Autoformatting (#106)

* autoformatting, linting, and removed unnecessary dependencies

* update lint github action

* update .clang-format for lint action

* attempt to fix linting github action

* attempt to fix linting github action round 2

* attempt to fix linting github action round 3

* attempt to fix linting github action round 4

* adjust minimum packages to support python3.6 and add cpu-only ubuntu dockerfile

* update testing dependecy versions for python3.6

* force build to use setuptools in pyproject.toml

* adjust pip install for github workflow

* install test dependencies in github workflow

* install test dependencies in github workflow

* try using sudo for pip install

* fix stupid typo

* only run pyspark tests if pyspark is installed

Co-authored-by: rogerwaleffe <[email protected]>
Co-authored-by: Jason Mohoney <[email protected]>

.clang-format

@@ -0,0 +1,226 @@
+---
+Language:        Cpp
+# BasedOnStyle:  Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
+AlignArrayOfStructures: None
+AlignConsecutiveMacros: None
+AlignConsecutiveAssignments: None
+AlignConsecutiveBitFields: None
+AlignConsecutiveDeclarations: None
+AlignEscapedNewlines: Left
+AlignOperands:   Align
+AlignTrailingComments: true
+AllowAllArgumentsOnNextLine: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortEnumsOnASingleLine: true
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortLambdasOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: WithoutElse
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: Yes
+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:     160
+CommentPragmas:  '^ IWYU pragma:'
+QualifierAlignment: Leave
+CompactNamespaces: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DeriveLineEnding: true
+DerivePointerAlignment: true
+DisableFormat:   false
+EmptyLineAfterAccessModifier: Never
+EmptyLineBeforeAccessModifier: LogicalBlock
+ExperimentalAutoDetectBinPacking: false
+PackConstructorInitializers: NextLine
+BasedOnStyle:    ''
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+AllowAllConstructorInitializersOnNextLine: true
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IfMacros:
+  - KJ_IF_MAYBE
+IncludeBlocks:   Regroup
+IncludeCategories:
+  - Regex:           '^<ext/.*\.h>'
+    Priority:        2
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '^<.*'
+    Priority:        2
+    SortPriority:    0
+    CaseSensitive:   false
+  - Regex:           '.*'
+    Priority:        3
+    SortPriority:    0
+    CaseSensitive:   false
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IncludeIsMainSourceRegex: ''
+IndentAccessModifiers: false
+IndentCaseLabels: true
+IndentCaseBlocks: false
+IndentGotoLabels: true
+IndentPPDirectives: None
+IndentExternBlock: AfterExternBlock
+IndentRequires:  false
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+InsertTrailingCommas: None
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+LambdaBodyIndentation: Signature
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: None
+ObjCBinPackProtocolList: Never
+ObjCBlockIndentWidth: 2
+ObjCBreakBeforeNestedBlockParam: true
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: true
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakOpenParenthesis: 0
+PenaltyBreakString: 1000
+PenaltyBreakTemplateDeclaration: 10
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PenaltyIndentedWhitespace: 0
+PointerAlignment: Left
+PPIndentWidth:   -1
+RawStringFormats:
+  - Language:        Cpp
+    Delimiters:
+      - cc
+      - CC
+      - cpp
+      - Cpp
+      - CPP
+      - 'c++'
+      - 'C++'
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+  - Language:        TextProto
+    Delimiters:
+      - pb
+      - PB
+      - proto
+      - PROTO
+    EnclosingFunctions:
+      - EqualsProto
+      - EquivToProto
+      - PARSE_PARTIAL_TEXT_PROTO
+      - PARSE_TEST_PROTO
+      - PARSE_TEXT_PROTO
+      - ParseTextOrDie
+      - ParseTextProtoOrDie
+      - ParseTestProto
+      - ParsePartialTestProto
+    CanonicalDelimiter: pb
+    BasedOnStyle:    google
+ReferenceAlignment: Pointer
+ReflowComments:  true
+RemoveBracesLLVM: false
+SeparateDefinitionBlocks: Leave
+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
+SpaceBeforeParensOptions:
+  AfterControlStatements: true
+  AfterForeachMacros: true
+  AfterFunctionDefinitionName: false
+  AfterFunctionDeclarationName: false
+  AfterIfMacros:   true
+  AfterOverloadedOperator: false
+  BeforeNonEmptyParentheses: false
+SpaceAroundPointerQualifiers: Default
+SpaceBeforeRangeBasedForLoopColon: true
+SpaceInEmptyBlock: false
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  Never
+SpacesInConditionalStatement: false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInLineCommentPrefix:
+  Minimum:         1
+  Maximum:         -1
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+SpaceBeforeSquareBrackets: false
+BitFieldColonSpacing: Both
+Standard:        Auto
+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
+...
+

