Adds support for running doctest as part of pytest #161
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Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #161 +/- ##
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+ Coverage 89.02% 89.48% +0.45%
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Files 17 17
Lines 2005 2006 +1
Branches 437 437
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+ Hits 1785 1795 +10
+ Misses 144 138 -6
+ Partials 76 73 -3 ☔ View full report in Codecov by Sentry. |
| >>> contig_one.add("NNN", 1) # doctest: +ELLIPSIS | ||
| <fgpyo.fasta.builder.ContigBuilder object at ...> |
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naive q: can the doctest: +ELLIPSIS pragma be moved to the following line, where the ellipsis actually exists? Or is it required to be on the line with the code being run, not the output?
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It has to be on the line :/
| @@ -9,10 +9,10 @@ | |||
| >>> import pysam | |||
| >>> from fgpyo.fasta.sequence_dictionary import SequenceDictionary | |||
| >>> sd: SequenceDictionary | |||
| >>> with pysam.AlignmentFile("./fgpyo/sam/tests/data/valid.sam") as fh: | |||
| ... sd = SequenceDictionary.from_sam(header=fh.header) | |||
| >>> with pysam.AlignmentFile("./tests/fgpyo/sam/data/valid.sam") as fh: | |||
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For clarity I might SKIP this and replace with a dummy path, as in the test for FastxZipped below
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I like this since it actually runs!
| Assert that a path exists and is readable | ||
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| ```python | ||
| >>> tmp_dir = Path(getfixture("tmp_path")) |
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It's probably because Griffe's parsers will only detect and remove doctest flags in raw pycon code block (not wrapped in fences), and only in examples section: """Summary.
Examples:
Some example.
>>> print("hey")
hey
"""I have written a Python-Markdown extension that enables such raw pycon code blocks anywhere in Markdown (stripping doctest flags again), but it's only available to sponsors for now: https://pawamoy.github.io/markdown-pycon/. |
I have futzed with the
trim_doctest_flagswithin themkdocstringsoptions inpyproject.ymlbut still don't get the# doctest +FLAGremoved. Help is welcome.