de0bb21fb3
Apply isort (forcing single lines, not sorting by type) via ruff
...
$ ruff check --fix --select=I \
--config=lint.isort.force-single-line=true \
--config=lint.isort.order-by-type=false \
BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py
Using ruff version 0.4.10
2024-06-26 15:31:39 +09:00
a47460e59a
Misc spellings flagged by codespell ( #4716 )
...
Note the childs to children changes in Bio/Phylo/Consensus.py
included fixing internal variable names only.
Not applying all the catergories ==> categories fixes
to the (deprecated) EMBOSS wrappers as some would be
functional changes.
Also no more LaTeX files (for spell checking)
2024-05-01 14:21:12 +01:00
f40d6b7aa7
ruff fix most F401 unused imports in Tests
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(base) Peters-iMac:biopython pc40583$ ruff check --fix --select F401 Tests/ --exclude "Tests/common_BioSQL_online.py,Tests/seq_tests_common.py,Tests/test_SearchIO_blast_text.py,Tests/test_codonalign.py,Tests/test_Cluster.py,Tests/test_codonalign.py"
...
Found 82 errors (54 fixed, 28 remaining)
2023-11-02 09:34:48 +00:00
d2e7b6baa5
Remove executable flags and shebang ( #2826 )
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Remove executable flags and hashbangs from tests; make run_tests.py executable
2020-05-26 13:09:54 +01:00
68a0eddb3f
Apply black style to test_BioSQL* files, version 19.10b0.
...
test_BioSQL_mysql_connector_online.py
test_BioSQL_MySQLdb_online.py
test_BioSQL_psycopg2_online.py
test_BioSQL_sqlite3.py
test_BioSQL_sqlite3_online.py
2020-05-09 16:40:44 +01:00
1b9e569a7f
Using tool unify to convert Tests/ to use double quotes
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Using https://github.com/myint/unify for this:
$ unify --quote \" --in-place Tests/*.py Tests/*/*.py
2019-08-02 14:10:22 +01:00
18bf3628ea
flake8: F405 - names defined via import star
2019-04-23 10:18:22 +01:00
7ba260652a
flake8 D400: Add missing dot to Tests/ docstrings
...
These last cases were done by hand.
2019-04-22 09:00:41 +01:00
61864cacfc
Mark BioSQL test import * with noqa for flake8
...
The entire design of the BioSQL tests puts the classes
in the common files for importing into the back-end
specific test files. Here using import * is by design.
2017-02-10 17:09:16 +00:00
b2fd95b06f
Avoid import * and other flake8 cleanup.
...
Still have some potentially unused imports:
$ flake8 Bio/Restriction/Restriction.py
Bio/Restriction/Restriction.py💯 1: F401 'Bio.Restriction.RanaConfig.ConsoleWidth' imported but unused
Bio/Restriction/Restriction.py💯 1: F401 'Bio.Restriction.RanaConfig.NameWidth' imported but unused
Bio/Restriction/Restriction.py💯 1: F401 'Bio.Restriction.RanaConfig.Indent' imported but unused
Bio/Restriction/Restriction.py💯 1: F401 'Bio.Restriction.RanaConfig.MaxSize' imported but unused
Bio/Restriction/Restriction.py:101:1: F401 'Bio.Restriction.RanaConfig.ftp_proxy' imported but unused
Bio/Restriction/Restriction.py:101:1: F401 'Bio.Restriction.RanaConfig.ftp_Rebase' imported but unused
Bio/Restriction/Restriction.py:102:1: F401 'Bio.Restriction.RanaConfig.ftp_emb_e' imported but unused
Bio/Restriction/Restriction.py:102:1: F401 'Bio.Restriction.RanaConfig.ftp_emb_s' imported but unused
Bio/Restriction/Restriction.py:102:1: F401 'Bio.Restriction.RanaConfig.ftp_emb_r' imported but unused
2017-02-10 16:55:32 +00:00
513192e0e8
Skip these test with run_tests.py --offline
2016-06-09 17:22:21 +01:00
762146ea0b
Split online tests for BioSQL
...
We need internet access for NCBI Entrez to load taxonomy
information automatically.
Based on a pull request from @ctSkennerton which was updated
by @peterjc following changes on the master branch, with some
painful workarounds for global BioSQL configuration variables.
2016-06-09 17:22:21 +01:00
