Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / PEtab-dev/libpetab-python issues and pull requests

#353 - Update/use ProblemConfig

Pull Request - State: open - Opened by dweindl about 1 month ago - 1 comment

#352 - Create output directories in write_*

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#351 - v2: fixes to validation and upconversion

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#350 - Fix version checks

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#349 - v2: version check

Issue - State: open - Opened by FFroehlich about 1 month ago - 3 comments

#348 - Problem.add_parameter: Rename kwarg estimated->estimate

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#347 - petab.calculate: compare all common columns

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#346 - Fix v2 import Deprecation warning

Pull Request - State: closed - Opened by dweindl about 1 month ago - 1 comment

#345 - v2: Observable/conditions/experiments/... objects

Pull Request - State: open - Opened by dweindl about 1 month ago - 1 comment

#344 - antlr runtime version

Issue - State: open - Opened by fbergmann about 1 month ago - 4 comments

#343 - Doc: fix deprecated petablint invocation

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#342 - Fix petablint v2 warning

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#341 - Fix Prior.from_par_dict for missing priorParameters columns

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#340 - Fix `get_required_parameters_for_parameter_table`

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#339 - v2: Adapt to long conditions table

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#338 - Store problem configuration in `v2.Problem`

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#337 - Use proper object model for petab.v2

Issue - State: open - Opened by dweindl about 2 months ago - 1 comment

#336 - Fix test_priors_to_measurements

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#335 - Implement proper truncation for prior distributions

Pull Request - State: open - Opened by dweindl about 2 months ago - 2 comments

#334 - Add constants + I/O + validation for new conditions/experiments tables

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#333 - Sbml model enhancements

Pull Request - State: closed - Opened by fbergmann about 2 months ago - 1 comment

#332 - Support for petab v2 experiments

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#331 - Add `SbmlModel.from_antimony`

Pull Request - State: closed - Opened by dweindl about 2 months ago - 2 comments

#329 - Refactor priors

Pull Request - State: closed - Opened by dweindl about 2 months ago - 2 comments

#328 - Functions for adding conditions/observables/parameter to Problem

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#327 - Enable passing the base path to Problem.from_yaml

Pull Request - State: closed - Opened by dweindl about 2 months ago - 1 comment

#326 - Store problem configuration in Problem

Pull Request - State: closed - Opened by dweindl about 2 months ago - 3 comments

#325 - Bump codecov/codecov-action from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] about 2 months ago - 1 comment
Labels: dependencies

#324 - Path management

Issue - State: open - Opened by FFroehlich 2 months ago - 1 comment

#323 - fix error message for missing cols in mapping df

Pull Request - State: closed - Opened by FFroehlich 2 months ago - 1 comment

#322 - Bump codecov/codecov-action from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago - 1 comment
Labels: dependencies

#321 - Bump codecov/codecov-action from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 2 months ago
Labels: dependencies

#320 - Release 0.5.0

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#319 - Implement `Model.__repr__`

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#318 - Make model id optional for PySBModel

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#317 - Preserve column ordering in `priors_to_measurements`

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#316 - remove visualization df if invalid

Pull Request - State: closed - Opened by m-philipps 3 months ago - 1 comment

#315 - doc: add petab.v1.priors

Pull Request - State: closed - Opened by dweindl 3 months ago - 1 comment

#312 - Add functionality for computing posteriors

Issue - State: open - Opened by dweindl 4 months ago
Labels: enhancement

#311 - Refactor priors

Issue - State: open - Opened by dweindl 4 months ago
Labels: enhancement

#310 - Feature to automate handling of replicate data

Issue - State: open - Opened by egeissen 4 months ago - 1 comment

#309 - Function for replacing `objectivePrior*` by observables/measurements

Pull Request - State: closed - Opened by dweindl 4 months ago - 1 comment

#308 - PEtab lint requires indices

Issue - State: open - Opened by PaulJonasJost 4 months ago - 1 comment
Labels: question

