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Fix error on empty bib files #15

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merged 8 commits into from
Aug 12, 2021
Merged

Fix error on empty bib files #15

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60fef48
Add warning on empty `CITATION.bib` files
SebastianM-C Aug 9, 2021
4c8e6a7
Don't error if there is no citation for a package
SebastianM-C Aug 9, 2021
4825b93
Update Symbolics test env
SebastianM-C Aug 11, 2021
f9598c0
Update tests
SebastianM-C Aug 11, 2021
9f40e4f
Fix line endings
SebastianM-C Aug 11, 2021
04ace17
Update doi for WriteVTK
SebastianM-C Aug 11, 2021
9f8d9b3
Sort citations
SebastianM-C Aug 12, 2021
b06a43d
Fix deprecation
SebastianM-C Aug 12, 2021
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2 changes: 1 addition & 1 deletion Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,8 @@ InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

[compat]
Bibliography = "0.2"
BibParser = "0.1"
Bibliography = "0.2"
DataStructures = "0.18"
HTTP = "0.9"
julia = "1.6"
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9 changes: 7 additions & 2 deletions src/citations.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,12 @@ function get_citation(pkg; badge=false)
if !isnothing(bib_path)
@debug "Reading CITATION.bib for $(pkg.name)"
try
import_bibtex(bib_path)
bib = import_bibtex(bib_path)
if isempty(bib)
@warn "The CITATION.bib file for $(pkg.name) is empty."
end

bib
catch e
@warn "There was an error reading the CITATION.bib file for $(pkg.name)" exception=e
end
Expand Down Expand Up @@ -47,7 +52,7 @@ function collect_citations(only_direct::Bool; badge=false)
end
end

return pkg_citations
return sort!(DataStructures.OrderedDict(pkg_citations))
end

function bibliography(pkg_citations)
Expand Down
1 change: 1 addition & 0 deletions src/tool_report.jl
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Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
function cite_package(name, bib; cite_commands)
isempty(bib) && return ""
if length(bib) == 1
key = only(keys(bib))
cmd = get(cite_commands, name, DEFAULT_CITE)
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79 changes: 39 additions & 40 deletions test/cite_str.jl
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Original file line number Diff line number Diff line change
@@ -1,40 +1,39 @@
const CITE_STR_JL =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the following packages: "*
"LabelledArrays.jl\\cite[LabelledArrays]{DifferentialEquations.jl-2017}, "*
"QuadGK.jl\\cite[QuadGK]{quadgk}, Symbolics.jl\\cite[Symbolics]{gowda2021high}, "*
"RecursiveArrayTools.jl\\cite[RecursiveArrayTools]{DifferentialEquations.jl-2017}, "*
"ArrayInterface.jl\\cite[ArrayInterface]{DifferentialEquations.jl-2017} and "*
"AbstractAlgebra.jl\\cite[AbstractAlgebra]{AbstractAlgebra.jl-2017}."

const CITE_STR_JL_AUTO =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the following packages: "*
"LabelledArrays.jl\\cite[LabelledArrays]{DifferentialEquations.jl-2017}, "*
"QuadGK.jl\\cite[QuadGK]{quadgk}, Symbolics.jl\\cite[Symbolics]{gowda2021high}, "*
"RecursiveArrayTools.jl\\cite[RecursiveArrayTools]{DifferentialEquations.jl-2017}, "*
"ArrayInterface.jl\\cite[ArrayInterface]{DifferentialEquations.jl-2017} and "*
"AbstractAlgebra.jl\\autocite[AbstractAlgebra]{AbstractAlgebra.jl-2017}."

const CITE_STR_JL_SINGLE =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the Symbolics.jl\\cite[Symbolics]{gowda2021high} package."

const CITE_STR_JL_SINGLE_TT =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the \\texttt{Symbolics.jl}\\cite[Symbolics]{gowda2021high} package."


const CITE_STR =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the following packages: "*
"LabelledArrays\\cite[LabelledArrays]{DifferentialEquations.jl-2017}, "*
"QuadGK\\cite[QuadGK]{quadgk}, Symbolics\\cite[Symbolics]{gowda2021high}, "*
"RecursiveArrayTools\\cite[RecursiveArrayTools]{DifferentialEquations.jl-2017}, "*
"ArrayInterface\\cite[ArrayInterface]{DifferentialEquations.jl-2017} and "*
"AbstractAlgebra\\cite[AbstractAlgebra]{AbstractAlgebra.jl-2017}."

