Fixing pydantic dependency, updating others

[bergsalex]

No description provided.

[github-actions]

Test Coverage Report

---------- coverage: platform linux, python 3.11.9-final-0 -----------
Name                                          Stmts   Miss  Cover
-----------------------------------------------------------------
src/geneweaver/core/__init__.py                   1      0   100%
src/geneweaver/core/config.py                     2      0   100%
src/geneweaver/core/config_class.py               9      0   100%
src/geneweaver/core/enum.py                     301     11    96%
src/geneweaver/core/exc.py                        4      0   100%
src/geneweaver/core/mapping.py                    2      2     0%
src/geneweaver/core/parse/__init__.py             0      0   100%
src/geneweaver/core/parse/batch.py              112      2    98%
src/geneweaver/core/parse/csv.py                 54      0   100%
src/geneweaver/core/parse/enum.py                 9      0   100%
src/geneweaver/core/parse/exceptions.py          21      0   100%
src/geneweaver/core/parse/numpy.py               45      0   100%
src/geneweaver/core/parse/score.py               41      0   100%
src/geneweaver/core/parse/threshold.py           15      0   100%
src/geneweaver/core/parse/utils.py               24      3    88%
src/geneweaver/core/parse/xlsx.py                88     26    70%
src/geneweaver/core/publication/__init__.py       0      0   100%
src/geneweaver/core/publication/pubmed.py        71      0   100%
src/geneweaver/core/render/__init__.py            0      0   100%
src/geneweaver/core/render/batch.py              19      0   100%
src/geneweaver/core/render/csv.py                10      0   100%
src/geneweaver/core/render/gene_list.py           4      0   100%
src/geneweaver/core/schema/__init__.py            8      0   100%
src/geneweaver/core/schema/api_response.py       16      0   100%
src/geneweaver/core/schema/batch.py              74      4    95%
src/geneweaver/core/schema/gene.py               45      2    96%
src/geneweaver/core/schema/geneset.py            82      0   100%
src/geneweaver/core/schema/group.py              14      0   100%
src/geneweaver/core/schema/legacy_api.py         27      0   100%
src/geneweaver/core/schema/messages.py           16      0   100%
src/geneweaver/core/schema/ontology.py           19      0   100%
src/geneweaver/core/schema/project.py            12      0   100%
src/geneweaver/core/schema/publication.py        14      0   100%
src/geneweaver/core/schema/score.py              27      6    78%
src/geneweaver/core/schema/species.py            17     17     0%
src/geneweaver/core/schema/stubgenerator.py       6      0   100%
src/geneweaver/core/schema/user.py               23      0   100%
src/geneweaver/core/threshold.py                 12      0   100%
src/geneweaver/core/types.py                      8      0   100%
src/geneweaver/core/utils.py                      4      0   100%
-----------------------------------------------------------------
TOTAL                                          1256     73    94%
Coverage HTML written to dir htmlcov

Required test coverage of 90% reached. Total coverage: 94.19%
=== 48103 passed, 2 skipped, 1 xfailed, 21775 warnings in 111.87s (0:01:51) ====