.flake8

@@ -0,0 +1,25 @@
+#########################
+# Flake8 Configuration  #
+# (.flake8)             #
+#########################
+[flake8]
+ignore =
+    # first argument of a classmethod should be named 'cls'
+    N804
+    # line break before binary operator
+    W503
+    # whitespace before ':'
+    E203
+exclude =
+    .tox
+    .git,
+    __pycache__,
+    build,
+    *.pyc,
+    *third_party*,
+    scripts
+max-line-length = 120
+max-complexity = 25
+import-order-style = pycharm
+application-import-names =
+    marius

.github/workflows/build_and_test.yml

@@ -37,9 +37,9 @@ jobs:
       shell: bash
       run:   |
         if [ "$RUNNER_OS" == "Linux" ]; then
-             pip3 install torch --extra-index-url https://download.pytorch.org/whl/cpu
+             sudo python3 -m pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
         elif [ "$RUNNER_OS" == "macOS" ]; then
-             pip3 install torch
+             sudo python3 -m pip install torch
         else
              echo "$RUNNER_OS not supported"
              exit 1
@@ -48,7 +48,7 @@ jobs:
     - name: Install Marius
       working-directory: ${{github.workspace}}
       shell: bash
-      run: pip3 install . --verbose
+      run: sudo python3 -m pip install .[tests] --verbose
 
     - name: Run Tests
       working-directory: ${{github.workspace}}

.github/workflows/lint.yml

@@ -0,0 +1,15 @@
+name: Lint
+
+on: [push, pull_request]
+
+jobs:
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - name: Install Tox
+      run: pip3 install tox
+    - name: Update clang-format
+      run: pip3 install --upgrade pip; pip3 install clang-format
+    - name: Check linting with Flake8
+      run: tox -e check_lint

.gitignore

@@ -10,6 +10,7 @@ CTestTestfile.cmake
 .idea/
 cmake-*/
 logs/
+data/
 test/test_data/generated/
 *.dylib
 
@@ -28,6 +29,8 @@ __pycache__/
 # Distribution / packaging
 .Python
 build/
+docs_build/
+docs_html/
 develop-eggs/
 dist/
 downloads/

MANIFEST.in

@@ -1,10 +1,3 @@
-graft test
-graft marius_package
 graft src
-graft include
-graft third_party
-graft cmake
-graft python_bindings
-
 include CMakeLists.txt
 global-exclude *.py[cod] __pycache__ *.so *.dylib .DS_Store *.gpickle

docs/conf.py

@@ -17,12 +17,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'Marius'
+project = "Marius"
 # copyright = '2020, Jason Mohoney'
-author = 'Jason Mohoney'
+author = "Jason Mohoney"
 
 # The full version, including alpha/beta/rc tags
-release = '0.0.2'
+release = "0.0.2"
 
 
 # -- General configuration ---------------------------------------------------
@@ -36,33 +36,31 @@
 breathe_default_project = "Marius"
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 autodoc_typehints = "description"
-autodoc_member_order = 'bysource'
+autodoc_member_order = "bysource"
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
-html_style = 'css/marius_theme.css'
+html_style = "css/marius_theme.css"
 
-html_logo = 'marius_logo_scaled.png'
+html_logo = "marius_logo_scaled.png"
 
-html_favicon = 'favicon.ico'
+html_favicon = "favicon.ico"
 
-html_theme_options = {
-    'logo_only': True
-}
+html_theme_options = {"logo_only": True}
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]