text:
// Copyright (c) 2014 David R. Jenni. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.

package main

import (
	"bytes"
	"reflect"
	"testing"
)

type offsetTest struct {
	data       []byte
	offset     int
	byteOffset int
}

var offsetTests = []offsetTest{
	{[]byte("abcdef"), 0, 0},
	{[]byte("abcdef"), 1, 1},
	{[]byte("abcdef"), 5, 5},
	{[]byte("日本語def"), 0, 0},
	{[]byte("日本語def"), 1, 3},
	{[]byte("日本語def"), 5, 11},
}

func TestByteOffset(t *testing.T) {
	for _, test := range offsetTests {
		off, err := byteOffset(bytes.NewReader(test.data), test.offset)
		if err != nil {
			t.Errorf("got error %v", err)
		}
		if off != test.byteOffset {
			t.Errorf("expected byte offset %d, got %d", test.byteOffset, off)
		}
	}
}

type empty struct{}

var importDir = reflect.TypeOf(empty{}).PkgPath()

func TestCurrImportPath(t *testing.T) {
	currDir, err := currImportDir()
	if err != nil {
		t.Fatal(err)
	}

	if currDir != importDir {
		t.Fatalf("expected '%s', got '%s'\n", importDir, currDir)
	}
}

var searchTests = []struct {
	prg   string
	off   int
	path  string
	ident string
}{
	// Imports
	{`package main; import _ "io"`, 21, "io", ""},
	{`package main; import _ "io"`, 22, "io", ""},
	{`package main; import _ "io"`, 23, "io", ""},
	{`package main; import _ "io"`, 24, "io", ""},
	{`package main; import _ "io"`, 25, "io", ""},
	{`package main; import _ "io"`, 26, "io", ""},
	{`package main; import _ "io"`, 27, "io", ""},
	{`package main; import foo "io"`, 21, "io", ""},
	{`package main; import _ "text/scanner"`, 27, "text/scanner", ""},
	{`package main; import "io"; func main() { var _ io.Reader } `, 22, "io", ""},
	{`package main; import ( "bytes"; "io" ); func main() { var _ io.Reader; var _ bytes.Buffer } `, 24, "bytes", ""},

	// Builtin type, function, const and variable
	{`package main; func main() { var _ bool }`, 34, "builtin", "bool"},
	{`package main; func main() { _ = make([]byte, 0) }`, 32, "builtin", "make"},
	{`package p; func main() { var _ bool = true }`, 39, "builtin", "true"},
	{`package p; func main() { var _ interface{} = nil }`, 47, "builtin", "nil"},

	// Declaration of a type, function, method, const and variable
	{`package p; type T struct{}`, 16, importDir, "T"},
	{`package p; func F() {}`, 16, importDir, "F"},
	{`package p; type T struct{}; func (_ T) M()`, 39, importDir, "M"},
	{`package p; const C = 42`, 17, importDir, "C"},
	{`package p; var V int = 42`, 15, importDir, "V"},

	// Usage of package local defined type, function, method, const and variable
	{`package p; type T struct{}; func main() { var _ T }`, 48, importDir, "T"},
	{`package p; type T struct{}; func (_ T) m() {}`, 36, importDir, "T"},
	{`package p; type T struct{}; func (_ *T) m() {}`, 37, importDir, "T"},
	{`package p; type T struct{}; type U struct{ t T }`, 46, importDir, "T"},
	{`package p; type T struct{}; type U struct{ T }`, 44, importDir, "T"},
	{`package p; func F() {}; func main() { F() }`, 38, importDir, "F"},
	{`package p; type T struct{}; func (_ T) M() {}; func main() { t := T{}; t.M() }`, 73, importDir, "M"},
	{`package p; const C = 42; func main() { var _ int = C }`, 51, importDir, "C"},
	{`package p; var V = 42; func main() { var _ int = V }`, 49, importDir, "V"},

	// Usage of imported type, function, field, const and variable
	{`package p; import "io"; func main() { var _ io.Reader }`, 46, "io", ""},
	{`package p; import "io"; func main() { var _ io.Reader }`, 47, "io", "Reader"},
	{`package p; import foo "io"; func main() { var _ foo.Reader }`, 52, "io", "Reader"},
	{`package p; import "io"; type T struct{ r io.Reader}`, 44, "io", "Reader"},
	{`package p; import "io"; type U struct{ io.Reader }`, 43, "io", "Reader"},
	{`package p; import "io"; type Reader struct{}; func main() { var _ io.Reader }`, 69, "io", "Reader"},
	{`package p; import "fmt"; func main() { fmt.Println("Hello World!") }`, 43, "fmt", "Println"},
	{`package p; import "math"; func main() { var _ int = math.MaxInt8 }`, 57, "math", "MaxInt8"},
	{`package p; import "net/http"; func main() { var _ int = http.StatusOK }`, 61, "net/http", "StatusOK"},
	{`package p; import "os"; func main() { var _ *os.File = os.Stdout }`, 58, "os", "Stdout"},
}

func TestIdentAtOffset(t *testing.T) {
	for i, test := range searchTests {
		path, ident, err := searchAtOff(test.off, test.prg)
		if err != nil {
			t.Errorf("Test %d: %v", i, err)
			continue
		}
		if path != test.path || ident != test.ident {
			t.Errorf("Test %d: expected '%s' '%s', got '%s' '%s'\n", i, test.path, test.ident, path, ident)
		}
	}
}

repository: davidrjenni/agodoc

repo_name: davidrjenni/agodoc

gha_language: Go


text:
@inproceedings{klockgether1970two,
  title={Two-phase nozzle and hollow core jet experiments},
  author={Klockgether, Jurgen and Schwefel, Hans-Paul},
  booktitle={Proc. 11th Symp. Engineering Aspects of Magnetohydrodynamics},
  pages={141--148},
  year={1970},
  organization={Pasadena, CA: California Institute of Technology}
}
@article{fogel1966artificial,
  title={Artificial intelligence through simulated evolution},
  author={Fogel, Lawrence J and Owens, Alvin J and Walsh, Michael J},
  year={1966},
  publisher={John Wiley}
}
@techreport{holland1987genetic,
  title={Genetic algorithms and classifier systems: foundations and future directions},
  author={Holland, John H},
  year={1987},
  institution={Michigan Univ., Ann Arbor (USA)}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

extension: bib


text:
# VERSION must follow pattern : <major>.<minor>.<patch>
set(KRIGING_VERSION_MAJOR 0)
set(KRIGING_VERSION_MINOR 8)
set(KRIGING_VERSION_PATCH 0)
set(KRIGING_VERSION "${KRIGING_VERSION_MAJOR}.${KRIGING_VERSION_MINOR}.${KRIGING_VERSION_PATCH}")

repository: libKriging/libKriging

repo_name: libKriging/libKriging

extension: cmake


text:
package util

import (
	"bufio"
	"crypto/rand"
	"encoding/base64"
	"math/big"
	"os"
	"path/filepath"
	"sort"
	"strconv"
	"time"
)

const (
	ISO8601            = "2006-01-02T15:04:05.999Z"
	databaseFolderName = "MimaWebDB"
)

func NewID() string {
	var max int64 = 100_000_000
	n, err := rand.Int(rand.Reader, big.NewInt(max))
	if err != nil {
		panic(err)
	}
	timestamp := time.Now().Unix()
	idInt64 := timestamp*max + n.Int64()
	return strconv.FormatInt(idInt64, 36)
}

func Base64Encode(data []byte) string {
	return base64.StdEncoding.EncodeToString(data)
}

func Base64Decode(s string) ([]byte, error) {
	return base64.StdEncoding.DecodeString(s)
}

func NewFileScanner(fullPath string) (*bufio.Scanner, *os.File, error) {
	file, err := os.Open(fullPath)
	if err != nil {
		return nil, nil, err
	}
	return bufio.NewScanner(file), file, nil
}

func GetPathsByExt(dir, ext string) ([]string, error) {
	pattern := filepath.Join(dir, "*"+ext)
	filePaths, err := filepath.Glob(pattern)
	if err != nil {
		return nil, err
	}
	sort.Strings(filePaths)
	return filePaths, nil
}

func DatabaseDefaultDir() string {
	home, err := os.UserHomeDir()
	if err != nil {
		panic(err)
	}
	return filepath.Join(home, databaseFolderName)
}

func TimestampFilename(ext string) string {
	name := strconv.FormatInt(time.Now().UnixNano(), 10)
	return name + ext
}

func BufWriteln(w *bufio.Writer, box64 string) (err error) {
	_, err = w.WriteString(box64 + "\n")
	return
}

func DeleteFiles(filePaths []string) error {
	for _, f := range filePaths {
		if err := os.Remove(f); err != nil {
			return err
		}
	}
	return nil
}

func TimeNow() string {
	return time.Now().Format(ISO8601)
}

repository: jbjian/mima-web

repo_name: jbjian/mima-web

extension: go


text:
@book{noauthor__1972,
 date = {1972},
 langid = {french},
 location = {Paris},
 publisher = {Université de Paris-Sud},
 title = { Résolution de problèmes de Cauchy par la méthode d'Ovcyannikov, Thèse de Doctorat de 3e cycle}
}


text:
package ast

import (
	"fmt"
)

type Meta struct {
	Filename string
	Line     int
	Col      int
	Offset   int
	Original string
}

func (m Meta) String() string {
	if len(m.Filename) == 0 {
		return fmt.Sprintf("%d:%d", m.Line, m.Col)
	}
	return fmt.Sprintf("%s %d:%d", m.Filename, m.Line, m.Col)
}

func (m Meta) Wrap(err error) error {
	return fmt.Errorf("%s: %s", m.String(), err)
}

func (m Meta) Errorf(format string, args ...interface{}) error {
	return m.Wrap(fmt.Errorf(format, args...))
}

func (a Meta) Format(st fmt.State, verb rune) {
	format(a, st, verb)
}

func (a Meta) MarshalJSON() ([]byte, error) {
	m := map[string]interface{}{
		"Filename": a.Filename,
		"Line":     a.Line,
		"Col":      a.Col,
		"Offset":   a.Offset,
		"Original": a.Original,
	}

	return toJSON(a, m)
}

repository: gobuffalo/lush

repo_name: gobuffalo/lush

gha_license_id: MIT


text:
include themes.inc

DESCRIPTION = "${PRE_DESCRIPTION}"
HOMEPAGE = "https://github.com/neutrino-images/ni-neutrino"
MAINTAINER = "NI-Team"
SUMMARY = "${DESCRIPTION} by ${MAINTAINER}"

SRC_URI = "git://github.com/neutrino-images/ni-neutrino.git;protocol=https;subpath=${SUBPATH}"

PR = "r4"
SRCREV = "${AUTOREV}"
PV = "3.60"

do_install () {
	install -d ${D}/var/tuxbox/themes
	install -m 644 ${S}/data/themes/Material*.theme ${D}/var/tuxbox/themes
	install -m 644 ${S}/data/themes/Adult*.theme ${D}/var/tuxbox/themes
	install -m 644 ${S}/data/themes/Dark*.theme ${D}/var/tuxbox/themes

	THEME_LIST=`ls ${D}/var/tuxbox/themes`

	install -d ${D}/var/tuxbox/themes/${PN}-icons/icons

	ICONS=`find ${S}/data/icons -name *.png`
	for i in  ${ICONS} ; do
		install -m 644 ${i} ${D}/var/tuxbox/themes/${PN}-icons/icons
	done

	rm -f ${D}/var/tuxbox/themes/${PN}-icons/icons/hint_imagelogo.png
	rm -f ${D}/var/tuxbox/themes/${PN}-icons/icons/mainmenue.png

	for t in  ${THEME_LIST} ; do
		LINKNAME=${D}/var/tuxbox/themes/`echo ${t%.*}`
		ln -sf /var/tuxbox/themes/${PN}-icons ${LINKNAME}
	done
}

repository: neutrino-hd/meta-neutrino

repo_name: neutrino-hd/meta-neutrino

gha_language: BitBake

extension: bb


text:
DESCRIPTION = "A lightweight PDF viewer and toolkit written in portable C."
HOMEPAGE = "http://www.mupdf.com"
SECTION = "x11/applications"

LICENSE = "GPLv3"
LIC_FILES_CHKSUM = "file://COPYING;md5=73f1eb20517c55bf9493b7dd6e480788"

inherit gitpkgv pkgconfig

TAG = "1.3"
BRANCH = "master"

# what happened to the git fetcher? no more tags as SRCREVs?
#### this is 1.3 hash
#SRCREV = "8530783a10e467947f8698cf44d38313b5454cb2"
#### this is 1.2 hash
SRCREV = "9d20a4f3a69fdea855f8678c1ad50b5db7472d81"
PKGV = "${GITPKGVTAG}"

#PV = "${TAG}"
PR = "r0"

DEPENDS = "openjpeg-native jbig2dec-native jpeg-native freetype-native libpng-native openjpeg jbig2dec jpeg freetype zlib bzip2 ${X11_DEPS}"
X11_DEPS = "virtual/libx11 libxext libxau libxdmcp libxcb"

SRC_URI = "git://git.ghostscript.com/mupdf.git;protocol=http;branch=${BRANCH} \
           file://${PN}-1.1_p20121127-buildsystem.patch \
           file://${PN}-1.1_p20121127-desktop-integration.patch \
           file://${PN}-1.2-mubusy_rename_fix.patch \
           file://${PN}-1.2-pkg-config.patch \
           file://${PN}-1.1_rc1-zoom-2.patch \
"

S = "${WORKDIR}/git"

LEAD_SONAME = "libfitz.so.1.2"

