Merge commit '07b72a402d2e74f2a5a99ba2621f08364fd517ba' into ammr4-beta

.github/workflows/ammr-doc.yaml

@@ -28,17 +28,17 @@ jobs:
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
 
       - name: Link check
+        shell: pixi run -e docs bash {0}
         run: |
           cd Docs
-          pixi run -e docs \
-            sphinx-build -M linkcheck . _build -W --keep-going -a -q 
+          sphinx-build -M linkcheck . _build -W --keep-going -a -q 
                             
       - name: Build Documentation
+        shell: pixi run -e docs bash {0}
         run: |
           cd Docs
-          pixi run -e docs clean
-          pixi run -e docs \
-            sphinx-build -M html . _build -W --keep-going -a -t draft
+          rm -rf _build
+          sphinx-build -M html . _build -W --keep-going -a -t draft
 
       - uses: actions/upload-artifact@v4
         with:
@@ -61,31 +61,16 @@ jobs:
           git checkout $(git describe --tags `git rev-list --tags=ammr* --max-count=1`);
       
       - uses: prefix-dev/setup-pixi@v0.5.1
-        continue-on-error: true
-        id: pixisetup
         with:
             environments: docs
             cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
 
       - name: Build Documentation
-        if: steps.pixisetup.outcome == 'success'
+        shell: pixi run -e docs bash {0}
         run: |
           cd Docs
-          pixi run -e docs \
-           sphinx-build -M html . _build -a
-    
-      # Fall back to mamba when buildig old versions
-      - name: Install mamba
-        if: steps.pixisetup.outcome == 'failure'
-        uses: mamba-org/setup-micromamba@v1
-        with:
-          environment-file: Docs/environment.yaml
-
-      - name: build with mamba
-        if: steps.pixisetup.outcome == 'failure'
-        shell: bash -leo pipefail {0} {0}
-        run: sphinx-build -M html Docs Docs/_build -a
-
+          sphinx-build -M html . _build -a
+
       - uses: actions/upload-artifact@v4
         with:
           name: tagged-version

.github/workflows/nightly-tests.yml

@@ -3,7 +3,12 @@ name: Nightly Full AMMR tests
 on:
   schedule:
     - cron: 0 3 * * *
-  workflow_dispatch: {}
+  workflow_dispatch:
+    inputs:
+      force-update-durations:
+          type: boolean
+          description: 'Force creation of new .test-duration files and create a PR with them. Default is false.'
+          default: false
 
 
 concurrency: 
@@ -19,7 +24,6 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        ams_version: ["8.0_Beta"]
         test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
 
     env:
@@ -36,17 +40,18 @@ jobs:
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
 
       - name: Run full AMMR tests
-        env:
-          RLM_LICENSE_PASSWORD: ${{ secrets.LICENSE_PASSWORD }}
-          RLM_LICENSE: ${{ secrets.LICENSE_SERVER }}
         run: |
             cd Tests
-            pixi run -e test `
-              pytest -n auto --dist worksteal `
+            pytest -n auto --dist worksteal `
               --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration `
               --durations=20 `
               --store-durations --clean-durations `
               --runslow
+        shell: pwsh -command "pixi run -e test pwsh '{0}'"
+
+        env:
+          RLM_LICENSE_PASSWORD: ${{ secrets.LICENSE_PASSWORD }}
+          RLM_LICENSE: ${{ secrets.LICENSE_SERVER }}
 
       - name: Upload partial durations
         uses: actions/upload-artifact@v4
@@ -60,35 +65,38 @@ jobs:
   test-linux:
     if: github.repository == 'anybody/ammr'
     runs-on: ubuntu-latest
-    container: ghcr.io/anybody/anybodycon-github-actions:${{ matrix.ams_version }}
+    container: ghcr.io/anybody/anybodycon-github-actions:8.0
     env:
-      ANYBODY_SUPPRESS_DEPRECATION_MESSAGES: ${{ fromJSON('{"7.4":"Off","7.5_Beta":"On"}')[matrix.ams_version] }}
+      ANYBODY_SUPPRESS_DEPRECATION_MESSAGES: "Off"
 
     strategy:
       fail-fast: false
       matrix:
-        ams_version: ["7.4", "8.0_Beta"]
-        test_group: [1, 2, 3, 4, 5]
+        test_group: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
 
     steps:
       - uses: actions/checkout@v4
-        with:
-          ref: ${{ fromJSON('{"7.4":"master-ammr-2.4.x","8.0_Beta":"master"}')[matrix.ams_version] }}
 
       - name: Set debug env vars
         run: echo ${{ github.event.inputs.debug_config }} >> $GITHUB_ENV
+
+      - uses: prefix-dev/setup-pixi@v0.5.1
+        with:
+          environments: test
+          cache-write: ${{ github.event_name == 'push' && github.ref_name == 'master' }}
 
