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Bring old dev branch up-to-date #23

Merged
merged 427 commits into from
Jul 7, 2022
Merged

Bring old dev branch up-to-date #23

merged 427 commits into from
Jul 7, 2022
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Feb 21, 2022

  1. test bf16 with same batch size

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  2. not possible, try boring f16

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  3. Doesn't seem any quicker - but perhaps I can increase the batch size

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  4. add back in dr12/dr8, change project. Keep f16/b512

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    mwalmsley committed Feb 21, 2022
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  5. swap exp dir

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Commits on Feb 22, 2022

  1. load encoded jpegs into memory

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  2. adjust to do what I intend

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  3. debugging

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  4. implementing albumentations 

    This time ... without bugs I think.
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  5. Fixing to allow for conflict free merge

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  6. Removing channel check

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  7. Merge pull request #6 from mwalmsley/pytorch-albumentations 

    implementing albumentations + simplejpeg in-memory loading
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  8. inplace vs ref error

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  9. Merge branch 'pytorch' of github.com:mwalmsley/zoobot into pytorch

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  10. missing import

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  11. debugging

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  12. single gpu for debugging

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  13. disable wandb

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  14. adjust transpose

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  15. that gave CHW now, but album. actually wants HWC

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  16. tweak torch cast

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  17. tweak channels

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  18. add colour support

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  19. seems to work single gpu, let's crank it up

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  20. update exp dir

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  21. debug aug hanging

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  22. back to debug mode, but multi-gpu

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  23. adjust dataloader

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  24. see if still hangs with cv2 changed

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  25. no longer hangs. Turn off debug mode, test speed.

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  26. doesn't hang but seems very very slow - 4 min for sanity check. 

    Turn off cv2 tweak and set num workers back to 0 for main process
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  27. hmm, it's now 12 minutes per epoch :/ turn torchvision back to debug

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  28. missed a line

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  29. okay, works, turn off debug mode

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  30. with in-memory and torchvision, v v slow. try switch to OOM+album

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  31. missed a conversion

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  32. fix transpose

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  33. album (with non-grey) clocks in at 11-12 mins, out-of-mem

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  34. add scripts to move catalog to local

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  35. echo

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  36. typo

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  37. seems happy, do for realz

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  38. dr5 first

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  39. enable/disable albumentations dynamically

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  40. testing vison speed

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  41. typo

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  42. typo

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  43. debugging

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  44. remove extra tensor cast

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  45. forgot to reduce channels

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  46. torchvison still 4-5 mins per, v quick. Try album w/ actual greyscale

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  47. album unhappy. try local training

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  48. oops I copied the png

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  49. debug saving

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  50. add assert

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  51. do the jpegs

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  52. debug

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  53. maybe ref error?

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  54. tweak locs

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  55. hmm, it's slower. try /share with prefetch

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  56. prefetch=5 went from 4 mins to 3 mins? Try 40

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  57. turn wandb on

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  58. try pass the strategy as a plugin

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  59. working well on wandb, a little over 4 mins. try 6 workers

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  60. measured cpu use is lower but time v similar, gpu use v similar. Try 24

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  61. similar speed again. 

    Is it CPU limited and augs are expensive? turn off all possible augs
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  62. a little under 3 mins per epoch! augs are important, but not critically. 

    try also swap read_image for simplejpeg to further reduce cpu.
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  63. oops, I forgot to put num_workers back to 12 from 24!

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  64. rename

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  65. 2:30! turn augs back on, then compare simplejpeg vs tv

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  66. and rename

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  67. 02:50 for simplejpeg. How about tv read_image?

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  68. 3:00 for tv, very similar. 

    Best config: 12 workers, prefetch 40, vision augs (no second flip), simplejpeg reader, jpegs on networked drive.

Run for realz on DR8 - how long will it take?
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Commits on Feb 24, 2022

  1. add replication folder (tf)

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Commits on Mar 3, 2022

  1. adjust warnings

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Commits on Mar 14, 2022

  1. hdf5 tweak

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  2. refactor hdf5 loading

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  3. typo

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Commits on Mar 15, 2022

  1. minor cleanup

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Commits on Mar 24, 2022

  1. minor changes for pytorch and tf2.8

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  2. to `

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  3. complete quick docs pass to get compiling again

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  4. Merge pull request #9 from mwalmsley/pytorch-docs 

    Pytorch docs
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  5. change to furo from alabaster

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Commits on Apr 1, 2022

  1. fix broken links

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Commits on Apr 2, 2022

  1. Merge pull request #10 from camallen/patch-1 - thanks Cam! 

    fix broken doc links

Will do a pass now to update the links for the latest branch also :)
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  2. Updating docs ahead of torch pr

