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Refactor xopen #143

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Refactor xopen #143

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6d35655
Make piped readers and writers binary only
rhpvorderman Jan 17, 2024
9e73de6
Text wrapping occurs in xopen function rather than in helper functions
rhpvorderman Jan 17, 2024
414ca0e
Make sure binary mode selection works
rhpvorderman Jan 19, 2024
abebb9e
Implement readable and writable interface for PipedCompressionWriter
rhpvorderman Jan 19, 2024
7205750
Fix writer tests for only binary
rhpvorderman Jan 19, 2024
5544a13
Fix compatibility issue from removing the mode argument
rhpvorderman Jan 19, 2024
3c2079e
Adapt piped tests for binary reading only
rhpvorderman Jan 19, 2024
193ce9c
Start consolidating reader and writers
rhpvorderman Jan 19, 2024
34356b9
Fix most of the errors on closing
rhpvorderman Jan 19, 2024
63f2dba
Fix all xopen issues
rhpvorderman Jan 19, 2024
aec107c
Make tests run with programs rather than readers/writers
rhpvorderman Jan 19, 2024
91c8591
Return emptied file to original state
rhpvorderman Jan 19, 2024
e46da2f
Make sure outfile is only created for writers
rhpvorderman Jan 19, 2024
68191b4
Fix a few issues with test_piped test fails
rhpvorderman Jan 19, 2024
d4972eb
Use a temporary file to store error messages
rhpvorderman Jan 19, 2024
a42720a
Fix mypy and flake8 errors
rhpvorderman Jan 19, 2024
1077f9b
Make sure stderr file is closed
rhpvorderman Jan 19, 2024
dc5013c
Fix a few warnings
rhpvorderman Jan 19, 2024
08132b2
Refactor init function for PipedCompressionProgram
rhpvorderman Jan 19, 2024
c978863
Replace .format with f-strings
rhpvorderman Jan 22, 2024
1f402bc
Simplify next method to prevent performance regression
rhpvorderman Jan 22, 2024
3067a96
Small refactorings
rhpvorderman Jan 22, 2024
325a42a
Initialize allowed_exit_cde and allowed_exit_message via init method
rhpvorderman Jan 22, 2024
fd52747
Ignore complexity warning
rhpvorderman Jan 22, 2024
d2c5622
Use PipedCompressionProgram rather than derived baseclasses
rhpvorderman Jan 22, 2024
565f70a
Make PipedCompressionProgram private
rhpvorderman Jan 22, 2024
07f03d0
Use a ProgramSettings class to allow for easier testing
rhpvorderman Jan 22, 2024
ea7d34f
Rewrite test_piped.py for only compression writer
rhpvorderman Jan 22, 2024
202b9be
Change default mode for PipedCompressionProgram to binary read
rhpvorderman Jan 22, 2024
7fd5027
Test for acceptable compression level in _PipedCompressionProgram
rhpvorderman Jan 22, 2024
f219a34
Remove deprecated function
rhpvorderman Jan 22, 2024
3d39854
Do not import subprocess attributes in global namespace
rhpvorderman Jan 22, 2024
4043ec6
Remove redundant comment
rhpvorderman Jan 22, 2024
ff324b9
Do not install on github actions
rhpvorderman Jan 22, 2024
e59d603
Fix append mode oversights
rhpvorderman Jan 22, 2024
5c8555d
Remove redundant text_mode_kwargs argument
rhpvorderman Jan 22, 2024
dbbf8bb
Slightly simplify test_piped
rhpvorderman Jan 23, 2024
9569234
Make PipedCompressionProgram.__init__ less complex
rhpvorderman Jan 23, 2024
1a67359
Remove redundant noqa: C901 tag
rhpvorderman Jan 23, 2024
7c5ad95
Make sure threads are passed to igzip_threaded if specified
rhpvorderman Jan 23, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -62,7 +62,7 @@ jobs:
run: brew install pigz pbzip2 isa-l zstd
- name: Install optional tools Linux
if: runner.os == 'Linux' && matrix.optional-deps
run: sudo apt-get install pigz pbzip2 isal zstd
run: sudo apt-get install pigz pbzip2 zstd
- name: Remove xz
if: runner.os == 'Linux' && !matrix.optional-deps
run: while which xz; do sudo rm $(which xz); done
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