Merge remote-tracking branch 'refs/remotes/origin/master' into cylc_profiler

Author: ChrisPaulBennett

.github/workflows/1_create_release_pr.yml

@@ -34,7 +34,7 @@ jobs:
         uses: cylc/release-actions/stage-1/sanitize-inputs@v1
 
       - name: Checkout repo
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           ref: ${{ env.BASE_REF }}
           fetch-depth: 0  # need to fetch all commits to check contributors
@@ -43,7 +43,7 @@ jobs:
         uses: cylc/release-actions/check-shortlog@v1
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: '3.x'
 

.github/workflows/2_auto_publish_release.yml

@@ -33,12 +33,12 @@ jobs:
     steps:
 
     - name: Checkout repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         ref: ${{ env.MERGE_SHA }}
 
     - name: Setup Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
 

.github/workflows/bash.yml

@@ -51,20 +51,21 @@ jobs:
           - '4.2'
           # if you use a value like 5.0, YAML will round it to 5, which will cause an error later on
           - '5.0'
+    env:
+      IMAGE: 'ghcr.io/cylc/cylc-bash-testing-2:master'
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Run Docker container
         run: |
-          docker pull ghcr.io/cylc/cylc-bash-testing:master
-          docker run --name bash -v $(pwd -P):/root/cylc-flow --rm -t -d -m 1G --memory-swap 1G ghcr.io/cylc/cylc-bash-testing:master /bin/bash
+          docker pull "$IMAGE"
+          docker run --name bash -v $(pwd -P):/root/cylc-flow --rm -t -d -m 1G --memory-swap 1G "$IMAGE" /bin/bash
           docker ps -a
 
       - name: Install Cylc dependencies in the container
         run: |
-          docker exec bash python3.7 -m pip install six==1.12
-          docker exec -w /root/cylc-flow bash python3.7 -m pip install .[all]
+          docker exec -w /root/cylc-flow bash python3.12 -m pip install .[all] --break-system-packages
 
       - name: Set the container bash version
         run: docker exec bash update-alternatives --set bash /bash/bash-${{ matrix.bash-version }}
@@ -94,7 +95,7 @@ jobs:
 
       - name: Upload artifact
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: 'cylc-run (bash-${{ matrix.bash-version }})'
           path: cylc-run

.github/workflows/build.yml

@@ -33,13 +33,10 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-latest', 'macos-latest']
-        python: ['3.7', '3.8', '3.9', '3.10', '3']
-        exclude:
-          - os: 'macos-latest'
-            python: '3.7'
+        python: ['3.12', '3']
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup Python
         uses: mamba-org/setup-micromamba@v2

.github/workflows/shortlog.yml

@@ -16,7 +16,7 @@ jobs:
     timeout-minutes: 10
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 0  # need to fetch all commits to check contributors
           ref: ${{ github.event.pull_request.head.sha }}

.github/workflows/test_conda-build.yml

@@ -5,6 +5,8 @@ on:
     paths:
       - 'conda-environment.yml'
       - '.github/workflows/test_conda-build.yml'
+      - 'pyproject.toml'
+      - 'setup.cfg'
   schedule:
     - cron: '17 22 * * 6'  # Every Saturday at 22:17
   workflow_dispatch:
@@ -28,16 +30,19 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8', '3']
+        python-version: ['3.12', '3']
     env:
       ENV_FILE: conda-environment.yml
+      # prevent pip from meddling with the conda installed dependencies (during the conda build step)
+      PIP_NO_DEPS: True
     steps:
       - name: checkout cylc-flow
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: modify conda env file
         run: |
           # write environment file
+          echo "  - python = ${{ matrix.python-version }}" >> "$ENV_FILE"
           echo "  - pip"  >> "$ENV_FILE"  # list pip as a dependency
           echo "  - pip:" >> "$ENV_FILE"  # add a pip section
           echo "    - ."  >> "$ENV_FILE"  # install cylc-flow (pip install .)
@@ -46,14 +51,18 @@ jobs:
       - name: build conda env
         uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.python-version }}
           environment-file: ${{ env.ENV_FILE }}
 
       - name: check cylc installation
         shell: bash -el {0}
         run: |
+          # make sure Cylc is functioning
           conda run -n test cylc version --long
 
+          # make sure pip is happy with the packages installed
+          # (checks pip deps are compatible with conda deps)
+          conda run -n test pip check
+
       - name: check for activate scripts
         shell : bash -el {0}
         run: |

