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custom clustering now takes position matrix instead of distance^2 matrix #87

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custom clustering now takes position matrix instead of distance^2 matrix #87

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Commits on May 19, 2022

  1. neighbor spelling (assuming we're sticking to American spelling!)

    @AdamOrmondroyd
    AdamOrmondroyd committed May 19, 2022
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Commits on May 23, 2022

  1. custom clustering now takes position matrix instead of distance^2 mat… 

    …rix, to allow more general clustering algorithms
    @AdamOrmondroyd
    AdamOrmondroyd committed May 23, 2022
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Commits on May 24, 2022

  1. corrected order of dimensions of position_matrix

    @AdamOrmondroyd
    AdamOrmondroyd committed May 24, 2022
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  2. renamed calculate_similarity_matrix() to calculate_position_matrix()

    @AdamOrmondroyd
    AdamOrmondroyd committed May 24, 2022
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  3. renamed calculate_similarity_matrix() to calculate_position2_matrix()

    @AdamOrmondroyd
    AdamOrmondroyd committed May 24, 2022
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  4. Merge branch 'ormorod-custom_cluster' of github.com:Ormorod/PolyChord… 

    …Lite into ormorod-custom_cluster
    @AdamOrmondroyd
    AdamOrmondroyd committed May 24, 2022
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Commits on May 25, 2022

  1. corrected index in default_cluster

    @AdamOrmondroyd
    AdamOrmondroyd committed May 25, 2022
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Commits on May 26, 2022

  1. added new dimension to cluster input as position_matrix is not square… 

    …. I believe this is consistent with m = number of dimensions, n = number of clusters
    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  2. changed cluster interfaces to add extra dimension for position_matrix

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  3. Merge branch 'master' into ormorod-custom_cluster

    @williamjameshandley
    williamjameshandley committed May 26, 2022
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  4. Updated CI to work on pull request to all branches

    @williamjameshandley
    williamjameshandley committed May 26, 2022
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  5. changed cluster interfaces to add extra dimension for position_matrix

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  6. changed distance2_matrix to no longer be square

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  7. added extra dimension to cluster argument for non-square distance2_ma… 

    …trix
    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  8. Merge branch 'ormorod-custom_cluster' of github.com:Ormorod/PolyChord… 

    …Lite into ormorod-custom_cluster
    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  9. renamed m to nDims, n to nPoints, and position_matrix (and distance2_… 

    …matrix where still required) to points
    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  10. changed neighbour to ~~correct~~ UK spelling

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  11. forgot to change the interface in clustering itself

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  12. another clustering interface using the wrong dimension of points

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  13. swapped indices over

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  14. Merge branch 'ormorod-custom_cluster' of github.com:Ormorod/PolyChord… 

    …Lite into ormorod-custom_cluster
    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  15. Revert "swapped indices over" 

    This reverts commit e4622f5.
    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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  16. now uses c indexing in c and python, and fortran indexing in fortran

    @AdamOrmondroyd
    AdamOrmondroyd committed May 26, 2022
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Commits on May 28, 2022

  1. Merge branch 'PolyChord:master' into master

    @AdamOrmondroyd
    AdamOrmondroyd authored May 28, 2022
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Commits on Jun 13, 2022

  1. similarity matrix renamed to distance^2 in comments

    @AdamOrmondroyd
    AdamOrmondroyd committed Jun 13, 2022
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Commits on Jun 30, 2022

  1. wrap_cluster() adds one to the cluster list, as Python algos number c… 

    …lusters from 0, but fortran wants them numbered from 1
    @AdamOrmondroyd
    AdamOrmondroyd committed Jun 30, 2022
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  2. Merge branch 'ormorod-custom_cluster' of github.com:Ormorod/PolyChord… 

    …Lite into ormorod-custom_cluster
    @AdamOrmondroyd
    AdamOrmondroyd committed Jun 30, 2022
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  3. example cluster now returns -1

    @AdamOrmondroyd
    AdamOrmondroyd committed Jun 30, 2022
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Commits on Jul 29, 2022

  1. Merge branch 'master' into ormorod-custom_cluster

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  2. Merge branch 'custom_cluster' of github.com:PolyChord/PolyChordLite i… 

    …nto ormorod-custom_cluster
    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  3. example to test custom clustering

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  4. equal weights of each Gaussian peak, corrected comments

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  5. remove mutual_nearest_neighbours function

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  6. replace sklearn dependence with compute_knn

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  7. compute_knn() computed the full nn ordering, then returned the first … 

    …k, so instead just return all of them (compute_nn()) and don't bother recalculating.
    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  8. realised the for loop in the copied knn clustering is actually a whil… 

    …e loop in disguise
    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  9. Removed unused num_clusters_old from native clustering

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  10. comment reminds that clustering algorithm should be 0-indexed

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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  11. updated run_pypolychord.ipynb with py2nb

    @AdamOrmondroyd
    AdamOrmondroyd committed Jul 29, 2022
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Commits on Sep 22, 2022

  1. correct docstring to clarify cluster function must number clusters fr… 

    …om 0
    @AdamOrmondroyd
    AdamOrmondroyd committed Sep 22, 2022
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  2. further correction to clustering in docstring

    @AdamOrmondroyd
    AdamOrmondroyd committed Sep 22, 2022
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  3. change cluster function example comments to docstring

    @AdamOrmondroyd
    AdamOrmondroyd committed Sep 22, 2022
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  4. remove unnecessary np.sqrt import

    @AdamOrmondroyd
    AdamOrmondroyd committed Sep 22, 2022
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Commits on Feb 7, 2023

  1. Correct root=root -> root=0 in make_resume_file (PolyChord#92) 

    * neighbor spelling (assuming we're sticking to American spelling!)

* change NameError catch to check whether mpy4py was installed

* set root=0 rather than erroneous root=root

* Revert "neighbor spelling (assuming we're sticking to American spelling!)"
This already appears in a different PR

This reverts commit f1f52ed.
    @AdamOrmondroyd
    AdamOrmondroyd authored Feb 7, 2023
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Commits on Feb 16, 2023

  1. PWD->CURDIR

    @williamjameshandley
    williamjameshandley committed Feb 16, 2023
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  2. Updated PWD to CURDIR in setup.py

    @williamjameshandley
    williamjameshandley committed Feb 16, 2023
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Commits on Feb 20, 2023

  1. Update python3.6 CI (PolyChord#96) 

    * neighbor spelling (assuming we're sticking to American spelling!)

* change to checkoutv4

* change to checkout@v3

* change to pythonv4

* change to ubuntu-20.04

* return to latest ubuntu for 3.7 and 3.8, and separately include 3.6 case

* include pythons up to 3.11

* enclose versions in quotes

* revert spelling changes
    @AdamOrmondroyd
    AdamOrmondroyd authored Feb 20, 2023
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  2. Merge branch 'master' into ormorod-custom_cluster

    @AdamOrmondroyd
    AdamOrmondroyd committed Feb 20, 2023
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