Merge pull request #3568 from Open-Systems-Pharmacology/develop

Version 12.3

Author: Yuri05

.github/workflows/build-and-test-pr_12.2.yml

@@ -0,0 +1,21 @@
+name: Build and Test 12.3
+
+on:
+  pull_request:
+    branches:
+    - develop
+  push:
+    branches:
+    - develop
+
+permissions:
+  contents: read
+  packages: read
+  
+jobs:
+
+  build:
+    uses: Open-Systems-Pharmacology/Workflows/.github/workflows/test-csharp.yml@main
+    secrets: inherit
+    with:
+      temp-version: "12.3.9999"

.github/workflows/build-and-test.yml

@@ -1,15 +1,12 @@
-name: Build Nightly 12.2
-run-name: Version 12.2.${{ github.run_number }}
+name: Build Nightly 12.3
+run-name: Version 12.3.${{ github.run_number }}
 
 on:
   workflow_dispatch:
   schedule:
     - cron: '0 2 * * *'
 
 env:
-  MAJOR: 12
-  MINOR: 2
-  RUN: ${{ github.run_number }}
   TARGET_FRAMEWORK: net8
 
 permissions:
@@ -23,7 +20,7 @@ jobs:
       LATEST_COMMIT_TIMESPAN: ${{ steps.get-latest-commit-timespan.outputs.LATEST_COMMIT_TIMESPAN}}
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
@@ -42,11 +39,14 @@ jobs:
 
   build-nightly:
     needs: get-latest-commit-timespan
-    if: needs.get-latest-commit-timespan.outputs.LATEST_COMMIT_TIMESPAN < 86400
+    # the build-nightly job should be run in 2 cases:
+    # - either the workflow was triggered manually (on 'workflow_dispatch')
+    # - or the workflow was triggered on schedule and last repository commit is not older than 24h (=86400 sec)
+    if: needs.get-latest-commit-timespan.outputs.LATEST_COMMIT_TIMESPAN < 86400 || github.event_name == 'workflow_dispatch'
     runs-on: windows-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: 'true'
 
@@ -57,15 +57,15 @@ jobs:
 
       - name: define env variables
         run: |
-          echo "APP_VERSION=${{ env.MAJOR }}.${{ env.MINOR }}.${{ env.RUN }}" | Out-File -FilePath $env:GITHUB_ENV -Append
+          echo "APP_VERSION=12.3.${{ github.run_number }}" | Out-File -FilePath $env:GITHUB_ENV -Append
 
       - name: Build
         run: |
           rake "update_go_license[ApplicationStartup.cs, ${{ secrets.GO_DIAGRAM_KEY }}]"
-          dotnet build PKSim.sln /p:Version=${{env.APP_VERSION}}
+          dotnet build /p:Version=${{env.APP_VERSION}}
 
       - name : Test
-        run: dotnet test .\tests\**\bin\Debug\net472\PKSim*Tests.dll -v normal --no-build  --logger:"html;LogFileName=../testLog_Windows.html"
+        run: dotnet test -v normal --no-build  --logger:"html;LogFileName=../testLog_Windows.html"
 
       - name: Sign PKSim.exe with CodeSignTool
         uses: Open-Systems-Pharmacology/Workflows/.github/actions/codesigner-SSL@main
@@ -120,32 +120,34 @@ jobs:
           file_path: ./setup/deploy/PK-Sim.${{ env.APP_VERSION }}.msi
 
       - name: Push test log as artifact
-        uses: actions/upload-artifact@v4
+        if: always()
+        uses: actions/upload-artifact@v7
         with:
           name: testLog_Windows
           path: ./testLog*.html
 
       - name: Push nightly installer as artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: PKSim Installer ${{env.APP_VERSION}}
           path: setup\deploy\*.msi
 
       - name: Push nightly portable as artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: PKSim Portable ${{env.APP_VERSION}}
           path: setup\PK-Sim ${{env.APP_VERSION}}
 
       - name: Push R dependencies as artifact
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@v7
         with:
           name: PKSim R Dependencies
           path: src\PKSimRDependencyResolution\bin\Debug\${{env.TARGET_FRAMEWORK}}\pk-sim-r-dependencies.zip
 
   cleanup-job:
-    needs: get-latest-commit-timespan
-    if: needs.get-latest-commit-timespan.outputs.LATEST_COMMIT_TIMESPAN >= 86400
+    needs: build-nightly
+    # run only if the build-nightly job was skipped
+    if: always() && needs.build-nightly.result == 'skipped'
     runs-on: ubuntu-latest
     permissions:
       actions: write

.github/workflows/build-and-test_12.2.yml

@@ -0,0 +1,20 @@
+name: Build Nightly 13.0
+run-name: Version 13.0.${{ github.run_number }}
+
+on:
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: read
+
+jobs:
+  check-branch:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Validate source branch
+      run: |
+        if [ "${{ github.ref_name }}" != "V13" ]; then
+          echo "::error::Please call the workflow from the V13 branch"
+          exit 1
+        fi

