Update dependencies in fence after running deptry #1302

nss10 · 2025-10-10T19:54:28Z

Link to JIRA ticket if there is one: PD-77

New Features

Breaking Changes

Support for local_settings.py is removed completely.

Bug Fixes

Improvements

Dependency updates

Cleanup unused dependencies using deptry, add transitive dependencies in pyproject.toml

Deployment changes

Deployment changes are being done as a part of this gen3-helm PR (#426)

coveralls · 2025-10-10T20:00:14Z

Pull Request Test Coverage Report for Build 19682826605

Details

0 of 0 changed or added relevant lines in 0 files are covered.
220 unchanged lines in 3 files lost coverage.
Overall coverage increased (+0.02%) to 74.987%

Files with Coverage Reduction	New Missed Lines	%
config.py	17	68.06%
init.py	24	89.84%
scripting/fence_create.py	179	60.65%

Totals
Change from base Build 19682819011:	0.02%
Covered Lines:	8424
Relevant Lines:	11234

💛 - Coveralls

github-actions · 2025-10-10T20:38:24Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_oidc_client.py	2	0	2
tests/test_user_token.py	5	0	5
tests/test_google_data_access.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_register_user.py	0	2	2
TOTAL	66	10	76

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-10-13T15:49:24Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_oidc_client.py	2	0	2
tests/test_user_token.py	5	0	5
tests/test_google_data_access.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_register_user.py	0	2	2
TOTAL	66	10	76

Please find the detailed integration test report here

Please find the Github Action logs here

Avantol13 · 2025-10-13T18:25:49Z

bin/fence_create.py

If we want to be complete about this, take a look at the old cloud auto k8s configmaps and secrets that were relying on this: https://github.com/uc-cdis/cloud-automation/blob/master/kube/services/fence/fence-deploy.yaml#L69

And remove them from Helm: https://github.com/uc-cdis/gen3-helm/blob/ae911bca4a44c673d44f92f3827957a9338e79b9/helm/fence/values.yaml#L438

And make sure nothing breaks

And update the Breaking Changes bullet point for this PR so its clear that local_settings is no longer supported.

…ocal_settings.py`

nss10 · 2025-10-31T19:02:29Z

tests/test_import_fence.py

@@ -1,104 +0,0 @@
-"""


Deleting this test seems appropriate, since the main purpose of these tests was to ensure that Fence doesn’t crash when local_settings.py is missing. This made sense when local_settings.py was optional after being deprecated, but it now seems unnecessary. Thoughts?

…dependency_updates

github-actions · 2025-11-03T15:34:11Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_oidc_client.py	2	0	2
tests/test_user_token.py	5	0	5
tests/test_google_data_access.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_register_user.py	0	2	2
TOTAL	66	10	76

Please find the detailed integration test report here

Please find the Github Action logs here

…dependency_updates

github-actions · 2025-11-07T18:00:03Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_oidc_client.py	2	0	2
tests/test_user_token.py	5	0	5
tests/test_google_data_access.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_register_user.py	0	2	2
TOTAL	66	10	76

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-11-07T21:20:30Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_oidc_client.py	2	0	2
tests/test_user_token.py	5	0	5
tests/test_google_data_access.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
tests/test_register_user.py	0	2	2
TOTAL	66	10	76

Please find the detailed integration test report here

Please find the Github Action logs here

Avantol13 · 2025-11-19T17:09:07Z

.gitignore


 # Django stuff:
 *.log
-local_settings.py


let's still keep this in the .gitignore just in case some one has one, we don't want to check it in

Avantol13 · 2025-11-19T17:09:31Z

pyproject.toml

 # NOTE: for testing with updated libaries as git repos:
 # foobar = {git = "https://github.com/uc-cdis/some-repo", rev = "feat/test"}
-jinja2 = "^3.1.6"
+wtforms = "^3.2.1"


if possible, change all these ^ to >=

github-actions · 2025-11-19T18:16:15Z

Failed to Prepare CI environment

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paulineribeyre

lgtm just need to finish changing ^ to >=

github-actions · 2025-11-19T19:07:49Z

Failed to Prepare CI environment

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Avantol13 · 2025-11-19T19:10:04Z

fence/settings.py

can we remove this whole file safely?

Please help me understand this. With local_settings being gone, does fence still need the ability to search for the cofig in paths described by CONFIG_SEARCH_FOLDERS

Am I to reposition this variable such that we can get rid of this file, or am I to see if it is safe to eliminate this variable altogether?

reposition this variable such that we can get rid of this file

This is what I meant, sorry for being unclear. This was placed here as a bridge between the old and new config at the time (so if you had old config, it could find the new config). But now, we should just place that variable somewhere else and remove this file altogether.

We still need to search for the new config, but it can be put somewhere else. Maybe directly in the config.py:

fence/fence/config.py

Lines 12 to 14 in 4173550

DEFAULT_CFG_PATH = os.path.join(

os.path.dirname(os.path.abspath(__file__)), "config-default.yaml"

)

@nss10 it looks like the file is still here even though you removed the config. Can we just delete the entire file?

