[BUG]: maybe the h5ad is invalid, need to check it and replace it #33
Description
Version
main
Which installation method(s) does this occur on?
No response
Describe the bug.
url = "https://exampledata.scverse.org/rapids-singlecell/dli_census.h5ad"
wget.download(url, output)
Got HTTP 403 Forbidden
Minimum reproducible example
Relevant log output
cuml 25.6.0 requires nvidia-curand, which is not installed.
cuml 25.6.0 requires nvidia-cusolver, which is not installed.
cuml 25.6.0 requires nvidia-cusparse, which is not installed.
cuxfilter 25.6.0 requires cupy-cuda11x>=12.0.0, which is not installed.
nx-cugraph 25.6.0 requires cupy-cuda11x>=12.0.0, which is not installed.
cucim 25.6.0 requires cupy-cuda11x>=12.0.0, which is not installed.
cuxfilter 25.6.0 requires bokeh<=3.6.3,>=3.1, but you have bokeh 3.7.3 which is incompatible.
cuxfilter 25.6.0 requires shapely<2.1.0, but you have shapely 2.1.1 which is incompatible.
Successfully installed anndata-0.11.4 array-api-compat-1.12.0 asciitree-0.3.3 deprecated-1.2.18 fasteners-0.20 fonttools-4.61.1 h5py-3.13.0 legacy-api-wrap-1.4.1 natsort-8.4.0 networkx-3.4.2 numcodecs-0.15.1 pynndescent-0.5.13 rapids-singlecell-0.12.6 scanpy-1.11.1 scikit-image-0.25.2 scikit-learn-1.5.2 scikit-misc-0.5.1 scipy-1.15.3 session-info2-0.1.2 tifffile-2025.5.10 umap-learn-0.5.7 wget-3.2 wrapt-1.17.2 zarr-2.18.7
Input Notebook: notebooks/03_scRNA_analysis_with_pearson_residuals.ipynb
Output Notebook: notebook_output/result_03_scRNA_analysis_with_pearson_residuals.ipynb
Executing: 0%| | 0/52 [00:00<?, ?cell/s]Executing notebook with kernel: python3
Executing Cell 1---------------------------------------
Ending Cell 1------------------------------------------
Executing: 2%|▏ | 1/52 [00:01<00:58, 1.14s/cell]Executing Cell 2---------------------------------------
Ending Cell 2------------------------------------------
Executing: 4%|▍ | 2/52 [00:06<02:55, 3.52s/cell]Executing Cell 3---------------------------------------
Ending Cell 3------------------------------------------
Executing: 6%|▌ | 3/52 [00:06<01:39, 2.03s/cell]Executing Cell 4---------------------------------------
Ending Cell 4------------------------------------------
Executing Cell 5---------------------------------------
Ending Cell 5------------------------------------------
Executing Cell 6---------------------------------------
creating data directory
Downloading cell data..
Ending Cell 6------------------------------------------
Executing: 12%|█▏ | 6/52 [00:07<00:39, 1.17cell/s]
Executing: 12%|█▏ | 6/52 [00:08<01:06, 1.44s/cell]
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "/opt/conda/lib/python3.12/site-packages/papermill/__main__.py", line 4, in <module>
papermill()
File "/opt/conda/lib/python3.12/site-packages/click/core.py", line 1442, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/click/core.py", line 1363, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/click/core.py", line 1226, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/click/core.py", line 794, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/click/decorators.py", line 34, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/lib/python3.12/site-packages/papermill/cli.py", line 235, in papermill
execute_notebook(
File "/opt/conda/lib/python3.12/site-packages/papermill/execute.py", line 131, in execute_notebook
raise_for_execution_errors(nb, output_path)
File "/opt/conda/lib/python3.12/site-packages/papermill/execute.py", line 251, in raise_for_execution_errors
raise error
papermill.exceptions.PapermillExecutionError:
---------------------------------------------------------------------------
Exception encountered at "In [3]":
---------------------------------------------------------------------------
HTTPError Traceback (most recent call last)
Cell In[3], line 18
16 if not os.path.isfile(output): # as it's not there, let's see if we have our downloaded file. If not, let's get it!
17 print('Downloading cell data..')
---> 18 wget.download(url, output)
20 adata = ad.read_h5ad(output)
21 adata= adata[adata.obs["assay"].isin(["10x 3' v3", "10x 5' v1", "10x 5' v2"])].copy()
File /opt/conda/lib/python3.12/site-packages/wget.py:526, in download(url, out, bar)
524 else:
525 binurl = url
--> 526 (tmpfile, headers) = ulib.urlretrieve(binurl, tmpfile, callback)
527 filename = detect_filename(url, out, headers)
528 if outdir:
File /opt/conda/lib/python3.12/urllib/request.py:240, in urlretrieve(url, filename, reporthook, data)
223 """
224 Retrieve a URL into a temporary location on disk.
225
(...) 236 data file as well as the resulting HTTPMessage object.
237 """
238 url_type, path = _splittype(url)
--> 240 with contextlib.closing(urlopen(url, data)) as fp:
241 headers = fp.info()
243 # Just return the local path and the "headers" for file://
244 # URLs. No sense in performing a copy unless requested.
File /opt/conda/lib/python3.12/urllib/request.py:215, in urlopen(url, data, timeout, cafile, capath, cadefault, context)
213 else:
214 opener = _opener
--> 215 return opener.open(url, data, timeout)
File /opt/conda/lib/python3.12/urllib/request.py:521, in OpenerDirector.open(self, fullurl, data, timeout)
519 for processor in self.process_response.get(protocol, []):
520 meth = getattr(processor, meth_name)
--> 521 response = meth(req, response)
523 return response
File /opt/conda/lib/python3.12/urllib/request.py:630, in HTTPErrorProcessor.http_response(self, request, response)
627 # According to RFC 2616, "2xx" code indicates that the client's
628 # request was successfully received, understood, and accepted.
629 if not (200 <= code < 300):
--> 630 response = self.parent.error(
631 'http', request, response, code, msg, hdrs)
633 return response
File /opt/conda/lib/python3.12/urllib/request.py:559, in OpenerDirector.error(self, proto, *args)
557 if http_err:
558 args = (dict, 'default', 'http_error_default') + orig_args
--> 559 return self._call_chain(*args)
File /opt/conda/lib/python3.12/urllib/request.py:492, in OpenerDirector._call_chain(self, chain, kind, meth_name, *args)
490 for handler in handlers:
491 func = getattr(handler, meth_name)
--> 492 result = func(*args)
493 if result is not None:
494 return result
File /opt/conda/lib/python3.12/urllib/request.py:639, in HTTPDefaultErrorHandler.http_error_default(self, req, fp, code, msg, hdrs)
638 def http_error_default(self, req, fp, code, msg, hdrs):
--> 639 raise HTTPError(req.full_url, code, msg, hdrs, fp)
HTTPError: HTTP Error 403: ForbiddenFull env printout
Other/Misc.
No response
Code of Conduct
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- I have searched the open bugs and have found no duplicates for this bug report