GHA: test python3.12 #2179

dweindl · 2023-10-18T15:06:33Z

Run nightly tests also on python3.12

Waiting for

Remove setuptools<64 restriction #2180
sympy 1.12.1 / 1.13.0

codecov · 2023-10-18T15:27:02Z

Codecov Report

Merging #2179 (00aae73) into develop (594b07e) will increase coverage by 0.00%.
The diff coverage is n/a.

Additional details and impacted files

@@            Coverage Diff            @@
##           develop    #2179    +/-   ##
=========================================
  Coverage    76.64%   76.65%            
=========================================
  Files           91       91            
  Lines        15112    14998   -114     
=========================================
- Hits         11583    11497    -86     
+ Misses        3529     3501    -28

Flag	Coverage Δ
cpp	`73.11% <ø> (ø)`
cpp_python	`37.08% <ø> (ø)`
petab	`53.74% <ø> (-0.04%)`	⬇️
python	`78.00% <ø> (+0.55%)`	⬆️
sbmlsuite	`?`

Flags with carried forward coverage won't be shown. Click here to find out more.

see 8 files with indirect coverage changes

dweindl · 2023-10-18T18:13:54Z

@FFroehlich Can you please rebase https://github.com/FFroehlich/pysb/tree/fix_pattern_matching onto the latest pysb? In the current state it's not installable with python3.12.

Details

https://github.com/AMICI-dev/AMICI/actions/runs/6564520748/job/17831043835:

Collecting git+https://github.com/FFroehlich/pysb@fix_pattern_matching
  Cloning https://github.com/FFroehlich/pysb (to revision fix_pattern_matching) to /tmp/pip-req-build-5o91yuil
  Running command git clone --filter=blob:none --quiet https://github.com/FFroehlich/pysb /tmp/pip-req-build-5o91yuil
  Running command git checkout -b fix_pattern_matching --track origin/fix_pattern_matching
  Switched to a new branch 'fix_pattern_matching'
  branch 'fix_pattern_matching' set up to track 'origin/fix_pattern_matching'.
  Resolved https://github.com/FFroehlich/pysb to commit c400f1c49fc2f59b153b64e0a86e0e6886bedb41
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'error'
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [20 lines of output]
      /tmp/pip-req-build-5o91yuil/versioneer.py:467: SyntaxWarning: invalid escape sequence '\s'
        LONG_VERSION_PY['git'] = '''
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 34, in <module>
        File "/tmp/pip-req-build-5o91yuil/setup.py", line 53, in <module>
          main()
        File "/tmp/pip-req-build-5o91yuil/setup.py", line 16, in main
          version=versioneer.get_version(),
                  ^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-req-build-5o91yuil/versioneer.py", line 1405, in get_version
          return get_versions()["version"]
                 ^^^^^^^^^^^^^^
        File "/tmp/pip-req-build-5o91yuil/versioneer.py", line 1339, in get_versions
          cfg = get_config_from_root(root)
                ^^^^^^^^^^^^^^^^^^^^^^^^^^
        File "/tmp/pip-req-build-5o91yuil/versioneer.py", line 399, in get_config_from_root
          parser = configparser.SafeConfigParser()
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'?
      [end of output]

FFroehlich · 2023-10-19T12:54:01Z

done, also bumping up getting that branch merged on my todo list

dweindl · 2023-10-23T08:54:36Z

Generally works. Some sympy DeprecationWarnings (see also sympy/sympy#25837), one of them causing a BnglImportError (https://github.com/AMICI-dev/AMICI/actions/runs/6609653584/job/17950132739):

FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[CaOscillate_Func] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[gene_expr] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[gene_expr_func] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[gene_expr_simple] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[Motivating_example_cBNGL] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[motor] - pysb.importers.bngl.BnglImportError: Could not parse expression kPlus:  w*exp(((g1/2.0)*((1.0/2.0)-((CheYp/((cellVolume*_Na)*(10^-6)))/(Kd+(CheYp/((cellVolume*_Na)*(10^-6)))))))) 

Error: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[test_setconc] - DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[Repressilator] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_bngl.py::test_compare_to_pysb_simulation[test_paramname] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_pysb.py::test_compare_to_pysb_simulation[localfunc] - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_pysb.py::test_energy - DeprecationWarning: ast.NameConstant is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_splines_short.py::test_spline_piecewise - DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_splines_short.py::test_two_splines - DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead
FAILED python/tests/test_splines_short.py::test_splines_plist - DeprecationWarning: ast.Num is deprecated and will be removed in Python 3.14; use ast.Constant instead

We had to require setuptools<64 because it change its temporary build directory from a known path to a randomly named temporary directory. However, setuptools<64 doesn't work with for Python3.12 (#2179). Therefore, this adds an option to change the setuptools temporary build directory via the `AMICI_BUILD_TEMP` environment variable, so we have those temp files in a known path for coverage analysis. Not meant to be used by users.

dweindl · 2023-12-14T21:01:45Z

PySB is currently restricts sympy to <1.12 pysb/pysb@e83937c

This reverts commit f3d6efe.

dweindl · 2023-12-14T22:09:48Z

works with sympy@master https://github.com/AMICI-dev/AMICI/actions/runs/7214927173/job/19658093049

sonarqubecloud · 2023-12-14T22:41:01Z

Quality Gate passed

Kudos, no new issues were introduced!

0 New issues
0 Security Hotspots
No data about Coverage
No data about Duplication

See analysis details on SonarCloud

FFroehlich

👍

Run nightly tests also on python3.12

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 <[email protected]> * 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 <[email protected]>

GHA: test python3.12

f980d86

Why setuptools<64? Remove.

993e617

dweindl added 3 commits October 23, 2023 07:57

dateutil

90e5da4

..

f77f6cf

..

8abc37d

dweindl mentioned this pull request Nov 1, 2023

Remove setuptools<64 restriction #2180

Merged

dweindl self-assigned this Nov 1, 2023

dweindl and others added 9 commits November 3, 2023 05:47

Merge branch 'develop' into py312

e705cc3

..

50e527c

Merge branch 'develop' into py312

c75fdb3

test_pypi.yml

4e6e5c4

Merge branch 'develop' into py312

d1e5ef8

Merge branch 'develop' into py312

d233d5d

Merge branch 'develop' into py312

1a1bf89

sympy-master

3f65f04

..

f3d6efe

dweindl added 3 commits December 14, 2023 22:38

Revert ".."

7337364

This reverts commit f3d6efe.

..

299f47a

..

00aae73

dweindl marked this pull request as ready for review December 14, 2023 22:09

dweindl requested a review from a team as a code owner December 14, 2023 22:09

FFroehlich approved these changes Dec 18, 2023

View reviewed changes

dweindl merged commit 5ba5821 into develop Dec 18, 2023
34 checks passed

dweindl deleted the py312 branch December 18, 2023 13:22

dweindl added a commit to dweindl/AMICI that referenced this pull request Dec 18, 2023

GHA: test python3.12 (AMICI-dev#2179)

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Run nightly tests also on python3.12

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GHA: test python3.12 #2179

GHA: test python3.12 #2179

dweindl commented Oct 18, 2023 •

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GHA: test python3.12 #2179

GHA: test python3.12 #2179

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