Adding smaller test data

.coveragerc

@@ -1,6 +1,7 @@
 [run]
 omit =
-    pyedr/pyedr/tests/data/*
+    pyedr/pyedr/tests/*
+
 
 [report]
 exclude_lines =

.github/workflows/gh-ci.yaml

@@ -45,7 +45,7 @@ jobs:
 
     - name: install package deps
       run: |
-        mamba install pytest pytest-xdist pytest-cov codecov pbr numpy
+        mamba install pytest pytest-xdist pytest-cov codecov pbr numpy tqdm
 
     - name: check install
       run: |

ChangeLog

@@ -14,6 +14,18 @@ The rules for this file:
   * Note: rules were not applied before v0.6.0
 
 ------------------------------------------------------------------------------
+XX/XX/2022 BFedder, IAlibay
+
+  * 0.7.1
+
+  Changes
+
+  * Stopped using time.time() in verbose reporting and switched to using
+    tqdm for progress bars (PR # 55)
+  * Replaced some of the test data files with smaller counterparts to reduce
+    total file size (PR #55)
+  * Added Python 3.11 support (PR #59)
+
 02/09/2022 BFedder, IAlibay
 
   * 0.7.0

panedr/panedr/tests/test_edr.py

@@ -116,41 +116,6 @@ def test_verbosity(self):
         print(ref_content - content)
         assert_allclose(ref_content, content, atol=prec/2)
 
-    def test_progress(self):
-        """
-        Test the progress meter displays what is expected.
-        """
-        output = StringIO()
-        with redirect_stderr(output):
-            df = panedr.edr_to_df(EDR, verbose=True)
-        progress = output.getvalue().split('\n')[0].split('\r')
-        print(progress)
-        dt = 2000.0
-        # We can already iterate on `progress`, but I want to keep the cursor
-        # position from one for loop to the other.
-        progress_iter = iter(progress)
-        assert '' == next(progress_iter)
-        self._assert_progress_range(progress_iter, dt, 0, 21, 1)
-        self._assert_progress_range(progress_iter, dt, 30, 201, 10)
-        self._assert_progress_range(progress_iter, dt, 300, 2001, 100)
-        self._assert_progress_range(progress_iter, dt, 3000, 14101, 1000)
-        # Check the last line
-        print(df.iloc[-1, 0])
-        ref_line = 'Last Frame read : 14099, time : 28198000.0 ps'
-        last_line = next(progress_iter)
-        assert ref_line == last_line
-        # Did we leave stderr clean with a nice new line at the end?
-        assert output.getvalue().endswith('\n'), \
-               'New line missing at the end of output.'
-
-    def _assert_progress_range(self, progress, dt, start, stop, step):
-        for frame_idx in range(start, stop, step):
-            ref_line = 'Read frame : {},  time : {} ps'.format(frame_idx,
-                                                               dt * frame_idx)
-            progress_line = next(progress)
-            print(frame_idx, progress_line)
-            assert ref_line == progress_line
-
     def test_edr_dict_to_df_match(self, edr):
         array_df = pandas.DataFrame.from_dict(edr.edr_dict).set_index(
                 "Time", drop=False)

pyedr/pyedr/pyedr.py

@@ -46,7 +46,7 @@
 import warnings
 import sys
 import itertools
-import time
+from tqdm import tqdm
 from typing import List, Tuple, Dict
 
 import numpy as np
@@ -439,30 +439,15 @@ def read_edr(path: str, verbose: bool = False) -> read_edr_return_type:
     times: list[float]
         A list containing the time of each step/frame.
     """
-    begin = time.time()
     edr_file = EDRFile(str(path))
     all_energies = []
     all_names = [u'Time'] + [nm.name for nm in edr_file.nms]
     times = []
-    for ifr, frame in enumerate(edr_file):
-        if verbose:
-            if ((ifr < 20 or ifr % 10 == 0) and
-                    (ifr < 200 or ifr % 100 == 0) and
-                    (ifr < 2000 or ifr % 1000 == 0)):
-                print('\rRead frame : {},  time : {} ps'.format(ifr, frame.t),
-                      end='', file=sys.stderr)
+    for ifr, frame in tqdm(enumerate(edr_file), disable=(not verbose)):
         if frame.ener:
             # Export only frames that contain energies
             times.append(frame.t)
             all_energies.append([frame.t] + [ener.e for ener in frame.ener])
-
-    end = time.time()
-    if verbose:
-        print('\rLast Frame read : {}, time : {} ps'
-              .format(ifr, frame.t),
-              end='', file=sys.stderr)
-        print('\n{} frame read in {:.2f} seconds'.format(ifr, end - begin),
-              file=sys.stderr)
     return all_energies, all_names, times
 
