Add Aqua and JET tests

.gitignore

@@ -1,3 +1,4 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
+Manifest.toml

Project.toml

@@ -1,17 +1,26 @@
 name = "EmpiricalCDFs"
 uuid = "0dcf7749-4f9f-5e13-9c57-506664207bbc"
+license = "MIT"
 version = "0.2.2"
-license= "MIT"
 
 [deps]
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+Aqua = ">= 0.8"
+JET = ">= 0.0"
+Printf = ">= 0.0"
+Random = ">= 0.0"
+Statistics = "1"
+Test = ">= 0.0"
 julia = "1"
 
 [extras]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test", "Aqua", "JET"]

README.md

@@ -1,23 +1,18 @@
+[![Build Status](https://github.com/jlapeyre/EmpiricalCDFs.jl/actions/workflows/CI.yml/badge.svg?branch=main)](https://github.com/jlapeyre/EmpiricalCDFs.jl/actions/workflows/CI.yml?query=branch%3Amain)
+[![Coverage](https://codecov.io/gh/jlapeyre/EmpiricalCDFs.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/jlapeyre/EmpiricalCDFs.jl)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
+[![JET QA](https://img.shields.io/badge/JET.jl-%E2%9C%88%EF%B8%8F-%23aa4444)](https://github.com/aviatesk/JET.jl)
+
 # EmpiricalCDFs.jl
 
 *Empirical cumulative distribution functions*
 
-[![](https://img.shields.io/badge/docs-latest-blue.svg)](https://jlapeyre.github.io/EmpiricalCDFs.jl/latest)
-Linux, OSX: [![Build Status](https://travis-ci.org/jlapeyre/EmpiricalCDFs.jl.svg?branch=master)](https://travis-ci.org/jlapeyre/EmpiricalCDFs.jl)
- 
-Windows: [![Build Status](https://ci.appveyor.com/api/projects/status/github/jlapeyre/EmpiricalCDFs.jl?branch=master&svg=true)](https://ci.appveyor.com/project/jlapeyre/empiricalcdfs-jl)
-     
-[![Coverage Status](https://coveralls.io/repos/jlapeyre/EmpiricalCDFs.jl/badge.svg?branch=master&service=github)](https://coveralls.io/github/jlapeyre/EmpiricalCDFs.jl?branch=master)
-[![codecov.io](http://codecov.io/github/jlapeyre/EmpiricalCDFs.jl/coverage.svg?branch=master)](http://codecov.io/github/jlapeyre/EmpiricalCDFs.jl?branch=master)
-
 Provides [empirical cumulative distribution functions (CDFs)](https://en.wikipedia.org/wiki/Empirical_distribution_function)
 (or "empirical distribution functions" as they are know to probabalists).
 
 See the documentation [https://jlapeyre.github.io/EmpiricalCDFs.jl/latest](https://jlapeyre.github.io/EmpiricalCDFs.jl/latest).
 
-~~I'm surprised that this module is not more popular (if stars are a good measure) because it's rather generic,
-I use it frequently for new projects,
-and the functionality is not available elsewhere.~~ In the meantime it's gained some stars.
+
 
 *EmpiricalCDFs* implements empirical CDFs; building, evaluating, random sampling, evaluating the inverse, etc.
 It is useful especially for examining the
@@ -26,6 +21,10 @@ For this purpose, you specify a lower cutoff; data points below this value will
 resulting CDF will still be properly normalized. This ability to process and filter data [online](https://en.wikipedia.org/wiki/Online_algorithm)
 is absent in `StatsBase.ecdf`.
 
+~~I'm surprised that this module is not more popular (if stars are a good measure) because it's rather generic,
+I use it frequently for new projects,
+and the functionality is not available elsewhere.~~ In the meantime it's gained some stars.
+
 <!-- LocalWords:  EmpiricalCDFs jl OSX codecov io CDFs probabalists CDF eg -->
 <!-- LocalWords:  julia cdf EmpiricalCDF xmin logprint linprint getinverse -->
 <!-- LocalWords:  quantile CDFfile AbstractEmpiricalCDF readcdf mle mleKS -->

src/IOcdf.jl

@@ -89,14 +89,36 @@ Return the version number of the file format.
 """
 version(cdff::CDFfile) = cdff.vn
 
-for f in (:sort!, :push!, :append!, :getindex, :length, :size, :firstindex, :lastindex, :rand, :minimum, :maximum)
+for f in (:sort!, :push!, :append!, :getindex, :length, :size, :firstindex, :lastindex)
     @eval Base.$(f)(cdff::CDFfile, args...) = $(f)(cdff.cdf, args...)
 end
 
