WIP PlanemoLintBear.py: Add linter bear for planemo #1337

Shade5 · 2017-01-22T14:01:31Z

Added a linter bear for planemo lint
Used planemo lint command

Nosferatul · 2017-01-24T11:46:20Z

bears/planemo/PlanemoLintBear.py

+    Checks the code with pylint. This will run pylint over each file
+    separately.
+    """
+    LANGUAGES = {'xml'}


Can we have asciinema too?

I didn't understand what you meant. Isn't assciinema a recorder?

If you look at the bears documentation, we have asciinemas for a lot of the bears that showcase how they work

See other bears.
git grep -i asciinema

Right, I'll do that

jayvdb · 2017-01-25T20:33:05Z

test-requirements.txt

@@ -6,3 +6,4 @@ pytest-timeout~=1.2
 pytest-xdist~=1.15
 requests_mock~=0.7.0
 wheel~=0.29
+planemo~=0.36


this should appear in bear-requirements.txt , and not in test-requirements.txt.

That will solve the error you can see at https://travis-ci.org/coala/coala-bears/jobs/195095556#L5596

jayvdb · 2017-01-25T20:34:08Z

bears/planemo/PlanemoLintBear.py

+    CAN_DETECT = {'Syntax'}
+
+    @staticmethod
+    def create_arguments(filename, file, config_file,):


please remove the trailing comma here.

jayvdb · 2017-01-25T20:34:35Z

bears/planemo/PlanemoLintBear.py

+    @staticmethod
+    def create_arguments(filename, file, config_file,):
+        """
+        :param pylint_disable:     Disable the message, report, category or


these arguments do not exist for this bear;

jayvdb · 2017-01-25T20:36:37Z

tests/planemo/PlanemoLintBearTest.py

+                                      'planemolint_test.xml')
+
+    def test_run(self):
+        self.check_validity(


this checks an invalid file.

this test module also needs to run a test that is a successful valid file.

I would like to see a test with the check_results method.

sims1253

aaaand I never sent this >.>

sims1253 · 2017-01-25T16:33:22Z

bears/planemo/PlanemoLintBear.py

+    Checks the code with pylint. This will run pylint over each file
+    separately.
+    """
+    LANGUAGES = {'xml'}


If you look at the bears documentation, we have asciinemas for a lot of the bears that showcase how they work

sims1253 · 2017-01-25T16:34:40Z

bears/planemo/PlanemoLintBear.py

+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with pylint. This will run pylint over each file


planemo == pylint?

sims1253 · 2017-01-25T16:36:51Z

tests/planemo/PlanemoLintBearTest.py

+            self.uut,
+            [],  # Doesn't matter, planemo lint will parse the file
+            self.test_file,
+            valid=False)


You only test for one valid file. We wanted to improve testing, although I myself am not familiar with the details. Ask on the gitter channel about it.

We prefer the check_results method because we actually get to know the other attributes such as the message, the line no. etc.

gitmate-bot · 2017-01-26T04:29:28Z

bears/planemo/PlanemoLintBear.py

+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with planemo lint. This will run planemo lint over each file


E501 line too long (80 > 79 characters)'

PycodestyleBear (E501), severity NORMAL, section autopep8.

gitmate-bot · 2017-01-26T04:29:29Z

bears/planemo/PlanemoLintBear.py

+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with planemo lint. This will run planemo lint over each file


Line is longer than allowed. (80 > 79)

LineLengthBear, severity NORMAL, section linelength.

gitmate-bot · 2017-01-26T05:21:32Z

bears/planemo/PlanemoLintBear.py

+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with planemo lint. This will run planemo lint over each file


E501 line too long (80 > 79 characters)'

PycodestyleBear (E501), severity NORMAL, section autopep8.

gitmate-bot · 2017-01-26T05:21:33Z

bears/planemo/PlanemoLintBear.py

+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with planemo lint. This will run planemo lint over each file


Line is longer than allowed. (80 > 79)

LineLengthBear, severity NORMAL, section linelength.

Shade5 · 2017-01-26T08:37:58Z

Appveyor is failing because there is no planemo for windows right?
How do I exclude it ?

jayvdb

Tests havent yet been improved; they are still inadequate.

jayvdb · 2017-01-26T09:20:52Z

bears/planemo/PlanemoLintBear.py

+
+    @staticmethod
+    def create_arguments(filename, file, config_file):
+


Remove this blank line please

jayvdb · 2017-01-26T09:22:26Z

tests/planemo/test_files/valid_planemo_test.xml

+   <from>Jani</from>
+   <heading>Reminder</heading>
+   <body>Don't forget me this weekend!</body>
+</note>


You need to review your own patches. Github shows you a red marker here.