 

pyedr/pyedr/tests/data/cat_small.xvg

@@ -0,0 +1,78 @@
+# This file was created Tue Aug  2 10:36:39 2022
+# Created by:
+#                      :-) GROMACS - gmx energy, 2021.5 (-:
+# 
+# Executable:   /biggin/b149/mert4328/gromacs2021.5/bin/gmx
+# Data prefix:  /biggin/b149/mert4328/gromacs2021.5
+# Working dir:  /biggin/b149/mert4328/Downloads/panedr/pyedr/pyedr/tests/data
+# Command line:
+#   gmx energy -f cat.edr -o cat.xvg
+# gmx energy is part of G R O M A C S:
+#
+# Green Red Orange Magenta Azure Cyan Skyblue
+#
+@    title "GROMACS Energies"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "(kJ/mol), (K), (bar), (), (nm), (nm^3), (kg/m^3), (bar nm), (nm/ps)"
+@TYPE xy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ s0 legend "Bond"
+@ s1 legend "Angle"
+@ s2 legend "Proper Dih."
+@ s3 legend "Ryckaert-Bell."
+@ s4 legend "LJ-14"
+@ s5 legend "Coulomb-14"
+@ s6 legend "LJ (SR)"
+@ s7 legend "Disper. corr."
+@ s8 legend "Coulomb (SR)"
+@ s9 legend "Coul. recip."
+@ s10 legend "Potential"
+@ s11 legend "Kinetic En."
+@ s12 legend "Total Energy"
+@ s13 legend "Conserved En."
+@ s14 legend "Temperature"
+@ s15 legend "Pres. DC"
+@ s16 legend "Pressure"
+@ s17 legend "Constr. rmsd"
+@ s18 legend "Box-X"
+@ s19 legend "Box-Y"
+@ s20 legend "Box-Z"
+@ s21 legend "Volume"
+@ s22 legend "Density"
+@ s23 legend "pV"
+@ s24 legend "Enthalpy"
+@ s25 legend "Vir-XX"
+@ s26 legend "Vir-XY"
+@ s27 legend "Vir-XZ"
+@ s28 legend "Vir-YX"
+@ s29 legend "Vir-YY"
+@ s30 legend "Vir-YZ"
+@ s31 legend "Vir-ZX"
+@ s32 legend "Vir-ZY"
+@ s33 legend "Vir-ZZ"
+@ s34 legend "Pres-XX"
+@ s35 legend "Pres-XY"
+@ s36 legend "Pres-XZ"
+@ s37 legend "Pres-YX"
+@ s38 legend "Pres-YY"
+@ s39 legend "Pres-YZ"
+@ s40 legend "Pres-ZX"
+@ s41 legend "Pres-ZY"
+@ s42 legend "Pres-ZZ"
+@ s43 legend "#Surf*SurfTen"
+@ s44 legend "Box-Vel-XX"
+@ s45 legend "Box-Vel-YY"
+@ s46 legend "Box-Vel-ZZ"
+@ s47 legend "T-Protein"
+@ s48 legend "T-non-Protein"
+@ s49 legend "Lamb-Protein"
+@ s50 legend "Lamb-non-Protein"
+    0.000000  1374.823242  3764.527344  231.283890  1769.977173  2654.552490  7772.819824  93403.531250  -4571.847656  -634643.937500  3080.209717  -525164.062500  86616.812500  -438547.250000  -438527.062500  303.022461  -226.715179  120.662346    0.000003    6.946903    6.946903    6.946903  335.253754  1021.368042   20.189453  -438527.062500  26742.484375  -1014.244263  -428.990967  -1014.437500  27074.781250  -1649.407959  -428.967163  -1649.536377  29145.390625  204.548508   99.160240   16.660902   99.179382  215.034927  138.859970   16.658545  138.872696  -57.596401  -1857.519287    0.000000    0.000000    0.000000  305.216461  302.853333    1.000000    1.000000
+    0.020000  1426.225220  3752.830322  263.692535  1819.986816  2681.986084  7719.875977  93969.390625  -4571.750488  -634577.250000  2922.847168  -524592.125000  86058.304688  -438533.812500  -438520.187500  301.068573  -226.705521  127.012749    0.000003    6.946952    6.946952    6.946952  335.260864  1021.346375   20.189880  -438513.625000  29358.015625  404.244843  1123.673584  404.736359  24486.328125  -524.118896  1123.208862  -525.036743  28367.406250  -77.379997  -34.419483  -122.969460  -34.468178  436.573883   42.815838  -122.923424   42.906754   21.844366  -1095.899536    0.002461    0.002461    0.002461  302.409576  300.965179    1.000000    1.000000
+    0.040000  1482.009888  3731.591797  261.267670  1802.421021  2664.599365  7685.277344  94167.468750  -4571.551758  -634705.562500  3063.695312  -524418.812500  86040.515625  -438378.312500  -438527.031250  301.006317  -226.685791  172.537247    0.000003    6.947053    6.947053    6.947053  335.275482  1021.301880   20.190762  -438358.125000  26755.218750  -1644.403564  1042.608276  -1644.735718  24932.406250  -618.195557  1041.680420  -618.909668  29127.406250  216.510681  150.174057  -84.276016  150.206955  373.560364   47.772625  -84.184113   47.843361  -72.459267  -2553.005859    0.005053    0.005053    0.005053  299.224762  301.143646    1.000000    1.000000
+    0.060000  1470.337524  3683.409424  237.611053  1862.587646  2639.180664  7770.815430  93807.351562  -4571.210938  -634513.875000  2964.734863  -524649.062500  86426.179688  -438222.875000  -438543.031250  302.355530  -226.652084   40.944675    0.000003    6.947225    6.947225    6.947225  335.300385  1021.226013   20.192261  -438202.687500  27163.343750  -2570.930908  1478.509766  -2571.069824  30978.859375  -990.745056  1477.574463  -991.381042  27043.828125  160.203705  262.667664  -130.225845  262.681427  -189.501358  113.234261  -130.133194  113.297256  152.131683  1158.661621    0.008582    0.008582    0.008582  299.770569  302.554779    1.000000    1.000000

