text:
package testflight_test

import (
	"os"
	"path/filepath"

	. "github.com/onsi/ginkgo/v2"
	. "github.com/onsi/gomega"
	"github.com/onsi/gomega/gbytes"
)

var _ = Describe("Flying with an image_resource", func() {
	var (
		fixture string
	)

	BeforeEach(func() {
		fixture = filepath.Join(tmp, "fixture")

		err := os.MkdirAll(fixture, 0755)
		Expect(err).NotTo(HaveOccurred())

		err = os.WriteFile(
			filepath.Join(fixture, "run"),
			[]byte(`#!/bin/sh
ls /bin
`),
			0755,
		)
		Expect(err).NotTo(HaveOccurred())
	})

	It("propagates the rootfs and metadata to the task", func() {
		err := os.WriteFile(
			filepath.Join(fixture, "task.yml"),
			[]byte(`---
platform: linux

image_resource:
  type: mock
  source:
    mirror_self: true
    initial_version: hello-version

inputs:
- name: fixture

run:
  path: sh
  args:
  - -c
  - |
    ls /opt/resource/check
    env
`),
			0644,
		)
		Expect(err).NotTo(HaveOccurred())

		exec := spawnFlyIn(fixture, "execute", "-c", "task.yml")
		wait(exec, false)
		Expect(exec).To(gbytes.Say("/opt/resource/check"))
		Expect(exec).To(gbytes.Say("VERSION=hello-version"))
	})

	It("allows a version to be specified", func() {
		err := os.WriteFile(
			filepath.Join(fixture, "task.yml"),
			[]byte(`---
platform: linux

image_resource:
  type: mock
  source: {mirror_self: true}
  version: {version: hi-im-a-version}

inputs:
- name: fixture

run:
  path: env
`),
			0644,
		)
		Expect(err).NotTo(HaveOccurred())

		exec := spawnFlyIn(fixture, "execute", "-c", "task.yml")
		wait(exec, false)
		Expect(exec).To(gbytes.Say("VERSION=hi-im-a-version"))
	})
})

repository: concourse/concourse

repo_name: concourse/concourse


text:
@article{anderson1981estimation,
  title     = {Estimation of dynamic models with error components},
  author    = {Anderson, Theodore Wilbur and Hsiao, Cheng},
  journal   = {Journal of the American statistical Association},
  volume    = {76},
  number    = {375},
  pages     = {598--606},
  year      = {1981},
  publisher = {Taylor \& Francis}
}

@misc{baldwin_2013,
  title     = {Paying for College: Section 127 Employer Aid},
  url       = {https://www.forbes.com/sites/baldwin/2013/02/28/section-127-tuition-aid/},
  journal   = {Forbes},
  publisher = {Forbes Magazine},
  author    = {Baldwin, William},
  year      = {2013},
  month     = {Mar}
}

@misc{bea_2020,
  title     = {Personal Consumption Expenditures},
  url       = {https://fred.stlouisfed.org/series/PCE},
  journal   = {FRED, Federal Reserve Bank of St. Louis},
  publisher = {BEA, U.S. Bureau of Economic Analysis},
  author    = {BEA, U.S. Bureau of Economic Analysis},
  year      = {2020},
  month     = {Feb}
}

@techreport{bound2017understanding,
  title       = {Understanding the Economic Impact of the H-1B Program on the US},
  author      = {Bound, John and Khanna, Gaurav and Morales, Nicolas},
  year        = {2017},
  institution = {National Bureau of Economic Research}
}

@misc{bureauof_2020,
  title     = {Nonimmigrant Visa Statistics, Nonimmigrant Visas by Individual Class of Admission (e.g. A1, A2, etc.)},
  url       = {https://travel.state.gov/content/travel/en/legal/visa-law0/visa-statistics/nonimmigrant-visa-statistics.html},
  journal   = {Travel.State.Gov},
  publisher = {U.S. Department of State},
  author    = {Bureau of, Consular Affairs},
  year      = {2020}
}

@article{cappelli2004employers,
  title     = {Why do employers pay for college?},
  author    = {Cappelli, Peter},
  journal   = {Journal of Econometrics},
  volume    = {121},
  number    = {1-2},
  pages     = {213--241},
  year      = {2004},
  publisher = {Elsevier}
}

@misc{cb_excel_2019,
  title   = {Trends in Student Aid 2019 Excel Data, Table 2\_UG},
  url     = {https://research.collegeboard.org/xlsx/trends-student-aid-excel-data.xlsx},
  journal = {The College Board},
  author  = {College Board, The},
  year    = {2019}
}

@misc{cb_trends_2019,
  title   = {Trends in Student Aid 2019},
  url     = {https://research.collegeboard.org/trends/student-aid},
  journal = {The College Board},
  author  = {College Board, The},
  year    = {2019}
}

@article{cherry2014rejuvenating,
  title   = {Rejuvenating tuition reimbursement programs},
  author  = {Cherry, T},
  journal = {HR Magazine},
  volume  = {59},
  number  = {6},
  year    = {2014}
}

@article{dennison2019crime,
  title     = {The crime-reducing benefits of a college degree: evidence from a nationally representative US sample},
  author    = {Dennison, Christopher R},
  journal   = {Criminal Justice Studies},
  volume    = {32},
  number    = {4},
  pages     = {297--316},
  year      = {2019},
  publisher = {Taylor \& Francis}
}

@misc{edvisors_2019,
  title   = {Why Do Tuition Rates Rise Faster Than Inflation?},
  url     = {https://www.edvisors.com/plan-for-college/saving-for-college/tuition-inflation/},
  journal = {Edvisors},
  author  = {Edvisors},
  year    = {2019},
  month   = {Dec}
}

@misc{finaid_2020,
  title   = {Loans: Historical Loan Limits},
  url     = {https://www.finaid.org/loans/historicallimits.phtml},
  journal = {FinAid},
  author  = {FinAid},
  year    = {2020}
}
@misc{glass_2010,
  title   = {Roosevelt signs the GI Bill of Rights into law, June 22, 1944},
  url     = {https://www.politico.com/story/2010/06/roosevelt-signs-the-gi-bill-of-rights-into-law-june-22-1944-038814},
  journal = {Politico},
  author  = {Glass, Andrew},
  year    = {2010},
  month   = {Jun}
}

@misc{glover_2017,
  title   = {The Case for Talent Investment},
  url     = {https://www.luminafoundation.org/news-and-views/the-case-for-talent-investment/},
  journal = {Lumina Foundation},
  author  = {Glover, Haley},
  year    = {2017},
  month   = {Feb}
}

@article{ivanov2005practitioner,
  title     = {A practitioner's guide to lag order selection for VAR impulse response analysis},
  author    = {Ivanov, Ventzislav and Kilian, Lutz},
  journal   = {Studies in Nonlinear Dynamics \& Econometrics},
  volume    = {9},
  number    = {1},
  year      = {2005},
  publisher = {De Gruyter}
}

@misc{jones_2010,
  title     = {Who Benefits from Section 127? A study of employee education assistance provided under section 127 of the internal revenue code},
  url       = {http://www.cpepea.com/wp-content/uploads/2017/05/10-0418-Coalition-Report-on-Public-Policy-Issue-E-P-E-A_FNL.pdf},
  journal   = {The Coalition To Preserve Employer Provided Education Assistance (CPEPEA)},
  publisher = {The Society for Human Resource Management (SHRM)},
  author    = {Jones, Gigi},
  year      = {2010}
}

@article{law1990law,
  title   = {Law 101-649},
  author  = {Law, Public},
  journal = {Immigration Act, November},
  volume  = {29},
  year    = {1990}
}

@article{maldonado2018price,
  title   = {Price of College Increasing Almost 8 Times Faster Than Wages},
  author  = {Maldonado, C},
  journal = {Forbes Magazine Online},
  year    = {2018}
}

@misc{merrick_2019,
  title     = {Education Benefits Present a Learning Opportunity},
  url       = {https://www.shrm.org/hr-today/news/hr-magazine/spring2019/pages/education-benefits-present-learning-opportunity.aspx},
  journal   = {SHRM},
  publisher = {SHRM},
  author    = {Merrick, Amy},
  year      = {2019},
  month     = {Aug}
}

@misc{nces_2017,
  title   = {Table 330.10, Average undergraduate tuition and fees and room and board rates charged for full-time students in degree-granting postsecondary institutions, by level and control of institution: Selected years, 1963-64 through 2016-17},
  url     = {https://nces.ed.gov/programs/digest/d17/tables/dt17_330.10.asp},
  journal = {Digest of Education Statistics, 2017},
  author  = {National Center for Education Statistics, (NCES)},
  year    = {2017}
}

@misc{nces_2019,
  title   = {Table 303.10, Total fall enrollment in degree-granting postsecondary institutions, by attendance status, sex of student, and control of institution: Selected years, 1947 through 2028},
  url     = {https://nces.ed.gov/programs/digest/d18/tables/dt18_303.10.asp},
  journal = {Digest of Education Statistics, 2018},
  author  = {National Center for Education Statistics, (NCES)},
  year    = {2019}
}

@book{plaw95_600_1978,
  volume    = {92 STAT. 2763},
  publisher = {95th Congress},
  url       = {https://www.govinfo.gov/content/pkg/STATUTE-92/pdf/STATUTE-92-Pg2763.pdf},
  year      = {1978}
}

@book{plaw99_514_1986,
  volume    = {100 STAT. 2510},
  publisher = {99th Congress},
  url       = {https://www.govtrack.us/congress/bills/99/hr3838/text},
  year      = {1986}
}

@misc{powers_2018,
  title     = {Learn About the GI Bill for Post-9/11 Active Duty Service Members},
  url       = {https://www.thebalancecareers.com/gi-bill-for-the-21st-century-3347143},
  journal   = {The Balance Careers},
  publisher = {The Balance Careers},
  author    = {Powers, Rod},
  year      = {2018},
  month     = {Dec}
}

@article{ruiz2017key,
  title   = {Key facts about the US H-1B visa program},
  author  = {Ruiz, Neil G},
  journal = {Washington, DC: Brookings},
  year    = {2017}
}

@misc{schenck_2016,
  title   = {Structural vector autoregression models},
  url     = {https://blog.stata.com/2016/09/20/structural-vector-autoregression-models/},
  journal = {The Stata Blog},
  author  = {Schenck, David},
  year    = {2016},
  month   = {Sep}
}

@misc{schiavo_2020,
  title     = {What the CARES Act means for student loan benefits},
  url       = {https://www.benefitnews.com/news/what-the-cares-act-means-for-student-loan-benefits},
  journal   = {Employee Benefit News},
  publisher = {Employee Benefit News},
  author    = {Schiavo, Amanda},
  year      = {2020},
  month     = {Apr}
}

@misc{stamour_2019,
  title   = {Most college students work, and that's both good and bad},
  url     = {https://www.insidehighered.com/news/2019/11/18/most-college-students-work-and-thats-both-good-and-bad},
  journal = {Inside Higher Ed},
  author  = {St. Amour, Madeline},
  year    = {2019},
  month   = {Nov}
}

