pharmpy/pharmpy issues and pull requests

#2896 - Improve testing of tools

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

#2895 - Get 100% coverage for the model class modules

Issue - State: closed - Opened by rikardn 7 months ago - 2 comments

#2894 - Get 100% coverage for the basic module

Issue - State: closed - Opened by rikardn 7 months ago

#2893 - Get 100% test coverage of the tests themselves

Issue - State: closed - Opened by rikardn 7 months ago

#2892 - Change simulation path

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

#2891 - docutils 0.21.1 cannot be used with Pharmpy

Issue - State: closed - Opened by rikardn 7 months ago - 2 comments
Labels: dependencies

#2890 - Bump pyright from 1.1.357 to 1.1.358

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

#2889 - Bump pandas from 2.2.1 to 2.2.2

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

#2888 - Bump docutils from 0.20.1 to 0.21.1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 2 comments
Labels: dependencies

#2887 - Avoid labeling IOV effects as covariate

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

#2886 - Rename SAEMOBJ to OBJ in ext file

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

#2885 - Parse SAEM OFV

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

#2884 - Clearer NONMEM config error messages

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

#2883 - Change path for simulation tool in amd

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

#2882 - Move all_models outside of if statement

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

#2881 - Add adaptive scope reduction to covsearch

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

#2880 - Add option to limit number of maximum evaluations in covsearch

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

#2879 - Alternative location of config file for Windows

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

#2878 - Add modeling function to round numbers

Issue - State: open - Opened by stellabelin 7 months ago
Labels: enhancement

#2877 - Bump docutils from 0.20.1 to 0.21.post1

Pull Request - State: closed - Opened by dependabot[bot] 7 months ago - 2 comments
Labels: dependencies

#2876 - Bump filelock from 3.13.3 to 3.13.4

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

#2875 - Raise proper error if config file is incorrect

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

#2874 - Remove all config-options in model and modeling

Issue - State: open - Opened by stellabelin 7 months ago - 1 comment

#2873 - Bump execnet from 2.1.0 to 2.1.1

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

#2872 - New Context (ToolDatabase) and ModelDatabase design

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

#2871 - Update AMD TMDD documentation

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

#2870 - Initiate empty MFL object if argument is None (fix #2838)

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

#2869 - Apply strictness in each step in bottom_up_stepwise IIVSearch

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

#2868 - Correct extraction of redundant K-rate individual parameters

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

#2867 - Change peripherals to tuple

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

#2866 - Bump typing-extensions from 4.10.0 to 4.11.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2865 - Bump networkx from 3.2.1 to 3.3

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2864 - Bump parso from 0.8.3 to 0.8.4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2863 - Bump execnet from 2.0.2 to 2.1.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2862 - Fix failing RxODE conversion without ODE system

Pull Request - State: closed - Opened by JohanWBorg 8 months ago

#2861 - Remove IPREDADJ when going to an additive error model

Issue - State: open - Opened by stellabelin 8 months ago

#2860 - Bump nbformat from 5.10.3 to 5.10.4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2859 - Bump distributed from 2024.4.0 to 2024.4.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 2 comments
Labels: dependencies

#2858 - Bump dask from 2024.4.0 to 2024.4.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#2857 - Bump pyright from 1.1.356 to 1.1.357

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2856 - Fonts incorrectly displayed in svg diagram in documentation

Issue - State: open - Opened by stellabelin 8 months ago
Labels: docs

#2855 - Add SIR as parameter uncertainty method

Issue - State: open - Opened by stellabelin 8 months ago

#2854 - Add Bootstrap as parameter uncertainty method

Issue - State: open - Opened by stellabelin 8 months ago - 1 comment

#2853 - Split API reference into two pages for Python and R

Issue - State: open - Opened by stellabelin 8 months ago
Labels: docs

#2852 - Add tutorials in modeling user guide

Issue - State: open - Opened by stellabelin 8 months ago
Labels: docs

#2851 - Bump scipy from 1.12.0 to 1.13.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2850 - Bump lxml from 5.2.0 to 5.2.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2849 - Bump keyring from 25.0.0 to 25.1.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2848 - Bump numexpr from 2.9.0 to 2.10.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2847 - Bump dask from 2024.3.1 to 2024.4.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#2846 - Bump distributed from 2024.3.1 to 2024.4.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#2845 - Bump pycparser from 2.21 to 2.22

