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Fix_function_category #155

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Commits on Jul 8, 2024

  1. create linear_intensity_profile.ipynb haesleinhuepf#36

    @marabuuu
    marabuuu committed Jul 8, 2024
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Commits on Jul 17, 2024

  1. update linear_intensity_profile haesleinhuepf#36

    @marabuuu
    marabuuu committed Jul 17, 2024
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  2. add docstring haesleinhuepf#36

    @marabuuu
    marabuuu committed Jul 17, 2024
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Commits on Jul 31, 2024

  1. Added identify_centroids evaluation task

    @shinzlet
    shinzlet committed Jul 31, 2024
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  2. Add find_closest_neighbors test

    @shinzlet
    shinzlet committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. Added load_bgr_tif_and_output_rgb test case

    @shinzlet
    shinzlet committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. Merge pull request haesleinhuepf#82 from marabuuu/linear-intensity-pr… 

    …ofile

Linear intensity profile
    @haesleinhuepf
    haesleinhuepf authored Aug 2, 2024
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  2. Adjusted floating point comparison to account for error, made dtype e… 

    …xplicit on image data
    @shinzlet
    shinzlet committed Aug 2, 2024
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Commits on Aug 4, 2024

  1. Add local_maxima_from_distance_transform test case

    @ilan-theodoro
    ilan-theodoro committed Aug 4, 2024
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Commits on Aug 5, 2024

  1. Add flow_field_deformation test case

    @ilan-theodoro
    ilan-theodoro committed Aug 5, 2024
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  2. Add detect_ellipse test case

    @ilan-theodoro
    ilan-theodoro committed Aug 5, 2024
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Commits on Aug 7, 2024

  1. Fix typo

    @JoOkuma
    JoOkuma committed Aug 7, 2024
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  2. readme typo

    @JoOkuma
    JoOkuma committed Aug 7, 2024
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  3. Adding test case for selecting cells that co-express some gene (inten… 

    …sity)
    @JoOkuma
    JoOkuma committed Aug 7, 2024
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  4. clean up jupyter outputs

    @JoOkuma
    JoOkuma committed Aug 7, 2024
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  5. Add new test to register 3D timelapses

    @JoOkuma
    JoOkuma committed Aug 7, 2024
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Commits on Aug 10, 2024

  1. added two test cases: gaussian fit to spot, and distance between two … 

    …image maxima
    Teun Huijben authored and Teun Huijben committed Aug 10, 2024
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Commits on Aug 12, 2024

  1. Merge pull request haesleinhuepf#87 from JoOkuma/fix-positive-typo 

    Fix typo
    @haesleinhuepf
    haesleinhuepf authored Aug 12, 2024
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  2. more detailed prompt, more asserts

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  3. Merge branch 'main' of https://github.com/shinzlet/human-eval-bia int… 

    …o pr/85
    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  4. rerun notebook

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  5. renamed and rerun notebook

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  6. Merge pull request haesleinhuepf#85 from shinzlet/main 

    Add 3 new test cases (`identify_centroids`, `find_closest_neighbors`, `load_bgr_tif_and_output_rgb`)
    @haesleinhuepf
    haesleinhuepf authored Aug 12, 2024
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  7. made test more flexible, added test-cases

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  8. tiny documentation update

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  9. test ignoring order of points, return points as list of coordinates

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  10. Merge pull request haesleinhuepf#86 from ilan-theodoro/main 

    Add `local_maxima_from_distance_transform`, `flow_field_deformation`, and `detect_ellipse` test cases
    @haesleinhuepf
    haesleinhuepf authored Aug 12, 2024
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  11. add another example assert, rerun notebook

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  12. Merge pull request haesleinhuepf#91 from TeunHuijben/two-test-cases 

    Added two new test cases: `fit_gaussian_to_spot` and `distance_between_maxima`
    @haesleinhuepf
    haesleinhuepf authored Aug 12, 2024
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  13. reran notebook

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  14. be more precise in the docstring

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  15. Merge pull request haesleinhuepf#90 from JoOkuma/registration 

