Nicola Soranzo
7fee81607c
Add linting with ruff
...
ruff (https://github.com/charliermarsh/ruff ) is a new and extremely fast
Python linter, written in Rust.
Ruff can be used to replace Flake8 (plus a variety of plugins), isort,
pydocstyle, yesqa, eradicate, pyupgrade, and autoflake.
Here ruff is added to our current linters (flake8, flake8-bugbear and isort)
while we assess its reliability.
I've not enabled the isort rules because many of the options we use are not
implemented yet. I have instead enabled the pyupgrade rules (a tool which I
run manually every few months).
Also:
- Fix new linting errors reported by ruff.
2023-01-16 14:34:56 +00:00
Dannon Baker
03351d2a9f
Apply black to tools as well
2022-02-03 09:12:13 -05:00
Dannon Baker
623a5e165a
Apply black formatting.
...
Apply isort.
2022-02-03 07:42:20 -05:00
Alex Ostrovsky
f884f9b149
Allow any format in export tool
2022-01-11 13:10:03 -08:00
Marius van den Beek and Nicola Soranzo
94881812a0
Tweak tool options
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Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com >
2021-08-25 18:03:19 +03:00
mvdbeek
ee63fcc736
Allow skipping sanitization of / char
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and allow using collection name as outer directory
2021-08-25 10:51:13 +03:00
mvdbeek
8bf9de4e1a
Provide $input.serialize(), allow wrap_json to serialize collections
2021-05-28 22:49:49 +02:00
mvdbeek
d6e58fb898
Implement export of FileParameter / MetadataFile files
2021-05-27 17:23:42 +02:00
mvdbeek
05d517a384
Mirror collection structure on exported filesystem
2021-05-27 17:21:01 +02:00
mvdbeek
f5d05fb545
Allow creation of subdirectories on export
2021-05-27 17:21:01 +02:00
mvdbeek
a4c0468813
Sanitize exported filenames
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Now can't include leading `.`, `/` and utf null, and is truncated at 255
characters. Duplicate filenames will raise an error.
2021-05-27 17:21:01 +02:00
mvdbeek
920a4b3f77
Provide files to export as json configfile
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This avoids shell limits and quoting issues.
2021-05-27 17:21:01 +02:00
mvdbeek
f24024c0d7
Add name_and_ext shortcut
2021-05-27 17:21:01 +02:00
mvdbeek
97af023140
Enable datatype aliases for stuff that has weird extensions in Galaxy
2021-05-27 17:21:01 +02:00
John Chilton
e9081759ca
Add tool for exporting individual files to Galaxy.
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Stolen wholesale from EU. Trying to make it a bit more general though.
2021-05-27 17:21:01 +02:00
Nicola Soranzo