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/[email protected]
- 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/[email protected]
+ 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