Release 0.1.15

Merge pull request #45 from PEtab-dev/release_0.11.15

Author: dweindl

.github/ISSUE_TEMPLATE/petab-specification-changes.md

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8]
+        python-version: [3.7, 3.8, 3.9]
 
     steps:
     - name: Check out repository

.github/workflows/ci_tests.yml

@@ -2,32 +2,49 @@
 
 ## 0.1 series
 
+### 0.1.15
+
+**NOTE:** The original PEtab format + petab package repository has been split
+up (PEtab-dev/libpetab-python#41). This repository now only contains the petab
+Python package. The PEtab specifications and related information are available
+at https://github.com/PEtab-dev/PEtab.
+
+* Improved `petab.flatten_timepoint_specific_output_overrides` (PEtab-dev/libpetab-python#42)
+* Validator: output message in case of successful check is added (PEtab-dev/PEtab#487)
+* Update how-to-cite (Closes PEtab-dev/PEtab#432) (PEtab-dev/PEtab#509)
+* Broadcast and mapping of scale and unscale functions (PEtab-dev/PEtab#505)
+* Update Python requirement (3.7.1) (PEtab-dev/PEtab#502)
+* Fix `petab.get_required_parameters_for_parameter_table`
+  (PEtab-dev/libpetab-python#43)
+* Fix `petab.measurement_table_has_timepoint_specific_mappings`
+  (PEtab-dev/libpetab-python#44)
+
 ### 0.1.14
 
-* Fix sampling of priors in `parameterScale` (#492)
+* Fix sampling of priors in `parameterScale` (PEtab-dev/PEtab#492)
 * Clarify documentation of `parameterScale` priors
-* Improvements in `petab.simulate` (#479):
+* Improvements in `petab.simulate` (PEtab-dev/PEtab#479):
   * Fix default noise distributions
   * Add option for non-negative synthetic data
 
 ### 0.1.13
 
 * Fix for pandas 1.2.0 -- use `get_handle` instead of `get_filepath_or_buffer`
-* Fix erroneous `petab_test_suite` symlink (all #493)
+* Fix erroneous `petab_test_suite` symlink (all PEtab-dev/PEtab#493)
 
 ### 0.1.12
 
 * Documentation update:
   * Added SBML2Julia to list of tools supporting PEtab
   * Extended PEtab introduction
   * Tutorial for creating PEtab files
-* Minor fix: Default argument for optional 'model' parameter in 
-  `petab.lint.check_condition_df`` (#477)
+* Minor fix: Default argument for optional 'model' parameter in
+  `petab.lint.check_condition_df`` (PEtab-dev/PEtab#477)
 
 ### 0.1.11
 
-* Function for generating synthetic data (#472)
-* Minor documentation updates (#470)
+* Function for generating synthetic data (PEtab-dev/PEtab#472)
+* Minor documentation updates (PEtab-dev/PEtab#470)
 
 ### 0.1.10
 
@@ -37,42 +54,42 @@
 
 Library:
 
-* Allow URL as filenames for YAML files and SBML models (Closes #187) (#459)
-* Allow model time in observable formulas (#445)
-* Make float parsing from CSV round-trip (#444)
-* Validator: Error message for missing IDs, with line numbers. (#467)
-* Validator: Detect duplicated observable IDs (#446)
+* Allow URL as filenames for YAML files and SBML models (Closes PEtab-dev/PEtab#187) (PEtab-dev/PEtab#459)
+* Allow model time in observable formulas (PEtab-dev/PEtab#445)
+* Make float parsing from CSV round-trip (PEtab-dev/PEtab#444)
+* Validator: Error message for missing IDs, with line numbers. (PEtab-dev/PEtab#467)
+* Validator: Detect duplicated observable IDs (PEtab-dev/PEtab#446)
 * Some documentation and CI fixes / updates
-* Visualization: Add option to save visualization specification (#457)
-* Visualization: Column XValue not mandatory anymore (#429)
+* Visualization: Add option to save visualization specification (PEtab-dev/PEtab#457)
+* Visualization: Column XValue not mandatory anymore (PEtab-dev/PEtab#429)
 * Visualization: Add sorting of indices of dataframes for the correct sorting
-  of x-values (#430)
-* Visualization: Default value for the column x_label in vis_spec (#431)
+  of x-values (PEtab-dev/PEtab#430)
+* Visualization: Default value for the column x_label in vis_spec (PEtab-dev/PEtab#431)
 
