Added tqdm bar for: pca.transform() (#4531)

Fixes #3773

Adds tqdm progress bar to  the `pca.transform` method.

package/AUTHORS

@@ -236,6 +236,7 @@ Chronological list of authors
   2024
   - Aditya Keshari
   - Philipp Stärk
+  - Sampurna Mukherjee
 
 External code
 -------------

package/CHANGELOG

@@ -16,7 +16,7 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
-         tyler.je.reddy
+         tyler.je.reddy, SampurnaM
 
  * 2.8.0
 
@@ -34,6 +34,8 @@ Fixes
  * Fix deploy action to use the correct version of the pypi upload action.
 
 Enhancements
+ * Added a tqdm progress bar for `MDAnalysis.analysis.pca.PCA.transform()`
+   (PR #4531)
  * Improved performance of PDBWriter (Issue #2785, PR #4472)
  * Added parsing of arbitrary columns of the LAMMPS dump parser. (Issue #3504)
  * Documented the r0 attribute in the `Contacts` class and added the 

package/MDAnalysis/analysis/pca.py

@@ -118,6 +118,7 @@
 
 import numpy as np
 import scipy.integrate
+from tqdm.auto import tqdm
 
 from MDAnalysis import Universe
 from MDAnalysis.analysis.align import _fit_to
@@ -355,12 +356,12 @@ def n_components(self, n):
                 n = len(self._variance)
             self.results.variance = self._variance[:n]
             self.results.cumulated_variance = (np.cumsum(self._variance) /
-                                       np.sum(self._variance))[:n]
+                                               np.sum(self._variance))[:n]
             self.results.p_components = self._p_components[:, :n]
         self._n_components = n
 
     def transform(self, atomgroup, n_components=None, start=None, stop=None,
-                  step=None):
+                  step=None, verbose=False):
         """Apply the dimensionality reduction on a trajectory
 
         Parameters
@@ -382,6 +383,11 @@ def transform(self, atomgroup, n_components=None, start=None, stop=None,
             Include every `step` frames in the PCA transform. If set to
             ``None`` (the default) then every frame is analyzed (i.e., same as
             ``step=1``).
+        verbose : bool, optional
+            ``verbose = True`` option displays a progress bar for the
+            iterations of transform. ``verbose = False`` disables the
+            progress bar, just returns the pca_space array when the
+            calculations are finished.
 
         Returns
         -------
@@ -391,14 +397,17 @@ def transform(self, atomgroup, n_components=None, start=None, stop=None,
         .. versionchanged:: 0.19.0
            Transform now requires that :meth:`run` has been called before,
            otherwise a :exc:`ValueError` is raised.
+        .. versionchanged:: 2.8.0
+           Transform now has shows a tqdm progressbar, which can be toggled
+           on with ``verbose = True``, or off with ``verbose = False``
         """
         if not self._calculated:
             raise ValueError('Call run() on the PCA before using transform')
 
         if isinstance(atomgroup, Universe):
             atomgroup = atomgroup.atoms
 
-        if(self._n_atoms != atomgroup.n_atoms):
+        if self._n_atoms != atomgroup.n_atoms:
             raise ValueError('PCA has been fit for'
                              '{} atoms. Your atomgroup'
                              'has {} atoms'.format(self._n_atoms,
@@ -415,7 +424,10 @@ def transform(self, atomgroup, n_components=None, start=None, stop=None,
 
         dot = np.zeros((n_frames, dim))
 
-        for i, ts in enumerate(traj[start:stop:step]):
+        for i, ts in tqdm(enumerate(traj[start:stop:step]), disable=not verbose,
+                          total=len(traj[start:stop:step])
+                          ):
+
             xyz = atomgroup.positions.ravel() - self._xmean
             dot[i] = np.dot(xyz, self._p_components[:, :dim])
 
@@ -561,7 +573,7 @@ def project_single_frame(self, components=None, group=None, anchor=None):
             for res in group.residues:
                 # n_common is the number of pca atoms in a residue
                 n_common = pca_res_counts[np.where(
-                           pca_res_indices == res.resindex)][0]
+                            pca_res_indices == res.resindex)][0]
                 non_pca_atoms = np.append(non_pca_atoms,
                                           res.atoms.n_atoms - n_common)
             # index_extrapolate records the anchor number for each non-PCA atom

package/MDAnalysis/lib/log.py

@@ -135,7 +135,8 @@ def create(logger_name="MDAnalysis", logfile="MDAnalysis.log"):
 
     # handler that writes to logfile
     logfile_handler = logging.FileHandler(logfile)
-    logfile_formatter = logging.Formatter('%(asctime)s %(name)-12s %(levelname)-8s %(message)s')
+    logfile_formatter = logging.Formatter(
+        '%(asctime)s %(name)-12s %(levelname)-8s %(message)s')
     logfile_handler.setFormatter(logfile_formatter)
     logger.addHandler(logfile_handler)
 
@@ -172,6 +173,7 @@ class NullHandler(logging.Handler):
     see the advice on logging and libraries in
     http://docs.python.org/library/logging.html?#configuring-logging-for-a-library
     """
+
     def emit(self, record):
         pass
 
@@ -327,6 +329,7 @@ class ProgressBar(tqdm):
     .. _`tqdm documentation`: https://tqdm.github.io/
 
     """
+
     def __init__(self, *args, **kwargs):
         """"""
         # ^^^^ keep the empty doc string to avoid Sphinx doc errors with the