Removed FilePath dependency.

FilePaths is no longer used to enforce distinction between a
String and a filesystem location.  New method 'cif_from_string'
should be used where the string content is in CIF format. The
CIF constructor will still work when passed a FilePath type.

Project.toml

@@ -1,12 +1,11 @@
 name = "CrystalInfoFramework"
 uuid = "6007d9b0-c6b2-11e8-0510-1d10e825f3f1"
 authors = ["James.Hester <[email protected]>"]
-version = "0.6.3"
+version = "0.7.0"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
-FilePaths = "8fc22ac5-c921-52a6-82fd-178b2807b824"
 Lerche = "d42ef402-04e6-4356-9f73-091573ea58dc"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
@@ -16,7 +15,6 @@ cif_api_jll = "6fcef0ae-1c05-5fc1-b206-1cf994addbad"
 
 [compat]
 DataFrames = "^1.1.0"
-FilePaths = "^0.8.0"
 Lerche = "^0.5.0"
 PrecompileTools = "1.2.0"
 URIs = "1.5.0"

src/CrystalInfoFramework.jl

@@ -21,14 +21,14 @@
 module CrystalInfoFramework
 using DataFrames
 using URIs
-using FilePaths   #easy cross-platform URI
 using Lerche # for native parser
 using cif_api_jll # for cif API parser
 using PrecompileTools #for fast startup
 
 # **Exports**
 
 export CifValue,Cif,Block,CifBlock
+export cif_from_string
 export CifContainer, NestedCifContainer
 export get_frames,get_contents
 export get_loop, eachrow, add_to_loop!, create_loop!
@@ -81,8 +81,8 @@ end
 
 #
 @compile_workload begin
-    c = Cif(joinpath(@__PATH__,"../test/nick1.cif"), native=true)
-    d = DDLm_Dictionary(joinpath(@__PATH__,"../test/ddl.dic"), ignore_imports=true)
+    c = Cif(joinpath(@__DIR__, "../test/nick1.cif"), native=true)
+    d = DDLm_Dictionary(joinpath(@__DIR__, "../test/ddl.dic"), ignore_imports=true)
 end
 
 end

src/cif2_transformer.jl

@@ -31,7 +31,7 @@ already been processed.
 ==#
 
 struct TreeToCif <: Transformer
-    source_name::AbstractPath
+    source_name::AbstractString
     header_comments::AbstractString
 end
 

src/cif_base.jl

@@ -191,11 +191,11 @@ A CIF data block or save frame containing no nested save frames.
 mutable struct Block{V} <: CifContainer{V}
     loop_names::Vector{Vector{String}} #one loop is a list of datanames
     data_values::Dict{String,Vector{V}}
-    original_file::AbstractPath
+    original_file::AbstractString
 end
 
 Block{V}() where V = begin
-    Block(Vector{String}[],Dict{String,Vector{V}}(),p"")
+    Block(Vector{String}[],Dict{String,Vector{V}}(),"")
 end
 
 """
@@ -205,7 +205,7 @@ mutable struct CifBlock{V} <: NestedCifContainer{V}
     save_frames::Dict{String,Block{V}}
     loop_names::Vector{Vector{String}} #one loop is a list of datanames
     data_values::Dict{String,Vector{V}}
-    original_file::AbstractPath
+    original_file::AbstractString
 end
 
 Block(f::CifBlock) = Block(get_loop_names(f),get_data_values(f),get_source_file(f))
@@ -356,12 +356,12 @@ recording the source of the collection.
 """
 struct Cif{V,T <: CifContainer{V}} <: CifCollection{V}
     contents::Dict{String,T}
-    original_file::AbstractPath
+    original_file::AbstractString
     header_comments::String
 end
 
 Cif{V,T}() where V where T = begin
-    return Cif(Dict{String,T}(), p"", "")
+    return Cif(Dict{String,T}(), "", "")
 end
 
 Cif() = Cif{ CifValue, CifBlock{CifValue} }
@@ -472,7 +472,7 @@ get_frames(f::CifBlock{V}) where V = Cif{V,Block{V}}(f.save_frames,get_source_fi
 mutable struct cif_builder_context
     actual_cif::Dict{String,CifContainer{CifValue}}
     block_stack::Array{CifContainer{CifValue}}
-    filename::AbstractPath
+    filename::AbstractString
     verbose::Bool
 end
 
@@ -662,7 +662,7 @@ end
 
 # This sets up the callbacks and configures the cifapi parser.
 
-default_options(s::AbstractPath;verbose=false) = begin
+default_options(s::AbstractString;verbose=false) = begin
     handle_cif_start_c = @cfunction(handle_cif_start,Cint,(cif_tp_ptr,Ref{cif_builder_context}))
     handle_cif_end_c = @cfunction(handle_cif_end,Cint,(cif_tp_ptr,Ref{cif_builder_context}))
     handle_block_start_c = @cfunction(handle_block_start,Cint,(cif_container_tp_ptr,Ref{cif_builder_context}))
@@ -693,7 +693,7 @@ default_options(s::AbstractPath;verbose=false) = begin
 end
 
