remove BioCore test dependency

Author: jgreener64

.gitignore

@@ -9,3 +9,4 @@ benchmark/results
 Manifest.toml
 *.swp
 extractdata/protein.ff14SB.*
+BioFmtSpecimens

benchmark/benchmarks.jl

@@ -8,15 +8,14 @@
 using BioStructures
 using BenchmarkTools
 using BioAlignments
-import BioCore # Imported to avoid clash with BioGenerics distance
 using BioSequences
 using Graphs
 import MMTF # Imported to avoid clash with writemmtf
 using MetaGraphs
 using Random
 
 # Use files in BioFmtSpecimens
-fmtdir = BioCore.Testing.get_bio_fmt_specimens()
+fmtdir = BioStructures.get_bio_fmt_specimens()
 testfilepath(path::AbstractString...) = joinpath(fmtdir, path...)
 
 # All writing is done to one temporary file

src/download.jl

@@ -411,3 +411,17 @@ function retrievepdb(pdbid::AbstractString;
     end
     read(pdbpath, format; structure_name=structure_name, kwargs...)
 end
+
+const FMT_SPECIMEN_PATH = joinpath(dirname(dirname(@__FILE__)), "BioFmtSpecimens")
+
+# Get the path to BioFmtSpecimens and download it if required
+# See https://github.com/BioJulia/BioCore.jl/blob/master/src/Testing.jl
+function get_bio_fmt_specimens(fresh=false)
+    if fresh
+        rm(FMT_SPECIMEN_PATH; force=true, recursive=true)
+    end
+    if !isdir(FMT_SPECIMEN_PATH)
+        run(`git clone https://github.com/BioJulia/BioFmtSpecimens.git $FMT_SPECIMEN_PATH`)
+    end
+    return FMT_SPECIMEN_PATH
+end

test/Project.toml

@@ -1,7 +1,6 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
-BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 CodecZlib = "944b1d66-785c-5afd-91f1-9de20f533193"
 DSSP_jll = "74334e00-59ce-546d-b517-81f3b7e1d491"
@@ -18,5 +17,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 Aqua = "0.8"
-BioCore = "2"
 Test = "1.9"

test/runtests.jl

@@ -3,7 +3,6 @@ module TestBioStructures
 using Aqua
 using BioAlignments
 using BioSequences
-import BioCore # Imported to avoid clash with BioGenerics distance
 using CodecZlib
 using DSSP_jll
 using DataFrames
@@ -54,7 +53,7 @@ using BioStructures:
     pdb_download_prefix
 
 # Get the path to BioFmtSpecimens and download it if required
-fmtdir = BioCore.Testing.get_bio_fmt_specimens("master", false)
+fmtdir = BioStructures.get_bio_fmt_specimens()
 
 # Access files in BioFmtSpecimens to test against
 testfilepath(path::AbstractString...) = joinpath(fmtdir, path...)