@misc{talentculture_2018,
  title   = {What Does Tuition Assistance Look Like in 2018?},
  url     = {https://talentculture.com/tuition-assistance-look-like-2018/},
  journal = {TalentCulture},
  author  = {TalentCulture},
  year    = {2018},
  month   = {May}
}

@misc{veteransaffairs_2017,
  title   = {Veterans Educational Assistance Program (VEAP)},
  url     = {https://www.benefits.va.gov/gibill/veap.asp},
  journal = {VA.gov},
  author  = {Veterans Affairs, Department of},
  year    = {2017},
  month   = {Mar}
}

@misc{veteransaffairs_2020,
  title   = {Forever GI Bill - Harry W. Colmery Veterans Educational Assistance Act},
  url     = {https://www.benefits.va.gov/GIBILL/FGIBSummaries.asp},
  journal = {VA.gov},
  author  = {Veterans Affairs, Department of},
  year    = {2020},
  month   = {Jan}
}

license: MIT

license_type: permissive

branch_name: refs/heads/master

gha_license_id: MIT

gha_language: TeX

extension: bib


text:
package auth

import (
	"crypto/hmac"
	"crypto/md5"
	"crypto/sha1"
	"encoding/hex"
)

func Md5Sum(b []byte) string {
	h := md5.New()
	h.Write(b)
	return hex.EncodeToString(h.Sum(nil))
}

func Sha1Sum(b []byte) string {
	h := sha1.New()
	h.Write(b)
	return hex.EncodeToString(h.Sum(nil))
}

func HmacSha1(message, key []byte) string {
	mac := hmac.New(sha1.New, key)
	mac.Write(message)
	return Bytes2String(mac.Sum(nil))
}

func CheckHmacSha1(message, messageMAC, key []byte) bool {
	mac := hmac.New(sha1.New, key)
	mac.Write(message)
	expectedMAC := mac.Sum(nil)
	return hmac.Equal(messageMAC, expectedMAC)
}

extension: go


text:
require bash.inc
PR = "r14"

SRC_URI += "\
  file://bash-3.0-fixes.patch \
  file://default_path.patch \
  file://signames-mipsel.diff \
"

SRC_URI[archive.md5sum] = "26c4d642e29b3533d8d754995bc277b3"
SRC_URI[archive.sha256sum] = "72d3f9d80fb4622e79ee5019314668b7bd6747182fa0928c8742002b7568586f"

repository: overo/overo-oe-natty

repo_name: overo/overo-oe-natty

branch_name: HEAD

extension: bb


text:
/*
Copyright 2022 The Kubernetes Authors.

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
*/

package v1alpha1

import (
	"sigs.k8s.io/kubebuilder/v3/pkg/config"
	cfgv3 "sigs.k8s.io/kubebuilder/v3/pkg/config/v3"
	"sigs.k8s.io/kubebuilder/v3/pkg/model/stage"
	"sigs.k8s.io/kubebuilder/v3/pkg/plugin"
	"sigs.k8s.io/kubebuilder/v3/pkg/plugins/golang"
)

const pluginName = "deploy-image." + golang.DefaultNameQualifier

var (
	pluginVersion            = plugin.Version{Number: 1, Stage: stage.Alpha}
	supportedProjectVersions = []config.Version{cfgv3.Version}
	pluginKey                = plugin.KeyFor(Plugin{})
)

var _ plugin.CreateAPI = Plugin{}

// Plugin implements the plugin.Full interface
type Plugin struct {
	createAPISubcommand
}

// Name returns the name of the plugin
func (Plugin) Name() string { return pluginName }

// Version returns the version of the plugin
func (Plugin) Version() plugin.Version { return pluginVersion }

// SupportedProjectVersions returns an array with all project versions supported by the plugin
func (Plugin) SupportedProjectVersions() []config.Version { return supportedProjectVersions }

// GetCreateAPISubcommand will return the subcommand which is responsible for scaffolding apis
func (p Plugin) GetCreateAPISubcommand() plugin.CreateAPISubcommand { return &p.createAPISubcommand }

type PluginConfig struct {
	Resources []ResourceData `json:"resources,omitempty"`
}

type ResourceData struct {
	Group   string  `json:"group,omitempty"`
	Domain  string  `json:"domain,omitempty"`
	Version string  `json:"version"`
	Kind    string  `json:"kind"`
	Options options `json:"options,omitempty"`
}

type options struct {
	Image            string `json:"image,omitempty"`
	ContainerCommand string `json:"containerCommand,omitempty"`
	ContainerPort    string `json:"containerPort,omitempty"`
	RunAsUser        string `json:"runAsUser,omitempty"`
}

func (p Plugin) DeprecationWarning() string {
	return ""
}

repository: kubernetes-sigs/kubebuilder

repo_name: kubernetes-sigs/kubebuilder

gha_language: Go


text:
SUMMARY = "Wi-Fi Test Suite Linux Control Agent"
LICENSE = "ISC"
LIC_FILES_CHKSUM = "file://LICENSE.txt;md5=0542427ed5c315ca34aa09ae7a85ed32"

SRC_URI = " \
  git://ssh.dev.azure.com/v3/HQV-Gardena/SG-Gateway/sg-gateway-wifi-alliance-test-suite;protocol=ssh;branch=main \
  file://eth0.network.disabled \
  file://wifi-testsuite-install.sh \
"

PR = "r4"
PV = "10.10.1+git${SRCPV}"
SRCREV = "63cd320851e875ee278a4b019b9ad537104cc21b"

DEPENDS = "libtirpc"

# procps supports the arguments 'a' and 'x' which are used by WTS
RDEPENDS:${PN} = "\
  procps \
  wpa-supplicant-cli \
"

S = "${WORKDIR}/git"
FILES:${PN} += "\
    /usr/local/sbin/ \
    ${systemd_unitdir}/network \
"

do_install () {
    install -d ${D}${bindir}
    install -m 0755 ${S}/ca/wfa_ca ${D}${bindir}
    install -m 0755 ${S}/dut/wfa_dut ${D}${bindir}
    install -m 0755 ${WORKDIR}/wifi-testsuite-install.sh ${D}${bindir}/wifi-testsuite-install
    install -m 0755 -D ${S}/scripts/*.sh ${D}${bindir}
    # Workaround for the hardcoded paths
    install -d ${D}/usr/local/sbin
    ln -s ${bindir}/getipconfig.sh ${D}/usr/local/sbin/
    ln -s ${bindir}/findprocess.sh ${D}/usr/local/sbin/

    # Configure static address on eth0
    install -d 0755 ${D}${systemd_unitdir}/network
    install -m 0644 ${WORKDIR}/eth0.network.disabled ${D}${systemd_unitdir}/network
}

branch_name: refs/heads/main


text:
DESCRIPTION = "This is a modified version of the icecc-create-env script in order to\
make it work with OE."
SECTION = "base"
PRIORITY = "optional"
LICENSE = "GPL"

DEPENDS = ""
INHIBIT_DEFAULT_DEPS = "1"

inherit native

SRC_URI = "http://www.digital-opsis.com/openembedded/icecc-create-env-${PV}.tar.gz"

S = "${WORKDIR}/icecc-create-env-${PV}"

do_stage() {
	install -d ${STAGING_DIR}/ice
	install -m 0755 ${WORKDIR}/icecc-create-env ${STAGING_DIR}/ice/icecc-create-env
}

SRC_URI[md5sum] = "641ec45fe377529c7fd914f77b11b44f"
SRC_URI[sha256sum] = "9ff8360375432a7a5c476cc6d55b3fdea9d6f3edc080d295a60421d8f47b1834"


text:
package main

import (
	"fmt"
	"testing"
)

func TestArray(t *testing.T) {
	res := array
	fmt.Println(res())
}

repository: aystzh/go-hello

repo_name: aystzh/go-hello


text:
@inproceedings{las-12-comparisoncloud,
 address = {Honolulu and HI},
 author = {von Laszewski, Gregor and Javier Diaz and Fugang Wang and Geoffrey C. Fox},
 booktitle = {IEEE Cloud 2012},
 doi = {10.1109/CLOUD.2012.104},
 month = {June},
 title = {Comparison of Multiple Cloud Frameworks},
 url = {https://laszewski.github.io/papers/laszewski-IEEECloud2012_id-4803.pdf},
 year = {2012}
}


text:
@unpublished{quandenser,
  author = "The M. and Käll L.",
  title = "Focus on the spectra that matter by clustering of quantification data in shotgun proteomics",
  year = "2018"
}

@ARTICLE{nextflow,
    author = "Tommaso P et al",  %bib can only use max 3 people in author
    title = "Nextflow enables reproducible computational workflows",
    journal = "Nature Biotechnology",
    volume = "35",
    DOI = "10.1038/nbt.3820",
    pages = "316–319",
    year = "2017"
}

@ARTICLE{snakemake,
    author = "Köster, Johannes and Rahmann, Sven",
    title = "{Snakemake—a scalable bioinformatics workflow engine}",
    journal = "Bioinformatics",
    volume = "28",
    number = "19",
    pages = "2520-2522",
    doi = "10.1093/bioinformatics/bts480",
    year = "2012"
}

@ARTICLE{singularity,
    author = "Kurtzer GM. Sochat V. Bauer MW",
    title = "Singularity: Scientific containers for mobility of compute",
    journal = "PLoS ONE",
    volume = "5",
    DOI = "10.1371/journal.pone.0177459",
    year = "2017"
}

@ARTICLE{biocontainers,
    autohor = "Leprevost F V. et al",
    title = "BioContainers: an open-source and community-driven framework for software standardization",
    journal = "Bioinformatics",
    volume = "33",
    number = "16",
    pages = "2580-2582",
    DOI = "10.1093/bioinformatics/btx192",
    year = "2017"
}

@ARTICLE{docker,
  author = "Merkel, Dirk",
  year = "2014",
  month = "03",
  pages = "",
  title = "Docker: lightweight Linux containers for consistent development and deployment",
  volume = "2014",
  journal = "Linux Journal"
}

@ARTICLE{singularity-hub,
    author = "Sochat V. Prybol CJ. Kurtzer GM",
    title = "Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers",
    journal = "PLoS ONE",
    volume = "12",
    number = "11",
    DOI = "10.1371/journal.pone.0188511",
    year = "2017"
}

@MISC{singularity-documentation,
    title = "Singularity Container Documentation Release 3.1",
    howpublished = "\url{https://www.sylabs.io/guides/3.1/user-guide.pdf}",
    note = "Accessed: 2019-04-05"
}

@MISC{singularity-uppmax,
    title = "Singularity User Guide",
    howpublished = "\url{https://www.uppmax.uu.se/support/user-guides/singularity-user-guide/}",
    note = "Accessed: 2019-03-27"
}

