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Adds sequence optimization #8

Merged
merged 135 commits into from
Sep 11, 2024
Merged

Adds sequence optimization #8

merged 135 commits into from
Sep 11, 2024

Commits on Apr 19, 2024

  1. Adds the Gamma class to handle multiple parameters

    @cabb99
    cabb99 committed Apr 19, 2024
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  2. Adds sample gamma arrays

    @cabb99
    cabb99 committed Apr 19, 2024
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Commits on Apr 26, 2024

  1. Corrects Gamma reading of AWSEM files

    @cabb99
    cabb99 committed Apr 26, 2024
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Commits on May 20, 2024

  1. changed valid_indices=range(len(_AA)) default argument to valid_indic… 

    …es=np.arange(len(_AA))
    Finley Clark committed May 20, 2024
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  2. Merge branch 'cabb99:main' into main

    @ftclark3
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  3. Merge branch 'main' of https://github.com/cabb99/Frustratometer 

    pulling merged fork to local
    Finley Clark committed May 20, 2024
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Commits on May 21, 2024

  1. Adds simpler handling for gammas

    @cabb99
    cabb99 committed May 21, 2024
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  2. Adds methods to calculate AB

    @cabb99
    cabb99 committed May 21, 2024
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Commits on May 28, 2024

  1. Merge remote-tracking branch 'refs/remotes/origin/main' 

    sync with remote to test frustratometer code against server
    Finley Clark committed May 28, 2024
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  2. Merge branch 'main' of https://github.com/cabb99/Frustratometer

    Finley Clark committed May 28, 2024
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Commits on Jun 1, 2024

  1. Update README.md 

    Changes CI badge location. (Displays failing even if fails are passing)
    @cabb99
    cabb99 authored Jun 1, 2024
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  2. Update README.md 

    Adds easter egg
    @cabb99
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  3. Update README.md

    @cabb99
    cabb99 authored Jun 1, 2024
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  4. Merge pull request #5 from cabb99/cabb99-readme 

    Edits readme
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    cabb99 authored Jun 1, 2024
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Commits on Jun 3, 2024

  1. added tests for sequence0 and sequence12

    Finley Clark committed Jun 3, 2024
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  2. added commented lines to tests/test_awsem_frustratometer.py which use… 

    …r can uncomment to modify tests if desired
    Finley Clark committed Jun 3, 2024
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  3. fixed Frustratometer.frustration(kind='configurational') call to Frus… 

    …tratometer.configurational_frustration()
    Finley Clark committed Jun 3, 2024
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  4. Merge remote-tracking branch 'ftclark3/main' 

    getting up to date
    Finley Clark committed Jun 3, 2024
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  5. removed .rar file generated by frustratometer server (decompressed fi… 

    …les already present in tests/data)
    Finley Clark committed Jun 3, 2024
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Commits on Jun 5, 2024

  1. added additional tests for sequences of varying heterogeneity and energy

    Finley Clark committed Jun 5, 2024
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  2. building on on previous commit

    Finley Clark committed Jun 5, 2024
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  3. building on on previous commit

    Finley Clark committed Jun 5, 2024
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  4. building on on previous commit

    Finley Clark committed Jun 5, 2024
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  5. finished test updates -- increased tolerance so that low heterogeneit… 

    …y sequences pass
    Finley Clark committed Jun 5, 2024
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  6. removed sequence parameter from frustratometer.Frustratometer.vmd() t… 

    …o prevent accidental misuse
    Finley Clark committed Jun 5, 2024
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  7. added sequence argument back to vmd function but raise warning if seq… 

    …uence passed to vmd is different from self.sequence
    Finley Clark committed Jun 5, 2024
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  8. raise tolerance for sequence0 configurational frustration again

    Finley Clark committed Jun 5, 2024
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Commits on Jun 13, 2024

  1. Merge remote-tracking branch 'origin/main' 

    bringing in carlos's stuff before push my commits back
    Finley Clark committed Jun 13, 2024
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  2. Merge pull request #6 from ftclark3/main 

