[SYNPY-1798]: updated black to 26.3.1 and reran pre-commit by linglp · Pull Request #1341 · Sage-Bionetworks/synapsePythonClient

linglp · 2026-03-20T14:32:40Z

Problem:

There's a high security risk of black 23.3.0. I updated black to the latest version of 26.3.1
see: https://github.com/Sage-Bionetworks/synapsePythonClient/security/dependabot/42

Solution:

updated black in pre-commit to 26.3.1
updated lock file to match the latest version of black
re-installed pre-commit and ran it to fix all files

BryanFauble · 2026-03-20T18:01:25Z

 7. Delete wiki pages

 """
+


This is going to cause the line numbers in the tutorial to be incorrect by 1 line.

BryanFauble

Thanks for the updates. I didn't see any logic changes, just formatting updates. LGTM!

andrewelamb · 2026-03-20T19:12:27Z

@linglp Should we put min version of back in the setup.cfg file?

linglp · 2026-03-20T20:52:54Z

@andrewelamb

@linglp Should we put min version of back in the setup.cfg file?

I think if you just do pip install -e ".[dev]", it installs the latest version from PyPI at install time anyway.

thomasyu888 · 2026-03-31T18:49:00Z

Wait for 4.12 release to be completed to merge

Copilot

Pull request overview

Updates the repository’s formatting/tooling baseline by bumping the black pre-commit hook to 26.3.1, regenerating the Pipenv lockfile, and applying the resulting reformatting across code, tests, and docs.

Changes:

Bumped black in .pre-commit-config.yaml to 26.3.1.
Updated Pipfile.lock to reflect the new formatter dependency set.
Ran pre-commit/black across the repo, producing mostly whitespace/format-only diffs (plus a few incidental code edits).

Reviewed changes

Copilot reviewed 82 out of 83 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/unit/synapseutils/unit_test_synapseutils_walk.py	Reformatted multi-patch contexts
tests/unit/synapseutils/unit_test_synapseutils_sync.py	Reformatted multi-patch contexts
tests/unit/synapseutils/unit_test_synapseutils_monitor.py	Reformatted multi-patch contexts
tests/unit/synapseutils/unit_test_synapseutils_migrate.py	Reformatted SQL triple-quote usage
tests/unit/synapseutils/unit_test_synapseutils_describe.py	Reformatted multi-patch contexts
tests/unit/synapseutils/unit_test_synapseutils_copy.py	Reformatted multi-patch contexts
tests/unit/synapseclient/unit_test_tables.py	Reformatted multi-patch contexts
tests/unit/synapseclient/unit_test_get_permissions.py	Added blank line after docstring
tests/unit/synapseclient/unit_test_Entity.py	Tuple-unpacking style cleanup
tests/unit/synapseclient/unit_test_commandline.py	Docstring normalization
tests/unit/synapseclient/services/unit_test_json_schema.py	Added blank line after docstring
tests/unit/synapseclient/operations/unit_test_utility_operations.py	Added blank line after docstring
tests/unit/synapseclient/models/unit_test_entityview.py	Added blank line after docstring
tests/unit/synapseclient/models/synchronous/unit_test_docker.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_wiki_async.py	Reformatted multi-patch/raises contexts
tests/unit/synapseclient/models/async/unit_test_submission_bundle_async.py	Reformatted async-for binding
tests/unit/synapseclient/models/async/unit_test_submission_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_schema_organization_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_recordset_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_project_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_link_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_form_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_folder_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_file_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_evaluation_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_docker_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/models/async/unit_test_curation_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/extensions/unit_test_create_json_schema.py	Reformatted nested `open()` contexts
tests/unit/synapseclient/extensions/test_schema_management.py	Reformatted multi-patch contexts
tests/unit/synapseclient/core/upload/unit_test_multipart_upload.py	Reformatted multi-patch contexts
tests/unit/synapseclient/core/unit_test_version_check.py	Removed extra blank line
tests/unit/synapseclient/core/unit_test_sts_transfer.py	Reformatted conditional expression
tests/unit/synapseclient/core/unit_test_remote_storage_file_wrappers.py	Reformatted multi-patch contexts
tests/unit/synapseclient/core/unit_test_doze.py	Added blank line after module docstring
tests/unit/synapseclient/core/unit_test_Cache.py	Reformatted multi-patch contexts
tests/unit/synapseclient/core/multithread_download/unit_test_download_threads.py	Reformatted multi-patch contexts
tests/unit/synapseclient/core/download/unit_test_download_async.py	Reformatted multi-patch contexts
tests/unit/synapseclient/core/credentials/unit_test_cred_provider.py	Reformatted multi-patch contexts
tests/unit/synapseclient/api/unit_test_web_services.py	Added blank line after docstring
tests/unit/synapseclient/api/unit_test_entity_services.py	Added blank line after docstring
tests/test_utils.py	Trailing comma in signature
tests/integration/synapseclient/test_command_line_client.py	Reformatted multi-patch contexts
tests/integration/synapseclient/operations/async/test_utility_operations_async.py	Added blank line after docstring
tests/integration/synapseclient/operations/async/test_delete_operations_async.py	Added blank line after docstring
tests/integration/synapseclient/models/async/test_submission_bundle_async.py	Reformatted async-for binding
tests/integration/synapseclient/models/async/test_schema_organization_async.py	Added blank line after docstring
tests/integration/synapseclient/models/async/test_form_async.py	Added blank line after docstring
tests/integration/synapseclient/integration_test.py	Reformatted nested string writes
tests/integration/synapseclient/extensions/curator/test_schema_management.py	Added blank line after docstring
tests/integration/synapseclient/core/upload/test_multipart_upload.py	Tuple-unpacking style cleanup
tests/integration/synapseclient/core/upload/test_multipart_upload_async.py	Tuple-unpacking style cleanup
tests/integration/synapseclient/core/test_external_storage.py	Reformatted multi-patch contexts
synapseutils/sync.py	Formatting-only line wrapping
synapseutils/migrate_functions.py	Formatting-only SQL string wrapping
synapseclient/models/schema_organization.py	Trailing comma in signature
synapseclient/models/recordset.py	Formatting-only ternary wrapping
synapseclient/models/protocols/docker_protocol.py	Added blank line after docstring
synapseclient/models/mixins/table_components.py	Formatting-only line wrapping
synapseclient/models/link.py	Formatting-only ternary wrapping
synapseclient/models/file.py	Formatting-only ternary wrapping
synapseclient/models/entityview.py	Formatting-only ternary wrapping
synapseclient/models/curation.py	Trailing comma in signature
synapseclient/models/annotations.py	Signature formatting
synapseclient/models/agent.py	Formatting-only line wrapping
synapseclient/extensions/curator/schema_generation.py	Type-ignore spacing & commas
synapseclient/extensions/curator/record_based_metadata_task.py	Added blank line after docstring
synapseclient/core/utils.py	Trailing commas in signatures
synapseclient/core/transfer_bar.py	Added blank line after docstring
synapseclient/core/otel_config.py	Added blank line after docstring
synapseclient/core/models/custom_json.py	Added blank line after docstring
synapseclient/core/dozer.py	Added blank line after docstring
synapseclient/core/download/download_functions.py	Formatting-only await wrapping
synapseclient/client.py	Formatting-only line wrapping
synapseclient/api/file_services.py	Tuple-unpacking style cleanup
synapseclient/api/docker_commit_services.py	Added blank line after docstring
synapseclient/activity.py	Formatting-only line wrapping
Pipfile.lock	Updated lock for black 26.3.1
docs/tutorials/python/wiki.md	Adjusted snippet line range
docs/tutorials/python/tutorial_scripts/wiki.py	Added blank line after docstring
docs/tutorials/python/tutorial_scripts/upload_data_in_bulk.py	Formatting-only line wrapping
docs/scripts/object_orientated_programming_poc/synapse_project.py	Added blank line after docstring
.pre-commit-config.yaml	Bumped black rev to 26.3.1