-for f in (:mean, :std, :quantile )
+import Random
+for f in (:rand,)
+    @eval Base.$(f)(cdff::CDFfile) = $(f)(cdff.cdf)
+    @eval Base.$(f)(X::Random.AbstractRNG, cdff::CDFfile) = $(f)(X, cdff.cdf)
+end
+
+for f in (:extrema, :maximum, :minimum)
+    @eval begin
+        Base.$(f)(cdf::CDFfile; kws...) = $(f)(cdf.cdf; kws...)
+        Base.$(f)(func, cdf::CDFfile; kws...) = $(f)(func, cdf.cdf; kws...)
+    end
+end
+
+
+for f in (:std, :quantile )
     @eval Statistics.$(f)(cdff::CDFfile, args...) = $(f)(cdff.cdf, args...)
 end
 
+for f in (:mean,)
+    @eval begin
+        Statistics.$(f)(cdf::CDFfile; kws...) = Statistics.$(f)(cdf.cdf; kws...)
+        Statistics.$(f)(func, cdf::CDFfile; kws...) = Statistics.$(f)(func, cdf.cdf; kws...)
+    end
+end
+
+
 for f in (:getcdfindex, :counts)
 #           :mle, :KSstatistic, :mleKS, :scanmle)
     @eval $(f)(cdff::CDFfile, args...) = $(f)(cdff.cdf, args...)
@@ -111,7 +133,7 @@ end
 
 ####
 
-function make_CDFfile_version_string(v)
+function make_CDFfile_version_string(v::VersionNumber)
     nchars = 100
     s::String = "CDFfile " * string(v)
     s = s * " "^(nchars-length(s))

src/cdfs.jl

@@ -20,19 +20,37 @@ return the array holding samples for `cdf`.
 data(cdf::AbstractEmpiricalCDF) = cdf.xdata
 
 # Extend base functions
-for f in (:length, :size, :minimum, :maximum, :extrema, :issorted, :iterate, :getindex, :lastindex, :firstindex)
+for f in (:length, :size, :issorted, :iterate, :getindex, :lastindex, :firstindex)
     @eval begin
         Base.$(f)(cdf::AbstractEmpiricalCDF, args...) = $(f)(cdf.xdata, args...)
     end
 end
 
+for f in (:extrema, :maximum, :minimum)
+    @eval begin
+        Base.$(f)(cdf::AbstractEmpiricalCDF; kws...) = $(f)(cdf.xdata; kws...)
+        Base.$(f)(func, cdf::AbstractEmpiricalCDF; kws...) = $(f)(func, cdf.xdata; kws...)
+    end
+end
+
+# Base.extrema(cdf::AbstractEmpiricalCDF, a::AbstractArray) = extrema(cdf.xdata, a)
+import Base.Order
+Base.issorted(cdf::AbstractEmpiricalCDF, ord::Order.Ordering) = issorted(cdf.xdata, ord)
+
 # Extend Statistics functions
-for f in (:mean, :median, :middle, :std, :stdm, :var, :varm, :quantile)
+for f in (:median, :middle, :std, :stdm, :var, :varm, :quantile)
     @eval begin
         Statistics.$(f)(cdf::AbstractEmpiricalCDF, args...; kws...) = Statistics.$(f)(cdf.xdata, args...; kws...)
     end
 end
 
+for f in (:mean,)
+    @eval begin
+        Statistics.$(f)(cdf::AbstractEmpiricalCDF; kws...) = Statistics.$(f)(cdf.xdata; kws...)
+        Statistics.$(f)(func, cdf::AbstractEmpiricalCDF; kws...) = Statistics.$(f)(func, cdf.xdata; kws...)
+    end
+end
+
 # Same as above, but the return value is the cdf
 
 @doc """
@@ -226,12 +244,14 @@ function _inverse(cdf::EmpiricalCDFHi, x)
     cdf.xdata[ind]
 end
 
+import Random
 """
     rand(cdf::EmpiricalCDF)
 
 Pick a random sample from the distribution represented by `cdf`.
 """
 Base.rand(cdf::AbstractEmpiricalCDF) = _inverse(cdf,rand())
+Base.rand(X::Random.AbstractRNG, cdf::AbstractEmpiricalCDF) = _inverse(cdf,rand(X))
 