# mupdf crashes when built with -ggdb3
# http://bugs.ghostscript.com/show_bug.cgi?id=691578
FULL_OPTIMIZATION := "${@oe_filter_out('-ggdb3', '${FULL_OPTIMIZATION}', d)}"

do_configure_prepend() {
    cd ${S}
    rm -rf ${S}/thirdparty

    sed -i -e "/^prefix=/s:=.*:=/usr:" \
        ${S}/debian/${PN}.pc

    # http://bugs.ghostscript.com/show_bug.cgi?id=693467
    sed -i -e '/^\(Actions\|MimeType\)=/s:\(.*\):\1;:' \
        ${S}/debian/${PN}.desktop

    my_soname="${LEAD_SONAME}"

    sed -i -e "\$a\$(FITZ_LIB):" \
        -e "\$a\\\t\$(QUIET_LINK) \$(CC) \$(LDFLAGS) --shared -Wl,-soname -Wl,${my_soname} -Wl,--no-undefined -o \$@ \$^ \$(LIBS)" \
        -e "/^FITZ_LIB :=/s:=.*:= build/release/${my_soname}:" \
        ${S}/Makefile

    # we don't include CJK fonts to make binary more slim
    # comment out following two lines if you need support for CJK
    sed -i 's:^\t\$.GENDIR./font_cjk.c::g' ${S}/Makefile
}

do_compile() {
    cd ${S}
    unset CFLAGS LDFLAGS
    export PKG_CONFIG_PATH=${STAGING_LIBDIR_NATIVE}/pkgconfig
    oe_runmake build=release build/release
    oe_runmake build=release build/release/cmapdump LD="${BUILD_CC}" CFLAGS="-I${S}/pdf -I${S}/fitz -I${STAGING_INCDIR_NATIVE}" LDFLAGS="-L${STAGING_LIBDIR_NATIVE} -Wl,-rpath-link,${STAGING_LIBDIR_NATIVE}" CC=${BUILD_CC}
    oe_runmake build=release build/release/fontdump LD="${BUILD_CC}" CFLAGS="-I${S}/pdf -I${S}/fitz -I${STAGING_INCDIR_NATIVE}" LDFLAGS="-L${STAGING_LIBDIR_NATIVE} -Wl,-rpath-link,${STAGING_LIBDIR_NATIVE}" CC=${BUILD_CC}

    cd ${S}
    export PKG_CONFIG="pkg-config"
    export PKG_CONFIG_PATH=${STAGING_LIBDIR}/pkgconfig
    oe_runmake build=release XCFLAGS="-fpic"
}

do_install() {
    cd ${S}
    oe_runmake DESTDIR="${D}" install build=release
    install -d ${D}${datadir}/applications
    install -d ${D}${datadir}/pixmaps
    install -d ${D}${includedir}
    install -d ${D}${libdir}/pkgconfig
    install -m 0644 ${S}/debian/mupdf.xpm ${D}/${datadir}/pixmaps/
    install -m 0644 ${S}/debian/mupdf.desktop ${D}${datadir}/applications/
    install -m 0644 ${S}/pdf/mupdf-internal.h ${D}${includedir}/
    install -m 0644 ${S}/fitz/fitz-internal.h ${D}${includedir}/
    install -m 0644 ${S}/xps/muxps-internal.h ${D}${includedir}/
    install -m 0644 ${S}/debian/mupdf.pc ${D}${libdir}/pkgconfig

    ln -s ${LEAD_SONAME} ${D}${libdir}/libfitz.so
}

FILES_${PN}-dev += "${includedir}"

repository: sarnold/meta-alt-desktop-extras

repo_name: sarnold/meta-alt-desktop-extras


text:
@article{derrien_autograph_2007,
 abstract = {AutoGRAPH is an interactive web server for automatic multi-species comparative genomics analyses based on personal datasets or pre-inserted public datasets. This program automatically identifies conserved segments (CS) and breakpoint regions, assesses the conservation of marker/gene order between organisms, constructs synteny maps for two to three species and generates high-quality, interactive displays facilitating the identification of chromosomal rearrangements. AutoGRAPH can also be used for the integration and comparison of several types of genomic resources (meiotic maps, radiation hybrid maps and genome sequences) for a single species, making AutoGRAPH a versatile tool for comparative genomics analysis. AVAILABILITY: http://genoweb.univ-rennes1.fr/tom_dog/AutoGRAPH/. SUPPLEMENTARY INFORMATION: A description of the algorithm and additional information are available at http://genoweb.univ-rennes1.fr/tom_dog/AutoGRAPH/Tutorial.php.},
 author = {Derrien, Thomas and Andre, Catherine and Galibert, Francis and Hitte, Christophe and André, Catherine and Galibert, Francis and Hitte, Christophe},
 doi = {10.1093/bioinformatics/btl618},
 file = {Attachment:/Users/admin/Zotero/storage/4XIRKVKU/Derrien et al. - 2007 - AutoGRAPH An interactive web server for automating and visualizing comparative genome maps.pdf:application/pdf},
 issn = {13674803},
 journal = {Bioinformatics},
 keywords = {DNA, Algorithms, Base Sequence, Chromosome Mapping, Computer Graphics, Database Management Systems, Databases, Genetic, Information Storage and Retrieval, Internet, methods, Molecular Sequence Data, Sequence Alignment, Sequence Analysis, Software, User-Computer Interface},
 language = {eng},
 month = {February},
 note = {ISBN: 13674803},
 number = {4},
 pages = {498--499},
 pmid = {17145741},
 title = {AutoGRAPH: An interactive web server for automating and visualizing comparative genome maps},
 volume = {23},
 year = {2007}
}


text:
DESCRIPTION = "The gSOAP toolkit provides a unique SOAP-to-C/C++ language binding \
for the development of SOAP Web Services and clients."
SECTION = "devel"
LICENSE = "GPL-2.0-with-OpenSSL-exception"
LIC_FILES_CHKSUM = "file://LICENSE.txt;md5=4f40a941379143186f9602242c3fb729 \
                    file://GPLv2_license.txt;md5=a33672dbe491b6517750a0389063508b"

SRC_URI = "https://prdownloads.sourceforge.net/${BPN}2/${BPN}_${PV}.zip"
SRC_URI:append:libc-musl = " file://0001-Simplify-check-for-gethostbyname_r.patch"
SRC_URI[sha256sum] = "b65190ebf8c2517d6fafbdc2000bc7bc650d921a02f4aa53eb1e3df267592c4a"

inherit autotools

BBCLASSEXTEND = "native"

S = "${WORKDIR}/${BPN}-2.8"

EXTRA_OECONF += "--enable-ipv6 --enable-c-locale"
PARALLEL_MAKE = ""

EXTRA_OEMAKE:class-target = "SOAP=${STAGING_BINDIR_NATIVE}/soapcpp2"

DEPENDS = "openssl zlib flex bison bison-native"
DEPENDS:append:class-target = " gsoap-native"

do_install:append() {
    install -d ${D}${libdir}
    for lib in libgsoapssl libgsoapssl++ libgsoap libgsoapck++ libgsoap++ libgsoapck
    do
        oe_libinstall -C gsoap $lib ${D}${libdir}
    done
}

do_install:class-native() {
    oe_runmake DESTDIR=${D} BINDIR=${D}${bindir} install
}

FILES:${PN} = "${bindir}/wsdl2h ${bindir}/soapcpp2"
FILES:${PN} += "${datadir}"
FILES:${PN}-staticdev = "${libdir}"
FILES:${PN}-dev = "${includedir}"
RRECOMMENDS:${PN}-dev = "${PN}-staticdev"

repository: openembedded/meta-openembedded

repo_name: openembedded/meta-openembedded


text:
@online{noauthor_roxygen_nodate,
	title = {Roxygen},
	url = {http://roxygen.org/},
	urldate = {2013-08-05}
}

repository: pmean/build-website

repo_name: pmean/build-website


text:
import React, { Component, PropTypes } from 'react';

class ColumnTitle extends Component {
    render() {
        const { title, style } = this.props;
        return (

                {title}

        );
    }
}

ColumnTitle.propTypes = {
    title: PropTypes.string.isRequired,
    style: PropTypes.object,
};
ColumnTitle.defaultProps = {
    style: {}
}
export default ColumnTitle;

repository: NamBker/Reapeater

repo_name: NamBker/Reapeater

extension: js


text:
@article{tamura2013mega6,
  title={MEGA6: molecular evolutionary genetics analysis version 6.0},
  author={Tamura, Koichiro and Stecher, Glen and Peterson, Daniel and Filipski, Alan and Kumar, Sudhir},
  journal={Molecular biology and evolution},
  volume={30},
  number={12},
  pages={2725--2729},
  year={2013},
  publisher={SMBE}
}

@article{sturmbauer2010evolutionary,
  title={Evolutionary history of the Lake Tanganyika cichlid tribe Lamprologini (Teleostei: Perciformes) derived from mitochondrial and nuclear DNA data},
  author={Sturmbauer, Christian and Salzburger, Walter and Duftner, Nina and Schelly, Robert and Koblm{\"u}ller, Stephan},
  journal={Molecular Phylogenetics and Evolution},
  volume={57},
  number={1},
  pages={266--284},
  year={2010},
  publisher={Elsevier}
}

@article{kishe2008dietary,
  title={Dietary shift in benthivorous cichlids after the ecological changes in Lake Victoria},
  author={Kishe-Machumu, Mary and Witte, Frans and Wanink, Jan H},
  journal={Animal Biology},
  volume={58},
  number={4},
  pages={401--417},
  year={2008},
  publisher={Brill}
}

@book{greenwood1976review,
  title={A Review of the Family Centropomidae (Pisces, Perciformes)},
  author={Greenwood, P.H.},
  lccn={76376278},
  %series={British Museum (Natural History): Bulletin. Zoology series},
  %url={https://books.google.com/books?id=6GPMSAAACAAJ},
  year={1976},
  publisher={British Museum (Natural History)}
}

@article{schwartz2006effects,
  title={Effects of Nile perch, Lates niloticus, on functional and specific fish diversity in Uganda's Lake Kyoga system},
  author={Schwartz, Jesse DM and Pallin, Marla J and Michener, Robert H and Mbabazi, Dismiss and Kaufman, Les},
  journal={African Journal of Ecology},
  volume={44},
  number={2},
  pages={145--156},
  year={2006},
  publisher={Wiley Online Library}
}

@article{witte2013cichlid,
  title={Cichlid species diversity in naturally and anthropogenically turbid habitats of Lake Victoria, East Africa},
  author={Witte, Frans and Seehausen, Ole and Wanink, Jan H and Kishe-Machumu, Mary A and Rensing, Marjolein and Goldschmidt, Tijs},
  journal={Aquatic Sciences},
  volume={75},
  number={2},
  pages={169--183},
  year={2013},
  publisher={Springer}
}

@article{seehausen1997patterns,
  title={Patterns of the remnant cichlid fauna in southern Lake Victoria},
  author={Seehausen, Ole and Witte, Frans and Katunzi, Egid F and Smits, Jan and Bouton, Niels},
  journal={Conservation Biology},
  volume={11},
  number={4},
  pages={890--904},
  year={1997},
  publisher={Wiley Online Library}
}

@article{janitza2013auc,
  title={An AUC-based permutation variable importance measure for random forests},
  author={Janitza, Silke and Strobl, Carolin and Boulesteix, Anne-Laure},
  journal={BMC Bioinformatics},
  volume={14},
  number={1},
  pages={119},
  year={2013},
  publisher={BioMed Central}
}

@misc{hothorn2010party,
  title={Party: A laboratory for recursive partytioning},
  author={Hothorn, Torsten and Hornik, Kurt and Strobl, Carolin and Zeileis, Achim},
  year={2010}
}

@article{hothorn2006unbiased,
  title={Unbiased recursive partitioning: A conditional inference framework},
  author={Hothorn, Torsten and Hornik, Kurt and Zeileis, Achim},
  journal={Journal of Computational and Graphical statistics},
  volume={15},
  number={3},
  pages={651--674},
  year={2006},
  publisher={Taylor \& Francis}
}

@book{daget1991check,
  title={Check-list of the freshwater fishes of Africa, vol. 4},
  author={Daget, J. and Gosse, J.P. and van den Audenaerde, D.F.E.T. and O.R.S.T.O.M. (Agency : France)},
  isbn={9789073242036},
  lccn={85184297},
  series={Check-list of the Freshwater Fishes of Africa, Cloffa: Catalogue Des Poissons D'eau Douce D'Afrique},
  url={https://books.google.com/books?id=uZEWAQAAIAAJ},
  year={1991},
  publisher={ORSTOM}
}

@article{de2013two,
  title={Two new species of zooplanktivorous haplochromine cichlids from Lake Victoria, Tanzania},
  author={De Zeeuw, Marnix P and Westbroek, Irene and Van Oijen, Martien JP and Witte, Frans},
  journal={ZooKeys},
  number={256},
  pages={1},
  year={2013},
  publisher={Pensoft Publishers}
}

@article{de2010seven,
  title={Seven new species of detritivorous and phytoplanktivorous haplochromines from Lake Victoria},
  author={De Zeeuw, MP and Mietes, M and Niemantsverdriet, P and Ter Huurne, S and Witte, F},
  journal={Zoologische Mededelingen},
  volume={84},
  pages={201--250},
  year={2010}
}

@article{van2008haplochromis,
  title={Haplochromis vonlinnei spec. nov., a piscivorous haplochromine cichlid (Teleostei, Perciformes) from the Mwanza Gulf area of Lake Victoria, Tanzania},
  author={van Oijen, MJ and de Zeeuw, MP},
  journal={Zoologische Mededelingen},
  volume={82},
  year={2008}
}

