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Merging dev into stable (1.3.0 release) #1067

Merged
merged 677 commits into from
Sep 23, 2024
Merged

Merging dev into stable (1.3.0 release) #1067

merged 677 commits into from
Sep 23, 2024
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Commits on May 31, 2024

  1. Fix topoMap boost link issue (windows, #1033)

    @julien-tierny
    julien-tierny committed May 31, 2024
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  2. Merge pull request #1034 from julien-tierny/dev 

    Fix topoMap boost link issue (windows, #1033)
    @julien-tierny
    julien-tierny authored May 31, 2024
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Commits on Jun 7, 2024

  1. added mt-wae example to vtk layer

    @julien-tierny
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  2. adding mt-wae example in base layer

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  3. added mt-wae example in pv plugin

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  4. xml reformatting

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  5. clang-formatting

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  6. Revert "clang-formatting" 

    This reverts commit 1dbee0c.
    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  7. clang-formatting

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  8. fighting VM old clang-format

    @julien-tierny
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  9. adding pd-wae example to vtk layer

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  10. adding pd-wae example to core layer

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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  11. added pd-wae example to the pv plugin

    @julien-tierny
    julien-tierny committed Jun 7, 2024
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Commits on Jun 10, 2024

  1. [SignedDistanceField] add module

    @MatPont
    MatPont committed Jun 10, 2024
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  2. [SignedDistanceField] clang format

    @MatPont
    MatPont committed Jun 10, 2024
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  3. [SignedDistanceField] missing priority queue header

    @MatPont
    MatPont committed Jun 10, 2024
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  4. [SignedDistanceField] missing override keyword

    @MatPont
    MatPont committed Jun 10, 2024
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  5. [SignedDistanceField] fix unsigned template abs

    @MatPont
    MatPont committed Jun 10, 2024
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  6. [SignedDistanceField] use bool literals

    @MatPont
    MatPont committed Jun 10, 2024
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  7. [SignedDistanceField] remove redundant virtual

    @MatPont
    MatPont committed Jun 10, 2024
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Commits on Jun 18, 2024

  1. fixes for new windows build chain

    @julien-tierny
    julien-tierny committed Jun 18, 2024
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Commits on Jun 20, 2024

  1. [MergeTree] debug messages

    @MatPont
    MatPont committed Jun 20, 2024
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Commits on Jun 25, 2024

  1. Merge branch 'dev' of github.com:topology-tool-kit/ttk into dev

    @eve-le-guillou
    eve-le-guillou committed Jun 25, 2024
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Commits on Jun 26, 2024

  1. Fix getCellRank in regular grids

    @eve-le-guillou
    eve-le-guillou committed Jun 26, 2024
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  2. Init array

    @eve-le-guillou
    eve-le-guillou committed Jun 26, 2024
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  3. init variable

    @eve-le-guillou
    eve-le-guillou committed Jun 26, 2024
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Commits on Jun 27, 2024

  1. Merge pull request #1006 from MatPont/mt_wae 

    Wasserstein Auto-Encoders of Merge Trees (and Persistence Diagrams)
    @julien-tierny
    julien-tierny authored Jun 27, 2024
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  2. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into m… 

    …pi_getCellRank
    @julien-tierny
    julien-tierny committed Jun 27, 2024
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  3. Updating ChangeLog

    @julien-tierny
    julien-tierny committed Jun 27, 2024
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  4. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into sdf

    @julien-tierny
    julien-tierny committed Jun 27, 2024
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  5. Merge pull request #1037 from eve-le-guillou/mpi_getCellRank 

    [MPI] Fix getCellRank in RegularGrid
    @julien-tierny
    julien-tierny authored Jun 27, 2024
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  6. Merge pull request #1038 from julien-tierny/dev 

    Updating ChangeLog
    @julien-tierny
    julien-tierny authored Jun 27, 2024
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  7. ripser 128bits indices only for gcc/clang

    @MClemot
    MClemot committed Jun 27, 2024
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  8. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into i… 

    …ndices128
    @MClemot
    MClemot committed Jun 27, 2024
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Commits on Jun 28, 2024

  1. advanced option for 128bits indices

    @MClemot
    MClemot committed Jun 28, 2024
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  2. trying to add torch to the CI

    @julien-tierny
    julien-tierny committed Jun 28, 2024
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  3. Merge pull request #1039 from MClemot/ripser128 

    [RipsPersistenceDiagram] 128 bits indices option
    @julien-tierny
    julien-tierny authored Jun 28, 2024
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  4. fixed file path