 """
-    Cif(s::AbstractPath;verbose=false,native=true,version=0)
+    Cif(somepath; verbose=false, native=true, version=0)
 
 Read in filename `s` as a CIF file. If `verbose` is true, print
 progress information during parsing. If `native` is `false`, use the
@@ -711,33 +711,33 @@ uses 6-10 times as much memory. However, from a cold start
 (e.g. in a standalone script) the cif_api parser is around 
 30% faster.
 """
-Cif(s::AbstractPath;verbose=false,native=true,version=0) = begin
-    ## get the full filename
-    full = realpath(s)
+Cif(somepath; verbose=false, native=true, version=0) = begin
+    ## get the full filename and make sure we have a string.
+    full = convert(String, realpath(somepath))
     if !Sys.iswindows() && !native
         pathstring = URI(full).path
         p_opts = default_options(full,verbose=verbose)
         result = cif_tp_ptr(p_opts)
         ## the real result is in our user data context
-        return Cif(p_opts.user_data.actual_cif,full,"")
+        return Cif(p_opts.user_data.actual_cif, full ,"")
     end
     if Sys.iswindows() && !native
         @debug "Did not use cif_api on Windows"
     end
-    full_contents = read(full,String)
-    Cif(full_contents,verbose=verbose,version=version,source=full)
+    full_contents = read(full, String)
+    cif_from_string(full_contents, verbose=verbose, version=version, source=full)
 end
 
 """
-    Cif(s::AbstractString;verbose=false,version=0,source=p"")
+    cif_from_string(s::AbstractString; verbose=false, version=0, source="")
 
-Process contents of `s` as a CIF file using the native Julia parser.
+Process `s` as the text of a CIF file using the native Julia parser.
 If `verbose` is true, print progress information during parsing.
 `version` may be `1`, `2` or `0` (default) for auto-detected CIF
 version. If `source` is provided, it is a filesystem location to
 record as the source for `s`.
 """
-Cif(s::AbstractString;verbose=false,version=0,source=p"") = begin
+cif_from_string(s::AbstractString; verbose=false, version=0, source="") = begin
     if length(s) > 1 && s[1] == '\ufeff'
         s = s[(nextind(s,1)):end]
     end

src/ddl2_dictionary_ng.jl

@@ -31,13 +31,12 @@ DDL2_Dictionary(c::Cif) = begin
 end
 
 """
-    DDL2_Dictionary(a::AbstractPath;verbose=false)
+    DDL2_Dictionary(a; verbose=false)
 
 Create a `DDL2_Dictionary` given filename `a`. `verbose = true` will print
 extra debugging information during reading.
 """
-DDL2_Dictionary(a::AbstractPath;verbose=false) = DDL2_Dictionary(Cif(a,verbose=verbose))
-DDL2_Dictionary(a::String;verbose=false) = DDL2_Dictionary(Cif(Path(a),verbose=verbose))
+DDL2_Dictionary(a; verbose=false) = DDL2_Dictionary(Cif(a,verbose=verbose))
 
 DDL2_Dictionary(b::CifBlock,blockname::AbstractString) = begin
     all_dict_info = Dict{Symbol,DataFrame}()

src/ddlm_dictionary_ng.jl

@@ -95,7 +95,7 @@ DDLm_Dictionary(c::Cif;kwargs...) = begin
 end
 
 """
-    DDLm_Dictionary(a::AbstractPath;verbose=false,ignore_imports="None",
+    DDLm_Dictionary(a; verbose=false, ignore_imports="None",
     cache_imports=false)
 
 Create a `DDLm_Dictionary` given filename `a`. `verbose = true` will print
@@ -121,15 +121,11 @@ unless `import_dir` is specified, in which case the search is relative to
 that directory.
 
 """
-DDLm_Dictionary(a::AbstractPath;verbose=false,kwargs...) = begin
-    c = Cif(a,verbose=verbose,native=true) #Native to catch header comments
+DDLm_Dictionary(a; verbose=false, kwargs...) = begin
+    c = Cif(a, verbose=verbose, native=true) #Native to catch header comments
     DDLm_Dictionary(c;kwargs...)
 end
 
