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Release 3.24.06 #888

Merged
merged 855 commits into from
Jun 12, 2024
Merged

Release 3.24.06 #888

merged 855 commits into from
Jun 12, 2024
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Nov 3, 2023

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Commits on Nov 7, 2023

  1. Merge branch 'devel' into compilation_database_xmippCore

    # Conflicts:
    #	.github/workflows/build.yml
    albertmena committed Nov 7, 2023
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Commits on Nov 10, 2023

  1. remove model pick options

    fede-pe committed Nov 10, 2023
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  3. remove model pick option

    fede-pe committed Nov 10, 2023
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Commits on Nov 13, 2023

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Commits on Nov 15, 2023

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  2. Moved shift correction

    oierlauzi committed Nov 15, 2023
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Commits on Nov 17, 2023

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  2. Code smell

    MartinSalinas98 committed Nov 17, 2023
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  3. Better naming

    MartinSalinas98 committed Nov 17, 2023
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  4. CIF support

    MartinSalinas98 committed Nov 17, 2023
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  5. Code smell

    MartinSalinas98 committed Nov 17, 2023
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  6. Code smell

    MartinSalinas98 committed Nov 17, 2023
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  7. Readability

    MartinSalinas98 committed Nov 17, 2023
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  8. More compact

    MartinSalinas98 committed Nov 17, 2023
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  9. Rollback last commit

    MartinSalinas98 committed Nov 17, 2023
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Commits on Nov 28, 2023

  1. Update xmipp

    albertmena authored Nov 28, 2023
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  2. Merge pull request #844 from I2PC/release-3.23.11

    Release 3.23.11 to devel
    oierlauzi authored Nov 28, 2023
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Commits on Nov 29, 2023

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  2. Minor changes

    oierlauzi committed Nov 29, 2023
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Commits on Nov 30, 2023

  1. Merge pull request #845 from I2PC/olz_fix_pyxmipp

    Fixed PyXmipp installation
    albertmena authored Nov 30, 2023
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  3. graphene first commit

    Vilax committed Nov 30, 2023
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  4. upate

    Vilax committed Nov 30, 2023
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Commits on Dec 1, 2023

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  5. Removal of ambiguous type

    cossorzano committed Dec 1, 2023
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Commits on Dec 4, 2023

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Commits on Dec 5, 2023

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  2. Merge pull request #846 from I2PC/co_bugFixes

    Co bug fixes
    albertmena authored Dec 5, 2023
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Commits on Dec 7, 2023

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Commits on Dec 11, 2023

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  3. Comments

    MartinSalinas98 committed Dec 11, 2023
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  4. Rollback

    MartinSalinas98 committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. update model names

    fede-pe committed Dec 12, 2023
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Commits on Dec 14, 2023

  1. Merge pull request #847 from I2PC/co_deepCenter

    Deep center interface simplified
    albertmena authored Dec 14, 2023
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Commits on Dec 15, 2023

  1. Merge pull request #848 from I2PC/fi_DMD_updateModel

    Fi dmd update model
    Vilax authored Dec 15, 2023
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Commits on Dec 18, 2023

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  2. Code smell

    MartinSalinas98 authored Dec 18, 2023
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  3. Extra object removal

    oierlauzi committed Dec 18, 2023
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  4. Moved external actions to master/main

    To avoid needing manual updates
    MartinSalinas98 authored Dec 18, 2023
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Commits on Dec 19, 2023

  1. Merge pull request #849 from I2PC/olz_cif_pdb_label_from_volume

    Added CIF format support to pdb_label_from_volume
    albertmena authored Dec 19, 2023
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  2. Merge pull request #850 from I2PC/ms_action_simplification

    Moved external actions to master/main
    albertmena authored Dec 19, 2023
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  3. graphene update

    Vilax committed Dec 19, 2023
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  5. Merge pull request #851 from I2PC/olz_fix_pdb_write

    Fixed PDB write function when no categories are present
    oierlauzi authored Dec 19, 2023
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Commits on Dec 23, 2023

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Commits on Jan 3, 2024

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Commits on Jan 8, 2024

  1. adding tomo reconstructoin

    Vilax committed Jan 8, 2024
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  3. checking

    Vilax committed Jan 8, 2024
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  4. restoring dose filter

    Vilax committed Jan 8, 2024
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  5. enhancing subtomo extraction

