Merge pull request #6 from JakobAsslaender/UpdateCompatNTests

update compat + tests
dfsp-spirit · Nov 13, 2024 · 1f5a4ab · 1f5a4ab
2 parents 66ae868 + 2a2d348
commit 1f5a4ab
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Showing 15 changed files with 44 additions and 56 deletions.
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,5 @@
 *.jl.cov
 *.jl.mem
 /docs/build/
+Manifest.toml
+test/Manifest.toml
diff --git a/Project.toml b/Project.toml
@@ -15,12 +15,13 @@ Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 
 [compat]
-CSV = "0.8"
+CSV = "0.8, 0.10"
 CodecZlib = "0.6, 0.7"
-Colors = "0.12"
+Colors = "0.12, 0.13"
 DataFrames = "0.22, 1.0"
+DelimitedFiles = "1"
 Reexport = "1.0"
-TranscodingStreams = "0.9.5"
+TranscodingStreams = "0.9.5, 0.11"
 julia = "1"
 
 [extras]

diff --git a/src/fs_label.jl b/src/fs_label.jl
@@ -47,7 +47,7 @@ function read_label(file::AbstractString)
     csv_data_reader = CSV.File(file; header=column_names, delim=" ", ignorerepeated=true, skipto=3, limit=num_vertices, types=column_types, comment="#")
 
     df = DataFrame(csv_data_reader)
-    return(df)
+    return df
 end
 
 """

diff --git a/test/Project.toml b/test/Project.toml
@@ -0,0 +1,3 @@
+[deps]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -6,10 +6,7 @@ import Base.length, Base.maximum, Base.minimum, Base.fieldcount
 # The easiest way to run these tests with the current version of your code
 # seems to be the following one:
 # - start a JULIA interpreter with `cd develop/NeuroFormats.jl; julia --project=.`, then:
-# - run: `using Pkg; Pkg.test("NeuroFormats");` 
-
-
-include("./utils_for_testing.jl")
+# - run: `using Pkg; Pkg.test("NeuroFormats");`
 
 # Common utility tests
 include("./test_utils.jl")

diff --git a/test/test_dti_tck.jl b/test/test_dti_tck.jl
@@ -1,8 +1,8 @@
 # Tests for reading TCK files.
 
 @testset "Read DTI tracks from a MRtrix3 TCK file." begin
-    
-    TCK_FILE = joinpath(get_testdata_dir(), "DTI/simple_big_endian.tck")
+
+    TCK_FILE = joinpath(Base.source_dir(), "data/DTI/simple_big_endian.tck")
     tck = read_tck(TCK_FILE)
 
     # test header

diff --git a/test/test_dti_trk.jl b/test/test_dti_trk.jl
@@ -1,8 +1,8 @@
 # Tests for reading TRK files.
 
 @testset "Read DTI tracks from a DiffusionToolkit TRK file." begin
-    
-    TRK_FILE = joinpath(get_testdata_dir(), "DTI/complex_big_endian.trk")
+
+    TRK_FILE = joinpath(Base.source_dir(), "data/DTI/complex_big_endian.trk")
     trk = read_trk(TRK_FILE)
 
     @test trk.header.hdr_size == 1000

diff --git a/test/test_fs_annot.jl b/test/test_fs_annot.jl
@@ -3,7 +3,7 @@
 
 @testset "Read a FreeSurfer annotation and compute properties" begin
 
-    ANNOT_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/label/lh.aparc.annot")
+    ANNOT_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/label/lh.aparc.annot")
     fs_annot = read_annot(ANNOT_FILE)
 
     @test Base.length(fs_annot.vertex_indices) == 149244
@@ -29,7 +29,7 @@ end
 
 @testset "Derive per-vertex color information from a FreeSurfer annotation" begin
 
-    ANNOT_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/label/lh.aparc.annot")
+    ANNOT_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/label/lh.aparc.annot")
     fs_annot = read_annot(ANNOT_FILE)
 
     @test Base.length(vertex_colors(fs_annot)) == 149244

diff --git a/test/test_fs_common.jl b/test/test_fs_common.jl
@@ -2,8 +2,8 @@
 
 
 @testset "fs_common.jl: read fs int24" begin
-    
-    CURV_LH_THICKNESS_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.thickness")
+
+    CURV_LH_THICKNESS_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.thickness")
     file_io = open(CURV_LH_THICKNESS_FILE, "r")
     int24 = NeuroFormats.FreeSurfer._read_fs_int24(file_io)
     close(file_io)
@@ -14,11 +14,11 @@ end
 
 @testset "fs_common.jl: interpret fs int24" begin
 
-    CURV_LH_THICKNESS_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.thickness")
+    CURV_LH_THICKNESS_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.thickness")
     curv = read_curv(CURV_LH_THICKNESS_FILE, with_header = true)
-    
+
     int24 = NeuroFormats.FreeSurfer._interpret_fs_int24(curv.header.curv_magic_b1, curv.header.curv_magic_b2, curv.header.curv_magic_b3)
-    
+
     @test int24 == 16777215
 end
 

diff --git a/test/test_fs_curv.jl b/test/test_fs_curv.jl
@@ -1,8 +1,8 @@
 
 
 @testset "fs_curv.jl: read curv with header" begin
-    
-CURV_LH_THICKNESS_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.thickness")
+
+CURV_LH_THICKNESS_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.thickness")
 curv = read_curv(CURV_LH_THICKNESS_FILE, with_header = true)
 
