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Feature misc jv #547

Merged
merged 6 commits into from
Jan 14, 2021
Merged

Feature misc jv #547

merged 6 commits into from
Jan 14, 2021

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jvanhoefer
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  • Fixes the broken sampling via the new PEtab release
  • Adds installation advice for all optimizers
  • Checks if fides is installed and throws a meaningful error message...

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codecov-io commented Jan 13, 2021

Codecov Report

Merging #547 (b86019a) into develop (24f3ce3) will decrease coverage by 3.71%.
The diff coverage is 50.00%.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop     #547      +/-   ##
===========================================
- Coverage    90.91%   87.19%   -3.72%     
===========================================
  Files           69       69              
  Lines         4403     4405       +2     
===========================================
- Hits          4003     3841     -162     
- Misses         400      564     +164     
Impacted Files Coverage Δ
pypesto/optimize/optimizer.py 90.61% <50.00%> (-0.22%) ⬇️
pypesto/petab/pysb_importer.py 0.00% <0.00%> (-100.00%) ⬇️
pypesto/prediction/amici_predictor.py 14.08% <0.00%> (-83.10%) ⬇️
pypesto/prediction/prediction.py 22.50% <0.00%> (-72.50%) ⬇️
pypesto/startpoint/util.py 50.00% <0.00%> (-35.00%) ⬇️
pypesto/objective/amici_util.py 75.89% <0.00%> (-8.93%) ⬇️
pypesto/engine/multi_process.py 84.61% <0.00%> (-7.70%) ⬇️
pypesto/petab/importer.py 76.64% <0.00%> (-5.11%) ⬇️
pypesto/objective/amici_calculator.py 90.00% <0.00%> (-3.34%) ⬇️
pypesto/objective/amici.py 90.96% <0.00%> (-0.61%) ⬇️
... and 1 more

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pypesto/optimize/optimizer.py Outdated Show resolved Hide resolved
pypesto/optimize/optimizer.py Outdated Show resolved Hide resolved
@@ -577,7 +579,9 @@ def minimize(
ub = problem.ub
if pyswarm is None:
raise ImportError(
"This optimizer requires an installation of pyswarm.")
"This optimizer requires an installation of pyswarm.You can "
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Suggested change
"This optimizer requires an installation of pyswarm.You can "
"This optimizer requires an installation of pyswarm. You can "

@@ -641,7 +645,9 @@ def minimize(

if cma is None:
raise ImportError(
"This optimizer requires an installation of cma.")
"This optimizer requires an installation of cma. You can "
"install cma via pip install cma."
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Suggested change
"install cma via pip install cma."
"install cma via `pip install cma`."

pypesto/optimize/optimizer.py Outdated Show resolved Hide resolved
jvanhoefer and others added 4 commits January 14, 2021 08:52
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
Co-authored-by: Yannik Schälte <31767307+yannikschaelte@users.noreply.github.com>
@jvanhoefer jvanhoefer merged commit df705ce into develop Jan 14, 2021
@yannikschaelte yannikschaelte mentioned this pull request Jan 19, 2021
@jvanhoefer jvanhoefer deleted the feature_misc_jv branch January 27, 2021 09:36
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4 participants