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Merge dev and do new release #386

Merged
merged 124 commits into from
Aug 26, 2024
Merged

Merge dev and do new release #386

merged 124 commits into from
Aug 26, 2024

Commits on Apr 21, 2023

  1. First addition of FastShermanMorrison for testing

    @vhaasteren
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  2. Added numpy and cython extensions to setup.py

    @vhaasteren
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Commits on Apr 24, 2023

  1. Updated docstrings and method selector for fast-sherman-morrison

    @vhaasteren
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  2. Merge remote-tracking branch 'github-vhaasteren/fastshermanmorrison' … 

    …into fastshermanmorrison
    @vhaasteren
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  3. Added numpy and cython to requirements_dev.txt

    @vhaasteren
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  4. Moved FastShermanMorrison to external package

    @vhaasteren
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  5. Removed fastshermanmorrison from setup.py

    @vhaasteren
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  6. Conform to black linter

    @vhaasteren
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Commits on Apr 26, 2023

  1. Added test for fast-sherman-morrison

    @vhaasteren
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  2. Added requirements_tests.txt, so that the extensions can be loaded fo… 

    …r testing.
    @vhaasteren
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  3. Added decorator to show fastshermanmorrison-pulsar warning only once

    @vhaasteren
    vhaasteren committed Apr 26, 2023
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  4. Proper linting corrections

    @vhaasteren
    vhaasteren committed Apr 26, 2023
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  5. Changed the EcorrKernelWarning machanism

    @vhaasteren
    vhaasteren committed Apr 26, 2023
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  6. Blacking

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  7. Lint update

    @vhaasteren
    vhaasteren committed Apr 26, 2023
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  8. Removed the have_shown stuff for now

    @vhaasteren
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Commits on May 4, 2023

  1. Placed fastshermanmorrison into requirements_dev.txt

    @vhaasteren
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Commits on Sep 21, 2023

  1. Added Percentage Point Function for all parameters

    @vhaasteren
    vhaasteren committed Sep 21, 2023
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  2. Added PPF tests

    @vhaasteren
    vhaasteren committed Sep 21, 2023
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  3. Done linting on parameter.py and test_parameter.py

    @vhaasteren
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Commits on Sep 22, 2023

  1. Allow for index arrays in ShermanMorrison, so we do not need sorted T… 

    …OAs for EcorrKernelNoise signals
    @vhaasteren
    vhaasteren committed Sep 22, 2023
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Commits on Sep 24, 2023

  1. Updated all the white signals and block matrix code for index array i… 

    …ndexing
    @vhaasteren
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Commits on Sep 25, 2023

  1. Provided mechanism for showing warning message about fastshermanmorri… 

    …son, and updated fastshermanmorrison-pulsar in requirements_dev.txt
    @vhaasteren
    vhaasteren committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Added pragmas for no coverage of exception results

    @vhaasteren
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  2. Linting: forgot a space in a pragma

    @vhaasteren
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Commits on Sep 27, 2023

  1. Modified pulsar.py to allow for additional pulsar types from external… 

    … packages
    @vhaasteren
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  2. Moved drop t2pulsar code

    @vhaasteren
    vhaasteren committed Sep 27, 2023
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Commits on Sep 28, 2023

  1. Bugfix for bug #358

    @vhaasteren
    vhaasteren committed Sep 28, 2023
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  2. Linting

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  3. Added tests for scrambled/unsorted IPTA datasets for EcorrKernelNoise

    @vhaasteren
    vhaasteren committed Sep 28, 2023
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Commits on Sep 29, 2023

  1. Changed logdet=True in one call in MarginalizingNmat, so we don't nee… 

    …d to include cumbersome tests to not decrease coverage. Is never called anyway, and it doesn't slow things down.
    @vhaasteren
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Commits on Oct 1, 2023

  1. Add Python 3.11, Remove Python 3.7

    @AaronDJohnson
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Commits on Oct 5, 2023

  1. Merge branch 'master' into python311

    @vallis
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Commits on Oct 6, 2023

  1. Merge branch 'nanograv:master' into bugfix_358

    @vhaasteren
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  2. Merge branch 'nanograv:master' into quant2ind_returns_indices

    @vhaasteren
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  3. Merge branch 'nanograv:master' into ppf_parameters

    @vhaasteren
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  4. Merge branch 'nanograv:master' into fastshermanmorrison

    @vhaasteren
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Commits on Nov 6, 2023

  1. Merge branch 'master' into ppf_parameters

    @vhaasteren
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  2. Merge remote-tracking branch 'github-vhaasteren/ppf_parameters' into … 

    …ppf_parameters
    @vhaasteren
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  3. Merge branch 'master' into bugfix_358

    @vhaasteren
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  4. Merge remote-tracking branch 'github-vhaasteren/bugfix_358' into bugf… 

    …ix_358
    @vhaasteren
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  5. Merge branch 'master' into quant2ind_returns_indices