       - name: Run tests
+        run: |
+          cd Tests
+          pytest -n auto \
+            --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration \
+            --only-load \
+            --runslow
+        shell: pixi run -e test bash {0}
         env:
           RLM_LICENSE_PASSWORD: ${{ secrets.LICENSE_PASSWORD }}
           RLM_LICENSE: ${{ secrets.LICENSE_SERVER }}
-        run: |
-            cd Tests
-            pytest -n auto \
-              --splits 5 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration \
-              --only-load \
-              --runslow
-      
+
 
   combine-and-upload-timings:
     runs-on: ubuntu-latest
@@ -108,7 +116,7 @@ jobs:
               data.update(json.loads(file.read_text()))
           data = {k: v for k, v in sorted(data.items(), key=lambda x: x[1], reverse=True)}
           test_durations = pathlib.Path('Tests/.test_durations')
-          if set(data) != set(json.loads(test_durations.read_text())):
+          if set(data) != set(json.loads(test_durations.read_text())) or "${{ github.event.inputs.force-update-durations }}" == "true":
               test_durations.write_text(json.dumps(data, indent=2))
         shell: python
 

.github/workflows/test-forks.yml

@@ -39,13 +39,14 @@ jobs:
           & $HOME/.pixi/bin/pixi.exe install
             
       - name: Run AMMR tests
+        shell: pixi run -e test pwsh -Command {0}
+
         run: |
           cd Tests
-          pixi run -e test `
-            pytest -n 5 --dist worksteal `
-             --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration `
-             --durations=10 `
-             --runslow
+          pytest -n 5 --dist worksteal `
+            --splits 10 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration `
+            --durations=10 `
+            --runslow
         env:
           RLM_LICENSE: ${{ secrets.LICENSE_SERVER }}
           RLM_LICENSE_PASSWORD: ${{ secrets.LICENSE_PASSWORD }}

.github/workflows/test-self-hosted.yml

@@ -55,10 +55,11 @@ jobs:
           connection-string:  ${{ secrets.AZURE_CONN_STR }}
 
       - name: Run AMMR tests
+        shell: pixi run -e test pwsh -Command {0}
+
         run: |
           cd Tests
-          pixi run -e test `
-            pytest -n 5 --dist worksteal `
+          pytest -n 5 --dist worksteal `
             --splits 5 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration `
             --durations=10 `
             --anybodycon="$Env:ANYBODYCON" `

.github/workflows/test.yml

@@ -58,12 +58,13 @@ jobs:
       - name: Run AMMR tests
         run: |
           cd Tests
-          pixi run -e test `
-             pytest -n auto --dist worksteal `
-             --splits 20 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration `
-             --durations=10 `
-             --runslow
-             ${{ github.event.inputs.custom-pytest-arg  || '' }}
+          pytest -n auto --dist worksteal `
+          --splits 20 --group ${{ matrix.test_group }} --splitting-algorithm=least_duration `
+          --durations=10 `
+          --runslow
+          ${{ github.event.inputs.custom-pytest-arg  || '' }}
+        shell: pixi run -e test pwsh -Command {0}
+
         env:
           RLM_LICENSE: ${{ secrets.LICENSE_SERVER }}
           RLM_LICENSE_PASSWORD: ${{ secrets.LICENSE_PASSWORD }}

Docs/README.md

@@ -3,14 +3,13 @@
 # AnyBody Managed Model Repository 4 ✨ Beta
 > The beta version of the AMMR 4 with a full thoracic model and new abdominal pressure model
 
+> [!TIP]
+> For the the latest AMMR 4 release, with full thoracic model please see [AMMR4-beta](https://github.com/anybody/ammr4-beta)
+
 The AnyBody Model Repository (AMMR), is an open library of musculoskeletal
 models and examples for the [AnyBody Modeling
 System](https://www.anybodytech.com/software/ams/).
 
-> [!IMPORTANT]
-An AnyBody license with active maintenance is required to use the models from GitHub. 
-Please see the [beta program](https://forum.anyscript.org/t/become-a-beta-tester/5056/6), or request a [trial license ](https://www.anybodytech.com/contact/)
-
 <p align="center">
   <img src = "https://github.com/AnyBody/ammr/blob/master/Docs/_static/ammr_bodyparts.png" width=350>
 </p>
@@ -30,6 +29,11 @@ institutions. The models are maintained by [AnyBody
 Technology](https://www.anybodytech.com) who ensure that various body part models
 can be used together as a full body, scalable musculoskeletal model.
 
+> [!IMPORTANT]
+An AnyBody license with active maintenance is required to use the models from GitHub. 
+Please see the [beta program](https://forum.anyscript.org/t/become-a-beta-tester/5056/6), or request a [trial license ](https://www.anybodytech.com/contact/)
+
+
 
 ## Getting Started