Closed ZhixuNi closed 4 years ago
Hi,
thank you very much for reporting and fixing this issue! I'll wait for the CI/CD to finish and then merge it. I'll also try to upload the new version to pip as soon as possible
Best, Manuel
Merging #203 into dev will increase coverage by
63.96%
. The diff coverage is84%
.
@@ Coverage Diff @@
## dev #203 +/- ##
==========================================
+ Coverage 15.94% 79.9% +63.96%
==========================================
Files 13 33 +20
Lines 1844 3951 +2107
==========================================
+ Hits 294 3157 +2863
+ Misses 1550 794 -756
Impacted Files | Coverage Δ | |
---|---|---|
tests/file_io_indexed_gzip_reader_test.py | 96.55% <ø> (ø) |
|
pymzml/file_classes/bytesMzml.py | 40% <0%> (ø) |
:arrow_up: |
pymzml/file_classes/indexedGzip.py | 96.96% <100%> (+54.54%) |
:arrow_up: |
tests/utils_decoder_test.py | 66.66% <100%> (ø) |
|
pymzml/regex_patterns.py | 100% <100%> (ø) |
:arrow_up: |
pymzml/file_classes/standardGzip.py | 97.14% <100%> (+60%) |
:arrow_up: |
tests/main_chromatogram_test.py | 89.47% <100%> (ø) |
|
tests/file_io_indexed_gzip_writer_test.py | 99% <100%> (ø) |
|
tests/test_file_paths.py | 100% <100%> (ø) |
|
tests/plot_spec_test.py | 98.38% <100%> (ø) |
|
... and 52 more |
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Hi!
Thanks for the response!
There are some problems to access the ndarrays in the pymzml.spec.Spectrum
This only happens in some windows 10 machines with anaconda.
Don't know if it is this UnicodeDecodeError issue or numpy issue.
Currently it solved on our PCs with this fix, but still do not know if this fits to other people or not.
Best,
Could you tell me the numpy and anaconda versions which gave you that error? I'm not too familiar with anaconda, but I'll try to have a closer look as soon as I can
I'm using conda/4.7.12 requests/2.22.0 CPython/3.7.4 Windows/10 Windows/10.0.18362
The develop environment info (Ptyhon 3.7.6) is as follows:
# packages in environment at C:\Users\winadmin\.conda\envs\envpy37:
#
# Name Version Build Channel
atomicwrites 1.3.0 pypi_0 pypi
attrs 19.3.0 pypi_0 pypi
ca-certificates 2019.11.27 0
certifi 2019.11.28 py37_0
chardet 3.0.4 pypi_0 pypi
codecov 2.0.15 pypi_0 pypi
colorama 0.4.3 pypi_0 pypi
coverage 5.0.3 pypi_0 pypi
cycler 0.10.0 pypi_0 pypi
cython 0.29.14 pypi_0 pypi
et-xmlfile 1.0.1 pypi_0 pypi
idna 2.8 pypi_0 pypi
importlib-metadata 1.4.0 pypi_0 pypi
jdcal 1.4.1 pypi_0 pypi
kiwisolver 1.1.0 pypi_0 pypi
llvmlite 0.31.0 pypi_0 pypi
matplotlib 3.1.2 pypi_0 pypi
more-itertools 8.1.0 pypi_0 pypi
natsort 7.0.0 pypi_0 pypi
numba 0.47.0 pypi_0 pypi
numpy 1.18.1 pypi_0 pypi
openpyxl 3.0.3 pypi_0 pypi
openssl 1.1.1d he774522_3
packaging 20.0 pypi_0 pypi
pandas 0.25.3 pypi_0 pypi
pip 19.3.1 py37_0
plotly 4.4.1 pypi_0 pypi
pluggy 0.13.1 pypi_0 pypi
py 1.8.1 pypi_0 pypi
pymzml 2.4.5 pypi_0 pypi
pyparsing 2.4.6 pypi_0 pypi
pyside2 5.14.0 pypi_0 pypi
pytest 5.3.4 pypi_0 pypi
pytest-cov 2.8.1 pypi_0 pypi
python 3.7.6 h60c2a47_2
python-dateutil 2.8.1 pypi_0 pypi
pytz 2019.3 pypi_0 pypi
regex 2020.1.8 pypi_0 pypi
requests 2.22.0 pypi_0 pypi
retrying 1.3.3 pypi_0 pypi
scipy 1.4.1 pypi_0 pypi
setuptools 44.0.0 py37_0
shiboken2 5.14.0 pypi_0 pypi
six 1.14.0 pypi_0 pypi
sqlite 3.30.1 he774522_0
urllib3 1.25.8 pypi_0 pypi
vc 14.1 h0510ff6_4
vs2015_runtime 14.16.27012 hf0eaf9b_1
wcwidth 0.1.8 pypi_0 pypi
wheel 0.33.6 py37_0
wincertstore 0.2 py37_0
xlrd 1.2.0 pypi_0 pypi
xlwt 1.3.0 pypi_0 pypi
zipp 2.0.0 pypi_0 pypi
I tried Numpy version 1.18.0 1.18.1 from conda and pip, the pip version 1.18.1 + this fix solved the issue.
Hope this info helps.
obo encode issue:
UnicodeDecodeError observed under Windows 10 1909 64bit. The windows 10 VM is using EN-US as default, with DE-DE and ZH-CN installed. For some mzml files, following error messages will occur:
or any access to
spectrum.mz
can lead to freeze of the program.Hot fix is applied by changing line 195 in
obo.py
fromto
Problems solved and all tests passed.
Add latest psi-ms.obo files:
Now files in 2020 should be fine while using psi-ms-4.1.33.obo.gz releaseon on date: 21:01:2020