Open victorlin opened 3 months ago
From @jameshadfield in https://github.com/nextstrain/augur/pull/1246#discussion_r1604241775:
I looked at a few of these - totally fine if we want to defer any and all to separate PRs beyond this one:
reportUnusedExpression
- single failure, should fixreportUndefinedVariable
- single failure, already with a flake8 ignore commentreportPrivateImportUsage
- no failuresreportGeneralTypeIssues
- 9 errors, but all seem worth fixing
reportPrivateImportUsage
- no failures
I didn't get any errors locally but did in CI (noted in e5ced1c8b5e1aeb1923bc00219594336e8ceeb34):
2024-05-17T00:31:30.1458148Z tests/test_pyright.py::test_pyright /home/runner/work/augur/augur/augur/clades.py
2024-05-17T00:31:30.1466206Z /home/runner/work/augur/augur/augur/clades.py:328:18 - error: "read" is not exported from module "Bio.Phylo" (reportPrivateImportUsage)
…
2024-05-17T00:31:30.1553703Z 20 errors, 0 warnings, 0 informations
2024-05-17T00:31:30.3631414Z FAILED
I now realize that it's specific to the Biopython version. Pyright passed in CI with biopython=1.80 but failed on latest (1.83).
Pyright was added in #1246. The default Pyright configuration options result in many violations from Augur's code as-is. To allow incremental adoption of Pyright, all default rule violations were disabled.
Tasks
Go through each of these and either (1) decide to keep the exception or (2) remove the exception and fix all violations in the code.