Format all Python files with black

src/start/python/setup.py

@@ -8,6 +8,7 @@
 
 try:
     from Cython.Build import cythonize
+
     USE_CYTHON = True
     EXT = "pyx"
 except ImportError:
@@ -16,13 +17,12 @@
     cythonize = lambda ext: ext
 
 extensions = [
-    Extension("cp2k", ["cp2k.{}".format(EXT)],
+    Extension(
+        "cp2k",
+        ["cp2k.{}".format(EXT)],
         include_dirs=[numpy.get_include()],
         libraries=["cp2k"],
-        ),
+    ),
 ]
 
-setup(
-    name="cp2k",
-    ext_modules=cythonize(extensions)
-)
+setup(name="cp2k", ext_modules=cythonize(extensions))

tools/autotune_grid/xyz_to_vab/template_parser.py

@@ -34,10 +34,11 @@
 
 import sys
 
+
 def load_template(template_filename):
     """ Load the routine template string from a file and return the object """
     # template_str = "\n".join([e.rstrip() for e in open(template_filename).readlines()])
-    return  pyratemp.Template(filename = template_filename)
+    return pyratemp.Template(filename=template_filename)
 
 
 def create_ordered_pairs():
@@ -50,18 +51,21 @@ def create_ordered_pairs():
         (0, 1)--3750300
     """
     # Order the most common cases
-    l = [ (1,0) , (1,1), (0,0), (0,1) ]
+    l = [(1, 0), (1, 1), (0, 0), (0, 1)]
     # The rest are appended as is
-    for i in range(0,la_max_local_end+1):
-        for j in range(0,lb_max_local_end+1):
-            if not (i,j) in l:
-                l.append((i,j,))
+    for i in range(0, la_max_local_end + 1):
+        for j in range(0, lb_max_local_end + 1):
+            if not (i, j) in l:
+                l.append((i, j,))
     return l
 
+
 if __name__ == "__main__":
     if len(sys.argv) != 3:
         print(" Incorrect number of parameters ")
-        print(" Usage: " + str(sys.argv[0]) + " <template_file> " + " <destination_file>")
+        print(
+            " Usage: " + str(sys.argv[0]) + " <template_file> " + " <destination_file>"
+        )
         sys.exit(1)
 
     template_file_name = sys.argv[1]
@@ -70,8 +74,13 @@ def create_ordered_pairs():
     l = create_ordered_pairs()
     # Initialize the templates
     module_template = load_template(template_file_name)
-    source_str = module_template(cray_tracing = False, la_max_local=la_max_local_end, lb_max_local=lb_max_local_end, pairs = l)
-    source_file = open(output_file_name,'w+')
+    source_str = module_template(
+        cray_tracing=False,
+        la_max_local=la_max_local_end,
+        lb_max_local=lb_max_local_end,
+        pairs=l,
+    )
+    source_file = open(output_file_name, "w+")
     print(source_str, file=source_file)
 
     source_file.close()

tools/benchmark_plots/plot_benchmark.py

@@ -9,9 +9,10 @@
 import argparse
 
 # Base directory
-BASE = '/home/jeremy/cp2k-uk/results/'
+BASE = "/home/jeremy/cp2k-uk/results/"
 YSHIFT = 1.1
 
+
 def makePlot(benchmarkName, machineName, shift, showPlot):
     """
     Make a plot of benchmark results.
@@ -27,69 +28,81 @@ def makePlot(benchmarkName, machineName, shift, showPlot):
     plt.ioff()
 
     # Construct file name based on machine name and benchmark name
-    fileName = BASE \
-               + machineName.lower() \
-               + '_benchmarks/' \
-               + benchmarkName \
-               + '/' \
-               + benchmarkName \
-               + '_besttimes.txt'
-
-    print('Processing benchmark results for %s from file:' %  machineName)
+    fileName = (
+        BASE
+        + machineName.lower()
+        + "_benchmarks/"
+        + benchmarkName
+        + "/"
+        + benchmarkName
+        + "_besttimes.txt"
+    )
+
+    print("Processing benchmark results for %s from file:" % machineName)
     print(fileName)
 
