Release 0.5.0 / Merge pull request #413 from ICB-DCM/develop

## What's Changed

### Features

* Updated AMICI to v0.29.0 which comes with many new features and bug fixes (by @dweindl in #412)
* Added support for support for forward sensitivities (by @dweindl in #393)
* Use amici default options in generated HDF5 input files (by @dweindl in #392, #406)
* Set python package version via setuptools_scm (by @dweindl in #395)
* PEtab import: option to ignore initialization prior (by @dweindl in #402)
* Added scaffold for objective function / gradient evaluation with JSON I/O (by @dweindl in #400)

### Fixes

* Fixed data race in aggregateLikelihood (by @dweindl in #411)
* PEtab pipeline: 
  * Fixed potentially incorrect initial state from condition table (by @dweindl in #408)
  * Fail on problems using priors (they aren't supported and never have been) (by @dweindl in #384)
  * Only compute sensitivities with respect to optimized parameters (by @dweindl in #394)
  * HDF5 generation: Don't write obsolete sens_ind (by @dweindl in #407)
* Reduced clang warnings (by @dweindl in #397)


**Full Changelog**: v0.4.10...v0.5.0

.clang-tidy

@@ -2,7 +2,6 @@
 Checks:          '*,-cppcoreguidelines-pro-type-vararg,-google-readability-braces-around-statements,-google-readability-todo,-llvm-include-order,-fuchsia-default-arguments,-hicpp-vararg,-google-default-arguments'
 WarningsAsErrors: ''
 HeaderFilterRegex: ''
-AnalyzeTemporaryDtors: false
 User:            dweindl
 CheckOptions:    
   - key:             google-readability-braces-around-statements.ShortStatementLines

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+

.gitattributes

@@ -0,0 +1,3 @@
+.git_archival.txt  export-subst
+python/.git_archival.txt  export-subst
+

.github/workflows/benchmark_models.yml

@@ -33,17 +33,15 @@ jobs:
             -DCMAKE_BUILD_TYPE=Debug \
             -DENABLE_PYTHON=ON \
             -DBUILD_TESTS=OFF \
+            -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install parPE Python deps
-      run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt
-
     - name: Configure parpe
       run: |
         cmake \
           -S"${PARPE_BASE}" \
           -B"${PARPE_BUILD}" \
+          -DPARPE_ENABLE_CERES=OFF \
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOVR_REPORT=TRUE \
@@ -66,11 +64,19 @@ jobs:
         BM_REPO_URL: https://github.com/Benchmarking-Initiative/Benchmark-Models-PEtab.git
       run: |
         cd $PARPE_BASE/benchmark_collection \
-          && git clone --depth 1 $BM_REPO_URL
+          && git clone --depth 1 $BM_REPO_URL \
+          && echo "BENCHMARK_COLLECTION=$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" >> $GITHUB_ENV \
+          && . $PARPE_BASE/build/venv/bin/activate \
+          && python -m pip install -e Benchmark-Models-PEtab/src/python
 
     - name: Benchmark models --- tests
+      env:
+        # parallel compilation
+        MAKE_OPTS: "-j"
       run: |
         cd $PARPE_BASE/benchmark_collection \
-          && AMICI_PARALLEL_COMPILE="" \
-             BENCHMARK_COLLECTION="$(pwd)/Benchmark-Models-PEtab/Benchmark-Models/" \
-             $PARPE_BASE/misc/run_in_venv.sh $PARPE_BASE/build/venv ./all.sh
+          && . $PARPE_BASE/build/venv/bin/activate \
+          && python -m pip uninstall -y petab \
+          && python -m pip install https://github.com/PEtab-dev/libpetab-python/archive/develop.zip \
+          && python priors_to_measurements.py \
+          && AMICI_PARALLEL_COMPILE="" ./all.sh

.github/workflows/deploy_dockerhub.yml

@@ -2,9 +2,26 @@
 name: Deploy to dockerhub
 on: [push, workflow_dispatch]
 jobs:
+  check-secret:
+    runs-on: ubuntu-latest
+    outputs:
+      secrets-defined: ${{ steps.secret-check.outputs.defined }}
+    steps:
+      - name: Check for Secret availability
+        id: secret-check
+        shell: bash
+        run: |
+          if [ "${{ secrets.DOCKER_USERNAME }}" != '' ]; then
+            echo "defined=true" >> $GITHUB_OUTPUT;
+          else
+            echo "defined=false" >> $GITHUB_OUTPUT;
+          fi
+
   build:
     name: Deploy to dockerhub
     runs-on: ubuntu-latest
+    needs: [check-secret]
+    if: needs.check-secret.outputs.secrets-defined == 'true'
     steps:
     - uses: actions/checkout@master
     - run: git archive -v -o container/charliecloud/parpe_base/parpe.tar.gz --format=tar.gz HEAD

.github/workflows/parpe_tests.yml

@@ -18,7 +18,6 @@ jobs:
       # If we are running in docker, we generally don't have SYS_PTRACE
       #  permissions  and thus, cannot use vader. Also disable Infiniband.
       PARPE_TESTS_MPIEXEC: mpiexec -n 5 --oversubscribe --allow-run-as-root --mca btl_vader_single_copy_mechanism none --mca btl ^openib --mca oob_tcp_if_include lo --mca btl_tcp_if_include lo --mca orte_base_help_aggregate 0
-
     steps:
     - uses: actions/checkout@master
     - name: chown checkout directory
@@ -56,12 +55,12 @@ jobs:
           -DCMAKE_BUILD_TYPE=Debug \
           -DENABLE_PYTHON=ON \
           -DBUILD_TESTS=OFF \
+          -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install parPE Python deps
+    - name: Install parPE deps
       run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt \
-          && sudo apt install lcov
+        sudo apt install lcov
 
     - name: "Install parPE deps: fides"
       run: |
@@ -77,7 +76,8 @@ jobs:
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOV_REPORT=TRUE \
           -DBUILD_TESTING=TRUE \
-          -DPARPE_ENABLE_FIDES=TRUE
+          -DPARPE_ENABLE_FIDES=TRUE \
+          -DPARPE_ENABLE_CERES=FALSE
 
     - name: Build parPE
       # with sonar build wrapper
@@ -107,7 +107,7 @@ jobs:
 
     - name: Cache sonar files
       id: cache-sonar
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: sonar_cache
         key: ${{ runner.os }}-sonar_cache

.github/workflows/petab_testsuite.yml

@@ -34,17 +34,15 @@ jobs:
             -DCMAKE_BUILD_TYPE=Debug \
             -DENABLE_PYTHON=ON \
             -DBUILD_TESTS=OFF \
+            -DCMAKE_PREFIX_PATH="${CMAKE_PREFIX_PATH};${AMICI_PATH}/ThirdParty/SuiteSparse/install" \
           && cmake --build "${AMICI_PATH}/build" --parallel -- VERBOSE=1
 
-    - name: Install parPE Python deps
-      run: |
-        pip install -r ${PARPE_BASE}/python/requirements.txt
-
     - name: Configure parpe
       run: |
         cmake \
           -S"${PARPE_BASE}" \
           -B"${PARPE_BUILD}" \
+          -DPARPE_ENABLE_CERES=OFF \
           -DIPOPT_INCLUDE_DIRS=/usr/include/coin/ \
           -DIPOPT_LIBRARIES=/usr/lib/libipopt.so \
           -DGCOVR_REPORT=TRUE \