@article{seegers2008fishes,
  title={The fishes collected by GA Fischer in East Africa in 1883 and 1885/86},
  author={Seegers, Lothar},
  journal={Zoosystematics and Evolution},
  volume={84},
  number={2},
  pages={149--195},
  year={2008},
  publisher={Wiley Online Library}
}

@article{van2004haplochromis,
  title={Haplochromis ushindi spec. nov., the largest piscivorous cichlid in the Mwanza Gulf area of Lake Victoria (East Africa) before the Nile perch upsurge},
  author={van Oijen, MJP},
  journal={Zoologische Mededelingen},
  volume={78},
  pages={249--255},
  year={2004}
}

@article{seehausen1998mbipi,
  title={Mbipi, the rock-dwelling cichlids of Lake Victoria: description of three new genera and fifteen new species (Teleostei)},
  author={Seehausen, Ole and Lippitsch, E and Bouton, N and Zwennes, H},
  journal={Ichthyological Exploration of Freshwaters},
  volume={9},
  number={2},
  pages={129--228},
  year={1998},
  publisher={Verlag Dr. Friedrich Pfeil}
}

@book{seehausen1996lake,
  title={Lake Victoria rock cichlids: taxonomy, ecology and distribution},
  author={Seehausen, Ole},
  year={1996},
  publisher={Verduyn Cichlids}
}

@article{van1996taxonomical,
  title={Taxonomical and ecological descriptions of a species complex of zoopianktivorous and insectivorous cichlids from Lake Victoria},
  author={Van Oijen, MJP and Witte, F},
  journal={Zoologische Verhandelingen},
  pages={3--56},
  year={1996},
  publisher={NATIONAAL NATUURHISTORISCH MUSEUM}
}

@article{van1992haplochromis,
  title={Haplochromis hozvesi spec, nov., a crab and fish eating cichlid from Lake Victoria},
  journal={Zoologische Mededelingen},
  publisher={National Museum of Natural History, Netherlands},
  author={van Oijen, MJP},
  year={1992}
}

@article{van1991systematic,
  title={A systematic revision of the piscivorous haplochromine Cichlidae (Pisces: Teleostei) of Lake Victoria (East Africa). Part I},
  author={Van Oijen, MJP},
  journal={Zoologische Verhandelingen},
  volume={272},
  pages={1--95},
  year={1991}
}

@article{hoogerhoud1982ecological,
  title={The ecological differentiation of two closely resembling Haplochromis species from Lake Victoria (H. iris and H. hiatus; Pisces, Cichlidae)},
  author={Hoogerhoud, RJC and Witte, F and Barel, CDN},
  journal={Netherlands Journal of Zoology},
  volume={33},
  number={3},
  pages={283--305},
  year={1982},
  publisher={Brill}
}

@article{witte1980haplochromine,
  title={Haplochromine cleaner fishes: a taxonomic and eco-morphological description of two new species},
  author={Witte, F and Witte-Maas, ELM},
  journal={Netherlands Journal of Zoology},
  volume={31},
  number={1},
  pages={203--230},
  year={1980},
  publisher={Brill}
}

@book{witte1990taxonomy,
  title={Taxonomy, ecology and fishery of Lake Victoria haplichromine trophic groups},
  author={Witte, Frans and Van Oijen, MJP},
  year={1990},
  publisher={Nationaal Natuurhistorisch Museum}
}

@misc{redlist,
  title={The IUCN Red List of Threatened Species. Version 2014.1. \url{http://www.iucnredlist.org} (2013)},
  author={IUCN},
  year={2014},
  publisher={IUCN}
}

@misc{kuznetsova2013lmertest,
  title={lmerTest: Tests for Random and Fixed Effects for Linear Mixed Effect Models},
  author={Kuznetsova, A and Brockhoff, PB and Christensen, RHB},
  year={2013}
}

@misc{bates2010lme4,
  title={lme4: Mixed-effects modeling with R},
  author={Bates, Douglas M},
  year={2010},
  publisher={Springer New York}
}

@article{hoyle1987effect,
  title={The effect of prey morphology and size on handling time in a piscivore, the largemouth bass (Micropterus salmoides)},
  author={Hoyle, James A and Keast, Allen},
  journal={Canadian Journal of Zoology},
  volume={65},
  number={8},
  pages={1972--1977},
  year={1987},
  publisher={NRC Research Press}
}

@article{wagner2013genome,
  title={Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation},
  author={Wagner, Catherine E and Keller, Irene and Wittwer, Samuel and Selz, Oliver M and Mwaiko, Salome and Greuter, Lucie and Sivasundar, Arjun and Seehausen, Ole},
  journal={Molecular ecology},
  volume={22},
  number={3},
  pages={787--798},
  year={2013},
  publisher={Wiley Online Library}
}

@article{nagl2000origin,
  title={The origin and age of haplochromine fishes in Lake Victoria, East Africa},
  author={Nagl, Sandra and Tichy, Herbert and Mayer, Werner E and Takezaki, Naoko and Takahata, Naoyuki and Klein, Jan},
  journal={Proceedings of the Royal Society of London B: Biological Sciences},
  volume={267},
  number={1447},
  pages={1049--1061},
  year={2000},
  publisher={The Royal Society}
}

@article{hellig2010allometric,
  title={Allometric shape change of the lower pharyngeal jaw correlates with a dietary shift to piscivory in a cichlid fish},
  author={Hellig, Christoph J and Kerschbaumer, Michaela and Sefc, Kristina M and Koblm{\"u}ller, Stephan},
  journal={Naturwissenschaften},
  volume={97},
  number={7},
  pages={663--672},
  year={2010},
  publisher={Springer}
}

@article{muschick2012convergent,
  title={Convergent evolution within an adaptive radiation of cichlid fishes},
  author={Muschick, Moritz and Indermaur, Adrian and Salzburger, Walter},
  journal={Current biology},
  volume={22},
  number={24},
  pages={2362--2368},
  year={2012},
  publisher={Elsevier}
}

@article{lopez2013testing,
  title={Testing for ancient adaptive radiations in Neotropical cichlid fishes},
  author={L{\'o}pez-Fern{\'a}ndez, Hern{\'a}n and Arbour, Jessica H and Winemiller, Kirk and Honeycutt, Rodney L and others},
  journal={Evolution},
  volume={67},
  number={5},
  pages={1321--1337},
  year={2013},
  publisher={Wiley Online Library}
}

@misc{openscad,
  author = {Marius Kintel},
  title = {OpenSCAD},
  year = {2014},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/openscad/openscad}}
}

@phdthesis{kwik2011biology,
  title={The biology and ecology of small tropical scorpaenoids inhabiting shallow coastal habitats in Singapore},
  author={Kwik Teik Beng, Jeffery},
  year={2011}
}

@article{betancur2013tree,
  title={The tree of life and a new classification of bony fishes},
  author={Betancur-R, Ricardo and Broughton, Richard E and Wiley, Edward O and Carpenter, Kent and L{\'o}pez, J Andr{\'e}s and Li, Chenhong and Holcroft, Nancy I and Arcila, Dahiana and Sanciangco, Millicent and Cureton Ii, James C and others},
  journal={PLOS Currents Tree of Life},
  year={2013},
  publisher={Public Library of Science}
}

@article{boettiger2012rfishbase,
  title={rfishbase: exploring, manipulating and visualizing FishBase data from R},
  author={Boettiger, C and Lang, DT and Wainwright, PC},
  journal={Journal of Fish Biology},
  volume={81},
  number={6},
  pages={2030--2039},
  year={2012},
  publisher={Wiley Online Library}
}

@article{froese2013fishbase,
  title={Fishbase, a Global Information System on Fishes},
  author={Froese, R and Pauly, D},
  journal={World Wide Web electronic publication (accessed February 2013)},
  year={2013}
}

@book{tiercelin1991lake,
  title={Lake Tanganyika and its life},
  author={Tiercelin, J-J and Coulter, GW},
  year={1991},
  publisher={Oxford univ. press London etc}
}

@article{greenwood1981haplochromine,
  title={The haplochromine fishes of the East African Lakes; collected papers on their taxonomy, biology and evolution (with an introduction and species index)},
  author={Greenwood, Peter Humphry},
  year={1981},
  publisher={Muenchen (Germany, FR) Kraus International Pub.}
}

@article{heard1995key,
  title={Key evolutionary innovations and their ecological mechanisms},
  author={Heard, Stephen B and Hauser, David L},
  journal={Historical biology},
  volume={10},
  number={2},
  pages={151--173},
  year={1995},
  publisher={Taylor \& Francis}
}

@book{mayr1963animal,
  title={Animal species and evolution},
  author={Mayr, E.},
  lccn={63009552},
  series={Belknap Press},
  url={https://books.google.com/books?id=GDwuAAAAMAAJ},
  year={1963},
  publisher={Belknap Press of Harvard University Press}
}

@book{pfennig2012evolution,
  title={Evolution's wedge: competition and the origins of diversity},
  author={Pfennig, David W and Pfennig, Karin S},
  number={12},
  year={2012},
  publisher={Univ of California Press}
}

@book{schluter2000ecology,
  title={The ecology of adaptive radiation},
  author={Schluter, Dolph},
  year={2000},
  publisher={OUP Oxford}
}

@article{revell2012phytools,
  title={phytools: an R package for phylogenetic comparative biology (and other things)},
  author={Revell, Liam J},
  journal={Methods in Ecology and Evolution},
  volume={3},
  number={2},
  pages={217--223},
  year={2012},
  publisher={Wiley Online Library}
}

@article{harmon2008geiger,
  title={GEIGER: investigating evolutionary radiations},
  author={Harmon, Luke J and Weir, Jason T and Brock, Chad D and Glor, Richard E and Challenger, Wendell},
  journal={Bioinformatics},
  volume={24},
  number={1},
  pages={129--131},
  year={2008},
  publisher={Oxford Univ Press}
}

@article{alfaro_does_2009,
	title = {Does evolutionary innovation in pharyngeal jaws lead to rapid lineage diversification in labrid fishes?},
	volume = {9},
	issn = {1471-2148},
	doi = {10.1186/1471-2148-9-255},
	abstract = {Background: Major modifications to the pharyngeal jaw apparatus are widely regarded as a recurring evolutionary key innovation that has enabled adaptive radiation in many species-rich clades of percomorph fishes. However one of the central predictions of this hypothesis, that the acquisition of a modified pharyngeal jaw apparatus will be positively correlated with explosive lineage diversification, has never been tested. We applied comparative methods to a new time-calibrated phylogeny of labrid fishes to test whether diversification rates shifted at two scales where major pharyngeal jaw innovations have evolved: across all of Labridae and within the subclade of parrotfishes. Results: Diversification patterns within early labrids did not reflect rapid initial radiation. Much of modern labrid diversity stems from two recent rapid diversification events; one within julidine fishes and the other with the origin of the most species-rich clade of reef-associated parrotfishes. A secondary pharyngeal jaw innovation was correlated with rapid diversification within the parrotfishes. However diversification rate shifts within parrotfishes are more strongly correlated with the evolution of extreme dichromatism than with pharyngeal jaw modifications. Conclusion: The temporal lag between pharyngeal jaw modifications and changes in diversification rates casts doubt on the key innovation hypothesis as a simple explanation for much of the richness seen in labrids and scarines. Although the possession of a secondarily modified PJA was correlated with increased diversification rates, this pattern is better explained by the evolution of extreme dichromatism (and other social and behavioral characters relating to sexual selection) within Scarus and Chlorurus. The PJA-innovation hypothesis also fails to explain the most dominant aspect of labrid lineage diversification, the radiation of the julidines. We suggest that pharyngeal jaws might have played a more important role in enabling morphological evolution of the feeding apparatus in labrids and scarines rather than in accelerating lineage diversification.},
	journal = {Bmc Evolutionary Biology},
	author = {Alfaro, Michael E. and Brock, Chad D. and Banbury, Barbara L. and Wainwright, Peter C.},
	month = oct,
	year = {2009},
	note = {WOS:000271889300002},
	pages = {255}
}

@article{brawand_genomic_2014,
	title = {The genomic substrate for adaptive radiation in {African} cichlid fish},
	volume = {513},
	issn = {0028-0836},
	doi = {10.1038/nature13726},
	abstract = {Cichlid fishes are famous for large, diverse and replicated adaptive radiations in the Great Lakes of East Africa. To understand themolecular mechanisms underlying cichlid phenotypic diversity, we sequenced the genomes and transcriptomes of five lineages of African cichlids: the Nile tilapia (Oreochromis niloticus), an ancestral lineage with low diversity; and four members of the East African lineage: Neolamprologus brichardi/pulcher (older radiation, Lake Tanganyika), Metriaclima zebra (recent radiation, Lake Malawi), Pundamilia nyererei (very recent radiation, Lake Victoria), and Astatotilapia burtoni (riverine species around Lake Tanganyika). We found an excess of gene duplications in the East African lineage compared to tilapia and other teleosts, an abundance of non-coding element divergence, accelerated coding sequence evolution, expression divergence associated with transposable element insertions, and regulation by novel microRNAs. In addition, we analysed sequence data from sixty individuals representing six closely related species from Lake Victoria, and show genome-wide diversifying selection on coding and regulatory variants, some of which were recruited from ancient polymorphisms. We conclude that a number of molecular mechanisms shaped East African cichlid genomes, and that amassing of standing variation during periods of relaxed purifying selection may have been important in facilitating subsequent evolutionary diversification.},
	number = {7518},
	journal = {Nature},
	author = {Brawand, David and Wagner, Catherine E. and Li, Yang I. and Malinsky, Milan and Keller, Irene and Fan, Shaohua and Simakov, Oleg and Ng, Alvin Y. and Lim, Zhi Wei and Bezault, Etienne and Turner-Maier, Jason and Johnson, Jeremy and Alcazar, Rosa and Noh, Hyun Ji and Russell, Pamela and Aken, Bronwen and Alfoeldi, Jessica and Amemiya, Chris and Azzouzi, Naoual and Baroiller, Jean-Francois and Barloy-Hubler, Frederique and Berlin, Aaron and Bloomquist, Ryan and Carleton, Karen L. and Conte, Matthew A. and D'Cotta, Helena and Eshel, Orly and Gaffney, Leslie and Galibert, Francis and Gante, Hugo F. and Gnerre, Sante and Greuter, Lucie and Guyon, Richard and Haddad, Natalie S. and Haerty, Wilfried and Harris, Rayna M. and Hofmann, Hans A. and Hourlier, Thibaut and Hulata, Gideon and Jaffe, David B. and Lara, Marcia and Lee, Alison P. and MacCallum, Iain and Mwaiko, Salome and Nikaido, Masato and Nishihara, Hidenori and Ozouf-Costaz, Catherine and Penman, David J. and Przybylski, Dariusz and Rakotomanga, Michaelle and Renn, Suzy C. P. and Ribeiro, Filipe J. and Ron, Micha and Salzburger, Walter and Sanchez-Pulido, Luis and Santos, M. Emilia and Searle, Steve and Sharpe, Ted and Swofford, Ross and Tan, Frederick J. and Williams, Louise and Young, Sarah and Yin, Shuangye and Okada, Norihiro and Kocher, Thomas D. and Miska, Eric A. and Lander, Eric S. and Venkatesh, Byrappa and Fernald, Russell D. and Meyer, Axel and Ponting, Chris P. and Streelman, J. Todd and Lindblad-Toh, Kerstin and Seehausen, Ole and Di Palma, Federica},
	month = sep,
	year = {2014},
	note = {WOS:000341814900051},
	pages = {375--+}
}