-DDLm_Dictionary(a::String;kwargs...) = begin
-    DDLm_Dictionary(Path(a);kwargs...)
-end
-
 DDLm_Dictionary(b::CifBlock;ignore_imports=:None,header="",cache_imports=true,import_dir="") = begin
     all_dict_info = Dict{Symbol,DataFrame}()
     # Namespace
@@ -1325,57 +1321,30 @@ const ddlm_categories = [
 Turn a possibly relative URL into an absolute one. Will probably fail if file
 component starts with "."
 """
-fix_url(s::String,parent) = begin
+fix_url(s::String, parent) = begin
     scheme = match(r"^[a-zA-Z]+:",s)
     if scheme == nothing
         if s[1]=='/'
-            return URI(Path(s))
+            return URI(path = s, scheme = "file")
         elseif s[1]=="."  # really shouldn't accept this
-            return URI(Path(joinpath(parent,s)))
+            return URI(path = joinpath(parent,s), scheme = "file")
         else
-            return URI(Path(joinpath(parent,s)))
+            return URI(path = joinpath(parent,s), scheme = "file")
         end
     end
     return URI(s)
 end
 
-# Following code copied from URIs/uris.jl. For some reason
-# this function was not recognised during precompilation
-
-const absent = SubString("absent", 1, 0)
-
-function URIs.URI(p::AbstractPath; query=absent, fragment=absent)
-    if isempty(p.root)
-        throw(ArgumentError("$p is not an absolute path"))
-    end
-
-    b = IOBuffer()
-    print(b, "file://")
-
-    if !isempty(p.drive)
-        print(b, "/")
-        print(b, p.drive)
-    end
-
-    for s in p.segments
-        print(b, "/")
-        print(b, URIs.escapeuri(s))
-    end
-
-    return URIs.URI(URIs.URI(String(take!(b))); query=query, fragment=fragment)
-end
-
 """
     to_path(::URI)
 
-Convert a file: URI to a Path.
-Really belongs in FilePaths.jl but for now this will work.
+Convert a file: URI to a path.
 """
 to_path(u::URI) = begin
     if Sys.iswindows()
-        Path(unescapeuri(u.path[2:end]))
+        unescapeuri(u.path[2:end])
     else
-        Path(unescapeuri(u.path))
+        unescapeuri(u.path)
     end
 end
 
@@ -1657,7 +1626,7 @@ check_import_block(d::DDLm_Dictionary,name,cat,obj,val) = begin
     spec = x[:import].get[]
     for one_spec in spec
         if get(one_spec,"mode","Contents") == "Full" continue end
-        templ_file_name = joinpath(Path(d.import_dir), one_spec["file"])
+        templ_file_name = joinpath(d.import_dir, one_spec["file"])
         if !(templ_file_name in keys(d.cached_imports))
             println("Warning: cannot find $templ_file_name when checking imports for $name")
             continue

test/Project.toml

@@ -1,5 +1,4 @@
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-FilePaths = "8fc22ac5-c921-52a6-82fd-178b2807b824"
 Lerche = "d42ef402-04e6-4356-9f73-091573ea58dc"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

test/creation.jl

@@ -1,7 +1,6 @@
 # Test CIF object creation and destruction
-# Now adapted for NativeCif
 
-testdir = @__PATH__
+testdir = @__DIR__
 
 @testset "Test simple CIF creation and destruction" begin
 

test/data_and_dictionaries.jl

@@ -1,8 +1,8 @@
 # Test combinations of data and dictionaries
 
 prepare_dd() = begin
-    t = DDLm_Dictionary(joinpath(@__PATH__,"cif_core.dic"))
-    n = first(Cif(joinpath(@__PATH__,"nick1.cif"))).second
+    t = DDLm_Dictionary(joinpath(@__DIR__,"cif_core.dic"))
+    n = first(Cif(joinpath(@__DIR__,"nick1.cif"))).second
     return t,n
 end
 
@@ -40,8 +40,8 @@ is_looped(b, n) = any(x -> n in x, CrystalInfoFramework.get_loop_names(b))
 end
 
 @testset "Merging blocks" begin
-    t = DDLm_Dictionary(joinpath(@__PATH__,"cif_core.dic"))
-    n = Cif(joinpath(@__PATH__,"nick1_mergeable.cif"))
+    t = DDLm_Dictionary(joinpath(@__DIR__,"cif_core.dic"))
+    n = Cif(joinpath(@__DIR__,"nick1_mergeable.cif"))
     println("About to merge blocks")
     merge_blocks!(n,t)
     f = first(n).second

test/dc_base.jl

@@ -5,9 +5,9 @@ using Test
 
 # Test a plain CIF as data source
 
-const cif_test_file = joinpath(@__PATH__,"nick1.cif")
-const multi_block_test_file = joinpath(@__PATH__,"cif_img_1.7.11.dic")
-const core_dic = joinpath(@__PATH__,"cif_core.dic")
+const cif_test_file = joinpath(@__DIR__,"nick1.cif")
+const multi_block_test_file = joinpath(@__DIR__,"cif_img_1.7.11.dic")
+const core_dic = joinpath(@__DIR__,"cif_core.dic")
 
 prepare_files() = begin
     c = Cif(cif_test_file)