    @vhaasteren
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  6. Merge remote-tracking branch 'github-vhaasteren/quant2ind_returns_ind… 

    …ices' into quant2ind_returns_indices
    @vhaasteren
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  7. Merge branch 'master' into python311

    @AaronDJohnson
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  8. Merge branch 'master' into bugfix_358

    @vhaasteren
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  9. Merge branch 'master' into ppf_parameters

    @vhaasteren
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  10. Merge branch 'master' into quant2ind_returns_indices

    @vhaasteren
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  11. Merge branch 'master' into fastshermanmorrison

    @vhaasteren
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  12. Merge remote-tracking branch 'github-vhaasteren/fastshermanmorrison' … 

    …into fastshermanmorrison
    @vhaasteren
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  13. Merge branch 'master' into pulsar_mods

    @vhaasteren
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  14. Linting of test_white_signals.py

    @vhaasteren
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Commits on Nov 7, 2023

  1. Provided extra unit tests for the PPF functionality and parameters in… 

    … general
    @vhaasteren
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  2. Linting: extra line of whitespace

    @vhaasteren
    vhaasteren committed Nov 7, 2023
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  3. Updated the ci_tests.yml to include the dev branch

    @vhaasteren
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  4. Merge pull request #362 from AaronDJohnson/python311 

    Add Python 3.11, Remove Python 3.7
    @vhaasteren
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  5. Added more unit tests for the parameter module

    @vhaasteren
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Commits on Nov 8, 2023

  1. Updated version of fastshermanmorrison-pulsar to 0.4.0, which has bin… 

    …ary builds
    @vhaasteren
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Commits on Nov 9, 2023

  1. Merge pull request #359 from vhaasteren/bugfix_358 

    Bugfix for bug #358
    @AaronDJohnson
    AaronDJohnson authored Nov 9, 2023
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  2. Fixed typo

    @vhaasteren
    vhaasteren committed Nov 9, 2023
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  3. Added the necessary unit tests

    @vhaasteren
    vhaasteren committed Nov 9, 2023
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  4. Linting

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  5. Added extra unit test

    @vhaasteren
    vhaasteren committed Nov 9, 2023
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  6. Updated the test_pulsar.py

    @vhaasteren
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Commits on Nov 15, 2023

  1. add conda stuff to docs (#336) 

    * add conda stuff to docs

* add conda stuff to docs

* add flake8 to dev build

* split out runtime deps from development deps in example

* remove make lint from instructions (already run in make test)

* link to apple silicon tips

* update conda install instructions

add test dependencies to conda env initialization following @aarchiba's suggestion

---------

Co-authored-by: Rutger van Haasteren <[email protected]>
    @paulthebaker @vhaasteren
    paulthebaker and vhaasteren authored Nov 15, 2023
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Commits on Nov 17, 2023

  1. Merge pull request #343 from vhaasteren/fastshermanmorrison 

    Fast Sherman Morrison for Kernel Ecorr
    @AaronDJohnson
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  2. Merge branch 'dev' into quant2ind_returns_indices

    @vhaasteren
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  3. Added tests for indices_from_slice and quant2ind

    @vhaasteren
    vhaasteren committed Nov 17, 2023
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  4. Added error message

    @vhaasteren
    vhaasteren committed Nov 17, 2023
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  5. Merge pull request #356 from vhaasteren/quant2ind_returns_indices 

    Allow for index arrays in ShermanMorrison
    @AaronDJohnson
    AaronDJohnson authored Nov 17, 2023
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Commits on Nov 29, 2023

  1. Make astropy optional in pulsar.py

    @vhaasteren
    vhaasteren committed Nov 29, 2023
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  2. Added space for black

    @vhaasteren
    vhaasteren committed Nov 29, 2023
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  3. Changed the location of the pragma: no cover

    @vhaasteren
    vhaasteren committed Nov 29, 2023
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  4. Merge pull request #368 from vhaasteren/astropy_optional 

    Astropy optional
    @AaronDJohnson
    AaronDJohnson authored Nov 29, 2023
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Commits on Nov 30, 2023

  1. Properly address units in PintPulsar position

    @vhaasteren
    vhaasteren committed Nov 30, 2023
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  2. Fix typo

    @vhaasteren
    vhaasteren committed Nov 30, 2023
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Commits on Dec 23, 2023

  1. add new EPTA and general selection functions

    Chen Siyuan committed Dec 23, 2023
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  2. Update gp_bases.py

    @siyuan-chen
    siyuan-chen authored Dec 23, 2023
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  3. Update gp_signals.py

    @siyuan-chen
    siyuan-chen authored Dec 23, 2023
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  4. Update signal_base.py

    @siyuan-chen
    siyuan-chen authored Dec 23, 2023
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  5. Update utils.py

    @siyuan-chen
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Commits on Feb 6, 2024

  1. added doc string and explanation

    Chen Siyuan committed Feb 6, 2024
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Commits on Feb 14, 2024