@book{cracraft_origin_1990,
	title = {The origin of the evolutionary novelties -- Pattern and process at different hierarchical levels},
	isbn = {0-226-58695-2},
	author = {Cracraft, J.},
	year = {1990},
	note = {WOS:A1990BU03X00002}
}

@article{futuyma_evolution_1988,
	title = {The evolution of the ecological specialization},
	volume = {19},
	issn = {0066-4162},
	doi = {10.1146/annurev.es.19.110188.001231},
	journal = {Annual Review of Ecology and Systematics},
	author = {Futuyma, D.J. and Moreno, G.},
	year = {1988},
	note = {WOS:A1988R137700009},
	pages = {207--233}
}

@book{givnish_adaptive_1998,
	title = {Adaptive plant evolution on islands: {Classical} patterns, molecular data, new insights},
	isbn = {0-19-850171-4},
	author = {Givnish, Thomas J.},
	editor = {Grant, P. R.},
	year = {1998},
	note = {BCI:BCI199800412732}
}

@article{givnish_molecular_2000,
	title = {Molecular evolution, adaptive radiation, and geographic diversification in the amphiatlantic family {Rapateaceae}: {Evidence} from {ndhF} sequences and morphology},
	volume = {54},
	issn = {0014-3820},
	abstract = {Rapateaceae (16 genera, similar to 100 species) is largely restricted to the tepuis and sandplains of the Guayana Shield in northern South America, with Maschalocephalus endemic to West Africa. The family has undergone extensive radiation in flower form, leaf shape, habit, and habitat. To analyze the evolution of these distributions and traits, we derived a molecular phylogeny for representatives of 14 genera, based on sequence variation in the chloroplast-encoded ndhF gene. The lowland subfamily Rapateoideae is paraphyletic and includes the largely montane subfamily Saxofridericioideae as a monophyletic subset. Overall, the morphological/anatomical data differ significantly from ndhF sequences in phylogenetic structure, but show a high degree of concordance with the molecular tree in three of four tribes. Branch lengths are consistent with the operation of a molecular clock. Maschalocephalus diverges only slightly from other Monotremae: it is the product of relatively recent, long-distance dispersal, not continental drift-only its habitat atop rifted, nutrient-poor sandstones is vicariant. The family appears to have originated approximately 65 Mya in inundated lowlands of the Guayana Shield, followed by: (1) wide geographic spread of lowland taxa along riverine corridors; (2) colonization of Amazonian white-sand savannas in the western Shield; (3) invasion of tepui habitats with frequent speciation, evolution of narrow endemism, and origin of hummingbird pollination in the western Shield; and (4) reinvasion of lowland white-sand savannas. The apparent timing of speciation in the Stegolepis alliance about 6-12 Mya occurred long after the tepuis began to be dissected from each other as the Atlantic rifted approximately 90 Mya. Given the narrow distributions of most montane taxa, this suggests that infrequent long-distance dispersal combined with vicariance accounts for speciation atop tepuis in the Stegolepis alliance.},
	number = {6},
	journal = {Evolution},
	author = {Givnish, T. J. and Evans, T. M. and Zjhra, M. L. and Patterson, T. B. and Berry, P. E. and Sytsma, K. J.},
	month = dec,
	year = {2000},
	note = {WOS:000166682500007},
	pages = {1915--1937}
}

@article{hodges_spurring_1995,
	title = {Spurring plant diversification: {Are} floral nectar spurs a key innovation?},
	volume = {262},
	issn = {0962-8452},
	doi = {10.1098/rspb.1995.0215},
	abstract = {High levels of species diversity in taxonomic groups have often been explained by a key innovation. However, the difficulty in establishing a causal role between a proposed key innovation and increased species diversity, as well as in substantiating that diversity patterns are different from null models has led to major criticisms of key innovation hypotheses. Here we show chat patterns of diversification within and among clades that have evolved floral nectar spurs strongly support the hypothesis that floral nectar spurs represent a key innovation. Both reproductive success and reproductive isolation can be influenced by simple changes in nectar spur morphology and the acquisition of nectar spurs in a wide array of plant groups is highly correlated with increased species diversity.},
	number = {1365},
	journal = {Proceedings of the Royal Society B-Biological Sciences},
	author = {Hodges, S. A. and Arnold, M. L.},
	month = dec,
	year = {1995},
	note = {WOS:A1995TQ73800013},
	pages = {343--348}
}

@article{hunter_key_1998,
	title = {Key innovations and the ecology of macroevolution},
	volume = {13},
	issn = {0169-5347},
	doi = {10.1016/S0169-5347(97)01273-1},
	abstract = {The origin or evolutionary 'success' of taxa is often attributed to key innovations aspects of organismal phenotype that promote diversification. Different ways of delimiting taxa and measuring 'success' (i.e. number or longevity of species, morphological variety or differential control of energy) give rise to different ideas of how key innovations might operate. Key innovations may enhance competitive ability, relax adaptive trade offs or permit exploitation of a new productive resource base. Recent key Innovation studies comparing species richness in extant sister clades may miss important observations possible only with consideration of the fossil record, traditional higher taxa and phenotypic diversity.},
	number = {1},
	journal = {Trends in Ecology \& Evolution},
	author = {Hunter, J. P.},
	month = jan,
	year = {1998},
	note = {WOS:000071133600016},
	pages = {31--36}
}

@article{liem_evolutionary_1973,
	title = {Evolutionary strategies and morphological innovations -- Cichlid pharyngeal jaws},
	volume = {22},
	issn = {0039-7989},
	doi = {10.2307/2412950},
	number = {4},
	journal = {Systematic Zoology},
	author = {Liem, K.F.},
	year = {1973},
	note = {WOS:A1973R919100010},
	pages = {425--441}
}

@article{maia_key_2013,
	title = {Key ornamental innovations facilitate diversification in an avian radiation},
	volume = {110},
	issn = {0027-8424},
	doi = {10.1073/pnas.1220784110},
	abstract = {Patterns of biodiversity are often explained by ecological processes, where traits that promote novel ways of interacting with the environment (key innovations) play a fundamental role in promoting diversification. However, sexual selection and social competition can also promote diversification through rapid evolution of ornamental traits. Because selection can operate only on existing variation, the tendency of ornamental traits to constrain or enable the production of novel phenotypes is a crucial but often overlooked aspect of diversification. Starlings are a speciose group characterized by diverse iridescent colors produced by nanometer-scale arrays of melanin-containing organelles (melanosomes) that play a central role in sexual selection and social competition. We show that evolutionary lability of these colors is associated with both morphological and lineage diversification in African starlings. The solid rod-like melanosome morphology has evolved in a directional manner into three more optically complex forms that can produce a broader range of colors than the ancestral form, resulting in (i) faster color evolution, (ii) the occupation of novel, previously unreachable regions of colorspace, and ultimately (iii) accelerated lineage diversification. As in adaptive radiations, key innovations in ornament production can provide high phenotypic trait variability, leading to dramatic effects on the tempo and mode of diversification.},
	number = {26},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Maia, Rafael and Rubenstein, Dustin R. and Shawkey, Matthew D.},
	month = jun,
	year = {2013},
	note = {WOS:000321503700057},
	pages = {10687--10692}
}

@article{mitter_phylogenetic_1988,
    title = {The phylogenetic study of adaptive zones - Has phytophagy promoted insect diversification},
	%title = {{THE} {PHYLOGENETIC} {STUDY} {OF} {ADAPTIVE} {ZONES} - {HAS} {PHYTOPHAGY} {PROMOTED} {INSECT} {DIVERSIFICATION}},
	volume = {132},
	issn = {0003-0147},
	doi = {10.1086/284840},
	number = {1},
	journal = {American Naturalist},
	author = {Mitter, C. and Farrell, B. and Wiegmann, B.},
	month = jul,
	year = {1988},
	note = {WOS:A1988P824400007},
	pages = {107--128}
}

@article{rabosky2013rates,
  title={Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation},
  author={Rabosky, Daniel L and Santini, Francesco and Eastman, Jonathan and Smith, Stephen A and Sidlauskas, Brian and Chang, Jonathan and Alfaro, Michael E},
  journal={Nature communications},
  volume={4},
  year={2013},
  publisher={Nature Publishing Group}
}

@incollection{rabosky_diversity-dependence_2013,
	title = {Diversity-{Dependence}, {Ecological} {Speciation}, and the {Role} of {Competition} in {Macroevolution}},
	volume = {44},
	isbn = {978-0-8243-1444-6},
	abstract = {Variation in the rate of species diversification underlies many large-scale patterns in the organization of biological diversity. Here, I explore the phenomenon of diversity-dependent diversification and its contribution to differential species proliferation in time and space. Diversity-dependence can be a pattern of asymptotic diversity change through time as well as a process by which interspecific competition influences the dynamics of speciation and extinction. I review the evidence for diversity-dependence as revealed by phylogenies and fossils and discuss the close relationship between diversity-dependence and Darwin's proposed mechanism for the origin of species. An emerging body of research suggests that diversity-dependence contributes to the formation and persistence of incipient species and raises new questions about the meaning of ecological speciation. Diversity-dependence provides a conceptual framework for unifying biodiversity patterns across scales that vary by many orders of magnitude, from the dynamics of geographic range evolution to speciation and adaptive radiation.},
	booktitle = {Annual {Review} of {Ecology}, {Evolution}, and {Systematics}, {Vol} 44},
	author = {Rabosky, Daniel L.},
	editor = {Futuyma, D. J.},
	year = {2013},
	note = {WOS:000329821800023},
	pages = {481--502}
}

@article{rabosky_automatic_2014,
	title = {Automatic {Detection} of {Key} {Innovations}, {Rate} {Shifts}, and {Diversity}-{Dependence} on {Phylogenetic} {Trees}},
	volume = {9},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0089543},
	abstract = {A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify heterogeneous mixtures of dynamic processes within single phylogenies. I developed a method that can identify arbitrary numbers of time-varying diversification processes on phylogenies without specifying their locations in advance. The method uses reversible-jump Markov Chain Monte Carlo to move between model subspaces that vary in the number of distinct diversification regimes. The model assumes that changes in evolutionary regimes occur across the branches of phylogenetic trees under a compound Poisson process and explicitly accounts for rate variation through time and among lineages. Using simulated datasets, I demonstrate that the method can be used to quantify complex mixtures of time-dependent, diversity-dependent, and constant-rate diversification processes. I compared the performance of the method to the MEDUSA model of rate variation among lineages. As an empirical example, I analyzed the history of speciation and extinction during the radiation of modern whales. The method described here will greatly facilitate the exploration of macroevolutionary dynamics across large phylogenetic trees, which may have been shaped by heterogeneous mixtures of distinct evolutionary processes.},
	number = {2},
	journal = {Plos One},
	author = {Rabosky, Daniel L.},
	month = feb,
	year = {2014},
	note = {WOS:000332389000056},
	pages = {e89543}
}

@article{seehausen_cichlid_1997,
	title = {Cichlid fish diversity threatened by eutrophication that curbs sexual selection},
	volume = {277},
	issn = {0036-8075},
	doi = {10.1126/science.277.5333.1808},
	abstract = {Cichlid fish species of Lake Victoria can interbreed without loss of fertility but are sexually isolated by mate choice. Mate choice is determined on the basis of coloration, and strong assortative mating can quickly lead to sexual isolation of color morphs. Dull fish coloration, few color morphs, and low species diversity are found in areas that have become turbid as a result of recent eutrophication, By constraining color vision, turbidity interferes with mate choice, relaxes sexual selection, and blocks the mechanism of reproductive isolation, In this way, human activities that increase turbidity destroy both the mechanism of diversification and that which maintains diversity.},
	number = {5333},
	journal = {Science},
	author = {Seehausen, O. and vanAlphen, J. J. M. and Witte, F.},
	month = sep,
	year = {1997},
	note = {WOS:A1997XX29800043},
	pages = {1808--1811}
}