 # Header
@@ -22,7 +22,7 @@ end
 
 @testset "fs_curv.jl: read curv without header" begin
 
-CURV_LH_THICKNESS_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.thickness")
+CURV_LH_THICKNESS_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.thickness")
 curv_data = read_curv(CURV_LH_THICKNESS_FILE, with_header = false)
 
 # Content
@@ -34,13 +34,13 @@ end
 
 @testset "fs_curv.jl: write and re-read curv file" begin
 
-CURV_LH_THICKNESS_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.thickness")
+CURV_LH_THICKNESS_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.thickness")
 curv_data = read_curv(CURV_LH_THICKNESS_FILE, with_header = false)
 
 # Write and re-read
 tf = tempname()
 write_curv(tf, curv_data)
-curv_re = read_curv(tf, with_header = true) 
+curv_re = read_curv(tf, with_header = true)
 
 # Header
 @test curv_re.header.curv_magic_b1 == 0xff

diff --git a/test/test_fs_label.jl b/test/test_fs_label.jl
@@ -3,7 +3,7 @@ using DataFrames
 
 @testset "A FreeSurfer surface label file can be read" begin
 
-    LABEL_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/label/lh.entorhinal_exvivo.label")
+    LABEL_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/label/lh.entorhinal_exvivo.label")
     fs_label = read_label(LABEL_FILE)
 
     @test typeof(fs_label) == DataFrames.DataFrame
@@ -14,7 +14,7 @@ end
 
 @testset "A FreeSurfer surface label file can be read, written and re-read" begin
 
-    LABEL_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/label/lh.entorhinal_exvivo.label")
+    LABEL_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/label/lh.entorhinal_exvivo.label")
     fs_label = read_label(LABEL_FILE)
 
     @test typeof(fs_label) == DataFrames.DataFrame

diff --git a/test/test_fs_mgh.jl b/test/test_fs_mgh.jl
@@ -3,7 +3,7 @@
 
 @testset "Read a 3D/4D FreeSurfer MGH file." begin
 
-    MGH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/mri/brain.mgz")
+    MGH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/mri/brain.mgz")
     mgh = read_mgh(MGH_FILE)
 
     # Test header.
@@ -31,7 +31,7 @@ end
 
 @testset "Compute vox2ras matrix for MGH file." begin
 
-    MGH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/mri/brain.mgz")
+    MGH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/mri/brain.mgz")
     mgh = read_mgh(MGH_FILE)
 
     # Use FreeSurfer's `mri_info` command line tool on the brain.mgz file to get this info:
@@ -45,9 +45,9 @@ end
 
 @testset "fs_mgh.jl: write and re-read MGH file uncompressed" begin
 
-    MGH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/mri/brain.mgz")
+    MGH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/mri/brain.mgz")
     mgh = read_mgh(MGH_FILE)
-    
+
     # Write and re-read
     tf = tempname()
     write_mgh(tf, mgh, format = "mgh")
@@ -81,15 +81,15 @@ end
     @test mgh_re.data[110, 110, 110, 1] == 71
     @test mgh_re.data[1, 1, 1, 1] == 0
     @test sum(Int32.(mgh_re.data)) == 121035479
-    
+
 end
 
 
 @testset "fs_mgh.jl: write and re-read MGZ file compressed" begin
 
-    MGH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/mri/brain.mgz")
+    MGH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/mri/brain.mgz")
     mgh = read_mgh(MGH_FILE)
-    
+
     # Write and re-read
     tf = tempname()
     write_mgh(tf, mgh, format = "mgz")
@@ -122,6 +122,6 @@ end
     @test mgh_re.data[100, 100, 100, 1] == 77   # try on command line: mri_info --voxel 99 99 99 test/data/subjects_dir/subject1/mri/brain.mgz
     @test mgh_re.data[110, 110, 110, 1] == 71
     @test mgh_re.data[1, 1, 1, 1] == 0
-    @test sum(Int32.(mgh_re.data)) == 121035479    
+    @test sum(Int32.(mgh_re.data)) == 121035479
 end
 
diff --git a/test/test_fs_surface.jl b/test/test_fs_surface.jl
@@ -1,7 +1,7 @@
 
 @testset "fs_surface.jl: read brain mesh" begin
-        
-    BRAIN_MESH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.tinysurface")
+
+    BRAIN_MESH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.tinysurface")
     surface = read_surf(BRAIN_MESH_FILE) # a mesh with 5 vertices and 3 faces.
 
     known_num_verts = 5
@@ -25,8 +25,8 @@ end
 
 
 @testset "fs_surface.jl: export brain mesh to OBJ file" begin
-       
-    BRAIN_MESH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.tinysurface")
+
+    BRAIN_MESH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.tinysurface")
     surface = read_surf(BRAIN_MESH_FILE) # a mesh with 5 vertices and 3 faces.
 
     tf = tempname()

diff --git a/test/test_utils.jl b/test/test_utils.jl
@@ -1,11 +1,11 @@
 
 @testset "utils.jl: read a fixed length string from a binary file" begin
-        
-    BRAIN_MESH_FILE = joinpath(get_testdata_dir(), "subjects_dir/subject1/surf/lh.tinysurface")
+
+    BRAIN_MESH_FILE = joinpath(Base.source_dir(), "data/subjects_dir/subject1/surf/lh.tinysurface")
     file_io = open(BRAIN_MESH_FILE, "r")
 
     @test Base.position(file_io) == 0
-    
+
     b1 = read(file_io, UInt8)
     b2 = read(file_io, UInt8)
     b3 = read(file_io, UInt8)

diff --git a/test/utils_for_testing.jl b/test/utils_for_testing.jl