Update pre-commit hooks and add other checks

.clang-format

@@ -0,0 +1,178 @@
+---
+Language:        Cpp
+# BasedOnStyle:  LLVM
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
+AlignArrayOfStructures: None
+AlignConsecutiveMacros: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Right
+AlignOperands:   Align
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: true
+AllowAllConstructorInitializersOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: MultiLine
+AttributeMacros:
+  - __capability
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterCaseLabel:  false
+  AfterClass:      false
+  AfterControlStatement: Never
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  BeforeLambdaBody: false
+  BeforeWhile:     false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
+BreakBeforeConceptDeclarations: true
+BreakBeforeBraces: Attach
+BreakBeforeInheritanceComma: false
+BreakInheritanceList: BeforeColon
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: false
+DisableFormat:   false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IfMacros:
+  - KJ_IF_MAYBE
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority:        2
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '^(<|"(gtest|gmock|isl|json)/)'
+    Priority:        3
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '.*'
+    Priority:        1
+    SortPriority:    0
+    CaseSensitive:   false
+IncludeIsMainRegex: '(Test)?$'
+IncludeIsMainSourceRegex: ''
+IndentAccessModifiers: false
+IndentCaseLabels: false
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentExternBlock: AfterExternBlock
+IndentRequires:  false
+IndentWidth:     2
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: true
+LambdaBodyIndentation: Signature
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Auto
+ObjCBlockIndentWidth: 2
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 19
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 60
+PenaltyIndentedWhitespace: 0
+PointerAlignment: Right
+PPIndentWidth:   -1
+ReferenceAlignment: Pointer
+ReflowComments:  false
+ShortNamespaceLines: 1
+SortIncludes:    CaseSensitive
+SortJavaStaticImport: Before
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterLogicalNot: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCaseColon: false
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: true
+SpaceBeforeInheritanceColon: true
+SpaceBeforeParens: ControlStatements
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles:  Never
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInLineCommentPrefix:
+  Minimum:         1
+  Maximum:         -1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+BitFieldColonSpacing: Both
+Standard:        Latest
+StatementAttributeLikeMacros:
+  - Q_EMIT
+StatementMacros:
+  - Q_UNUSED
+  - QT_REQUIRE_VERSION
+TabWidth:        8
+UseCRLF:         false
+UseTab:          Never
+WhitespaceSensitiveMacros:
+  - STRINGIZE
+  - PP_STRINGIZE
+  - BOOST_PP_STRINGIZE
+  - NS_SWIFT_NAME
+  - CF_SWIFT_NAME
+...
+

.pre-commit-config.yaml

@@ -5,22 +5,26 @@ exclude: '^tools/(build_utils/fypp)'
 fail_fast: false
 repos:
 - repo: https://github.com/ambv/black
-  rev: 21.5b1
+  rev: 22.1.0
   hooks:
   - id: black
+    name: Reformat Python files with the black code formatter
+    files: '^.*(/PACKAGE)|(\.py)$'
 - repo: https://gitlab.com/pycqa/flake8
-  rev: 3.8.4
+  rev: 4.0.1
   hooks:
   - id: flake8
     exclude: >-
       (?x)^(
         .cp2k/.*|
       )$
 - repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: v3.4.0
+  rev: v4.1.0
   hooks:
   - id: check-ast
   - id: check-yaml
+  - id: check-symlinks
+  - id: trailing-whitespace
 - repo: https://github.com/pseewald/fprettify
   rev: v0.3.7
   hooks:

LICENSE

@@ -291,7 +291,7 @@ convey the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
     DBCSR: Distributed Block Compressed Sparse Row matrix library
-    Copyright (C) by the DBCSR developers group - All rights reserved 
+    Copyright (C) by the DBCSR developers group - All rights reserved
 
     This program is free software; you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by

docs/guide/3-developer-guide/1-tooling/index.md

@@ -2,7 +2,7 @@ title: Tooling
 
 # Build System
 
-We support CMake for compilation. See [here](../../2-user-guide/1-installation/index.html) on how to compile and 
+We support CMake for compilation. See [here](../../2-user-guide/1-installation/index.html) on how to compile and
 [here](../../2-user-guide/1-installation/1-cmake-build-recipes.html) for more CMake details.
 