    Vilax committed Jan 8, 2024
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  7. fixing pr

    Vilax committed Jan 8, 2024
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  9. removing comments

    Vilax committed Jan 8, 2024
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  10. bug fixed

    Vilax committed Jan 8, 2024
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  11. Merge pull request #854 from I2PC/fastExtraction

    Fast subtomo extraction
    Vilax authored Jan 8, 2024
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  13. extract remove form xtomo

    Vilax committed Jan 8, 2024
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  15. Merge pull request #852 from I2PC/xtomo

    xtomo tigre reconstruction
    Vilax authored Jan 8, 2024
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Commits on Jan 9, 2024

  1. Update README.md

    albertmena authored Jan 9, 2024
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Commits on Jan 10, 2024

  1. update pythorch version

    albertmena committed Jan 10, 2024
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Commits on Jan 11, 2024

  1. deprecating deep_denoising

    albertmena committed Jan 11, 2024
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  2. Merge pull request #840 from I2PC/ms_pdb_standard_read

    Cif support (standard function calls)
    albertmena authored Jan 11, 2024
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  3. Merge pull request #856 from I2PC/agm_deprecating

    Deprecated deep_denoising
    albertmena authored Jan 11, 2024
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  5. Update xmipp_pyTorch.yml

    albertmena authored Jan 11, 2024
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  7. Merge pull request #855 from I2PC/agm_pytorch_version

    update pythorch version
    albertmena authored Jan 11, 2024
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Commits on Jan 15, 2024

  1. Removing unused programs

    oierlauzi committed Jan 15, 2024
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  2. Removed more unused changes

    oierlauzi committed Jan 15, 2024
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  3. More of the same

    oierlauzi committed Jan 15, 2024
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Commits on Jan 19, 2024

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  3. Rewritten

    cossorzano committed Jan 19, 2024
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  4. Using generator

    oierlauzi committed Jan 19, 2024
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  5. Update xmipp_pyTorch-gpu.yml

    Versions of torchvision and python were not compatible with the specified pytorch.
    Ratolon authored Jan 19, 2024
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  6. Update xmipp_pyTorch.yml

    Fix broken installation due to incompatibility between stated pytorch + torchvision + python
    Ratolon authored Jan 19, 2024
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Commits on Jan 23, 2024

  1. Merge pull request #857 from I2PC/co_deepCenter2

    deep center: calculate shift for particles
    cossorzano authored Jan 23, 2024
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Commits on Jan 24, 2024

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  2. Merge pull request #858 from I2PC/mit_fix_dltkenv

    Fix DLTK installation
    albertmena authored Jan 24, 2024
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  6. Merge branch 'devel' into compilation_database_XmippCore

    # Conflicts:
    #	.github/workflows/build.yml
    DavidHerreros committed Jan 24, 2024
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  8. Added missing operator

    oierlauzi committed Jan 24, 2024
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  9. Removed extra imports

    oierlauzi committed Jan 24, 2024
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  10. Bugfix

    oierlauzi committed Jan 24, 2024
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  11. Fixed some code smells

    oierlauzi committed Jan 24, 2024
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  12. Fix equations

    DavidHerreros committed Jan 24, 2024
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Commits on Jan 25, 2024

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  5. Merge pull request #860 from I2PC/dh_bug_cufft

    Wipe out memory ouptut in cuFFT
    albertmena authored Jan 25, 2024
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  6. fix Fix this attribute access on a value that can be 'None' in src/xm…

    …ipp/tests/test_programs.py
    fede-pe committed Jan 25, 2024
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  9. fix Identical sub-expressions on both sides of operator , in src/xmip…

    …p/libraries/reconstruction_starpu/reconstruct_fourier_codelet_padded_image_to_fft.cpp
    fede-pe committed Jan 25, 2024
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  12. fix Throw the exception by value in src/xmipp/libraries/reconstructi…

    …on_cuda/cuda_angular_sph_alignment.cpp
    fede-pe committed Jan 25, 2024
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  13. fix Throw the exception by value in src/xmipp/libraries/reconstructi…

    …on_cuda/cuda_angular_sph_alignment.cpp
    fede-pe committed Jan 25, 2024
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  14. fix Throw the exception by value in src/xmipp/libraries/reconstructi…

