed
+      run: pip freeze
+      shell: bash

.github/pull_request_template.md

@@ -0,0 +1,13 @@
+**JIRA ticket**: [TICKET-123](https://link.to.jira)
+
+**Summary**:
+
+A brief description of what this pull request aims to achieve
+
+**Changes**:
+
+- List changes made in this pull request
+
+**To test**:
+
+- List actions that should be taken to test that functionality works as expected

.github/workflows/_check.yml

@@ -0,0 +1,27 @@
+on:
+  workflow_call:
+    outputs:
+      branch-pr:
+        description: The PR number if the branch is in one
+        value: ${{ jobs.pr.outputs.branch-pr }}
+
+jobs:
+  pr:
+    runs-on: "ubuntu-latest"
+    outputs:
+      branch-pr: ${{ steps.script.outputs.result }}
+    steps:
+      - uses: actions/github-script@v7
+        id: script
+        if: github.event_name == 'push'
+        with:
+          script: |
+            const prs = await github.rest.pulls.list({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              head: context.repo.owner + ':${{ github.ref_name }}'
+            })
+            if (prs.data.length) {
+              console.log(`::notice ::Skipping CI on branch push as it is already run in PR #${prs.data[0]["number"]}`)
+              return prs.data[0]["number"]
+            }

.github/workflows/_dist.yml

@@ -0,0 +1,47 @@
+name: Create and publish a Docker image
+
+on:
+  workflow_call:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    name: Build and push image
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v2
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true

.github/workflows/_integration.yml

@@ -0,0 +1,41 @@
+name: Integration Tests
+
+on:
+  workflow_call:
+    secrets:
+      CODECOV_TOKEN:
+        required: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    services:
+      integration-db:
+        image: ghcr.io/diamondlightsource/scaup-backend-db:master
+        ports:
+          - 5432:5432
+    strategy:
+      matrix:
+        python-version: ["3.12", "3.13"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install .[dev]
+      - name: Test with pytest
+        env:
+          CONFIG_PATH: /home/runner/work/scaup-backend/scaup-backend/config.json
+        run: |
+          tox -e pytest
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          name: ${{ inputs.python-version }}/${{ inputs.runs-on }}
+          files: cov.xml
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/_tox.yml

@@ -0,0 +1,21 @@
+on:
+  workflow_call:
+    inputs:
+      tox:
+        type: string
+        description: What to run under tox
+        required: true
+
+jobs:
+  run:
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Install python packages
+        uses: ./.github/actions/install_requirements
+
+      - name: Run tox
+        run: tox -e ${{ inputs.tox }}

.github/workflows/ci.yml

@@ -0,0 +1,33 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  check:
+    uses: ./.github/workflows/_check.yml
+
+  lint:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_tox.yml
+    with:
+      tox: pre-commit
+
+  test:
+    needs: check
+    if: needs.check.outputs.branch-pr == ''
+    uses: ./.github/workflows/_integration.yml
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  release:
+    if: github.ref_type == 'tag'
+    needs: test
+    uses: ./.github/workflows/_dist.yml
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write

.github/workflows/db-docker-image.yml

@@ -0,0 +1,49 @@
+name: Create database Docker image
+
+on:
+  workflow_dispatch:
+    inputs:
+      environment:
+        type: string
+        default: DEV
+        required: true
+  push:
+    paths:
+      - "database/**"
+    branches: ["master"]
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}-db
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: database
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.gitlab-ci.yml

@@ -7,6 +7,20 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
++++++++++
+v0.9.2 (11/04/2025)
++++++++++
+
+**Changed**
+
+- Allow users to push unassigned samples
+- Improve logic for ordinal suffixes on samples
+- Display more information in tracking labels
+
+**Fixed**
+
+- More accurately pair up samples from Expeye with samples in SCAUP database
+
 +++++++++
 v0.9.1 (26/02/2025)
 +++++++++