    Fixing configurational call
    @cabb99
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Commits on Jun 14, 2024

  1. Merge branch 'main' of https://github.com/cabb99/DCA_Frustratometer i… 

    …nto ML
    @cabb99
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  2. Adds test for inner product calculation

    @cabb99
    cabb99 committed Jun 14, 2024
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  3. replaces numy.math with math to avoid deprecation

    @cabb99
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Commits on Jun 17, 2024

  1. fixed tcl visualization script so that highly or minimally frustrated… 

    … interactions are not drawn between residues adjacent in sequence
    Finley Clark committed Jun 17, 2024
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Commits on Jun 18, 2024

  1. Adds dE2 to sequence montecarlo method

    @cabb99
    cabb99 committed Jun 18, 2024
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Commits on Jun 21, 2024

  1. Optimizes all functions with numba

    @cabb99
    cabb99 committed Jun 21, 2024
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  2. Adds some function signatures to optimize compilation time

    @cabb99
    cabb99 committed Jun 21, 2024
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  3. Adds abstract class EnergyTerm

    @cabb99
    cabb99 committed Jun 21, 2024
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Commits on Jun 24, 2024

  1. Changes dictionaries to arrays

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  2. Maximum difference found was 0.51. Added more tolerace due to randomn… 

    …ess.
    @cabb99
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  3. Merged low heterogeneity sequences to have the same tolerance

    @cabb99
    cabb99 committed Jun 24, 2024
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  4. Fixes inner product test

    @cabb99
    cabb99 committed Jun 24, 2024
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Commits on Jul 20, 2024

  1. Defines types to reduce compilation time

    @cabb99
    cabb99 committed Jul 20, 2024
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  2. Moves mask creation and region mean computation outside of the mean i… 

    …nner product calculation
    @cabb99
    cabb99 committed Jul 20, 2024
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  3. Reordered functions

    @cabb99
    cabb99 committed Jul 20, 2024
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  4. Adds diff methods

    @cabb99
    cabb99 committed Jul 20, 2024
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  5. Defines initial energy terms

    @cabb99
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Commits on Jul 28, 2024

  1. committing changes i previously forgot to commit

    Finley Clark committed Jul 28, 2024
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Commits on Jul 30, 2024

  1. Updates numpy types to ndarray

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Commits on Jul 31, 2024

  1. Merge branch 'main' of https://github.com/HanaJaafari/DCA_Frustratometer

    @cabb99
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  2. Changes input to 2D masks

    @cabb99
    cabb99 committed Jul 31, 2024
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  3. Sets mean_inner_product as a 1D array

    @cabb99
    cabb99 committed Jul 31, 2024
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  4. Changes function to if conditions to optimize compilation time

    @cabb99
    cabb99 committed Jul 31, 2024
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  5. Removes masks

    @cabb99
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  6. Moves repeated indices out of internal loops 

    - 5x fold optimization
    @cabb99
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  7. Defines diff mean_inner_product_2_by_2 with test

    @cabb99
    cabb99 committed Jul 31, 2024
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  8. Defines inner product difference with tests

    @cabb99
    cabb99 committed Jul 31, 2024
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  9. Changes types to ndarray

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    cabb99 committed Jul 31, 2024
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  10. Makes numba types explicit

    @cabb99
    cabb99 committed Jul 31, 2024
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  11. Removes old functions from dE2 calculation

    @cabb99
    cabb99 committed Jul 31, 2024
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  12. Activates dE, HET and dE2 tests

    @cabb99
    cabb99 committed Jul 31, 2024
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  13. Adds summed energy example

    @cabb99
    cabb99 committed Jul 31, 2024
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  14. Adds support for multiplication and addition from other side

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Commits on Aug 5, 2024

  1. Adds caching to functions

    @cabb99
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  2. Adds caching to functions