    @julien-tierny
    julien-tierny committed Jun 28, 2024
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  5. fixed C++ version for examples

    @julien-tierny
    julien-tierny committed Jun 28, 2024
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Commits on Jul 1, 2024

  1. fast persistence update

    @MohamedKISSI
    MohamedKISSI committed Jul 1, 2024
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  2. Merge branch 'topology-tool-kit:dev' into dev

    @MohamedKISSI
    MohamedKISSI authored Jul 1, 2024
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Commits on Jul 2, 2024

  1. code formatting

    @MohamedKISSI
    MohamedKISSI committed Jul 2, 2024
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  2. removing saveGradient function

    @MohamedKISSI
    MohamedKISSI committed Jul 2, 2024
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  3. [SignedDistanceField] remove scalar template

    @MatPont
    MatPont committed Jul 2, 2024
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  4. [SignedDistanceField] fix english variable name

    @MatPont
    MatPont committed Jul 2, 2024
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  5. [SignedDistanceField] fix include, protected and doc

    @MatPont
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Commits on Jul 3, 2024

  1. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into dev

    @julien-tierny
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Commits on Jul 4, 2024

  1. removed unnecessary include

    @julien-tierny
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  2. removed unnecessary include

    @julien-tierny
    julien-tierny committed Jul 4, 2024
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  3. unnecessary includes

    @julien-tierny
    julien-tierny committed Jul 4, 2024
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  4. added developer warnings

    @julien-tierny
    julien-tierny committed Jul 4, 2024
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  5. removing unnecessary includes

    @julien-tierny
    julien-tierny committed Jul 4, 2024
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  6. Processing change requests

    @MohamedKISSI
    MohamedKISSI committed Jul 4, 2024
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  7. [SurfaceGeometrySmoother] move functions to geometry

    @MatPont
    MatPont committed Jul 4, 2024
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  8. [Geometry] missing doc

    @MatPont
    MatPont committed Jul 4, 2024
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  9. [SignedDistanceField] doc

    @MatPont
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  10. [SignedDistanceField] clang format

    @MatPont
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  11. Merge pull request #1041 from MohamedKISSI/fastPersistenceUpdate 

    Fast persistence update
    @julien-tierny
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  12. Merge pull request #1035 from MatPont/sdf 

    [SignedDistanceField] add module
    @julien-tierny
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  13. gui shuffle

    @julien-tierny
    julien-tierny committed Jul 4, 2024
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  14. Merge pull request #1042 from MatPont/sdf 

    SDF gui shuffle
    @julien-tierny
    julien-tierny authored Jul 4, 2024
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  15. add Topological Optimization code

    @MohamedKISSI
    MohamedKISSI committed Jul 4, 2024
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  16. clang-format the code

    @MohamedKISSI
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Commits on Jul 5, 2024

  1. Fixing torch dependency issue

    @MohamedKISSI
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  2. Give a default value to the constraintDiagram variable so that the tt… 

    …k examples work
    @MohamedKISSI
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  3. set constraintDiagram variable to const

    @MohamedKISSI
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  4. We remove the default initialization for certain variables

    @MohamedKISSI
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  5. fix odr violations

    @MohamedKISSI
    MohamedKISSI committed Jul 5, 2024
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  6. fix odr violations getCoordinatesInformations

    @MohamedKISSI
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Commits on Jul 15, 2024

  1. restored original gui for existing backends

    @julien-tierny
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  2. progress on ui shuffling

    @julien-tierny
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  3. work on solver gui

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Commits on Jul 16, 2024

  1. updated optimization gui

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Commits on Jul 17, 2024

  1. [Torch] fix external project linkage

    @MatPont
    MatPont committed Jul 17, 2024
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  2. [Example] vtk-c++ example from 14 to 17

    @MatPont
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  3. [Torch] fix TORCH_FOUND condition

    @MatPont
    MatPont committed Jul 17, 2024
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  4. Avoid crash when unstructured grid with invalid cells 

    before this commit, invalid unstructured grid lead to crash.
the only removed check are completely trivials and should not impact compute time.
    @CharlesGueunet
    CharlesGueunet committed Jul 17, 2024
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  5. Set default variable values to match XML file and updated PyTorch war… 

    …ning messages.
    @MohamedKISSI
    MohamedKISSI committed Jul 17, 2024
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Commits on Jul 18, 2024

  1. Merge pull request #1044 from MatPont/torch_example_fix 

    [Torch] fix external project linkage
    @julien-tierny
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  2. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into dev

    @julien-tierny
    julien-tierny committed Jul 18, 2024
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  3. disable binary torch for mac