Sorry, I missed deleting the actual file. Thanks @paulineribeyre for taking care of this :)

github-actions · 2025-11-19T20:18:37Z

filepath	passed	failed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	0	15
tests/test_centralized_auth.py	16	0	0	16
tests/test_audit_service.py	3	0	3	6
tests/test_data_upload.py	8	0	1	9
tests/test_presigned_url.py	7	0	0	7
tests/test_user_token.py	5	0	0	5
tests/test_dbgap.py	4	0	1	5
tests/test_drs_endpoint.py	4	0	0	4
tests/test_client_credentials.py	1	0	0	1
tests/test_register_user.py	1	1	0	2
tests/test_oidc_client.py	2	0	0	2
tests/test_google_data_access.py	1	0	0	1
tests/test_ras_authn.py	0	0	3	3
TOTAL	67	1	8	76

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-11-21T17:26:17Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_user_token.py	5	0	5
tests/test_register_user.py	2	0	2
tests/test_client_credentials.py	1	0	1
tests/test_oidc_client.py	2	0	2
tests/test_google_data_access.py	1	0	1
tests/test_ras_authn.py	0	3	3
TOTAL	68	8	76

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-11-24T18:40:11Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_user_token.py	5	0	5
tests/test_register_user.py	2	0	2
tests/test_client_credentials.py	1	0	1
tests/test_oidc_client.py	2	0	2
tests/test_google_data_access.py	1	0	1
tests/test_ras_authn.py	0	3	3
TOTAL	68	8	76

Please find the detailed integration test report here

Please find the Github Action logs here

github-actions · 2025-11-25T20:55:24Z

filepath	passed	skipped	SUBTOTAL
tests/test_oauth2.py	15	0	15
tests/test_centralized_auth.py	16	0	16
tests/test_audit_service.py	3	3	6
tests/test_data_upload.py	8	1	9
tests/test_presigned_url.py	7	0	7
tests/test_dbgap.py	4	1	5
tests/test_drs_endpoint.py	4	0	4
tests/test_user_token.py	5	0	5
tests/test_register_user.py	2	0	2
tests/test_oidc_client.py	2	0	2
tests/test_google_data_access.py	1	0	1
tests/test_client_credentials.py	1	0	1
tests/test_ras_authn.py	0	3	3
TOTAL	68	8	76

Please find the detailed integration test report here

Please find the Github Action logs here

Update dependencies in fence

4feccd7

nss10 changed the title ~~Update dependencies in fence~~ Update dependencies in fence after running deptry Oct 10, 2025

Remove Deprecated local_settings.py

44a6eea

nss10 marked this pull request as ready for review October 13, 2025 15:50

nss10 requested a review from Avantol13 October 13, 2025 16:40

Avantol13 reviewed Oct 13, 2025

View reviewed changes

Delete references of local_settings and files that are linked to `l…

71102ee

…ocal_settings.py`

nss10 commented Oct 31, 2025

View reviewed changes

Merge branch 'master' of https://github.com/uc-cdis/fence into chore/…

c04e664

…dependency_updates

nss10 added 2 commits November 7, 2025 11:17

Merge branch 'master' of https://github.com/uc-cdis/fence into chore/…

ce9c522

…dependency_updates

Update poetry lock

62909d0

nss10 added 2 commits November 7, 2025 14:20

Update poetry lock to resolve snyk errors

bb89c64

Add a forced dependency on idna, to overcome a snyk dependency

fc45c35

nss10 requested review from Avantol13, k-burt-uch and paulineribeyre November 19, 2025 15:31

Avantol13 requested changes Nov 19, 2025

View reviewed changes

Replace ^ with >= and update gitignore

286fbb3

nss10 requested a review from Avantol13 November 19, 2025 17:40

paulineribeyre reviewed Nov 19, 2025

View reviewed changes

Update ^ tp >= for all entries in pyproject.toml

078abca

nss10 requested a review from paulineribeyre November 19, 2025 18:46

paulineribeyre previously approved these changes Nov 19, 2025

View reviewed changes

Avantol13 requested changes Nov 19, 2025

View reviewed changes

Update poetry lock

3cc527b

nss10 dismissed paulineribeyre’s stale review via 3cc527b November 19, 2025 19:37

Remove settings.py and test_settings.py completely

8277f53

nss10 requested review from Avantol13 and paulineribeyre November 21, 2025 18:14

Delete fence/settings.py

b40a424

paulineribeyre approved these changes Nov 24, 2025

View reviewed changes

Avantol13 approved these changes Nov 25, 2025

View reviewed changes

Merge branch 'master' into chore/dependency_updates

b215912

nss10 merged commit 34b17e1 into master Nov 25, 2025
12 checks passed

nss10 deleted the chore/dependency_updates branch November 25, 2025 21:02

	DEFAULT_CFG_PATH = os.path.join(
	os.path.dirname(os.path.abspath(__file__)), "config-default.yaml"
	)

Update dependencies in fence after running deptry #1302

Update dependencies in fence after running deptry #1302

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Pull Request Test Coverage Report for Build 19682826605

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