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add validation of certificate identifier in codechecl.yml validation
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‎DESCRIPTION‎

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Package: codecheck
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Title: Helper Functions for CODECHECK Project
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Version: 0.17.0
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Version: 0.18.0
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Authors@R:
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c(person(given = "Stephen",
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family = "Eglen",

‎R/configuration.R‎

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@@ -204,6 +204,13 @@ validate_codecheck_yml <- function(configuration) {
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stop("Could not load codecheck configuration from input '", configuration, "'")
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}
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# MUST have a non-empty certificate identifier matching the pattern NNNN-NNN
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assertthat::assert_that(isTRUE(grepl("^\\d{4}-\\d{3}$", codecheck_yml$certificate)), # if certificate is missing, grepl returns a logical(0)
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msg = paste0("The certificate identifier '",
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codecheck_yml$certificate,
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"' is missing or invalid")
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)
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# MUST have manifest
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assertthat::assert_that(assertthat::has_name(codecheck_yml, "manifest"),
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msg = paste0("codecheck.yml must have a root-level node 'manifest'",
@@ -235,9 +242,8 @@ validate_codecheck_yml <- function(configuration) {
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# Check if the paper_link contains a valid URL. We only check that it starts with https?://
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url_regex <- "^https?://"
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if (!grepl(url_regex, codecheck_yml$paper$reference)) {
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warning("The paper reference in the codecheck.yml is not a valid URL")
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}
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assertthat::assert_that(grepl(url_regex, codecheck_yml$paper$reference),
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msg = paste0(codecheck_yml$paper$reference, " is not a valid URL"))
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# if ORCID are used, they must be without URL prefix and valid form, actual checking requires login, see #11
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orcid_regex <- "^(\\d{4}\\-\\d{4}\\-\\d{4}\\-\\d{3}(\\d|X))$"

‎inst/tinytest/test_codecheck_yml.R‎

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expect_silent(validate_codecheck_yml("yaml/codecheck.yml"))
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expect_true(validate_codecheck_yml("yaml/codecheck.yml"))
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# certificate ID ----
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expect_error(validate_codecheck_yml("yaml/certificate_id_missing/codecheck.yml"),
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pattern = "'' is missing or invalid")
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expect_error(validate_codecheck_yml("yaml/certificate_id_invalid/codecheck1.yml"),
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pattern = "'20XX-000' is missing or invalid")
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expect_error(validate_codecheck_yml("yaml/certificate_id_invalid/codecheck2.yml"),
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pattern = "'2025-99' is missing or invalid")
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expect_error(validate_codecheck_yml("yaml/certificate_id_invalid/codecheck3.yml"),
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pattern = "'' is missing or invalid")
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# manifest ----
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expect_error(validate_codecheck_yml("yaml/manifest_missing/codecheck.yml"),
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pattern = "root-level node 'manifest'")

‎inst/tinytest/yaml/author_name_missing/codecheck.yml‎

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@@ -26,5 +26,5 @@ summary: >
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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate: 2020-XYZ
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certificate: 2020-999
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report: https://doi.org/10.5281/zenodo.FIXME

‎inst/tinytest/yaml/certificate_id_invalid/codecheck1.yml‎

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---
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version: https://codecheck.org.uk/spec/config/1.0
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paper:
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title: >
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The principal components of natural images
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authors:
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- name: Peter J. B. Hancock
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- name: Roland J. Baddeley
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- name: Leslie S. Smith
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ORCID: 0000-0002-3716-8013
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reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
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manifest:
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- file: Figure2.png
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comment: manuscript Figure 2
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- file: Figure3.png
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comment: manuscript Figure 3
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- file: Figure4.png
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comment: manuscript Figure 4
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- file: Figure5.png
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comment: manuscript Figure 5
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- file: Figure6.png
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comment: manuscript Figure 6
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- file: Figure7.png
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comment: manuscript Figure 7
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- file: Figure8.png
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comment: manuscript Figure 8
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codechecker:
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- name: Stephen J. Eglen
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ORCID: 0000-0001-8607-8025
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- name: Daniel Nüst
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ORCID: 0000-0002-0024-5046
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summary: >
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Matlab code written by Iain Davies to reproduce original
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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate: 20XX-000
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report: https://doi.org/10.5281/zenodo.FIXME