  1. Only do numerical Cholesky update once the likelihood has been calcul… 

    …ated already
    @vhaasteren
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  2. Linting of course

    @vhaasteren
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Commits on Mar 5, 2024

  1. Merge pull request #381 from nanograv/master 

    Fix CI issues on dev
    @AaronDJohnson
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  2. Merge branch 'dev' into faster_sparse

    @vhaasteren
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Commits on Apr 7, 2024

  1. liniting

    Chen Siyuan committed Apr 7, 2024
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  2. more linting

    Chen Siyuan committed Apr 7, 2024
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  3. linting

    Chen Siyuan committed Apr 7, 2024
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Commits on Apr 9, 2024

  1. Merge pull request #373 from siyuan-chen/selections 

    Merge EPTA version part 1
    @vhaasteren
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  2. Merge branch 'dev' into gp_bases

    @vhaasteren
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  3. Merge pull request #374 from siyuan-chen/gp_bases 

    Merge EPTA version part 2
    @vhaasteren
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Commits on Apr 18, 2024

  1. Merge branch 'dev' into faster_sparse

    @vhaasteren
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Commits on Apr 19, 2024

  1. Added test for the sparse matrix in-place solve

    @vhaasteren
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  2. Oopsie, timing model addition was not committed enough

    @vhaasteren
    vhaasteren committed Apr 19, 2024
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  3. Added test for PINT pulsar with RAJ/DECJ

    @vhaasteren
    vhaasteren committed Apr 19, 2024
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Commits on Apr 20, 2024

  1. Merge pull request #376 from vhaasteren/faster_sparse 

    Faster sparse matrix Cholesky
    @AaronDJohnson
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Commits on Apr 21, 2024

  1. Merge branch 'dev' into ppf_parameters

    @vhaasteren
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  2. Changed dimensionality constraint for normal ppf

    @vhaasteren
    vhaasteren committed Apr 21, 2024
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  3. Merge branch 'dev' into ppf_parameters

    @vhaasteren
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  4. Merge pull request #383 from nanograv/master 

    Merging master into dev
    @vhaasteren
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  5. Merge branch 'dev' into fix_posunits

    @vhaasteren
    vhaasteren committed Apr 21, 2024
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  6. Fix merge errors

    @vhaasteren
    vhaasteren committed Apr 21, 2024
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  7. Fixed extra pulsar test

    @vhaasteren
    vhaasteren committed Apr 21, 2024
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  8. Merge pull request #353 from vhaasteren/ppf_parameters 

    Percentage Point Functions for parameters
    @AaronDJohnson
    AaronDJohnson authored Apr 21, 2024
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Commits on May 9, 2024

  1. Merge pull request #365 from vhaasteren/pulsar_mods 

    Modifications to the Pulsar class
    @vhaasteren
    vhaasteren authored May 9, 2024
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  2. Merge pull request #370 from vhaasteren/fix_posunits 

    Properly address units in PintPulsar position
    @vhaasteren
    vhaasteren authored May 9, 2024
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Commits on Aug 12, 2024

  1. Extra comment to make tests re-run

    @vhaasteren
    vhaasteren committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. move to macos-13

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  2. Merge branch 'dev' into fix_ci

    @AaronDJohnson
    AaronDJohnson authored Aug 13, 2024
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  3. add 3.12, update codecov

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  4. Merge branch 'fix_ci' of https://github.com/AaronDJohnson/enterprise … 

    …into fix_ci
    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  5. Add Python 3.12

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  6. undo codecov upgrade

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  7. redo upgrade codecov, lower max healpy version

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  8. spacing is important...

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  9. missed one...

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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  10. undo upper limit on healpy

    @AaronDJohnson
    AaronDJohnson committed Aug 13, 2024
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Commits on Aug 15, 2024

  1. Update selections.py for "CHIME" 

    Add "CHIME" to 
def nanograv_backends(backend_flags):
    @alyssacassity
    alyssacassity authored Aug 15, 2024
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Commits on Aug 22, 2024

  1. Update selections.py 

    added "VEGAS" to list as requested
    @alyssacassity
    alyssacassity authored Aug 22, 2024
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Commits on Aug 24, 2024

  1. try to get verbose output

    @AaronDJohnson
    AaronDJohnson committed Aug 24, 2024
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Commits on Aug 25, 2024

  1. attempt 7896868

    @AaronDJohnson
    AaronDJohnson committed Aug 25, 2024
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  2. try to skip the problematic test

    @AaronDJohnson
    AaronDJohnson committed Aug 25, 2024
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Commits on Aug 26, 2024

  1. Merge pull request #391 from AaronDJohnson/fix_ci 

    Fix CI
    @vhaasteren
    vhaasteren authored Aug 26, 2024
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  2. Merge pull request #393 from alyssacassity/patch-1 

    Update selections.py for "CHIME" and "VEGAS"
    @AaronDJohnson
    AaronDJohnson authored Aug 26, 2024
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