libpetab-python v0.1.27.dev1

Features:

• Added method to check if measurement time is at steady-state by @dilpath in #124
• Create dummy simulation conditions dataframe for empty measurements by @dilpath in #127
• Validator: Report empty noiseFormula by @dweindl in #134
• Speedup visspec assembly / fix deprecation warning by @dweindl in #135
• Handle incomplete PEtab problems in petab.Problem.from_yaml by @dweindl in #138
• Argument forwarding for Problem.get_optimization_to_simulation_parameter_mapping by @dweindl in #159
• Added candidate schema for version 2 by @dweindl in #142
• get_parameter_df: Allow any collection of parameter tables by @dweindl in #153, @m-philipps in #156, @dilpath in #157
• Updated visualization example notebooks by @dweindl in #137, by @plakrisenko in #146, by @plakrisenko in #147
• Added support for PEtab problems with multiple condition files by @dweindl in #152
• Added abstraction for (SBML) models by @dweindl in #133

Fixes:

• Apply get table method before write table method to ensure correct index by @dilpath in #126
• petablint: Fix incorrect noise-parameter-mismatch error message by @dweindl in #129
• Fixed handling of NaN values for parameters in condition table by @dweindl in #150
• More informative petab.calculate errors by @dweindl in #151

Removals:

• Removed ancient/deprecated default file naming scheme by @dweindl in #132
• Removed ancient deprecated functions related to specifying observables/noise models inside SBML
  by @dweindl in #140 #131
• Removed deprecated visualization functions by @dweindl in #130

New Contributors

• @m-philipps made their first contribution in #156

Full Changelog: v0.1.26...v0.1.27

libpetab-python v0.1.26

What's Changed

• Fix SBML Rule handling logic by @dweindl in #120

libpetab-python v0.1.25

• Fix for pytest 7.1 by @yannikschaelte in #112
• Fix jinja version by @dilpath in #115
• Add steady state constant by @dilpath in #114
• Omit measurement processing if not relevant for parameter mapping by @FFroehlich in #117

Full Changelog: v0.1.24...v0.1.25

libpetab-python v0.1.24

• GHA: Regular package installation instead of -e by @dweindl in #106
• Fix unclosed file warnings by @dilpath in #107
• Generation of condition-specific SBML models by @dweindl in #108

Full Changelog: v0.1.23...v0.1.24

libpetab-python v0.1.23

• Added command line interface for plotting by @dweindl in #98
• Fixed petab.visualize.data_overview.create_report by @dweindl in #96, #104
• Vis: Fixed cropped errorbars by @dweindl in #99
• Fixed pandas deprecation warning by @dweindl in #103

... and other changes by @plakrisenko, @dweindl

Full Changelog: v0.1.22...v0.1.23

libpetab-python v0.1.22

• Allow zero bounds for log parameters by @FFroehlich in #83
• Adapt to Matplotlib 3.5 by @dweindl in #86
• Allow specifying file format for visualization by @dweindl in #85
• Visualization: Don't mess with rcParams by @dweindl in #90
• Linter: Check condition IDs are unique by @dweindl in #92
• Add support for pathlib for reading PEtab tables by @dweindl, @dilpath in #93, #91
• Run tests also on Python 3.10 by @dweindl in #88
• Fix remote file retrieval on Windows @dweindl, @dilpath in #91
• Fix test suite for Windows @dweindl, @dilpath in #91

Full Changelog: v0.1.21...v0.1.22

libpetab-python v0.1.21

• PEtab spec compliance: measurements must now be not null, and numeric (#76)
  • Users who relied on null measurements for simulation/plotting are
    recommended to store these dummy simulation-only measurements in an
    additional file, separate to real measurements used for calibration
• Improve Unicode support (#79, fixes #77)
• Convenience methods to scale or unscale a parameter vector (#78)

libpetab-python v0.1.20

• Visualization: plot additional simulation points (not only at measurements) (#62), bugfix (#68)
• Documentation: visualization, observables, simulation, Sphinx fixes (#67)
• Lint: ensure valid parameter IDs in observable and noise parameters (#69)
• Convenience method for quick export of a PEtab problem to files (#71)

PEtab v0.1.19

• Visualization: refactoring (#58) including various bug fixes
• Validation: Fixed detection of missing observable/noise parameter overrides
  (#64)
• Optional relative paths in generated YAML (#57)

PEtab v0.1.18

• Fixed various documentation issues
• Parameter mapping: Added option to ignore time-point specific
  noiseParameters (#51)