 Compilations is based on [Fypp](https://github.com/aradi/fypp) meta-progamming package, which is available as submodule.

docs/guide/3-developer-guide/4-performance/1-insights.md

@@ -102,7 +102,7 @@ The columns describe:
     - `AVERAGE`: averaged over all MPI ranks
     - `MAXIMUM`: maximum over all MPI ranks
     - `AVERAGE` and `MAXIMUM` can be used to locate load-imbalance or synchronization points.
-- `MAXRANKS`: 
+- `MAXRANKS`:
 
 #### Time spent in Just-In-Time (JIT) Compilation
 

src/acc/libsmm_acc/predict/README.md

@@ -96,7 +96,7 @@ Explore the data interactively using the [provided Jupyter notebook](notebooks/i
 
 #### 4. Train
 
-For each algorithm, build a predictive model using decision trees and feature selection based on the features' permutation importance. 
+For each algorithm, build a predictive model using decision trees and feature selection based on the features' permutation importance.
 
 ```bash
 ./predict_train.py  # --algo medium --folder /scratch/autotuning_dataset, e.g.

src/acc/libsmm_acc/predict/predict_helpers.py

@@ -29,7 +29,7 @@ def safe_pickle(data, file):
     :param data: data to be pickled
     :param file: file to pickle it into
     """
-    max_bytes = 2 ** 31 - 1  # Maximum number of bytes to write in one chunk
+    max_bytes = 2**31 - 1  # Maximum number of bytes to write in one chunk
     pickle_out = pickle.dumps(data)
     n_bytes = len(pickle_out)
     with open(file, "wb") as f:
@@ -47,7 +47,7 @@ def safe_pickle_load(file_path):
     :param data: data to be loaded through pickle
     :param file: file to read from
     """
-    max_bytes = 2 ** 31 - 1  # Maximum number of bytes to read in one chunk
+    max_bytes = 2**31 - 1  # Maximum number of bytes to read in one chunk
     bytes_in = bytearray(0)
     input_size = os.path.getsize(file_path)
     with open(file_path, "rb") as f:

src/acc/libsmm_acc/predict/predict_train.py

@@ -489,7 +489,7 @@ def read_data(algo, read_from, nrows, folder, log):
     X = X.drop(cols_to_drop, axis=1)
     log += print_and_log(
         "X    : {:>8,} x {:>8,} ({:>2.2} MB)".format(
-            len(X), len(X.columns), sys.getsizeof(X) / 10 ** 6
+            len(X), len(X.columns), sys.getsizeof(X) / 10**6
         )
     )
     log += print_and_log("Head:")
@@ -505,7 +505,7 @@ def read_data(algo, read_from, nrows, folder, log):
     log += print_and_log("\nRead Y")
     Y = dd.read_parquet(parquet_data_file, columns=["perf_scaled"])
     log += print_and_log(
-        "Y    : {:>8,} ({:>2.2} MB)".format(len(Y), sys.getsizeof(Y) / 10 ** 6)
+        "Y    : {:>8,} ({:>2.2} MB)".format(len(Y), sys.getsizeof(Y) / 10**6)
     )
     log += print_and_log("Head:")
     log += print_and_log(Y.head())
@@ -516,7 +516,7 @@ def read_data(algo, read_from, nrows, folder, log):
     X_mnk = dd.read_parquet(parquet_data_file, columns=["mnk"])
     nrows_data = len(X_mnk.index)
     log += print_and_log(
-        "X_mnk : {:>8,} ({:>2.2} MB)".format(nrows_data, sys.getsizeof(X_mnk) / 10 ** 6)
+        "X_mnk : {:>8,} ({:>2.2} MB)".format(nrows_data, sys.getsizeof(X_mnk) / 10**6)
     )
     log += print_and_log("Head:")
     log += print_and_log(X_mnk.head())

src/acc/libsmm_acc/tune/README.md

@@ -160,7 +160,7 @@ Each tune-directory contains a job file. Since there might be many tune-director
 When `tune_submit.py` is called without arguments, it will just list the jobs that could be submitted:
 