@article{seehausen_african_2006,
	title = {African cichlid fish: a model system in adaptive radiation research},
	volume = {273},
	issn = {0962-8452},
	doi = {10.1098/rspb.2006.3539},
	abstract = {The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory. The past few years have seen major advances in the phylogenetics, evolutionary biogeography and ecology of cichlid fish.. Most of this work has concentrated on the most diverse radiations. Unfortunately, a large number of small radiations and,non-radiations' have been overlooked, potentially limiting the contribution of the cichlid system to our understanding of speciation and adaptive radiation. I have reviewed the literature to identify 33 intralacustrine radiations and 76 failed radiations. For as many as possible I collected information on lake size, age and phylogenetic relationships. I use these data to address two questions: (i) whether the rate of speciation and the resulting species richness are related to temporal and spatial variation in ecological opportunity and (ii) whether the likelihood of undergoing adaptive radiation is similar for different African cichlid lineages. The former is a key prediction of the ecological theory of adaptive radiation that has been presumed true but remains untested for cichlid radiations. The second is based on the hypothesis that the propensity of cichlids to radiate is due to a key evolutionary innovation shared by all African cichlids. The evidence suggests that speciation rate declines through time as niches get filled up during adaptive radiation: young radiations and early stages of old radiations are characterized by high rates of speciation, whereas at least 0.5 Myr into a radiation speciation becomes a lot less frequent. The number of species in cichlid radiations increases with lake size, supporting the prediction that species diversity increases with habitat heterogeneity, but also with opportunity for isolation by distance. Finally, the data suggest that the propensity to radiate within lakes is a derived property that evolved during the evolutionary history of some African cichlids, and the appearance of which does not coincide with the appearance of proposed key innovations in morphology and life history.},
	number = {1597},
	journal = {Proceedings of the Royal Society B-Biological Sciences},
	author = {Seehausen, Ole},
	month = aug,
	year = {2006},
	note = {WOS:000239728000001},
	pages = {1987--1998}
}

@article{van_oijen_ecological_1982,
	title = {Ecological differentiation among the piscivorous haplochromine cichlids},
	volume = {32},
	issn = {0028-2960},
	number = {3},
	journal = {Netherlands Journal of Zoology},
	author = {Van Oijen, M.J.P},
	year = {1982},
	note = {WOS:A1982PM30400006},
	pages = {336--363}
}

@article{van_rijssel_adaptive_2013,
	title = {Adaptive responses in resurgent {Lake} {Victoria} cichlids over the past 30 years},
	volume = {27},
	issn = {0269-7653},
	doi = {10.1007/s10682-012-9596-9},
	abstract = {Textbook examples of adaptive radiation like the Galapagos finches and the East-African cichlids form a subject of major interest in evolutionary biology. Many of these species often show rapid morphological changes in response to a perturbed environment. The dramatic ecological changes in Lake Victoria during the past three decades, e.g. Nile perch predation and eutrophication, provide a unique opportunity to study environmental effects on cichlid morphology. Preliminary research has revealed that the lake's haplochromines tend to be extremely plastic and sensitive to these environmental changes. So far, long-term ecomorphological studies at short-term intervals are extremely rare. In this study, we examined morphological changes over a},
	number = {2},
	journal = {Evolutionary Ecology},
	author = {van Rijssel, Jacco C. and Witte, Frans},
	month = mar,
	year = {2013},
	note = {WOS:000314524900002},
	pages = {253--267}
}

@article{vermeij_crucibles_2012,
  title={Crucibles of creativity: the geographic origins of tropical molluscan innovations},
  author={Vermeij, Geerat J},
  journal={Evolutionary Ecology},
  volume={26},
  number={2},
  pages={357--373},
  year={2012},
  publisher={Springer}
}

@article{vermeij_ecology_2007,
	title = {The ecology of invasion: acquisition and loss of the siphonal canal in gastropods},
	volume = {33},
	issn = {0094-8373},
	doi = {10.1666/06061.1},
	number = {3},
	journal = {Paleobiology},
	author = {Vermeij, Geerat J.},
	year = {2007},
	note = {WOS:000248471200007},
	pages = {469--493}
}

@article{vermeij_innovation_2001,
	title = {Innovation and evolution at the edge: origins and fates of gastropods with a labral tooth},
	volume = {72},
	issn = {0024-4066},
	doi = {10.1006/bijl.2001.0524},
	abstract = {I combined data from the taxonomy, phylogeny, functional morphology, biogeography, and fossil record of gastropods to probe the origins, distribution, and fates of predatory gastropod clades characterized by the presence of a labral tooth, a downwardly projecting tooth or spine formed at the edge of the outer lip of the shell. A labral tooth occurs in at least 608 species, of which 251 are Recent. Studies of the type and position of the labral tooth, along with other characters, indicate that the labral tooth has evolved independently at least 58 times, beginning in the Campanian epoch of the late Cretaceous. The labral tooth plays a more or less active part in predation on relatively large prey animals that are protected by a hard skeleton. In the Recent fauna, tooth-bearing species are overwhelmingly warm-temperate to tropical in distribution (240 of 251 species; 96\%. Within Muricidae (excluding Coralliophilinae), however, there is no discernible latitudinal gradient in the number of tooth-bearing species relative to total regional diversity. First appearances of clades with a labral tooth are overwhelmingly concentrated in the late Oligocene to Pleistocene interval, with the largest number appearing during the early Miocene (12 clades). The temporal pattern differs significantly from that expected on the basis of the number of faunas available per time interval, and is therefore not an artifact of sampling or fossil preservation. The most consistent factor associated with, and permitting the repeated evolution of, the labral tooth is high planktonic primary productivity. Two factors may account for the link between primary productivity and the evolution of labral teeth: (1) the general economic opportunity afforded by ready availability of an access to nutrients, and (2) the greater abundance and sizes range of available suspension-feeding prey animals. Incumbency-the presence of already well-adapted species-often controls evolutionary opportunity. The complementary distributions of major tooth-bearing clades in many parts of the world point to the role of well-adapted incumbents in limiting the adaptive exploration by other clades that could in principle evolve a labral tooth. The elimination of incumbents by extinction, however, does not provide opportunities for other clades to fill the adaptive void. (C) 2001 The Linnean Society of London.},
	number = {4},
	journal = {Biological Journal of the Linnean Society},
	author = {Vermeij, G. J.},
	month = apr,
	year = {2001},
	note = {WOS:000169007400001},
	pages = {461--508}
}

@article{wainwright_biomechanical_1987,
    title = {Biomechanical limits to ecological performance - mollusk-crushing by the Caribbean hogfish, {\em Lachnolaimus maximus} (Labridae)},
	%title = {{BIOMECHANICAL} {LIMITS} {TO} {ECOLOGICAL} {PERFORMANCE} - {MOLLUSK}-{CRUSHING} {BY} {THE} {CARIBBEAN} {HOGFISH}, {LACHNOLAIMUS}-{MAXIMUS} ({LABRIDAE})},
	volume = {213},
	issn = {0952-8369},
	journal = {Journal of Zoology},
	author = {wainwright, P.C.},
	month = oct,
	year = {1987},
	note = {WOS:A1987K433500010},
	pages = {283--297}
}

@article{wainwright_evolution_2012,
	title = {The {Evolution} of {Pharyngognathy}: {A} {Phylogenetic} and {Functional} {Appraisal} of the {Pharyngeal} {Jaw} {Key} {Innovation} in {Labroid} {Fishes} and {Beyond}},
	volume = {61},
	issn = {1063-5157},
	doi = {10.1093/sysbio/sys060},
	abstract = {The perciform group Labroidei includes approximately 2600 species and comprises some of the most diverse and successful lineages of teleost fishes. Composed of four major clades, Cichlidae, Labridae (wrasses, parrotfishes, and weed whitings), Pomacentridae (damselfishes), and Embiotocidae (surfperches); labroids have been an icon for studies of biodiversity, adaptive radiation, and sexual selection. The success and diversification of labroids have been largely attributed to the presence of a major innovation in the pharyngeal jaw apparatus, pharyngognathy, which is hypothesized to increase feeding capacity and versatility. We present results of large-scale phylogenetic analyses and a survey of pharyngeal jaw functional morphology that allow us to examine the evolution of pharyngognathy in a historical context. Phylogenetic analyses were based on a sample of 188 acanthomorph (spiny-rayed fish) species, primarily percomorphs (perch-like fishes), and DNA sequence data collected from 10 nuclear loci that have been previously used to resolve higher level ray-finned fish relationships. Phylogenies inferred from this dataset using maximum likelihood, Bayesian, and species tree analyses indicate polyphyly of the traditional Labroidei and clearly separate Labridae from the remainder of the traditional labroid lineages (Cichlidae, Embiotocidae, and Pomacentridae). These three "chromide" families grouped within a newly discovered clade of 40 families and more than 4800 species ({\textgreater}27\% of percomorphs and {\textgreater}16\% of all ray-finned fishes), which we name Ovalentaria for its characteristic demersal, adhesive eggs with chorionic filaments. This fantastically diverse clade includes some of the most species-rich lineages of marine and freshwater fishes, including all representatives of the Cichlidae, Embiotocidae, Pomacentridae, Ambassidae, Gobiesocidae, Grammatidae, Mugilidae, Opistognathidae, Pholidichthyidae, Plesiopidae (including Notograptus), Polycentridae, Pseudochromidae, Atherinomorpha, and Blennioidei. Beyond the discovery of Ovalentaria, this study provides a surprising, but well-supported, hypothesis for a convictblenny (Pholidichthys) sister group to the charismatic cichlids and new insights into the evolution of pharyngognathy. Bayesian stochastic mapping ancestral state reconstructions indicate that pharyngognathy has evolved at least six times in percomorphs, including four separate origins in members of the former Labroidei, one origin in the Centrogenyidae, and one origin within Beloniformes. Our analyses indicate that all pharyngognathous fishes have a mechanically efficient biting mechanism enabled by the muscular sling and a single lower jaw element. However, a major distinction exists between Labridae, which lacks the widespread, generalized percomorph pharyngeal biting mechanism, and all other pharyngognathous clades, which possess this generalized biting mechanism in addition to pharyngognathy. Our results reveal a remarkable history of pharyngognathy: far from a single origin, it appears to have evolved at least six times, and its status as a major evolutionary innovation is reinforced by it being a synapomorphy for several independent major radiations, including some of the most species rich and ecologically diverse percomorph clades of coral reef and tropical freshwater fishes, Labridae and Cichlidae.},
	number = {6},
	journal = {Systematic Biology},
	author = {Wainwright, Peter C. and Smith, W. Leo and Price, Samantha A. and Tang, Kevin L. and Sparks, John S. and Ferry, Lara A. and Kuhn, Kristen L. and Eytan, Ron I. and Near, Thomas J.},
	month = dec,
	year = {2012},
	note = {WOS:000310376400007},
	pages = {1001--1027}
}

@article{witte_destruction_1992,
    title = {The destruction of an endemic species flock - quantitatative data on the decline of the haplochromine cichlids of Lake Victoria},
	%title = {{THE} {DESTRUCTION} {OF} {AN} {ENDEMIC} {SPECIES} {FLOCK} - {QUANTITATIVE} {DATA} {ON} {THE} {DECLINE} {OF} {THE} {HAPLOCHROMINE} {CICHLIDS} {OF} {LAKE} {VICTORIA}},
	volume = {34},
	issn = {0378-1909},
	doi = {10.1007/BF00004782},
	abstract = {The Lake Victoria fish fauna included an endemic cichlid flock of more than 300 species. To boost fisheries, Nile perch (Lates sp.) was introduced into the lake in the 1950s. In the early 1980s an explosive increase of this predator was observed. Simultaneously, catches of haplochromines decreased. This paper describes thc species composition of haplochromines in a research area in the Mwanza Gulf of Lake Victoria prior to the Nile perch upsurge. The decline of the haplochromines as a group and the decline of the number of species in various habitats in the Mwanza Gulf was monitored between 1979 and 1990. Of the 123+ species originally caught at a series of sampling stations ca. 80 had disappeared from the catches after 1986. In deepwater regions and in sub-littoral regions haplochromine catches decreased to virtually zero after the Nile perch boom. Haplochromines were still caught in the littoral regions where Nile perch densities were lower. However, a considerable decrease of species occurred in these regions too. It is expected that a remnant of the original haplochromine fauna will survive in the littoral region of the lake. Extrapolation of the data of the Mwanza Gulf to the entire lake would imply that approximately 200 of the 300+ endemic haplochromine species have already disappeared, or are threatened with extinction. Although fishing had an impact on the haplochromine stocks, the main cause of their decline was predation by Nile perch. The speed of decline differed between species and appeared to depend on their abundance and size, and on the degree of habitat overlap with Nile perch. Since the Nile perch upsurge, the food web of Lake Victoria has changed considerably and the total yield of the fishery has increased three to four times. Dramatic declines of native species have also been observed in other lakes as a result of the introduction of alien predators. However, such data concern less speciose communities and, in most cases, the actual process of extinction has not been monitored.},
	number = {1},
	journal = {Environmental Biology of Fishes},
	author = {Witte, F. and Goldschmidt, T. and Wanink, J. and Van Oijen, M.J.P. and Goudswaard, K. and Wittemaas, E. and Bouton, N.},
	month = may,
	year = {1992},
	note = {WOS:A1992HY87100001},
	pages = {1--28}
}

repository: ryneches/dissertation

repo_name: ryneches/dissertation


text:
LICENSE = "LGPL"
DEPENDS = "gupnp"

require gupnp.inc

SRC_URI[md5sum] = "5940df3c1152894685c3fc38ee95fd78"
SRC_URI[sha256sum] = "a909129997f79dcb6d35221ce205854d64c47a7390843e420cfba753485087bd"

inherit autotools pkgconfig

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD


text:
##===-------------------------------------------------------------------------------------------===##
##                        _..._
##                     .-'_..._''.                                    .---._______
##  __  __   ___     .' .'      '.\  .         /|                 .--.|   |\  ___ `'.
## |  |/  `.'   `.  / .'           .'|         ||                 |__||   | ' |--.\  \
## |   .-.  .-.   '. '            <  |         ||                 .--.|   | | |    \  '
## |  |  |  |  |  || |             | |         ||  __             |  ||   | | |     |  '
## |  |  |  |  |  || |             | | .'''-.  ||/'__ '.   _    _ |  ||   | | |     |  |
## |  |  |  |  |  |. '             | |/.'''. \ |:/`  '. ' | '  / ||  ||   | | |     ' .'
## |  |  |  |  |  | \ '.          .|  /    | | ||     | |.' | .' ||  ||   | | |___.' /'
## |__|  |__|  |__|  '. `._____.-'/| |     | | ||\    / '/  | /  ||__||   |/_______.'/
##                     `-.______ / | |     | | |/\'..' /|   `'.  |    '---'\_______|/
##                              `  | '.    | '.'  `'-'` '   .'|  '/
##                                 '---'   '---'         `-'  `--'
##
##  This file is distributed under the MIT License (MIT).
##  See LICENSE.txt for details.
##
##===------------------------------------------------------------------------------------------===##

