Python: PEP8 fixes (#1926)

* fix [E401](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)

* fix [E711](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)

* fix [E713](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)

* fix [E722](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)

* fix [W601](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)

* fix [W605](https://github.com/PyCQA/pycodestyle/blob/2.8.0/docs/intro.rst#error-codes)

tools/build_utils/check_archives.py

@@ -2,7 +2,8 @@
 
 # author: Ole Schuett
 
-import sys, os
+import os
+import sys
 from subprocess import check_output
 from os import path
 from glob import glob

tools/build_utils/discover_programs.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python3
 
-import re, sys, os
+import os
+import re
+import sys
 from os import path
 
 # pre-compiled regular expressions
@@ -45,7 +47,7 @@ def is_fortran_program(fn):
     tail = f.read()
     f.close()
     m = re_program.search(tail.lower())
-    return m != None
+    return m is not None
 
 
 # ============================================================================
@@ -54,7 +56,7 @@ def has_main_function(fn):
     content = f.read()
     f.close()
     m = re_main.search(content)
-    return m != None
+    return m is not None
 
 
 # ===============================================================================

tools/coverage/test_coverage.py

@@ -49,7 +49,7 @@ def main():
     for fn in coverage.keys():
         cov_rate, nlines = coverage[fn]
         uncov_lines = nlines * (100.0 - cov_rate) / 100.0
-        if ref_coverage.has_key(fn):
+        if fn in ref_coverage:
             cov_rate0, nlines0 = ref_coverage[fn]
             uncov_lines0 = nlines0 * (100.0 - cov_rate0) / 100.0
             tol = max(nlines, nlines0) * 0.001  # uncov_lines has limited precision

tools/dashboard/generate_dashboard.py

@@ -29,7 +29,7 @@ from typing import Any, List, Dict, cast, Optional, ValuesView, NewType
 
 try:
     from typing import Literal
-except:
+except ImportError:
     from typing_extensions import Literal  # type: ignore
 
 import matplotlib as mpl  # type: ignore
@@ -687,7 +687,7 @@ def retrieve_report(url: str) -> Optional[str]:
             etag_file.write_text(r.headers["ETag"])
         return report_text
 
-    except:
+    except Exception:
         traceback.print_exc()
         return None
 
@@ -722,7 +722,7 @@ def parse_report(report_txt: Optional[str], log: GitLog) -> Report:
             return Report("FAILED", "Unknown CommitSHA.")
 
         return Report(status, summary, sha=sha, plots=plots, plot_points=points)
-    except:
+    except Exception:
         traceback.print_exc()
         return Report("UNKNOWN", "Error while parsing report.")
 

tools/dashboard/generate_regtest_survey.py

@@ -306,7 +306,7 @@ def parse_report(report_url):
             try:
                 float(parts[1])  # try parsing float...
                 values[test_name] = parts[1]  # ... but pass on the original string
-            except:
+            except TypeError:
                 pass  # ignore values which can not be parsed
         else:
             pass  # ignore line

tools/doxify/is_fypp.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
-import sys, re
+import re
+import sys
 
 FYPP_SYMBOLS = r"(#|\$|@)"
 FYPP_LINE = r"^\s*" + FYPP_SYMBOLS + r":"

tools/fix_unused_public.py

@@ -2,7 +2,8 @@
 
 # author: Ole Schuett
 
-import re, sys
+import re
+import sys
 from os import path
 from os.path import dirname, basename, normpath
 import os
@@ -118,7 +119,7 @@ def parse_file(fn):
     # re.IGNORECASE is horribly expensive. Converting to lower-case upfront
     content = content.lower()
     content = re.sub("!.*\n", "\n", content)
-    content = re.sub("&\s*\n", "", content)
+    content = re.sub("&\\s*\n", "", content)
     content = re.sub("&", " ", content)
 
     mods = re_module.findall(content)

tools/maple2f90/maple2f90.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
-import re, sys
+import re
+import sys
 
 """Script to help the conversion of maple generated fortran code to f90"""
 

tools/minimax_tools/minimax_to_fortran_source.py

@@ -79,7 +79,7 @@ def parse_data_set(input_path: Path) -> List[Approximation]:
                 if err == 0.0 or k >= 58:
                     continue
                 # slight change of notation e.g. 6E09 --> 6_9
-                Rc_filename = re.sub("E0?(?=\d)", "_", Rc_str.strip())
+                Rc_filename = re.sub(r"E0?(?=\d)", "_", Rc_str.strip())
                 filename = input_path / f"1_xk{k:02d}.{Rc_filename}"
                 assert filename.exists()
 

tools/package_planner/plan_packages.py

@@ -4,7 +4,9 @@
 
 # A tool to help planning CP2K packages, listing currently violated dependencies if any
 
-import re, sys, os
+import os
+import re
+import sys
 from os import path
 from os.path import dirname, basename, normpath, abspath
 
