From 5fa2e57e162903914966cd43c1ce4ba634d4c070 Mon Sep 17 00:00:00 2001
From: ljwoods2 <145226270+ljwoods2@users.noreply.github.com>
Date: Mon, 12 Feb 2024 06:19:22 -0700
Subject: [PATCH] ChainedReader __repr__ fix for MemoryReader sub-readers
 (#4407)

* Reset branch and added pytest

* PEP8 and CHANGELOG

* Assert statement fix

* Full iteration and repr() change

* typo

* typo

* Update package/CHANGELOG

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>

* Added direct test to u.trajectory.filenames

* Removing print

---------

Co-authored-by: Rocco Meli <r.meli@bluemail.ch>
---
 package/CHANGELOG                             |  5 +++-
 package/MDAnalysis/coordinates/chain.py       | 24 ++++++++++++++-----
 .../coordinates/test_chainreader.py           | 19 +++++++++++++++
 3 files changed, 41 insertions(+), 7 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index d4ba2ca05e7..c825d7094df 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -14,11 +14,14 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
-??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli
+??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
+         ljwoods2
 
  * 2.8.0
 
 Fixes
+ * Fix ChainReader `__repr__()` method when sub-reader is MemoryReader 
+   (Issue #3349, PR #4407)
  * Fix bug in PCA preventing use of `frames=...` syntax (PR #4423)
  * Fix `analysis/diffusionmap.py` iteration through trajectory to iteration
    over `self._sliced_trajectory`, hence supporting
diff --git a/package/MDAnalysis/coordinates/chain.py b/package/MDAnalysis/coordinates/chain.py
index bdfdeff3523..0c09a596d95 100644
--- a/package/MDAnalysis/coordinates/chain.py
+++ b/package/MDAnalysis/coordinates/chain.py
@@ -269,8 +269,17 @@ def __init__(self, filenames, skip=1, dt=None, continuous=False,
             kwargs['dt'] = dt
         self.readers = [core.reader(filename, convert_units=convert_units, **kwargs)
                         for filename in filenames]
-        self.filenames = np.array([fn[0] if isinstance(fn, tuple) else fn
-                                                        for fn in filenames])
+        # Iterate through all filenames, appending NoneType None for ndarrays
+        self.filenames = []
+        for fn in filenames:
+            if isinstance(fn, np.ndarray):
+                self.filenames.append(None)
+            elif isinstance(fn, tuple):
+                self.filenames.append(fn[0])
+            else:
+                self.filenames.append(fn)
+        self.filenames = np.array(self.filenames)
+
         # pointer to "active" trajectory index into self.readers
         self.__active_reader_index = 0
 
@@ -598,11 +607,14 @@ def close(self):
 
     def __repr__(self):
         if len(self.filenames) > 3:
-            fnames = "{fname} and {nfanmes} more".format(
-                    fname=os.path.basename(self.filenames[0]),
-                    nfanmes=len(self.filenames) - 1)
+            fname = (os.path.basename(self.filenames[0])
+                     if self.filenames[0] else "numpy.ndarray")
+            fnames = "{fname} and {nfnames} more".format(
+                    fname=fname,
+                    nfnames=len(self.filenames) - 1)
         else:
-            fnames = ", ".join([os.path.basename(fn) for fn in self.filenames])
+            fnames = ", ".join([os.path.basename(fn) if fn else "numpy.ndarray"
+                                for fn in self.filenames])
         return ("<{clsname} containing {fname} with {nframes} frames of {natoms} atoms>"
                 "".format(
                     clsname=self.__class__.__name__,
diff --git a/testsuite/MDAnalysisTests/coordinates/test_chainreader.py b/testsuite/MDAnalysisTests/coordinates/test_chainreader.py
index ba0687ffd76..2049b687279 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_chainreader.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_chainreader.py
@@ -455,3 +455,22 @@ def wrapped(ts):
     # in the issue report values of ~25 were seen before the fix
     # with the fix all values should be <1e-6
     assert np.abs(com).max() < 1e-6
+
+
+def test_issue_3349():
+    # test for repr of a chainreader when the subreaders are memoryreaders
+    cdx = np.random.random(3341 * 3 * 10)
+    cdx = cdx.reshape(-1, 3341, 3).astype(np.float32) * 10
+    u = mda.Universe(PSF, (cdx, DCD))
+    u2 = mda.Universe(PSF, (cdx, cdx, cdx, DCD))
+    u_expected_filenames = np.array([None, str(DCD)])
+    u2_expected_filenames = np.array([None, None, None, str(DCD)])
+
+    assert_equal("<ChainReader containing numpy.ndarray, adk_dims.dcd with " +
+                 "108 frames of 3341 atoms>",
+                 u.trajectory.__repr__())
+    assert_equal(u_expected_filenames, u.trajectory.filenames)
+    assert_equal("<ChainReader containing numpy.ndarray and 3 more with " +
+                 "128 frames of 3341 atoms>",
+                 u2.trajectory.__repr__())
+    assert_equal(u2_expected_filenames, u2.trajectory.filenames)