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2844 - Bump lxml from 5.1.0 to 5.2.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2843 - Bump altair from 5.2.0 to 5.3.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2842 - Bump ipython from 8.22.2 to 8.23.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2841 - Bump jaraco-classes from 3.3.1 to 3.4.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2840 - Bump build from 1.2.0 to 1.2.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2839 - Fix allometry issue for PKPD models

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

#2838 - Bug in AMD for PKPD models

Issue - State: closed - Opened by antoniaih 8 months ago
Labels: bug

#2837 - Fix dataset filtering ruvsearch

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

#2836 - Bump ipykernel from 6.29.3 to 6.29.4

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2835 - Bump build from 1.1.1 to 1.2.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2834 - Bump pyright from 1.1.355 to 1.1.356

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2833 - validate kwargs in model.replace (fix #2824)

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

#2832 - PKPD ruv_search

Issue - State: closed - Opened by Orwa-bit 8 months ago - 2 comments

#2831 - Fix failing nlmixr error model test

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

#2830 - Update AMD PKPD documentation with removed structural covariates

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

#2829 - Filter dataset for tmdd models with dv_types

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

#2828 - IIV_RUV included in the iivsearch when running the amd tool with strategy "RSI"

Issue - State: open - Opened by schaedeli 8 months ago - 3 comments

#2827 - Bump nh3 from 0.2.15 to 0.2.17

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2826 - Expand logic for covariate effect extraction

Pull Request - State: closed - Opened by JohanWBorg 8 months ago

#2825 - FREM post processing crash if no ext-file for input model

Issue - State: open - Opened by rikardn 8 months ago
Labels: bug

#2824 - Validate kwargs in replace methods

Issue - State: closed - Opened by stellabelin 8 months ago

#2823 - Bump filelock from 3.13.1 to 3.13.3

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2822 - Remove structural covariates from amd for pkpd models

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

#2821 - PKPD ruv_search: the RUV is estimated for PK in the final PKPD model

Issue - State: closed - Opened by Orwa-bit 8 months ago - 2 comments

#2820 - PKPD iiv_search: Covariances are tested between PK IIVs and PD IIVs

Issue - State: closed - Opened by Orwa-bit 8 months ago - 2 comments

#2819 - PKPD models are not being generated in Pharmr-v0.108.0 using run_amd

Issue - State: closed - Opened by Orwa-bit 8 months ago - 1 comment

#2818 - TMDD is not generating all models for 2 types of DVs

Issue - State: open - Opened by Orwa-bit 8 months ago - 6 comments

#2817 - Bump keyring from 24.3.1 to 25.0.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2816 - Bump tox from 4.14.1 to 4.14.2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2815 - Modelsearch fails for zero transits

Issue - State: open - Opened by antoniaih 8 months ago - 2 comments

#2814 - Update covsearch and amd documentation

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

#2813 - Bump nbconvert from 7.16.2 to 7.16.3

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2812 - Allow list of lists of parameters in iovsearch (#2807)

Pull Request - State: closed - Opened by antoniaih 8 months ago

#2811 - Add method ModelFeatures.replace_features

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

#2810 - Remove hardcoding of DVID column name

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

#2809 - Implement get_individual_parameters within get_rv_parameters

Pull Request - State: closed - Opened by JohanWBorg 8 months ago

#2808 - Allow adding IOV on parameters without IIV

Issue - State: open - Opened by stellabelin 8 months ago
Labels: bug

#2807 - Support list of distributions in IOVSearch

Issue - State: closed - Opened by stellabelin 8 months ago - 2 comments
Labels: bug

#2806 - Bump importlib-metadata from 7.0.2 to 7.1.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2805 - Bump pyright from 1.1.354 to 1.1.355

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2804 - Correct drug metabolite description

Pull Request - State: closed - Opened by JohanWBorg 8 months ago

#2803 - Parent - Metabolite modeling v0.108

Issue - State: open - Opened by SylvieRetout 8 months ago - 1 comment

#2802 - Bump pytest-asyncio from 0.23.5.post1 to 0.23.6

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2801 - Add info to dv_types for TMDD

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

#2800 - Add documentation to vpc plot and add path to simulation type

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

#2799 - Implement a way to store dataset operations in Pharmpy

Issue - State: closed - Opened by antoniaih 8 months ago - 1 comment

#2798 - Bump fsspec from 2024.3.0 to 2024.3.1

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#2797 - Add VPC plot to AMD results report

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

GitHub / pharmpy/pharmpy issues and pull requests