Add Python linter

.github/workflows/CI.yaml

@@ -35,10 +35,13 @@ jobs:
       - run: bundle install
       - run: bundle exec danger || true
       - run: BML_OPENMP=no EMACS=emacs27 ./build.sh check_indent
+      - run: sudo apt-get install --yes pycodestyle
+      - run: pycodestyle $(git ls-files '*.py')
 
   build:
     name: Build and test (${{ matrix.JOBNAME }})
     runs-on: ubuntu-20.04
+    needs: lint
     strategy:
       fail-fast: false
       matrix:

examples/gpmd/get_energy.py

@@ -1,26 +1,23 @@
 #!/usr/bin/env python
-import os, sys
+import sys
 import numpy
 
-MyFileName=str(sys.argv[1])
-#print 'File name:', MyFileName
+MyFileName = str(sys.argv[1])
 
-count=-1
-MyFile = open(MyFileName,"r")
+count = -1
+MyFile = open(MyFileName, "r", encoding="utf-8")
 
 for lines in MyFile:
-  count = count + 1
-Dim=count
-#print 'Dim', Dim
+    count = count + 1
+Dim = count
 datos = numpy.zeros(Dim+1)
 
-count=-1
-MyFile = open(MyFileName,"r")
+count = -1
+MyFile = open(MyFileName, "r", encoding="utf-8")
 for lines in MyFile:
-  lines_split = lines.split()
-  count = count + 1
-  if(len(lines_split) > 2):
-    if(lines_split[0] == "Energy"):
-        if(lines_split[1] == "Total"):
-                    print " ", lines_split[4]
-
+    lines_split = lines.split()
+    count = count + 1
+    if len(lines_split) > 2:
+        if lines_split[0] == "Energy":
+            if lines_split[1] == "Total":
+                print(" ", lines_split[4])

examples/gpmd/test-energy.py

@@ -1,4 +1,7 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
+
+import argparse
+
 
 def compare_MD(reference, current, reltol):
     """Compare MD energies.
@@ -8,29 +11,24 @@ def compare_MD(reference, current, reltol):
 
     """
 
-    import sys
-    #energy = re.compile("MD_data\s+([0-9eE.+-]+)\s+([0-9eE.+-]+)")
-
-    fd = open(reference)
-    reference_energies = []
-    for line in fd:
-        result = line.split()
-        reference_energies.append(float(result[0]))
-    fd.close()
-
-    fd = open(current)
-    current_energies = []
-    for line in fd:
-        result = line.split()
-        current_energies.append(float(result[0]))
-    fd.close()
-
-
+    with open(reference, encoding="utf-8") as fd:
+        reference_energies = []
+        for line in fd:
+            result = line.split()
+            reference_energies.append(float(result[0]))
+
+    with open(current, encoding="utf-8") as fd:
+        current_energies = []
+        for line in fd:
+            result = line.split()
+            current_energies.append(float(result[0]))
+
     if len(reference_energies) != len(current_energies):
-        raise Exception("[error] different number of MD steps\n"
-                        + ("  reference ran for %4d steps\n" % (len(reference_energies)))
-                        + ("  current ran for   %4d steps\n" % (len(current_energies)))
-                        + "  can not compare")
+        raise Exception(
+            "[error] different number of MD steps\n"
+            + ("  reference ran for %4d steps\n" % (len(reference_energies)))
+            + ("  current ran for   %4d steps\n" % (len(current_energies)))
+            + "  can not compare")
 
     result = True
     for i in range(len(reference_energies)):
@@ -41,29 +39,34 @@ def compare_MD(reference, current, reltol):
             print("failure in MD step %d" % (i+1))
             result = False
     if not result:
-        raise Exception(("[error] when comparing '%s' with '%s'" % (reference, current))
-                        + "energies do not agree")
+        raise Exception(
+            ("[error] when comparing '%s' with '%s'" % (reference, current))
+            + "energies do not agree")
+
+    print("Energy test passed without failure ...")
 
