Allow the use of ReTest during development

diegozea · Dec 11, 2023 · 55cbc99 · 55cbc99
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commit 55cbc99
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diff --git a/test/Information/CorrectedMutualInformation.jl b/test/Information/CorrectedMutualInformation.jl
@@ -1,10 +1,10 @@
 @testset "CorrectedMutualInformation" begin
 
-    Gaoetal2011 = joinpath(pwd(), "data", "Gaoetal2011.fasta")
+    Gaoetal2011 = joinpath(DATA, "Gaoetal2011.fasta")
 
     function gao11_buslje09(measure)
         filename = string("data_Gaoetal2011_soft_Busljeetal2009_measure_", measure, ".txt")
-        joinpath(pwd(), "data", filename)
+        joinpath(DATA, filename)
     end
 
     ## Column numbers for the output of Buslje et. al. 2009
@@ -223,9 +223,9 @@
     @testset "Results from Buslje et. al. 2009" begin
 
         @testset "Simple" begin
-            data = readdlm(joinpath(pwd(), "data",
+            data = readdlm(joinpath(DATA,
                            "data_simple_soft_Busljeetal2009_measure_MI.txt"), comments=true)
-            results = buslje09(joinpath(pwd(), "data", "simple.fasta"), FASTA,
+            results = buslje09(joinpath(DATA, "simple.fasta"), FASTA,
                                lambda=0.0, clustering=false, apc=false)
 
             @test isapprox(Float64(data[1, SCORE]), results[MIToS_SCORE][1,2], atol=1e-6)
@@ -297,7 +297,7 @@
     @testset "BLMI" begin
 
         @testset "Simple" begin
-            file = joinpath(pwd(), "data", "simple.fasta")
+            file = joinpath(DATA, "simple.fasta")
             busl = buslje09(file, FASTA)
             blmi = BLMI(file, FASTA)
 

diff --git a/test/Information/Gaps.jl b/test/Information/Gaps.jl
@@ -1,7 +1,7 @@
 @testset "Pairwise Gap Percentage" begin
 
     @testset "Simple" begin
-        file = joinpath(pwd(), "data", "simple.fasta")
+        file = joinpath(DATA, "simple.fasta")
         mat = [ 0. 0.
                 0. 0. ]
 
@@ -12,7 +12,7 @@
 
     @testset "Gaps" begin
 
-        file = joinpath(pwd(), "data", "gaps.txt")
+        file = joinpath(DATA, "gaps.txt")
         cl = hobohmI(read(file, Raw), 62)
         gu, gi = pairwisegapfraction(file, Raw)
         ncl = nclusters(cl)

diff --git a/test/Information/Iterations.jl b/test/Information/Iterations.jl
@@ -7,7 +7,7 @@
         # New methods to measure residues coevolution in proteins.
         # BMC bioinformatics, 12(1), 206.
 
-        aln = read(joinpath(pwd(), "data", "Gaoetal2011.fasta"), FASTA)
+        aln = read(joinpath(DATA, "Gaoetal2011.fasta"), FASTA)
         result = Float64[ 0     0     0     0     0     0
                           0     0     0     0     0     0
                           0     0     0     1     1     0.296
@@ -36,7 +36,7 @@
 
         table = ContingencyTable(Float64, Val{1}, GappedAlphabet())
 
-        gaps = read(joinpath(pwd(), "data", "gaps.txt"), Raw)
+        gaps = read(joinpath(DATA, "gaps.txt"), Raw)
 
         # THAYQAIHQV 0
         # THAYQAIHQ- 0.1

diff --git a/test/MIToSTests.jl b/test/MIToSTests.jl
@@ -0,0 +1,10 @@
+"""
+You need to `include` this file (and module) into your Julia session to run the tests using 
+`ReTest`. `ReTest` is not a dependency of `MIToS`, so you need to install it manually.
+Then, you can do `MIToSTests.retest()` to setup the tests. After that, you can use 
+regular expressions to filter the tests you want to run, e.g. `MIToSTests.retest(r"MSA")`.
+"""
+module MIToSTests
+    using ReTest
+    include("tests.jl")
+end
diff --git a/test/MSA/Concatenation.jl b/test/MSA/Concatenation.jl
@@ -1,5 +1,5 @@
 @testset "hcat" begin
-    simple = joinpath(pwd(), "data", "simple.fasta")
+    simple = joinpath(DATA, "simple.fasta")
     msa = read(simple, FASTA, generatemapping=true)
     setannotresidue!(msa, "ONE", "example", "ab")
     setannotresidue!(msa, "TWO", "example", "cd")

diff --git a/test/MSA/General.jl b/test/MSA/General.jl
@@ -7,8 +7,8 @@
         AnnotatedMultipleSequenceAlignment
         )
 
