Skip to content

Update changelog #514

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
dweindl wants to merge 1 commit into
base: main
Choose a base branch
from
+46 −0
Open

Update changelog #514

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
46 changes: 46 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,51 @@
# PEtab changelog

## 0.9 series

### 0.9.0

This release will require Python>=3.12 and numpy>=2.1.

**Fixes**
* Fixed the mean of residuals and added an option to choose between
normalized and unnormalized errors in `plot_goodness_of_fit`
(by @plakrisenko in https://github.com/PEtab-dev/libpetab-python/pull/473)
* Made `scipy` a lazy import, so it is no longer required unless
probability distributions are actually used
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/486)
* Fixed `PetabStrPrinter` for non-integer rational exponents
(by @wshlavacek in https://github.com/PEtab-dev/libpetab-python/pull/489)
* Fixed spurious `nan`-related warnings in `Subplot.from_df`
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/496)
* Fixed a missing `return` in the noise distribution merge of
`petab1to2`, which caused `noiseDistribution` to always be `NaN` after
conversion
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/502)
* Fixed the PEtab v2 extension config model
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/506)
* Fixed SBML math parsing by using `sbmlmath` instead of
`sympy.sympify`
(by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/509)

**Features**
* Added support for PEtab SciML problems, including a dedicated linter
(by @BSnelling, @m-philipps and @dilpath in https://github.com/PEtab-dev/libpetab-python/pull/482
https://github.com/PEtab-dev/libpetab-python/pull/505,
https://github.com/PEtab-dev/libpetab-python/pull/499,
https://github.com/PEtab-dev/libpetab-python/pull/498,
https://github.com/PEtab-dev/libpetab-python/pull/511, and
https://github.com/PEtab-dev/libpetab-python/pull/513)
* Added support for BNGL models
(by @wshlavacek in https://github.com/PEtab-dev/libpetab-python/pull/508)
* Added linting of the mapping table, and allowed pure annotation-only
mapping entries
(by @m-philipps and @BSnelling in
https://github.com/PEtab-dev/libpetab-python/pull/480 and
https://github.com/PEtab-dev/libpetab-python/pull/500)
* Minor improvements to the v1-to-v2 converter: warn when dropping
`parameterScale`/`initializationPriorType`/`initializationPriorParameters`,
and use the experiments table column order suggested by the PEtab format
(by @m-philipps in https://github.com/PEtab-dev/libpetab-python/pull/479)

## 0.8 series

Expand Down