-    print("Energy test passed without failure ...")  
 
 def main():
     """The main function.
     """
 
-    import argparse, os, sys
-
-    parser = argparse.ArgumentParser(description="""Script to compare MD results by using the total energy""")
-    parser.add_argument("--reference",
-                        help="The reference output")
-    parser.add_argument("--current",
-                        help="The current output")
-    parser.add_argument("--reltol",
-                        help="Relative tolerance when comparing, default is %(default)s",
-                        type=float,
-                        default=1e-10)
+    parser = argparse.ArgumentParser(description="""Script to compare
+                                     MD results by using the total energy""")
+    parser.add_argument(
+        "--reference",
+        help="The reference output")
+    parser.add_argument(
+        "--current",
+        help="The current output")
+    parser.add_argument(
+        "--reltol",
+        help="Relative tolerance when comparing, default is %(default)s",
+        type=float,
+        default=1e-10)
     options = parser.parse_args()
 
     compare_MD(options.reference, options.current, options.reltol)
 
+
 if __name__ == "__main__":
     main()

examples/gpmdcov/get_energy.py

@@ -3,14 +3,13 @@
 import argparse
 import re
 
-energy_re = re.compile("Energy Total.*=\s+([0-9-.]+)")
+energy_re = re.compile(r"Energy Total.*=\s+([0-9-.]+)")
 
 parser = argparse.ArgumentParser()
-parser.add_argument("OUT",
-                    help="The output")
+parser.add_argument("OUT", help="The output")
 options = parser.parse_args()
 
-with open(options.OUT) as fd:
+with open(options.OUT, encoding="utf-8") as fd:
     for line in fd:
         result = energy_re.search(line)
         if result:

examples/gpmdcov/test-energy.py

@@ -1,5 +1,8 @@
 #!/usr/bin/env python
 
+import argparse
+
+
 def compare_MD(reference, current, reltol):
     """Compare MD energies.
 
@@ -8,29 +11,24 @@ def compare_MD(reference, current, reltol):
 
     """
 
-    import sys
-    #energy = re.compile("MD_data\s+([0-9eE.+-]+)\s+([0-9eE.+-]+)")
-
-    fd = open(reference)
-    reference_energies = []
-    for line in fd:
-        result = line.split()
-        reference_energies.append(float(result[0]))
-    fd.close()
-
-    fd = open(current)
-    current_energies = []
-    for line in fd:
-        result = line.split()
-        current_energies.append(float(result[0]))
-    fd.close()
-
-
+    with open(reference, encoding="utf-8") as fd:
+        reference_energies = []
+        for line in fd:
+            result = line.split()
+            reference_energies.append(float(result[0]))
+
+    with open(current, encoding="utf-8") as fd:
+        current_energies = []
+        for line in fd:
+            result = line.split()
+            current_energies.append(float(result[0]))
+
     if len(reference_energies) != len(current_energies):
-        raise Exception("[error] different number of MD steps\n"
-                        + ("  reference ran for %4d steps\n" % (len(reference_energies)))
-                        + ("  current ran for   %4d steps\n" % (len(current_energies)))
-                        + "  can not compare")
+        raise Exception(
+            "[error] different number of MD steps\n"
+            + ("  reference ran for %4d steps\n" % (len(reference_energies)))
+            + ("  current ran for   %4d steps\n" % (len(current_energies)))
+            + "  can not compare")
 
     result = True
     for i in range(len(reference_energies)):
@@ -41,29 +39,34 @@ def compare_MD(reference, current, reltol):
             print("failure in MD step %d" % (i+1))
             result = False
     if not result:
-        raise Exception(("[error] when comparing '%s' with '%s'" % (reference, current))
-                        + "energies do not agree")
+        raise Exception(
+            ("[error] when comparing '%s' with '%s'" % (reference, current))
+            + "energies do not agree")
+
+    print("Energy test passed without failure ...")
 
-    print("Energy test passed without failure ...")  
 
 def main():
     """The main function.
     """
 
-    import argparse, os, sys
-
-    parser = argparse.ArgumentParser(description="""Script to compare MD results by using the total energy""")
-    parser.add_argument("--reference",
-                        help="The reference output")
-    parser.add_argument("--current",
-                        help="The current output")
-    parser.add_argument("--reltol",
-                        help="Relative tolerance when comparing, default is %(default)s",
-                        type=float,
-                        default=1e-10)
+    parser = argparse.ArgumentParser(description="""Script to compare MD
+                                     results by using the total energy""")
+    parser.add_argument(
+        "--reference",
+        help="The reference output")
+    parser.add_argument(
+        "--current",
+        help="The current output")
+    parser.add_argument(
+        "--reltol",
+        help="Relative tolerance when comparing, default is %(default)s",
+        type=float,
+        default=1e-10)
     options = parser.parse_args()
 
     compare_MD(options.reference, options.current, options.reltol)
 
+
 if __name__ == "__main__":
     main()