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Merge pull request ICB-DCM#1298 from ICB-DCM/develop
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Release v0.4.2
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PaulJonasJost authored Feb 6, 2024
2 parents b4a187f + f46ca20 commit 34e89b3
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22 changes: 14 additions & 8 deletions .github/CODEOWNERS
Validating CODEOWNERS rules …
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@@ -1,27 +1,31 @@
# see https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-code-owners

# default owners
* @ICB-DCM/pypesto-maintainers
# default owners = active maintainers
* @Doresic @PaulJonasJost @m-philipps

/doc/example/censored.ipynb @Doresic
# Examples
/doc/example/censored_data.ipynb @Doresic
/doc/example/hdf5_storage.ipynb @PaulJonasJost
/doc/example/hierarchical.ipynb @dilpath @dweindl
/doc/example/julia.ipynb @PaulJonasJost
/doc/example/model_selection.ipynb @dilpath
/doc/example/nonlinear_monotone.ipynb @Doresic
/doc/example/ordinal.ipynb @Doresic
/doc/example/ordinal_data.ipynb @Doresic
/doc/example/petab_import.ipynb @dweindl @FFroehlich
/doc/example/relative_data.ipynb @dilpath @dweindl
/doc/example/sampler_study.ipynb @dilpath
/doc/example/sampling_diagnostics.ipynb @dilpath
/doc/example/semiquantitative_data.ipynb @Doresic
/doc/example/store.ipynb @PaulJonasJost
/doc/example/synthetic_data.ipynb @dilpath
/docker/ @dweindl

# Code
/pypesto/engine/ @PaulJonasJost
/pypesto/engine/mpi_pool.py @PaulJonasJost
/pypesto/ensemble/ @dilpath @PaulJonasJost
/pypesto/hierarchical/ @dweindl @Doresic
/pypesto/hierarchical/optimal_scaling_approach/ @Doresic
/pypesto/hierarchical/spline_approximation/ @Doresic
/pypesto/hierarchical/ordinal/ @Doresic
/pypesto/hierarchical/relative/ @dweindl @Doresic
/pypesto/hierarchical/semiquantitative/ @Doresic
/pypesto/history/ @PaulJonasJost
/pypesto/objective/ @PaulJonasJost
/pypesto/objective/amici/ @dweindl @FFroehlich
Expand All @@ -38,6 +42,8 @@
/pypesto/startpoint/ @PaulJonasJost
/pypesto/store/ @PaulJonasJost
/pypesto/visualize/ @stephanmg @m-philipps

# Tests
/test/base/ @PaulJonasJost @m-philipps
/test/doc/ @PaulJonasJost
/test/hierarchical/ @dweindl @doresic
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32 changes: 18 additions & 14 deletions .github/workflows/ci.yml
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Expand Up @@ -5,6 +5,7 @@ on:
push:
branches:
- main
- develop
pull_request:
workflow_dispatch:
schedule:
Expand All @@ -14,6 +15,8 @@ on:
env:
# use all available cores for compiling amici models
AMICI_PARALLEL_COMPILE: ""
# non-interactive backend for matplotlib
MPLBACKEND: "agg"

# jobs
jobs:
Expand All @@ -36,7 +39,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -75,9 +78,8 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
~/Library/Caches/Homebrew
key: ${{ runner.os }}-${{ matrix.python-version }}-ci

- name: Install dependencies
Expand Down Expand Up @@ -145,7 +147,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -189,7 +191,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand All @@ -205,7 +207,9 @@ jobs:
run: .github/workflows/install_deps.sh

- name: Install PEtabJL dependencies
run: julia -e 'using Pkg; Pkg.add("PEtab"); Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")'
run: >
julia -e 'using Pkg; Pkg.add(Pkg.PackageSpec(;name="PEtab", version="2.5.0"));
Pkg.add("OrdinaryDiffEq"); Pkg.add("Sundials")'
- name: Run tests
timeout-minutes: 25
Expand Down Expand Up @@ -237,7 +241,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -273,7 +277,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -309,7 +313,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -345,7 +349,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -377,7 +381,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand All @@ -388,7 +392,7 @@ jobs:
run: pip install cffconvert && cffconvert --validate