    …on_cuda/cuda_volume_deform_sph.cpp
    fede-pe committed Jan 25, 2024
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  15. fix Remove the unary minus operator or change the expression's underl…

    …ying type in src/xmipp/legacy/libraries/reconstruction/volume_validate_pca.cpp
    fede-pe committed Jan 25, 2024
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  19. Bugfix

    oierlauzi committed Jan 25, 2024
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  21. swap condiciotn

    fede-pe committed Jan 25, 2024
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  22. Bugfix

    oierlauzi committed Jan 25, 2024
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Commits on Jan 26, 2024

  1. Merge pull request #862 from I2PC/dh_add_wedge

    Fix WEDGE option in FourierFilter
    albertmena authored Jan 26, 2024
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  2. Merge pull request #864 from I2PC/olz_fix_random_generator

    Fixing random generator
    albertmena authored Jan 26, 2024
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  5. Merge pull request #835 from I2PC/compilation_database_xmippCore

    Add XmippCore libraries to compilied database on compiling Xmipp
    albertmena authored Jan 26, 2024
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  7. Merge pull request #834 from I2PC/compilation_database_XmippCore

    XmippCore libraries added to compilation database
    albertmena authored Jan 26, 2024
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  8. Merge pull request #861 from I2PC/olz_whd

    Using upsample and downsample functions in extract subtomograms
    albertmena authored Jan 26, 2024
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Commits on Jan 31, 2024

  1. Merge pull request #865 from I2PC/co_fixes202401

    Co fixes202401
    albertmena authored Jan 31, 2024
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Commits on Feb 1, 2024

  1. Merge pull request #863 from I2PC/fi_xhd_25.01.2024

    Fi xhd 25.01.2024
    albertmena authored Feb 1, 2024
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  3. fix comment indent

    jamesmkrieger committed Feb 1, 2024
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Commits on Feb 2, 2024

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Commits on Feb 6, 2024

  1. fixes for subtomo extraction

    fede-pe committed Feb 6, 2024
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  2. do not debug code

    fede-pe committed Feb 6, 2024
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  3. remove debug CODE

    fede-pe committed Feb 6, 2024
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  6. Merge pull request #866 from I2PC/jmk_res_bfac

    fix unaccounted column in res bfac pdb
    Vilax authored Feb 6, 2024
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Commits on Feb 7, 2024

  1. Update README.md

    albertmena authored Feb 7, 2024
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  2. Merge pull request #867 from I2PC/fi_fixes_extractSubtomos

    Fi fixes extract subtomos
    oierlauzi authored Feb 7, 2024
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Commits on Feb 13, 2024

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  2. Removed commented code

    oierlauzi committed Feb 13, 2024
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  3. Simplified code

    oierlauzi committed Feb 13, 2024
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  4. Using isinstance

    oierlauzi committed Feb 13, 2024
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Commits on Feb 14, 2024

  1. Merge pull request #859 from I2PC/olz_split_volume

    New split volume program
    albertmena authored Feb 14, 2024
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Commits on Feb 16, 2024

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Commits on Feb 26, 2024

  1. Merge pull request #868 from I2PC/monotomo

    accelarating monotomo with float
    oierlauzi authored Feb 26, 2024
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  2. adding tigre working

    Vilax committed Feb 26, 2024
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  3. fixing sonar cloud bugs

    Vilax committed Feb 26, 2024
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Commits on Feb 29, 2024

  1. fixing issues in PR

    Vilax committed Feb 29, 2024
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Commits on Mar 1, 2024

  1. Merge pull request #871 from I2PC/tigre

    tigre reconstruction added to tomo
    Vilax authored Mar 1, 2024
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Commits on Mar 15, 2024

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Commits on Mar 18, 2024

  1. Renamed program file

    oierlauzi committed Mar 18, 2024
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  2. Simplified code

    oierlauzi committed Mar 18, 2024
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  3. Merge pull request #872 from I2PC/_visimTS

    simualtion of ts, tomograms and coordinates
    oierlauzi authored Mar 18, 2024
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Commits on Apr 29, 2024

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Commits on Apr 30, 2024

  1. Local average added

    cossorzano committed Apr 30, 2024
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  2. Merge pull request #875 from I2PC/co_ice

    Local average added
    oierlauzi authored Apr 30, 2024
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Commits on May 6, 2024

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Commits on May 13, 2024

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  2. Merge pull request #878 from I2PC/jmk_typos