Sorry 😓 didn't notice this

jayvdb · 2017-01-26T09:23:43Z

bears/planemo/PlanemoLintBear.py

+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with planemo lint. This will run


What is planemo?

https://github.com/galaxyproject/planemo

The description needs to improve IMO. A naiive user wouldn't understand much by the given description.

jayvdb · 2017-01-26T09:25:15Z

bears/planemo/PlanemoLintBear.py

+    Checks the code with planemo lint. This will run
+    planemo lint over each file separately.
+    """
+    LANGUAGES = {'xml'}


This bear cand handle any xml file. If this was committed, that is what you are saying this bear can accept, and for e.g.coala-quickstart will try to use it for all xml files.

Techievena · 2017-04-24T16:18:31Z

Ask maintainers to trigger the rebuild. It occasionally fails.

yash-nisar · 2017-04-25T03:27:39Z

Or maybe you can repush too.

gitmate-bot · 2017-05-03T15:47:41Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-05-11T07:43:39Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

yash-nisar · 2017-05-11T10:01:09Z

bears/planemo/PlanemoLintBear.py

+    ASCIINEMA_URL = 'https://asciinema.org/a/0kiduzg55d59nxhm8wuwfvl3n'
+    LICENSE = 'AGPL-3.0'
+    CAN_DETECT = {'Syntax'}
+


I would like to see the SEE_MORE attribute.

yash-nisar · 2017-05-11T10:04:36Z

tests/planemo/PlanemoLintBearTest.py

+            self.uut,
+            [],  # Doesn't matter, planemo lint will parse the file
+            self.test_file,
+            valid=True)


We're working towards writing all the future tests with check_results, so it would be nice if you could use check_results which would help us to verify the output and see if the regex is working. :)

yash-nisar · 2017-05-11T10:06:27Z

bears/planemo/PlanemoLintBear.py

@@ -0,0 +1,30 @@
+


Any reason for leaving this line ?

yash-nisar · 2017-05-11T10:08:48Z

bears/planemo/PlanemoLintBear.py

@@ -0,0 +1,30 @@
+
+from coalib.bearlib.abstractions.Linter import linter
+from dependency_management.requirements.PipRequirement import PipRequirement


We prefer the parenthesis like below...
from dependency_management.requirements.PipRequirement import ( PipRequirement)

yash-nisar · 2017-05-11T10:11:33Z

bears/planemo/PlanemoLintBear.py

+    @staticmethod
+    def create_arguments(filename, file, config_file):
+        args = ('lint',)
+        return args + (filename,)


return 'lint', filename could suffice IMO.

yash-nisar · 2017-05-11T10:14:31Z

tests/planemo/PlanemoLintBearTest.py

+    def setUp(self):
+        self.section = Section('test section')
+        self.uut = PlanemoLintBear(self.section, Queue())
+        self.test_file = os.path.join(os.path.dirname(__file__),


Any particular reason of including this in the setUp method ?

gitmate-bot · 2017-05-18T17:30:19Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

yash-nisar · 2017-05-18T18:04:51Z

Ping @Shade5

Shade5 · 2017-05-19T05:52:28Z

I've been trying to fix this for a while now. Got appyer working but then circle failed. No idea now 😓

yash-nisar · 2017-05-19T05:58:39Z

Can you spot the reason for CircleCI failure ?

Shade5 · 2017-05-19T09:07:03Z

I've tried a lot, couldn't fix it. Please have a look.

Added a linter bear for planemo lint Used `planemo lint` command Closes coala#1321

gitmate-bot · 2017-05-27T01:30:47Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-06-03T00:10:21Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-06-10T09:57:12Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-06-17T08:36:59Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-06-24T07:17:41Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-06-24T07:17:42Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-07-01T05:57:26Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-07-08T04:36:55Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-07-15T03:17:25Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-07-15T03:17:26Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

gitmate-bot · 2017-07-22T01:57:15Z

Hey! This pull request hasn't been updated for a while :/ It would be nice if we could get this going again!

Shade5 mentioned this pull request Jan 22, 2017

Bear proposal planemo lint #1321

Open

Shade5 force-pushed the bug branch from 99b18fd to 87be1e9 Compare January 22, 2017 17:28

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bears/planemo/PlanemoLintBear.py

@@ -0,0 +1,30 @@

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yash-nisar reviewed May 11, 2017

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PlanemoLintBear.py: Add linter bear for planemo

b465827

Added a linter bear for planemo lint Used `planemo lint` command Closes coala#1321

Shade5 force-pushed the bug branch from 1889dfa to b465827 Compare May 19, 2017 09:11

gitmate-bot added the status/STALE label Aug 31, 2017


		@staticmethod
		def create_arguments(filename, file, config_file):

		@@ -0,0 +1,30 @@

		from coalib.bearlib.abstractions.Linter import linter
		from dependency_management.requirements.PipRequirement import PipRequirement

WIP PlanemoLintBear.py: Add linter bear for planemo #1337

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WIP PlanemoLintBear.py: Add linter bear for planemo #1337

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