Python 3 support #14
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Example pull request: galaxyproject#2453 Useful commands:
When done with changing the python file(s), make sure all tests pass and both python2 and 3 lint is OK. Then add the file(s) that are OK to this file, to check them automatically with python 3 lint: |
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Smaller PRs or are we going to merge a bunch of stuff together? |
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@jmchilton Still have to figure how to split the work among people, suggestions welcome! |
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Regarding bx-python, code is now here and the tests run/pass. I will merge any Python 3 changes that don't break the tests under 2. |
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@jxtx Thanks! I've removed it from the list. |
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List of files that do not pass py34-lint tests: |
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@nsoranzo Sorry, to be clear the tests run/pass under Python 2. Still needs work for python 3. |
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@jxtx Ohhh, OK. I don't think we will have time for that today, but I'll open an issue on your repo. |
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@jmchilton I've created a |
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I will start with |
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Doing OK, done. |
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Doing ./test/api/helpers.py |
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WIP on getting an unit test to run in Python 3. |
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doing ./test/api/test_datasets.py |
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I've done |
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doing ./test/unit/managers/base.py |
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doing ./test/api/test_tool_data.py |
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doing ./test/api/test_workflow_extraction.py |
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doing ./test/unit/managers/test_DatasetManager.py |
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Doing |
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doing ./test/unit/managers/test_HDAManager.py |
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Done |
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found something interesting maybe helpful for this project Cheat Sheet: Writing Python 2-3 compatible code |
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Done: |
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test/unit/datatypes/dataproviders/test_line_dataproviders.py |
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Doing |
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I'm doing |
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lib/galaxy/datatypes/sequence.py |
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Doing lib/galaxy/datatypes/converters/interval_to_bed_converter.py |
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./lib/galaxy/datatypes/sniff.py |
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./lib/galaxy/datatypes/converters/fastq_to_fqtoc.py |
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./lib/galaxy/datatypes/tabular.py |
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lib/galaxy/datatypes/converters/bed_to_gff_converter.py |
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./lib/galaxy/datatypes/converters/lped_to_fped_converter.py |
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scripts/api/example_watch_folder.py |
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./lib/galaxy/datatypes/util/gff_util.py |
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./lib/galaxy/datatypes/dataproviders/line.py |
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./lib/galaxy/datatypes/dataproviders/column.py |
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./lib/galaxy/managers/context.py |
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./scripts/bootstrap_history.py |
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./lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py |
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./lib/galaxy/visualization/genomes.py |
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./lib/galaxy/model/migrate/versions/0006_change_qual_datatype.py |
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lib/galaxy/visualization/data_providers/phyloviz/newickparser.py |
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./lib/galaxy/model/migrate/versions/0014_pages.py |
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+lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py |
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Hey, so I was looking at lending a hand in this, and trying to read up on porting methods. I notice that the example pull request doesn't really touch strings, instead of using any of the methods I've seen like unicode_literals or six.u(). What was the reasoning in going with this strategy? Are there things to watch out for when applying it? |
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@NickSto You are very welcome to contribute to this effort, feel free to add commits to the Regarding your question, there is no need to use If you want a short introduction of the recommended approach to do the porting, we can meet for 10' tomorrow at some point. |
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@tshtatland @ericenns Do not forget to add at the top of a file when you change |
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I've opened PR galaxyproject#2574, thank you all for the fantastic contribution! |
Python 2.7 will not be maintained past 2020.
Add support for Python >= 3.3 while maintaining support for Python 2.6 and 2.7.
xref.: https://trello.com/c/dZcCVf9I/2702-migrate-to-python-3
The list of files already fixed is in
.ci/py3_sources.txtUseful tools and documentation:
https://docs.python.org/3/howto/pyporting.html
https://docs.python.org/2/library/2to3.html
https://python-modernize.readthedocs.org/
https://pythonhosted.org/six/
http://python3porting.com/preparing.html
Requirements which need to be ported or dropped:
xref: galaxyproject#1715
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