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equal area penalty slower than expected #598

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jsnel opened this issue Mar 15, 2021 · 0 comments · Fixed by #618
Closed

equal area penalty slower than expected #598

jsnel opened this issue Mar 15, 2021 · 0 comments · Fixed by #618
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Priority: Medium Business as usual Status: Needs Profiling Type: Bug Minor issues, non-crashing bug, slowdowns

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@jsnel
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jsnel commented Mar 15, 2021

  • glotaran version: v0.3.2
  • Python version: all
  • Operating System: all

Description

Use of equal area spectral penalty is much slower than expected.
@jsnel jsnel added Priority: Medium Business as usual Type: Bug Minor issues, non-crashing bug, slowdowns Status: Needs Profiling labels Mar 15, 2021
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 15, 2021
@jsnel
Remove unneeded check in spectral_penalties._get_area
b28a024 
Remove check if any area_index is close to all element in global_axis result which generated a lot of extra checks resulting in a massive slowdown.
Fixes glotaran#598
@jsnel jsnel mentioned this issue Mar 15, 2021
Merged
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 18, 2021
@jsnel
Remove unneeded check in spectral_penalties._get_area
3525a02 
Remove check if any area_index is close to all element in global_axis result which generated a lot of extra checks resulting in a massive slowdown.
Fixes glotaran#598
jsnel added a commit that referenced this issue Mar 18, 2021
@jsnel
Maintenance/patches for v0.3.3 (#599)
67dacce 
* Force recalculation of SVD attributes in scheme._prepare_data Fixes #597
* 🔨 Remove no-op code related to new_dims 
* Remove unneeded check in spectral_penalties._get_area Fixes #598
* Add python 3.9 support (#450)
* Bump numba dependencies as needed for Python 3.9
@jsnel jsnel mentioned this issue Mar 18, 2021
Merged
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 28, 2021
@jsnel
Maintenance/patches for v0.3.3 (glotaran#599)
0f56c03 
* Remove unneeded check in spectral_penalties._get_area Fixes glotaran#598
* Add python 3.9 support (glotaran#450)
* Bump numba dependencies as needed for Python 3.9
@jsnel jsnel mentioned this issue Mar 28, 2021
Merged
jsnel added a commit to jsnel/pyglotaran that referenced this issue Mar 28, 2021
@jsnel
Maintenance/patches for v0.3.3 (glotaran#599) 1/2
fb18061 
* Remove unneeded check in spectral_penalties._get_area Fixes glotaran#598
@jsnel jsnel linked a pull request Mar 28, 2021 that will close this issue
Maintenance/forward port v0.3.3 changes #618
Merged
jsnel added a commit that referenced this issue Mar 28, 2021
@jsnel
Maintenance/forward port v0.3.3 changes (#618)
0d41d63 
* Prepare v0.3.3 release (#603)
Bumped version and added release notes

* Maintenance/patches for v0.3.3 (#599) 1/2
* Remove unneeded check in spectral_penalties._get_area Fixes #598
* Maintenance/patches for v0.3.3 (#599) 2/2
* Force recalculation of SVD attributes in scheme._prepare_data Fixes #597
* 🔨 Remove no-op code related to new_dims
Changes that were lost because code was moved from scheme.py to problem.py

* Add a Zenodo config file
Added config file based on the example generated by zenodo
JSON Export example found at: https://zenodo.org/account/settings/github/repository/glotaran/pyglotaran#
Closes #579

* Update readme
Clarified Python version support
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Priority: Medium Business as usual Status: Needs Profiling Type: Bug Minor issues, non-crashing bug, slowdowns
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Maintenance/forward port v0.3.3 changes jsnel/pyglotaran
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