    Add new test to register 3D timelapses
    @haesleinhuepf
    haesleinhuepf authored Aug 12, 2024
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  16. more precise docstring

    @haesleinhuepf
    haesleinhuepf committed Aug 12, 2024
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  17. Merge pull request haesleinhuepf#88 from JoOkuma/cell-coexp 

    Adding test case for selecting cells that co-express some gene (image intensity)
    @haesleinhuepf
    haesleinhuepf authored Aug 12, 2024
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Commits on Aug 13, 2024

  1. Added FFT spectrum testcase. It is a hard one :-)

    @royerloic
    royerloic committed Aug 13, 2024
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  2. Addressed feedback from Robert.

    @royerloic
    royerloic committed Aug 13, 2024
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  3. Addressed feedback from Robert and fixed typos

    @royerloic
    royerloic committed Aug 13, 2024
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Commits on Aug 27, 2024

  1. add test case translate 3d image haesleinhuepf#7

    @marabuuu
    marabuuu committed Aug 27, 2024
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Commits on Aug 29, 2024

  1. update function name in check function haesleinhuepf#7

    @marabuuu
    marabuuu committed Aug 29, 2024
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Commits on Sep 3, 2024

  1. test case for image histogram

    @pr4deepr
    pr4deepr committed Sep 3, 2024
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  2. updated to include num_bins as argument

    @pr4deepr
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  3. Merge pull request haesleinhuepf#105 from pr4deepr/main 

    new test cases: image histogram
    @haesleinhuepf
    haesleinhuepf authored Sep 3, 2024
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  4. Update open_image_return_dimensions.ipynb 

    Make the order of the height and width return values more explicit.
    @tischi
    tischi authored Sep 3, 2024
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  5. Merge pull request haesleinhuepf#106 from haesleinhuepf/tischi-patch-1 

    Update open_image_return_dimensions.ipynb
    @haesleinhuepf
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  6. reran the notebook

    @haesleinhuepf
    haesleinhuepf committed Sep 3, 2024
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  7. Merge pull request haesleinhuepf#94 from royerloic/main 

    Added FFT spectrum testcase. It is a hard one :-)
    @haesleinhuepf
    haesleinhuepf authored Sep 3, 2024
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  8. renamed notebook, simplified docstring

    @haesleinhuepf
    haesleinhuepf committed Sep 3, 2024
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  9. Merge pull request haesleinhuepf#101 from marabuuu/translate-image 

    Add test case for translating an image
    @haesleinhuepf
    haesleinhuepf authored Sep 3, 2024
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  10. save_image_voxel_size notebook

    @pr4deepr
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Commits on Sep 4, 2024

  1. modified function to save the image and return save path

    @pr4deepr
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Commits on Sep 5, 2024

  1. creating new categories

    @pr4deepr
    pr4deepr committed Sep 5, 2024
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Commits on Sep 6, 2024

  1. ensured all tasks are in categories. Plot results

    @pr4deepr
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  2. remove all samples and result data except gpt-4o-2024-05-13, deepseek… 

    …-coder-v2 and reference
    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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  3. rephrased almost all prompts, to have more precise type hints 

    e.g. images are now described as "image provided as numpy array"
    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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  4. renamed old result files file to have "_old_prompt" in their model name

    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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  5. regenerated prompt list and problem file with new prompts

    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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  6. recreated samples for gpt-4o2024-05-13 and reference

    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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  7. sampled deepseek-coder-v2 with new prompts

    @haesleinhuepf
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  8. evaluated samples

    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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  9. redraw all figures with old and new prompts comparison

    @haesleinhuepf
    haesleinhuepf committed Sep 6, 2024
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Commits on Sep 7, 2024

  1. Fixed sum_intensity_projection docstring

    @ian-coccimiglio
    ian-coccimiglio committed Sep 7, 2024
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  2. Merge pull request haesleinhuepf#117 from ian-coccimiglio/fix_docstring 

    Fixed sum_intensity_projection docstring
    @haesleinhuepf
    haesleinhuepf authored Sep 7, 2024
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  3. fix sum images notebook to add two images rather than lists