pyedr/pyedr/tests/datafiles.py

@@ -28,9 +28,9 @@
 from pkg_resources import resource_filename
 
 
-EDR = resource_filename(__name__, 'data/cat.edr')
-EDR_XVG = resource_filename(__name__, 'data/cat.xvg')
-EDR_UNITS = resource_filename(__name__, 'data/cat_units.p')
+EDR = resource_filename(__name__, 'data/cat_small.edr')
+EDR_XVG = resource_filename(__name__, 'data/cat_small.xvg')
+EDR_UNITS = resource_filename(__name__, 'data/cat_small_units.p')
 
 EDR_IRREG = resource_filename(__name__, 'data/irregular.edr')
 EDR_IRREG_XVG = resource_filename(__name__, 'data/irregular.xvg')

pyedr/pyedr/tests/test_edr.py

@@ -79,7 +79,6 @@ def test_columns(self, edr):
 
         for ref, val in zip(edr.xvgcols, edr.edr_dict.keys()):
             assert ref == val, "mismatching column entries"
-
     def test_times(self, edr):
         """
         Test that the time is read correctly when dt is regular.
@@ -109,40 +108,6 @@ def test_verbosity(self):
             assert_allclose(ref_content[:, i], edr_dict[key],
                             atol=prec/2)
 
-    def test_progress(self):
-        """
-        Test the progress meter displays what is expected.
-        """
-        output = StringIO()
-        with redirect_stderr(output):
-            edr_dict = pyedr.edr_to_dict(EDR, verbose=True)
-        progress = output.getvalue().split('\n')[0].split('\r')
-        print(progress)
-        dt = 2000.0
-        # We can already iterate on `progress`, but I want to keep the cursor
-        # position from one for loop to the other.
-        progress_iter = iter(progress)
-        assert '' == next(progress_iter)
-        self._assert_progress_range(progress_iter, dt, 0, 21, 1)
-        self._assert_progress_range(progress_iter, dt, 30, 201, 10)
-        self._assert_progress_range(progress_iter, dt, 300, 2001, 100)
-        self._assert_progress_range(progress_iter, dt, 3000, 14101, 1000)
-        # Check the last line
-        ref_line = 'Last Frame read : 14099, time : 28198000.0 ps'
-        last_line = next(progress_iter)
-        assert ref_line == last_line
-        # Did we leave stderr clean with a nice new line at the end?
-        assert output.getvalue().endswith('\n'), \
-               'New line missing at the end of output.'
-
-    def _assert_progress_range(self, progress, dt, start, stop, step):
-        for frame_idx in range(start, stop, step):
-            ref_line = 'Read frame : {},  time : {} ps'.format(frame_idx,
-                                                               dt * frame_idx)
-            progress_line = next(progress)
-            print(frame_idx, progress_line)
-            assert ref_line == progress_line
-
 
 def read_xvg(path):
     """

pyedr/requirements.txt

@@ -1,2 +1,3 @@
 numpy>=1.19.0
 pbr
+tqdm

pyedr/setup.cfg

@@ -29,6 +29,7 @@ python_requires = >= 3.6
 install_requires =
     numpy
     pbr
+    tqdm
 
 [options.extras_require]
 test =