#.rst:
# FindGridTools
# ----------------
#
# .. code-block:: cmake
#
#   find_package(GridTools [REQUIRED] [QUIET])
#
# Find the GridTools include paths.
#
# Result Variables
# ^^^^^^^^^^^^^^^^
#
# Defines the following variables:
#
# ``GridTools_FOUND``
#   True if GridTools was found.
# ``GRIDTOOLS_INCLUDE_DIRS``
#   Where to find GridTools includes.
#
if( NOT GRIDTOOLS_FOUND )

  find_path( GRIDTOOLS_INCLUDE_DIR
             NAMES gridtools.hpp
             PATHS
                ${CMAKE_INSTALL_PREFIX}
                "${GRIDTOOLS_PATH}"
                "${GRIDTOOLS_ROOT}"
                ENV GRIDTOOLS_PATH
            PATH_SUFFIXES include/gridtools
  )

  include(FindPackageHandleStandardArgs)

  # handle the QUIETLY and REQUIRED arguments and set GRIDTOOLS_FOUND to TRUE
  find_package_handle_standard_args( gridtools DEFAULT_MSG
                                     GRIDTOOLS_INCLUDE_DIR )

  mark_as_advanced( GRIDTOOLS_INCLUDE_DIRS GRIDTOOLS_LIBRARIES )

  set( GridTools_FOUND ${GRIDTOOLS_FOUND} )
  set( GRIDTOOLS_INCLUDE_DIRS
    ${GRIDTOOLS_INCLUDE_DIR}
  )
endif()

repository: MeteoSwiss-APN/mchbuild

repo_name: MeteoSwiss-APN/mchbuild

gha_language: CMake


text:
@InProceedings{Lan_2015_CVPR,
author = {Lan, Zhengzhong and Lin, Ming and Li, Xuanchong and Hauptmann, Alex G. and Raj, Bhiksha},
title = {Beyond Gaussian Pyramid: Multi-Skip Feature Stacking for Action Recognition},
booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR)},
month = {June},
year = {2015}
}

branch_name: refs/heads/main


text:
@Article{machimbarrena_internet_2018,
  title = {Internet Risks: An Overview of Victimization in Cyberbullying, Cyber Dating Abuse, Sexting, Online Grooming and Problematic Internet Use},
  volume = {15},
  issn = {1660-4601},
  shorttitle = {Internet Risks},
  url = {http://www.mdpi.com/1660-4601/15/11/2471},
  doi = {10.3390/ijerph15112471},
  abstract = {The advance of digital media has created risks that affect the bio-psycho-social well-being of adolescents. Some of these risks are cyberbullying, cyber dating abuse, sexting, online grooming and problematic Internet use. These risks have been studied individually or through associations of some of them but they have not been explored conjointly. The main objective is to determine the comorbidity between the described Internet risks and to identify the profiles of victimized adolescents. An analytical and cross-sectional study with 3212 participants (46.3% males) from 22 Spanish schools was carried out. Mean age was 13.92 ± 1.44 years (range 11–21). Assessment tools with adequate standards of reliability and validity were used. The main results indicate that the most prevalent single risk is cyberbullying victimization (30.27%). The most prevalent two-risk associations are cyberbullying-online grooming (12.61%) and cyberbullying-sexting (5.79%). The three-risk combination of cyberbullying-sexting-grooming (7.12%) is highlighted, while 5.49% of the adolescents present all the risks. In addition, four profiles are distinguished, with the profile Sexualized risk behaviour standing out, with high scores in grooming and sexting and low scores in the rest of the risks. Determining the comorbidity of risks is useful for clinical and educational interventions, as it can provide information about additional risks.},
  language = {en},
  number = {11},
  urldate = {2020-01-23},
  journal = {International Journal of Environmental Research and Public Health},
  author = {Juan Manuel Machimbarrena and Esther Calvete and Liria Fernandez-Gonzalez and Aitor alvarez-Bardon and Lourdes alvarez-Fernandez and Joaquin Gonzalez-Cabrera},
  month = {nov},
  year = {2018},
  pages = {2471},
  file = {Machimbarrena et al. - 2018 - Internet Risks An Overview of Victimization in Cy.pdf:C\:\\Users\\mmach\\Zotero\\storage\\2C6EMWUK\\Machimbarrena et al. - 2018 - Internet Risks An Overview of Victimization in Cy.pdf:application/pdf},
  pubtype = {2},
}

repository: mmachimbarrena/Pruebaweb

repo_name: mmachimbarrena/Pruebaweb


text:
add_library(module-header)
target_sources(module-header
  INTERFACE
    FILE_SET fs TYPE CXX_MODULE_HEADER_UNITS FILES
      sources/module-header.h)
target_compile_features(module-header
  PRIVATE
    cxx_std_20)

repository: JKorbelRA/CMake

repo_name: JKorbelRA/CMake

gha_license_id: NOASSERTION

gha_language: C


text:
package netlib

import (
	"math"
	"errors"
	"time"

	"github.com/idealeak/goserver.v2/core/logger"
	"github.com/idealeak/goserver.v2/core/module"
	"github.com/idealeak/goserver.v2/core/profile"
	"github.com/idealeak/goserver.v2/core/utils"
)

const (
	IoServiceMaxCount int = 10
)

var (
	NetModule = newNetEngine()
)

type NetEngine struct {
	pool     map[int]ioService
	childAck chan int
	quit     bool
	reaped   bool
}

func newNetEngine() *NetEngine {
	e := &NetEngine{
		pool:     make(map[int]ioService),
		childAck: make(chan int, IoServiceMaxCount),
	}

	return e
}

func (e *NetEngine) newIoService(sc *SessionConfig) ioService {
	var s ioService
	if sc.IsClient {
		if !sc.AllowMultiConn && ConnectorMgr.IsConnecting(sc) {
			return nil
		}
		if sc.Protocol == "ws" {
			s = newWsConnector(e, sc)
		} else {
			s = newTcpConnector(e, sc)
		}
	} else {
		if sc.Protocol == "ws" {
			s = newWsAcceptor(e, sc)
		} else {
			s = newTcpAcceptor(e, sc)
		}
	}
	return s
}

func (e *NetEngine) GetAcceptors() []Acceptor {
	acceptors := make([]Acceptor, 0, len(e.pool))
	for _, v := range e.pool {
		if a, is := v.(Acceptor); is {
			acceptors = append(acceptors, a)
		}
	}

	return acceptors
}

func (e *NetEngine) Connect(sc *SessionConfig) error {
	if e.quit {
		return errors.New("NetEngine already quiting")
	}
	SendStartNetIoService(sc)
	return nil
}

func (e *NetEngine) Listen(sc *SessionConfig) error {
	if e.quit {
		return errors.New("NetEngine already quiting")
	}
	SendStartNetIoService(sc)
	return nil
}

func (e *NetEngine) ShutConnector(ip string, port int) {
	for _, v := range e.pool {
		if c, is := v.(Connector); is {
			sc := c.GetSessionConfig()
			if sc.Ip == ip && sc.Port == port {
				c.shutdown()
				return
			}
		}
	}
}

////////////////////////////////////////////////////////////////////
/// Module Implement [beg]
////////////////////////////////////////////////////////////////////
func (e *NetEngine) ModuleName() string {
	return module.ModuleName_Net
}

func (e *NetEngine) Init() {
	var err error
	for i := 0; i < len(Config.IoServices); i++ {
		s := e.newIoService(&Config.IoServices[i])
		if s != nil {
			e.pool[Config.IoServices[i].Id] = s
			err = s.start()
			if err != nil {
				logger.Logger.Error(err)
			}
		}
	}

	//time.AfterFunc(time.Minute*5, func() { e.dump() })
}

func (e *NetEngine) Update() {
	defer utils.DumpStackIfPanic("NetEngine.Update")

	watch := profile.TimeStatisticMgr.WatchStart(e.ModuleName())
	defer watch.Stop()

	e.clearClosedIo()

	for _, v := range e.pool {
		v.update()
	}
}

func (e *NetEngine) Shutdown() {
	if e.quit {
		return
	}

	e.quit = true

	if len(e.pool) > 0 {
		for _, v := range e.pool {
			v.shutdown()
		}
		go e.reapRoutine()
	} else {
		e.destroy()
	}
}

////////////////////////////////////////////////////////////////////
/// Module Implement [end]
////////////////////////////////////////////////////////////////////

func (e *NetEngine) clearClosedIo() {
	for {
		select {
		case k := <-e.childAck:
			delete(e.pool, k)
		default:
			return
		}
	}
}

func (e *NetEngine) reapRoutine() {
	if e.reaped {
		return
	}

	e.reaped = true

	for {
		select {
		case k := <-e.childAck:
			delete(e.pool, k)
			if len(e.pool) == 0 {
				e.destroy()
				return
			}
		}
	}
}

func (e *NetEngine) destroy() {
	module.UnregisteModule(e)
}

func (e *NetEngine) dump() {
	for _, v := range e.pool {
		v.dump()
	}
	time.AfterFunc(time.Minute*5, func() { e.dump() })
}
func init() {
	module.RegisteModule(NetModule, 0, math.MaxInt32)
}

func Connect(sc *SessionConfig) error {
	return NetModule.Connect(sc)
}

func Listen(sc *SessionConfig) error {
	return NetModule.Listen(sc)
}

func GetAcceptors() []Acceptor {
	return NetModule.GetAcceptors()
}

func ShutConnector(ip string, port int) {
	NetModule.ShutConnector(ip, port)
}

repository: konser/go-pack

repo_name: konser/go-pack


text:
@Article{lavallee_identification_2016,
  title = {Identification of {MYC} mutations in acute myeloid leukemias with {NUP98}-{NSD1} translocations},
  volume = {30},
  doi = {10.1038/leu.2016.19},
  number = {7},
  journal = {Leukemia},
  author = {V. P. Lavall{\a'e}e and S. Lemieux and G. Boucher and P. Gendron and I. Boivin and S. Girard and J. H{\a'e}bert and G. Sauvageau},
  year = {2016},
  note = {Type: Journal Article},
  pages = {1621--4},
  issn = {0887-6924},
  date = {2016-01-01},
}


text:
@article{lewis2016improved,
 author = {Lewis, Richard A and Fan, Ailin},
 journal = {Statistics in Biopharmaceutical Research},
 number = {1},
 pages = {40--48},
 publisher = {Taylor & Francis},
 title = {Improved acceptance limits for ASTM Standard E2810},
 volume = {8},
 year = {2016}
}

repository: ailinf/academic-kickstart

repo_name: ailinf/academic-kickstart


text:
SUMMARY = "rebar is an Erlang build tool that makes it easy to compile and test Erlang applications, port drivers and releases."
DESCRIPTION = "rebar is a self-contained Erlang script, so it's easy to distribute or even embed directly in a project. Where possible, rebar uses standard Erlang/OTP conventions for project structures, thus minimizing the amount of build configuration work. rebar also provides dependency management, enabling application writers to easily re-use common libraries from a variety of locations (git, hg, etc)."
LICENSE = "Apache-2.0"
LIC_FILES_CHKSUM = "file://LICENSE;md5=ff253ad767462c46be284da12dda33e8"

S = "${WORKDIR}/git"
SRCREV = "365ac649dc818619757f96a699ddb174f004cff9"
PV = "2.6.1-git${SRCPV}"
PR = "r0"

SRC_URI = "git://github.com/rebar/rebar;branch=master"

DEPENDS += "erlang-native"

do_compile () {
    ./bootstrap
}

do_install() {
        install -d 0755 ${D}/${bindir}
	install -m 0755 ${S}/rebar ${D}/${bindir}/rebar
}

FILES_${PN} = "${bindir}"
FILES_${PN}-dbg += "/.debug"

BBCLASSEXTEND = "native nativesdk"

repository: Seept/meta-erlang

repo_name: Seept/meta-erlang


text:
SUMMARY = "User configurable main windows"
LICENSE = "GPLv2 | LGPLv2.1"
LIC_FILES_CHKSUM = " \
	file://COPYING;md5=5c213a7de3f013310bd272cdb6eb7a24 \
	file://COPYING.LIB;md5=2d5025d4aa3495befef8f17206a5b0a1 \
"

inherit kde-kf5

DEPENDS += " \
    kitemviews \
    kconfig \
    kconfig-native \
    kglobalaccel \
    kconfigwidgets \
    ki18n \
    kiconthemes \
    ktextwidgets \
    kwidgetsaddons \
    kwindowsystem \
    attica \
    kcoreaddons-native \
    kauth-native \
    sonnet-native \
    gettext-native \
"