    @julien-tierny
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  4. install torch when CI testing

    @julien-tierny
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  5. Merge pull request #1040 from julien-tierny/dev 

    trying to add torch to the CI
    @julien-tierny
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  6. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into t… 

    …opologicalOptimization
    @julien-tierny
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  7. Merge pull request #1045 from CharlesGueunet/ContourTreeCleanCheck 

    Avoid crash on unstructured grid with invalid cells, when using Contour / Merge tree
    @julien-tierny
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Commits on Jul 19, 2024

  1. [MergeTree] debug messages

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Commits on Aug 14, 2024

  1. [MergeTree] remove some debug messages

    @MatPont
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  2. [MergeTree] debug messages

    @MatPont
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Commits on Aug 21, 2024

  1. [MergeTree] debug messages

    @MatPont
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  2. [MergeTree] debug messages

    @MatPont
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  3. Merge https://github.com/topology-tool-kit/ttk into pdBaryFix

    @MatPont
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  4. [MergeTree] debug messages

    @MatPont
    MatPont committed Aug 21, 2024
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Commits on Aug 23, 2024

  1. updated adam unavailability message

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  2. topological optimization backend refactoring

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  3. Reformatting console outputs

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  4. [SignedDistanceField] not expanded box precision

    @MatPont
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  5. trying to debug windows ci

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  6. listing conda installation

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  7. added missing files

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  8. listing more conda install

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  9. exploring conda install

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  10. try to add libboost-devel

    @julien-tierny
    julien-tierny committed Aug 23, 2024
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  11. searching for conda's boost cmake files

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  12. simpler windows CI fix

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  13. windows ci, fixing boost dep

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  14. disabling websocket on windows

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  15. fix refactoring

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  16. removed unnecessary headers

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  17. updated var names

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  18. remvod comments

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  19. fixed vtk layer

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  20. used proper indices, removed unused functions

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  21. updated var names

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  22. typo fix

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  23. updated paper references

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  24. Merge pull request #1046 from MatPont/sdf_box_precision 

    [SignedDistanceField] not expanded box precision
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  25. [MergeTree] first barycenter fix attempt

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Commits on Aug 24, 2024

  1. Removed getNeighborsIndices function and updated dataVector type to d… 

    …ataType.
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Commits on Aug 26, 2024

  1. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into t… 

    …opologicalOptimization
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  2. clang-format

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  3. removed unnecessary headers

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Commits on Aug 28, 2024

  1. Use double format for dataVectors and computations, ensure consistenc… 

    …y between kFloat64 and kDouble, remove unnecessary copies of smoothedScalars. Normalize input data in pre-process and de-normalize in post-process. Report status message every k iterations.
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Commits on Aug 29, 2024

  1. Solving problems by normalizing the values ​​of the critical points o… 

    …f the target diagram.
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  2. Merge https://github.com/topology-tool-kit/ttk into pdBaryFix

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  3. [MergeTreeBarycenter] remove debug messages

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  4. [MergeTreeBarycenter] remove debug messages

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  5. [MergeTreeBarycenter] remove double to template function

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  6. Revert "[MergeTreeBarycenter] remove debug messages" 

    This reverts commit 24a2b7b.

Revert "[MergeTreeBarycenter] remove debug messages"

This reverts commit 7b9a820.
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Commits on Aug 30, 2024

  1. [MergeTreeBarycenter] debug messages

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  2. [MergeTreeBarycenter] debug messages

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  3. [MergeTreeBarycenter] debug

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  4. [MergeTreeBarycenter] debug

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  5. [MergeTreeBarycenter] remove debug messages

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  6. [MergeTreeBarycenter] volatile update

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  7. CI: Use sccache action from marketplace

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  8. fixup linux

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Commits on Sep 2, 2024

  1. Merge pull request #1048 from MatPont/pdBaryFix 

    Fix Merge Tree (and Persistence Diagram) barycenter precision
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  1. Merge pull request #1043 from MohamedKISSI/topologicalOptimization 

    add Topological Optimization code
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  2. Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows 

    Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 3 to 4.1.7.
- [Release notes](https://github.com/actions/download-artifact/releases)
- [Commits](actions/download-artifact@v3...v4.1.7)

---
updated-dependencies:
- dependency-name: actions/download-artifact
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
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Commits on Sep 4, 2024

  1. [ci] upgrade upload-artifacts

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  2. [ci] upgraded checkout

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  3. [ci] testing delete upgrade

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  4. [ci] fixing brew warnings

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  5. [ci] fix delete artifact upgrade

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  6. Merge pull request #1050 from topology-tool-kit/dependabot/github_act… 