@ARTICLE{proteowizard,
    author = "Kessner D. et al",
    title = "ProteoWizard: open source software for rapid proteomics tools development",
    journal = "Bioinformatics",
    volume = "24",
    number = "21",
    DOI = "10.1093/bioinformatics/btn323",
    pages = "2534–2536",
    year = "2008"
}

@ARTICLE{crux,
    author = "McIlwain S. et al",
    title = "Crux: rapid open source protein tandem mass spectrometry analysis",
    journal = "Journal of Proteome Research",
    volume = "13",
    number = "10",
    pages = "4488-4491",
    year = "2014"
}

@ARTICLE{tide-search,
    author = "Diament J. B. and Noble S. W.",
    title = "Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra",
    journal = "Journal of Proteome Research",
    volume = "10",
    number = "9",
    pages = "3871-3879",
    year = "2010"
}

@ARTICLE{percolator,
    author = "Käll L. et al",
    title = "Semi-supervised learning for peptide identification from shotgun proteomics datasets",
    journal = "Nature Methods",
    volume = "4",
    number = "11",
    pages = "923-925",
    year = "2007"
}

@ARTICLE{triqler,
    author = "The M. and Käll L.",
    title = "Integrated identification and quantification error probabilities for shotgun proteomics",
    journal = "Molecular and Cellular Proteomics",
    volume = "18",
    number = "3",
    DOI = "10.1074/mcp.RA118.001018",
    year = "2019",
    pages = "561-570"
}

@ARTICLE{mzml-format,
    author = "Deutsch W. E.",
    title = "Mass Spectrometer Output File Format mzML",
    journal = "Methods in Molecular Biology",
    volume = "604",
    DOI = "10.1007/978-1-60761-444-9_22",
    year = "2010",
    pages = "319-331"
}

@MISC{wine,
    title = "About Wine",
    howpublished = "\url{https://www.winehq.org/about}",
    note = "Accessed: 2019-03-28"
}

@MISC{docker-image,
    title = "Chambm/wine-dotnet",
    howpublished = "\url{https://hub.docker.com/r/chambm/wine-dotnet}",
    note = "Accessed: 2019-03-28"
}

@MISC{docker-howto,
    title = "Msconvert Wine",
    howpublished = "\url{http://tools.proteomecenter.org/wiki/index.php?title=Msconvert_Wine}",
    note = "Accessed: 2019-03-28"
}

@MISC{pyside2,
    title = "Qt for Python",
    howpublished = "\url{https://wiki.qt.io/Qt_for_Python}",
    note = "Accessed: 2019-03-28"
}

@INPROCEEDINGS{knime,
    author = "Michael R. et al",
    title = "{KNIME}: The Konstanz Information Miner",
    booktitle = "Studies in Classification, Data Analysis, and Knowledge Organization (GfKL 2007)",
    publisher = "Springer",
    ISBN = "978-3-540-78239-1",
    ISSN = "1431-8814",
    year = "2007"
}

@ARTICLE{openms,
    author = "Röst H.L. et al",
    title = "OpenMS: A flexible open-source software platform for mass spectrometry data analysis",
    DOI = "10.1038/nmeth.3959",
    journal = "Nature Methods",
    volume = "13",
    year = "2016"
}

@ARTICLE{openms-hpc,
    author = "Pfeuffe J. et al",
    title = "OpenMS–A platform for reproducible analysis of mass spectrometry data",
    DOI = "10.1016/j.jbiotec.2017.05.016",
    journal = "Journal of Biotechnology",
    volume = "261",
    pages = "142-148",
    year = "2017"
}

@MISC{m-jahn-pipeline,
    author = "Jahn M.",
    title = "m-jahn/openMS-workflows",
    howpublished = "\url{https://github.com/m-jahn/openMS-workflows}",
    note = "Accessed: 2019-04-05"
}

@ARTICLE{maxquant,
    author = "Cox J. and Mann M.",
    title = "MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification",
    journal = "Nature Biotechnology",
    volume = "26",
    pages = "1367-1372",
    year = "2008"
}

@MISC{maxquant-installation,
    title = "MaxQuant Documentation: Download and install guide",
    howpublished = "\url{http://www.coxdocs.org/doku.php?id=maxquant:common:download_and_installation}",
    note = "Accessed: 2019-04-05"
}

@ARTICLE{q-value,
    title = "Philosopher, a data processing toolkit for shotgun proteomics.",
    author = "Käll L. et al",
    title = "Posterior error probabilities and false discovery rates: two sides of the same coin",
    journal = "Journal of Proteome Research",
    volume = "7",
    number = "1",
    pages = "40 -44",
    year = "2008"
}

@MISC{scipy,
    author = "Jones E. et al",
    title = "{SciPy}: Open source scientific tools for Python",
    year = "2001--",
    url = "http://www.scipy.org/",
    note = "[Online; accessed 2019-05-19]"
}

@MISC{ncbi-search,
    title = "Gene [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information",
    year = "2004",
    howpublished = "\url{https://www.ncbi.nlm.nih.gov/gene/}",
    note = "Accessed: 2019-05-20"
}

@ARTICLE{cyano-low-light,
    author = "Golden S.",
    title = "Light-responsive gene expression in cyanobacteria",
    journal = "Journal of Bacteriology",
    volume = "177",
    number = "7",
    pages = "1651-1654",
    DOI = "10.1128/jb.177.7.1651-1654.1995",
    year = "1995"
}

@ARTICLE{phytochrome,
	author = "Yeh, Kuo-Chen and Wu, Shu-Hsing and Murphy, John T. and Lagarias, J. Clark",
	title = "A Cyanobacterial Phytochrome Two-Component Light Sensory System",
	volume = "277",
	number = "5331",
	pages = "1505--1508",
	year = "1997",
	doi = "10.1126/science.277.5331.1505",
	publisher = "American Association for the Advancement of Science",
	URL = "https://science.sciencemag.org/content/277/5331/1505",
	journal = "Science"
}

@ARTICLE{phytochrome-dark,
    author = "García-Domínguez M. et al",
    title = "Light-Dependent Regulation of Cyanobacterial Phytochrome Expression",
    journal = "Journal of Bacteriology",
    volume = "182",
    number = "1",
    pages = "38-44",
    doi = "10.1128/JB.182.1.38-44.2000",
    year = "2000",
}

@MISC{min-span-tree,
    title = "Minimum spanning tree",
    howpublished = "\url{https://en.wikipedia.org/wiki/Minimum_spanning_tree}",
    note = "Accessed: 2019-05-22"
}

@ARTICLE{phycobilisomes,
    author = "Lu-Ning Liu et al.",
    title = "Characterization, structure and function of linker polypeptides in phycobilisomes of cyanobacteria and red algae: An overview",
    DOI = "10.1016/j.bbabio.2005.04.001",
    volum = "1708",
    number = "2",
    pages = "133-142"
}

@ARTICLE{michael-jahn-cyano,
    author = "Jahn M. et al",
    title = "Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins",
    journal = "Cell Reports",
    year = "2018",
    volume = "25",
    pages = "478-486",
    month = "oct"
}

@ARTICLE{boxcar,
    author = "Meier F. et al.",
    title = "BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes",
    DOI = "10.1038/s41592-018-0003-5",
    volume = "15",
    year = "2017"
}

@ARTICLE{boxcar-data,
    author = "Albrechtsen N. et al",
    title = "Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery",
    journal = "Cell Systems",
    volume = "7",
    number = "6",
    pages = "601-612",
    DOI = "10.1016/j.cels.2018.10.012",
    year = "2018"
}

@ARTICLE{heme-oxygenase,
    author="Willows D.R et al",
    title="Phytobilin biosynthesis: the Synechocystis sp. PCC 6803 heme oxygenase-encoding ho1 gene complements a phytochrome-deficient Arabidopsis thaliana hy1 mutant",
    journal="Plant Molecular Biology",
    volume="43",
    number="1",
    pages="113-120",
    doi="10.1023/A:1006489129449",
    year="2000",
}

@ARTICLE{heme-oxygenase-2,
    author = "Okada K.",
    title = "HO1 and PcyA proteins involved in phycobilin biosynthesis form a 1:2 complex with ferredoxin-1 required for photosynthesis",
    journal = "FEBS Letters",
    volume = "583",
    number = "8",
    pages = "1251-1256",
    DOI = "https://doi.org/10.1016/j.febslet.2009.03.052",
    year = "2009"
}

@ARTICLE{fdr,
    author = "Aggarwal S. et al",
    title = "False Discovery Rate Estimation in Proteomics",
    bookTitle = "Statistical Analysis in Proteomics",
    year = "2016",
    publisher = "Springer New York",
    pages = "119-128",
    doi = "10.1007/978-1-4939-3106-4_7",
}

@MISC{nonlinear,
    title = "P-values, False Discovery Rate (FDR) and q-values",
    howpublished = "\url{http://www.nonlinear.com/support/progenesis/comet/faq/v2.0/pq-values.aspx}",
    note = "Accessed: 2019-05-27"
}

@ARTICLE{slr2032,
    author="Jansén T. et al",
    title="Characterization of trophic changes and a functional oxidative pentose phosphate pathway in Synechocystis sp. PCC 6803",
    journal="Acta Physiologiae Plantarum",
    year="2010",
    volume="32",
    number="3",
    pages="511--518",
    doi="10.1007/s11738-009-0428-7",
}

@ARTICLE{ssl2501,
    author="Matthew A. et al.",
    title="Photoautotrophic Polyhydroxybutyrate Granule Formation Is Regulated by Cyanobacterial Phasin PhaP in Synechocystis sp. Strain PCC 6803",
    journal="Applied and environmental microbiology",
    volume = "81",
    year="2015"
}

@ARTICLE{phasins,
    author = "Mezzina, Mariela P. and Pettinari, M. Juli",
    title = "Phasins, Multifaceted Polyhydroxyalkanoate Granule-Associated Proteins",
    journal = "Applied and environmental microbiology",
    year = "2016",
    publisher = "American Society for Microbiology",
    volume = "82",
    number = "17",
    pages = "5060-5067",
    doi = "10.1128/AEM.01161-16"
}

@ARTICLE{hypothetical-protein1,
    author = "Naveed M. et al",
    title = "Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets",
    volume = "10",
    year = "2017",
    DOI = "doi:10.1186/s13104-017-2992-z"
}

@ARTICLE{hypothetical-protein2,
    author = "Oliveira L. W. et al.",
    title = "Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance.",
    volume = "13",
    year = "2018",
    DOI = "doi:10.1371/journal.pone.0198965"
}

@BOOK{quantitative_analysis,
    author    = "Daniel C. Harris",
    title     = "Quantitative chemical analysis",
    publisher = "W.H Freeman and Company",
    year      = "2010",
    note      = "ISBN: 978-1-4292-18-15-3"
}

gha_language: Shell


text:
// Copyright 2020 The ChromiumOS Authors
// Use of this source code is governed by a BSD-style license that can be
// found in the LICENSE file.

