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MAINT: Backports for 1.4.0rc2 #11161

Merged
merged 26 commits into from
Dec 7, 2019
Merged

MAINT: Backports for 1.4.0rc2 #11161

merged 26 commits into from
Dec 7, 2019

Commits on Dec 2, 2019

  1. REL: set version to 1.4.0rc2 

    * set version to 1.4.0rc2 unreleased
    @tylerjereddy
    tylerjereddy committed Dec 2, 2019
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  2. API: Restore Rotation.match_vectors, deprecated in favors of align_ve… 

    …ctors
    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  3. ENH: Return loss value from Rotation.align_vectors

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  4. TST: Add a test of Rotation.align_vectors comparing results with prop… 

    …ortional weights
    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  5. MAINT: Change error to warning in Rotation.align_vectors

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  6. MAINT: Add lower bound of 0 for returned loss in Rotation.align_vectors

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  7. API: Return RMSD instead of loss function from Rotation.align_vectors

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  8. MAINT: Remove docstring of deprecated match_vectors 

    It is causing some errors in documentation build due to unused references
    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  9. API: Add return_sensitivity argument to Rotation.align_vectors

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  10. MAINT: Make Rotation.align_vectors work with single observations

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  11. TST: Add tests with invalid inputs to Rotation.align_vectors

    @nmayorov @tylerjereddy
    nmayorov authored and tylerjereddy committed Dec 2, 2019
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  12. BUG: remove repeated insertion of the same node to the heap in dijkstra

    @krzysztofpioro @tylerjereddy
    krzysztofpioro authored and tylerjereddy committed Dec 2, 2019
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  13. MAINT: move current_node=&nodes[j_source] line up

    @krzysztofpioro @tylerjereddy
    krzysztofpioro authored and tylerjereddy committed Dec 2, 2019
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  14. add missing types to _stats.pyx 

    change a few size/index related variables from int -> int_p

disable wraparound and boundscheck in a few other places
    @grlee77 @tylerjereddy
    grlee77 authored and tylerjereddy committed Dec 2, 2019
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  15. avoid warning about a potentially uninitialized variable

    @grlee77 @tylerjereddy
    grlee77 authored and tylerjereddy committed Dec 2, 2019
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  16. BUG: interpolate/fitpack: fix leak in splprep for task!=0 

    This is the non-default code path, not realised usually.
    @pv @tylerjereddy
    pv authored and tylerjereddy committed Dec 2, 2019
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  17. BUG: interpolate/fitpack: fix memory leak in splprep

    @pv @tylerjereddy
    pv authored and tylerjereddy committed Dec 2, 2019
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  18. FIX: Avoid potential segfault when slicing CSR or CSC matrices 

    The issue could occur for CSR matrices with row start index > stop index.

This fixes the same issue for column slice of CSC matrices.
    @grlee77 @tylerjereddy
    grlee77 authored and tylerjereddy committed Dec 2, 2019
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  19. TST: add test cases for invalid indexing of CSR/CSC matrices

    @grlee77 @tylerjereddy
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  20. MAINT: PR 11127 reviewer adjustments 

    * add out-of-bounds and invalid sparse
indexing test cases requested by reviewer

* adjust compressed.py source code such
that start index > stop index case now returns
an empty object (of same class as input)
    @tylerjereddy
    tylerjereddy committed Dec 2, 2019
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  21. Revert "TST: add test cases for invalid indexing of CSR/CSC matrices" 

    This reverts commit 1e870bb.
    @tylerjereddy
    tylerjereddy committed Dec 2, 2019
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  22. DOC: update 1.4.0 release notes 

    * account for backported PRs: 11081,
11096, 11124, 11126, 11127
    @tylerjereddy
    tylerjereddy committed Dec 2, 2019
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Commits on Dec 4, 2019

  1. BUG: Fix random state bug multiscale_graphcorr (scipy#11152) 

    * BUG: Fix random state bug multiscale_graphcorr

* BUG: Fix index error in multiscale_graphcorr

* BUG: fix nonetype exception

* ENH: Remove workers dependence for random_state in multiscale_graphcorr

* MAIN: Move random state keyword to end of parameter list

* MAIN: change list comprehension so it is more clear

* MAIN: fix typo in seed parameter

* ENH: Change seed generation in multiscale_graphcorr

* DOC: Use random_state keyword in example

* MAIN: Add whitespace around bitwise operator
    @sampan501 @tylerjereddy
    sampan501 authored and tylerjereddy committed Dec 4, 2019
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  2. BUG: empty sparse slice shapes (scipy#11166) 

    * BUG: empty sparse slice shapes

* CSC and CSR sparse matrix slices
that return empty matrices should
now correctly preserve a shape
of (0, original_shape[1])

* refactor _process_slice

replace use of 'empty' with i0=i1 which gives an empty slice
this will keep the existing logic for shape handling

* TST: add additional CSR and CSC slicing test cases
    @tylerjereddy
    tylerjereddy committed Dec 4, 2019
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  3. remove redundant fft in signal.resample

    @wenhui-prudencemed @tylerjereddy
    wenhui-prudencemed authored and tylerjereddy committed Dec 4, 2019
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Commits on Dec 7, 2019

  1. DOC: update 1.4.0 release notes 

    * update 1.4.0 release notes to reflect
backported PRs: 11152, 11166, 11167

* remove a redundant mention of multiscale_graphcorr
in the release notes and improve spacing around the original
mention of multiscale_graphcorr
    @tylerjereddy
    tylerjereddy committed Dec 7, 2019
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