rewrite the module for best practices

Author: vcanogil

.gitignore

@@ -1,6 +1,6 @@
 # MacOS default directory
 *.DS_Store
-.CondaPkg
+*.CondaPkg
 
 # Files generated by invoking Julia with --code-coverage
 *.jl.cov

src/Cclib.jl

@@ -1,6 +1,9 @@
 module Cclib
+using PythonCall
+using CondaPkg
 
-include("./functions.jl")
+include("functions.jl")
+include("config.jl")
 
 const cclib = Ref{Py}()
 

src/data.jl renamed to src/config.jl

@@ -1,3 +1,5 @@
+export cclibtypes
+
 cclibtypes = Dict(
     "aonames" => Array{String},
     "aooverlaps" => Array{Float64, 2},
@@ -72,13 +74,3 @@ cclibtypes = Dict(
     "vibsyms" => Array{String},
     "zpve" => Float64
 )
-
-using Cclib
-using PythonCall
-m3 = ccread("./test/data/Trp_polar_tdhf.out")
-
-for (key, value) in m3
-    type = cclibtypes[key]
-    m3[key] = pyconvert(type, value)
-end
-m3

src/functions.jl

@@ -1,12 +1,18 @@
-using PythonCall
-using CondaPkg
-
 export ccread
 
 
-function ccread(file)
+function pyccread(file)
     data = cclib[].io.ccread(file)
     keys = pyconvert(Array, data.__dict__.keys())
     values = pyconvert(Array, data.__dict__.values())
     return Dict(zip(keys, values))
+end
+
+function ccread(pydict)
+    datadict = pyccread(pydict)
+    for (key, value) in datadict
+        type = cclibtypes[key]
+        datadict[key] = pyconvert(type, value)
+    end
+    return datadict
 end

test/runtests.jl

@@ -3,6 +3,15 @@ using Test
 
 
 @testset "Cclib.jl" begin
+
+    # Start with something simple
     @test ccread("./test/data/uracil_two.xyz")["natom"] == 12
+    @test ccread("./test/data/uracil_two.xyz")["atomnos"] == [7, 6, 1, 8, 7, 6, 8, 6, 6, 1, 1, 1]
+    @test ccread("./test/data/uracil_two.xyz")["atomcoords"] == [5.435 4.091 6.109 3.647 3.253 3.636 2.79 5.065 5.906 2.243 5.448 7.003;
+                                                                 5.42432 4.08846 6.05396 3.68445 3.24195 3.62987 2.83542 5.0864 5.91213 2.2534 5.42415 6.9915;;;
+                                                                 3.248 3.266 3.347 3.394 3.118 2.955 2.842 2.953 3.101 3.138 2.833 3.119;
+                                                                 3.24732 3.26356 3.354 3.39863 3.11963 2.96568 2.83961 2.95832 3.09904 3.12801 2.83814 3.10206;;;
+                                                                 -0.916 -0.635 -0.144 0.495 -1.717 -3.039 -3.923 -3.239 -2.202 -1.514 -4.258 -2.345;
+                                                                 -0.9432 -0.64127 -0.15563 0.50851 -1.70419 -3.0054 -3.9297 -3.25044 -2.21101 -1.51035 -4.27067 -2.32366]
 end