- name: Build doc
timeout-minutes: 10
timeout-minutes: 30
run: tox -e doc

notebooks1:
Expand All @@ -410,7 +414,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

Expand Down Expand Up @@ -440,7 +444,7 @@ jobs:
uses: actions/cache@v3
with:
path: |
~/.cache
~/.cache/pip
.tox/
key: ${{ runner.os }}-${{ matrix.python-version }}-ci-${{ github.job }}

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31 changes: 31 additions & 0 deletions .github/workflows/clear-cache.yml
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@@ -0,0 +1,31 @@
# Save cache space by deleting cache entries from a PR after it was merged.
# https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows#force-deleting-cache-entries
name: Delete after PR merge
on:
pull_request:
types:
- closed

jobs:
cleanup:
runs-on: ubuntu-latest
steps:
- name: Cleanup
run: |
gh extension install actions/gh-actions-cache
echo "Fetching list of cache key"
cacheKeysForPR=$(gh actions-cache list -R $REPO -B $BRANCH -L 100 | cut -f 1 )
## Setting this to not fail the workflow while deleting cache keys.
set +e
echo "Deleting caches..."
for cacheKey in $cacheKeysForPR
do
gh actions-cache delete $cacheKey -R $REPO -B $BRANCH --confirm
done
echo "Done"
env:
GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
REPO: ${{ github.repository }}
BRANCH: refs/pull/${{ github.event.pull_request.number }}/merge
4 changes: 2 additions & 2 deletions .github/workflows/install_deps.sh
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Expand Up @@ -10,7 +10,7 @@ pip install wheel setuptools
pip install tox

# Update package lists
if [ "$(uname)" == "Darwin" ]; then
if [ "$(uname)" = "Darwin" ]; then
# MacOS
:
else
Expand All @@ -28,7 +28,7 @@ for par in "$@"; do

amici)
# for amici
if [ "$(uname)" == "Darwin" ]; then
if [ "$(uname)" = "Darwin" ]; then
brew install swig hdf5 libomp
else
sudo apt-get install \
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6 changes: 4 additions & 2 deletions .readthedocs.yml
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Expand Up @@ -19,9 +19,11 @@ python:
- doc

build:
os: "ubuntu-20.04"
os: "ubuntu-22.04"
apt_packages:
- clang
- libatlas-base-dev
- libhdf5-serial-dev
- swig
tools:
python: "3.10"
python: "3.11"
44 changes: 44 additions & 0 deletions CHANGELOG.rst
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Expand Up @@ -6,6 +6,50 @@ Release notes
..........


0.4.2 (2024-01-30)
-------------------

* General
* Stabilize tests (#1240, #1254, #1300, #1302, #1303)
* Update type annotations and documentations (#1239, #1248, #1255, #1258, #1251, #1268, #1275)
* GHA/Codeowner changes (#1260, #1261, #1259, #1262, #1285)
* Update utility functions (#1243)
* Refactor progress bars (#1272)
* Clear Notebook output(#1246, #1277, #1274, #1271, #1276, #1278)
* Optimize
* (Sac)ESSOptimizer: History of best objective values (#1212)
* Fix missing fixed parameters in scatter search results (#1265)
* Fix TypeError in pypesto.result.optimize.OptimizerResult.summary if x0 is None (#1266)
* ESSOptimizer: Include results for local searches in OptimizeResult (#1270)
* **New Feature**: Spline Approximation (#1222)
* Select
* Allow for hierarchical problems (#1241)
* custom minimize method (#1264)
* Set estimated parameters in petab_select.Models (#1287)
* Hierarchical
* Log space startpoint sampling (#1242)
* Support for box constraints on offset and scaling parameters (#1238)
* restructuring and add relative to InnerCalculatorCollector (#1245)
* Semiquantitative: Robust regularization calculation (#1297)
* History
* Support pathlib.Path for result/history files (#1247)
* Extended Amici history (#1263)
* Visualize
* Fix time trajectories for hierarchical problems (#1213)
* Fix hierarchical parameter plotting for all optimizers (#1244)
* Sacess history plot (#1250)
* Objective
* Fix PEtab.jl version to before 2.5.0 (temporarily) (#1256)
* PEtab
* Enable Importer passing verbose to create_model (#1269)
* PetabImporter: version-specific amici model directories (#1283)
* Problem
* Problem: add inner problem names, bounds and hierarchical flag (#1282)
* Use warnings.warn instead of logging.warn when loading Problem from HDF5 without an Objective (#1253)
* Ensemble
* EnsemblePrediction: remove "no predictor" warning (#1293)


