Commit Graph

13 Commits

Author SHA1 Message Date
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
d2e7b6baa5 Remove executable flags and shebang (#2826)
Remove executable flags and hashbangs from tests; make run_tests.py executable
2020-05-26 13:09:54 +01:00
1b9e569a7f Using tool unify to convert Tests/ to use double quotes
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
ccf88fc058 Tests do not require postgresql CREATE DATABASE permissions
Test framework changes so as not to require a postgres user with createdb privileges.

Under TravisCI / AppVeyor a dedicated postgres user is setup.

Squashed commit of pull request #1420.
2017-10-27 14:11:39 +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
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
955472ef49 Read BioSQL test settings from INI file 2016-05-20 08:04:38 +01:00
b67cebf60e Fix common PEP8 violation in unittest verbosity argument 2014-11-11 14:38:37 +09:00
82272b1f36 autopep8 E265 - Format block comments.
$ autopep8 --version
autopep8 1.0.4
$ autopep8 -r -i --select E265 ...
2014-10-27 14:27:12 +00:00
471d69c7b4 pure python mysql driver for BioSQL using Oracle's mysql-connector
Note VARCHAR BINARY problem under Python 3 (bytes vs unicode), thus
includes a Cursor wrapper for mysql.connector under python3 to
convert bytes to strings.
2014-05-25 13:03:58 +01:00