Fix coverage drop in coordinates module #1441

utkbansal · 2017-06-27T17:29:02Z

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Tests?
Docs?
CHANGELOG updated?
Issue raised/referenced?

utkbansal · 2017-06-27T18:40:04Z

With the last commit, I might have bloated the tests. I'll revisit that aspect later. I'm currently only focused on getting coverage back.

richardjgowers · 2017-06-28T06:18:27Z

@utkbansal how do you mean bloated? Some unnecessary tests or just linecount?

utkbansal · 2017-06-28T06:41:28Z

@richardjgowers In the terms of the number of lines. I should be able to make some fixtures global. Stuff like tempdir can be easily done. But I'll need to play around with scopes and see figure out the greatest scope I can use them in. But I think this work is better suited for Phase 2. Thoughst??

richardjgowers · 2017-06-28T07:08:38Z

Yeah don't worry about line counts for now

…

On Wed, 28 Jun 2017, 7:41 a.m. Utkarsh Bansal, ***@***.***> wrote: @richardjgowers <https://github.com/richardjgowers> In the terms of the number of lines. I should be able to make some fixtures global. Stuff like tempdir can be easily done. But I'll need to play around with scopes and see figure out the greatest scope I can use them in. But I think this work is better suited for Phase 2. Thoughst?? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1441 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AI0jBzX2enarCYJh6BokSKboRk8vbd2Aks5sIfWZgaJpZM4OG8qd> .

utkbansal · 2017-06-28T12:26:36Z

Woah! We actually crossed 90% in coverage!

utkbansal · 2017-06-28T13:09:51Z

@kain88-de @richardjgowers A review at this point would be helpful. I'm mostly done porting the stuff. I now need to look for the tests that are missed out.

utkbansal · 2017-06-28T13:16:21Z

I have restarted the build for the merge of 1414 - https://travis-ci.org/MDAnalysis/mdanalysis/builds/246515054

Want to see the drop in coverage caused by it. This PR + 1414 should ideally sum up to no drop in coverage.

kain88-de · 2017-06-28T15:58:17Z

testsuite/MDAnalysisTests/coordinates/base.py

-        with self.ref.writer(outfile, self.reader.n_atoms) as W:
-            for ts in self.reader:
+    def tmp_file(self, name, ref, tmpdir):
+        return tmpdir.name + name + '.' + ref.ext


this might need to be changed since tmpdir is a pytest internal fixture. @utkbansal do you know where tmpdirs are created here?

kain88-de · 2017-06-28T15:59:52Z

testsuite/MDAnalysisTests/coordinates/test_gro.py

+    def reader(ref):
+        reader = ref.reader(ref.trajectory)
+        reader.add_auxiliary('lowf', ref.aux_lowf, dt=ref.aux_lowf_dt, initial_time=0, time_selector=None)
+        reader.add_auxiliary('highf', ref.aux_highf, dt=ref.aux_highf_dt, initial_time=0, time_selector=None)


Can we find a solution that doesn't require us to repeat this for every child class of BaseReaderTests?

Can't this be defined in the base class?

kain88-de · 2017-06-28T19:35:50Z

testsuite/MDAnalysisTests/coordinates/base.py

+    def tmp_file(self, name, ref, tmpdir):
+        return tmpdir.name + name + '.' + ref.ext
+
+    def test_write_trajectory_timestep(self,ref, reader, tmpdir):


I'm confused here. Is tmpdir here using the tmpdir-fixture of pytest? Because later you use tmpdir.name but the path.local variable that the tmpdir-fixture returns doesn't have a name attribute.

kain88-de · 2017-06-28T19:39:04Z

testsuite/MDAnalysisTests/coordinates/test_gro.py

+    @staticmethod
+    @pytest.fixture()
+    def tmpdir():
+        return tempdir.TempDir()


Oh man overwriting the pytest tmpdir fixture isn't a good idea. rather call it tempdir to make it distinctively different. Also this fixture shouldn't be repeated for every class that inherits BaseTestWriter. Can't it be part of the base class?

