Update protein-translation tests #1115

sjwarner-bp · 2017-11-20T11:36:46Z

sjwarner-bp · 2017-11-20T12:41:07Z

I've just seen this error - can someone let me know if there is a maximum line size, as this seems to be the error (but I'd like to check first) 🙂

N-Parsons · 2017-11-20T22:29:26Z

Hi @sjwarner-bp, if you click through to Travis-CI using the "details" link in the bottom box, it will take you to an overview of the tests. You can then pick one of the Python versions (usually doesn't matter which) and then it will show an output of what's wrong.

In your case, it looks like flake8 formatting errors (link:

$ flake8
./exercises/protein-translation/protein_translation_test.py:7:1: E302 expected 2 blank lines, found 1
./exercises/protein-translation/protein_translation_test.py:49:80: E501 line too long (80 > 79 characters)
./exercises/protein-translation/protein_translation_test.py:54:80: E501 line too long (82 > 79 characters)
./exercises/protein-translation/protein_translation_test.py:59:80: E501 line too long (83 > 79 characters)
./exercises/protein-translation/protein_translation_test.py:61:33: E231 missing whitespace after ','
./exercises/protein-translation/protein_translation_test.py:61:44: E231 missing whitespace after ','

You can also install flake8 locally using pip install flake8, and then run it with flake8 <path>.

cmccandless · 2017-11-20T22:35:23Z

@N-Parsons (cc @sjwarner-bp )

You can also install flake8 locally using pip install flake8, and then run it with flake8 [path].

I think you accidentally dropped an "8". Also note that path is optional and defaults to "./" 😄

sjwarner-bp · 2017-11-21T08:36:14Z

Perfect - thanks for letting me know guys, I've installed it locally and will remember to use it in future! 🙂

cmccandless · 2017-11-21T15:43:08Z

exercises/protein-translation/protein_translation_test.py

@@ -35,25 +37,34 @@ def test_identifies_stop_codons(self):
        for codon in ['UAA', 'UAG', 'UGA']:
            self.assertEqual('STOP', of_codon(codon))


Per discussion in exercism/problem-specifications#997, I don't think we should test for intermediate results. Thus, all tests should test of_rna() (proteins() in the spec).

cmccandless · 2017-11-21T15:43:56Z

exercises/protein-translation/protein_translation_test.py

@@ -35,25 +37,34 @@ def test_identifies_stop_codons(self):
        for codon in ['UAA', 'UAG', 'UGA']:
            self.assertEqual('STOP', of_codon(codon))

-    def test_translates_rna_strand_into_correct_protein(self):
+    def test_translates_rna_strand_into_correct_protein_list(self):
        strand = 'AUGUUUUGG'
        expected = ['Methionine', 'Phenylalanine', 'Tryptophan']
        self.assertEqual(expected, of_rna(strand))


In an effort to maintain consistency with the spec, of_rna() should probably be renamed to proteins().

sjwarner-bp · 2017-11-21T15:47:24Z

Hi @cmccandless - just to double check so I don't make the wrong edits, all of_codon() and of_rna() should be renamed to proteins()?

cmccandless · 2017-11-21T15:49:38Z

@sjwarner-bp Correct, however note that the tests that currently use of_codon() will need to be modified to expect a list (albeit with only 1 element each).

sjwarner-bp · 2017-11-21T15:52:48Z

Perfect, I understand you 😄

sjwarner-bp · 2017-11-30T10:42:22Z

Sorry, I have just picked this up again after a hectic week! I'm trying to do this but running into trouble.

Just to clarify, the things I need to do to satisfy this is:

Change all reference of of_codon and of_strand to protein
Update the skeleton file with a single definition for protein and nothing else
Update the reference solution

So I have done the first two, but the final one is causing me a little confusion - do you have any guidance?

cmccandless · 2017-11-30T16:06:54Z

@sjwarner-bp Have you tried simply renaming (in example.py) of_rna->protein, with no other changes?

sjwarner-bp · 2017-12-01T16:16:02Z

Hi @cmccandless , I have renamed of_rna to protein and I end up with 13 failed tests, all of which have AssertationError <some_output> != None

cmccandless · 2017-12-01T16:25:30Z

@sjwarner-bp Can you please drop the contents of your example.py and protein_translation_test.py in a multi-file gist so I can take a look?

sjwarner-bp · 2017-12-01T16:30:18Z

Sure thing - here it is

cmccandless · 2017-12-01T16:32:46Z

Don't forget to change

from protein_translation import protein

to

from example import protein

when running tests locally (revert before committing).

sjwarner-bp · 2017-12-01T16:34:59Z

Yup, done that - I still end up with 8 failing tests for some reason though 😱. I've tried the (previously) of_codon with and without list notation around the parameter.

cmccandless · 2017-12-01T16:37:29Z

Make sure the tests that were previously of_codon tests both pass in and expect a list.

sjwarner-bp · 2017-12-01T16:40:47Z

Do you mean something like the following?

def test_AUG_translates_to_methionine(self):
        self.assertEqual(['Methionine'], protein(['AUG']))

I've tried this (and then without the [ ]) but it doesn't seem to work.

cmccandless · 2017-12-01T17:07:30Z

Sorry; I wasn't paying full attention to this and I didn't take the time to fully understand the inputs/outputs.

According to the canonical data, here are a few notes:

Tests should only reference proteins() (I told you to call it protein, but should pluralize for consistency)
proteins() expected a string (my bad, told you to provide a list, but that's wrong)
proteins() returns a list, regardless of the number of elements in the input
If proteins() encounters a STOP codon, translation ceases and the results so far are returned. The STOP protein itself is not included.

See if any of that helps. I was able to make a few quick edits to your code to make it work, but you will benefit more from this if you figure it out yourself 😄

cmccandless · 2017-12-04T17:49:15Z

exercises/protein-translation/protein_translation_test.py

-from protein_translation import of_codon, of_rna
+from protein_translation import proteins
+
+# Tests adapted from problem-specifications/canonical-data.json @ v1.0.0


For consistency with other exercises, can you please change the spacing around this line? Should be 2 blank lines above, 1 below. (In the back of my mind I have a feeling I may have already said this, but switched the numbers; if so, I apologize for the misinformation)

cmccandless · 2017-12-06T20:22:26Z

@sjwarner-bp Merged. Thanks for working on this!

sjwarner-bp · 2017-12-06T20:39:32Z

Thanks for helping me out!

Update protein-translation tests

e7f6cca

Fix formatting issues

15b62a0

cmccandless suggested changes Nov 21, 2017

View reviewed changes

cmccandless mentioned this pull request Nov 29, 2017

update protein_translations tests from canonical #1122

Closed

protein-translation: remove testing of intermediate results

3702fc0

cmccandless suggested changes Dec 4, 2017

View reviewed changes

protein-translation: adjust spacing

d19c19d

cmccandless approved these changes Dec 6, 2017

View reviewed changes

Merge branch 'master' into protein-translation-test-update

25ba10f

cmccandless merged commit e78fd80 into exercism:master Dec 6, 2017

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Update protein-translation tests #1115

Update protein-translation tests #1115

sjwarner-bp commented Nov 20, 2017

sjwarner-bp commented Nov 20, 2017

N-Parsons commented Nov 20, 2017 •

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cmccandless commented Dec 6, 2017

sjwarner-bp commented Dec 6, 2017

		@@ -35,25 +37,34 @@ def test_identifies_stop_codons(self):
		for codon in ['UAA', 'UAG', 'UGA']:
		self.assertEqual('STOP', of_codon(codon))

Update protein-translation tests #1115

Update protein-translation tests #1115

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