Allow ChainReader to accept format keyword

package/CHANGELOG

@@ -79,6 +79,7 @@ Changes
   * changed the water bridge analysis output format (PR #2087)
 
 Fixes
+  * fixed ChainReader setting format with format keyword (Issue #2334)
   * fixed lack of check for scaling of NCDFReader velocities (Issue #2323)
   * fixed PDBReader and PDBWriter newlines for PDB header (Issue #2324)
   * fixes ProgressMeter issues with older Jupyter Lab versions (Issue #2078)

package/MDAnalysis/coordinates/core.py

@@ -46,7 +46,7 @@
 from ..core._get_readers import get_reader_for, get_writer_for
 
 
-def reader(filename, **kwargs):
+def reader(filename, format=None, **kwargs):
     """Provide a trajectory reader instance for *filename*.
 
     This function guesses the file format from the extension of *filename* and
@@ -78,10 +78,14 @@ def reader(filename, **kwargs):
     if isinstance(filename, tuple):
         Reader = get_reader_for(filename[0],
                                 format=filename[1])
-        return Reader(filename[0], **kwargs)
+        filename = filename[0]
     else:
-        Reader = get_reader_for(filename)
+        Reader = get_reader_for(filename, format=format)
+    try:
         return Reader(filename, **kwargs)
+    except ValueError:
+        raise TypeError('Unable to read {fn} with {r}.'.format(fn=filename,
+                                                                r=Reader))
 
 
 def writer(filename, n_atoms=None, **kwargs):

package/MDAnalysis/core/universe.py

@@ -601,7 +601,7 @@ def load_new(self, filename, format=None, in_memory=False, **kwargs):
         # supply number of atoms for readers that cannot do it for themselves
         kwargs['n_atoms'] = self.atoms.n_atoms
 
-        self.trajectory = reader(filename, **kwargs)
+        self.trajectory = reader(filename, format=format, **kwargs)
         if self.trajectory.n_atoms != len(self.atoms):
             raise ValueError("The topology and {form} trajectory files don't"
                              " have the same number of atoms!\n"

testsuite/MDAnalysisTests/coordinates/test_chainreader.py

@@ -200,13 +200,29 @@ def test_set_all_format_tuples(self):
         assert universe.trajectory.n_frames == 21
         assert_equal(universe.trajectory.filenames, [PDB, XTC, TRR])
 
+    def test_set_format_tuples_and_format(self):
+        universe = mda.Universe(GRO, [(PDB, 'pdb'), GRO, GRO, (XTC, 'xtc'), 
+                                      (TRR, 'trr')], format='gro')
+        assert universe.trajectory.n_frames == 23
+        assert_equal(universe.trajectory.filenames, [PDB, GRO, GRO, XTC, TRR])
+
+        with pytest.raises(TypeError) as errinfo:
+            mda.Universe(GRO, [(PDB, 'pdb'), GRO, GRO, (XTC, 'xtc'), 
+                                      (TRR, 'trr')], format='pdb')
+        assert 'Unable to read' in str(errinfo.value)
+
+
     def test_set_one_format_tuple(self):
         universe = mda.Universe(PSF, [(PDB_small, 'pdb'), DCD])
         assert universe.trajectory.n_frames == 99
 
     def test_set_all_formats(self):
-        universe = mda.Universe(PSF, [PDB_small, PDB_closed], format='pdb')
-        assert universe.trajectory.n_frames == 2
+        with pytest.raises(TypeError) as errinfo:
+            mda.Universe(PDB, [PDB, GRO], format='gro')
+        assert 'Unable to read' in str(errinfo.value)
+
+        universe = mda.Universe(GRO, [PDB, PDB, PDB], format='pdb')
+        assert_equal(universe.trajectory.filenames, [PDB, PDB, PDB])
 
 
 def build_trajectories(folder, sequences, fmt='xtc'):