Merge pull request #233 from astro-informatics/development

Release 3.0

.ci/coverage.sh

@@ -0,0 +1,6 @@
+
+lcov --directory . --capture --output-file coverage.info # capture coverage info
+lcov --remove coverage.info '/usr/*' --output-file coverage.info # filter out system
+lcov --list coverage.info #debug info
+# Uploading report to CodeCov
+bash <(curl -s https://codecov.io/bash) || echo "Codecov did not collect coverage reports"

.ci/create_gource.sh

@@ -0,0 +1,62 @@
+#!/bin/env bash
+
+# Generates gource video: https://gource.io/
+# To run it from the root directory
+# Needs gource and ffmpeg for the video
+# Usage:
+#
+# cd repository
+# .ci/create_gource
+#
+# or, to save it into a video:
+#
+# create_gource --video
+#
+
+
+function is_installed () {
+    is_installed=$(which $1 2> /dev/null)
+    if [[ $? != 0 ]]; then
+        echo " ${1} is not available. Try installing it with"
+        echo "     brew install ${1}"
+        exit 1
+    fi
+}
+
+pic_dir=".git/avatar"
+
+# name,github
+cat <<EOF > names.csv
+Adrian Jackson,adrianjhpc
+David Pérez-Suárez,dpshelio
+Ilektra Christidi,ilectra
+Jason McEwen,jasonmcewen
+Luke Pratley,Luke-Pratley
+Mayeul d'Avezac,mdavezac
+Ole Streicher,olebole
+Rafael Carrillo,rafael-carrillo
+rc-softdev-admin,rc-softdev-admin
+Roland Guichard,UCLGuichard
+Sinan Shi,sinanshi
+Xiaohao Cai,XiaohaoCai
+EOF
+
+mkdir -p ${pic_dir}
+url="https://github.com/username.png"
+n_images=$(ls ${pic_dir} | wc -l)
+n_names=$(wc -l names.csv)
+if [[ ${n_images[1]} < ${n_names[1]} ]]; then
+    while IFS="," read fullname username; do
+        curl -L ${url/username/${username}} > "${pic_dir}/${fullname}.png"
+    done < names.csv
+fi
+
+is_installed gource || exit 1
+
+
+if [[ ${1} == "--video" ]]; then
+    is_installed ffmpeg || exit 1
+    gource --user-image-dir ${pic_dir} --seconds-per-day 0.05 -1280x720 -o - | ffmpeg -y -r 60 -f image2pipe -vcodec ppm -i - -vcodec libx264 -preset ultrafast -pix_fmt yuv420p -crf 1 -threads 0 -bf 0 gource.mp4
+else
+    gource --user-image-dir ${pic_dir} --seconds-per-day 0.05 -1280x720
+fi

.ci/install_spack.sh

@@ -0,0 +1,24 @@
+#!/bin/bash -xe
+
+cwd=$(pwd)
+cd $HOME
+
+# Are we using the cache directory or it's empty?
+if [ ! -f $HOME/spack/README.md ]
+then
+    rm -rf spack
+    git clone https://github.com/spack/spack.git
+fi
+
+. spack/share/spack/setup-env.sh
+
+
+while sleep 540 ; do echo "=========== make is taking more than 9m - pinging travis =========="; done &
+spack compiler list
+spack compiler remove [email protected]
+spack compiler list
+# spack install -y [email protected]
+# spack compiler add `spack location -i [email protected]`
+spack install -y [email protected]
+
+cd $cwd

.ci/spack_env.sh

@@ -0,0 +1,5 @@
+
+export SPACK_ROOT=$HOME/spack
+. $SPACK_ROOT/share/spack/setup-env.sh
+
+spack load [email protected]

