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Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn3/fs_helpers.py: Remove unused "pathlib" import.
(cache_ipfs_file): Disable "unused-argument" warting.
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This library pollutes the Genenetwork2 profile with an old version
"dataclasses" thereby causing it to fail.
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When the encoding is not specified explicitly, the system default encoding is
used. This is not recommended.
* gn3/computations/ctl.py (call_ctl_script),
gn3/computations/gemma.py (generate_pheno_txt_file),
gn3/computations/parsers.py (parse_genofile),
gn3/computations/partial_correlations.py (partial_correlations_fast),
gn3/computations/rqtl.py (process_rqtl_output, process_perm_output),
gn3/computations/wgcna.py (dump_wgcna_data, call_wgcna_script),
gn3/fs_helpers.py (jsonfile_to_dict): Explicitly specify UTF-8 to be the file
encoding.
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tests/unit/computations/test_gemma.py (TestGemma.test_generate_pheno_txt_file),
tests/unit/computations/test_wgcna.py (TestWgcna.test_create_json_file): Test
for call to open with encoding='utf-8' argument.
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* Use `with` in place of plain `open`
* Use f-strings in place of `str.format()`
* Remove string interpolation from queries - provide data as query parameters
* other minor fixes
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Generally avoid naming things with a "utils" prefix/ suffix since it
encourages contributors to dump any new functions there; and over time, as the
code grows, things get messy...
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