I don't like that this is defined in the child class. This is common for all tests and should be defined in the base class. Similar to the universe fixtures above

Also the name is NOT OK. It overwrites a pytest fixture which can lead to confusion. See above comment for alternative name suggestions

richardjgowers · 2017-06-29T09:27:28Z

testsuite/MDAnalysisTests/coordinates/test_xyz.py

+
+    @staticmethod
+    @pytest.fixture()
+    def u_no_resnames():


These Universe fixtures don't need to be defined in each format's tests, they're format agnostic. I would either, define them in the base class (BaseWriterTest?) or just call them in the test function. They're very light, so we're unlikely to have them has a large-scoped fixture.

utkbansal · 2017-06-29T09:42:36Z

@richardjgowers @kain88-de Is there an easy way to compare two(or more coverage reports). Coveralls can do that but it doesn't work. I might have an idea why it doesn't work though, it would be great if we could fix it.

kain88-de · 2017-06-30T08:44:20Z

@utkbansal any progress on this?

utkbansal · 2017-06-30T08:57:30Z

Not yet, It has the same yield problem which is causing the coverage to drop. The problem is smaller in the core module, so I'm trying to fix that first so that I'm more comfortable dealing with tricky cases here.

…

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utkbansal · 2017-07-02T09:46:43Z

Missing test cases due to yield

test_dcd.py - Leaving this out because @kain88-de is already working on it.
test_reader_api.py
test_timestep_api.py

Other than tests in these files, all are executed.

utkbansal · 2017-07-02T10:04:11Z

@richardjgowers @kain88-de In test_timestep_api.py we have the following test class -

class TestBaseTimestep(BaseTimestepTest):
    @dec.skipif(parser_not_found('DCD'),
                'DCD parser not available. Are you using python 3?')
    def test_other_timestep(self):
        # use a subclass to base.Timestep to check it works
        ts1 = mda.coordinates.base.Timestep(10)
        ts1.positions = self._get_pos()

        # can't do TRR Timestep here as it always has vels and forces
        # so isn't actually equal to a position only timestep
        for otherTS in [mda.coordinates.DCD.Timestep,
                        mda.coordinates.TRJ.Timestep,
                        mda.coordinates.DMS.Timestep,
                        mda.coordinates.GRO.Timestep,
                        mda.coordinates.TRZ.Timestep,
                        ]:
            ts2 = otherTS(10)
            ts2.positions = self._get_pos()
            yield (self._check_ts_equal, ts1, ts2,
                   "Failed on {0}".format(otherTS))

If we change it to something like the following, the test will be executed.

class TestBaseTimestep(BaseTimestepTest):
    @dec.skipif(parser_not_found('DCD'),
                'DCD parser not available. Are you using python 3?')
    def test_other_timestep(self):
        # use a subclass to base.Timestep to check it works
        ts1 = mda.coordinates.base.Timestep(10)
        ts1.positions = self._get_pos()

        # can't do TRR Timestep here as it always has vels and forces
        # so isn't actually equal to a position only timestep
        for otherTS in [mda.coordinates.DCD.Timestep,
                        mda.coordinates.TRJ.Timestep,
                        mda.coordinates.DMS.Timestep,
                        mda.coordinates.GRO.Timestep,
                        mda.coordinates.TRZ.Timestep,
                        ]:
            ts2 = otherTS(10)
            ts2.positions = self._get_pos()


            ##### THIS IS THE CHANGE #######
            self._check_ts_equal( ts1, ts2,
                   "Failed on {0}".format(otherTS))

This is a band-aid fix for now. But I want to do this for now because the right way will casue a lot of changes - BaseTimestepTest inherits from TestCase, I need to get rid of TestCase and use fixtures. But then I will also have to modify all the other subclasses to use fixtures too.

kain88-de · 2017-07-02T13:47:10Z

testsuite/MDAnalysisTests/coordinates/test_gro.py

+    def reader(ref):
+        reader = ref.reader(ref.trajectory)
+        reader.add_auxiliary('lowf', ref.aux_lowf, dt=ref.aux_lowf_dt, initial_time=0, time_selector=None)
+        reader.add_auxiliary('highf', ref.aux_highf, dt=ref.aux_highf_dt, initial_time=0, time_selector=None)


Can't this be defined in the base class?

kain88-de · 2017-07-02T13:47:10Z

testsuite/MDAnalysisTests/coordinates/test_gro.py

+    @staticmethod
+    @pytest.fixture()
+    def tmpdir():
+        return tempdir.TempDir()


I don't like that this is defined in the child class. This is common for all tests and should be defined in the base class. Similar to the universe fixtures above

kain88-de · 2017-07-02T13:47:10Z

testsuite/MDAnalysisTests/coordinates/test_gro.py

+    @staticmethod
+    @pytest.fixture()
+    def tmpdir():
+        return tempdir.TempDir()


Also the name is NOT OK. It overwrites a pytest fixture which can lead to confusion. See above comment for alternative name suggestions

richardjgowers · 2017-07-02T17:07:40Z

@utkbansal with the band-aid above, why does that yield not work? Also, why can't we quickly put in the parametrize over classes?

utkbansal · 2017-07-02T17:23:36Z

@richardjgowers yield doesn't work if you have setUp in the class (see #1443 (comment)) and parameterize doesn't work if we inherit from TestCase (see #1443 (comment)).