-    pf09645_sto = joinpath(pwd(), "data", "PF09645_full.stockholm")
-    gaoetal2011 = joinpath(pwd(), "data", "Gaoetal2011.fasta")
+    pf09645_sto = joinpath(DATA, "PF09645_full.stockholm")
+    gaoetal2011 = joinpath(DATA, "Gaoetal2011.fasta")
 
     gaoetal_msas = [ read(gaoetal2011, FASTA, T) for T in msa_types ]
     pfam_msas    = [ read(pf09645_sto, Stockholm, T) for T in msa_types ]

diff --git a/test/MSA/GetIndex.jl b/test/MSA/GetIndex.jl
@@ -1,5 +1,5 @@
 @testset "getindex" begin
-    simple = joinpath(pwd(), "data", "simple.fasta")
+    simple = joinpath(DATA, "simple.fasta")
 
     @testset "MSA" begin
         msa = read(simple, FASTA, generatemapping=true)

diff --git a/test/MSA/Hobohm.jl b/test/MSA/Hobohm.jl
@@ -14,7 +14,7 @@ end
     # DAYCMT  33.3  83.3
     # DAYCMT  33.3  83.3
 
-    fasta = read(joinpath(pwd(), "data", "Gaoetal2011.fasta"), FASTA)
+    fasta = read(joinpath(DATA, "Gaoetal2011.fasta"), FASTA)
     clusters = hobohmI(fasta, 62)
 
     @test nclusters(clusters) == 2

diff --git a/test/MSA/IO.jl b/test/MSA/IO.jl
@@ -18,8 +18,8 @@
     # > Pfam version 28.0, based on UniProt release 2014_07
     @testset "Stockholm" begin
 
-        pf09645_sto = joinpath(pwd(), "data", "PF09645_full.stockholm")
-        rna_sto = joinpath(pwd(), "data", "upsk_rna.sto")
+        pf09645_sto = joinpath(DATA, "PF09645_full.stockholm")
+        rna_sto = joinpath(DATA, "upsk_rna.sto")
 
         @testset "Read" begin
 
@@ -139,8 +139,8 @@
 
     @testset "FASTA" begin
 
-        pf09645_fas = joinpath(pwd(), "data", "PF09645_full.fasta.gz")
-        gaoetal2011 = joinpath(pwd(), "data", "Gaoetal2011.fasta")
+        pf09645_fas = joinpath(DATA, "PF09645_full.fasta.gz")
+        gaoetal2011 = joinpath(DATA, "Gaoetal2011.fasta")
 
         @testset "Read" begin
 
@@ -278,7 +278,7 @@
 
         @testset "Non standard residues and mapping" begin
 
-            seqs = read(joinpath(pwd(), "data", "alphabet.fasta"), FASTA,
+            seqs = read(joinpath(DATA, "alphabet.fasta"), FASTA,
                         generatemapping=true)
 
             @test vec(seqs[1,:]) == res"ARNDCQEGHILKMFPSTWYV"
@@ -292,7 +292,7 @@
     @testset "Raw" begin
 
         # AnnotatedMultipleSequenceAlignment
-        raw = read(joinpath(pwd(), "data", "gaps.txt"), Raw)
+        raw = read(joinpath(DATA, "gaps.txt"), Raw)
         mat = getresidues(raw)
         raw_string = """THAYQAIHQV
                         THAYQAIHQ-
@@ -360,16 +360,16 @@
 
         # Example NBRF file: http://iubio.bio.indiana.edu/soft/molbio/readseq/classic/src/Formats
         # "The sequence is free format and may be interrupted by blanks for ease of reading"
-        example = joinpath(pwd(), "data", "example.nbrf")
+        example = joinpath(DATA, "example.nbrf")
         # Alignment file (PIR) from https://salilab.org/modeller/9v7/manual/node445.html
-        modeller = joinpath(pwd(), "data", "modeller.pir.gz")
+        modeller = joinpath(DATA, "modeller.pir.gz")
         # http://emboss.sourceforge.net/docs/themes/seqformats/NbrfFormat.html
         # "sequence may contain punctuation symbols to indicate various degrees of
         # reliability of the data"
-        emboss = joinpath(pwd(), "data", "emboss.pir")
+        emboss = joinpath(DATA, "emboss.pir")
         # http://caps.ncbs.res.in/pass2v3/pir.html
         # Example from pass2 with spaces added at the end of the id lines.
-        pass2 = joinpath(pwd(), "data", "pass2.pir")
+        pass2 = joinpath(DATA, "pass2.pir")
 
