Import fails after clean installation

[jolaem]

After installing profet as per instructions I get the following traceback:

Python 3.10.12 (main, Feb  4 2025, 14:57:36) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import profet
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/sxy26921/myenvs/perc/lib/python3.10/site-packages/profet/__init__.py", line 1, in <module>
    from .profet import Fetcher
  File "/home/sxy26921/myenvs/perc/lib/python3.10/site-packages/profet/profet.py", line 1, in <module>
    from .alphafold import Alphafold_DB
  File "/home/sxy26921/myenvs/perc/lib/python3.10/site-packages/profet/alphafold.py", line 9, in <module>
    from requests_html import HTMLSession
  File "/home/sxy26921/myenvs/perc/lib/python3.10/site-packages/requests_html.py", line 14, in <module>
    from lxml.html.clean import Cleaner
  File "/home/sxy26921/myenvs/perc/lib/python3.10/site-packages/lxml/html/clean.py", line 18, in <module>
    raise ImportError(
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.

pip show profet shows:

Name: profet
Version: 0.0.1
Summary: Protein structure Fetcher from online databases
Home-page: https://github.com/alan-turing-institute/profet
Author: mooniean
Author-email: bcostagomes@turing.ac.uk
License: UNKNOWN
Location: /home/sxy26921/myenvs/perc/lib/python3.10/site-packages
Requires: bs4, numpy, pandas, pypdb, requests, requests-html
Required-by: 

So even though lxml_html_clean is included in setup.cfg, it looks like the version on pypi is older and does not have that package. I confirmed that instalaling profet from source pip install . does not raise this error.

Pypi package needs updating.

[jmp1985]

I've updated the workflows and the information on pypi to allow releases to be published. This should be fixed in #57

[jolaem]

@jmp1985 This still fails for me when installing from pypi.

