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Cleanup package building #1384

Merged
merged 10 commits into from
Jan 29, 2021
Merged

Cleanup package building #1384

merged 10 commits into from
Jan 29, 2021

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dweindl
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@dweindl dweindl commented Jan 29, 2021 •
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  • Use PEP 517 pyproject.toml (taking proper care of dependencies of setup.py itself)
  • Use setup.cfg
  • NOTE: creating a source distribution now requires https://github.com/pypa/build (or manual installation of the build requirements)

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codecov bot commented Jan 29, 2021 •
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Codecov Report

Merging #1384 (8620da1) into develop (8c440e9) will increase coverage by 3.40%.
The diff coverage is n/a.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    #1384      +/-   ##
===========================================
+ Coverage    75.31%   78.71%   +3.40%     
===========================================
  Files           22       63      +41     
  Lines         3168     9920    +6752     
===========================================
+ Hits          2386     7809    +5423     
- Misses         782     2111    +1329
Flag Coverage Δ
cpp 75.23% <ø> (?)
petab 69.50% <ø> (ø)
python 68.09% <ø> (?)

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

Impacted Files Coverage Δ
src/spline.cpp 71.57% <0.00%> (ø)
src/model_ode.cpp 75.64% <0.00%> (ø)
include/amici/solver_cvodes.h 100.00% <0.00%> (ø)
include/amici/misc.h 80.00% <0.00%> (ø)
src/model.cpp 83.59% <0.00%> (ø)
include/amici/steadystateproblem.h 100.00% <0.00%> (ø)
include/amici/sundials_linsol_wrapper.h 100.00% <0.00%> (ø)
include/amici/solver.h 100.00% <0.00%> (ø)
include/amici/solver_idas.h 100.00% <0.00%> (ø)
src/backwardproblem.cpp 64.77% <0.00%> (ø)
... and 42 more

@dweindl dweindl marked this pull request as ready for review January 29, 2021 13:52
FFroehlich
FFroehlich approved these changes Jan 29, 2021
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nice 👍

python/sdist/pyproject.toml Show resolved Hide resolved
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sonarcloud bot commented Jan 29, 2021

Kudos, SonarCloud Quality Gate passed!

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

0.0% 0.0% Coverage
0.0% 0.0% Duplication

@dweindl dweindl merged commit d7392e2 into develop Jan 29, 2021
@dweindl dweindl deleted the cleanup_setup branch January 29, 2021 17:58
@dweindl dweindl linked an issue Feb 19, 2021 that may be closed by this pull request
error: invalid command 'bdist_wheel' #1077
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@dweindl dweindl mentioned this pull request Feb 19, 2021
Merged
dweindl added a commit that referenced this pull request Feb 20, 2021
@dweindl
Release 0.11.13 (Merge pull request #1431 from AMICI-dev/release_0.11…
b090fbb 
….13)

Breaking changes:
* AMICI requires Python>=3.7
* Updated package installation (PEP517/518): 
  Creating source distributions requires https://github.com/pypa/build (#1384)
  (but now handles all package building dependencies properly)

Features:
* More flexible state reinitialization (#1417)

Updated dependencies:
* Upgrade to sundials 5.7.0 (#1392)

Fixes:
* Python: account for heaviside functions in expressions (#1382)
* Python: allow loading of existing models in import_petab_problem (#1383)
* Python: Don't override user-provided compiler/linker flags (#1389)
* Python: PEtab import reinitialization fixes (#1417)
* Python: Fix PEtab observables for pysb models (#1390)
* Python: Substitute expressions in event condition expressions (#1404)
* Python: Unspecified initial states in PEtab conditions table default to SBML initial value (#1397)
* C++: Fix timepoint out of bounds access (#1402)
* C++: Fix exported CMake config (#1388)
* Fixed Dockerfile: add python3-venv (#1398, #1408)

Other:
* Slim exported swig interface (#1425)
* Updated documentation
    * Getting started tutorial (#1423)
    * List supported SBML test tags (#1428)
    * Add AMICI C++/Python/Matlab feature comparison (#1409)
    * ...
* Various minor CI improvements
* ...
@dweindl dweindl mentioned this pull request Feb 22, 2021
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@FFroehlich FFroehlich FFroehlich approved these changes

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error: invalid command 'bdist_wheel'
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@dweindl @FFroehlich