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bwm_usage_notebook.ipynb fails on colab #176
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Description
cell 18 fails for a known reason
# Workaround: brainglobe-atlasapi 2.3.1 fetches its atlas-version manifest
# from a Colab-unfriendly S3 endpoint that returns 403 for some Colab IPs.
# Pre-seed the cache so BrainGlobeAtlas() below can find a version manifest
# even when the live fetch fails. See https://github.com/brainglobe/brainglobe-atlasapi/issues/738
However it seems that the fallback doesnt work either.
Full output
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Could not fetch the latest atlas versions: 403
Using the last cached version from /root/.brainglobe/last_versions.conf
Downloading... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0.0% • 0/93 bytes • speed: ? • ETA: -:--:--
---------------------------------------------------------------------------
ReadError Traceback (most recent call last)
[/usr/local/lib/python3.12/dist-packages/brainglobe_atlasapi/bg_atlas.py](https://localhost:8080/#) in download_extract_file(self)
203 try:
--> 204 tar = tarfile.open(destination_path)
205 tar.extractall(path=self.brainglobe_dir)
3 frames
ReadError: file could not be opened successfully:
- method gz: ReadError('not a gzip file')
- method bz2: ReadError('not a bzip2 file')
- method xz: ReadError('not an lzma file')
- method tar: ReadError('truncated header')
The above exception was the direct cause of the following exception:
ReadError Traceback (most recent call last)
[/usr/local/lib/python3.12/dist-packages/brainglobe_atlasapi/bg_atlas.py](https://localhost:8080/#) in download_extract_file(self)
208 # Delete corrupted file so we can try again later
209 destination_path.unlink(missing_ok=True)
--> 210 raise tarfile.ReadError(
211 f"Atlas download was interrupted or corrupted. "
212 f"Please try again. Details: {e}"
ReadError: Atlas download was interrupted or corrupted. Please try again. Details: file could not be opened successfully:
- method gz: ReadError('not a gzip file')
- method bz2: ReadError('not a bzip2 file')
- method xz: ReadError('not an lzma file')
- method tar: ReadError('truncated header')
I tried clearing the cache, and retrying the download but this error seems to persist.
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bendichter commentedon Jun 29, 2026
Thanks for this issue, @asmacdo. I suspect brainglobe changed the way they are serving their atlas data in a way that has broken earlier versions of the brainglobe API. I'm investigating now.
bendichter commentedon Jul 1, 2026
See brainglobe/brainglobe-atlasapi#847