Update python dependencies

[afuetterer]

Some dependency versions are quite dated. Let's update those.

Versions

$ python -m pip list --outdated
Package                  Version Latest Type
------------------------ ------- ------ -----
beautifulsoup4           4.8.2   4.12.2 wheel
chardet                  3.0.4   5.2.0  wheel
click                    7.1.2   8.1.7  wheel
configparser             5.0.2   6.0.0  wheel
connexion                2.9.0   2.14.2 wheel
extruct                  0.13.0  0.16.0 wheel
Flask                    1.1.4   2.3.3  wheel
Flask-Cors               3.0.10  4.0.0  wheel
Flask-Limiter            2.0.0   3.5.0  wheel
idna                     2.10    3.4    wheel
IDUtils                  1.1.14  1.2.1  wheel
itsdangerous             1.1.0   2.1.2  wheel
Jinja2                   2.11.3  3.1.2  wheel 
jmespath                 0.10.0  1.0.1  wheel
jsonschema               3.2.0   4.19.0 wheel
levenshtein              0.12.0  0.21.1 wheel
MarkupSafe               2.0.1   2.1.3  wheel
openapi-schema-validator 0.1.6   0.6.0  wheel
openapi-spec-validator   0.3.3   0.6.0  wheel
pandas                   1.5.3   2.1.0  wheel
pyrsistent               0.16.1  0.19.3 wheel
PyYAML                   5.3.1   6.0.1  wheel
rapidfuzz                3.1.2   3.2.0  wheel
rdflib                   6.1.1   7.0.0  wheel
requests                 2.24.0  2.31.0 wheel
SPARQLWrapper            1.8.5   2.0.0  wheel
tika                     1.25    2.6.0  sdist
tldextract               3.1.2   3.4.4  wheel
urlextract               1.2.0   1.8.0  wheel
urllib3                  1.25.11 2.0.4  wheel
Werkzeug                 1.0.1   2.3.7  wheel

Tasks

• [x] autosemver #376
• [x] beautifulsoup4 #407
• [x] lxml #407
• [x] jmespath #407
• [x] configparser #407
• [x] idutils #407
• [x] requests #407
• [x] waitress #407
• [x] remove werkzeug (transitive dependency (connexion, flask)) #407
• [x] remove markupsafe (transitive dependency (connexion, jinja2)) #407
• [x] flask-cors #407
• [x] levenshtein #407
• [x] rapidfuzz #407
• [x] pyld #407
• [x] feedparser #407
• [x] connexion[swagger-ui]
• [x] pandas -> update requires Python >=3.9 #410
• [x] extruct: https://github.com/scrapinghub/extruct/blob/master/HISTORY.rst #410
• [x] flask-limiter: https://github.com/alisaifee/flask-limiter/blob/master/HISTORY.rst #410
• [x] pyyaml #410
• [x] tldextract: https://github.com/john-kurkowski/tldextract/blob/master/CHANGELOG.md #410
• [x] urlextract: https://github.com/lipoja/URLExtract/blob/master/CHANGELOG.rst #410
• [x] tika: https://github.com/chrismattmann/tika-python/compare/1.25...2.6.0 #410
• [x] sparqlwrapper: https://github.com/RDFLib/sparqlwrapper/blob/master/ChangeLog.txt #410
• [x] rdflib: https://github.com/RDFLib/rdflib/blob/main/CHANGELOG.md #410
• [x] flask updated to 2.2.5, 2.3 is not compatible with connexion #410

Relevant

• pyRdfa3 -> project has been archived by the owner on Jun 21, 2022

Related: #357 #409

[afuetterer]

Is there a reason for the version constraint flask-limiter<=2.0.0 @huberrob? What was the intention?

[huberrob]

I think there was a conflict with connexion or Werkzeug, but not sure..

[afuetterer]

Alright, I will investigate. I updated to the last version 2.14 of connexion in #407. Which works fine. If it works with flask-limiter 3.5 I will drop this constraint.

connexion team is also working on a version 3.0.0.

[afuetterer]

All done.