Merge pull request #1173 from ICB-DCM/develop

release v0.4.0
ICB-DCM · Nov 22, 2023 · d0d2a73 · d0d2a73
2 parents 883138a + ffe5c6e
commit d0d2a73
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diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS
@@ -15,32 +15,32 @@
 /docker/ @dweindl
 /pypesto/engine/ @PaulJonasJost
 /pypesto/engine/mpi_pool.py @PaulJonasJost
-/pypesto/ensemble/ @dilpath
-/pypesto/hierarchical/ @dilpath @dweindl
+/pypesto/ensemble/ @dilpath @PaulJonasJost
+/pypesto/hierarchical/ @dweindl @doresic
 /pypesto/hierarchical/optimal_scaling_approach/ @doresic
 /pypesto/history/ @PaulJonasJost
 /pypesto/objective/ @PaulJonasJost
-/pypesto/objective/amici/ @PaulJonasJost @dweindl @FFroehlich
+/pypesto/objective/amici/ @dweindl @FFroehlich
 /pypesto/objective/jax/ @FFroehlich
 /pypesto/objective/aesara/ @FFroehlich
 /pypesto/optimize/ @PaulJonasJost
 /pypesto/petab/ @dweindl @FFroehlich
-/pypesto/predict/ @PaulJonasJost @dilpath
-/pypesto/problem/ @PaulJonasJost
+/pypesto/predict/ @dilpath
+/pypesto/problem/ @PaulJonasJost @m-philipps
 /pypesto/profile/ @PaulJonasJost
 /pypesto/result/ @PaulJonasJost
-/pypesto/sample/ @dilpath
+/pypesto/sample/ @dilpath @vwiela
 /pypesto/select/ @dilpath
 /pypesto/startpoint/ @PaulJonasJost
 /pypesto/store/ @PaulJonasJost
-/pypesto/visualize/ @plakrisenko @stephanmg
-/test/base/ @PaulJonasJost
+/pypesto/visualize/@stephanmg @m-philipps
+/test/base/ @PaulJonasJost @m-philipps
 /test/doc/ @PaulJonasJost
-/test/hierarchical/ @dilpath @dweindl
+/test/hierarchical/ @dweindl @doresic
 /test/julia/ @PaulJonasJost
 /test/optimize/ @PaulJonasJost
 /test/petab/ @dweindl @FFroehlich
 /test/profile/ @PaulJonasJost
 /test/sample/ @dilpath
 /test/select/ @dilpath
-/test/visualize/ @plakrisenko @stephanmg
+/test/visualize/ @stephanmg @m-philipps
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -11,6 +11,10 @@ on:
     # run Monday and Thursday at 03:42 UTC
     - cron: '42 3 * * MON,THU'
 
+env:
+  # use all available cores for compiling amici models
+  AMICI_PARALLEL_COMPILE: ""
+
 # jobs
 jobs:
   base:
@@ -31,15 +35,20 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-base
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
 
     - name: Run tests
-      timeout-minutes: 25
+      timeout-minutes: 30
       run: tox -e base
+      env:
+        CC: clang
+        CXX: clang++
 
     - name: Coverage
       uses: codecov/codecov-action@v3
@@ -65,7 +74,10 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
+        path: |
+          ~/.cache
+          .tox/
+          ~/Library/Caches/Homebrew
         key: ${{ runner.os }}-${{ matrix.python-version }}-ci
 
     - name: Install dependencies
@@ -96,6 +108,14 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Cache
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~\AppData\Local\pip\Cache
+          .tox
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci
+
     - name: Install dependencies
       run: |
         pip install --upgrade pip
@@ -124,15 +144,20 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-petab
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici pysb
 
     - name: Run tests
       timeout-minutes: 35
       run: tox -e petab
+      env:
+        CC: clang
+        CXX: clang++
 
     - name: Coverage
       uses: codecov/codecov-action@v3
@@ -165,8 +190,9 @@ jobs:
       with:
         path: |
           ~/.cache
+          .tox/
           ~/.julia/artifacts
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-julia
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh
@@ -203,14 +229,16 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-optimize
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh ipopt
 
     - name: Run tests
-      timeout-minutes: 20
+      timeout-minutes: 25
       run: tox -e optimize
 
     - name: Coverage
@@ -237,8 +265,10 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-hierarchical
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
@@ -271,8 +301,10 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-select
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici
@@ -305,19 +337,17 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-quality
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: pip install tox pre-commit
 
     - name: Check repository size
       run: tox -e size
 
-    - name: Run quality checks
-      timeout-minutes: 5
-      run: tox -e project,flake8
-
     - name: Run pre-commit hooks
       run: pre-commit run --all-files
 