 
 ### 0.1.8
 
 Library:
 
-* Use ``core.is_empty`` to check for empty values (#434)
-* Move tests to python 3.8 (#435)
-* Update to libcombine 0.2.6 (#437)
-* Make float parsing from CSV round-trip (#444)
-* Lint: Allow model time in observable formulas (#445)
-* Lint: Detect duplicated observable ids (#446)
-* Fix likelihood calculation with missing values (#451)
+* Use ``core.is_empty`` to check for empty values (PEtab-dev/PEtab#434)
+* Move tests to python 3.8 (PEtab-dev/PEtab#435)
+* Update to libcombine 0.2.6 (PEtab-dev/PEtab#437)
+* Make float parsing from CSV round-trip (PEtab-dev/PEtab#444)
+* Lint: Allow model time in observable formulas (PEtab-dev/PEtab#445)
+* Lint: Detect duplicated observable ids (PEtab-dev/PEtab#446)
+* Fix likelihood calculation with missing values (PEtab-dev/PEtab#451)
 
 Documentation:
 
-* Move format documentation to restructuredtext format (#452)
-* Document all noise distributions and observable scales (#452)
-* Fix documentation for prior distribution (#449)
+* Move format documentation to restructuredtext format (PEtab-dev/PEtab#452)
+* Document all noise distributions and observable scales (PEtab-dev/PEtab#452)
+* Fix documentation for prior distribution (PEtab-dev/PEtab#449)
 
 Visualization:
 
-* Make XValue column non-mandatory (#429)
-* Apply correct condition sorting (#430)
-* Apply correct default x label (#431)
+* Make XValue column non-mandatory (PEtab-dev/PEtab#429)
+* Apply correct condition sorting (PEtab-dev/PEtab#430)
+* Apply correct default x label (PEtab-dev/PEtab#431)
 
 
 ### 0.1.7
@@ -87,43 +104,43 @@ Documentation:
 
 Library:
 
-* Fix handling of empty columns for residual calculation (#392)
-* Allow optional fixing of fixed parameters in parameter mapping (#399)
-* Fix function to flatten out time-point specific overrides (#404)
-* Add function to create a problem yaml file (#398)
-* Allow merging of multiple parameter files (#407)
+* Fix handling of empty columns for residual calculation (PEtab-dev/PEtab#392)
+* Allow optional fixing of fixed parameters in parameter mapping (PEtab-dev/PEtab#399)
+* Fix function to flatten out time-point specific overrides (PEtab-dev/PEtab#404)
+* Add function to create a problem yaml file (PEtab-dev/PEtab#398)
+* Allow merging of multiple parameter files (PEtab-dev/PEtab#407)
 
 Documentation:
 
 * In README, add to the overview table the coverage for the supporting tools,
   and links and usage examples (various commits)
-* Show REAMDE on readthedocs documentation front page (#400)
-* Correct description of observable and noise formulas (#401)
-* Update documentation on optional visualization values (#405, #419)
+* Show REAMDE on readthedocs documentation front page (PEtab-dev/PEtab#400)
+* Correct description of observable and noise formulas (PEtab-dev/PEtab#401)
+* Update documentation on optional visualization values (PEtab-dev/PEtab#405, PEtab-dev/PEtab#419)
 
 Visualization:
 
-* Fix sorting problem (#396)
-* More generously handle optional values (#405, #419)
-* Create dataset id also for simulation dataframe (#408)
-* Extend test suite for visualization (#418)
+* Fix sorting problem (PEtab-dev/PEtab#396)
+* More generously handle optional values (PEtab-dev/PEtab#405, PEtab-dev/PEtab#419)
+* Create dataset id also for simulation dataframe (PEtab-dev/PEtab#408)
+* Extend test suite for visualization (PEtab-dev/PEtab#418)
 
 
 ### 0.1.5
 
 Library:
 
