update tests, add error handling

Author: vcanogil

Project.toml

@@ -5,6 +5,7 @@ version = "0.1.0"
 
 [deps]
 CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d"
 

src/Cclib.jl

@@ -1,6 +1,7 @@
 module Cclib
 using PythonCall
 using CondaPkg
+using Logging
 
 include("functions.jl")
 include("config.jl")

src/functions.jl

@@ -1,18 +1,33 @@
 export ccread
 
-
 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)
+function get_data(file)
+    datadict = pyccread(file)
     for (key, value) in datadict
         type = cclibtypes[key]
         datadict[key] = pyconvert(type, value)
     end
     return datadict
-end
+end
+
+function ccread(file)
+    try
+        if !isfile(file)
+            @error "$(file) is not file"
+            return nothing
+        end
+        data = get_data(file)
+        return data
+    catch e
+        if isa(e, PythonCall.PyException)
+            @error "Unsupported file format"
+            return nothing
+        end
+    end
+end

test/data/invalid_file.txt

@@ -0,0 +1 @@
+test invalid file

test/runtests.jl

@@ -1,10 +1,11 @@
 using Cclib
+using PythonCall
 using Test
 
 
 @testset "Cclib.jl" begin
 
-    # Start with something simple
+    # Check that input is read correctly
     @test ccread("./data/uracil_two.xyz")["natom"] == 12
     @test ccread("./data/uracil_two.xyz")["atomnos"] == [7, 6, 1, 8, 7, 6, 8, 6, 6, 1, 1, 1]
     @test ccread("./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;
@@ -13,4 +14,8 @@ using Test
                                                                  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]
+
+    # Check that it handles unsupported files correctly
+    @test isnothing(ccread("./data/invalid_file.txt"))
+    @test isnothing(ccread("./data/"))
 end