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Commits on Apr 4, 2022

  1. Continue updating documentation

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  2. add resnet/detectron integration

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  3. tweak run params

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  4. remove nodelist

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  5. cuda debugging

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  6. adjust node

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  7. post-refactor update

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  8. return res4 as output

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  9. enable variable representaiton_dim

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  10. fix shapes with a flatten

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  11. 4x batch size, full dr8

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  12. works, but let's do with b512 just for easy comparison

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Commits on Apr 5, 2022

  1. switch to res5 output

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  2. test batch size 256, as with original paper

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  3. add s244, color, back to batch=512

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  4. typo re transforms

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  5. check images

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  6. exited before upload

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  7. try single gpu

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  8. transpose images for wandb

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  9. transpose earlier

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  10. try to log earlier

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  11. restrict dataset size

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  12. debugging

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  13. try without colour

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  14. change node

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  15. back to greyscale, 224, low prefactor

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  16. new node

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  17. new node

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  18. refactor for speed

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  19. faster - try debug

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  20. debug torchvision

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  21. works, add greyscale back

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  22. typo, add custom greyscale

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  23. typo

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  24. adjust mean

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  25. works, add color back

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  26. works - now, finally, log the images

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  27. works and logs, try with 244 images on 1 gpu

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  28. works, do full 2xgpu run

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  29. increase prefetch

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  30. begin adjusting data notes

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Commits on Apr 6, 2022

  1. restart?

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  2. hmm, color broken, try greyscale

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  3. seems to work in greyscale...try again with color

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  4. typo

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  5. color definitely unhappy - check images on wandb

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  6. color images look perfect...try 1 gpu

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  7. enable albumentations

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  8. check if effnet still works

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  9. effnet works in color, so not data loading. 

    Try torchvision resnet in color
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  10. typo

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  11. 2 gpu -2cpu, see if dataloader still times out

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  12. try with unfrozen bn

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  13. works :) unfreezing batch norm was crucial 

    experiment with 1024 batch size, 16b
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  14. reduce prefetch factor

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  15. still prefetching too much

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  16. mem still high, try num workers 1

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  17. try one gpu - maybe it's smth with batchnorm

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  18. seems the memory keeps going up slowly, even with 1 gpu, 1 worker - t… 

    …ry effnet
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  19. drop batch size

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  20. try with normal dataloaders etc

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  21. add emptycache

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  22. clearing cache on each batch seems to solve the problem :)

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  23. try enforce catalog dtypes, columns

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  24. typo

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  25. JUST fits with effnet. Switch to detectron resnet, 2gpu (same num of … 

    …workers in total I think)
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  26. got a nan - maybe from b16, let's disable

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  27. another node

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  28. galahad still crashing - try with 1 gpu

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  29. try for real and cross fingers

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Commits on Apr 7, 2022

  1. add resnet->detectron2 example

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  2. train effnet greyscale on dr5

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  3. typo from refactoring

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  4. expand on pytorch/tf docs

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  5. data tweaks before adding resnet

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  6. minor cleanup throughout

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  7. Merge branch 'pytorch' into resnet

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  8. Merge pull request #11 from mwalmsley/resnet 

    Add Resnet50 (torchvision and detectron2) arch to PyTorch branch
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  9. major refactor to sep. user choice from zoobot api

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  10. remove extra arg

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  11. typo

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  12. update cols

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  13. wandb default on

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  14. epochs typo

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  15. add more defaults

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  16. typo

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  17. set default precision correctly

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  18. enable mixed precision

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  19. works - add color version

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  20. works, let's do detectron with greyscale

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  21. fix typo, increase prefetch to 8

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  22. actually, keep prefetch=4, set num_workers=8

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  23. restart effnet greyscale

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  24. restart effnet color

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  25. okay, back to detectron

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  26. Running well, bump to num_workers=11, add color

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  27. oops forgot name

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  28. start color torchvision

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  29. and run torchvision without color

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  30. rebuild docs

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  31. add training with pytorch guide

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  32. update components guide

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  33. Merge branch 'main' into pytorch

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  34. Merge pull request #12 from mwalmsley/pytorch 

    Add PyTorch version of Zoobot. Update all docs.
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  35. hotfix index link

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  36. Merge branch 'main' of github.com:mwalmsley/zoobot

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  37. restart detectron with full precision

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  38. and with color

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  39. and with torchvision

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  40. detectron color

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  41. and greyscale

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Commits on Apr 8, 2022

  1. refactor tf api to match pytorch

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  2. add replication slurm scripts for tensorflow

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  3. adjust slurm reqs

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  4. adjust docs to account for new tf api

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  5. Merge pull request #13 from mwalmsley/tf-api 

    Adjust API to use train_with_keras.train function
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  6. hotfix some readme links