    @cabb99
    cabb99 committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. Sets gap energy to 0

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Commits on Aug 7, 2024

  1. Corrects and adds a test for correct indicator and gamma arrays

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Commits on Aug 9, 2024

  1. Fixes dE2 calculation for short peptide

    @cabb99
    cabb99 committed Aug 9, 2024
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  2. allows the dummy decorator to take any parameter

    @cabb99
    cabb99 committed Aug 9, 2024
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  3. Defines functions for testing

    @cabb99
    cabb99 committed Aug 9, 2024
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  4. Moves test_ernegy_term class

    @cabb99
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Commits on Aug 10, 2024

  1. Moves inner product tests

    @cabb99
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Commits on Aug 12, 2024

  1. Creates tests for energy terms including variance

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  2. Adds small pdb for tests

    @cabb99
    cabb99 committed Aug 12, 2024
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  3. Fixes math using Energy Terms

    @cabb99
    cabb99 committed Aug 12, 2024
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Commits on Aug 13, 2024

  1. Fixes montecarlo benchmarking

    @cabb99
    cabb99 committed Aug 13, 2024
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  2. Reduces size of sample

    @cabb99
    cabb99 committed Aug 13, 2024
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  3. Adds benchmark function

    @cabb99
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  4. Fixes benchmark for swapping and mutations

    @cabb99
    cabb99 committed Aug 13, 2024
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  5. Moves energy term testing

    @cabb99
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  6. Adds profiling to benchmarks to locate slow process in variance

    @cabb99
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  7. Creates optimized function for the difference

    @cabb99
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  8. diff optimization 

    diff_mean_inner_product_2_by_2: 0.000599 seconds
Compiled signatures: [(int64, int64, Array(int64, 1, 'A', True, aligned=True), Array(float64, 1, 'A', True, aligned=True))]
No timing information available

diff_mean_inner_product_2_by_2_v2: 0.000157 seconds
Compiled signatures: [(int64, int64, Array(int64, 1, 'A', True, aligned=True), Array(float64, 1, 'A', True, aligned=True))]
No timing information available
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  9. Further optimizes diff_inner_product 

    diff_mean_inner_product_2_by_2: 0.000591 seconds
Compiled signatures: [(int64, int64, Array(int64, 1, 'A', True, aligned=True), Array(float64, 1, 'A', True, aligned=True))]
No timing information available

diff_mean_inner_product_2_by_2_v2: 0.000144 seconds
Compiled signatures: [(int64, int64, Array(int64, 1, 'A', True, aligned=True), Array(float64, 1, 'A', True, aligned=True))]
No timing information available
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  10. Removes paralellization to avoid double paralelization and reduce ove… 

    …rhead
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  11. Removes extra comments

    @cabb99
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  12. Adds numba signature to functions

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  13. Fixes AWSEM energy average

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    cabb99 committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. denergy_mutation passing tests

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  2. Removes debugging code

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    cabb99 committed Aug 14, 2024
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  3. Fixes variance calculation for numba (matrix product was too slow)

    @cabb99
    cabb99 committed Aug 14, 2024
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  4. Optimizes variance calculation

    @cabb99
    cabb99 committed Aug 14, 2024
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  5. Fixes montecarlo annealing

    @cabb99
    cabb99 committed Aug 14, 2024
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  6. Fixes parallel tempering

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  7. Removes initial seq_index for montecarlo initialization

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  8. Fixes montecarlo sequence being modified by mistake

    @cabb99
    cabb99 committed Aug 14, 2024
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  9. Allows ability to print other energies during annealing

    @cabb99
    cabb99 committed Aug 14, 2024
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  10. Adds Energy standard deviation calculation

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    cabb99 committed Aug 14, 2024
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Commits on Aug 15, 2024

  1. Simplifies writing to a file

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  2. Adds csv_writter wrapper

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    cabb99 committed Aug 15, 2024
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  3. Changes descriptions

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  4. Reorders imports

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  5. Adds Energy bound - Energy free example