To fix this properly I will have to get rid of TestCase inheritance (in BaseTimestepTest ) and then I wil have to update all the sublasses of BaseTimestepTest to use fixtures.
This can be, IMHO, done in the next phase.

kain88-de · 2017-07-02T17:30:07Z

@utkbansal this is one of the last classes and the coordinates tests are already set to pytest. You might as well go full on at least for the BaseTimestepTest. I don't mind if this takes a bit longer. You can also start working on porting the analysis tests.

utkbansal · 2017-07-02T17:44:55Z

@kain88-de Okay, I'll fix it completely then. I'm also starting analysis - it's the only module left.

utkbansal · 2017-07-02T18:50:16Z

@richardjgowers @kain88-de I overestimated the amount of work needed to fix this. Apologies.

utkbansal · 2017-07-02T21:45:53Z

@richardjgowers @kain88-de Should be better now.

richardjgowers · 2017-07-03T06:49:32Z

testsuite/MDAnalysisTests/coordinates/base.py

-
-    def test_getitem(self):
-        assert_equal(self.ts[1], self.refpos[1])
+    # def setUp(self):


delete this

richardjgowers · 2017-07-03T06:52:04Z

testsuite/MDAnalysisTests/coordinates/test_reader_api.py


        assert_raises(TypeError, sl)

-    def _check_getitem(self, sl):
-        res = [ts.frame for ts in self.reader[sl]]
+    @pytest.mark.parametrize('sl', [


why can't this use a double parametrize?

We should be able to do that.

I'm not really sure how I can do this.

@pytest.mark.parametrize('slice_cls', [list, np.array]) @pytest.mark.parametrize('sl', []) def test_thing(self, slice_cls, sl): sl = slice_cls(sl) etc

We want to turn res = [ts.frame for ts in reader[sl]] into a fixture, right? I am unable to access the reader fixture in the parametrize call.

I think this has to do with static checking, If I define the fixture in the subclass itself, then I'm able to access it in the parameterize call.

kain88-de · 2017-07-08T19:51:39Z

@utkbansal you haven't updated the DCD tests. As I said DCD can now be updated as well since we merged the new DCD reader

utkbansal · 2017-07-10T14:05:06Z

I think something is wrong with the precision in the DCD test. Can someone check?

kain88-de · 2017-07-10T15:08:00Z

@utkbansal did you have a look at the difference in these tests between your branch and develop?

orbeckst · 2017-07-10T19:01:06Z

I don't think that these failing tests should be using assert_equal when comparing floating point numbers. This should have been assert_almost_equal.

kain88-de · 2017-07-11T09:38:00Z

testsuite/MDAnalysisTests/coordinates/base.py

@@ -801,13 +801,13 @@ def test_time_with_offset(self):

        assert_equal(ts.time, reftime + ref_offset)

-    def test_dt(self):
+    def test_dt(self, ref):


looks like it doesn't know what ref is. Also you forgot a test_dt in the other test class. Did you run those tests on your local laptop?

Oddly enough the tests still fail. But if I directly change the files in where MD is installed (site-packages) then the same change works. Is there another build step I'm missing?!

utkbansal · 2017-07-12T05:05:27Z

@kain88-de DCD works now.

Comments have been addressed

utkbansal changed the title ~~Fix coverage drop in coordinates module~~ [WIP]Fix coverage drop in coordinates module Jun 27, 2017

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DCD-Cython #1372

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utkbansal changed the title ~~[WIP]Fix coverage drop in coordinates module~~ Fix coverage drop in coordinates module Jul 2, 2017

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testsuite/MDAnalysisTests/coordinates/base.py Outdated

def test_getitem(self):

assert_equal(self.ts[1], self.refpos[1])

# def setUp(self):

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Try using asser_almost_equals

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MDAnalysis / mdanalysis

Fix coverage drop in coordinates module #1441

Fix coverage drop in coordinates module #1441

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