package arc

import (
	"context"
	"fmt"
	"time"

	"chromiumos/tast/common/android/ui"
	"chromiumos/tast/ctxutil"
	"chromiumos/tast/local/arc"
	"chromiumos/tast/local/chrome/ash"
	"chromiumos/tast/local/chrome/ime"
	"chromiumos/tast/local/chrome/uiauto/faillog"
	"chromiumos/tast/local/input"
	"chromiumos/tast/testing"
)

func init() {
	testing.AddTest(&testing.Test{
		Func:         KeyCharacterMap,
		LacrosStatus: testing.LacrosVariantUnneeded,
		Desc:         "Checks KeyCharacterMap working in non-US layouts",
		Contacts:     []string{"yhanada@chromium.org", "arc-framework+tast@google.com"},
		Attr:         []string{"group:mainline", "informational"},
		SoftwareDeps: []string{"chrome"},
		Fixture:      "arcBooted",
		Timeout:      3 * time.Minute,
		Params: []testing.Param{{
			ExtraSoftwareDeps: []string{"android_p"},
		}, {
			Name:              "vm",
			ExtraSoftwareDeps: []string{"android_vm"},
		}},
	})
}

func KeyCharacterMap(ctx context.Context, s *testing.State) {
	cleanupCtx := ctx
	ctx, cancel := ctxutil.Shorten(ctx, 30*time.Second)
	defer cancel()

	p := s.FixtValue().(*arc.PreData)
	cr := p.Chrome
	a := p.ARC
	d := p.UIDevice

	tconn, err := cr.TestAPIConn(ctx)
	if err != nil {
		s.Fatal("Creating test API connection failed: ", err)
	}

	const (
		apk          = "ArcKeyCharacterMapTest.apk"
		pkg          = "org.chromium.arc.testapp.kcm"
		activityName = ".MainActivity"
		fieldID      = pkg + ":id/typed_character"
	)

	s.Log("Installing app")
	if err := a.Install(ctx, arc.APKPath(apk)); err != nil {
		s.Fatal("Failed installing app: ", err)
	}

	act, err := arc.NewActivity(a, pkg, activityName)
	if err != nil {
		s.Fatal("Failed to create an activity: ", err)
	}
	defer act.Close()

	if err := act.StartWithDefaultOptions(ctx, tconn); err != nil {
		s.Fatal("Failed to start an activity: ", err)
	}
	defer act.Stop(cleanupCtx, tconn)

	kb, err := input.Keyboard(ctx)
	if err != nil {
		s.Fatal("Failed to find keyboard: ", err)
	}
	defer kb.Close()

	imeID, err := ime.CurrentInputMethod(ctx, tconn)
	if err != nil {
		s.Fatal("Failed to get current ime: ", err)
	}
	imePrefix, err := ime.Prefix(ctx, tconn)
	if err != nil {
		s.Fatal("Failed to get ime prefix: ", err)
	}
	defer func(ctx context.Context) {
		if err := ime.SetCurrentInputMethod(ctx, tconn, imeID); err != nil {
			s.Error("Failed to set the default input method: ", err)
		}
	}(cleanupCtx)

	// Wait for the activity to have focus.
	if err := ash.WaitForCondition(ctx, tconn, func(window *ash.Window) bool {
		return window.ARCPackageName == act.PackageName() &&
			window.IsVisible && window.HasFocus && window.IsActive
	}, &testing.PollOptions{Timeout: 10 * time.Second}); err != nil {
		s.Fatal("Failed to wait for the app to be ready: ", err)
	}

	// Wait for the View inflated.
	if err := d.Object(ui.ID(fieldID)).WaitForExists(ctx, 10*time.Second); err != nil {
		s.Fatal("Failed to wait for the app to render: ", err)
	}

	for _, tc := range []struct {
		name     string
		im       *ime.InputMethod
		mappings []struct{ in, out string }
	}{
		{
			name: "QWERTY keyboard",
			im:   nil,
			mappings: []struct{ in, out string }{
				{"q", "q"},
				{"shift+q", "Q"},
			},
		},
		{
			name: "AZERTY keyboard",
			im:   &ime.FrenchFrance,
			mappings: []struct{ in, out string }{
				{"q", "a"},
				{"shift+q", "A"},
				{"5", "("},
				{"shift+5", "5"},
				{"altgr+5", "["},
				{"-", ")"},
				{"altgr+-", "]"},
				// Display values for dead keys are defined in android.view.KeyCharacterMap
				{"[", "\u02c6"},       //  ACCENT_CIRCUMFLEX
				{"shift+[", "\u00a8"}, //  ACCENT_UMLAUT
			},
		},
		{
			name: "JCUKEN keyboard",
			im:   &ime.Russian,
			mappings: []struct{ in, out string }{
				{"q", "й"},
				{"shift+q", "Й"},
			},
		},
	} {
		s.Run(ctx, tc.name, func(ctx context.Context, s *testing.State) {
			if tc.im != nil {
				if err := ime.AddAndSetInputMethod(ctx, tconn, imePrefix+tc.im.ID); err != nil {
					s.Fatalf("Failed to switch the IME %q: %v", tc.im.Name, err)
				}

				defer func(ctx context.Context) {
					if err := ime.RemoveInputMethod(ctx, tconn, imePrefix+tc.im.ID); err != nil {
						s.Errorf("Failed to remove the IME %q: %v", tc.im.Name, err)
					}
				}(ctx)
			}

			for i, v := range tc.mappings {
				if err := kb.Accel(ctx, v.in); err != nil {
					s.Fatal("Failed to type: ", err)
				}

				if err := d.Object(ui.ID(fieldID), ui.Text(v.out)).WaitForExists(ctx, 10*time.Second); err != nil {
					faillog.DumpUITreeWithScreenshotOnError(ctx, s.OutDir(), func() bool { return true }, cr, fmt.Sprintf("ui_root_%s_%d", tc.name, i))
					s.Errorf("Failed to find field %q after typing %q: %v", v.in, v.out, err)
				}
			}
		})
	}
}


text:
package dto

// MessageBlock child struct of SlackResponseEventMessage
type MessageBlock struct {
	BlockID  string `json:"block_id"`
	Elements []struct {
		Elements []struct {
			Type   string `json:"type"`
			UserID string `json:"user_id,omitempty"`
			Text   string `json:"text,omitempty"`
		} `json:"elements"`
		Type string `json:"type"`
	} `json:"elements"`
	Type string `json:"type"`
}

// SlackResponseEventMessage main event message object
type SlackResponseEventMessage struct {
	Channel      string         `json:"channel"`
	ClientMsgID  string         `json:"client_msg_id"`
	DisplayAsBot bool           `json:"display_as_bot"`
	EventTs      string         `json:"event_ts"`
	ThreadTS     string         `json:"thread_ts"`
	Files        []File         `json:"files"`
	SourceTeam   string         `json:"source_team"`
	Team         string         `json:"team"`
	Text         string         `json:"text"`
	Ts           string         `json:"ts"`
	Type         string         `json:"type"`
	Upload       bool           `json:"upload"`
	User         string         `json:"user"`
	UserTeam     string         `json:"user_team"`
	Blocks       []MessageBlock `json:"blocks"`
}

// ToBaseOriginalMessage converts the SlackResponseEventMessage to BaseOriginalMessage object
func (m SlackResponseEventMessage) ToBaseOriginalMessage() BaseOriginalMessage {
	return BaseOriginalMessage{
		Text:        m.Text,
		User:        m.User,
		Files:       m.Files,
		Channel:     m.Channel,
		ClientMsgID: m.ClientMsgID,
		EventTs:     m.EventTs,
		ThreadTS:    m.ThreadTS,
		Ts:          m.Ts,
		Type:        m.Type,
	}
}

repository: sharovik/devbot

repo_name: sharovik/devbot


text:
package config_test

import (
	"testing"

	"github.com/gokrazy/rsync/internal/config"
	"github.com/google/go-cmp/cmp"
)

func TestConfig(t *testing.T) {
	cfg, err := config.FromString(`
[[listener]]
rsyncd = "localhost:873"

[[listener]]
http_monitoring = "localhost:8738"

[[listener]]
anon_ssh = "localhost:22873"

[[module]]
name = "interop"
path = "/non/existant/path"

`)
	if err != nil {
		t.Fatal(err)
	}

	if got, want := len(cfg.Listeners), 3; got != want {
		t.Fatalf("unexpected number of listeners: got %d, want %d", got, want)
	}

	{
		want := []config.Listener{
			{Rsyncd: "localhost:873"},
			{HTTPMonitoring: "localhost:8738"},
			{AnonSSH: "localhost:22873"},
		}
		if diff := cmp.Diff(want, cfg.Listeners); diff != "" {
			t.Fatalf("unexpected listener config: diff (-want +got):\n%s", diff)
		}
	}

	{
		want := []config.Module{
			{Name: "interop", Path: "/non/existant/path"},
		}
		if diff := cmp.Diff(want, cfg.Modules); diff != "" {
			t.Fatalf("unexpected module config: diff (-want +got):\n%s", diff)
		}
	}
}

repository: pombredanne/rsync

repo_name: pombredanne/rsync


text:
DESCRIPTION = "Driver for at76 based usb-wifi devices"
SECTION = "base"
LICENSE = "GPL"

PR = "r3"

RDEPENDS_${PN} = "at76c503-firmware"

SRC_URI = "http://download.berlios.de/at76c503a/at76_usb-0.17.tar.gz"
SRC_URI_ixp4xx = "http://download.berlios.de/at76c503a/at76_usb-0.17.tar.gz \
                  file://at76_usb-0.17-.patch"
S = "${WORKDIR}/at76_usb-${PV}/"

inherit module

MODULES = "at76c503 at76_usbdfu at76c503-i3861 at76c503-rfmd at76c503-rfmd-acc \
	at76c505-rfmd at76c503-i3863 at76c505-rfmd2958"

do_install() {
	install -d ${D}${base_libdir}/modules/${KERNEL_VERSION}/kernel/drivers/usb/
	for i in *${KERNEL_OBJECT_SUFFIX}; do
		install -m 0644 $i ${D}${base_libdir}/modules/${KERNEL_VERSION}/kernel/drivers/usb/
	done
}

SRC_URI[md5sum] = "b47d4fa958aaf83916b6a917626102cd"
SRC_URI[sha256sum] = "9d1fff10d391cb64890bb8e0050d3f023520a8dd5aee43c4d3f9c6f8611da668"


text:
%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/

%% Created for Blaise Bourdin at 2018-12-12 22:11:46 +0900

%% Saved with string encoding Unicode (UTF-8)