Comments suppressed due to low confidence (1)

tests/integration/synapseclient/test_command_line_client.py:947

The call to run(...) passes "synapse" "--skip-checks" which Python concatenates into a single argument ("synapse--skip-checks"). Since run() sets sys.argv directly from these items, this will prevent argparse from seeing --skip-checks and likely makes the test fail. Pass these as separate arguments (e.g., "synapse", "--skip-checks", ...).

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

Copilot · 2026-04-07T19:47:00Z

+        with (
+            patch.object(self.syn, "get", return_value=self.file_ent) as patch_syn_get,
+            patch.object(
+                self.syn, "restGET", side_effects=[permissions, access_requirements]
+            ) as patch_rest_get,


In this patch context, patch.object(..., side_effects=[...]) uses an invalid keyword argument (side_effects). unittest.mock.patch expects side_effect, so this will raise a TypeError and the test will fail.

Copilot · 2026-04-07T19:47:00Z

+            file_handle_result: Dict[str, str] = (
+                await get_file_handle_for_download_async(
+                    file_handle_id=file_handle_id,
+                    synapse_id=synapse_id,
+                    entity_type=entity_type,


The type annotation for file_handle_result is incorrect: get_file_handle_for_download_async(...) returns a nested dict (e.g., containing a fileHandle dict), not Dict[str, str]. This annotation is misleading and will break static type checking; consider using Dict[str, Any] / Mapping[str, Any] (or a TypedDict) instead.