-* New create empty observable function (issue 386) (#387)
-* Deprecate petab.sbml.globalize_parameters (#381)
-* Fix computing log10 likelihood (#380)
-* Documentation update and typehints for visualization  (#372)
+* New create empty observable function (issue 386) (PEtab-dev/PEtab#387)
+* Deprecate petab.sbml.globalize_parameters (PEtab-dev/PEtab#381)
+* Fix computing log10 likelihood (PEtab-dev/PEtab#380)
+* Documentation update and typehints for visualization  (PEtab-dev/PEtab#372)
 * Ordered result of `petab.get_output_parameters`
 * Fix missing argument to parameters.create_parameter_df
 
 Documentation:
 * Add overview of supported PEtab feature in toolboxes
 * Add contribution guide
-* Fix optional values in documentation (#378)
+* Fix optional values in documentation (PEtab-dev/PEtab#378)
 
 
 ### 0.1.4
@@ -151,44 +168,44 @@ Library:
 File format:
 
 * Updated documentation
-* Observables table in YAML file now mandatory in schema (was implicitly 
+* Observables table in YAML file now mandatory in schema (was implicitly
   mandatory before, as observable table was required already)
 
 Library:
 * petablint:
-  * Fix: allow specifying observables file via CLI (Closes #302)
-  * Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes #303)
-  * Fix: handle undefined observables more gracefully (Closes #300) (#351)
-* Parameter mapping: 
-  * Fix / refactor parameter mapping (breaking change) (#344)
+  * Fix: allow specifying observables file via CLI (Closes PEtab-dev/PEtab#302)
+  * Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes PEtab-dev/PEtab#303)
+  * Fix: handle undefined observables more gracefully (Closes PEtab-dev/PEtab#300) (PEtab-dev/PEtab#351)
+* Parameter mapping:
+  * Fix / refactor parameter mapping (breaking change) (PEtab-dev/PEtab#344)
     (now performing parameter value and scale mapping together)
-  * check optional measurement cols in mapping (#350)
-* allow calculating llhs (#349), chi2 values (#348) and residuals (#345)
+  * check optional measurement cols in mapping (PEtab-dev/PEtab#350)
+* allow calculating llhs (PEtab-dev/PEtab#349), chi2 values (PEtab-dev/PEtab#348) and residuals (PEtab-dev/PEtab#345)
 * Visualization
-  * Basic Scatterplots & lot of bar plot fixes (#270)
-  * Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas 
-    (Closes #322)
-* make libcombine optional (#338)
+  * Basic Scatterplots & lot of bar plot fixes (PEtab-dev/PEtab#270)
+  * Fix incorrect length of bool `bool_preequ` when subsetting with ind_meas
+    (Closes PEtab-dev/PEtab#322)
+* make libcombine optional (PEtab-dev/PEtab#338)
 
 
 ### 0.1.2
 
 Library:
 
-* Extensions and fixes for the visualization functions (#255, #262)
-* Allow to extract fixed|free and scaled|non-scaled parameters (#256, #268, #273)
-* Various fixes (esp. #264)
-* Add function to get observable ids (#269)
-* Improve documentation (esp. #289)
+* Extensions and fixes for the visualization functions (PEtab-dev/PEtab#255, PEtab-dev/PEtab#262)
+* Allow to extract fixed|free and scaled|non-scaled parameters (PEtab-dev/PEtab#256, PEtab-dev/PEtab#268, PEtab-dev/PEtab#273)
+* Various fixes (esp. PEtab-dev/PEtab#264)
+* Add function to get observable ids (PEtab-dev/PEtab#269)
+* Improve documentation (esp. PEtab-dev/PEtab#289)
 * Set default column for simulation results to 'simulation'
-* Add support for COMBINE archives (#271)
+* Add support for COMBINE archives (PEtab-dev/PEtab#271)
 * Fix sbml observables to table
-* Improve prior and dataframe tests (#285, #286, #297)
-* Add function to get parameter table with all default values (#288)
-* Move tests to github actions (#281)
+* Improve prior and dataframe tests (PEtab-dev/PEtab#285, PEtab-dev/PEtab#286, PEtab-dev/PEtab#297)
+* Add function to get parameter table with all default values (PEtab-dev/PEtab#288)
+* Move tests to github actions (PEtab-dev/PEtab#281)
 * Check for valid identifiers
 * Fix handling of empty values in dataframes
-* Allow to get numeric values in parameter mappings in scaled form (#308)
+* Allow to get numeric values in parameter mappings in scaled form (PEtab-dev/PEtab#308)
 