.github/workflows/test_fast.yml

@@ -27,20 +27,20 @@ jobs:
       fail-fast: false # don't stop on first failure
       matrix:
         os: ['ubuntu-latest']
-        python-version: ['3.7', '3.8', '3.10', '3.11', '3.12', '3']
+        python-version: ['3.12', '3']
         include:
           - os: 'macos-latest'
-            python-version: '3.8'  # oldest version with arm64 builds
+            python-version: '3.12' # oldest version we support
           # non-utc timezone test
           - os: 'ubuntu-latest'
-            python-version: '3.9'  # not the oldest, not the most recent version
+            python-version: '3'
             time-zone: 'XXX-09:35'
     env:
       TZ: ${{ matrix.time-zone }}
       PYTEST_ADDOPTS: --cov --cov-append -n 5 --color=yes
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Install System Dependencies
         uses: mamba-org/setup-micromamba@v2
@@ -54,6 +54,7 @@ jobs:
             bash
             subversion
             sqlite
+            graphviz
 
       - name: Install Python Dependencies
         run: |
@@ -83,7 +84,7 @@ jobs:
 
       - name: Upload failed tests artifact
         if: failure()
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: cylc-run (${{ matrix.os }} py-${{ matrix.python-version }})
           path: ~/cylc-run/
@@ -95,7 +96,7 @@ jobs:
           coverage report
 
       - name: Upload coverage artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: coverage_${{ matrix.os }}_py-${{ matrix.python-version }}
           path: coverage.xml
@@ -111,7 +112,7 @@ jobs:
       FORCE_COLOR: 2
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Install System Dependencies
         uses: mamba-org/setup-micromamba@v2
@@ -154,10 +155,10 @@ jobs:
     timeout-minutes: 2
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Download coverage artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
 
       - name: Codecov upload
         uses: codecov/codecov-action@v5

.github/workflows/test_functional.yml

@@ -49,7 +49,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ['ubuntu-22.04']
-        python-version: ['3.7']
+        python-version: ['3.12'] # oldest version we support
         test-base: ['tests/f']
         chunk: ['1/4', '2/4', '3/4', '4/4']
         platform: ['_local_background* _local_at*']
@@ -65,27 +65,27 @@ jobs:
           # tests/k
           - name: 'flaky'
             os: 'ubuntu-latest'
-            python-version: '3.7'
+            python-version: '3.12'
             test-base: 'tests/k'
             chunk: '1/1'
             platform: '_local_background* _local_at*'
           # remote platforms
           - name: '_remote_background_indep_poll'
             os: 'ubuntu-latest'
-            python-version: '3.7'
+            python-version: '3.12'
             test-base: 'tests/f tests/k'
             chunk: '1/1'
             platform: '_remote_background_indep_poll _remote_at_indep_poll'
           - name: '_remote_background_indep_tcp'
             os: 'ubuntu-latest'
             test-base: 'tests/f tests/k'
-            python-version: '3.7'
+            python-version: '3.12'
             chunk: '1/1'
             platform: '_remote_background_indep_tcp _remote_at_indep_tcp'
           # macos
           - name: 'macos 1/5'
             os: 'macos-latest'
-            python-version: '3.8'  # oldest available
+            python-version: '3.12'  # oldest version we support
             test-base: 'tests/f'
             chunk: '1/5'
             platform: '_local_background*'
@@ -106,7 +106,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Configure Python
         uses: mamba-org/setup-micromamba@v2
@@ -275,7 +275,7 @@ jobs:
 
       - name: Upload failed tests artifact
         if: failure() && steps.test.outcome == 'failure'
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: cylc-run (${{ steps.uploadname.outputs.uploadname }})
           path: ~/cylc-run/
@@ -314,7 +314,7 @@ jobs:
           coverage report
 
       - name: Upload coverage artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v5
         with:
           name: coverage_${{ steps.uploadname.outputs.uploadname }}
           path: coverage.xml
@@ -326,10 +326,10 @@ jobs:
     timeout-minutes: 2
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Download coverage artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
 
       - name: Codecov upload
         uses: codecov/codecov-action@v5

.github/workflows/test_tutorial_workflow.yml

@@ -34,17 +34,17 @@ jobs:
           - os: 'ubuntu-latest'
             python-version: '3'
           - os: 'ubuntu-22.04'
-            python-version: '3.7'
+            python-version: '3.12'
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10
     steps:
       - name: configure python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Install docs/tutorial dependencies
         uses: cylc/cylc-doc/.github/actions/install-dependencies@master

.github/workflows/update_copyright.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
 
     - name: Checkout repo
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
 
     - name: Configure git
       uses: cylc/release-actions/configure-git@v1