Release 0.11.15

Merge pull request #1482 from AMICI-dev/release_0.11.15

.github/workflows/release_biosimulators.yml

@@ -0,0 +1,32 @@
+name: Release to BioSimulators
+
+on:
+ release:
+ types:
+ - published
+
+jobs:
+ updateCliAndDockerImage:
+ name: Build and release downstream command-line interface and Docker image
+ runs-on: ubuntu-latest
+ env:
+ # Owner/repository-id for the GitHub repository for the downstream command-line interface and Docker image
+ DOWNSTREAM_REPOSITORY: biosimulators/Biosimulators_AMICI
+
+ # Username/token to use the GitHub API to trigger an action on the GitHub repository for the downstream
+ # command-line interface and Docker image. Tokens can be generated at https:/settings/tokens.
+ # The token should have the scope `repo`
+ GH_ISSUE_USERNAME: ${{ secrets.BIOSIMULATORS_USERNAME }}
+ GH_ISSUE_TOKEN: ${{ secrets.BIOSIMULATORS_TOKEN }}
+ steps:
+ - name: Trigger GitHub action that will build and release the downstream command-line interface and Docker image
+ run: |
+ PACKAGE_VERSION="${GITHUB_REF/refs\/tags\/v/}"
+ WORKFLOW_FILE=ci.yml
+
+ curl \
+ -X POST \
+ -u ${GH_ISSUE_USERNAME}:${GH_ISSUE_TOKEN} \
+ -H "Accept: application/vnd.github.v3+json" \
+ https://api.github.com/repos/${DOWNSTREAM_REPOSITORY}/actions/workflows/${WORKFLOW_FILE}/dispatches \
+ -d "{\"inputs\": {\"simulatorVersion\": \"${PACKAGE_VERSION}\", \"simulatorVersionLatest\": \"true\"}}"

.github/workflows/test_performance.yml

@@ -4,7 +4,7 @@ on:
  branches:
  - develop
  - master
- - speedup_reaction_ids
+ - compile_without_optimization
 
  pull_request:
  branches:
@@ -50,12 +50,7 @@ jobs:
  # import test model
  - name: Import test model
  run: |
- cd CS_Signalling_ERBB_RAS_AKT \
- && check_time.sh \
- petab_import amici_import_petab -v \
- -n 'CS_Signalling_ERBB_RAS_AKT_petab' \
- -y 'FroehlichKes2018/PEtab/FroehlichKes2018.yaml' \
- --no-compile
+ check_time.sh petab_import python tests/performance/test.py import
 
  - name: "Upload artifact: CS_Signalling_ERBB_RAS_AKT_petab"
  uses: actions/upload-artifact@v1
@@ -65,29 +60,60 @@ jobs:
 
  # install model package
  - name: Install test model
- run: |
- check_time.sh install_model \
- python3 CS_Signalling_ERBB_RAS_AKT/CS_Signalling_ERBB_RAS_AKT_petab/setup.py install --user
+ run: >
+ check_time.sh install_model tests/performance/test.py compile;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh install_model_${opt} tests/performance/test.py compile_${opt};
+ done
 
  # run simulations
  - name: forward_simulation
- run: |
- check_time.sh forward_simulation tests/performance/test.py forward_simulation
+ run: >
+ check_time.sh forward_simulation tests/performance/test.py forward_simulation;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh forward_simulation tests/performance/test.py forward_simulation_${opt};
+ done
  - name: forward_sensitivities
- run: |
- check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities
+ run: >
+ check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh forward_sensitivities tests/performance/test.py forward_sensitivities_${opt};
+ done
  - name: adjoint_sensitivities
- run: |
- check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities
+ run: >
+ check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh adjoint_sensitivities tests/performance/test.py adjoint_sensitivities_${opt};
+ done
  - name: forward_simulation_non_optimal_parameters
  run: |
- check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters
+ check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh forward_simulation_non_optimal_parameters tests/performance/test.py forward_simulation_non_optimal_parameters_${opt};
+ done
  - name: adjoint_sensitivities_non_optimal_parameters
  run: |
- check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters
+ check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh adjoint_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_sensitivities_non_optimal_parameters_${opt};
+ done
  - name: forward_steadystate_sensitivities_non_optimal_parameters
  run: |
- check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters
+ check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh forward_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py forward_steadystate_sensitivities_non_optimal_parameters_${opt};
+ done
  - name: adjoint_steadystate_sensitivities_non_optimal_parameters
  run: |
- check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters
+ check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters;
+ for opt in O0 O1 O2;
+ do
+ check_time.sh adjoint_steadystate_sensitivities_non_optimal_parameters tests/performance/test.py adjoint_steadystate_sensitivities_non_optimal_parameters_${opt};
+ done

.github/workflows/test_sbml_semantic_test_suite.yml

@@ -4,6 +4,7 @@ on:
  branches:
  - develop
  - master
+ - release**
  pull_request:
  paths:
  - .github/workflows/test_sbml_semantic_test_suite.yml

.gitignore

@@ -193,3 +193,4 @@ coverage_SBMLSuite.xml
 Benchmark-Models-PEtab/
 
 
+CS_Signalling_ERBB_RAS_AKT/