Release v0.5.7 #1610
Merged
Release v0.5.7 #1610
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* CI: Update amici branch AMICI's main development branch changed from `develop` to `main`. This updates the test environment accordingly. * more recent python
We don't support the updated PEtab v2 tests yet.
Fixes `SetuptoolsDeprecationWarning: License classifiers are deprecated.`.
`disp` is deprecated for the L-BFGS-B optimizer and has no effect anymore, see https://docs.scipy.org/doc/scipy/reference/optimize.minimize-lbfgsb.html.
Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 5. - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@v4...v5) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: '5' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* fix cutoff based on chi2 distribution * update calculate_cutoff docstring * add cutoff computation test * add cutoff computation test * quality fix * quality * ruff * ruff * use amici branch main instead of develop in tox.ini * fix docstring * fix docstring --------- Co-authored-by: Daniel Weindl <[email protected]>
* Remove outdated pymc3 reference from getting-started notebook Co-authored-by: dweindl <[email protected]> * .. * Update getting_started.ipynb Add adaptive parallel tempering to available samplers list. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: dweindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Vincent Wieland <[email protected]>
* split ProfilerTask into descending and ascending parts * add explanatory comments
Previously, an optimization result with only non-finite values would result in an IndexError. Now this is handled more gracefully. Closes #1599.
Updated citation format for pyPESTO reference in README. Year was duplicated, volume and number were missing.
We need https://pypi.org/project/libroadrunner/ which is imported as `roadrunner`. We don't want https://pypi.org/project/roadrunner/.
Bumps [actions/setup-python](https://github.com/actions/setup-python) from 5 to 6. - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@v5...v6) --- updated-dependencies: - dependency-name: actions/setup-python dependency-version: '6' dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* Update getting_started.ipynb The comments on the results of the profiling in the getting started notebook were outdated. They refered to results of the old version with the Boehm model, rather than the new version with the conversion reaction model. * Update getting_started.ipynb --------- Co-authored-by: Polina Lakrisenko <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>
…scatter. (#1608) * Change cluster assignment and improve plotting efficiency using scatter plot. * Quality --------- Co-authored-by: Stephan Grein <[email protected]>
…w more steady state presimulation (#1604) Co-authored-by: Daniel Weindl <[email protected]>
https://github.com/aesara-devs/aesara is no longer maintained, and `pymc` does not require aesara.
As per our Python support policy, we drop support for Python 3.10. Also, run tests with Python 3.13 instead of 3.12.
|
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1610 +/- ##
==========================================
- Coverage 84.63% 83.70% -0.93%
==========================================
Files 163 163
Lines 14042 14088 +46
==========================================
- Hits 11885 11793 -92
- Misses 2157 2295 +138 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
Soonishly, there will be amici 1.0.0, which will break some things here. Require <1.0.0 until everything is updated (-> #1619).
Co-authored-by: Polina Lakrisenko <[email protected]> Co-authored-by: Polina Lakrisenko <[email protected]> Co-authored-by: Polina Lakrisenko <[email protected]>
* Fix Python requirement * Cross-references * Reword
* Fix OptimizerImportError (Closes #1615) * Fix names * Use currently unused optimization result * Fix incorrect typehints
There are issues with that release, at least on macos.
* add visualization of multiple CIs based on profiles * sort CLs in decreasing order * fix test * add legend, different colors for CIs by default * ruff format * add df parameter to profile_cis, profile_nested_cis * Update pypesto/visualize/profile_cis.py Co-authored-by: Daniel Weindl <[email protected]> * substitute rotation with orientation * update getting_started notebook * ruff * ruff format * Update doc/example/getting_started.ipynb Co-authored-by: Daniel Weindl <[email protected]> * move legend to the top --------- Co-authored-by: Daniel Weindl <[email protected]>
* remove unnecessary title and axes labels * fix * do in one line --------- Co-authored-by: Daniel Weindl <[email protected]> Co-authored-by: Stephan Grein <[email protected]>
… use `macos-latest` (#1633) * Test fails on (deprecated) `macos-13` runners due to issues with the current antimony version, and fails on `macos-15` for other reasons (#1597 (comment)). Disable for now. Related to #1597. * use macos-latest > GitHub Actions: macOS 13 runner image is closing down https://github.blog/changelog/2025-09-19-github-actions-macos-13-runner-image-is-closing-down/
…ed additional typecheck and possibility to use an integer as id (#1635)
* try errorbar * style * ruff * ruff * Update pypesto/visualize/profile_cis.py Co-authored-by: Daniel Weindl <[email protected]> * set strict=True --------- Co-authored-by: Daniel Weindl <[email protected]>
* accept all matlab color in assign_colors * fix colors * check color types in waterfall plots * fix colors in optimization_stats * fix colors in optimizer_history * color fixes in profile visualization * update colors in parameter visualization * update docstrings * improve typing and docstrings * fix annotations * set strict=True * Update pypesto/visualize/dimension_reduction.py Co-authored-by: Paul Jonas Jost <[email protected]> * ruff * background color in ensemble_scatter_lowlevel --------- Co-authored-by: Paul Jonas Jost <[email protected]>
* Change cluster assignment and improve plotting efficiency using scatter plot. * Quality * Add minimal alpha value for cluster color transparency Set a minimal alpha value to avoid non-visible colors when balancing alpha levels based on cluster size. * Revert * Add minimmal alpha value. * Update pypesto/visualize/clust_color.py Co-authored-by: Polina Lakrisenko <[email protected]> --------- Co-authored-by: Polina Lakrisenko <[email protected]>
* Updated version.py * Updated changelog
PaulJonasJost
requested review from
Doresic,
FFroehlich,
dilpath,
dweindl,
stephanmg and
vwiela
as code owners
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
monotonic_history#1632)