         @testset "Read" begin
 
@@ -461,7 +461,7 @@
 
         @testset "Duplicated identifiers" begin
 
-            duplicated_ids_file = joinpath(pwd(), "data", "duplicated_ids.pir")
+            duplicated_ids_file = joinpath(DATA, "duplicated_ids.pir")
             @test_throws ArgumentError read(duplicated_ids_file, PIR)
         end
     end

diff --git a/test/MSA/Identity.jl b/test/MSA/Identity.jl
@@ -55,7 +55,7 @@
 
     @testset "MSA" begin
 
-        fasta = read(joinpath(pwd(), "data", "Gaoetal2011.fasta"), FASTA)
+        fasta = read(joinpath(DATA, "Gaoetal2011.fasta"), FASTA)
         id = percentidentity(fasta)
 
         @test id[1,1] == 100.0
@@ -80,7 +80,7 @@
 
         @testset "Gaps" begin
 
-            aln = read(joinpath(pwd(), "data", "gaps.txt"), Raw)
+            aln = read(joinpath(DATA, "gaps.txt"), Raw)
             id = percentidentity(aln)
 
             @test id[1,1] == 100.0
@@ -110,7 +110,7 @@
 
     @testset "Percent Similarity" begin
 
-        fasta = read(joinpath(pwd(), "data", "Gaoetal2011.fasta"), FASTA)
+        fasta = read(joinpath(DATA, "Gaoetal2011.fasta"), FASTA)
 
         @testset "Gaps" begin
 

diff --git a/test/MSA/MSAAnnotations.jl b/test/MSA/MSAAnnotations.jl
@@ -1,12 +1,12 @@
 @testset "MSA Annotations" begin
 
-    pfam = read(joinpath(pwd(), "data", "PF09645_full.stockholm"), Stockholm,
+    pfam = read(joinpath(DATA, "PF09645_full.stockholm"), Stockholm,
         generatemapping=true, useidcoordinates=true)
 
     F112_SSV1 = collect(string(".....QTLNSYKMAEIMYKILEKKGELTLEDILAQFEISVPSAYNIQRALKAIC",
         "ERHPDECEVQYKNRKTTFKWIKQEQKEEQKQEQTQDNIAKIFDAQPANFEQTDQGFIKAKQ....."))
 
-    fasta = read(joinpath(pwd(), "data", "Gaoetal2011.fasta"), FASTA, generatemapping=true)
+    fasta = read(joinpath(DATA, "Gaoetal2011.fasta"), FASTA, generatemapping=true)
 
     @testset "Mapping" begin
 

diff --git a/test/MSA/MSAEditing.jl b/test/MSA/MSAEditing.jl
@@ -7,8 +7,8 @@
         AnnotatedMultipleSequenceAlignment
         )
 
-    pf09645_sto = joinpath(pwd(), "data", "PF09645_full.stockholm")
-    gaoetal2011 = joinpath(pwd(), "data", "Gaoetal2011.fasta")
+    pf09645_sto = joinpath(DATA, "PF09645_full.stockholm")
+    gaoetal2011 = joinpath(DATA, "Gaoetal2011.fasta")
 
     gaoetal_msas = [ read(gaoetal2011, FASTA, T) for T in msa_types ]
     pfam_msas    = [ read(pf09645_sto, Stockholm, T) for T in msa_types ]

diff --git a/test/MSA/MSAStats.jl b/test/MSA/MSAStats.jl
@@ -7,8 +7,8 @@
         AnnotatedMultipleSequenceAlignment
         )
 
-    pf09645_sto = joinpath(pwd(), "data", "PF09645_full.stockholm")
-    gaoetal2011 = joinpath(pwd(), "data", "Gaoetal2011.fasta")
+    pf09645_sto = joinpath(DATA, "PF09645_full.stockholm")
+    gaoetal2011 = joinpath(DATA, "Gaoetal2011.fasta")
 
     gaoetal_msas = [ read(gaoetal2011, FASTA, T) for T in msa_types ]
     pfam_msas    = [ read(pf09645_sto, Stockholm, T) for T in msa_types ]

diff --git a/test/MSA/Shuffle.jl b/test/MSA/Shuffle.jl
@@ -9,7 +9,7 @@
 
     N = length(msa_types)
 
-    pf09645_sto = joinpath(pwd(), "data", "PF09645_full.stockholm")
+    pf09645_sto = joinpath(DATA, "PF09645_full.stockholm")
 
     msas = [ read(pf09645_sto, Stockholm, T) for T in msa_types ]
     gaps = [ msa .== GAP for msa in msas ]

diff --git a/test/PDB/Contacts.jl b/test/PDB/Contacts.jl
@@ -1,6 +1,6 @@
 @testset "Contacts" begin
 
-    txt(code) = joinpath(pwd(), "data", string(uppercase(code), ".pdb"))
+    txt(code) = joinpath(DATA, string(uppercase(code), ".pdb"))
 
