Tutorial data is gone #10
Description
Hi
I wanted to follow today your tutorial, to test a few things.
Unfortunately, it seems that the very first dataset called all.bed is not anymore in the repo.
Maybe I am missing something here, but in the notebook one of the 1st steps is reading this file with the helper functional example_file which should download then the file.
I get the following error :
----> [1](vscode-notebook-cell:?execution_count=47&line=1) all_bed_file = example_file("doc/ipynb/all.*",endswith="*.bed")
File /opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:58, in example_file(pattern, endswith)
[20](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:20) def example_file(pattern, endswith=None):
[21](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:21) """
[22](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:22) Returns the local location of a PySnpTools example file, downloading it
[23](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:23) if needed.
(...)
[56](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:56)
[57](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:57) """
---> [58](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/_example_file.py:58) return pysnptools_hashdown._example_file(pattern, endswith=endswith)
File /opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:171, in Hashdown._example_file(self, pattern, endswith)
[169](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:169) return_file = None
[170](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:170) for filename in fnmatch.filter(self.file_to_hash, pattern):
--> [171](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:171) with self.open_read(filename) as local_file:
[172](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:172) if return_file is None and (
[173](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:173) endswith is None or fnmatch.fnmatch(filename, endswith)
[174](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:174) ):
[175](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:175) return_file = local_file
File /opt/conda/lib/python3.11/contextlib.py:137, in _GeneratorContextManager.__enter__(self)
...
[204](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:204) ), "URL return 'no item' ('{0}')".format(full_url)
[205](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:205) local_hash = Hashdown._get_hash(full_file)
[206](https://file+.vscode-resource.vscode-cdn.net/opt/conda/lib/python3.11/site-packages/pysnptools/util/filecache/hashdown.py:206) if hash is None:
AssertionError: URL return 'no item' ('https://github.com/fastlmm/PySnpTools/raw/ed14e050b2b75e7f4ddb73d512fbe928bbdb2b85/doc/ipynb/all.bed')If I am looking into older releases in the repo, I can find the file.
I downloaded this now manually and will continue that way, but wanted to raise this.
Cheers