#307 - Function for replacing `objectivePrior*` by observables/measurements

Issue - State: closed - Opened by dweindl 5 months ago
Labels: enhancement

#306 - Circumvent `SettingWithCopyWarning`

Pull Request - State: closed - Opened by m-philipps 5 months ago - 1 comment

#305 - PEtab Simulator update_parameters

Issue - State: open - Opened by PaulJonasJost 6 months ago
Labels: enhancement

#304 - Many `SettingWithCopyWarning`s during `plot_problem`

Issue - State: closed - Opened by dweindl 6 months ago

#303 - Add functions for setting series data types

Pull Request - State: open - Opened by dweindl 7 months ago - 1 comment

#302 - Add petab.v2.models

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#300 - Release v0.4.1

Pull Request - State: closed - Opened by dilpath 7 months ago - 1 comment

#299 - Add petab.v2.C

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#298 - Fix imports

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#297 - Implement `petab.*` deprecation with `__getattr__`

Pull Request - State: closed - Opened by dilpath 7 months ago - 3 comments

#296 - Remove obsolete flake8 files

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#295 - Release v0.4.0

Pull Request - State: closed - Opened by dilpath 7 months ago - 1 comment

#294 - Handle numpy types in sympify_petab

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#293 - Fix imports related to v1 subpackage

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#292 - Doc: fix formatting / missing type annotations

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#291 - v2: handle optional condition table

Issue - State: open - Opened by dweindl 7 months ago

#289 - v2 validation: atomize checks

Issue - State: open - Opened by dweindl 7 months ago

#288 - New validation API

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#287 - Fix validation for remote files

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#286 - Validation fails for remote files

Issue - State: closed - Opened by dweindl 7 months ago
Labels: bug

#285 - Add petab.v2.Problem

Pull Request - State: closed - Opened by dweindl 7 months ago - 2 comments

#284 - Separate v1 and v2 tests

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#283 - Fix SBML math parsing

Issue - State: open - Opened by dweindl 7 months ago
Labels: bug

#282 - Introduce petab.v1 package

Pull Request - State: closed - Opened by dweindl 7 months ago - 2 comments

#281 - PEtab v1 to v2 converter

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#280 - Refactor Problem.from_yaml, extract get_path_prefix

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#279 - Validator: check prior parameters

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#278 - Validator: check for positive bounds for log-scaled parameter

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#277 - Doc: versioning and deprecation policy

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#276 - Ruff pyupgrade: python3.10

Pull Request - State: closed - Opened by dweindl 7 months ago - 2 comments

#275 - setup.py -> pyproject.toml

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#274 - Deprecate petablint with individual tables

Pull Request - State: closed - Opened by dweindl 7 months ago - 1 comment

#273 - Integration of extensions

Issue - State: open - Opened by dweindl 7 months ago - 2 comments

#272 - Add converter for PEtab v1 problems to v2

Issue - State: closed - Opened by dweindl 7 months ago
Labels: enhancement

#271 - Library organization for petab v2

Issue - State: open - Opened by dweindl 7 months ago - 4 comments

#270 - Bump actions/setup-python from 4 to 5

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#269 - Bump codecov/codecov-action from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#268 - Bump actions/cache from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#267 - Bump actions/checkout from 3 to 4

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago
Labels: dependencies

#266 - Release 0.3.0

Pull Request - State: closed - Opened by dweindl 7 months ago

#265 - composite problem

Issue - State: open - Opened by MA-Kochen 8 months ago - 4 comments

#264 - Simplify yaml schema

Pull Request - State: closed - Opened by dweindl 8 months ago - 2 comments

#263 - Add support for experiments (previously named timecourses)

Pull Request - State: closed - Opened by dilpath 8 months ago - 2 comments

#262 - Drop an index if it's reset

Pull Request - State: closed - Opened by dilpath 8 months ago - 1 comment

#261 - Refactor sympification

Pull Request - State: closed - Opened by dweindl 9 months ago - 1 comment

#260 - Add PEtab math parser and sympy converter

Pull Request - State: closed - Opened by dweindl 9 months ago - 3 comments

#259 - Require positive bounds for log-scale parameters

Pull Request - State: closed - Opened by dweindl 9 months ago - 6 comments

#258 - Let dependabot update actions

Pull Request - State: closed - Opened by dweindl 9 months ago

#257 - fix typo

Pull Request - State: closed - Opened by m-philipps 9 months ago

#256 - Require python>=3.10

Pull Request - State: closed - Opened by dweindl 9 months ago - 1 comment

#255 - Validator: check datasetId in visualizations table exists in measurem…

Pull Request - State: closed - Opened by dweindl 10 months ago - 1 comment

#254 - Vis: Make line plot markers configurable

Pull Request - State: closed - Opened by dweindl 10 months ago - 2 comments