PV = "${KF5_VERSION}"
SRC_URI[md5sum] = "009205833a4135eee008b6ea55833bb2"
SRC_URI[sha256sum] = "cad50edb7692432adbd402dc1220b4b621acc1882987e8332bccf2a17cd14f73"

# REVISIT remove ugly hack for wayland-only environments
SRC_URI += " \
    file://0001-no-session-management-if-not-supported-by-qtbase-ind.patch \
"

EXTRA_OECMAKE += "-DBUILD_TESTING=OFF"

# evt. put ksendbugmail to separate package later
FILES_${PN}-dbg += "${libdir}/kxmlgui/kf5/.debug/"


text:
SUMMARY = "A Cross Platform and Open Source Electronics Design Automation Suite"
LICENSE = "LGPLv2.1 & OCCT_LGPL_EXCEPTION"
LIC_FILES_CHKSUM = " \
    file://LICENSE_LGPL_21.txt;md5=6ab17b41640564434dda85c06b7124f7 \
    file://OCCT_LGPL_EXCEPTION.txt;md5=509623a9302457aa45a3621bf7ca591c \
"

DEPENDS = " \
    doxygen-native \
    tcl-native \
    freetype \
    tk \
    ffmpeg \
    tbb \
    vtk \
"

inherit cmake features_check

REQUIRED_DISTRO_FEATURES = "opengl x11"

SRC_URI = " \
    git://github.com/Open-Cascade-SAS/OCCT.git \
    file://0001-Steal-some-fixes.patch \
"
SRCREV = "628c0211d53c7fe1036a85e7a7b2b067c9c50f7a"
PV = "7.5.0"
S = "${WORKDIR}/git"

VTKVER = "9.0"

EXTRA_OECMAKE = " \
    -DCMAKE_BUILD_TYPE=RelWithDebInfo \
    -D3RDPARTY_VTK_INCLUDE_DIR=${STAGING_INCDIR}/vtk-${VTKVER} \
    -D3RDPARTY_VTK_LIBRARY_DIR=${STAGING_LIBDIR} \
    -DUSE_FFMPEG=ON \
    -DUSE_TBB=ON \
    -DUSE_VTK=ON \
"

RDEPENDS_${PN} += "bash tk-lib"

repository: pschneiders/meta-microcontroller

repo_name: pschneiders/meta-microcontroller


text:
@misc{gutierrez2019systems,
  title={Systems, methods and, media for encoding and decoding signals used in time of flight imaging},
  author={Gutierrez, Felipe and Gupta, Mohit and Velten, Andreas and Breitbach, Eric and Nayar, Shree K},
  year={2019},
  publisher={Google Patents},
  note={US Patent App. 15/699,623}
  abstract={In accordance with some embodiments, systems, methods and media for encoding and decoding signals used in time-of-flight imaging are provided. In some embodiments, a method for estimating the depth of a scene is provided, comprising: causing a light source to emit modulated light toward the scene based on a modulation function; causing the image sensor to generate a first value based on the modulated light and a first demodulation function of K modulation functions; causing the image sensor to generate a second value; causing the image sensor to generate a third value; and determining a depth estimate for the portion of the scene based on the first value, the second value, the third value, and three correlation functions each including at least one half of a trapezoid wave.}
}

gha_language: TeX


text:
@inproceedings{2015InformationEF,
  title={Information extraction from clinical texts in Russian},
  author={Shelmanov Artem, Smirnov Ivan, Vishneva Elena},
  year={2015}
}


text:
require recipes-graphics/xorg-driver/xorg-driver-video.inc
DESCRIPTION = "X.Org X server -- Glamo display driver with KMS support"
DEPENDS += "libdrm"
RDEPENDS_${PN} += "xserver-xorg-module-exa"

LIC_FILES_CHKSUM = "file://COPYING;md5=d8cbd99fff773f92e844948f74ef0df8"

PE = "2"
PV = "1.0.0+gitr${SRCPV}"
PR = "${INC_PR}.4"

SRC_URI = "git://git.openmoko.org/git/xf86-video-glamo.git;branch=master \
           file://0001-glamo-kms-driver-drop-unused-xf86_config.patch \
           file://0001-fix-build-with-KMS-disabled.patch \
           file://0003-glamo-driver-adapt-to-xserver-0.13-video-API.patch \
           file://0001-glamo-driver-remove-references-to-mibstore.patch \
"

S = "${WORKDIR}/git"
SRCREV = "cb9ed17035a79e49dde26a1e7e2bc5f10fd8144b"

EXTRA_OECONF = " --disable-kms "

repository: ExorEmbedded/exor-workspace

repo_name: ExorEmbedded/exor-workspace

gha_language: Python


text:
package live

import "github.com/BPing/aliyun-live-go-sdk/aliyun"

// ---------------------------------------------------------------------------------------------------------------------
// 直播基本信息
type LiveBase struct {
	DomainName string `json:"DomainName" xml:"DomainName"` //    加速域名
	AppName    string `json:"AppName" xml:"AppName"`       //	应用名称
}

// 流基本信息
type StreamBase struct {
	LiveBase
	StreamName string //	直播流名称
}

// 在线
// ---------------------------------------------------------------------------------------------------------------------
type OnlineInfoResponse struct {
	aliyun.Response
	OnlineUserInfo  OnlineUserInfo
	TotalUserNumber int64
}

type OnlineUserInfo struct {
	LiveStreamOnlineUserNumInfo []LiveStreamOnlineInfo
}

type LiveStreamOnlineInfo struct {
	DomainName  string //
	AppName     string //
	StreamName  string //
	PublishTime string //
	PublishUrl  string //
}

// 黑名单
// ---------------------------------------------------------------------------------------------------------------------
type StreamListResponse struct {
	aliyun.Response
	DomainName string     //流所属加速域名
	StreamUrls StreamUrls //	流完整URL地址
}

type StreamUrls struct {
	StreamUrl []string
}

// ---------------------------------------------------------------------------------------------------------------------

// 直播流的操作记录
type LiveStreamControlInfo struct {
	StreamName string //	流的名字
	ClientIP   string //	用户端的IP地址
	Action     string //	执行的操作名称
	TimeStamp  string //	操作执行的时间 UTC时间
}

// RTMP直播流的在线人数
type OnlineUserNum struct {
	TotalUserNumber int64                         //	所有流的用户数总和
	OnlineUserInfo  []LiveStreamOnlineUserNumInfo //每条直播流的用户数信息
}

type LiveStreamOnlineUserNumInfo struct {
	StreamUrl  string //直播流的URL
	UserNumber int64  //	直播流的在线人数
}

// ---------------------------------------------------------------------------------------------------------------------

// 对象存储oss信息
type OssInfo struct {
	OssEndpoint     string //	oss endpoint，如：oss-cn-hangzhou.aliyuncs.com，详细请参照oss相关文档
	OssBucket       string //	oss存储bucket名称
	OssObject       string //	oss存储的录制文件名
	OssObjectPrefix string //	oss存储文件名，支持变量匹配，包含{AppName}、{StreamName}、{UnixTimestamp}、{Sequence}，如：record/live/{StreamName}/{UnixTimestamp}_{Sequence}
}

// ---------------------------------------------------------------------------------------------------------------------

// 录制配置
type LiveAppRecord struct {
	LiveBase
	OssInfo
	CreateTime string
}

// 录制
// ---------------------------------------------------------------------------------------------------------------------

type FrameRateAndBitRateInfosResponse struct {
	aliyun.Response
	FrameRateAndBitRateInfos FrameRateAndBitRateInfos
}

type FrameRateAndBitRateInfos struct {
	FrameRateAndBitRateInfo []FrameRateAndBitRateInfo
}

// 各直播流的帧率/码率信息
type FrameRateAndBitRateInfo struct {
	StreamUrl      string // 直播流的URL
	VideoFrameRate int    // 直播流的视频帧率
	AudioFrameRate int    // 直播流的音频帧率
	BitRate        int    // 直播流的码率
}

// ---------------------------------------------------------------------------------------------------------------------

// 录制配置列表
type RecordIndexInfoListResponse struct {
	aliyun.Response
	RecordIndexInfoList RecordIndexInfoList
}

type RecordInfoListResponse struct {
	aliyun.Response
	RecordInfoList RecordInfoList
}

// 录制配置单个
type RecordIndexInfoResponse struct {
	aliyun.Response
	RecordIndexInfo RecordIndexInfo
}

type RecordInfoResponse struct {
	aliyun.Response
	RecordInfo RecordInfo
}

type RecordIndexInfoList struct {
	RecordIndexInfo []RecordIndexInfo
}

type RecordInfoList struct {
	RecordIndexInfo []RecordInfo
}

type RecordInfo struct {
	RecordIndexInfo
}

//RecordId	String	索引文件Id
//RecordUrl	String	索引文件地址
//DomainName	String	流所属加速域名
//AppName	String	流所属应用名称
//StreamName	String	直播流名称
//OssEndpoint	String	oss endpoit
//OssBucket	String	oss存储bucket名称
//OssObject	String	oss存储的录制文件名
//CreateTime	String	创建时间
//StartTime	String	开始时间，格式：2015-12-01T17:36:00Z
//EndTime	String	结束时间，格式：2015-12-01T17:36:00Z
//Duration	String	录制时长，单位：秒
//Height	String	视频高
//Width	String	视频宽
//CreateTime	String	创建时间

// 录制配置信息
type RecordIndexInfo struct {
	StreamBase
	OssInfo          //oss存储
	RecordId  string //	索引文件Id
	RecordUrl string //	索引文件地址
	//OssObject  string //	oss存储的录制文件名 包含在OssInfo
	Height     string //	视频高
	Width      string //	视频宽
	CreateTime string //    创建时间
	StartTime  string //	开始时间，格式：2015-12-01T17:36:00Z
	EndTime    string //	结束时间，格式：2015-12-01T17:36:00Z
	Duration   string //	录制时长
}

// ---------------------------------------------------------------------------------------------------------------------

type RecordContentInfoListResponse struct {
	aliyun.Response
	RecordContentInfoList RecordContentInfoList
}

// 录制内容列表
type RecordContentInfoList struct {
	RecordContentInfo []RecordContentInfo
}

type RecordContentInfo struct {
	OssInfo
	StartTime string `json:"StartTime" xml:"StartTime"` //	开始时间，格式：2015-12-01T17:36:00Z
	EndTime   string `json:"EndTime" xml:"EndTime"`     //	结束时间，格式：2015-12-01T17:36:00Z
	Duration  string `json:"Duration" xml:"Duration"`   //	录制时长
}

// ---------------------------------------------------------------------------------------------------------------------

// 截图配置(参数)
type SnapshotConfig struct {
	OssInfo
	TimeInterval       int    `json:"TimeInterval" xml:"TimeInterval"`             // 截图周期
	OverwriteOssObject string `json:"OverwriteOssObject" xml:"OverwriteOssObject"` //oss存储文件名
	SequenceOssObject  string `json:"SequenceOssObject" xml:"SequenceOssObject"`   //oss存储文件名
}

// 查询域名下的截图配置返回结构
type LiveSnapshotConfigResponse struct {
	aliyun.Response
	LiveSnapshotParam
	LiveStreamSnapshotConfigList struct {
		LiveStreamSnapshotConfig []LiveStreamSnapshotConfig `json:"LiveStreamSnapshotConfig" xml:"LiveStreamSnapshotConfig"`
	} `json:"LiveStreamSnapshotConfigList" xml:"LiveStreamSnapshotConfigList"` //	截图配置
	TotalPage int `json:"TotalPage" xml:"TotalPage"` //	总页数
	TotalNum  int `json:"TotalNum" xml:"TotalNum"`   //	符合条件的总个数
}

// 查询域名下的截图配置参数
type LiveSnapshotParam struct {
	PageNum  int    `json:"PageNum" xml:"PageNum"`   //    分页的页码
	PageSize int    `json:"PageSize" xml:"PageSize"` //	每页大小
	Order    string `json:"Order" xml:"Order"`
}

type LiveStreamSnapshotConfig struct {
	LiveBase
	SnapshotConfig
	CreateTime string `json:"CreateTime" xml:"CreateTime"` //创建时间
}

// 查询截图信息
type StreamSnapshotInfoResponse struct {
	aliyun.Response
	LiveStreamSnapshotInfoList struct {
		StreamSnapshotInfo []StreamSnapshotInfo `json:"StreamSnapshotInfo" xml:"StreamSnapshotInfo"`
	} `json:"LiveStreamSnapshotInfoList" xml:"LiveStreamSnapshotInfoList"` //截图内容列表，没有则返回空数组
	NextStartTime string `json:"NextStartTime" xml:"NextStartTime"` //
}

// 单个截图数据类型
type StreamSnapshotInfo struct {
	OssInfo
	CreateTime string `json:"CreateTime" xml:"CreateTime"` //截图产生时间，格式：2015-12-01T17:36:00Z
}

// ---------------------------------------------------------------------------------------------------------------------
// 转码配置信息返回结构体
type StreamTranscodeInfoResponse struct {
	aliyun.Response
	DomainTranscodeList struct {
		DomainTranscodeInfo []DomainTranscodeInfo `json:"DomainTranscodeInfo" xml:"DomainTranscodeInfo"`
	} `json:"DomainTranscodeList" xml:"DomainTranscodeList"` //转码配置信息
}

type DomainTranscodeInfo struct {
	TranscodeName     string `json:"TranscodeName" xml:"TranscodeName"`         //	播放域名
	TranscodeApp      string `json:"TranscodeApp" xml:"TranscodeApp"`           //	应用名称
	TranscodeId       string `json:"TranscodeId" xml:"TranscodeId"`             //	数据库ID
	TranscodeTemplate string `json:"TranscodeTemplate" xml:"TranscodeTemplate"` //	转码模版
	TranscodeSnapshot string `json:"TranscodeSnapshot" xml:"TranscodeSnapshot"` //	是否实施截图
	TranscodeRecord   string `json:"TranscodeRecord" xml:"TranscodeRecord"`     //	是否实施录制
}