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  7. add docker setup

    @camallen
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  8. add package groups for tf and pytorch

    @camallen
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  9. ignore wandb stuff

    @camallen
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  10. add model training args 

    allow training under a cpu only regime and control the number of data loader workers
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  11. avoid dectectron 2 imports for now 

    this can go back in when the dependecy install is fixed
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Commits on Apr 20, 2022

  1. refactor out pytorch datasets

    @mwalmsley
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  2. fix imports

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Commits on Apr 21, 2022

  1. generic lightning vs plain pytorch

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Commits on Apr 25, 2022

  1. Update docs to point to dropbox and data more obviously

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  2. formatting error

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  3. add citation.cff

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  4. Add Zenodo info

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Commits on Apr 26, 2022

  1. update cff message, thanks Alice

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  2. and fix doi typo

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  3. gz2 label typo

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  4. Merge branch 'refactor-pytorch-datasets' into main

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  5. Merge pull request #15 from mwalmsley/main 

    Update refactor with latest changes
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  6. Merge branch 'main' into dockerize

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  7. Merge pull request #14 from camallen/dockerize 

    Dockerize zoobot for pytorch and tensorflow versions - thanks Cam. Couple of tweaks incoming.
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  8. only support GalaxyDataModule still

    @mwalmsley
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  9. Add travis support to check install approach

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  10. bump python version for tf 2.8

    @mwalmsley
    mwalmsley committed Apr 26, 2022
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  11. update pluggy for travis

    @mwalmsley
    mwalmsley committed Apr 26, 2022
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  12. hmm, pluggy is up2date, try pytest and 3.8

    @mwalmsley
    mwalmsley committed Apr 26, 2022
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  13. flail around a little solving module error on travis

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    mwalmsley committed Apr 26, 2022
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  14. typo

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    mwalmsley committed Apr 26, 2022
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  15. I think it's the inits - add them

    @mwalmsley
    mwalmsley committed Apr 26, 2022
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  16. Travis works :) update readme with new instructions

    @mwalmsley
    mwalmsley committed Apr 26, 2022
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Commits on Apr 27, 2022

  1. Merge branch 'main' into refactor-pytorch-datasets

    @mwalmsley
    mwalmsley committed Apr 27, 2022
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Commits on Apr 29, 2022

  1. Complete refactor to use pytorch-galaxy-datasets, with example

    @mwalmsley
    mwalmsley committed Apr 29, 2022
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  2. build is unhappy, maybe missing this syntax

    @mwalmsley
    mwalmsley committed Apr 29, 2022
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  3. Merge pull request #16 from mwalmsley/refactor-pytorch-datasets 

    Refactor pytorch datasets
    @mwalmsley
    mwalmsley committed Apr 29, 2022
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  4. missed a rename, thanks cam

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    mwalmsley committed Apr 29, 2022
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  5. Merge pull request #17 from mwalmsley/refactor-pytorch-datasets 

    missed a rename, thanks cam
    @mwalmsley
    mwalmsley committed Apr 29, 2022
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Commits on May 11, 2022

  1. Minor refactor + add ortho gz2 label cols etc

    @mwalmsley
    mwalmsley committed May 11, 2022
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Commits on May 16, 2022

  1. Move detectron import into conditional 

    Avoid errors when gpus=None
    @mwalmsley
    mwalmsley committed May 16, 2022
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Commits on May 20, 2022

  1. add gz2 ortho dependencies explicitly

    @mwalmsley
    mwalmsley committed May 20, 2022
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  2. typo

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    mwalmsley committed May 20, 2022
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Commits on May 24, 2022

  1. allow multiple catalog paths to be passed 

    combines multiple csv files into one pandas dataframe at load time before passing to the training system
    @camallen
    camallen committed May 24, 2022
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  2. allow install of git based packages (pytorch_galaxy_datasets)

    @camallen
    camallen committed May 24, 2022
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Commits on Jun 30, 2022

  1. Merge pull request #19 from camallen/add-multi-catalog-loading 

    allow multiple catalog paths to be passed
    @mwalmsley
    mwalmsley committed Jun 30, 2022
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  2. Merge pull request #20 from camallen/add-git-to-dockerfile 

    allow install of git based packages (pytorch_galaxy_datasets)

see also #21
    @mwalmsley
    mwalmsley committed Jun 30, 2022
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Commits on Jul 7, 2022

  1. minor cleanup

    @mwalmsley
    mwalmsley committed Jul 7, 2022
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  2. new gitignore

    @mwalmsley
    mwalmsley committed Jul 7, 2022
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  3. adjust main with minor changes from dev. 

    ignore dev changes to train_model_on_catalog.py
    @mwalmsley
    mwalmsley committed Jul 7, 2022
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