(perc) sxy26921@LNXSCLT487:~$ pip install profet
Collecting profet
  Using cached profet-0.0.1-py3-none-any.whl (5.6 kB)
Requirement already satisfied: numpy in ./myenv/perc/lib/python3.10/site-packages (from profet) (2.2.6)
Requirement already satisfied: pandas in ./myenv/perc/lib/python3.10/site-packages (from profet) (2.3.1)
Requirement already satisfied: requests in ./myenv/perc/lib/python3.10/site-packages (from profet) (2.32.4)
Requirement already satisfied: pypdb in ./myenv/perc/lib/python3.10/site-packages (from profet) (2.4)
Requirement already satisfied: requests-html in ./myenv/perc/lib/python3.10/site-packages (from profet) (0.10.0)
Requirement already satisfied: bs4 in ./myenv/perc/lib/python3.10/site-packages (from profet) (0.0.2)
Requirement already satisfied: beautifulsoup4 in ./myenv/perc/lib/python3.10/site-packages (from bs4->profet) (4.13.4)
Requirement already satisfied: tzdata>=2022.7 in ./myenv/perc/lib/python3.10/site-packages (from pandas->profet) (2025.2)
Requirement already satisfied: python-dateutil>=2.8.2 in ./myenv/perc/lib/python3.10/site-packages (from pandas->profet) (2.9.0.post0)
Requirement already satisfied: pytz>=2020.1 in ./myenv/perc/lib/python3.10/site-packages (from pandas->profet) (2025.2)
Requirement already satisfied: charset_normalizer<4,>=2 in ./myenv/perc/lib/python3.10/site-packages (from requests->profet) (3.4.2)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./myenv/perc/lib/python3.10/site-packages (from requests->profet) (1.26.20)
Requirement already satisfied: idna<4,>=2.5 in ./myenv/perc/lib/python3.10/site-packages (from requests->profet) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in ./myenv/perc/lib/python3.10/site-packages (from requests->profet) (2025.7.9)
Requirement already satisfied: pyppeteer>=0.0.14 in ./myenv/perc/lib/python3.10/site-packages (from requests-html->profet) (2.0.0)
Requirement already satisfied: parse in ./myenv/perc/lib/python3.10/site-packages (from requests-html->profet) (1.20.2)
Requirement already satisfied: fake-useragent in ./myenv/perc/lib/python3.10/site-packages (from requests-html->profet) (2.2.0)
Requirement already satisfied: pyquery in ./myenv/perc/lib/python3.10/site-packages (from requests-html->profet) (2.0.1)
Requirement already satisfied: w3lib in ./myenv/perc/lib/python3.10/site-packages (from requests-html->profet) (2.3.1)
Requirement already satisfied: tqdm<5.0.0,>=4.42.1 in ./myenv/perc/lib/python3.10/site-packages (from pyppeteer>=0.0.14->requests-html->profet) (4.67.1)
Requirement already satisfied: websockets<11.0,>=10.0 in ./myenv/perc/lib/python3.10/site-packages (from pyppeteer>=0.0.14->requests-html->profet) (10.4)
Requirement already satisfied: importlib-metadata>=1.4 in ./myenv/perc/lib/python3.10/site-packages (from pyppeteer>=0.0.14->requests-html->profet) (8.7.0)
Requirement already satisfied: pyee<12.0.0,>=11.0.0 in ./myenv/perc/lib/python3.10/site-packages (from pyppeteer>=0.0.14->requests-html->profet) (11.1.1)
Requirement already satisfied: appdirs<2.0.0,>=1.4.3 in ./myenv/perc/lib/python3.10/site-packages (from pyppeteer>=0.0.14->requests-html->profet) (1.4.4)
Requirement already satisfied: six>=1.5 in ./myenv/perc/lib/python3.10/site-packages (from python-dateutil>=2.8.2->pandas->profet) (1.17.0)
Requirement already satisfied: typing-extensions>=4.0.0 in ./myenv/perc/lib/python3.10/site-packages (from beautifulsoup4->bs4->profet) (4.14.1)
Requirement already satisfied: soupsieve>1.2 in ./myenv/perc/lib/python3.10/site-packages (from beautifulsoup4->bs4->profet) (2.7)
Requirement already satisfied: cssselect>=1.2.0 in ./myenv/perc/lib/python3.10/site-packages (from pyquery->requests-html->profet) (1.3.0)
Requirement already satisfied: lxml>=2.1 in ./myenv/perc/lib/python3.10/site-packages (from pyquery->requests-html->profet) (6.0.0)
Requirement already satisfied: zipp>=3.20 in ./myenv/perc/lib/python3.10/site-packages (from importlib-metadata>=1.4->pyppeteer>=0.0.14->requests-html->profet) (3.23.0)
Installing collected packages: profet
Successfully installed profet-0.0.1
(perc) sxy26921@LNXSCLT487:~$ python
Python 3.10.12 (main, May 27 2025, 17:12:29) [GCC 11.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import profet
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/sxy26921/myenv/perc/lib/python3.10/site-packages/profet/__init__.py", line 1, in <module>
    from .profet import Fetcher
  File "/home/sxy26921/myenv/perc/lib/python3.10/site-packages/profet/profet.py", line 1, in <module>
    from .alphafold import Alphafold_DB
  File "/home/sxy26921/myenv/perc/lib/python3.10/site-packages/profet/alphafold.py", line 9, in <module>
    from requests_html import HTMLSession
  File "/home/sxy26921/myenv/perc/lib/python3.10/site-packages/requests_html.py", line 14, in <module>
    from lxml.html.clean import Cleaner
  File "/home/sxy26921/myenv/perc/lib/python3.10/site-packages/lxml/html/clean.py", line 18, in <module>
    raise ImportError(
ImportError: lxml.html.clean module is now a separate project lxml_html_clean.
Install lxml[html_clean] or lxml_html_clean directly.
>>> 

[jolaem]

Okay I've just spotted that pip was using cache in the text above, but tried again with --no-cache-dir and --force_reinstall and same issue, it continues installing version 0.0.1: profet-0.0.1-py3-none-any.whl

[jmp1985]

This should now be fixed