    Typo fixes: fix scrach to scratch and fix lack of space after it
    albertmena authored May 13, 2024
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Commits on May 14, 2024

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  3. Merge pull request #880 from I2PC/olz_half_micrographs

    Added support for half precision float micrographs
    cossorzano authored May 14, 2024
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Commits on May 16, 2024

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Commits on May 20, 2024

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  3. Merge pull request #876 from I2PC/zart_cuda

    CUDA implementation of ZART
    albertmena authored May 20, 2024
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  4. header file forgotten

    Vilax committed May 20, 2024
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  6. Working on json

    albertmena committed May 20, 2024
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  7. working on data collection

    albertmena committed May 20, 2024
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  8. working on data collection

    albertmena committed May 20, 2024
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Commits on May 21, 2024

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  5. Merge pull request #881 from I2PC/deprecate_zart_cpu

    Deprecating ZART CPU version
    albertmena authored May 21, 2024
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  7. working on data collection

    albertmena committed May 21, 2024
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  10. minor fixes

    albertmena committed May 21, 2024
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Commits on May 23, 2024

  1. curl to test

    albertmena committed May 23, 2024
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  2. timeout

    albertmena committed May 23, 2024
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Commits on May 24, 2024

  1. branchName

    albertmena committed May 24, 2024
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Commits on May 29, 2024

  1. http conection without ssl

    albertmena committed May 29, 2024
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  2. Merge pull request #879 from I2PC/vi_updateTomo

    solving some bugs and enhancing performance
    oierlauzi authored May 29, 2024
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  3. json.dumps

    albertmena committed May 29, 2024
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  4. Fix double json.dump error

    csimong committed May 29, 2024
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  5. working on general way

    albertmena committed May 29, 2024
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  6. working on general way

    albertmena committed May 29, 2024
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  8. hidden debug

    albertmena committed May 29, 2024
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  9. logTail fix

    albertmena committed May 29, 2024
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Commits on May 30, 2024

  1. several fixes from review

    albertmena committed May 30, 2024
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  2. logTail just if fails

    albertmena committed May 30, 2024
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  3. fixing paths

    albertmena committed May 30, 2024
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  4. minor bugs

    albertmena committed May 30, 2024
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  5. statistics variable

    albertmena committed May 30, 2024
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  6. no prints

    albertmena committed May 30, 2024
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  7. Update xmipp_base.py

    albertmena authored May 30, 2024
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  8. no send statistics actions

    albertmena committed May 30, 2024
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  9. Merge pull request #883 from I2PC/agm_remove_force_flag

    Removed force flag on conda installations
    albertmena authored May 30, 2024
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Commits on May 31, 2024

  1. last review

    albertmena committed May 31, 2024
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  4. last last review

    albertmena committed May 31, 2024
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  5. Fixing missing cone

    oierlauzi committed May 31, 2024
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  7. Merge pull request #882 from I2PC/agm_api_old_installer

    API statistics
    albertmena authored May 31, 2024
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  8. Merge pull request #886 from I2PC/vi_olz_fix_missing_cone

    Fixing missing cone
    albertmena authored May 31, 2024
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Commits on Jun 3, 2024

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  2. Merge pull request #884 from I2PC/recover_zart_cpu

    Delete ZART GPU and recover ZART CPU for release
    albertmena authored Jun 3, 2024
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  4. Update CHANGELOG.md

    albertmena authored Jun 3, 2024
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  5. Update CHANGELOG.md

    albertmena authored Jun 3, 2024
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  6. Update CHANGELOG.md

    albertmena authored Jun 3, 2024
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  7. Update CHANGELOG.md

    albertmena authored Jun 3, 2024
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  8. cleaning code

    erneyramirez committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. posting with certified

    albertmena committed Jun 4, 2024
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  2. posting with certified

    albertmena committed Jun 4, 2024
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  3. Merge pull request #887 from I2PC/agm_certifications

    Adding certifications ssl
    csimong authored Jun 4, 2024
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  4. cleaning code

    erneyramirez committed Jun 4, 2024
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Commits on Jun 7, 2024

  1. Merge pull request #885 from I2PC/er_pca2dClass_merge_devel

    pca 2dclassification
    albertmena authored Jun 7, 2024
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Commits on Jun 10, 2024

  1. release version

    albertmena committed Jun 10, 2024
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