    @ian-coccimiglio
    ian-coccimiglio committed Sep 7, 2024
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Commits on Sep 8, 2024

  1. add interpolate_stack.ipynb haesleinhuepf#6

    @marabuuu
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Commits on Sep 9, 2024

  1. Fixed functions requesting images providing lists

    @ian-coccimiglio
    ian-coccimiglio committed Sep 9, 2024
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  2. More flexible standard deviation acceptance

    @ian-coccimiglio
    ian-coccimiglio committed Sep 9, 2024
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  3. Allowed flexible interpretation of image dimensions based on PIL or N… 

    …umpy
    @ian-coccimiglio
    ian-coccimiglio committed Sep 9, 2024
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  4. Removed extra blocks

    @ian-coccimiglio
    ian-coccimiglio committed Sep 9, 2024
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  5. replace function with np.linspace to allow more intermediate slices h… 

    …aesleinhuepf#6
    @marabuuu
    marabuuu committed Sep 9, 2024
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  6. add categorise_functions yaml

    @pr4deepr
    pr4deepr committed Sep 9, 2024
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  7. Code to check if all test cases in yaml file

    @pr4deepr
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  8. removed old files

    @pr4deepr
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  9. read new yaml file and plot model performance by category

    @pr4deepr
    pr4deepr committed Sep 9, 2024
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  10. updated pull request template

    @pr4deepr
    pr4deepr committed Sep 9, 2024
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Commits on Sep 10, 2024

  1. update dock string haesleinhuepf#6 

    Co-authored-by: Robert Haase <[email protected]>
    @marabuuu @haesleinhuepf
    marabuuu and haesleinhuepf authored Sep 10, 2024
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  2. test case for scaling and affine transform

    @pr4deepr
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  3. Merge branch 'haesleinhuepf:development-collecting-new-test-cases' in… 

    …to development-collecting-new-test-cases
    @pr4deepr
    pr4deepr authored Sep 10, 2024
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  4. scale image affine transform test case

    @pr4deepr
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Commits on Sep 11, 2024

  1. remove print statement and added clarity for return values

    @pr4deepr
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  2. cleared outputs

    @pr4deepr
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  3. polygon and multipolygon test cases shapely

    @pr4deepr
    pr4deepr committed Sep 11, 2024
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  4. Revert "scale image affine transform test case" 

    This reverts commit 77bcb51.
    @pr4deepr
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  5. Merge pull request haesleinhuepf#132 from pr4deepr/shapely 

    Test cases using shapely
    @haesleinhuepf
    haesleinhuepf authored Sep 11, 2024
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  6. remove comment, too obvious

    @haesleinhuepf
    haesleinhuepf authored Sep 11, 2024
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  7. remove comment

    @haesleinhuepf
    haesleinhuepf authored Sep 11, 2024
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  8. just added another simple assert

    @haesleinhuepf
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  9. Merge pull request haesleinhuepf#125 from marabuuu/interpolate-stack 

    Add test case interpolating stack
    @haesleinhuepf
    haesleinhuepf authored Sep 11, 2024
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  10. rename notebook, format prompt

    @haesleinhuepf
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  11. Merge pull request haesleinhuepf#110 from pr4deepr/development-collec… 

    …ting-new-test-cases

save_image_voxel_size notebook
    @haesleinhuepf
    haesleinhuepf authored Sep 11, 2024
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Commits on Sep 12, 2024

  1. Updated label images for more flexible inputs

    @ian-coccimiglio
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Commits on Sep 13, 2024

  1. clean rerun notebook

    @haesleinhuepf
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  2. Merge pull request haesleinhuepf#126 from ian-coccimiglio/fix_stdev 

    Adjust mean_std_column to accept both pandas and numpy stdev
    @haesleinhuepf
    haesleinhuepf authored Sep 13, 2024
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  3. Reverted change to workflow_batch_process_folder_count_labels

    @ian-coccimiglio
    ian-coccimiglio committed Sep 13, 2024
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Commits on Oct 14, 2024

