hoho2b

[BUG] Float coordinate cause error (ValueError: invalid literal for int() with base 10)

2

Float in the coordinate will cause error: ``` Traceback (most recent call last): File "voc2coco.py", line 154, in convert(xml_files, args.json_file) File "voc2coco.py", line 109, in convert ymin = int(get_and_check(bndbox, "ymin",...

## Modifications - Suppress `VisibleDeprecationWarning` in [`nep-0034`](https://numpy.org/neps/nep-0034-infer-dtype-is-object.html) - Add progress bar for `tqdm` ## Message - Also shown in #285 ``` bonito/cli/convert.py:76: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences...

## Links - Fix #271 - Bug from https://github.com/nanoporetech/bonito/commit/21c1b4966d748731176e9ef70374f9c35ce81d8b ## Code https://github.com/nanoporetech/bonito/blob/fd4086ae55a73a2f99da5992a8b5300b96fbca0c/bonito/ctc/model.py#L48-L57 ```diff - return self.ctc_label_smoothing_loss(self, log_probs, targets, lengths) + return self.ctc_label_smoothing_loss(log_probs, targets, lengths) ```

## Modifications - Use [`np.ogrid`](https://numpy.org/doc/stable/reference/generated/numpy.ogrid.html) instead of double for loop to speed up the `build_mask` - Inspired by a StackOverflow post [link](https://stackoverflow.com/a/44874588) ## Tests & results #### Code ```python #...

## Notes - **[Why make this PR]** At first, I just want the `export` function for `PointwiseAvgPool`, then I found the 3D and 2D are in separate files with similar...

Hi, I'm trying to build 3D equivariant CNN and I found the tetrahedron symmetry group ("Describes 3D rotation symmetries of a tetrahedron in the space R3") is missing in [action-on-volume](https://quva-lab.github.io/escnn/api/escnn.gspaces.html#action-on-volume)....

**To Reproduce** 1. Edit the `1vsn.pdb` file, add an empty line in the end. (mimic the fix will be applied to the pdb) 2. Run the code ```bash docker run...