‎inst/tinytest/yaml/certificate_id_invalid/codecheck2.yml‎

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---
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version: https://codecheck.org.uk/spec/config/1.0
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paper:
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title: >
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The principal components of natural images
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authors:
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- name: Peter J. B. Hancock
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- name: Roland J. Baddeley
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- name: Leslie S. Smith
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ORCID: 0000-0002-3716-8013
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reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
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manifest:
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- file: Figure2.png
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comment: manuscript Figure 2
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- file: Figure3.png
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comment: manuscript Figure 3
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- file: Figure4.png
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comment: manuscript Figure 4
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- file: Figure5.png
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comment: manuscript Figure 5
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- file: Figure6.png
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comment: manuscript Figure 6
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- file: Figure7.png
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comment: manuscript Figure 7
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- file: Figure8.png
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comment: manuscript Figure 8
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codechecker:
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- name: Stephen J. Eglen
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ORCID: 0000-0001-8607-8025
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- name: Daniel Nüst
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ORCID: 0000-0002-0024-5046
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summary: >
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Matlab code written by Iain Davies to reproduce original
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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate: 2025-99
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report: https://doi.org/10.5281/zenodo.FIXME

‎inst/tinytest/yaml/certificate_id_invalid/codecheck3.yml‎

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---
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version: https://codecheck.org.uk/spec/config/1.0
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paper:
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title: >
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The principal components of natural images
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authors:
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- name: Peter J. B. Hancock
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- name: Roland J. Baddeley
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- name: Leslie S. Smith
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ORCID: 0000-0002-3716-8013
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reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
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manifest:
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- file: Figure2.png
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comment: manuscript Figure 2
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- file: Figure3.png
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comment: manuscript Figure 3
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- file: Figure4.png
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comment: manuscript Figure 4
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- file: Figure5.png
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comment: manuscript Figure 5
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- file: Figure6.png
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comment: manuscript Figure 6
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- file: Figure7.png
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comment: manuscript Figure 7
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- file: Figure8.png
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comment: manuscript Figure 8
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codechecker:
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- name: Stephen J. Eglen
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ORCID: 0000-0001-8607-8025
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- name: Daniel Nüst
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ORCID: 0000-0002-0024-5046
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summary: >
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Matlab code written by Iain Davies to reproduce original
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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate: ""
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report: https://doi.org/10.5281/zenodo.FIXME

‎inst/tinytest/yaml/certificate_id_missing/codecheck.yml‎

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---
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version: https://codecheck.org.uk/spec/config/1.0
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paper:
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title: >
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The principal components of natural images
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authors:
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- name: Peter J. B. Hancock
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- name: Roland J. Baddeley
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- name: Leslie S. Smith
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ORCID: 0000-0002-3716-8013
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reference: http://pdfs.semanticscholar.org/7dcf/a42cfe3b59becb441844b72558b361693608.pdf
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manifest:
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- file: Figure2.png
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comment: manuscript Figure 2
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- file: Figure3.png
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comment: manuscript Figure 3
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- file: Figure4.png
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comment: manuscript Figure 4
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- file: Figure5.png
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comment: manuscript Figure 5
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- file: Figure6.png
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comment: manuscript Figure 6
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- file: Figure7.png
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comment: manuscript Figure 7
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- file: Figure8.png
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comment: manuscript Figure 8
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codechecker:
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- name: Stephen J. Eglen
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ORCID: 0000-0001-8607-8025
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- name: Daniel Nüst
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ORCID: 0000-0002-0024-5046
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summary: >
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Matlab code written by Iain Davies to reproduce original
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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate:
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report: https://doi.org/10.5281/zenodo.FIXME

‎inst/tinytest/yaml/codecheck.yml‎

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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate: 2020-XYZ
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certificate: 2020-000
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report: https://doi.org/10.5281/zenodo.FIXME

‎inst/tinytest/yaml/codechecker_name_missing/codecheck.yml‎

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paper; natural images provided by Peter Hancock.
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repository: https://github.com/codecheckers/Reproduction-Hancock
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check_time: "2020-04-13 10:00:00"
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certificate: 2020-XYZ
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certificate: 2020-999
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report: https://doi.org/10.5281/zenodo.FIXME

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