Merge branch 'main' into match-atlas-dcgs

Author: stephen-riggs

.github/workflows/ci.yml

@@ -17,7 +17,7 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
     services:
       mariadb:
-        image: mariadb:11.7.2 # released 2024-05-06
+        image: mariadb:12.1.2 # released 2024-05-06
         # Pulls image from DockerHub
         # Docker images: https://hub.docker.com/_/mariadb
         # Previous version(s):
@@ -40,10 +40,10 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Use Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -69,7 +69,7 @@ jobs:
           docker container list -a
 
       - name: Get ISPyB database
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
         with:
           name: database
           path: database/

.github/workflows/codeql.yml

@@ -24,19 +24,19 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@v4
         with:
           languages: ${{ matrix.language }}
           queries: +security-and-quality
 
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v3
+        uses: github/codeql-action/autobuild@v4
         if: ${{ matrix.language == 'javascript' || matrix.language == 'python' }}
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
+        uses: github/codeql-action/analyze@v4
         with:
           category: "/language:${{ matrix.language }}"

.github/workflows/publish-version.yml

@@ -16,9 +16,9 @@ jobs:
       doTag: ${{ steps.checkTag.outputs.doTag }}
       newVersion: ${{ steps.checkTag.outputs.newVersion }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Use Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Check current tag
@@ -46,7 +46,7 @@ jobs:
       - get-current-version
     if: ${{ needs.get-current-version.outputs.doTag == 'true' }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Push the new tag
         run: |
           git config --global user.name "DiamondLightSource-build-server"
@@ -64,9 +64,9 @@ jobs:
       - get-current-version
     if: ${{ needs.get-current-version.outputs.doTag == 'true' }}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install pypa/build
@@ -78,7 +78,7 @@ jobs:
       - name: Build python package
         run: python3 -m build
       - name: Store built package artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: package-distributions
           path: dist/
@@ -100,7 +100,7 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
         with:
           name: package-distributions
           path: dist/
@@ -123,12 +123,12 @@ jobs:
 
     steps:
       - name: Download all the dists
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
         with:
           name: package-distributions
           path: dist/
       - name: Sign the dists with Sigstore
-        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        uses: sigstore/gh-action-sigstore-python@v3.2.0
         with:
           inputs: >-
             ./dist/*.tar.gz

.github/workflows/test.yml

@@ -18,9 +18,9 @@ jobs:
     name: Static Analysis
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Syntax validation
@@ -35,9 +35,9 @@ jobs:
     name: Build package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install pypa/build
@@ -53,13 +53,13 @@ jobs:
     name: Build package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Download ISPyB DB schema v${{ env.ISPYB_DATABASE_SCHEMA }} for tests
         run: |
           mkdir database
           wget -t 3 --waitretry=20 https://github.com/DiamondLightSource/ispyb-database/releases/download/v${{ env.ISPYB_DATABASE_SCHEMA }}/ispyb-database-${{ env.ISPYB_DATABASE_SCHEMA }}.tar.gz -O database/ispyb-database.tar.gz
       - name: Store database artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: database
           path: database/

.github/workflows/version-bump.yml

@@ -34,9 +34,9 @@ jobs:
       contents: write
       pull-requests: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Set up Python 3.10
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Install package

pyproject.toml

@@ -96,7 +96,6 @@ GitHub = "https://github.com/DiamondLightSource/python-murfey"
 "murfey.sessions" = "murfey.cli.db_sessions:run"
 "murfey.simulate" = "murfey.cli.dummy:run"
 "murfey.spa_inject" = "murfey.cli.inject_spa_processing:run"
-"murfey.spa_ispyb_entries" = "murfey.cli.spa_ispyb_messages:run"
 "murfey.transfer" = "murfey.cli.transfer:run"
 [project.entry-points."murfey.config.extraction"]
 "murfey_machine" = "murfey.util.config:get_extended_machine_config"