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bwm_usage_notebook: work around brainglobe S3 403 on Colab #160

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Merged
bendichter merged 1 commit into from
May 13, 2026
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bwm_usage_notebook: work around brainglobe S3 403 on Colab #160

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25 changes: 25 additions & 0 deletions 000409/IBL/bwm_usage_notebook.ipynb
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Expand Up @@ -2277,6 +2277,31 @@
}
],
"source": [
"# Workaround: brainglobe-atlasapi 2.3.1 fetches its atlas-version manifest\n",
"# from a Colab-unfriendly S3 endpoint that returns 403 for some Colab IPs.\n",
"# Pre-seed the cache so BrainGlobeAtlas() below can find a version manifest\n",
"# even when the live fetch fails. See https://github.com/brainglobe/brainglobe-atlasapi/issues/738\n",
"from pathlib import Path\n",
"import urllib.request\n",
"\n",
"_bg_dir = Path.home() / \".brainglobe\"\n",
"_manifest_url = (\n",
" \"https://brainglobe.s3.us-west-2.amazonaws.com/atlas/atlases/last_versions.conf\"\n",
")\n",
"try:\n",
" _manifest = urllib.request.urlopen(_manifest_url, timeout=20).read().decode()\n",
"except Exception as _e: # noqa: BLE001\n",
" print(f\"Couldn't reach brainglobe manifest ({_e}); writing a minimal fallback.\")\n",
" _manifest = \"[atlases]\\nallen_mouse_25um = 3.0\\n\"\n",
"\n",
"# Write to both the V1 and V2 cache paths so whichever brainglobe-atlasapi\n",
"# code path reads from disk finds the file.\n",
"for _p in (_bg_dir / \"last_versions.conf\",\n",
" _bg_dir / \"brainglobe-atlasapi\" / \"atlases\" / \"last_versions.conf\"):\n",
" _p.parent.mkdir(parents=True, exist_ok=True)\n",
" if not _p.exists():\n",
" _p.write_text(_manifest)\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import numpy as np\n",
"from brainglobe_atlasapi import BrainGlobeAtlas\n",
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