@@ -339,8 +369,10 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-docs
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh doc amici
@@ -370,8 +402,10 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks1
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici ipopt
@@ -398,8 +432,10 @@ jobs:
     - name: Cache
       uses: actions/cache@v3
       with:
-        path: ~/.cache
-        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-notebooks2
+        path: |
+          ~/.cache
+          .tox/
+        key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}
 
     - name: Install dependencies
       run: .github/workflows/install_deps.sh amici

diff --git a/.github/workflows/install_deps.sh b/.github/workflows/install_deps.sh
@@ -12,7 +12,7 @@ pip install tox
 # Update package lists
 if [ "$(uname)" == "Darwin" ]; then
   # MacOS
-  brew update
+  :
 else
   # Linux
   sudo apt-get update
@@ -32,7 +32,7 @@ for par in "$@"; do
         brew install swig hdf5 libomp
       else
         sudo apt-get install \
-          swig libatlas-base-dev libhdf5-serial-dev
+          clang libatlas-base-dev libhdf5-serial-dev libomp-dev swig
       fi
     ;;
 

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -59,6 +59,7 @@ repos:
   - id: style
     name: Check style
     description: Check style
-    entry: tox -e project,flake8 --
-    language: python
+    pass_filenames: false
+    entry: tox -e project,flake8
+    language: system
     types: [python]
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,45 @@ Release notes
 =============
 
 
+0.4 series
+..........
+
+
+0.4.0 (2023-11-22)
+-------------------
+
+* General
+    * Documentation (#1140, #1146, #1152, #1149, #1192)
+    * Updated Jupyter Notebooks (#1141)
+    * Update code to avoid deprecations/warnings (#1158, #1184)
+    * Updated maintainers and codeownership (#1171, #1170)
+    * Improve tests and GHA (#1178, #1185, #1188, #1190, #1193, #1199, #1198, #1197, #1208)
+* Profile:
+    * Fix problem overwrite of profiling (#1153)
+    * Add warning, trying to profile fixed parameter (#1155)
+    * ProfileOptions: add some basic integrity checking (#1163)
+    * Fix pypesto.profile.parameter_profile incorrectly assuming symmetric bounds (#1166)
+    * Improve pypesto/profile/profile_next_guess.py (#1167)
+    * Parameter profile: retry optimization in case of failure (#1168)
+    * Fix incorrect types in pypesto.result.profile.ProfilerResult (#1210)
+* Problem:
+    * Add/forward startpoint_kwargs in PetabImporter.create_problem (#1135)
+    * Support valid AMICI noise distributions that are invalid in PEtab (#1157)
+    * Fix startpoint sampling for PEtab-derived problems with fixed parameters (#1169)
+* Optimize
+    * Log traceback in case of exceptions during optimizations (#1156)
+    * Saccess optimizer improvements (#1177, #1187, #1194, #1195, #1201, #1202, #1204)
+    * ESS optimizer improvements (#1176, #1181, #1182)
+    * Fix check for allow_failed_starts (#1180)
+    * Handle message and exitflag in histories (#1203)
+    * Fix indexing error for 0-dimensional HDF5 datasets (#1206)
+* Hierarchical:
+    * Fix HierarchicalAmiciCalculator.__call__ not setting 'hess' in result (#1161)
+* Visualization:
+    * Fix legend argument checking for waterfall/parameter/history plots (#1139)
+    * Fix waterfall start indices for multiple results (#1200)
+
+
 0.3 series
 ..........
 

diff --git a/doc/api.rst b/doc/api.rst
@@ -20,9 +20,11 @@ API reference
    pypesto.predict
    pypesto.problem
    pypesto.profile
+   pypesto.profile.profile_next_guess
    pypesto.result
    pypesto.sample
    pypesto.select
+   pypesto.select.postprocessors
    pypesto.startpoint
    pypesto.store
    pypesto.visualize

diff --git a/doc/conf.py b/doc/conf.py
@@ -56,6 +56,8 @@
     'sphinxcontrib.bibtex',
     # ensure that jQuery is installed
     'sphinxcontrib.jquery',
+    # type hint formatting
+    'sphinx_autodoc_typehints',
 ]
 
 # default autodoc options
@@ -81,8 +83,13 @@
         None,
     ),
     'amici': ('https://amici.readthedocs.io/en/latest/', None),
+    'fides': ('https://fides-optimizer.readthedocs.io/en/latest/', None),
 }
 
+
+typehints_document_rtype = True
+autodoc_typehints = "description"
+
 bibtex_bibfiles = ["using_pypesto.bib"]
 
 # Add any paths that contain templates here, relative to this directory.