Release 0.1.2 #311

yannikschaelte · 2020-02-20T09:47:21Z

Extensions and fixes for the visualization functions (Barplot uniform coloring & yScale=log fix #196 #255, Visu callobs par #262)
Allow to extract fixed|free and scaled|non-scaled parameters (allow to extract only estimate parameters #256, Add properties for fixed/free and scaled values #268, Add functions to get all of fixed|free, scaled parameter values #273)
Various fixes (esp. petablint fails with only numeric entries in noiseFormula in observable table #264)
Add function to get observable ids (Observables function #269)
Improve documentation (esp. Fix format documentation regarding parameter scale #289)
Set default column for simulation results to 'simulation'
Add support for COMBINE archives (PEtab COMBINE archive #271)
Fix sbml observables to table
Improve prior and dataframe tests (Prior tests #285, Fix prior scales #286, Add tests for petab.measurements.get_simulation_conditions #297)
Add function to get parameter table with all default values (Feature defaultvalues #288)
Move tests to github actions (GitHub actions #281)
Check for valid identifiers
Fix handling of empty values in dataframes
Allow to get numeric values in parameter mappings in scaled form (Scaled mappings #308)

* resolves #197 * small fix * change all barplot colors to blue

* allow to extract only estimate parameters * add docstrings

* fix #261 * corrected flake8 error - line too long * deleted white space * add F403 to falke8 tests

…ixes #264)

* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>

* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <[email protected]> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 Co-authored-by: Daniel Weindl <[email protected]>

* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <[email protected]> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 * fix typo * streamline fixed|free|all, and scaled values * fix default args * fix codacy * address reviewer comment: return empty list * add docstring# * add more docstrings * fix var type error * address reviewer comments Co-authored-by: Daniel Weindl <[email protected]>

* Add create_combine_archive for generation of COMBINE archives * Add support for reading PEtab COMBINE archives * Add tests for COMBINE archive r/w

* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <[email protected]> * add get_observables function * add observables test; use observables file in petab test * fix typo * move get_observables to ..._ids * remove unused arg * add docstring * fix lint * fix pylint * fix flake8 * fix typo * streamline fixed|free|all, and scaled values * fix default args * fix codacy * address reviewer comment: return empty list * add docstring# * add more docstrings * fix var type error * address reviewer comments * add parameter properties test * add tests for get/write_parameter_df * add measurements tests * add conditions tests * fix conditions create function * add parameter tests * add observables tests * fixup * add docstrings * address reviewer comments * random edit to see if codacy is happy * random stuff to annoy codecov Co-authored-by: Daniel Weindl <[email protected]>

* add test for valid prior parameters * add raising test * fix codacy * random edit to make codacy happy * address reviewer comments

* add test for valid prior parameters * add raising test * cont * fix codacy * fix errors in get_priors_from_df: wrong default scaling and empty values * random edit to make codacy happy * fix merge error * make codacy happy

* init parameter df normalization function * cont * add normalize_parameter_df function * make other dfs optional in check_parameter_df * fixup normalize_parameter_df * add test for normalize_parameter_df; rename test_parameter.py -> test_parameters.py * address reviewer comments and make codacy happy

* Github actions for CI and deployment * Updated links after repository move Co-authored-by: Daniel Weindl <[email protected]>

get_condition_df, get_measurement_df, get_observable_df, get_parameter_df are generalized a bit (#296)

* Add tests for petab.measurements.get_simulation_conditions * Apply suggestions from code review Co-authored-by: Yannik Schälte <[email protected]>

Rows with NaNs in grouped-by columns are dropped. This is generally not what we want.

This reverts commit 95a0f95.

* Fix handling of NaNs in pandas.DataFrame.groupby Rows with NaNs in grouped-by columns are dropped. This is generally not what we want.

* require newer pandas * allow scaled parameter mappings * add test * fix copy error * add scaling to problem function * address reviewer comments

codecov · 2020-02-20T09:48:08Z

Codecov Report

Merging #311 into master will increase coverage by 5.11%.
The diff coverage is 82.33%.

@@            Coverage Diff             @@
##           master     #311      +/-   ##
==========================================
+ Coverage   71.52%   76.63%   +5.11%     
==========================================
  Files          22       22              
  Lines        1661     1849     +188     
  Branches      361      411      +50     
==========================================
+ Hits         1188     1417     +229     
+ Misses        395      329      -66     
- Partials       78      103      +25

Impacted Files	Coverage Δ
petab/visualize/plot_data_and_simulation.py	`69.64% <ø> (ø)`	⬆️
petab/visualize/helper_functions.py	`89.47% <0%> (-0.53%)`	⬇️
petab/migrations.py	`0% <0%> (ø)`	⬆️
petab/version.py	`100% <100%> (ø)`	⬆️
petab/yaml.py	`86.04% <100%> (+1.04%)`	⬆️
petab/C.py	`100% <100%> (ø)`	⬆️
petab/visualize/plotting_config.py	`58.82% <66.66%> (-0.27%)`	⬇️
petab/conditions.py	`90.47% <73.33%> (+35.93%)`	⬆️
petab/observables.py	`93.75% <75%> (+64.71%)`	⬆️
petab/lint.py	`74.19% <78.04%> (+0.5%)`	⬆️
... and 12 more

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 8a4461c...8104059. Read the comment docs.

