Merge pull request #1468 from ICB-DCM/develop

Release v0.5.4
ICB-DCM · Oct 31, 2024 · 3b97e34 · 3b97e34
2 parents ead29b3 + a82e637
commit 3b97e34
Show file tree

Hide file tree

Showing 103 changed files with 5,347 additions and 2,050 deletions.
diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -1,7 +1,7 @@
 # see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners
 
 # default owners = active maintainers
-* @Doresic @PaulJonasJost @m-philipps
+* @Doresic @PaulJonasJost @vwiela
 
 # Examples
 /doc/example/censored_data.ipynb @Doresic
@@ -28,29 +28,28 @@
 /pypesto/hierarchical/semiquantitative/ @Doresic
 /pypesto/history/ @PaulJonasJost
 /pypesto/objective/ @PaulJonasJost
+/pypesto/objective/julia @vwiela
 /pypesto/objective/amici/ @dweindl @FFroehlich
 /pypesto/objective/jax/ @FFroehlich
 /pypesto/objective/aesara/ @FFroehlich
 /pypesto/optimize/ @PaulJonasJost
 /pypesto/petab/ @dweindl @FFroehlich
 /pypesto/predict/ @dilpath
-/pypesto/problem/ @PaulJonasJost @m-philipps
-/pypesto/profile/ @PaulJonasJost
+/pypesto/problem/ @PaulJonasJost @vwiela
+/pypesto/profile/ @PaulJonasJost @Doresic
 /pypesto/result/ @PaulJonasJost
-/pypesto/sample/ @dilpath @vwiela
+/pypesto/sample/ @dilpath @arrjon
 /pypesto/select/ @dilpath
 /pypesto/startpoint/ @PaulJonasJost
 /pypesto/store/ @PaulJonasJost
-/pypesto/visualize/ @stephanmg @m-philipps
 
 # Tests
-/test/base/ @PaulJonasJost @m-philipps
+/test/base/ @PaulJonasJost @vwiela
 /test/doc/ @PaulJonasJost
-/test/hierarchical/ @dweindl @doresic
-/test/julia/ @PaulJonasJost
+/test/hierarchical/ @dweindl @Doresic
+/test/julia/ @PaulJonasJost @vwiela
 /test/optimize/ @PaulJonasJost
 /test/petab/ @dweindl @FFroehlich
-/test/profile/ @PaulJonasJost
-/test/sample/ @dilpath
+/test/profile/ @PaulJonasJost @Doresic
+/test/sample/ @dilpath @arrjon
 /test/select/ @dilpath
-/test/visualize/ @stephanmg @m-philipps
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -8,6 +8,7 @@ on:
     - develop
   pull_request:
   workflow_dispatch:
+  merge_group:
   schedule:
     # run Monday and Thursday at 03:42 UTC
     - cron: '42 3 * * MON,THU'
@@ -28,15 +29,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -54,7 +55,7 @@ jobs:
         CXX: clang++
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -67,15 +68,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -90,7 +91,7 @@ jobs:
       run: ulimit -n 65536 65536 && tox -e base
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -103,15 +104,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~\AppData\Local\pip\Cache
@@ -136,15 +137,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -162,7 +163,7 @@ jobs:
         CXX: clang++
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -180,43 +181,40 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache tox and cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
           .tox/
         key: "${{ runner.os }}-${{ runner.arch }}-py${{ matrix.python-version }}-ci-${{ github.job }}"
 
     - name: Install julia
-      uses: julia-actions/setup-julia@v1
+      uses: julia-actions/setup-julia@v2
       with:
-        version: 1.9
-
-    - name: Cache Julia
-      uses: julia-actions/cache@v1
+        version: 1.11
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh
 
     - name: Install PEtabJL dependencies
       run: >
-        julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PEtab", version="2.5.0"));
+        julia -e 'using Pkg; Pkg.add("PEtab");
         Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")'
 
     - name: Run tests
       timeout-minutes: 25
       run: tox -e julia
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -229,15 +227,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -252,7 +250,7 @@ jobs:
       run: tox -e optimize
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -265,15 +263,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -288,7 +286,7 @@ jobs:
       run: tox -e hierarchical
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -301,15 +299,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -324,7 +322,7 @@ jobs:
       run: tox -e select
 
     - name: Coverage
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         file: ./coverage.xml
@@ -337,15 +335,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -369,15 +367,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -402,15 +400,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip
@@ -432,15 +430,15 @@ jobs:
 
     steps:
     - name: Check out repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Prepare python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: |
           ~/.cache/pip