filippocastelli / keggutils Goto Github PK
View Code? Open in Web Editor NEWUtils for working with KEGG data on NetworkX
License: GNU General Public License v3.0
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keggutils's Issues
CircleCI failing even if tests are ok
I'm trying to add OK notebook execution testing as a condition ci PASSED status, documentation notebooks intentionally produce errors right now to test if CircleCI can catch them.
AttributeError: 'KEGGpathway' object has no attribute 'node'
Executing
import KEGGutils as kg
pathway = kg.KEGGpathway(pathway_id='hsa05224')yields the error AttributeError: 'KEGGpathway' object has no attribute 'node'.
This can be fixed by editing "KEGGutils/KEGGpathway.py":
# line 164
self.pos.update({n: self.node[n]["xy"]})
# to
self.pos.update({n: self.nodes[n]["xy"]})
# line 484
"nodes": (self.node[e1]["name"], self.node[e2]["name"]),
# to
"nodes": (self.nodes[e1]["name"], self.nodes[e2]["name"]),File not found error in some of the API methods
After fresh install of KEGGutils in a virtual environment:
>>> import KEGGutils as kg
>>> kg.keggapi_list('hsa')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/erikhuckvale/tmp/.env/lib/python3.10/site-packages/KEGGutils/KEGGapi.py", line 533, in keggapi_list
org_codes = get_organism_codes()
File "/Users/erikhuckvale/tmp/.env/lib/python3.10/site-packages/KEGGutils/KEGGapi.py", line 1003, in get_organism_codes
organism_fulltext = org_codespath.read_text()
File "/usr/local/Cellar/[email protected]/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/pathlib.py", line 1134, in read_text
with self.open(mode='r', encoding=encoding, errors=errors) as f:
File "/usr/local/Cellar/[email protected]/3.10.8/Frameworks/Python.framework/Versions/3.10/lib/python3.10/pathlib.py", line 1119, in open
return self._accessor.open(self, mode, buffering, encoding, errors,
FileNotFoundError: [Errno 2] No such file or directory: '/path/to/virtualenv/.env/lib/python3.10/site-packages/KEGGutils/res/org_codes.txt'
README is not PyPi-friendly
The PyPi website cannot appropriately read the README.md and shows gibberish, I'll find a solution for that in the near future.
conda yml env configurator
The project would benefit from a dedicated conda env configurator, planning on writing one.
Missing files in sdist
It appears that the manifest is missing at least one file necessary to build
from the sdist for version 0.3.3. You're in good company, about 5% of other
projects updated in the last year are also missing files.
+ /tmp/venv/bin/pip3 wheel --no-binary keggutils -w /tmp/ext keggutils==0.3.3
Looking in indexes: http://10.10.0.139:9191/root/pypi/+simple/
Collecting keggutils==0.3.3
Downloading http://10.10.0.139:9191/root/pypi/%2Bf/26a/1f6f737c42cff/KEGGutils-0.3.3.tar.gz (22 kB)
ERROR: Command errored out with exit status 1:
command: /tmp/venv/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-ydlbw80p/keggutils/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-ydlbw80p/keggutils/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-wheel-ydlbw80p/keggutils/pip-egg-info
cwd: /tmp/pip-wheel-ydlbw80p/keggutils/
Complete output (13 lines):
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-wheel-ydlbw80p/keggutils/setup.py", line 31, in <module>
install_requires= get_requirements(),
File "/tmp/pip-wheel-ydlbw80p/keggutils/setup.py", line 15, in get_requirements
reqs = reqpath.read_text().splitlines()
File "/usr/lib/python3.8/pathlib.py", line 1227, in read_text
with self.open(mode='r', encoding=encoding, errors=errors) as f:
File "/usr/lib/python3.8/pathlib.py", line 1213, in open
return io.open(self, mode, buffering, encoding, errors, newline,
File "/usr/lib/python3.8/pathlib.py", line 1069, in _opener
return self._accessor.open(self, flags, mode)
FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
imghdr deprecation
imghdr is used in KEGGapi.py to infer image type, it is deprecated in python 3.11 and will be removed in 3.13.
In absence of standard lib alternatives one could use an external dependency like filetype https://github.com/h2non/filetype.py
definetly not an urgent issue but hey it's there
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