    …ions/dot-github/workflows/actions/download-artifact-4.1.7

Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows
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Commits on Sep 9, 2024

  1. changelog update

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  2. [ci] adding ubuntu 24.04

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  3. [ci] disabling ubuntu 24.04

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  4. [pd-pga] updted paraview xml doc

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  5. [pd-pga] updated vtk docuemntation

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  6. [pd-pga] update core documentation

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  7. clang-formatting doc

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Commits on Sep 10, 2024

  1. Merge pull request #1052 from julien-tierny/doc 

    Updated documentation
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  2. [ci] updated ttk-paraview packaging

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  3. [ci] updated ttk-paraview paths

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  4. Merge pull request #1053 from julien-tierny/patch 

    [ci] updated ttk-paraview packaging
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  5. updated patch set for pv513

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  6. updated patchset

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Commits on Sep 11, 2024

  1. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into s… 

    …ccache_support
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  2. [pv513] updated ymls

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  3. [pv513] fixed builtin examples

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  4. Merge pull request #1049 from mwestphal/sccache_support 

    CI: Use sccache action from marketplace
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  5. [pv513] Last dialog fix

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  6. [pv513] tuning down errors to warnings

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  7. [pv513] Long-term path for assets

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  8. [ci-pv513] Adjusting patch set

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Commits on Sep 12, 2024

  1. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into p… 

    …atch
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  2. [ci-pv513] Final ci packaging

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  3. Merge pull request #1054 from julien-tierny/patch 

    [ci-pv513] Updated patch set for ParaView 5.13
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  4. [ci] remove pip sklearn from tests

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  5. [ci] updating ubuntu dependencies

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  6. [ci] updated ubuntu tests

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  7. [ci] updated macos tests

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  8. [ci] updated windows tests

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  9. [ci] fix yml formatting

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  10. [ci] fix yml syntax

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  11. [ci] fix pv-headless package name for macos

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  12. [ci] fix pv headless package name for macos

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  13. [ci] debugging pvpython macos14

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  14. [ci] adding spectra to macos

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  15. [ci] continue on macos-14 pvpython errors

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  16. [ci] continue on all macos-14 pvpython errors

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  17. [ci-pv513] Momentarily disabling buggy example

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  18. [ci-pv513] Enabling ubuntu-22.04 on pv513 headless

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  19. [ci-pv513] Fixing buggy example disable win

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  20. Merge pull request #1056 from julien-tierny/patch 

    [ci-pv513] Enabling ubuntu-22.04 on pv513 headless
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  21. [ci-pv513] removed unnecessary comment

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  22. [pv513] Final patchset fix

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  23. [ci] fixing buggy example windows

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  24. Merge pull request #1057 from julien-tierny/patch 

    [pv513] Final patchset fix
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  25. [ci] adding ubuntu-24.04

    @julien-tierny
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  26. [ci] trying to fix ubuntu-24.04 issues

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  27. [ci] trying to fix ubuntu-24.04 issue

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  28. [ci] trying to fix ubuntu-24.04 issue

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Commits on Sep 13, 2024

  1. [ci] ubuntu-24.04 temp roll back

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  2. [ci-ubuntu-24.04] Fixing ifdef warning

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  3. [ci-ubuntu-24.04] workaround gcc-13 bug

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  4. [ci-ubuntu-24.04] workaround gcc-13 bug (bis)

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  5. [ci] clang-formatting dms edits

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  6. Revert "[ci] clang-formatting dms edits" 

    This reverts commit 09effc4.
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  7. [ci] clang-formatting DMS edits (bis)

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  8. [ci] clang-formatting DMS edits (ter)

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    julien-tierny committed Sep 13, 2024
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  9. [ci] trying to fix windows websocketio issue

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    julien-tierny committed Sep 13, 2024
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  10. Merge pull request #1058 from julien-tierny/ci 

    [CI] Updating test workflow to ParaView 5.13 (with extensions to Ubuntu 24.04 and MacOS 14)
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    julien-tierny authored Sep 13, 2024
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Commits on Sep 14, 2024

  1. [ci] migrating check to ubuntu-24.04

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Commits on Sep 15, 2024

  1. [ci-macos-14] trying to fix pvpython

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  2. [ci-macos-14] Fixing pvpython

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    julien-tierny committed Sep 15, 2024
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  3. [ci-macos-14] Resuming pvpython enforcement

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    julien-tierny committed Sep 15, 2024
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  4. Merge pull request #1059 from julien-tierny/fix 