 ### 0.1.1
 
@@ -199,18 +216,18 @@ Library:
 * Let get_placeholders return an (ordered) list of placeholders
 * Deprecate `petab.problem.from_folder` and related functions
   (obsolete after introducing more flexible YAML files for grouping tables
-  and models) 
+  and models)
 
 ### 0.1.0
 
 Data format:
 
 * Introduce observables table instead of SBML assignment rules for defining
-  observation model (#244) (moves observableTransformation and noiseModel
+  observation model (PEtab-dev/PEtab#244) (moves observableTransformation and noiseModel
   from the measurement table to the observables table)
-* Allow initial concentrations / sizes in condition table (#238)
+* Allow initial concentrations / sizes in condition table (PEtab-dev/PEtab#238)
 * Fixes and clarifications in the format documentation
-* Changes in prior columns of the parameter table (#222)
+* Changes in prior columns of the parameter table (PEtab-dev/PEtab#222)
 * Introduced separate version number of file format, this release being
   version 1
 
@@ -221,9 +238,9 @@ Library:
 * Parameter mapping changed to include all model parameters and not only
   those differing from the ones defined inside the SBML model
 * Introduced constants for all field names and string options, replacing
-  most string literals in the code (#228)
+  most string literals in the code (PEtab-dev/PEtab#228)
 * Added unit tests and additional format validation steps
-* Optional parallelization of parameter mapping (#205)
+* Optional parallelization of parameter mapping (PEtab-dev/PEtab#205)
 * Extended documentation (in-source and example Jupyter notebooks)
 
 ### 0.0.2
@@ -237,13 +254,13 @@ Bugfix release
 
 Data format:
 * Update format and documentation with respect to data and parameter scales
-  (#169)
+  (PEtab-dev/PEtab#169)
 * Define YAML schema for grouping PEtab files, also allowing for more complex
-  combinations of files (#183)
+  combinations of files (PEtab-dev/PEtab#183)
 
 Library:
 * Refactor library. Reorganize `petab.core` functions.
-* Fix visualization w/o condition names #142
+* Fix visualization w/o condition names PEtab-dev/PEtab#142
 * Extend validator
 * Removed deprecated functions petab.Problem.get_constant_parameters
   and petab.sbml.constant_species_to_parameters
@@ -258,21 +275,21 @@ Data format: *No changes*
 Library:
 * Extended visualization support
 * Add helper function and test case to deal with timepoint-specific parameters
-  flatten_timepoint_specific_output_overrides (#128) (Closes #125)
-* Fix get_noise_distributions: so far we got 'normal' everywhere due to 
-  wrong grouping (#147)
-* Fix create_parameter_df: Exclude rule targets (#149)
+  flatten_timepoint_specific_output_overrides (PEtab-dev/PEtab#128) (Closes PEtab-dev/PEtab#125)
+* Fix get_noise_distributions: so far we got 'normal' everywhere due to
+  wrong grouping (PEtab-dev/PEtab#147)
+* Fix create_parameter_df: Exclude rule targets (PEtab-dev/PEtab#149)
 * Verify condition table column names occur as model parameters
-  (Closes #150) (#151)
+  (Closes PEtab-dev/PEtab#150) (PEtab-dev/PEtab#151)
 * More informative error messages in case of wrongly set observable and
-  noise parameters (Closes #118) (#155)
-* Update doc for copasi import and github installation (#158) 
+  noise parameters (Closes PEtab-dev/PEtab#118) (PEtab-dev/PEtab#155)
+* Update doc for copasi import and github installation (PEtab-dev/PEtab#158)
 * Extend validator to check if all required parameters are present in
-  parameter table (Closes #43) (#159)
-* Setup documentation for RTD (#161)
-* Handle None in petab.core.split_parameter_replacement_list (Closes #121) 
+  parameter table (Closes PEtab-dev/PEtab#43) (PEtab-dev/PEtab#159)
+* Setup documentation for RTD (PEtab-dev/PEtab#161)
+* Handle None in petab.core.split_parameter_replacement_list (Closes PEtab-dev/PEtab#121)
 * Fix(lint) correct handling of optional columns. Check before access.
-* Remove obsolete generate_experiment_id.py (Closes #111) #166 
+* Remove obsolete generate_experiment_id.py (Closes PEtab-dev/PEtab#111) PEtab-dev/PEtab#166
 
 ### 0.0.0a16 and earlier