 ```bash
-$ ./tune_submit.py 
+$ ./tune_submit.py
           tune_5x5x5: Would submit, run with "doit!"
           tune_5x5x8: Would submit, run with "doit!"
           tune_5x8x5: Would submit, run with "doit!"

src/data/dbcsr.fypp

@@ -55,15 +55,15 @@
 #:set carry = 1
 #:for i in range(0,len(num))
 #:set outi = 0
-#:if carry == 1 
+#:if carry == 1
  #:if num[i] == 0
   #:set outi = 1
   #:set carry = 0
  #:else
   #:set outi = 0
   #:set carry = 1
  #:endif
-#:else 
+#:else
  #:set outi = num[i]
 #:endif
 #:mute
@@ -86,11 +86,11 @@ $: numout.append(outi)
  #! generates a list of permutations from n entries
  #! example n = 2 -> [[0,0],[0,1],[1,0],[1,1]] where 0/1 means present/not present
  #:set idx = []
- #:set newidx = [] 
+ #:set newidx = []
  ${init(idx,n)}$
 
  #:set imax = pow(2,n)
- #:for i in range(0,imax) 
+ #:for i in range(0,imax)
         $: permlist.append(idx)
         ${add_num(idx,newidx)}$
         #:set idx = newidx
@@ -104,8 +104,8 @@ $: numout.append(outi)
  #! generates permuted groups of variables from a variable list
  #! optional variables that appear together may be grouped
  #! example: varlist = [[var1], [var2,var3]]
- #! this gives: vargroups = [ [[var1],[var2,var3]], [[var1]], [[var2,var3]], []] 
- #:set permlist = [] 
+ #! this gives: vargroups = [ [[var1],[var2,var3]], [[var1]], [[var2,var3]], []]
+ #:set permlist = []
  ${gen_permlist(permlist,len(varlist))}$
  #:for p in permlist
     #:set group = []
@@ -141,7 +141,7 @@ $: prefix * (bool(len(group))) + ", ".join([str(i) + ' = ' + str(i) for i in fla
 #:def print_groupif(vargroups,varlist,i,check='PRESENT',prefix='')
 #! for a group [[var1]] and a varlist [[var1]],[var2,var3]]
 #! prints "(ELSE) IF (PRESENT(var1) .AND. .NOT. PRESENT(var2) .AND. .NOT. PRESENT(var3)) THEN"
-#! to be used in a loop 
+#! to be used in a loop
 #:set group = vargroups[i]
 #:set diff = [item for item in varlist if item not in group]
 #:set stat = "ELSE IF"
@@ -157,9 +157,9 @@ $: prefix * (bool(len(group))) + ", ".join([str(i) + ' = ' + str(i) for i in fla
 ${flatten(group,flatgroup)}$
 ${flatten(diff,flatdiff)}$
 #:endmute
-$: stat + "(" +  " .AND. ".join([check + "(" +  prefix + str(i) + ")" for i in flatgroup]) & 
+$: stat + "(" +  " .AND. ".join([check + "(" +  prefix + str(i) + ")" for i in flatgroup]) &
          + " .AND. " * (bool(len(diff)) * bool(len(diff) - len(varlist))) &
-         + " .AND. ".join([".NOT. " + check + "(" +  prefix + str(i) + ")" for i in flatdiff]) + ") THEN " 
+         + " .AND. ".join([".NOT. " + check + "(" +  prefix + str(i) + ")" for i in flatdiff]) + ") THEN "
 #:else
 ELSE
 #:endif

src/dbcsr_api_c.F

@@ -1406,7 +1406,7 @@ SUBROUTINE c_dbcsr_get_${var}$ (c_matrix, c_${var}$, c_size) BIND(C, name="c_dbc
             END DO
          #:else
             DO i = 1, c_size
-               c_${var}$ (i) = ${var}$ (i); 
+               c_${var}$ (i) = ${var}$ (i)
             END DO
          #:endif
          NULLIFY (${var}$)

src/ops/PACKAGE

@@ -1,6 +1,6 @@
 {
 "description": "High level DBCSR operations",
 "archive": "libdbcsr",
-"requires": ["../acc", "../mpi", "../data", "../base", "../dist", 
+"requires": ["../acc", "../mpi", "../data", "../base", "../dist",
 	     "../block", "../utils", "../core", "../mm", "../work"],
 }