Fix coverage drop in coordinates module #1441

utkbansal · Jun 27, 2017

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utkbansal · Jun 27, 2017

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 · Jun 28, 2017

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

utkbansal · Jun 28, 2017

@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 · Jun 28, 2017

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 · Jun 28, 2017

Woah! We actually crossed 90% in coverage!

utkbansal · Jun 28, 2017

@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 · Jun 28, 2017

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 · Jun 28, 2017

kain88-de reviewed Jun 28, 2017

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kain88-de · Jun 28, 2017

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 · Jun 28, 2017

kain88-de reviewed Jun 28, 2017

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kain88-de · Jun 28, 2017

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 · Jun 28, 2017

kain88-de reviewed Jun 28, 2017

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kain88-de · Jun 28, 2017

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 · Jun 28, 2017

kain88-de reviewed Jun 28, 2017

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kain88-de · Jun 28, 2017

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 · Jun 29, 2017

richardjgowers reviewed Jun 29, 2017

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richardjgowers · Jun 29, 2017

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 · Jun 29, 2017

@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 · Jun 30, 2017

@utkbansal any progress on this?

utkbansal · Jun 30, 2017

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.

…

On Fri, Jun 30, 2017 at 2:14 PM, Max Linke ***@***.***> wrote: @utkbansal <https://github.com/utkbansal> any progress on this? — 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/AH9W-KiDX8BTW02w1bD25zriAA3NMDwCks5sJLVlgaJpZM4OG8qd> .

utkbansal · Jul 2, 2017

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 · Jul 2, 2017

@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 · Jul 2, 2017

kain88-de requested changes Jul 2, 2017

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kain88-de · Jul 2, 2017

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 · Jul 2, 2017

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 · Jul 2, 2017

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 · Jul 2, 2017

@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 · Jul 2, 2017

@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 · Jul 2, 2017

@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 · Jul 2, 2017

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

utkbansal · Jul 2, 2017

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

utkbansal · Jul 2, 2017

@richardjgowers @kain88-de Should be better now.

richardjgowers · Jul 3, 2017

richardjgowers reviewed Jul 3, 2017

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richardjgowers · Jul 3, 2017

testsuite/MDAnalysisTests/coordinates/base.py

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


delete this

richardjgowers · Jul 3, 2017

richardjgowers reviewed Jul 3, 2017

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richardjgowers · Jul 3, 2017

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.

utkbansal · Jul 8, 2017

This PR is complete now, I think.

kain88-de · Jul 8, 2017

@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 · Jul 10, 2017

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

kain88-de · Jul 10, 2017

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

orbeckst · Jul 10, 2017

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 · Jul 11, 2017

kain88-de reviewed Jul 11, 2017

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kain88-de · Jul 11, 2017

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 · Jul 12, 2017

@kain88-de DCD works now.

kain88-de · Jul 12, 2017

kain88-de approved these changes Jul 12, 2017

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kain88-de · Jul 12, 2017

kain88-de dismissed richardjgowers’s stale review Jul 12, 2017

Comments have been addressed

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

kain88-de referenced this pull request Jul 1, 2017
Merged
DCD-Cython #1372
4 of 4 tasks complete

orbeckst added the testing label Jul 1, 2017

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

Try using asser_almost_equals

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Fix coverage drop in coordinates module #1441

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utkbansal commented Jun 27, 2017

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

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

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