* update changelog * fixup * Pylint ignore external packages * make codacy happy * make codacy even happier * FIX * test * test Co-authored-by: Daniel Weindl <[email protected]>

dweindl · 2020-02-20T10:22:39Z

tests/test_combine.py

@@ -0,0 +1,95 @@
+"""Test COMBINE archive"""


Issue found: Similar lines in 3 files

MerktSimon and others added 27 commits February 6, 2020 10:36

Barplot uniform coloring & yScale=log fix #196 (#255)

fd48e95

* resolves #197 * small fix * change all barplot colors to blue

allow to extract only estimate parameters (#256)

03ff27b

* allow to extract only estimate parameters * add docstrings

Visu callobs par (#262)

18317ba

* fix #261 * corrected flake8 error - line too long * deleted white space * add F403 to falke8 tests

Fix handling of numeric observable/noiseFormula in observable table (F…

30d817d

…ixes #264)

Add properties for fixed/free and scaled values (#268)

f766a50

* allow to extract only estimate parameters * add docstrings * return scaled versions of arrays * Update petab/problem.py Co-Authored-By: Daniel Weindl <[email protected]> Co-authored-by: Daniel Weindl <[email protected]>

Fix documentation hierarchy

2387ef9

Default column to look for simulation results should be 'simulation'

dde9b08

PEtab COMBINE archives (#271)

b4137bd

* Add create_combine_archive for generation of COMBINE archives * Add support for reading PEtab COMBINE archives * Add tests for COMBINE archive r/w

Fix sbml_observables_to_table - got broken in eb5453

c091cb2

Prior tests (#285)

85bd1b2

* add test for valid prior parameters * add raising test * fix codacy * random edit to make codacy happy * address reviewer comments

Fix prior scales (#286)

f302cab

* add test for valid prior parameters * add raising test * cont * fix codacy * fix errors in get_priors_from_df: wrong default scaling and empty values * random edit to make codacy happy * fix merge error * make codacy happy

GitHub actions (#281)

023f19e

* Github actions for CI and deployment * Updated links after repository move Co-authored-by: Daniel Weindl <[email protected]>

Fix format documentation regarding parameter scale (#289)

1dc87d9

Validator: Check for valid identifiers (Closes #291)

0ecf097

Generalization of get functions for PEtab data frames (#296 )

581492d

get_condition_df, get_measurement_df, get_observable_df, get_parameter_df are generalized a bit (#296)

Add tests for petab.measurements.get_simulation_conditions (#297)

c1e7d66

* Add tests for petab.measurements.get_simulation_conditions * Apply suggestions from code review Co-authored-by: Yannik Schälte <[email protected]>

Fix handling of NaNs in pandas.DataFrame.groupby

95a0f95

Rows with NaNs in grouped-by columns are dropped. This is generally not what we want.

Revert "Fix handling of NaNs in pandas.DataFrame.groupby"

7cda4f3

This reverts commit 95a0f95.

Validator: Observable ID must not shadow model entities (Closes #292)

1a7202c

Function-level import for libcombine

37575c6

Fix handling of NaNs in pandas.DataFrame.groupby (#298)

6b4cc08

* Fix handling of NaNs in pandas.DataFrame.groupby Rows with NaNs in grouped-by columns are dropped. This is generally not what we want.

require newer pandas (#299)

7a8a575

Scaled mappings (#308)

ae1aa35

* require newer pandas * allow scaled parameter mappings * add test * fix copy error * add scaling to problem function * address reviewer comments

prepare release 0.1.2 (#310)

8104059

* update changelog * fixup * Pylint ignore external packages * make codacy happy * make codacy even happier * FIX * test * test Co-authored-by: Daniel Weindl <[email protected]>

yannikschaelte requested a review from dweindl February 20, 2020 10:22

yannikschaelte self-assigned this Feb 20, 2020

dweindl reviewed Feb 20, 2020

View reviewed changes

tests/test_combine.py

@@ -0,0 +1,95 @@

"""Test COMBINE archive"""

Copy link

Member

dweindl Feb 20, 2020

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Issue found: Similar lines in 3 files

dweindl self-requested a review February 20, 2020 10:30

dweindl approved these changes Feb 20, 2020

View reviewed changes

yannikschaelte merged commit 8b03c8f into master Feb 20, 2020

yannikschaelte mentioned this pull request Feb 20, 2020

Cleanup PEtab documentation: Extension vs Optional fields #184

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Release 0.1.2 #311

Release 0.1.2 #311

yannikschaelte commented Feb 20, 2020 •

edited

Loading

codecov bot commented Feb 20, 2020 •

edited

Loading

dweindl Feb 20, 2020

Release 0.1.2 #311

Release 0.1.2 #311

Conversation

yannikschaelte commented Feb 20, 2020 • edited Loading

codecov bot commented Feb 20, 2020 • edited Loading

Codecov Report

dweindl Feb 20, 2020

Choose a reason for hiding this comment

yannikschaelte commented Feb 20, 2020 •

edited

Loading

codecov bot commented Feb 20, 2020 •

edited

Loading