.clang-format

@@ -1,60 +1,138 @@
 ---
 Language:        Cpp
-# BasedOnStyle:  LLVM
-AccessModifierOffset: -2
-AlignAfterOpenBracket: true
+# BasedOnStyle:  Google
+AccessModifierOffset: -1
+AlignAfterOpenBracket: Align
 AlignConsecutiveAssignments: false
-AlignEscapedNewlinesLeft: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
 AlignOperands:   true
 AlignTrailingComments: true
 AllowAllParametersOfDeclarationOnNextLine: true
 AllowShortBlocksOnASingleLine: false
 AllowShortCaseLabelsOnASingleLine: false
 AllowShortFunctionsOnASingleLine: All
-AllowShortIfStatementsOnASingleLine: false
-AllowShortLoopsOnASingleLine: false
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
 AlwaysBreakAfterDefinitionReturnType: None
-AlwaysBreakBeforeMultilineStrings: false
-AlwaysBreakTemplateDeclarations: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
 BinPackArguments: true
 BinPackParameters: true
-BreakBeforeBinaryOperators: All
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   false
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  AfterExternBlock: false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: true
+  SplitEmptyRecord: true
+  SplitEmptyNamespace: true
+BreakBeforeBinaryOperators: None
 BreakBeforeBraces: Attach
-BreakBeforeTernaryOperators: false
+BreakBeforeInheritanceComma: false
+BreakBeforeTernaryOperators: true
 BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
 ColumnLimit:     100
 CommentPragmas:  '^ IWYU pragma:'
-ConstructorInitializerAllOnOneLineOrOnePerLine: false
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
 ConstructorInitializerIndentWidth: 4
 ContinuationIndentWidth: 4
 Cpp11BracedListStyle: true
-DerivePointerAlignment: false
+DerivePointerAlignment: true
 DisableFormat:   false
 ExperimentalAutoDetectBinPacking: false
-ForEachMacros:   [ foreach, Q_FOREACH, BOOST_FOREACH ]
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeBlocks:   Preserve
+IncludeCategories:
+  - Regex:           '^(<|")sopt/config.h(>|")$'
+    Priority:        2
+  - Regex:           '^(<|")sopt/wavelets/'
+    Priority:        10
+  - Regex:           '^(<|")sopt/'
+    Priority:        9
+  - Regex:           '^(<.*/.*>)'
+    Priority:        7
+  - Regex:           '^(<.*>)'
+    Priority:        6
+  - Regex:           '".*"'
+    Priority:        8
+IncludeIsMainRegex: '(Test)?$'
 IndentCaseLabels: false
+IndentPPDirectives: None
 IndentWidth:     2
 IndentWrappedFunctionNames: false
-KeepEmptyLinesAtTheStartOfBlocks: true
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
 MacroBlockBegin: ''
 MacroBlockEnd:   ''
 MaxEmptyLinesToKeep: 1
 NamespaceIndentation: None
 ObjCBlockIndentWidth: 2
 ObjCSpaceAfterProperty: false
-ObjCSpaceBeforeProtocolList: true
-PenaltyBreakBeforeFirstCallParameter: 19
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
 PenaltyBreakComment: 300
 PenaltyBreakFirstLessLess: 120
 PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
-PenaltyReturnTypeOnItsOwnLine: 10
-PointerAlignment: Right
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
+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
+    CanonicalDelimiter: ''
+    BasedOnStyle:    google
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
 SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
 SpaceBeforeAssignmentOperators: true
-SpaceBeforeParens: false
+SpaceBeforeParens: ControlStatements
 SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 1
+SpacesBeforeTrailingComments: 2
 SpacesInAngles:  false
 SpacesInContainerLiterals: true
 SpacesInCStyleCastParentheses: false
@@ -63,18 +141,4 @@ SpacesInSquareBrackets: false
 Standard:        Cpp11
 TabWidth:        8
 UseTab:          Never
-IncludeCategories:
-  - Regex:           '^(<|")sopt/config.h(>|")$'
-    Priority:        2
-  - Regex:           '^(<|")sopt/wavelets/'
-    Priority:        10
-  - Regex:           '^(<|")sopt/'
-    Priority:        9
-  - Regex:           '^(<.*/.*>)'
-    Priority:        7
-  - Regex:           '^(<.*>)'
-    Priority:        6
-  - Regex:           '".\*"'
-    Priority:        8
 ...
-

.gitignore

@@ -78,3 +78,4 @@ build/
 .*.swp
 .settings
 python/tests/__pycache__
+*.h.gch

.mailmap

@@ -0,0 +1,29 @@
+Adrian Jackson <[email protected]> Adrian Jackson <[email protected]>
+David Pérez-Suárez <[email protected]> David Pérez-Suárez <[email protected]>
+David Pérez-Suárez <[email protected]> David Perez-Suarez <[email protected]>
+David Pérez-Suárez <[email protected]> dpshelio <[email protected]>
+Ilektra Christidi <[email protected]>
+Jason McEwen <[email protected]> Jason McEwen <[email protected]>
+Jason McEwen <[email protected]> Jason McEwen <[email protected]>
+Luke Pratley <[email protected]> Luke Pratley <[email protected]>
+Luke Pratley <[email protected]> luke <[email protected]>
+Luke Pratley <[email protected]> Luke Pratley <[email protected]>
+Luke Pratley <[email protected]> Luke Pratley <[email protected]>
+Mayeul d'Avezac <[email protected]> Mayeul d'Avezac <[email protected]>
+Ole Streicher <[email protected]> Ole Streicher <[email protected]>
+Rafael Carrillo <[email protected]> Rafael Carrillo <[email protected]>
+Rafael Carrillo <[email protected]> rafael-carrillo <[email protected]>
+Rafael Carrillo <[email protected]> rafael-carrillo <[email protected]>
+Rafael Carrillo <[email protected]> rafael-carrillo <[email protected]>
+Rafael Carrillo <[email protected]> rafael-carrillo <[email protected]>
+Rafael Carrillo <[email protected]> rafael-carrillo <[email protected]>
+Rafael Carrillo <[email protected]> rafael-carrillo <[email protected]>
+rc-softdev-admin <[email protected]> rc-softdev-admin <[email protected]>
+rc-softdev-admin <[email protected]> ccsprsd on Legion@UCL <[email protected]>
+Roland Guichard <[email protected]> Roland Guichard <[email protected]>
+Roland Guichard <[email protected]> Roland <[email protected]>
+Roland Guichard <[email protected]> UCLGuichard <[email protected]>
+Sinan Shi <[email protected]> Sinan Shi <[email protected]>
+Sinan Shi <[email protected]> sinanshi <[email protected]>
+Sinan Shi <[email protected]> sinanshi <[email protected]>
+Xiaohao Cai <[email protected]> Xiaohao Cai <[email protected]>