    [ci-macos-14] Fixing pvpython library loading issue
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    julien-tierny authored Sep 15, 2024
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Commits on Sep 16, 2024

  1. Revert "[ci] migrating check to ubuntu-24.04" 

    This reverts commit a173ddb.
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    julien-tierny committed Sep 16, 2024
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  2. [ci] migrating check workflow to pv513

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    julien-tierny committed Sep 16, 2024
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  3. [doc] adding topOpt dark sky to pv doc

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    julien-tierny committed Sep 16, 2024
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  4. [doc] links to dark sky example (vtk-layer)

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    julien-tierny committed Sep 16, 2024
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  5. [ci] continue on doxygen warnings

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    julien-tierny committed Sep 16, 2024
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  6. [ci] check code action upgrade

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    julien-tierny committed Sep 16, 2024
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  7. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into ci

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    julien-tierny committed Sep 16, 2024
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  8. Merge branch 'ci' of https://github.com/julien-tierny/ttk into doc

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  9. [doc] added dark sky links to base layer

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    julien-tierny committed Sep 16, 2024
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  10. [doc] added links for topoOpt torus (paraview)

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    julien-tierny committed Sep 16, 2024
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  11. [ci] removing topoOpt dark sky (out of mem)

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    julien-tierny committed Sep 16, 2024
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  12. [ci] remove examples that fill up memory

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  13. [doc] topoOpt torus link (vtk layer)

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    julien-tierny committed Sep 16, 2024
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Commits on Sep 17, 2024

  1. Merge pull request #1060 from julien-tierny/ci 

    Upgrading check_code workflow to pv513
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    julien-tierny authored Sep 17, 2024
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  2. [doc] adding topoOpt torus links (base layer)

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    julien-tierny committed Sep 17, 2024
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  3. [doc] add topoOpt pegasus links (paraview)

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    julien-tierny committed Sep 17, 2024
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  4. [doc] added topoOpt pegasus (vtk layer)

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    julien-tierny committed Sep 17, 2024
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  5. [doc] added topoOpt pegasus (base layer)

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    julien-tierny committed Sep 17, 2024
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  6. [ci] upgrading packaging (ubuntu-24.04, macos-14)

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    julien-tierny committed Sep 17, 2024
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  7. [versionBump] splash update

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  8. [versionBump] ParaView title

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    julien-tierny committed Sep 17, 2024
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  9. [ci] fixing windows packaging

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    julien-tierny committed Sep 17, 2024
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  10. [versionBump] updated changelog

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    julien-tierny committed Sep 17, 2024
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  11. [ci] fixing windows build

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    julien-tierny committed Sep 17, 2024
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  12. Merge pull request #1061 from julien-tierny/doc 

    [Doc] Adding Links to Topological Optimization examples (headers)
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    julien-tierny authored Sep 17, 2024
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  13. [ci] trying to fix windows packaging (using ninja)

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    julien-tierny committed Sep 17, 2024
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  14. [versionBump] incrementing version

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    julien-tierny committed Sep 17, 2024
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  15. [doc] Fix broken example links

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    julien-tierny committed Sep 17, 2024
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  16. [ci] Fixing macos packaging

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    julien-tierny committed Sep 17, 2024
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  17. [ci] fixing windows package tests

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    julien-tierny committed Sep 17, 2024
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  18. [doc] mpiExample (paraview)

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    julien-tierny committed Sep 17, 2024
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  19. [doc] mpiExample (vtk layer)

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  20. [doc] mpiExample (base layer)

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    julien-tierny committed Sep 17, 2024
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  21. [ci] disabling mpi example

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    julien-tierny committed Sep 17, 2024
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  22. Merge branch 'dev' of https://github.com/topology-tool-kit/ttk into doc

    @julien-tierny
    julien-tierny committed Sep 17, 2024
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  23. Merge pull request #1062 from julien-tierny/doc 

    [doc] Fix broken example links
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    julien-tierny authored Sep 17, 2024
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  24. [ci] fix macos-12 package tests

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    julien-tierny committed Sep 17, 2024
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  25. [ci] fix macos-14 package test

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    julien-tierny committed Sep 17, 2024
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  26. [ci] fix macos-12 test typo

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    julien-tierny committed Sep 17, 2024
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Commits on Sep 18, 2024

  1. Merge pull request #1063 from julien-tierny/ci 

    [ci] package workflow upgrade (ubuntu-24.04, macos-14, pv513)
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    julien-tierny authored Sep 18, 2024
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  2. Merge pull request #1064 from julien-tierny/versionBump 

    [release] Version bump (1.3.0)
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    julien-tierny authored Sep 18, 2024
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