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titipata / pubmed_parser

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset
http://titipata.github.io/pubmed_parser/
MIT License
577 stars 164 forks source link

[Bug report] No module find error #152

Closed jonghyunlee1993 closed 2 weeks ago

jonghyunlee1993 commented 3 weeks ago

Describe the bug Hi,

I encountered a module installation issue, specifically the "ModuleNotFoundError: No module named 'pubmed_parser'".

I downgraded to a previous version, 0.4.0, and it worked.

To install the package, I used pip commands. I also tried a Git-based installation, but that failed as well.

Please look into this issue.

Thanks!

To Reproduce I’m using an M1-based iMac, and I encountered the same issue when using Colab.

Screenshots

image
Michael-E-Rose commented 2 weeks ago

Can confirm, something is fishy:

Z:\>pip install pubmed_parser --upgrade
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: pubmed_parser in c:\users\rosm\appdata\roaming\python\python311\site-packages (0.4.0)
Collecting pubmed_parser
  Downloading pubmed_parser-0.5-py3-none-any.whl.metadata (17 kB)
Requirement already satisfied: lxml in c:\users\rosm\appdata\roaming\python\python311\site-packages (from pubmed_parser) (5.1.0)
Requirement already satisfied: unidecode in c:\users\rosm\appdata\roaming\python\python311\site-packages (from pubmed_parser) (1.3.8)
Requirement already satisfied: requests in c:\users\rosm\appdata\roaming\python\python311\site-packages (from pubmed_parser) (2.31.0)
Requirement already satisfied: six in c:\users\rosm\appdata\roaming\python\python311\site-packages (from pubmed_parser) (1.16.0)
Requirement already satisfied: numpy in c:\users\rosm\appdata\roaming\python\python311\site-packages (from pubmed_parser) (1.26.4)
Requirement already satisfied: charset-normalizer<4,>=2 in c:\users\rosm\appdata\roaming\python\python311\site-packages (from requests->pubmed_parser) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in c:\users\rosm\appdata\roaming\python\python311\site-packages (from requests->pubmed_parser) (3.6)
Requirement already satisfied: urllib3<3,>=1.21.1 in c:\users\rosm\appdata\roaming\python\python311\site-packages (from requests->pubmed_parser) (2.2.1)
Requirement already satisfied: certifi>=2017.4.17 in c:\users\rosm\appdata\roaming\python\python311\site-packages (from requests->pubmed_parser) (2024.2.2)
Downloading pubmed_parser-0.5-py3-none-any.whl (7.4 kB)
Installing collected packages: pubmed_parser
  Attempting uninstall: pubmed_parser
    Found existing installation: pubmed_parser 0.4.0
    Uninstalling pubmed_parser-0.4.0:
      Successfully uninstalled pubmed_parser-0.4.0
Successfully installed pubmed_parser-0.5

[notice] A new release of pip is available: 24.0 -> 24.2
[notice] To update, run: python.exe -m pip install --upgrade pip

Z:\>python
Python 3.11.6 (tags/v3.11.6:8b6ee5b, Oct  2 2023, 14:57:12) [MSC v.1935 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pubmed_parser
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ModuleNotFoundError: No module named 'pubmed_parser'
Michael-E-Rose commented 2 weeks ago

Found the mistake and fixed it. An installation from GitHub will deliver all the bugfixes and improvements of version 0.5.

@titipata , would you please bump a new version to PyPI? I suggest simply 0.5.1 - thanks!

titipata commented 1 week ago

@Michael-E-Rose This is done. Thank you!!