.github/workflows/build-nightly_12.2.yml .github/workflows/build-nightly_12.3.yml.github/workflows/build-nightly_12.2.yml renamed to .github/workflows/build-nightly_12.3.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: windows-latest
     steps:
       - name: Checkout code
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           submodules: 'true'
 
@@ -24,7 +24,7 @@ jobs:
           nuget restore
 
       - name: Build
-        run: dotnet build PKSim.sln /p:Version=12.2.9999
+        run: dotnet build PKSim.sln /p:Version=12.3.9999
 
 
       - name: Cover and report

.github/workflows/build-nightly_v13.yml

@@ -15,7 +15,7 @@ name: Badge for Nightly Build
 on:
   workflow_run:
     workflows:
-      - "Build Nightly 12.2"
+      - "Build Nightly 12.3"
     types:
       - completed
 
@@ -26,4 +26,4 @@ jobs:
   badge:
     uses: Open-Systems-Pharmacology/Workflows/.github/workflows/nightly-badge.yml@main
     with:
-      nightly-build-workflow: "build-nightly_12.2.yml"
+      nightly-build-workflow: "build-nightly_12.3.yml"

.github/workflows/coverage_12.2.yml .github/workflows/coverage.yml.github/workflows/coverage_12.2.yml renamed to .github/workflows/coverage.yml

@@ -1,17 +1,17 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio Version 17
-VisualStudioVersion = 17.0.31912.275
+# Visual Studio Version 18
+VisualStudioVersion = 18.1.11312.151
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{9B4D05BE-A0E7-41D6-8FCF-1C6005FBE801}"
 	ProjectSection(SolutionItems) = preProject
 		.gitattributes = .gitattributes
 		.gitignore = .gitignore
-		.github\workflows\build-and-test-pr_12.2.yml = .github\workflows\build-and-test-pr_12.2.yml
-		.github\workflows\build-and-test_12.2.yml = .github\workflows\build-and-test_12.2.yml
-		.github\workflows\build-nightly_12.2.yml = .github\workflows\build-nightly_12.2.yml
+		.github\workflows\build-nightly_12.3.yml = .github\workflows\build-nightly_12.3.yml
+		.github\workflows\build-and-test.yml = .github\workflows\build-and-test.yml
 		db_pre_commit.bat = db_pre_commit.bat
-		.github\workflows\coverage_12.2.yml = .github\workflows\coverage_12.2.yml
+		.github\workflows\coverage.yml = .github\workflows\coverage.yml
+		.github\workflows\nightly-badge.yml = .github\workflows\nightly-badge.yml
 		postclean.bat = postclean.bat
 		rakefile.rb = rakefile.rb
 		README.md = README.md

.github/workflows/nightly-badge.yml

@@ -6,7 +6,7 @@
 PK-Sim® uses building blocks that are grouped into [**Individuals**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-creating-individuals), [**Populations**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-creating-populations), [**Expression Profiles**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-expression-profile), [**Compounds**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-compounds-definition-and-work-flow), [**Formulations**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-formulations), [**Administration Protocols**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-administration-protocols), [**Events**](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-events), **Observers** and [**Observed Data**](https://docs.open-systems-pharmacology.org/shared-tools-and-example-workflows/import-edit-observed-data). Building blocks from these groups are combined to produce a [model](https://docs.open-systems-pharmacology.org/working-with-pk-sim/pk-sim-documentation/pk-sim-simulations). The advantage of building blocks is that they can be reused. For example, after having established a model for a drug after single dose intravenous administration to an animal species, just substitute the individual by a suitably parameterized virtual human population and obtain a first in man simulation model. Further substitute the formulation, to obtain a controlled-release per oral simulation model, substitute the protocol to obtain a multiple dose simulation model, or substitute the compound to obtain a simulation model for another drug. 
 
 ## Code Status
-[![Build status](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/PK-Sim/nightly-badge.yml?logo=GitHub&label=Build%20status)](https://github.com/Open-Systems-Pharmacology/PK-Sim/actions/workflows/build-nightly_12.2.yml)
+[![Build status](https://img.shields.io/github/actions/workflow/status/Open-Systems-Pharmacology/PK-Sim/nightly-badge.yml?logo=GitHub&label=Build%20status)](https://github.com/Open-Systems-Pharmacology/PK-Sim/actions/workflows/build-nightly_12.3.yml)
 [![Coverage status](https://codecov.io/gh/Open-Systems-Pharmacology/PK-Sim/branch/develop/graph/badge.svg)](https://codecov.io/gh/Open-Systems-Pharmacology/PK-Sim)
 
 ## Code of conduct