     # Load data from file
-    data = np.loadtxt(fileName, dtype={'names': ('nodes', 'time', 'label'), \
-                            'formats': ('i4', 'f4', 'a5')})
+    data = np.loadtxt(
+        fileName,
+        dtype={"names": ("nodes", "time", "label"), "formats": ("i4", "f4", "a5")},
+    )
 
     # Create plot
     fig = plt.figure()
     ax = fig.add_subplot(111)
     # Plot data
-    ax.loglog(data['nodes'], data['time'], marker='o')
+    ax.loglog(data["nodes"], data["time"], marker="o")
     # Change axes ticks to integers
-    ax.get_xaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter('%d'))
-    ax.get_yaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter('%d'))
+    ax.get_xaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter("%d"))
+    ax.get_yaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter("%d"))
     # Add title and axes labels
-    title = 'Performance of the ' + benchmarkName + ' benchmark on ' + machineName
+    title = "Performance of the " + benchmarkName + " benchmark on " + machineName
     plt.title(title)
-    plt.xlabel('Number of nodes used')
-    plt.ylabel('Time (seconds)')
+    plt.xlabel("Number of nodes used")
+    plt.ylabel("Time (seconds)")
     # Label the points with the best performance
-    for i, labelText in enumerate(data['label']):
-        ax.annotate(labelText, xy=(data['nodes'][i], data['time'][i]),
-                    xytext=(data['nodes'][i], shift*data['time'][i]))
+    for i, labelText in enumerate(data["label"]):
+        ax.annotate(
+            labelText,
+            xy=(data["nodes"][i], data["time"][i]),
+            xytext=(data["nodes"][i], shift * data["time"][i]),
+        )
 
     # Save plot to file
-    outFileName = benchmarkName + '-' + machineName.lower() + '.png'
+    outFileName = benchmarkName + "-" + machineName.lower() + ".png"
 
     plt.savefig(outFileName)
-    if (showPlot):
+    if showPlot:
         plt.show()
     plt.clf()
 
+
 if __name__ == "__main__":
     # Command line options
-    parser = argparse.ArgumentParser(description='Plot benchmark results.')
-    parser.add_argument('--name',
-                        default='fayalite-FIST',
-                        help='name of the benchmark to process')
-    parser.add_argument('--machine',
-                        default='Magnus',
-                        help='name of the machine used to obtain results')
-    parser.add_argument('--shift',
-                        default=YSHIFT,
-                        help='Fractional shift of label in y-direction',
-                        type=float)
-    parser.add_argument('--show',
-                        action='store_true',
-                        help='show the plot window as well as saving to file')
+    parser = argparse.ArgumentParser(description="Plot benchmark results.")
+    parser.add_argument(
+        "--name", default="fayalite-FIST", help="name of the benchmark to process"
+    )
+    parser.add_argument(
+        "--machine", default="Magnus", help="name of the machine used to obtain results"
+    )
+    parser.add_argument(
+        "--shift",
+        default=YSHIFT,
+        help="Fractional shift of label in y-direction",
+        type=float,
+    )
+    parser.add_argument(
+        "--show",
+        action="store_true",
+        help="show the plot window as well as saving to file",
+    )
 
     args = parser.parse_args()
 
     benchmarkName = args.name
     machineName = args.machine
-    shift=args.shift
+    shift = args.shift
     showPlot = args.show
 
-    makePlot(benchmarkName, machineName, shift, showPlot)
+    makePlot(benchmarkName, machineName, shift, showPlot)

tools/benchmark_plots/plot_comparison.py

@@ -10,9 +10,10 @@
 from itertools import cycle
 
 # Base directory
-BASE = '/home/jeremy/cp2k-uk/results/'
+BASE = "/home/jeremy/cp2k-uk/results/"
 YSHIFT = 1.1
 
+
 def makePlot(benchmarkName, machineNames, shifts, showPlot):
     """
     Make a comparison plot of benchmark results.
@@ -26,77 +27,89 @@ def makePlot(benchmarkName, machineNames, shifts, showPlot):
     # Turn interactive mode off (required in ipython)
     plt.ioff()
 