0.4.1 (2023-12-05)
-------------------

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5 changes: 3 additions & 2 deletions doc/api.rst
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Expand Up @@ -7,8 +7,9 @@ API reference
pypesto.engine
pypesto.ensemble
pypesto.hierarchical
pypesto.hierarchical.optimal_scaling
pypesto.hierarchical.spline_approximation
pypesto.hierarchical.ordinal
pypesto.hierarchical.relative
pypesto.hierarchical.semiquantitative
pypesto.history
pypesto.logging
pypesto.objective
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25 changes: 20 additions & 5 deletions doc/conf.py
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Expand Up @@ -22,6 +22,20 @@

sys.path.insert(0, os.path.abspath('../'))

# Silence:
# Debugger warning: It seems that frozen modules are being used, which may
# make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
# to python to disable frozen modules.
# Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
os.environ["PYDEVD_DISABLE_FILE_VALIDATION"] = "1"

# TQDM and nbsphinx do not play well together. Therefore, disable TQDM
# for the documentation build.
# (`Content block expected for the "raw" directive; none found.`)
os.environ["TQDM_DISABLE"] = "1"

# Enable parallel compilation of AMICI models
os.environ["AMICI_PARALLEL_COMPILE"] = ""

# -- General configuration ------------------------------------------------

Expand Down Expand Up @@ -70,24 +84,25 @@
'show-inheritance': True,
'autodoc_inherit_docstrings': True,
}
autodoc_mock_imports = ["amici"]
autodoc_class_signature = "separated"

# napoleon options
napoleon_use_rtype = False

# links for intersphinx
intersphinx_mapping = {
'python': ('https://docs.python.org/3', None),
'amici': ('https://amici.readthedocs.io/en/latest/', None),
'fides': ('https://fides-optimizer.readthedocs.io/en/latest/', None),
'matplotlib': ('https://matplotlib.org/stable/', None),
'numpy': ('https://numpy.org/devdocs/', None),
'scipy': ('https://docs.scipy.org/doc/scipy/', None),
'pandas': ('https://pandas.pydata.org/docs/', None),
'petab': (
'https://petab.readthedocs.io/projects/libpetab-python/en/latest/',
None,
),
'amici': ('https://amici.readthedocs.io/en/latest/', None),
'fides': ('https://fides-optimizer.readthedocs.io/en/latest/', None),
'petab_select': ('https://petab-select.readthedocs.io/en/develop/', None),
'python': ('https://docs.python.org/3', None),
'scipy': ('https://docs.scipy.org/doc/scipy/', None),
}


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8 changes: 4 additions & 4 deletions doc/example.rst
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Expand Up @@ -51,10 +51,10 @@ Algorithms and features
example/store.ipynb
example/model_selection.ipynb
example/julia.ipynb
example/hierarchical.ipynb
example/ordinal.ipynb
example/censored.ipynb
example/nonlinear_monotone.ipynb
example/relative_data.ipynb
example/ordinal_data.ipynb
example/censored_data.ipynb
example/semiquantitative_data.ipynb

Application examples
--------------------
Expand Down
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