 """
     finv(cdf::AbstractEmpiricalCDF) --> Function
@@ -253,14 +273,14 @@ julia> maximum(cdf)
 """
 function finv(cdf::EmpiricalCDF)
     function (c::Real)
-        (c < 0 || c >= 1) && throw(DomainError())
+        (c < 0 || c >= 1) && throw(DomainError(c))
         _inverse(cdf,c)
     end
 end
 
 function finv(cdf::EmpiricalCDFHi)
     function (c::Real)
-        (c < cdf.lowreject || c >= 1) && throw(DomainError())
+        (c < cdf.lowreject || c >= 1) && throw(DomainError(c))
         _inverse(cdf,c)
     end
 end

test/aqua_test.jl

@@ -0,0 +1,35 @@
+using EmpiricalCDFs
+using Aqua: Aqua
+
+const ThePackage = EmpiricalCDFs
+
+@testset "aqua deps compat" begin
+    Aqua.test_deps_compat(ThePackage)
+end
+
+@testset "aqua unbound_args" begin
+    Aqua.test_unbound_args(ThePackage)
+end
+
+@testset "aqua undefined exports" begin
+    Aqua.test_undefined_exports(ThePackage)
+end
+
+# TODO: Not sure exactly which versions are ok.
+if VERSION >= v"1.7"
+    @testset "aqua test ambiguities" begin
+        Aqua.test_ambiguities([ThePackage, Core, Base])
+    end
+end
+
+@testset "aqua piracies" begin
+    Aqua.test_piracies(ThePackage)
+end
+
+@testset "aqua project extras" begin
+    Aqua.test_project_extras(ThePackage)
+end
+
+@testset "aqua state deps" begin
+    Aqua.test_stale_deps(ThePackage)
+end

test/jet_test.jl

@@ -0,0 +1,101 @@
+using Test
+using EmpiricalCDFs
+using JET
+
+const package_to_analyze = EmpiricalCDFs
+
+## Ignore these errors. The first string in the pair is
+## the report message. The second is the file it occurs in.
+## Not very precise, but ok for now.
+const SKIP_MATCHES = [
+    # Trying to print a Sym could raise this error.
+#    ("type Nothing has no field den", "parameters.jl"),
+]
+
+## Skip reports for which return true
+## Skip reports for which return true
+const SKIP_REP_TESTS = [
+#    rep -> rep isa JET.UncaughtExceptionReport, # We intentionally throw MethodError
+#    rep -> rep isa JET.BuiltinErrorReport,
+#    rep -> string(rep) == "MethodErrorReport(no matching method found `eps(::Type{Union{}})`: eps(T::Type{Union{}}))",
+]
+
+##
+## JET. Static analysis of the package
+##
+
+function analyze_package(package_name=package_to_analyze)
+    result = report_package(
+        string(package_name);
+        report_pass=JET.BasicPass()
+        # ignored_modules=(
+        # )
+    )
+    reports = JET.get_reports(result)
+    return reports
+end
+
+"""
+    match_report(package, report::InferenceErrorReport, msg::String, file::String)
+
+Return `true` if the message is `msg` and the first file in the stack trace is `file`.
+
+`file` should be given relative to the `src` directory of `package`.
+"""
+function match_report(package, report, msg::String, file::String)
+    hasproperty(report, :msg) || return false
+    report.msg != msg && return false
+    filepath = joinpath(dirname(pathof(package)), file)
+    report_filepath = string(report.vst[1].file)
+    return report_filepath == filepath
+end
+
+function match_reports(package, report, match_data::Vector)
+    for (msg, file) in match_data
+        match_report(package, report, msg, file) && return true
+    end
+    return false
+end
+
+function do_rep_skip_test(rep, skip_rep_tests=SKIP_REP_TESTS)
+    for rep_test in skip_rep_tests
+        rep_test(rep) && return true
+    end
+    return false
+end
+
+# Filter out reports that we don't consider failures.
+# We could flag some that could be fixed as broken tests.
+# This could be more fine grained.
+
+function filter_reports(reports, package)
+    somereports = empty(reports)
+    for rep in reports
+        do_rep_skip_test(rep) && continue
+        match_reports(package, rep, SKIP_MATCHES) && continue
+        push!(somereports, rep)
+    end
+    return somereports
+end
+
+# print just some of the report
+function print_report(report)
+    hasproperty(report, :msg) && println(report.msg)
+    return hasproperty(report, :vst) && println(report.vst)
+end
+
+function run_reports()
+    reports = analyze_package(package_to_analyze)
+    somereports = filter_reports(reports, package_to_analyze)
+    @show somereports
+    number_of_ignored_jet_reports = length(reports) - length(somereports)
+    @info string(number_of_ignored_jet_reports, " reports ignored.")
+    @info string(length(somereports), " reports not ignored.")
+    for rep in somereports
+        print_report(rep)
+    end
+    @test isempty(somereports)
+    return (somereports, reports)
+end
+
+run_reports()

test/runtests.jl

@@ -5,6 +5,14 @@ using EmpiricalCDFs.IOcdf: readcdf, getcdf
 using Test
 using Statistics
 
+include("aqua_test.jl")
+
+if VERSION >= v"1.7" && VERSION <= v"1.11"
+    @testset "JET" begin
+        include("jet_test.jl")
+    end
+end
+
 @testset "construction" begin
     @test (cdf = EmpiricalCDF(); true)
     @test (cdf = EmpiricalCDF(); append!(cdf,rand(10^3)) ; true)