Description
Hi there,
using sc.read(filename, ext='txt') I get the following irrelevant warning:
WARNING: Your filename has more than two extensions: ['.5_E9', '.0_E9', '.5', '.txt']. Only considering the two last: ['.5', '.txt']. WARNING: Your filename has more than two extensions: ['.5_E9', '.0_E9', '.5', '.txt']. Only considering the two last: ['.5', '.txt'].
(filename is GSE136689_Counts_Matrix_AllCells_E8.5_E9.0_E9.5.txt)
digging in the error is raised by the readwrite module's function is_valid_filename(filename), that checks the extensions regardless of the 'ext' parameter the sc.read function gets, and if it passes it sends it to _read.
inside the _read function, there is a second call to is_valid_filename, which raises the second warning (with exactly the same text)
seeing as this is the process, i don't get why even have the ext parameter, because currently it seams like it is only used to indicate when someone uses an unsupported extension
Versions
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anndata 0.8.0
scanpy 1.9.1
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PIL 9.1.0
PyQt5 NA
appnope 0.1.3
atomicwrites 1.4.0
autoreload NA
backcall 0.2.0
beta_ufunc NA
binom_ufunc NA
brotli NA
bs4 4.11.1
certifi 2022.05.18.1
cffi 1.15.0
chardet 4.0.0
charset_normalizer 2.0.12
cloudpickle 2.0.0
colorama 0.4.4
cycler 0.10.0
cython_runtime NA
cytoolz 0.11.2
dask 2022.05.0
dateutil 2.8.2
debugpy 1.6.0
decorator 5.1.1
defusedxml 0.7.1
entrypoints 0.4
fastcluster 1.1.26
fsspec 2022.3.0
gprofiler 1.0.0
h5py 3.6.0
idna 3.3
igraph 0.9.9
ipykernel 6.13.0
ipython_genutils 0.2.0
ipywidgets 7.7.0
jedi 0.18.1
jinja2 3.1.2
joblib 1.1.0
jupyter_server 1.17.0
kiwisolver 1.4.2
leidenalg 0.8.8
llvmlite 0.38.0
louvain 0.7.1
markupsafe 2.1.1
matplotlib 3.5.1
matplotlib_inline NA
mpl_toolkits NA
natsort 8.1.0
nbinom_ufunc NA
networkx 2.6.3
numba 0.55.0
numpy 1.21.5
packaging 21.3
pandas 1.4.0
parso 0.8.3
pexpect 4.8.0
phyloproc NA
pickleshare 0.7.5
pkg_resources NA
prompt_toolkit 3.0.29
psutil 5.9.0
ptyprocess 0.7.0
pydev_ipython NA
pydevconsole NA
pydevd 2.8.0
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.12.0
pyparsing 3.0.9
pytz 2022.1
requests 2.27.1
scipy 1.7.3
seaborn 0.11.2
session_info 1.0.0
setuptools 62.2.0
sip NA
six 1.16.0
sklearn 1.0.2
socks 1.7.1
soupsieve 2.3.1
sphinxcontrib NA
spyder 5.2.2
spyder_kernels 2.2.1
spydercustomize NA
statsmodels 0.13.2
storemagic NA
texttable 1.6.4
threadpoolctl 3.1.0
tlz 0.11.2
toolz 0.11.2
tornado 6.1
traitlets 5.2.0
typing_extensions NA
unicodedata2 NA
urllib3 1.26.9
wcwidth 0.2.5
wurlitzer 3.0.2
yaml 6.0
zipp NA
zmq 22.3.0
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IPython 7.33.0
jupyter_client 7.3.1
jupyter_core 4.10.0
jupyterlab 3.2.8
notebook 6.4.11
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Python 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:27:05) [Clang 12.0.1 ]
macOS-12.4-x86_64-i386-64bit
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Session information updated at 2022-07-03 15:14