-    markers = ['o', 'v', '^', 's', '*']
+    markers = ["o", "v", "^", "s", "*"]
     markerCycler = cycle(markers)
     shiftCycler = cycle(shifts)
 
     fig = plt.figure()
     ax = fig.add_subplot(111)
-    title = 'Performance of the ' + benchmarkName + ' benchmark'
+    title = "Performance of the " + benchmarkName + " benchmark"
     plt.title(title)
-    plt.xlabel('Number of nodes used')
-    plt.ylabel('Time (seconds)')
+    plt.xlabel("Number of nodes used")
+    plt.ylabel("Time (seconds)")
 
     for machineName in machineNames:
-        fileName = BASE \
-                   + machineName.lower() \
-                   + '_benchmarks/' \
-                   + benchmarkName \
-                   + '/' \
-                   + benchmarkName \
-                   + '_besttimes.txt'
-        print('Processing benchmark results from file:')
+        fileName = (
+            BASE
+            + machineName.lower()
+            + "_benchmarks/"
+            + benchmarkName
+            + "/"
+            + benchmarkName
+            + "_besttimes.txt"
+        )
+        print("Processing benchmark results from file:")
         print(fileName)
-        data = np.loadtxt(fileName,
-                          dtype={'names': ('nodes', 'time', 'label'), \
-                                 'formats': ('i4', 'f4', 'a5')})
-        ax.loglog(data['nodes'], data['time'],
-                  marker=next(markerCycler),
-                  label=machineName)
+        data = np.loadtxt(
+            fileName,
+            dtype={"names": ("nodes", "time", "label"), "formats": ("i4", "f4", "a5")},
+        )
+        ax.loglog(
+            data["nodes"], data["time"], marker=next(markerCycler), label=machineName
+        )
 
         shift = next(shiftCycler)
-        alignment = 'left'
-        if (shift < 1.0):
-            alignment = 'right'
-        for i, labelText in enumerate(data['label']):
-            ax.annotate(labelText,
-                        xy=(data['nodes'][i], data['time'][i]),
-                        xytext=(data['nodes'][i], shift*data['time'][i]),
-                        horizontalalignment=alignment)
-
-    ax.get_xaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter('%d'))
-    ax.get_yaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter('%d'))
+        alignment = "left"
+        if shift < 1.0:
+            alignment = "right"
+        for i, labelText in enumerate(data["label"]):
+            ax.annotate(
+                labelText,
+                xy=(data["nodes"][i], data["time"][i]),
+                xytext=(data["nodes"][i], shift * data["time"][i]),
+                horizontalalignment=alignment,
+            )
+
+    ax.get_xaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter("%d"))
+    ax.get_yaxis().set_major_formatter(matplotlib.ticker.FormatStrFormatter("%d"))
     plt.legend()
 
-    outFileName = benchmarkName + '-comparison'
+    outFileName = benchmarkName + "-comparison"
     for machineName in machineNames:
-        outFileName = outFileName + '-' + machineName.lower()
-    outFileName = outFileName + '.png'
+        outFileName = outFileName + "-" + machineName.lower()
+    outFileName = outFileName + ".png"
 
     plt.savefig(outFileName)
 
-    if (showPlot):
+    if showPlot:
         plt.show()
     plt.clf()
 
+
 if __name__ == "__main__":
     # Command line arguments
-    parser = argparse.ArgumentParser(description='Plot benchmark results.')
-    parser.add_argument('--name',
-                        default='fayalite-FIST',
-                        help='name of the benchmark to process')
-    parser.add_argument('--machines',
-                        default='Magnus',
-                        help='name of the machines used to obtain results',
-                        nargs='*')
-    parser.add_argument('--shifts',
-                        default=[YSHIFT],
-                        help='Fractional shift of label in y-direction',
-                        nargs='*',
-                        type=float)
-    parser.add_argument('--show',
-                        action='store_true',
-                        help='show the plot window as well as saving to file')
+    parser = argparse.ArgumentParser(description="Plot benchmark results.")
+    parser.add_argument(
+        "--name", default="fayalite-FIST", help="name of the benchmark to process"
+    )
+    parser.add_argument(
+        "--machines",
+        default="Magnus",
+        help="name of the machines used to obtain results",
+        nargs="*",
+    )
+    parser.add_argument(
+        "--shifts",
+        default=[YSHIFT],
+        help="Fractional shift of label in y-direction",
+        nargs="*",
+        type=float,
+    )
+    parser.add_argument(
+        "--show",
+        action="store_true",
+        help="show the plot window as well as saving to file",
+    )
 
     args = parser.parse_args()