// ---------------------------------------------------------------------------------------------------------------------

// 混流信息返回结构体
type MixStreamsInfoResponse struct {
	aliyun.Response
	MixStreamsInfoList MixStreamsInfoList `json:"MixStreamsInfoList" xml:"MixStreamsInfoList"`
}

type MixStreamsInfoList struct {
	MixStreamsInfo []MixStreamsInfo `json:"MixStreamsInfo" xml:"MixStreamsInfo"`
}

type MixStreamsInfo struct {
	StreamBase
}

// ---------------------------------------------------------------------------------------------------------------------

// 拉流
// https://help.aliyun.com/document_detail/57733.html?spm=5176.doc57735.6.658.58h5BX
type PullStreamConfigResponse struct {
	aliyun.Response
	LiveAppRecordList AppRecordList `json:"LiveAppRecordList" xml:"LiveAppRecordList"`
}

type AppRecordList struct {
	LiveAppRecord []AppRecord `json:"LiveAppRecord" xml:"LiveAppRecord"`
}

type AppRecord struct {
	StreamBase
	SourceUrl string `json:"SourceUrl" xml:"SourceUrl"` // 	拉流源站
	StartTime string `json:"StartTime" xml:"StartTime"`
	EndTime   string `json:"EndTime" xml:"EndTime"`
}

// ---------------------------------------------------------------------------------------------------------------------

// 状态通知
type NotifyUrlConfigResponse struct {
	aliyun.Response
	NotifyUrlConfig struct {
		DomainName string `json:"DomainName" xml:"DomainName"` //    加速域名
		NotifyUrl  string `json:"NotifyUrl" xml:"NotifyUrl"`   //    回调地址
	}
}

// ---------------------------------------------------------------------------------------------------------------------

type MixNotifyConfigResponse struct {
	aliyun.Response
	NotifyUrl string `json:"NotifyUrl" xml:"NotifyUrl"` //    当前域名下连麦回调通知URL
}

repository: admpub/aliyun-live-go-sdk

repo_name: admpub/aliyun-live-go-sdk


text:
LINUX_VERSION ?= "4.1.0"

SRCREV = "0dd4dae3071d135836946ab1b990061c0899e9b5"
SRC_URI = "\
     git://github.com/raspberrypi/linux.git;protocol=git;branch=rpi-4.1.y \
     file://0001-bcm2835-Added-spi0-for-OpenLabs-802.15.4-chip-in-rpi.patch \
     file://0002-bcm2835-Added-spi0-for-OpenLabs-802.15.4-chip-in-rpi.patch \
     file://0001-bcm2708-Added-spi0-for-OpenLabs-802.15.4-chip.patch \
     file://0002-bcm2709-Added-spi0-for-OpenLabs-802.15.4-chip.patch \
     file://wpan.cfg \
"

do_kernel_configme_append() {
	# wpan.cfg does not seem to go into .config, so append wpan.cfg into
	# defconfig instead. This is probably not the right way to do it thou.
	cat ${WORKDIR}/wpan.cfg >> ${WORKDIR}/defconfig
}

do_install_prepend() {
	if [ -n "${KERNEL_DEVICETREE}" ]; then
		mkdir -p ${B}/arch/${ARCH}/boot/dts/overlays
	fi
}

# The linux-raspberrypi.inc file is found in meta-raspberrypi layer
# which is here git://git.yoctoproject.org/meta-raspberrypi
require recipes-kernel/linux/linux-raspberrypi.inc

repository: olegcherpak/meta-eca

repo_name: olegcherpak/meta-eca


text:
DESCRIPTION = "System::Image::Update::WebUI helps keeping up-to-date on embedded systems"

SECTION = "libs"
LICENSE = "Artistic-2.0"
PR = "r0"

MAINTAINER=	"Jens Rehsack <sno@netbsd.org>"
HOMEPAGE=	"https://github.com/rehsack/System-Image-Update-WebUI"

LIC_FILES_CHKSUM = "file://${COMMON_LICENSE_DIR}/Artistic-2.0;md5=8bbc66f0ba93cec26ef526117e280266 \
"

SRCREV="1ed79d5075037b3fdc26fab02ebd1f318b9c8121"

SRC_URI = "git://github.com/rehsack/System-Image-Update-WebUI.git \
           file://webui-run \
	   file://system-image-update-web.json \
	   file://system-image-update-web.conf \
"

inherit supervised record-installed-query system-image-update

PACKAGECONFIG ??= ""

PROVIDES:append = " ${PN}-nginx-proxy"
PACKAGES =+ "${PN}-nginx-proxy"
PACKAGECONFIG[nginx-proxy] = ""

RDEPENDS_${PN} += "system-image-update"

RDEPENDS_${PN} += "dancer2-perl"
RDEPENDS_${PN} += "datetime-format-duration-perl"
RDEPENDS_${PN} += "encode-perl"
RDEPENDS_${PN} += "file-find-rule-perl"
RDEPENDS_${PN} += "file-slurper-perl"
RDEPENDS_${PN} += "file-touch-perl"
RDEPENDS_${PN} += "hash-merge-perl"
RDEPENDS_${PN} += "hash-moreutils-perl"
RDEPENDS_${PN} += "http-tiny-perl"
RDEPENDS_${PN} += "json-perl"
RDEPENDS_${PN} += "module-pluggable-perl"
RDEPENDS_${PN} += "moo-perl"
RDEPENDS_${PN} += "namespace-clean-perl"
RDEPENDS_${PN} += "net-async-http-server-perl"
RDEPENDS_${PN} += "net-dns-perl"
RDEPENDS_${PN} += "netaddr-ip-perl"
RDEPENDS_${PN} += "perl-modules"
RDEPENDS_${PN} += "plack-perl"
RDEPENDS_${PN} += "scalar-list-utils-perl"
RDEPENDS_${PN} += "template-toolkit-perl"
RDEPENDS_${PN} += "unix-statgrab-perl"
RDEPENDS_${PN} += "yaml-libyaml-perl"

RDEPENDS_${PN} += "${@bb.utils.contains("PACKAGECONFIG", 'nginx-proxy', ' ${PN}-nginx-proxy ', '', d )}"

RDEPENDS_${PN}-dev += "devel-cycle-perl"
RDEPENDS_${PN}-dev += "devel-leak-object-perl"
RDEPENDS_${PN}-dev += "devel-stacktrace-perl"
RDEPENDS_${PN}-dev += "test-leaktrace-perl"
RDEPENDS_${PN}-dev += "test-memory-cycle-perl"

RDEPENDS_${PN}-nginx-proxy += "nginx"

SERVICE_NAME = "sysimg-update-webui"
SERVICE_RUN_SCRIPT_NAME_${PN} = "webui-run"
SERVICE_LOG_SCRIPT_NAME = "log.run"

SYSUPDATE_WEBUI_BASE ?= "/opt/${DISTRO}/${SERVICE_NAME}"

do_compile() {
	set -x
	sed -i -e "s,@SERVICE_NAME[@],${SERVICE_NAME},g" -e "s,@SYSUPDATE_WEBUI_BASE[@],${SYSUPDATE_WEBUI_BASE},g" \
	    -e "s,@SYSTEM_IMAGE_UPDATE_STATE_DIR[@],${SYSTEM_IMAGE_UPDATE_STATE_DIR},g" \
	    -e "s,@RECORD_INSTALLED_DEST[@],${RECORD_INSTALLED_DEST},g" \
	    ${WORKDIR}/webui-run
}

do_install() {
	set -x

	install -d -m 755 ${D}${sysconfdir}
	install -m 0644 ${WORKDIR}/system-image-update-web.json ${D}${sysconfdir}

	# create directory for source
	install -d ${D}${SYSUPDATE_WEBUI_BASE}

	# copy source
	(cd ${WORKDIR}/git && tar cf - bin config.yml environments lib public t views) | (cd ${D}${SYSUPDATE_WEBUI_BASE} && tar xf -)
	chown -R root:root ${D}${SYSUPDATE_WEBUI_BASE}

	install -d ${D}${sysconfdir}/nginx/conf.d/
	install -m 0644 ${WORKDIR}/system-image-update-web.conf ${D}${sysconfdir}/nginx/conf.d/
}

FILES_${PN}-nginx-proxy = "${sysconfdir}/nginx/conf.d/"
FILES_${PN}-dev += "${SYSUPDATE_WEBUI_BASE}/t"
FILES_${PN} += "${SYSUPDATE_WEBUI_BASE}"
FILES_${PN} += "${sysconfdir}"

BBCLASSEXTEND = "native"

repository: rehsack/meta-jens

repo_name: rehsack/meta-jens


text:
hunter_config(
    CURL
    VERSION ${HUNTER_CURL_VERSION}
    CMAKE_ARGS CMAKE_USE_BORINGSSL=ON
)

repository: cpp-pm/hunter

repo_name: cpp-pm/hunter


text:
@article{DeBofsky-2020-Differential,
    title = "Differential responses of gut microbiota of male and female fathead minnow (Pimephales promelas) to a short-term environmentally-relevant, aqueous exposure to benzo[a]pyrene",
    author = "DeBofsky, Abigail  and
      Xie, Yuwei  and
      Grimard, Chelsea  and
      Alcaraz, Alper James  and
      Brinkmann, Markus  and
      Hecker, Markus  and
      Giesy, John P.",
    journal = "Chemosphere, Volume 252",
    volume = "252",
    year = "2020",
    publisher = "Elsevier BV",
    url = "https://aclanthology.org/G20-69001",
    doi = "10.1016/j.chemosphere.2020.126461",
    pages = "126461",
}

repository: gwf-uwaterloo/gwf-publications

repo_name: gwf-uwaterloo/gwf-publications


text:
require bijin-assets.inc

SRC_URI[md5sum] = "65f0883878a0be36f7d83c5652708b1a"
SRC_URI[sha256sum] = "0bf2539bf8dc15617ba4c427a168c32fa1eaba70676f77d2c1adaa08db4627c8"


text:
SUMMARY = "Opusfile support library"
DESCRIPTION = "Opusfile provides application developers with a high-level API for decoding and seeking in .opus files. \
DLLs for the required libraries libogg 1.3.2, libopus 1.1.1 and openssl, are also included in the binary package. \
"

HOMEPAGE = "http://www.opus-codec.org"
SECTION = "libs/multimedia"

LICENSE = "BSD"
LIC_FILES_CHKSUM = "file://COPYING;md5=6ac22b992dde6a891f8949c3e2da8576"

SRC_URI = "https://archive.mozilla.org/pub/opus/opusfile-${PV}.tar.gz"

SRC_URI[md5sum] = "a08a6735476516d60fb226ad9ae191ff"
SRC_URI[sha256sum] = "f75fb500e40b122775ac1a71ad80c4477698842a8fe9da4a1b4a1a9f16e4e979"

DEPENDS = "libogg libopus openssl"

inherit autotools pkgconfig

repository: fgpolito/meta-clik

repo_name: fgpolito/meta-clik


text:
package version

var (
	Version            = "2.3.0"
	IntegreatlyVersion = "2.3.0"
)

repository: wtrocki/integreatly-operator

repo_name: wtrocki/integreatly-operator


text:
SECTION = "devel/chicken"
DESCRIPTION = "Chicken bindings for Cairo, a vector graphics library"
LICENSE = "LGPL-2.1"
LIC_FILES_CHKSUM = "file://cairo.meta;md5=cf2ed7913ed45c0b287e33d3c06bf3ed"
DEPENDS_append_class-cross = " cairo-native"
DEPENDS_append_class-crosssdk = " cairo-native"
DEPENDS_append_class-nativesdk = " nativesdk-cairo"
DEPENDS = " cairo"

SRC_URI = "http://code.call-cc.org/egg-tarballs/4/cairo/cairo-${PV}.tar.gz"

SRC_URI[md5sum] = "02e6852292a8a4f574064135d42931ae"
SRC_URI[sha256sum] = "846079c17055766fbebe53782789b357c7589a3c768bc45f074a7f7dd77efa02"

S = "${WORKDIR}/cairo-${PV}"

inherit chicken_install

BBCLASSEXTEND = "cross crosssdk nativesdk"

repository: OSSystems/meta-chicken

repo_name: OSSystems/meta-chicken


text:
@InProceedings{nguyen13a,
  pdf = {http://jmlr.org/proceedings/papers/v31/nguyen13a.pdf},
  title = {Competing with an Infinite Set of Models in Reinforcement Learning},
  author = {Nguyen, Phuong and Maillard, Odalric-Ambrym and Ryabko, Daniil and Ortner, Ronald},
  pages = {463--471},
  abstract = {We consider a reinforcement learning setting where the learner also has to deal with the problem of finding a suitable state-representation function from a given set of models. This has to be done while interacting with the environment in an online fashion (no resets), and the goal is to have small regret with respect to any Markov model in the set. For this setting, recently the BLB algorithm has been proposed, which achieves regret of order $T^{2/3}$, provided that the given set of models is finite. Our first contribution is to extend this result to a countably infinite set of models. Moreover, the BLB regret bound suffers from an additive term that can be exponential in the diameter of the MDP involved, since the diameter has to be guessed. The algorithm we propose avoids  guessing the diameter, thus improving the regret bound.},
}

repository: mreid/papersite

repo_name: mreid/papersite