@article{Chambolle-Conti-EtAl-2017a,
	Author = {Chambolle, A. and Conti, S. and Francfort, G. A.},
	Date-Added = {2018-12-12 22:11:41 +0900},
	Date-Modified = {2018-12-12 22:11:41 +0900},
	Journal = {Arch. Rat. Mech. Anal.},
	Note = {arXiv:1709.04208},
	Number = {3},
	Pages = {867--889},
	Title = {Approximation of a Brittle Fracture Energy with a Constraint of Non-Interpenetration},
	Volume = {228},
	Year = {2018},
	Bdsk-File-1 = {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}}

@phdthesis{Li-2016a,
	Author = {Li, T.},
	Date-Added = {2018-12-12 21:57:24 +0900},
	Date-Modified = {2018-12-12 21:57:24 +0900},
	Month = {October},
	School = {Universit{\'e} Paris-Saclay -- {\'E}cole Polytechnique},
	Title = {Gradient Damage Modeling of Dynamic Brittle Fracture},
	Year = {2016},
	Bdsk-File-1 = {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}}

@article{Alessi-Marigo-EtAl-2017a,
	Author = {Alessi, R. and Marigo, J.-J. and Maurini, C. and Vidoli, S.},
	Date-Added = {2018-12-12 21:37:15 +0900},
	Date-Modified = {2018-12-12 21:37:15 +0900},
	Doi = {10.1016/j.ijmecsci.2017.05.047},
	Journal = {Int. J. Mech. Sci.},
	Keywords = {Variational methods, Phase-field, Cohesive fracture, Ductile fracture},
	Title = {Coupling damage and plasticity for a phase-field regularisation of brittle, cohesive and ductile fracture: One-dimensional examples},
	Url = {http://www.sciencedirect.com/science/article/pii/S0020740317300322},
	Year = {2017},
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@phdthesis{Alessi-2013a,
	Author = {Alessi, R.},
	Date-Added = {2018-12-12 21:37:15 +0900},
	Date-Modified = {2018-12-12 21:37:15 +0900},
	Month = {July},
	School = {Universit\`a di Roma la Sapienza and \'Ecole Polytechnique},
	Title = {Variational approach to fracture mechanics with plasticity},
	Year = {2013},
	Bdsk-File-1 = {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}}

@phdthesis{Tanne-2017a,
	Address = {{\'E}cole Polytechnique},
	Author = {Tann{\'e}, E.},
	Date-Added = {2018-12-12 21:36:33 +0900},
	Date-Modified = {2018-12-12 21:36:33 +0900},
	Month = {December},
	Note = {available from https://pastel.archives-ouvertes.fr/tel-01758354},
	School = {Universit{\'e} Paris-Saclay},
	Title = {Variational phase-field models from brittle to ductile fracture: nucleation and propagation},
	Year = {2017},
	Bdsk-File-1 = {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}}

@article{Pham-Marigo-EtAl-2011a,
	Author = {Pham, K. and Marigo, J.-J. and Maurini, C.},
	Date-Added = {2016-10-25 19:49:10 +0000},
	Date-Modified = {2016-10-25 19:49:10 +0000},
	Doi = {DOI: 10.1016/j.jmps.2011.03.010},
	Issn = {0022-5096},
	Journal = {J. Mech. Phys. Solids},
	Keywords = {Bifurcation},
	Number = {6},
	Pages = {1163 - 1190},
	Title = {The issues of the uniqueness and the stability of the homogeneous response in uniaxial tests with gradient damage models},
	Url = {http://dx.doi.org/10.1016/j.jmps.2011.03.010},
	Volume = {59},
	Year = {2011},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S002250961100055X}}

@book{Zehnder-2012a,
	Author = {Zehnder, A T},
	Date-Added = {2014-02-11 04:48:44 +0000},
	Date-Modified = {2014-02-11 04:48:44 +0000},
	Publisher = {Springer-Verlag},
	Series = {Lecture Notes in Applied and Computational Mechanics, No 62},
	Title = {Fracture Mechanics},
	Year = {2012}}

@article{Bourdin-Francfort-EtAl-2000a,
	Author = {Bourdin, B. and Francfort, G.A. and Marigo, J.-J.},
	Coden = {JMPSA8},
	Date-Added = {2014-02-11 00:19:57 +0000},
	Date-Modified = {2014-02-11 00:19:57 +0000},
	Fjournal = {Journal of the Mechanics and Physics of Solids},
	Issn = {0022-5096},
	Journal = {J. Mech. Phys. Solids},
	Keywords = {fracture, fracture toughness, energy methods, variational calculus, finite elements},
	Local-Url = {Bourdin-EtAl-2000.pdf},
	Number = {4},
	Pages = {797--826},
	Title = {Numerical experiments in revisited brittle fracture},
	Url = {http://dx.doi.org/10.1016/S0022-5096(99)00028-9},
	Volume = {48},
	Year = {2000},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0022-5096(99)00028-9}}

@inproceedings{Amor-Marigo-EtAl-2008a,
	Author = {Amor, H. and Marigo, J.-J. and Maurini, C. and Pham, K.},
	Booktitle = {Proceedings of the 8th. World Congress on Computational Mechanics (WCCM8) 5th European Congress on Computational Methods in Applied Sciences and Engineeering (ECCOMAS 2008)},
	Date-Added = {2014-02-11 00:18:19 +0000},
	Date-Modified = {2014-02-11 00:18:19 +0000},
	Title = {Stability analysis and numerical implementation of non-local damage models via a global variational approach},
	Year = {2008},
	Bdsk-File-1 = {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}}

@article{Pham-Amor-EtAl-2011a,
	Author = {Pham, K. and Amor, H. and Marigo, J.-J. and Maurini, C.},
	Date-Added = {2014-02-11 00:18:19 +0000},
	Date-Modified = {2014-02-11 00:18:19 +0000},
	Doi = {10.1177/1056789510386852},
	Issn = {1056-7895},
	Journal = {International Journal of Damage Mechanics},
	Number = {4, SI},
	Pages = {618-652},
	Title = {Gradient Damage Models and Their Use to Approximate Brittle Fracture},
	Url = {http://dx.doi.org/10.1177/1056789510386852},
	Volume = {20},
	Year = {2011},
	Bdsk-File-1 = {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}}

@article{Giacomini-2005,
	Abstract = {We define a notion of quasistatic evolution for the elliptic approximation of the Mumford-Shah functional proposed by Ambrosio and Tortorelli. Then we prove that this regular evolution converges to a quasi static growth of brittle fractures in linearly elastic bodies. },
	Author = {Giacomini, A.},
	Date-Added = {2014-02-10 22:53:50 +0000},
	Date-Modified = {2014-02-10 22:53:50 +0000},
	Fjournal = {Calculus of Variations and Partial Differential Equations},
	Issn = {0944-2669},
	Journal = {Calc. Var. Partial Differential Equations},
	Local-Url = {Giacomini-2005.pdf},
	Mrclass = {35B27 (35R35 49J45 74G65 74R10)},
	Mrnumber = {MR2106765},
	Number = {2},
	Pages = {129--172},
	Title = {Ambrosio-{T}ortorelli approximation of quasi-static evolution of brittle fractures},
	Volume = {22},
	Year = {2005},
	Bdsk-File-1 = {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}}

@article{Knepley-Karpeev-2009a,
	Author = {Knepley, M. and Karpeev, D.},
	Date-Added = {2014-02-10 20:32:59 +0000},
	Date-Modified = {2014-02-10 20:32:59 +0000},
	Journal = {Scientific Programming},
	Number = {3},
	Pages = {215--230},
	Title = {Mesh Algorithms for PDE with {S}ieve {I}: Mesh Distribution},
	Volume = {17},
	Year = {2009},
	Bdsk-File-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxAyLi4vLi4vRG9jdW1lbnRzL1BhcGVycy9LbmVwbGV5LUthcnBlZXYtMjAwN2EtMC5wZGZPEQG+AAAAAAG+AAIAAAxNYWNpbnRvc2ggSEQAAAAAAAAAAAAAAAAAAAC2dQ0QSCsAAAAIk+kbS25lcGxleS1LYXJwZWV2LTIwMDdhLTAucGRmAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAiVDcYvQHcAAAAAAAAAAAACAAMAAAkgAAAAAAAAAAAAAAAAAAAABlBhcGVycwAQAAgAALZ1fZAAAAARAAgAAMYvoucAAAABABAACJPpAAhdAgAIOPsAByWpAAIARk1hY2ludG9zaCBIRDpVc2VyczpibGFpc2U6RG9jdW1lbnRzOlBhcGVyczpLbmVwbGV5LUthcnBlZXYtMjAwN2EtMC5wZGYADgA4ABsASwBuAGUAcABsAGUAeQAtAEsAYQByAHAAZQBlAHYALQAyADAAMAA3AGEALQAwAC4AcABkAGYADwAaAAwATQBhAGMAaQBuAHQAbwBzAGgAIABIAEQAEgA5VXNlcnMvYmxhaXNlL0RvY3VtZW50cy9QYXBlcnMvS25lcGxleS1LYXJwZWV2LTIwMDdhLTAucGRmAAATAAEvAAAVAAIADf//AAAACAANABoAJABZAAAAAAAAAgEAAAAAAAAABQAAAAAAAAAAAAAAAAAAAhs=}}

@inproceedings{petsc-efficient,
	Author = {Balay, S. and Gropp, W.D. and Curfman McInnes, L. and Smith, B.F.},
	Booktitle = {Modern Software Tools in Scientific Computing},
	Date-Added = {2014-02-10 20:31:51 +0000},
	Date-Modified = {2014-02-10 20:31:51 +0000},
	Editor = {Arge, E. and Bruaset, A. M. and Langtangen, H. P.},
	Pages = {163--202},
	Publisher = {Birkh{\"{a}}user Press},
	Title = {Efficient Management of Parallelism in Object Oriented Numerical Software Libraries},
	Year = {1997}}

@techreport{petsc-user-ref,
	Author = {Balay, S. and Brown, J. and and K. Buschelman and Eijkhout, V. and Gropp, W.D. and Kaushik, D. and Knepley, M.G. and Curfman McInnes, L. and Smith, B.F. and Zhang, H.},
	Date-Added = {2014-02-10 20:31:51 +0000},
	Date-Modified = {2014-02-10 20:31:51 +0000},
	Institution = {Argonne National Laboratory},
	Number = {ANL-95/11 - Revision 3.3},
	Title = {{PETS}c Users Manual},
	Year = {2012}}

@misc{petsc-web-page,
	Author = {Balay, S. and Brown, J. and Buschelman, K. and Gropp, W.D. and Kaushik, D. and Knepley, M.G. and McInnes, L. Curfman and Smith, B.F. and Zhang, H.},
	Date-Added = {2014-02-10 20:31:51 +0000},
	Date-Modified = {2014-02-10 20:31:51 +0000},
	Note = {http://www.mcs.anl.gov/petsc},
	Title = {{PETSc} {W}eb page},
	Year = {2012}}