    @cabb99
    cabb99 committed Aug 15, 2024
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  6. Removes extra tests

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  7. Moves awsem sample gamma files to test/data/gamma

    @cabb99
    cabb99 committed Aug 15, 2024
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  8. Removes plotting test

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  9. Adds sample awsem gamma files

    @cabb99
    cabb99 committed Aug 15, 2024
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  10. Adds function to compute energies in parallel

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    cabb99 committed Aug 15, 2024
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  11. Fixes edge case scenario when ni*nj==mi*mj but mi!=mj

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    cabb99 committed Aug 15, 2024
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  12. Changes test to new nersion of diff

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    cabb99 committed Aug 15, 2024
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  13. Changes integer return to float return

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    cabb99 committed Aug 15, 2024
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  14. Adds term to compute energy of selection

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    cabb99 committed Aug 15, 2024
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Commits on Aug 16, 2024

  1. Require numpy<2 (for prody)

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    cabb99 committed Aug 16, 2024
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Commits on Aug 17, 2024

  1. Adds sample energies for annealing

    @cabb99
    cabb99 committed Aug 17, 2024
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  2. Fixes error on yaml syntax

    @cabb99
    cabb99 committed Aug 17, 2024
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Commits on Aug 27, 2024

  1. Fixes numpy<2 requirement

    @cabb99
    cabb99 committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. Merge branch 'cabb99:main' into main

    @ftclark3
    ftclark3 authored Aug 28, 2024
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  2. Merge remote-tracking branch 'ftclark3/main' 

    latest updates from carlos and hana's modifications
    Finley Clark committed Aug 28, 2024
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  3. added option to write frustratogram to image file and exit instead of… 

    … making movie or opening vmd and leaving it there
    Finley Clark committed Aug 28, 2024
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  4. Adds utility function for naming time

    @cabb99
    cabb99 committed Aug 28, 2024
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  5. Minor formatting

    @cabb99
    cabb99 committed Aug 28, 2024
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  6. Install pydca with the constraint that numpy<2

    @cabb99
    cabb99 committed Aug 28, 2024
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  7. Adds nice time formatting to the benchmarks

    @cabb99
    cabb99 committed Aug 28, 2024
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  8. Removes parallelism from build_mean_inner_product_matrix

    @cabb99
    cabb99 committed Aug 28, 2024
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  9. Adds energy term benchmarks

    @cabb99
    cabb99 committed Aug 28, 2024
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  10. Removes extra tests

    @cabb99
    cabb99 committed Aug 28, 2024
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  11. Merge pull request #11 from ftclark3/main 

    write frustratogram image instead of movie
    @cabb99
    cabb99 authored Aug 28, 2024
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Commits on Sep 3, 2024

  1. Removes 3.12 test

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    cabb99 committed Sep 3, 2024
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Commits on Sep 5, 2024

  1. fixed numbification

    Finley Clark committed Sep 5, 2024
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Commits on Sep 8, 2024

  1. Merge pull request #12 from ftclark3/ML 

    fixed numbification
    @cabb99
    cabb99 authored Sep 8, 2024
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Commits on Sep 9, 2024

  1. Updates diff_mean_inner_product_2_by_2

    @cabb99
    cabb99 committed Sep 9, 2024
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  2. Merge branch 'ML' of https://github.com/cabb99/DCA_Frustratometer int… 

    …o ML
    @cabb99
    cabb99 committed Sep 9, 2024
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Commits on Sep 11, 2024

  1. Merges with main

    @cabb99
    cabb99 committed Sep 11, 2024
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  2. Merge pull request #10 from cabb99/ML 

    Sequence optimization
    @cabb99
    cabb99 authored Sep 11, 2024
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  3. Merges changes

    @cabb99
    cabb99 committed Sep 11, 2024
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  4. Merge branch 'HanaJaafari-main'

    @cabb99
    cabb99 committed Sep 11, 2024
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