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Python maintenance #4489

Merged
merged 10 commits into from
Apr 6, 2022
Merged

Python maintenance #4489

merged 10 commits into from
Apr 6, 2022

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jngrad
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@jngrad jngrad commented Apr 4, 2022 •
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Fixes #4488, fixes #4490, fixes #4491, fixes #4477

Description of changes:

  • require Python 3.8+ (as per NEP 29: new release schedule for scientific python packages #3421)
  • use contextlib in the testsuite to better handle ImportError from missing dependencies
  • use pathlib in the testsuite and scripts for portability on non-Posix environments
  • modernize python testsuite, fix broken test cases, improve code coverage
  • implement initial position offset for LEbc protocol OscillatoryShear
  • use new CI infrastructure: run jobs on 4 cores (reduce test runtime by 30%), update labels to better utilize GPU runners

@jngrad
CMake: Bump Python requirements
6e7baad
@jngrad
core: Dihedral code maintenance
0f1353b 
Replace raw pointers by references, make the regular and tabulated
dihedral bond kernels more similar, document singularity issue.
@jngrad
tests: Properly check dihedral bonds
1f562a2 
Fix broken analytical formula for the dihedral potential and forces
in the test case. Check regular and tabulated dihedral bond kernels
for multiple choices of multiplicity and phase.
@jngrad jngrad force-pushed the python_interface branch 4 times, most recently from fbfd372 to a3ffa9b Compare April 5, 2022 00:30
@jngrad
tests: Refactor IO test cases
4ddd129 
Use temporary directories in tests that need to output data to disk
to automate file cleanup. Use the pathlib module instead of the os
module for operations on filepaths to improve portability.
@jngrad
tests: Cleanup python testsuite
7bc8bc7 
Replace try/except import guards by contextlib.suppress(ImportError).
Remove unreachable code. Improve code coverage of utility functions.
Fix a minor bug when a variable assignment takes multiple lines. Run
the MMM1D tuning function once per test method to reduce overhead.
@jngrad
maintainer: Use pathlib module
72f35b3
@jngrad
python: Document Python classes
8031fba
@jngrad
core: Add initial_pos_offset to Oscillatory LEbc
ece1656
@jngrad
CI: Use new CI infrastructure
b3f4424 
Improve CPU/GPU load balancing by restricting CI jobs that don't
need a GPU on CI runners that don't provide a GPU. Use 4 cores
instead of 2 cores when the runner allows it. Execute slow jobs
on NUMA runners.
@jngrad jngrad marked this pull request as ready for review April 5, 2022 01:16
@jngrad jngrad requested a review from reinaual April 5, 2022 01:16
@jngrad jngrad added this to the Espresso 4.2 milestone Apr 6, 2022
@jngrad jngrad added the automerge Merge with kodiak label Apr 6, 2022
@kodiakhq kodiakhq bot merged commit a91b0dc into espressomd:python Apr 6, 2022
@jngrad jngrad deleted the python_interface branch April 6, 2022 14:12
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@reinaual reinaual reinaual approved these changes

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