  1. updated test cases jsonl + readme

    @haesleinhuepf
    haesleinhuepf committed Oct 14, 2024
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Commits on Oct 17, 2024

  1. Added new cases studies for metadata reading plus some image analysis… 

    … snippets
    @rmassei
    rmassei committed Oct 17, 2024
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Commits on Oct 18, 2024

  1. Correct the prompting of the new test cases

    @rmassei
    rmassei committed Oct 18, 2024
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Commits on Nov 21, 2024

  1. Remove test-case which didnt pass 

    see haesleinhuepf#144
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    haesleinhuepf committed Nov 21, 2024
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  2. Remove test which seems impossible to pass 

    see haesleinhuepf#145
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    haesleinhuepf committed Nov 21, 2024
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  3. remove dyfunctional test-case 

    see haesleinhuepf#146
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    haesleinhuepf committed Nov 21, 2024
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  4. remove test with to simple assert statements 

    see haesleinhuepf#147
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    haesleinhuepf committed Nov 21, 2024
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  5. renamed notebooks and functions, executed notebooks, refined docstrings

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    haesleinhuepf committed Nov 21, 2024
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  6. Merge pull request haesleinhuepf#142 from rmassei/main 

    New Test-Case - Metadata Reading plus some basics image processing
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    haesleinhuepf authored Nov 21, 2024
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  7. Merge branch 'main' into pr/129

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    haesleinhuepf committed Nov 21, 2024
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  8. reran notebook

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    haesleinhuepf committed Nov 21, 2024
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  9. Merge pull request haesleinhuepf#129 from pr4deepr/function_categorize 

    Categorise test cases
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    haesleinhuepf authored Nov 21, 2024
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  10. Merge pull request haesleinhuepf#134 from ian-coccimiglio/bfix_label 

    [Fixing Test Cases] Allow 0 in label image test cases
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    haesleinhuepf authored Nov 21, 2024
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  11. Merge pull request haesleinhuepf#127 from ian-coccimiglio/bfix_imdim 

    [Fixing-Test-Cases] Image Dimensions reading
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    haesleinhuepf authored Nov 21, 2024
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  12. Merge branch 'main' into prompt-refinement

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    haesleinhuepf committed Nov 21, 2024
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  13. sync with dev branch

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    haesleinhuepf committed Nov 21, 2024
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  14. sync with dev branch

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    haesleinhuepf committed Nov 21, 2024
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  15. Merge branch 'development-collecting-new-test-cases' into prompt-refi… 

    …nement
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    haesleinhuepf authored Nov 21, 2024
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  16. Merge pull request haesleinhuepf#118 from haesleinhuepf/prompt-refine… 

    …ment

Prompt refinement (discussion about if this should be merged or not)
    @haesleinhuepf
    haesleinhuepf authored Nov 21, 2024
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  17. Merge pull request haesleinhuepf#121 from ian-coccimiglio/fix_sum_images 

    Fixing test-cases related to Numpy I/O
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    haesleinhuepf authored Nov 21, 2024
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  18. deleted all sample files

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    haesleinhuepf committed Nov 21, 2024
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  19. Merge branch 'development-collecting-new-test-cases' of https://githu… 

    …b.com/haesleinhuepf/human-eval-bia into development-collecting-new-test-cases
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    haesleinhuepf committed Nov 21, 2024
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  20. deleted all sample files

    @haesleinhuepf
    haesleinhuepf committed Nov 21, 2024
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  21. remove test case which didn't pass 

    see haesleinhuepf#148
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    haesleinhuepf committed Nov 21, 2024
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  22. test-case formatting

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    haesleinhuepf committed Nov 21, 2024
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  23. categorised new test-cases, re-generated jsonl file + readme

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    haesleinhuepf committed Nov 21, 2024
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  24. sampled reference, redraw plots

    @haesleinhuepf
    haesleinhuepf committed Nov 21, 2024
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  25. update documentation

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    haesleinhuepf committed Nov 21, 2024
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Commits on Nov 27, 2024

  1. fixed summarize by case notebook for reference

    @pr4deepr
    pr4deepr committed Nov 27, 2024
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