Port test_pqr.py to BaseReaderTest/BaseWriterTest

package/AUTHORS

@@ -284,6 +284,7 @@ Chronological list of authors
   - Sai Udayagiri
   - Apoorva Verma
   - Aryaman Chaudhri
+  - Virvi Huta
 
 External code
 -------------

package/CHANGELOG

@@ -18,7 +18,7 @@ The rules for this file:
          spyke7, talagayev, tanii1125, BradyAJohnston, hejamu, jeremyleung521,
          harshitgajjela-droid, kunjsinha, aygarwal, jauy123, Dreamstick9,
          ollyfutur, Amarendra22, charity-g, ParthUppal523, apoorva-01, RMeli,
-         raulloiscuns, Aryaman-Chaudhri
+         raulloiscuns, Aryaman-Chaudhri, virvihuta
 
  * 2.11.0
 
@@ -101,6 +101,8 @@ Enhancements
 Changes
  * The msd.py inside analysis is changed, and ProgressBar is implemented inside
    _conclude_simple and _conclude_fft functions instead of tqdm (Issue #5144, PR #5153)
+ * Ported `test_pqr.py` to use the new `BaseReaderTest`/`BaseWriterTest`
+   classes (Issue #516).
 
 Deprecations
 

testsuite/MDAnalysisTests/coordinates/test_pqr.py

@@ -21,7 +21,12 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 import MDAnalysis as mda
-import os
+from MDAnalysis.coordinates.PQR import PQRReader, PQRWriter
+from MDAnalysisTests.coordinates.base import (
+    BaseReference,
+    BaseWriterTest,
+    BaseReaderTest,
+)
 import pytest
 
 from numpy.testing import (
@@ -31,11 +36,11 @@
 
 from MDAnalysisTests.coordinates.reference import RefAdKSmall
 from MDAnalysisTests.coordinates.base import _SingleFrameReader
-from MDAnalysisTests.datafiles import PQR
+from MDAnalysisTests.datafiles import PQR, COORDINATES_PQR
 from MDAnalysisTests import make_Universe
 
 
-class TestPQRReader(_SingleFrameReader):
+class TestPQRReaderOld(_SingleFrameReader):
     __test__ = True
 
     def setUp(self):
@@ -85,7 +90,7 @@ def test_dimensions(self):
         assert self.universe.dimensions is None
 
 
-class TestPQRWriter(RefAdKSmall):
+class TestPQRWriterOld(RefAdKSmall):
     @staticmethod
     @pytest.fixture
     def universe():
@@ -188,6 +193,53 @@ def test_total_charge(self, universe, tmpdir):
         )
 
 
+class PQRReference(BaseReference):
+    def __init__(self):
+        super(PQRReference, self).__init__()
+        self.trajectory = COORDINATES_PQR
+        self.topology = COORDINATES_PQR
+        self.reader = PQRReader
+        self.writer = PQRWriter
+        self.ext = "pqr"
+        self.n_frames = 1
+        self.prec = 3
+        self.totaltime = 0
+        self.container_format = False
+        self.dimensions = None
+        self.volume = 0
+
+
+class TestPQRReader(BaseReaderTest):
+    @staticmethod
+    @pytest.fixture(scope="class")
+    def ref():
+        return PQRReference()
+
+    def test_get_writer_1(self, ref, reader, tmpdir):
+        with tmpdir.as_cwd():
+            outfile = "test_writer." + ref.ext
+            with reader.Writer(outfile) as W:
+                assert_equal(isinstance(W, ref.writer), True)
+
+    def test_get_writer_2(self, ref, reader, tmpdir):
+        with tmpdir.as_cwd():
+            outfile = "test_writer." + ref.ext
+            with reader.Writer(outfile, n_atoms=100) as W:
+                assert_equal(isinstance(W, ref.writer), True)
+
+
+class TestPQRWriter(BaseWriterTest):
+    @staticmethod
+    @pytest.fixture(scope="class")
+    def ref():
+        return PQRReference()
+
+    def test_no_container(self, ref, tmpdir):
+        with tmpdir.as_cwd():
+            # PQRWriter doesnt require n_atoms at construction time
+            ref.writer("foo")
+
+
 class TestPQRWriterMissingAttrs(object):
     # pqr requires names, resids, resnames, segids, radii, charges
     @staticmethod

testsuite/MDAnalysisTests/data/coordinates/test.pqr

@@ -0,0 +1,6 @@
+REMARK   1 Test case for MDAnalysis
+ATOM 1 CA MET 1 0.000 1.000 2.000 0.0000 1.0000
+ATOM 2 CA ARG 2 3.000 4.000 5.000 0.0000 1.0000
+ATOM 3 CA ILE 3 6.000 7.000 8.000 0.0000 1.0000
+ATOM 4 CA LYS 4 9.000 10.000 11.000 0.0000 1.0000
+ATOM 5 CA LEU 5 12.000 13.000 14.000 0.0000 1.0000

testsuite/MDAnalysisTests/datafiles.py

@@ -308,6 +308,7 @@
     "COORDINATES_XYZ",
     "COORDINATES_XYZ_BZ2",
     "COORDINATES_GRO",
+    "COORDINATES_PQR",
     "COORDINATES_GRO_INCOMPLETE_VELOCITY",
     "Martini_membrane_gro",  # for testing the leaflet finder
     "COORDINATES_XTC",
@@ -431,6 +432,7 @@
 GRO_huge_box = (_data_ref / "huge_box.gro").as_posix()
 
 COORDINATES_GRO = (_data_ref / "coordinates/test.gro").as_posix()
+COORDINATES_PQR = (_data_ref / "coordinates/test.pqr").as_posix()
 COORDINATES_GRO_INCOMPLETE_VELOCITY = (
     _data_ref / "coordinates/test_incomplete_vel.gro"
 ).as_posix()