@article{Francfort-Marigo-1998,
	Author = {Francfort, G.A. and Marigo, J.-J.},
	Date-Added = {2014-02-10 17:09:23 +0000},
	Date-Modified = {2014-02-10 17:09:23 +0000},
	Journal = {J. Mech. Phys. Solids.},
	Keywords = {fracture, energy release rate, fracture toughness, energy methods, variational calculus},
	Local-Url = {Francfort-Marigo-1998.pdf},
	Number = 8,
	Pages = {1319--1342},
	Title = {Revisiting brittle fracture as an energy minimization problem},
	Url = {http://dx.doi.org/10.1016/S0022-5096(98)00034-9},
	Volume = 46,
	Year = 1998,
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/S0022-5096(98)00034-9}}

@article{Sicsic-Marigo-EtAl-2013a,
	Author = {Sicsic, P. and Marigo, J-J. and Maurini, C.},
	Date-Added = {2014-02-10 16:32:58 +0000},
	Date-Modified = {2014-02-10 16:32:58 +0000},
	Journal = {Journal of the Mechanics and Physics of Solids},
	Pages = {256--284},
	Title = {Initiation of a periodic array of cracks in the thermal shock problem: a gradient damage modeling},
	Url = {http://dx.doi.org/10.1016/j.jmps.2013.09.003},
	Volume = {63},
	Year = {2013},
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@article{Sicsic-Marigo-2013a,
	Author = {Sicsic, P. and Marigo, J.-J.},
	Date-Added = {2014-02-10 16:32:58 +0000},
	Date-Modified = {2014-02-10 16:32:58 +0000},
	Journal = {Journal of Elasticity},
	Number = {1},
	Pages = {55--74},
	Title = {From Gradient Damage Laws to {G}riffith's Theory of Crack Propagation},
	Url = {http://dx.doi.org/10.1007/s10659-012-9410-5},
	Volume = {113},
	Year = {2013},
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	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10659-012-9410-5}}

@article{Pham-Marigo-2013a,
	Affiliation = {Institut Jean Le Rond d'Alembert, Universit{\'e} Pierre et Marie Curie, 4 place Jussieu, 75252 Paris, France},
	Author = {Pham, K. and Marigo, J.-J.},
	Date-Added = {2014-02-10 16:26:46 +0000},
	Date-Modified = {2014-02-10 16:26:46 +0000},
	Issn = {0374-3535},
	Journal = {Journal of Elasticity},
	Keyword = {Physics and Astronomy},
	Note = {to appear in J. Elasticity},
	Number = {1},
	Pages = {63--93},
	Publisher = {Springer Netherlands},
	Title = {Stability of Homogeneous States with Gradient Damage Models: Size Effects and Shape Effects in the Three-Dimensional Setting},
	Url = {http://dx.doi.org/10.1007/s10659-012-9382-5},
	Volume = {110},
	Year = {2013},
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	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10659-012-9382-5}}

@article{Pham-Marigo-2011a,
	Author = {Pham, K. and Marigo, J.-J.},
	Date-Added = {2014-02-10 16:26:46 +0000},
	Date-Modified = {2014-02-10 16:26:46 +0000},
	Journal = {Continuum Mech. Thermodyn.},
	Number = {2-4},
	Pages = {147-171},
	Title = {From the onset of damage until the rupture: construction of the responses with damage localization for a general class of gradient damage models},
	Volume = {25},
	Year = {2013},
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	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00161-011-0228-3}}

@article{Chambolle-Francfort-EtAl-2009a,
	Author = {Chambolle, A. and Francfort, G.A. and Marigo, J.-J.},
	Date-Added = {2014-02-10 16:17:59 +0000},
	Date-Modified = {2014-02-10 16:17:59 +0000},
	Doi = {DOI: 10.1016/j.jmps.2009.05.009},
	Issn = {0022-5096},
	Journal = {Journal of the Mechanics and Physics of Solids},
	Keywords = {Stability},
	Number = {9},
	Pages = {1614--1622},
	Title = {When and how do cracks propagate?},
	Url = {http://www.sciencedirect.com/science/article/B6TXB-4WBK7K9-1/2/762979201c9bdccf70d8a65cd52053b6},
	Volume = {57},
	Year = {2009},
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	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TXB-4WBK7K9-1/2/762979201c9bdccf70d8a65cd52053b6}}

@article{Ambrosio-Tortorelli-1990,
	Author = {Ambrosio, L. and Tortorelli, V.M.},
	Coden = {CPAMA},
	Date-Added = {2014-02-10 16:17:39 +0000},
	Date-Modified = {2014-02-10 16:17:39 +0000},
	Fjournal = {Communications on Pure and Applied Mathematics},
	Issn = {0010-3640},
	Journal = {Comm. Pure Appl. Math.},
	Number = {8},
	Pages = {999--1036},
	Title = {Approximation of functionals depending on jumps by elliptic functionals via {$\Gamma$}-convergence},
	Volume = {43},
	Year = {1990},
	Bdsk-File-1 = {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}}

@article{Ambrosio-Tortorelli-1992,
	Author = {Ambrosio, L. and Tortorelli, V.M.},
	Coden = {BLUMAM},
	Date-Added = {2014-02-10 16:17:39 +0000},
	Date-Modified = {2014-02-10 16:17:39 +0000},
	Fjournal = {Unione Matematica Italiana. Bollettino. B. Serie VII},
	Journal = {Boll. Un. Mat. Ital. B (7)},
	Local-Url = {Ambrosio-Tortorelli-1992.pdf},
	Number = {1},
	Pages = {105--123},
	Title = {On the approximation of free discontinuity problems},
	Volume = {6},
	Year = {1992},
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@book{Braides-1998a,
	Author = {Braides, A.},
	Date-Added = {2014-02-10 16:17:27 +0000},
	Date-Modified = {2014-02-10 16:17:27 +0000},
	Number = {1694},
	Publisher = {Springer},
	Series = {Lecture Notes in Mathematics},
	Title = {Approximation of Free-Discontinuity Problems},
	Url = {http://www.springerlink.com/content/978-3-540-64771-3/},
	Year = {1998},
	Bdsk-File-1 = {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}}

@article{Bourdin-2007a,
	Author = {Bourdin, B.},
	Date-Added = {2014-02-10 15:50:47 +0000},
	Date-Modified = {2014-02-10 15:50:47 +0000},
	Journal = {Interfaces Free Bound.},
	Local-Url = {Bourdin-2007a.pdf},
	Month = {08},
	Pages = {411--430},
	Title = {Numerical implementation of a variational formulation of quasi-static brittle fracture},
	Volume = {9},
	Year = {2007},
	Bdsk-File-1 = {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}}

@article{Bourdin-Marigo-EtAl-2014a,
	Author = {Bourdin, B. and Marigo, J.-J. and Maurini, C. and Sicsic, P.},
	Date-Added = {2014-02-10 15:50:32 +0000},
	Date-Modified = {2014-02-10 21:40:42 +0000},
	Journal = {Phys. Rev. Lett.},
	Number = {1},
	Pages = {014301},
	Title = {Morphogenesis and Propagation of Complex Cracks Induced by Thermal Shocks},
	Url = {http://dx.doi.org/10.1103/PhysRevLett.112.014301},
	Volume = {112},
	Year = {2014},
	Bdsk-File-1 = {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},
	Bdsk-Url-1 = {http://arxiv.org/abs/1310.0501}}

@unpublished{Hossein-Hsueh-EtAl-2014a,
	Author = {Hossein, M.Z. and Hsueh, C.-J. and Bourdin, B. and Bhattacharya, K.},
	Date-Added = {2014-02-10 15:50:32 +0000},
	Date-Modified = {2014-02-10 15:50:32 +0000},
	Note = {Submitted to \emph{J. Mech. Phys. Solids}},
	Title = {Effective toughness of heterogeneous media},
	Year = {2014},
	Bdsk-File-1 = {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}}

@article{Bourdin-Francfort-EtAl-2008b,
	Author = {Bourdin, B. and Francfort, G.A. and Marigo, J.-J.},
	Date-Added = {2014-02-10 15:50:07 +0000},
	Date-Modified = {2014-02-10 15:50:07 +0000},
	Journal = {J. Elasticity},
	Number = {1-3},
	Pages = {1--148},
	Title = {The Variational Approach to Fracture},
	Url = {http://dx.doi.org/10.1007/s10659-007-9107-3},
	Volume = {91},
	Year = {2008},
	Bdsk-File-1 = {YnBsaXN0MDDSAQIDBFxyZWxhdGl2ZVBhdGhZYWxpYXNEYXRhXxBFLi4vLi4vLi4vLi4vRHJvcGJveC9BcnRpY2xlcy9MaWJyYXJ5L0JvdXJkaW4tRnJhbmNmb3J0LUV0QWwtMjAwOGEucGRmTxEB7AAAAAAB7AACAAAMTWFjaW50b3NoIEhEAAAAAAAAAAAAAAAAAAAAzKaAQkgrAAAAByeyH0JvdXJkaW4tRnJhbmNmb3J0LUV0QSM3Mjg4Ni5wZGYAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAHKIbIQUCZAAAAAAAAAAAABAAEAAAJIAAAAAAAAAAAAAAAAAAAAAdMaWJyYXJ5AAAQAAgAAMymxpIAAAARAAgAAMhBhukAAAABABQAByeyAAcndAAHHtwABk/MAAIGOwACAFdNYWNpbnRvc2ggSEQ6VXNlcnM6AGJsYWlzZToARHJvcGJveDoAQXJ0aWNsZXM6AExpYnJhcnk6AEJvdXJkaW4tRnJhbmNmb3J0LUV0QSM3Mjg4Ni5wZGYAAA4AQgAgAEIAbwB1AHIAZABpAG4ALQBGAHIAYQBuAGMAZgBvAHIAdAAtAEUAdABBAGwALQAyADAAMAA4AGEALgBwAGQAZgAPABoADABNAGEAYwBpAG4AdABvAHMAaAAgAEgARAASAEZVc2Vycy9ibGFpc2UvRHJvcGJveC9BcnRpY2xlcy9MaWJyYXJ5L0JvdXJkaW4tRnJhbmNmb3J0LUV0QWwtMjAwOGEucGRmABMAAS8AABUAAgAN//8AAAAIAA0AGgAkAGwAAAAAAAACAQAAAAAAAAAFAAAAAAAAAAAAAAAAAAACXA==},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10659-007-9107-3}}