* [SYNPY-1798]: updated black to 26.3.1 and reran pre-commit (#1341) * update black to 26.3.1 and rerun pre-commit * update the tutorial line --------- Co-authored-by: Lingling Peng <lpeng@w290.local> Co-authored-by: Lingling Peng <lpeng@Mac.SageCorpWiFi> * [SYNPY-1764] Add Trivy container vulnerability scanning (#1346) * [SYNPY-1764] Add Trivy container vulnerability scanning to Docker build Add Trivy scanning to gate Docker image publication on GHCR. Both release and develop Docker jobs now follow a build→scan→push pattern where images are only pushed if no Critical/High unfixed vulnerabilities are found. New workflows: - trivy.yml: reusable Trivy scanning workflow with SARIF upload to GitHub Security tab - docker_build.yml: reusable build/scan/push workflow for image rebuilds - trivy_periodic_scan.yml: daily rescan of latest published image with auto-remediation * Address PR review feedback from linglp and jaymedina - Fix push jobs to load scanned tar instead of rebuilding (build.yml) - Pin trivy-action to SHA for v0.35.0 to address supply chain attack - Fix env.repo_name output using $GITHUB_OUTPUT (trivy_periodic_scan.yml) - Pin all third-party actions to commit SHAs - Remove unnecessary permissions on get-image-reference job - Use !cancelled() for SARIF upload condition (trivy.yml) - Use LOCAL_IMAGE_TAG env var instead of hardcoded string (docker_build.yml) - Fix IMAGE_REFERENCES YAML line continuation * Prevent infinite rebuild loop in periodic Trivy scan Restructure trivy_periodic_scan.yml so the git tag is only created after a successful rebuild (not before). If the rebuild still has vulnerabilities, a GitHub issue is opened for manual triage instead of looping endlessly. - Rename bump-tag → compute-next-version (dry_run: true) - Add create-tag job gated on update-image success - Add alert-on-failure job that opens a GitHub issue with duplicate prevention when remediation fails * pre-commit * Update Trivy scan workflow to use previous tag and adjust image references * Address PR review feedback - Pin codeql-action/upload-sarif to SHA and upgrade to v3.35.1 - Guard update-image job on compute-next-version success - Use absolute URL for Security tab link in auto-created issues * Add actions read permission for Trivy scan job (#1355) * Add optional ARTIFACT_NAME_SUFFIX input to Trivy workflow and update artifact naming (#1357) * remove sort --------- Co-authored-by: Lingling <55448354+linglp@users.noreply.github.com> Co-authored-by: Lingling Peng <lpeng@w290.local> Co-authored-by: Lingling Peng <lpeng@Mac.SageCorpWiFi> Co-authored-by: BryanFauble <17128019+BryanFauble@users.noreply.github.com>

update black to 26.3.1 and rerun pre-commit

27a2995

linglp changed the title ~~[technical debt]: update black to 26.3.1 and rerun pre-commit~~ [technical debt]: updated black to 26.3.1 and reran pre-commit Mar 20, 2026

thomasyu888 requested a review from andrewelamb March 20, 2026 16:50

BryanFauble reviewed Mar 20, 2026

View reviewed changes

BryanFauble approved these changes Mar 20, 2026

View reviewed changes

Merge branch 'develop' into update-black

c312a02

linglp marked this pull request as ready for review March 23, 2026 16:25

linglp requested a review from a team as a code owner March 23, 2026 16:25

andrewelamb approved these changes Mar 23, 2026

View reviewed changes

update the tutorial line

da36afa

thomasyu888 changed the title ~~[technical debt]: updated black to 26.3.1 and reran pre-commit~~ [SYNPY-1798]: updated black to 26.3.1 and reran pre-commit Mar 31, 2026

Merge branch 'develop' into update-black

43a391e

Copilot AI review requested due to automatic review settings April 7, 2026 19:43

Copilot started reviewing on behalf of linglp April 7, 2026 19:44 View session

Copilot AI reviewed Apr 7, 2026

View reviewed changes

linglp merged commit 4f0721e into develop Apr 7, 2026
32 checks passed

linglp deleted the update-black branch April 7, 2026 21:16

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

[SYNPY-1798]: updated black to 26.3.1 and reran pre-commit#1341

[SYNPY-1798]: updated black to 26.3.1 and reran pre-commit#1341
linglp merged 4 commits intodevelopfrom
update-black

linglp commented Mar 20, 2026 •

edited

Loading

Uh oh!

BryanFauble Mar 20, 2026

Uh oh!

BryanFauble left a comment

Uh oh!

andrewelamb commented Mar 20, 2026

Uh oh!

linglp commented Mar 20, 2026

Uh oh!

thomasyu888 commented Mar 31, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Copilot AI Apr 7, 2026

Uh oh!

Copilot AI Apr 7, 2026

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

Conversation

linglp commented Mar 20, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Problem:

Solution:

Uh oh!

BryanFauble Mar 20, 2026

Choose a reason for hiding this comment

Uh oh!

BryanFauble left a comment

Choose a reason for hiding this comment

Uh oh!

andrewelamb commented Mar 20, 2026

Uh oh!

linglp commented Mar 20, 2026

Uh oh!

thomasyu888 commented Mar 31, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Copilot AI Apr 7, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI Apr 7, 2026

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

linglp commented Mar 20, 2026 •

edited

Loading