@@ -139,7 +141,7 @@ def parse_file(parsed_files, fn):
     content_lower = content.lower()
 
     mods = re_module.findall(content_lower)
-    prog = re_program.search(content_lower) != None
+    prog = re_program.search(content_lower) is not None
     uses = re_use.findall(content_lower)
     incl1_iter = re_incl1.finditer(content_lower)  # fortran includes
     incls = [content[m.start(1) : m.end(1)] for m in incl1_iter]
@@ -246,7 +248,7 @@ def find_cycles(parsed_files, mod2fn, fn, S=None):
     if "visited" in pf:
         return
 
-    if S == None:
+    if S is None:
         S = []
 
     for m in pf["module"]:
@@ -267,7 +269,7 @@ def find_cycles(parsed_files, mod2fn, fn, S=None):
 
 # =============================================================================
 def find_pkg_cycles(packages, p, S=None):
-    if S == None:
+    if S is None:
         S = []
 
     if p in S:

tools/precommit/precommit.py

@@ -219,7 +219,7 @@ def process_file(fn, allow_modifications):
             orig_lines = orig_content.decode("utf8").split("\n")
             new_lines = new_content.decode("utf8").split("\n")
             diff = unified_diff(orig_lines, new_lines, "before", "after", lineterm="")
-        except:
+        except Exception:
             diff = []  #
         raise Exception(f"File modified:\n" + "\n".join(diff))
 

tools/prettify/prettify.py

@@ -482,7 +482,7 @@ def main(argv):
                 print(f"prettified {filename}")
                 total_prettified += 1
 
-        except:
+        except Exception:
             logger.exception("processing file failed", extra={"ffilename": filename})
             failure += 1
 

tools/prettify/prettify_cp2k/normalizeFortranFile.py

@@ -65,7 +65,7 @@ use(\s+|(?P<intrinsic>\s*,\s*Intrinsic\s+::\s*))
     flags=re.IGNORECASE | re.VERBOSE,
 )
 
-COMMON_USES_RE = re.compile('^#include\s*"([^"]*(cp_common_uses.f90|base_uses.f90))"')
+COMMON_USES_RE = re.compile(r'^#include\s*"([^"]*(cp_common_uses.f90|base_uses.f90))"')
 LOCAL_NAME_RE = re.compile(
     rf"\s*(?P<localName>{VALID_NAME})(?:\s*=>\s*{VALID_NAME})?\s*$", re.VERBOSE
 )
@@ -320,7 +320,7 @@ def parseRoutine(inFile, logger):
                         break
                     routine["strippedCore"].append(subjline)
                 subF.close()
-            except:
+            except Exception:
                 import traceback
 
                 logger.debug(
@@ -484,7 +484,7 @@ def parseRoutine(inFile, logger):
                         break
                     routine["strippedCore"].append(subjline)
                 subF.close()
-            except:
+            except Exception:
                 import traceback
 
                 logger.debug(
@@ -921,7 +921,7 @@ def cleanDeclarations(routine, logger):
         if wrote:
             newDecl.write("\n")
         routine["declarations"] = [newDecl.getvalue()]
-    except:
+    except Exception:
         if "name" in routine.keys():
             logger.critical("exception cleaning routine " + routine["name"])
         logger.critical("parsedDeclartions={}".format(routine["parsedDeclarations"]))
@@ -1294,7 +1294,7 @@ def rewriteFortranFile(
                 with open(inc_absfn, "r", encoding="utf8") as fhandle:
                     implicitUsesRaw = parseUse(fhandle)
                 implicitUses = prepareImplicitUses(implicitUsesRaw["modules"])
-            except:
+            except Exception:
                 logger.critical(
                     "failed to parse use statements contained in common uses precompiler file {}".format(
                         inc_absfn

tools/regtesting/do_regtest.py

@@ -21,7 +21,7 @@ try:
     from typing import Literal  # not available before Python 3.8
 
     TestStatus = Literal["OK", "WRONG RESULT", "RUNTIME FAIL", "TIMED OUT"]
-except:
+except ImportError:
     TestStatus = str  # type: ignore
 
 # Some tests do not work with --keepalive (which is generally considered a bug).
@@ -255,7 +255,7 @@ class TestType:
             self.pattern = self.pattern.replace(c, f"\\{c}")  # escape special chars
         try:
             self.regex = re.compile(self.pattern)
-        except:
+        except Exception:
             print("Bad regex: " + self.pattern)
             raise
         self.column = int(parts[1])
@@ -458,7 +458,7 @@ async def run_unittests(batch: Batch, cfg: Config) -> List[TestResult]:
 
 # ======================================================================================
 async def run_regtests(batch: Batch, cfg: Config) -> List[TestResult]:
-    if cfg.keepalive and not batch.name in KEEPALIVE_SKIP_DIRS:
+    if cfg.keepalive and batch.name not in KEEPALIVE_SKIP_DIRS:
         return await run_regtests_keepalive(batch, cfg)
     else:
         return await run_regtests_classic(batch, cfg)