G3-328: Update requirements and Release version 0.8.0

[bergsalex]

This will release version v0.8.0. This is a small release compared to v0.7.0, but contains important updates for related projects.

What's Changed

• G3-305: Adding missing ingress definitions to jax-cluster-prod-10--prod environment. by @bergsalex in G3-305: Adding missing ingress definitions to jax-cluster-prod-10--prod environment. #85
• G3 325 api genset endpoint update by @francastell in G3 325 api genset endpoint update #89
• G3-348: Switching to thejacksonlaboratory Auth0 tenant. by @bergsalex in G3-348: Switching to thejacksonlaboratory Auth0 tenant.  #90
• Fix bug in link sso_id to email logic by @bergsalex in Fix bug in link sso_id to email logic #91

Full Changelog: v0.7.0...v0.8.0

---

⚠️ A Special Note on Authentication Changes ⚠️

Updating API to use thejacksonlaboratory Auth0 client by default, and updating manifests to define the same.

Using swagger authentication will continue to work for Geneweaver users.

Please expect the following changes to the login process:

1. You will to be asked to "Log in to The Jackson Laboratory to continue."
2. You will see The Jackson Laboratory's logo on the login page, instead of the Geneweaver logo.

Impact on Geneweaver Client

A note for users of the geneweaver-client library and CLI.

This will break the geneweaver-client authentication defaults, meaning
⚠️ you will not be able to log in without additional action. ⚠️

To fix this, you will need to either:

1. Update the geneweaver-client library to version 0.10.0 or higher (see this PR) , or
2. Set the following environment variables before running the gweave commands, and then re-authneticate

export AUTH_DOMAIN="thejacksonlaboratory.auth0.com"
export AUTH_CLIENT_ID="f8QZPcIrPIG6DIeWR2Rr3C8X5bzx8zBz"
gweaver beta auth login --reauth

[github-actions]

Test Coverage Report

============================= test session starts ==============================
platform linux -- Python 3.11.9, pytest-8.3.2, pluggy-1.5.0
rootdir: /home/runner/work/geneweaver-api/geneweaver-api
configfile: pyproject.toml
plugins: asyncio-0.21.2, anyio-4.4.0, cov-4.1.0
asyncio: mode=Mode.STRICT
collected 339 items

tests/controllers/test_api_standards.py ................................ [  9%]
....................................................................ssss [ 30%]
ssssssssssssssss                                                         [ 35%]
tests/controllers/test_genes.py .............                            [ 39%]
tests/controllers/test_genesets.py ..................................... [ 50%]
..............                                                           [ 54%]
tests/controllers/test_monitor.py .                                      [ 54%]
tests/controllers/test_publications.py ........                          [ 56%]
tests/controllers/test_search.py ..                                      [ 57%]
tests/controllers/test_species.py ....                                   [ 58%]
tests/core/test_security.py ..........                                   [ 61%]
tests/services/io/test_read_file_contents.py ...............             [ 66%]
tests/services/test_gene.py ..............                               [ 70%]
tests/services/test_genset.py .......................................... [ 82%]
.......................................                                  [ 94%]
tests/services/test_monitors.py ..                                       [ 94%]
tests/services/test_ontology.py ....                                     [ 95%]
tests/services/test_publications.py .......                              [ 97%]
tests/services/test_species.py .......                                   [100%]

=============================== warnings summary ===============================
tests/data/__init__.py:10
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:10: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    geneset_response_json = importlib.resources.read_text(

../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80: 11 warnings
  /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/importlib/resources/_legacy.py:80: DeprecationWarning: open_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    with open_text(package, resource, encoding, errors) as fp:

tests/data/__init__.py:13
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:13: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    geneset_w_gene_id_type_json = importlib.resources.read_text(

tests/data/__init__.py:17
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:17: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    geneset_list_response_json = importlib.resources.read_text("tests.data", "geneset.json")

tests/data/__init__.py:19
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:19: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    gene_homologus_ids_json = importlib.resources.read_text(

tests/data/__init__.py:23
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:23: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    gene_id_mapping_json = importlib.resources.read_text("tests.data", "gene_maping.json")

tests/data/__init__.py:25
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:25: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    publications_json = importlib.resources.read_text("tests.data", "publications.json")

tests/data/__init__.py:27
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:27: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    jwt_test_keys_json = importlib.resources.read_text(

tests/data/__init__.py:31
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:31: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    species_json = importlib.resources.read_text("tests.data", "species.json")

tests/data/__init__.py:33
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:33: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    genes_json = importlib.resources.read_text("tests.data", "genes.json")

tests/data/__init__.py:35
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:35: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    monitors_json = importlib.resources.read_text("tests.data", "monitors.json")

tests/data/__init__.py:37
  /home/runner/work/geneweaver-api/geneweaver-api/tests/data/__init__.py:37: DeprecationWarning: read_text is deprecated. Use files() instead. Refer to https://importlib-resources.readthedocs.io/en/latest/using.html#migrating-from-legacy for migration advice.
    ontology_json = importlib.resources.read_text("tests.data", "ontology.json")

tests/controllers/test_genes.py: 10 warnings
tests/controllers/test_genesets.py: 2 warnings
  /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/httpx/_content.py:202: DeprecationWarning: Use 'content=<...>' to upload raw bytes/text content.
    warnings.warn(message, DeprecationWarning)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

---------- coverage: platform linux, python 3.11.9-final-0 -----------
Name                                            Stmts   Miss  Cover
-------------------------------------------------------------------
src/geneweaver/api/__init__.py                      5      2    60%
src/geneweaver/api/controller/__init__.py           0      0   100%
src/geneweaver/api/controller/api.py               14      0   100%
src/geneweaver/api/controller/genes.py             38      0   100%
src/geneweaver/api/controller/genesets.py         126      3    98%
src/geneweaver/api/controller/message.py           27      0   100%
src/geneweaver/api/controller/monitors.py          15      0   100%
src/geneweaver/api/controller/publications.py      34      0   100%
src/geneweaver/api/controller/search.py            22      0   100%
src/geneweaver/api/controller/species.py           17      0   100%
src/geneweaver/api/core/__init__.py                 0      0   100%
src/geneweaver/api/core/config.py                   2      0   100%
src/geneweaver/api/core/config_class.py            27      0   100%
src/geneweaver/api/core/exceptions.py              13      1    92%
src/geneweaver/api/core/security.py               119     20    83%
src/geneweaver/api/dependencies.py                 61     30    51%
src/geneweaver/api/main.py                          1      0   100%
src/geneweaver/api/schemas/__init__.py              0      0   100%
src/geneweaver/api/schemas/apimodels.py            50      0   100%
src/geneweaver/api/schemas/auth.py                 18      0   100%
src/geneweaver/api/schemas/messages.py             18     18     0%
src/geneweaver/api/schemas/score.py                13     13     0%
src/geneweaver/api/services/__init__.py             0      0   100%
src/geneweaver/api/services/genes.py               45      0   100%
src/geneweaver/api/services/geneset.py            184      4    98%
src/geneweaver/api/services/io.py                   4      0   100%
src/geneweaver/api/services/monitors.py            10      0   100%
src/geneweaver/api/services/parse/__init__.py       0      0   100%
src/geneweaver/api/services/publications.py        47      0   100%
src/geneweaver/api/services/pubmeds.py              0      0   100%
src/geneweaver/api/services/species.py             18      3    83%
-------------------------------------------------------------------
TOTAL                                             928     94    90%
Coverage HTML written to dir htmlcov

Required test coverage of 60% reached. Total coverage: 89.87%
================= 319 passed, 20 skipped, 34 warnings in 5.56s =================