@article{Amor-Marigo-Maurini-2009,
	Abstract = {This paper presents a modified regularized formulation of the Ambrosio-Tortorelli type to introduce the crack non-interpenetration condition in the variational approach to fracture mechanics proposed by Francfort and Marigo [1998. Revisiting brittle fracture as an energy minimization problem. J. Mech. Phys. Solids 46 (8), 1319-1342]. We focus on the linear elastic case where the contact condition appears as a local unilateral constraint on the displacement jump at the crack surfaces. The regularized model is obtained by splitting the strain energy in a spherical and a deviatoric parts and accounting for the sign of the local volume change. The numerical implementation is based on a standard finite element discretization and on the adaptation of an alternate minimization algorithm used in previous works. The new regularization avoids crack interpenetration and predicts asymmetric results in traction and in compression. Even though we do not exhibit any gamma-convergence proof toward the desired limit behavior, we illustrate through several numerical case studies the pertinence of the new model in comparison to other approaches. {\textcopyright} 2009 Elsevier Ltd. All rights reserved.},
	Author = {Amor, Hanen and Marigo, Jean Jacques and Maurini, Corrado},
	Doi = {10.1016/j.jmps.2009.04.011},
	File = {:Users/Erwan/Documents/Mendeley/Amor, Marigo, Maurini/Amor, Marigo, Maurini - 2009 - Journal of the Mechanics and Physics of Solids(2).pdf:pdf},
	Isbn = {0022-5096},
	Issn = {00225096},
	Journal = {Journal of the Mechanics and Physics of Solids},
	Keywords = {Contact mechanics,Energy methods,Finite elements,Fracture,Free-discontinuity problems},
	Number = {8},
	Pages = {1209--1229},
	Title = {{Regularized formulation of the variational brittle fracture with unilateral contact: Numerical experiments}},
	Volume = {57},
	Year = {2009}}

@article{Freddi-Carfagni-2011,
	Author = {Freddi, Francesco and Royer-Carfagni, Gianni},
	Doi = {10.1007/s12356-011-0018-4},
	File = {:Users/Erwan/Documents/Mendeley/Freddi, Royer-Carfagni/Freddi, Royer-Carfagni - 2011 - Annals of Solid and Structural Mechanics.pdf:pdf},
	Issn = {18676936},
	Journal = {Annals of Solid and Structural Mechanics},
	Keywords = {Biaxial loading,Fracture mechanics,Strength domain,Uniaxial compression,Uniaxial tension,Variational calculus},
	Number = {2-4},
	Pages = {57--67},
	Title = {{Variational fracture mechanics to model compressive splitting of masonry-like materials}},
	Volume = {2},
	Year = {2011}}

gha_license_id: NOASSERTION

gha_language: Fortran


text:
@article{ahuja2020pats,
  title={PATS Dataset: Pose, Audio, Transcripts and Style},
  author={Ahuja, Chaitanya and Lee, Dong Won and Nakano, Yukiko I. and Morency, Louis-Philippe},
  journal={},
  _venue={},
  year={},
  webpage={https://chahuja.com/pats}
}

repository: chahuja/cv

repo_name: chahuja/cv


text:
require qt5-git.inc
require ${BPN}.inc

QT_MODULE_BRANCH = "release"
# v5.2.1 + 25 commits
SRCREV = "9902dfdbc44934ce2e8072bc237ca8cdbfb3402b"


text:
@article{Patel2019,
abstract = {The ability to make decisions based on quantities of interest that depend on variables inferred from measurement finds application in different fields of mechanics and physics. The evaluation of the inferred variables, and hence the quantities of interest, from the measurement typically requires the solution of an inverse problem. For example, in medical imaging the elastic heterogeneity of a tumor and its nonlinear elastic response can be used to distinguish benign tumors from their malignant counterparts. These images of linear and nonlinear elastic parameters of tissue are typically obtained by using a measured displacement field and solving a complex inverse elasticity problem. In this paper we consider circumventing the solution of the inverse problem by using measured displacements as input to a deep convolutional neural network (CNN) and training it to classify tumors on the basis of their elastic heterogeneity and nonlinearity. For a simple, 5-layer CNN trained with 8,000 samples for heterogeneity, and a 4-layer CNN trained with 4,000 samples for nonlinear elasticity we report classification accuracies in the range of 99.7{\%}−99.9{\%}. The training and testing data are both obtained from the forward solution of finite element models of samples. We also analyze the weights of the trained model to understand the process through which the network extracts features of elastic moduli from the input displacement images. Finally, we apply the nonlinear elasticity classifier, which is trained entirely using simulated data, to displacement images obtained from ten patients with breast lesions and note that it correctly classifies eight out of ten cases. This application illustrates how data from physics-based models can be used in improving the performance of a data-driven algorithm in data-sparse scenarios.},
author = {Patel, Dhruv and Tibrewala, Raghav and Vega, Adriana and Dong, Li and Hugenberg, Nicholas and Oberai, Assad A.},
doi = {10.1016/j.cma.2019.04.045},
issn = {00457825},
journal = {Computer Methods in Applied Mechanics and Engineering},
month = {may},
publisher = {Elsevier BV},
title = {{Circumventing the solution of inverse problems in mechanics through deep learning: Application to elasticity imaging}},
year = {2019}
}


text:
package ww

import (
	"reflect"
	"testing"
)

type wwTest struct {
	width  int
	input  string
	output []string
}

var wwTests = []wwTest{
	{
		width:  1,
		input:  "aaa bbb ccc",
		output: []string{"aaa bbb ccc"},
	},
	{
		width:  5,
		input:  "a b c d e f g h i",
		output: []string{"a b c", "d e f", "g h i"},
	},
	{
		width:  5,
		input:  "aaaaaa b c d efg hijk",
		output: []string{"aaaaaa", "b c d", "efg", "hijk"},
	},
	{
		width:  5,
		input:  "aaaaa bbbbb cccc dddd eee fff gg hh i j",
		output: []string{"aaaaa", "bbbbb", "cccc", "dddd", "eee", "fff", "gg hh", "i j"},
	},
	{
		width:  5,
		input:  "aaaaa bbbbb cccc dddd eee fff gg hh i j llllll",
		output: []string{"aaaaa", "bbbbb", "cccc", "dddd", "eee", "fff", "gg hh", "i j", "llllll"},
	},
	{
		width:  5,
		input:  "a bb c d e f gggg hh ii j",
		output: []string{"a bb", "c d e", "f", "gggg", "hh ii", "j"},
	},
	{
		width:  5,
		input:  "aa bbb c dddd eee f gggggg hh iii jjjj kkkkk llll m n o p",
		output: []string{"aa", "bbb c", "dddd", "eee f", "gggggg", "hh", "iii", "jjjj", "kkkkk", "llll", "m n o", "p"},
	},
}

func Test(t *testing.T) {
	for _, wwt := range wwTests {
		t.Run("", func(t *testing.T) {
			o := Wrap(wwt.input, wwt.width)
			if !reflect.DeepEqual(wwt.output, o) {
				t.Errorf("failed to wrap input %s", wwt.input)
				t.Logf("output  : %#v", o)
				t.Logf("expected: %#v", wwt.output)
			}
		})
	}
}

repository: osm/ww

repo_name: osm/ww


text:
# Try to find CAF headers and libraries.
#
# Use this module as follows:
#
#     find_package(CAF [COMPONENTS <core|io|opencl|...>*] [REQUIRED])
#
# Variables used by this module (they can change the default behaviour and need
# to be set before calling find_package):
#
#  CAF_ROOT_DIR  Set this variable either to an installation prefix or to wa
#                CAF build directory where to look for the CAF libraries.
#
# Variables defined by this module:
#
#  CAF_FOUND              System has CAF headers and library
#  CAF_VERSION            Found CAF release number
#  CAF_LIBRARIES          List of library files  for all components
#  CAF_INCLUDE_DIRS       List of include paths for all components

if(CAF_FIND_COMPONENTS STREQUAL "")
  message(FATAL_ERROR "FindCAF requires at least one COMPONENT.")
endif()

# iterate over user-defined components
foreach (comp ${CAF_FIND_COMPONENTS})
  # we use uppercase letters only for variable names
  string(TOUPPER "${comp}" UPPERCOMP)
  if ("${comp}" STREQUAL "core")
    set(HDRNAME "caf/all.hpp")
  elseif ("${comp}" STREQUAL "test")
    set(HDRNAME "caf/test/unit_test.hpp")
  else ()
    set(HDRNAME "caf/${comp}/all.hpp")
  endif ()
  if (CAF_ROOT_DIR)
    set(header_hints
        "${CAF_ROOT_DIR}/include"
        "${CAF_ROOT_DIR}/libcaf_${comp}"
        "${CAF_ROOT_DIR}/../libcaf_${comp}"
        "${CAF_ROOT_DIR}/../../libcaf_${comp}")
  endif ()
  find_path(CAF_INCLUDE_DIR_${UPPERCOMP}
            NAMES
              ${HDRNAME}
            HINTS
              ${header_hints}
              /usr/include
              /usr/local/include
              /opt/local/include
              /sw/include
              ${CMAKE_INSTALL_PREFIX}/include
              ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})
  mark_as_advanced(CAF_INCLUDE_DIR_${UPPERCOMP})
  if (NOT "${CAF_INCLUDE_DIR_${UPPERCOMP}}"
      STREQUAL "CAF_INCLUDE_DIR_${UPPERCOMP}-NOTFOUND")
    # mark as found (set back to false when missing library or build header)
    set(CAF_${comp}_FOUND true)
    # check for CMake-generated build header for the core component
    if ("${comp}" STREQUAL "core")
      find_path(caf_build_header_path
                NAMES
                  caf/detail/build_config.hpp
                HINTS
                  ${header_hints}
                  /usr/include
                  /usr/local/include
                  /opt/local/include
                  /sw/include
                  ${CMAKE_INSTALL_PREFIX}/include
                  ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR})
      if ("${caf_build_header_path}" STREQUAL "caf_build_header_path-NOTFOUND")
        message(WARNING "Found all.hpp for CAF core, but not build_config.hpp")
        set(CAF_${comp}_FOUND false)
      else()
        list(APPEND CAF_INCLUDE_DIRS "${caf_build_header_path}")
      endif()
    endif()
    list(APPEND CAF_INCLUDE_DIRS "${CAF_INCLUDE_DIR_${UPPERCOMP}}")
    # look for (.dll|.so|.dylib) file, again giving hints for non-installed CAFs
    # skip probe_event as it is header only
    if (NOT ${comp} STREQUAL "probe_event" AND NOT ${comp} STREQUAL "test")
      if (CAF_ROOT_DIR)
        set(library_hints "${CAF_ROOT_DIR}/lib")
      endif ()
      find_library(CAF_LIBRARY_${UPPERCOMP}
                   NAMES
                     "caf_${comp}"
                     "caf_${comp}_static"
                   HINTS
                     ${library_hints}
                     /usr/lib
                     /usr/local/lib
                     /opt/local/lib
                     /sw/lib
                     ${CMAKE_INSTALL_PREFIX}/lib
                     ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}
                     ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}/${CMAKE_BUILD_TYPE})
      mark_as_advanced(CAF_LIBRARY_${UPPERCOMP})
      if ("${CAF_LIBRARY_${UPPERCOMP}}"
          STREQUAL "CAF_LIBRARY_${UPPERCOMP}-NOTFOUND")
        set(CAF_${comp}_FOUND false)
      else ()
        set(CAF_LIBRARIES ${CAF_LIBRARIES} ${CAF_LIBRARY_${UPPERCOMP}})
      endif ()
    endif ()
  endif ()
endforeach ()

if (DEFINED CAF_INCLUDE_DIRS)
  list(REMOVE_DUPLICATES CAF_INCLUDE_DIRS)
endif()

if (NOT CAF_INCLUDE_DIR_CORE STREQUAL "CAF_INCLUDE_DIR_CORE-NOTFOUND")
  # read content of config.hpp
  file(READ "${CAF_INCLUDE_DIR_CORE}/caf/config.hpp" CONFIG_HPP)
  # get line containing the version
  string(REGEX MATCH "#define CAF_VERSION [0-9]+" VERSION_LINE "${CONFIG_HPP}")
  # extract version number from line
  string(REGEX MATCH "[0-9]+" VERSION_INT "${VERSION_LINE}")
  # calculate major, minor, and patch version
  math(EXPR CAF_VERSION_MAJOR "${VERSION_INT} / 10000")
  math(EXPR CAF_VERSION_MINOR "( ${VERSION_INT} / 100) % 100")
  math(EXPR CAF_VERSION_PATCH "${VERSION_INT} % 100")
  # create full version string
  set(CAF_VERSION "${CAF_VERSION_MAJOR}.${CAF_VERSION_MINOR}.${CAF_VERSION_PATCH}")
  if (NOT CAF_VERSION)
    unset(CAF_VERSION)
    message(WARNING "Unable to determine CAF version")
  endif ()
endif ()