const CITE_BADGE =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the Plots.jl\\cite[Plots]{https://doi.org/10.5281/zenodo.4725317} "*
"and WriteVTK.jl\\cite[WriteVTK]{https://doi.org/10.5281/zenodo.4692172} packages."
const CITE_STR_JL =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the following packages: "*
"ArrayInterface.jl\\cite[ArrayInterface]{DifferentialEquations.jl-2017}, "*
"LabelledArrays.jl\\cite[LabelledArrays]{DifferentialEquations.jl-2017}, "*
"QuadGK.jl\\cite[QuadGK]{quadgk}, "*
"RecursiveArrayTools.jl\\cite[RecursiveArrayTools]{DifferentialEquations.jl-2017} and "*
"Symbolics.jl\\cite[Symbolics]{gowda2021high}."

const CITE_STR_JL_AUTO =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the following packages: "*
"ArrayInterface.jl\\cite[ArrayInterface]{DifferentialEquations.jl-2017}, "*
"LabelledArrays.jl\\cite[LabelledArrays]{DifferentialEquations.jl-2017}, "*
"QuadGK.jl\\cite[QuadGK]{quadgk}, "*
"RecursiveArrayTools.jl\\cite[RecursiveArrayTools]{DifferentialEquations.jl-2017} and "*
"Symbolics.jl\\autocite[Symbolics]{gowda2021high}."

const CITE_STR_JL_SINGLE =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the Symbolics.jl\\cite[Symbolics]{gowda2021high} package."

const CITE_STR_JL_SINGLE_TT =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the \\texttt{Symbolics.jl}\\cite[Symbolics]{gowda2021high} package."

const CITE_STR =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the following packages: "*
"ArrayInterface\\cite[ArrayInterface]{DifferentialEquations.jl-2017}, "*
"LabelledArrays\\cite[LabelledArrays]{DifferentialEquations.jl-2017}, "*
"QuadGK\\cite[QuadGK]{quadgk}, "*
"RecursiveArrayTools\\cite[RecursiveArrayTools]{DifferentialEquations.jl-2017} and "*
"Symbolics\\cite[Symbolics]{gowda2021high}."

const CITE_BADGE =
"This work was done in \\cite[Julia v$VERSION]{Julia-2017} "*
"and made use of the Plots.jl\\cite[Plots]{https://doi.org/10.5281/zenodo.4725317} "*
"and WriteVTK.jl\\cite[WriteVTK]{https://doi.org/10.5281/zenodo.5068937} packages."
6 changes: 2 additions & 4 deletions test/runtests.jl
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Expand Up @@ -26,7 +26,6 @@ include("cite_str.jl")
@test "Symbolics" ∈ pkgs
@test "RecursiveArrayTools" ∈ pkgs
@test "ArrayInterface" ∈ pkgs
@test "AbstractAlgebra" ∈ pkgs
# There is an error in the CITATION.bib for Distributions
@test_broken haskey(citations, "Distributions")
end
Expand All @@ -35,7 +34,6 @@ include("cite_str.jl")
bib = bibliography(citations)
@test haskey(bib, "DifferentialEquations.jl-2017")
@test haskey(bib, "quadgk")
@test haskey(bib, "AbstractAlgebra.jl-2017")
@test haskey(bib, "gowda2021high")
end

Expand All @@ -48,7 +46,6 @@ include("cite_str.jl")

@test haskey(bib, "DifferentialEquations.jl-2017")
@test haskey(bib, "quadgk")
@test haskey(bib, "AbstractAlgebra.jl-2017")
@test haskey(bib, "gowda2021high")
end

Expand All @@ -68,7 +65,7 @@ include("cite_str.jl")
str = make_sentence(citations, jl=false)
@test str == CITE_STR

str = make_sentence(citations, cite_commands=Dict{String,String}("AbstractAlgebra"=>"\\autocite"))
str = make_sentence(citations, cite_commands=Dict{String,String}("Symbolics"=>"\\autocite"))
@test str == CITE_STR_JL_AUTO

@testset "Clipboard" begin
Expand All @@ -89,6 +86,7 @@ include("cite_str.jl")
@test_broken clipboard() == CITE_STR
end
end

@testset "PkgCite using badge" begin
zenodo_env = "badge_env"
Pkg.activate(zenodo_env)
Expand Down
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