Release 0.3.2

.github/workflows/ci.yml

@@ -17,8 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # update to 3.11 when numba allows (needed in umap)
-        python-version: ['3.9', '3.10']
+        python-version: ['3.9', '3.11']
 
     steps:
     - name: Check out repository
@@ -48,6 +47,65 @@ jobs:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
 
+  mac:
+    runs-on: macos-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: ~/.cache
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci
+
+    - name: Install dependencies
+      run: .github/workflows/install_deps.sh amici
+
+    - name: Run tests
+      timeout-minutes: 30
+      run: tox -e base
+
+    - name: Coverage
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./coverage.xml
+
+  windows:
+    runs-on: windows-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+
+    steps:
+    - name: Check out repository
+      uses: actions/checkout@v3
+
+    - name: Prepare python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install tox
+
+    - name: Run tests
+      shell: bash
+      timeout-minutes: 10
+      run: tox -e windows
+
   petab:
     runs-on: ubuntu-latest
     strategy:
@@ -100,7 +158,7 @@ jobs:
     - name: Install julia
       uses: julia-actions/setup-julia@v1
       with:
-        version: 1.7
+        version: 1.9
 
     - name: Cache
       uses: actions/cache@v3
@@ -113,8 +171,11 @@ jobs:
     - name: Install dependencies
       run: .github/workflows/install_deps.sh
 
+    - name: Install PEtabJL dependencies
+      run: julia -e 'using Pkg; Pkg.add("PEtab"); Pkg.add("OrdinaryDiffEq"), Pkg.add("Sundials")'
+
     - name: Run tests
-      timeout-minutes: 20
+      timeout-minutes: 25
       run: tox -e julia
 
     - name: Coverage

.github/workflows/install_deps.sh

@@ -9,8 +9,14 @@ pip install wheel setuptools
 # Used to create local test environments
 pip install tox
 
-# Update apt
-sudo apt-get update
+# Update package lists
+if [ "$(uname)" == "Darwin" ]; then
+  # MacOS
+  brew update
+else
+  # Linux
+  sudo apt-get update
+fi
 
 # Check arguments
 for par in "$@"; do
@@ -22,8 +28,12 @@ for par in "$@"; do
 
     amici)
       # for amici
-      sudo apt-get install \
-        swig libatlas-base-dev libhdf5-serial-dev
+      if [ "$(uname)" == "Darwin" ]; then
+        brew install swig hdf5 libomp
+      else
+        sudo apt-get install \
+          swig libatlas-base-dev libhdf5-serial-dev
+      fi
     ;;
 
     ipopt)

doc/example.rst

@@ -27,6 +27,7 @@ Getting started
 
    example/getting_started.ipynb
    example/custom_objective_function.ipynb
+   example/workflow_comparison.ipynb
 
 PEtab and AMICI
 ---------------

doc/example/boehm_JProteomeRes2014/Boehm_validation/Gradient.csv

@@ -0,0 +1,2 @@
+Epo_degradation_BaF3,k_exp_hetero,k_exp_homo,k_imp_hetero,k_imp_homo,k_phos,sd_pSTAT5A_rel,sd_pSTAT5B_rel,sd_rSTAT5A_rel
+-226.01431847863805,0.03263295726678998,0.05074978988074719,-273.3251522968395,-4.9353233689552945e-5,85.33308210815652,-57.82373022138993,6.47910944243548,1.5327970845176904

doc/example/boehm_JProteomeRes2014/Boehm_validation/Hessian.csv

@@ -0,0 +1,10 @@
+Epo_degradation_BaF3,k_exp_hetero,k_exp_homo,k_imp_hetero,k_imp_homo,k_phos,sd_pSTAT5A_rel,sd_pSTAT5B_rel,sd_rSTAT5A_rel
+2348.781845248937,-0.034169780647049425,-103.24202100672939,2772.675796487632,7.194796260472683e-5,-938.3560377189202,996.659728857624,31.143959976782426,13.030712117968559
+-0.034169780647049425,0.07739858784002018,-0.15899501912479183,0.7386693785162849,-4.187803035168086e-8,-0.17134098751539498,-0.2564122376627509,0.03372069395138544,0.07241122210747836
+-103.24202100672939,-0.15899501912479183,132.944794430612,95.49012010074641,-2.508362770407691e-6,-22.250883365424308,11.34374075166351,-3.886786248018129,-7.690665859911962
+2772.675796487632,0.7386693785162849,95.49012010074641,3563.661917245381,1.092950395076315e-5,-1110.2044314822922,1202.406495619125,41.717823566223906,14.58452306207908
+7.194796260472683e-5,-4.187803035168086e-8,-2.508362770407691e-6,1.092950395076315e-5,0.00011364116982094509,-0.00016740979955329535,0.0001089554236616266,0.00011027946613432109,8.045150373694503e-6
+-938.3560377189202,-0.17134098751539498,-22.250883365424308,-1110.2044314822922,-0.00016740979955329535,965.7762449769793,-416.0316410076297,-6.62255869644657,29.6808324053416
+996.659728857624,-0.2564122376627509,11.34374075166351,1202.406495619125,0.0001089554236616266,-416.0316410076297,435.9488576495015,0.0,0.0
+31.143959976782426,0.03372069395138544,-3.886786248018129,41.717823566223906,0.00011027946613432109,-6.62255869644657,0.0,139.82333729022352,0.0
+13.030712117968559,0.07241122210747836,-7.690665859911962,14.58452306207908,8.045150373694503e-6,29.6808324053416,0.0,0.0,162.6019478340014

doc/example/boehm_JProteomeRes2014/Boehm_validation/ObjectiveValue.csv

@@ -0,0 +1,2 @@
+ObjectiveValue
+149.05022585636098

doc/example/boehm_JProteomeRes2014/Boehm_validation/Parameter.csv

@@ -0,0 +1,2 @@
+Epo_degradation_BaF3,k_exp_hetero,k_exp_homo,k_imp_hetero,k_imp_homo,k_phos,sd_pSTAT5A_rel,sd_pSTAT5B_rel,sd_rSTAT5A_rel
+-1.665827601408055,-4.999704893599998,-2.2096987817000167,-1.78600654750001,4.9901140088,4.1977354885,0.5857552705999998,0.8189828191999999,0.49868440400000047

doc/example/conversion_reaction/PEtabJl_module.jl

@@ -0,0 +1,20 @@
+module MyPEtabJlModule
+
+using OrdinaryDiffEq
+using Sundials
+using PEtab
+
+pathYaml = "/Users/pauljonasjost/Documents/GitHub_Folders/pyPESTO/test/julia/../../doc/example/conversion_reaction/conversion_reaction.yaml"
+petabModel = readPEtabModel(pathYaml, verbose=true)
+
+# A full list of options for createPEtabODEProblem can be found at https://sebapersson.github.io/PEtab.jl/dev/API_choosen/#PEtab.setupPEtabODEProblem
+petabProblem = createPEtabODEProblem(
+	petabModel,
+	odeSolverOptions=ODESolverOptions(Rodas5P(), abstol=1e-08, reltol=1e-08, maxiters=Int64(1e4)),
+	gradientMethod=:ForwardDiff,
+	hessianMethod=:ForwardDiff,
+	sparseJacobian=nothing,
+	verbose=true
+)
+
+end