Use sourmash_args.get_moltype in "sig describe" #907
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Codecov Report
@@ Coverage Diff @@
## master #907 +/- ##
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+ Coverage 91.77% 91.8% +0.03%
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Files 70 70
Lines 4947 4941 -6
=========================================
- Hits 4540 4536 -4
+ Misses 407 405 -2
Continue to review full report at Codecov.
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thanks @olgabot! Can you also add a test that triggers the error, so we know it won't come back? =] It can be similar to this one: https://github.com/dib-lab/sourmash/pull/782/files#diff-036b5697ae6b2bd1ecc4f44d0f522c46R4 |
luizirber
reviewed
Feb 19, 2020
| ['signature', 'describe', | ||
| testdata1], | ||
| in_directory=location) | ||
| expected_output == """== This is sourmash version 3.2.2. == |
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Suggested change
| expected_output == """== This is sourmash version 3.2.2. == | |
| expected_output = """ |
there is an extra = here, and since versions change all the time we don't want that in the test
luizirber
reviewed
Feb 19, 2020
| signature: test.prot | ||
| source file: test.prot | ||
| md5: 57ae47c24a08a24b630dae80f0c6e256 | ||
| k=11 molecule=protein num=0 scaled=20 seed=42 track_abundance=1 |
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I think we can check for this line (and the equivalent on the other two sigs) instead of all the lines in the expected output.
This test as is will always require very stringent formatting of the sig describe output, which we might change in the future.
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Ah that makes sense. I can update the test!
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As to the installation issue, here's what I did: conda create sourmash-dev environmentconda install current sourmash on biocondaDid this because this has been the most painless way to get all the C/C++ dependencies installed in the past pip install requirementsThis was on a fresh macbook, using MacOS Catalina v 10.15.2 |
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I see, you don't have the Rust compiler installed. Two ways of fixing it:
Since you already have all other deps installed with conda, I think the first option will be easier. |
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Thank you Luiz, that worked!! Good to know about asking for Rust separately by |
Since we compile the Rust code into a shared library, the compiler is not needed if you're using sourmash (just as you didn't need a C/C++ compiler before), but if you're compiling from source/developing then you need it (just like you needed the C/C++ compiler before =]) |
8 tasks
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fixed in #1013 as a by-product of other changes. |
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Addressses #905 from @bluegenes
make testDid it pass the tests?make coverageIs the new code covered?without a major version increment. Changing file formats also requires a
major version number increment.
changes were made?