# let CMake check whether all requested components have been found
include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(CAF
                                  FOUND_VAR CAF_FOUND
                                  REQUIRED_VARS CAF_VERSION CAF_LIBRARIES CAF_INCLUDE_DIRS
                                  HANDLE_COMPONENTS)

# final step to tell CMake we're done
mark_as_advanced(CAF_ROOT_DIR
                 CAF_VERSION
                 CAF_LIBRARIES
                 CAF_INCLUDE_DIRS)

repository: dreambreaker-ds/cmake

repo_name: dreambreaker-ds/cmake

extension: cmake


text:
@article{khan_pre-hospital_2016,
 abstract = {© 2016 AMPCo Pty Ltd. Objective: The system of care in the Hunter New England Local Health District for patients with ST-segment elevation myocardial infarction (STEMI) foresees pre-hospital thrombolysis (PHT) administered by paramedics to patients more than 60 minutes from the cardiac catheterisation laboratory (CCL), and primary percutaneous coronary intervention (PCI) at the CCL for others. We assessed the safety and effectiveness of the pre-hospital diagnosis strategy, which allocates patients to PHT or primary PCI according to travel time to the CCL. Design, setting and participants: Prospective, non-randomised, consecutive, single-centre case series of STEMI patients diagnosed on the basis of a pre-hospital electrocardiogram (ECG), from August 2008 to August 2013. All patients were treated at the tertiary referral hospital (John Hunter Hospital, Newcastle). Main outcome measures: The primary efficacy endpoint was all-cause mortality at 12 months; the primary safety endpoint was bleeding. Results: STEMI was diagnosed in 484 patients on the basis of pre-hospital ECG; 150 were administered PHT and 334 underwent primary PCI. The median time from first medical contact (FMC) to PHT was 35 minutes (IQR, 28–43 min) and to balloon inflation 130 minutes (IQR, 100–150 min). In the PHT group, 37 patients (27%) needed rescue PCI (median time, 4 h; IQR, 3–5 h). The 12-month all-cause mortality rate was 7.0% (PHT, 6.7%; PCI, 7.2%). The incidence of major bleeding (TIMI criteria) in the PHT group was 1.3%; no patients in the primary PCI group experienced major bleeding. Conclusion: PHT can be delivered safely by paramedical staff in regional and rural Australia with good clinical outcomes.},
 author = {Khan, A.A. and Williams, T. and Savage, L. and Stewart, P. and Ashraf, A. and Davies, A.J. and Faddy, S. and Attia, J. and Oldmeadow, C. and Bhagwandeen, R. and Fletcher, P.J. and Boyle, A.J.},
 doi = {10.5694/mja15.01336},
 issn = {1326-5377},
 journal = {Medical Journal of Australia},
 keywords = {thrombolysis},
 month = {August},
 number = {3},
 pages = {121--125},
 title = {Pre-hospital thrombolysis in ST-segment elevation myocardial infarction: A regional Australian experience},
 volume = {205},
 year = {2016}
}

repository: ChrisOldmeadow/academic-kickstart

repo_name: ChrisOldmeadow/academic-kickstart


text:
DESCRIPTION = "Disko is an application framework, that can be used to develop GUI applications for embedded devices. It is closely connected to the DirectFB"
LICENSE = "GPL"
SRCREV = "f52597b8d5d584811cbe8f9e0bf25ea372526953"
PV = "1.6.1+gitr${SRCREV}"
PR = "r0"

DEFAULT_PREFERENCE = "-1"

require disko.inc

DEPENDS += "taglib directfb virtual/libx11 hal libxv libxxf86vm"

SRC_URI = "git://www.diskohq.org/disko.git;protocol=git \
	   file://pkgconfig.patch \
	  "

S = "${WORKDIR}/git"

do_compile() {
	${STAGING_BINDIR_NATIVE}/scons ${PARALLEL_MAKE} graphics=all prefix=${prefix}/ || \
        oefatal "scons build execution failed."
}

repository: trini/openembedded

repo_name: trini/openembedded


text:
@article{wang2018masd,
  title={MASD: A Multimodal Assembly Skill Decoding System for Robot Programming by Demonstration},
  author={Wang, Yue and Jiao, Yanmei and Xiong, Rong and Yu, Hongsheng and Zhang, Jiafan and Liu, Yong},
  journal={IEEE Transactions on Automation Science and Engineering},
  volume={15},
  number={4},
  pages={1722--1734},
  year={2018},
  publisher={IEEE}
}

repository: slinkle/academic-kickstart

repo_name: slinkle/academic-kickstart


text:
package api

import (
	"net/http"

	"github.com/DisgoOrg/log"
)

// Options is the configuration used when creating the client
type Options struct {
	Logger                    log.Logger
	GatewayIntents            GatewayIntents
	RestTimeout               int
	EnableWebhookInteractions bool
	ListenPort                int
	ListenURL                 string
	PublicKey                 string
	LargeThreshold            int
	RawGatewayEventsEnabled   bool
	HTTPClient                *http.Client
}


text:
package keeper

import (
	sdk "github.com/cosmos/cosmos-sdk/types"
	"github.com/summa-tx/relays/golang/x/relay/types"
)

func (k Keeper) emitProofProvided(
	ctx sdk.Context,
	filled types.FilledRequests,
) {
	filledIDs := []types.RequestID{}
	for _, f := range filled.Filled {
		filledIDs = append(filledIDs, f.ID)
	}
	ctx.EventManager().EmitEvent(types.NewProofProvidedEvent(filled.Proof.TxID, filledIDs))
}

// getConfs returns the number of confirmations of any given header
func (k Keeper) getConfs(ctx sdk.Context, header types.BitcoinHeader) (uint32, sdk.Error) {
	bestKnown, err := k.GetBestKnownDigest(ctx)
	if err != nil {
		return 0, err
	}
	bestKnownHeader, err := k.GetHeader(ctx, bestKnown)
	if err != nil {
		return 0, err
	}
	return bestKnownHeader.Height - header.Height, nil
}

// validateProof validates an SPV Proof and checks that it is stored correctly
func (k Keeper) validateProof(ctx sdk.Context, proof types.SPVProof) sdk.Error {
	// If it is not valid, it will return an error
	_, err := proof.Validate()
	if err != nil {
		return types.FromBTCSPVError(types.DefaultCodespace, err)
	}

	lca, lcaErr := k.GetLastReorgLCA(ctx)
	if lcaErr != nil {
		return lcaErr
	}
	isAncestor := k.IsAncestor(ctx, proof.ConfirmingHeader.Hash, lca, 240)
	if !isAncestor {
		return types.ErrNotAncestor(types.DefaultCodespace, proof.ConfirmingHeader.Hash)
	}

	return nil
}

func (k Keeper) checkRequestsFilled(ctx sdk.Context, filledRequests types.FilledRequests) ([]types.ProofRequest, sdk.Error) {
	// Validate Proof once
	err := k.validateProof(ctx, filledRequests.Proof)
	if err != nil {
		return nil, err
	}

	confs, confsErr := k.getConfs(ctx, filledRequests.Proof.ConfirmingHeader)
	if confsErr != nil {
		return nil, confsErr
	}

	var filled []types.ProofRequest

	for i := range filledRequests.Filled {
		// get request
		request, getErr := k.getRequest(ctx, filledRequests.Filled[i].ID)
		if getErr != nil {
			return nil, getErr
		}
		// check confirmations
		if confs < uint32(request.NumConfs) {
			return nil, types.ErrNotEnoughConfs(types.DefaultCodespace, filledRequests.Filled[i].ID)
		}

		// check request
		err := k.checkRequests(
			ctx,
			filledRequests.Filled[i].InputIndex,
			filledRequests.Filled[i].OutputIndex,
			filledRequests.Proof.Vin,
			filledRequests.Proof.Vout,
			filledRequests.Filled[i].ID)
		if err != nil {
			return nil, err
		}

		filled = append(filled, request)
	}

	k.emitProofProvided(ctx, filledRequests)
	return filled, nil
}

repository: summa-tx/relays

repo_name: summa-tx/relays


text:
find_path(NETCDF_INCLUDE_DIR netcdf.h)

find_library(NETCDF_LIBRARY NAMES netcdf)

set(NETCDF_LIBRARIES ${NETCDF_LIBRARY})
set(NETCDF_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})

include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(NetCDF REQUIRED_VARS NETCDF_INCLUDE_DIRS NETCDF_LIBRARIES)

repository: hmenke/ryuon-cmake

repo_name: hmenke/ryuon-cmake


text:
@Inbook{nielsen09clumnd,
  author="Nielsen, Frank and Nock, Richard",
  editor="Nielsen, Frank" ,
  title="Clustering Multivariate Normal Distributions",
  bookTitle="Emerging Trends in Visual Computing: LIX Fall Colloquium, ETVC 2008, Palaiseau, France, November 18-20, 2008. Revised Invited Papers",
  year="2009",
  publisher="Springer Berlin Heidelberg",
  address="Berlin, Heidelberg",
  pages="164--174",
  isbn="978-3-642-00826-9",
  doi="10.1007/978-3-642-00826-9_7",
  url="http://dx.doi.org/10.1007/978-3-642-00826-9_7"
}

@InProceedings{nielsen11staefd,
  author = "Frank Nielsen and Vincent Garcia",
  title = "Statistical exponential families: A digest with flash cards",
  note = "https://arxiv.org/abs/0911.4863",
  year = 2011
}

repository: vishalbelsare/crowdastro

repo_name: vishalbelsare/crowdastro