     @testset "Piccolo" begin
     # Using data from http://www-cryst.bioc.cam.ac.uk/~richard/piccolo/piccolo.php?PDB=1IGY (28/Sep/2015)
@@ -97,7 +97,7 @@
 
     @testset "1AKS" begin
 
-        pdb = read(joinpath(pwd(), "data", "1AKS.xml.gz"), PDBML)
+        pdb = read(joinpath(DATA, "1AKS.xml.gz"), PDBML)
 
         CA = @residuesdict pdb model "1" chain "A" group "ATOM" residue All
         CB = @residuesdict pdb model "1" chain "B" group "ATOM" residue All

diff --git a/test/PDB/Kabsch.jl b/test/PDB/Kabsch.jl
@@ -192,8 +192,8 @@
     end
 
     @testset "PDBResidue without alpha-carbon" begin
-        small_2WEL = read(joinpath(pwd(), "data", "2WEL_D_region.pdb"), PDBFile)
-        small_6BAB = read(joinpath(pwd(), "data", "6BAB_D_region.pdb"), PDBFile)
+        small_2WEL = read(joinpath(DATA, "2WEL_D_region.pdb"), PDBFile)
+        small_6BAB = read(joinpath(DATA, "6BAB_D_region.pdb"), PDBFile)
 
         aln_2WEL, aln_6BAB, RMSD = superimpose(small_2WEL, small_6BAB)
         @test length(aln_2WEL) == 3

diff --git a/test/PDB/PDB.jl b/test/PDB/PDB.jl
@@ -1,7 +1,7 @@
 @testset "Parse PDB and PDBML" begin
 
-    txt(code) = joinpath(pwd(), "data", string(uppercase(code), ".pdb"))
-    xml(code) = joinpath(pwd(), "data", string(uppercase(code), ".xml"))
+    txt(code) = joinpath(DATA, string(uppercase(code), ".pdb"))
+    xml(code) = joinpath(DATA, string(uppercase(code), ".xml"))
 
     @testset "2VQC: Missings" begin
 
@@ -289,7 +289,7 @@
     @testset "Foldseek" begin
         # PDB files generated by Foldseek have only 66 columns; element identifiers 
         # are missing (represented as empty strings). Those files only contain CA atoms.
-        pdb_file = joinpath(pwd(), "data", "foldseek_example.pdb")
+        pdb_file = joinpath(DATA, "foldseek_example.pdb")
         pdb = read(pdb_file, PDBFile)
 
         # The example file has only 8 residues and one chain (A)
@@ -316,7 +316,7 @@ end
 
 @testset "Write PDB files" begin
 
-    txt(code) = joinpath(pwd(), "data", string(uppercase(code), ".pdb"))
+    txt(code) = joinpath(DATA, string(uppercase(code), ".pdb"))
 
     @testset "2VQC" begin
         code = "2VQC"

diff --git a/test/PDB/Sequences.jl b/test/PDB/Sequences.jl
@@ -11,7 +11,7 @@ end
 
 @testset "Extract protein sequences from PDB" begin
 
-    file(code) = joinpath(pwd(), "data", string(uppercase(code), ".pdb"))
+    file(code) = joinpath(DATA, string(uppercase(code), ".pdb"))
 
     @testset "2VQC: Missings & selenomethionines" begin
         res = read(file("2VQC"), PDBFile)

diff --git a/test/Pfam/Pfam.jl b/test/Pfam/Pfam.jl
@@ -15,15 +15,15 @@ end
 
 @testset "PDB code" begin
 
-    msa = read(joinpath(pwd(), "data", "PF09645_full.stockholm"), Stockholm)
+    msa = read(joinpath(DATA, "PF09645_full.stockholm"), Stockholm)
     @test getseq2pdb(msa)["F112_SSV1/3-112"] == [("2VQC","A")]
 end
 
 @testset "Mapping PDB/Pfam" begin
 
-    msa_file   = joinpath(pwd(), "data", "PF09645_full.stockholm")
-    sifts_file = joinpath(pwd(), "data", "2vqc.xml.gz")
-    pdb_file   = joinpath(pwd(), "data", "2VQC.xml")
+    msa_file   = joinpath(DATA, "PF09645_full.stockholm")
+    sifts_file = joinpath(DATA, "2vqc.xml.gz")
+    pdb_file   = joinpath(DATA, "2VQC.xml")
     msa = read(msa_file, Stockholm, generatemapping=true, useidcoordinates=true)
     cmap = msacolumn2pdbresidue(msa, "F112_SSV1/3-112", "2VQC", "A", "PF09645", sifts_file)
     res = residuesdict(read(pdb_file, PDBML), "1", "A", "ATOM", All)