Fix AMICI hiding all warnings #2243
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Previously, importing amici would result in all warnings of the program being hidden, due to `logging.captureWarnings(True)`:
```sh
$ python -c "import warnings; warnings.warn('bla');"
<string>:1: UserWarning: bla
$ python -c "import amici; import warnings; warnings.warn('bla');"
$
```
This can't be the desired default.
Changes:
* Default to not capturing warnings
* If warnings are to be captured, at least handle them by amici loggers
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## develop #2243 +/- ##
===========================================
- Coverage 76.64% 76.63% -0.02%
===========================================
Files 91 91
Lines 15112 15005 -107
===========================================
- Hits 11583 11499 -84
+ Misses 3529 3506 -23
Flags with carried forward coverage won't be shown. Click here to find out more.
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FFroehlich
approved these changes
Dec 18, 2023
dweindl
added a commit
to dweindl/AMICI
that referenced
this pull request
Dec 18, 2023
Previously, importing amici would result in all warnings of the program being hidden, due to `logging.captureWarnings(True)`:
```sh
$ python -c "import warnings; warnings.warn('bla');"
<string>:1: UserWarning: bla
$ python -c "import amici; import warnings; warnings.warn('bla');"
$
```
This can't be the desired default.
Changes:
* Default to not capturing warnings
* If warnings are to be captured, at least handle them by amici loggers
Closes ICB-DCM/pyPESTO#1252
dweindl
added a commit
that referenced
this pull request
Dec 18, 2023
Improves model code generation by collapsing cases with identical statements. I.e. ``` switch(a) case b: case c: statements; break; ``` instead of ``` switch(a) case b: statements; break; case c: statements; break; ``` For my current model of interest, containing many events, this significantly reduces the generated code: E.g.: ``` 16K my_model/deltasx.cpp 6,6M my_model_old/deltasx.cpp ``` Overall, for this model, I got from 204201 LOC down to 7936 LOC (i.e. -96%). * .. * Apply suggestions from code review Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com> * GHA: test python3.12 (#2179) Run nightly tests also on python3.12 * Deterministic order of event assignments (#2242) Ensure event assignments targets are processed in deterministic order. Otherwise the ordering of state variables may change between subsequent model imports, which we'd like to avoid. Closes #2241. * Fix AMICI hiding all warnings (#2243) Previously, importing amici would result in all warnings of the program being hidden, due to `logging.captureWarnings(True)`: ```sh $ python -c "import warnings; warnings.warn('bla');" <string>:1: UserWarning: bla $ python -c "import amici; import warnings; warnings.warn('bla');" $ ``` This can't be the desired default. Changes: * Default to not capturing warnings * If warnings are to be captured, at least handle them by amici loggers Closes ICB-DCM/pyPESTO#1252 --------- Co-authored-by: Dilan Pathirana <59329744+dilpath@users.noreply.github.com>
dweindl
added a commit
to dweindl/AMICI
that referenced
this pull request
Jan 16, 2024
Fixes a "unused parameters" warning when using simulate_petab with default parameters. By default, fixed parameters are hard-coded during parameter mapping, and thus, must not be passed to `fill_in_edatas` later on. This warning was swallowed until recently (AMICI-dev#2243).
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Previously, importing amici would result in all warnings of the program being hidden, due to
logging.captureWarnings(True):This can't be the desired default.
Changes:
Closes ICB-DCM/pyPESTO#1252