daru 0.0.5 → 0.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (48) hide show
  1. checksums.yaml +4 -4
  2. data/.build.sh +14 -0
  3. data/.travis.yml +26 -4
  4. data/CONTRIBUTING.md +31 -0
  5. data/Gemfile +1 -2
  6. data/{History.txt → History.md} +110 -44
  7. data/README.md +21 -288
  8. data/Rakefile +1 -0
  9. data/daru.gemspec +12 -8
  10. data/lib/daru.rb +36 -1
  11. data/lib/daru/accessors/array_wrapper.rb +8 -3
  12. data/lib/daru/accessors/gsl_wrapper.rb +113 -0
  13. data/lib/daru/accessors/nmatrix_wrapper.rb +6 -17
  14. data/lib/daru/core/group_by.rb +0 -1
  15. data/lib/daru/dataframe.rb +1192 -83
  16. data/lib/daru/extensions/rserve.rb +21 -0
  17. data/lib/daru/index.rb +14 -0
  18. data/lib/daru/io/io.rb +170 -8
  19. data/lib/daru/maths/arithmetic/dataframe.rb +4 -3
  20. data/lib/daru/maths/arithmetic/vector.rb +4 -4
  21. data/lib/daru/maths/statistics/dataframe.rb +48 -27
  22. data/lib/daru/maths/statistics/vector.rb +215 -33
  23. data/lib/daru/monkeys.rb +53 -7
  24. data/lib/daru/multi_index.rb +21 -4
  25. data/lib/daru/plotting/dataframe.rb +83 -25
  26. data/lib/daru/plotting/vector.rb +9 -10
  27. data/lib/daru/vector.rb +596 -61
  28. data/lib/daru/version.rb +3 -0
  29. data/spec/accessors/wrappers_spec.rb +51 -0
  30. data/spec/core/group_by_spec.rb +0 -2
  31. data/spec/daru_spec.rb +58 -0
  32. data/spec/dataframe_spec.rb +768 -73
  33. data/spec/extensions/rserve_spec.rb +52 -0
  34. data/spec/fixtures/bank2.dat +200 -0
  35. data/spec/fixtures/repeated_fields.csv +7 -0
  36. data/spec/fixtures/scientific_notation.csv +4 -0
  37. data/spec/fixtures/test_xls.xls +0 -0
  38. data/spec/io/io_spec.rb +161 -24
  39. data/spec/math/arithmetic/dataframe_spec.rb +26 -7
  40. data/spec/math/arithmetic/vector_spec.rb +8 -0
  41. data/spec/math/statistics/dataframe_spec.rb +16 -1
  42. data/spec/math/statistics/vector_spec.rb +215 -47
  43. data/spec/spec_helper.rb +21 -2
  44. data/spec/vector_spec.rb +368 -12
  45. metadata +99 -16
  46. data/lib/version.rb +0 -3
  47. data/notebooks/grouping_splitting_pivots.ipynb +0 -529
  48. data/notebooks/intro_with_music_data_.ipynb +0 -303
data/spec/extensions/rserve_spec.rb ADDED
@@ -0,0 +1,52 @@
1
+ begin
2
+ require "rserve"
3
+ require 'daru/extensions/rserve'
4
+
5
+ describe "Daru rserve extension" do
6
+ before do
7
+ @r = Rserve::Connection.new
8
+ end
9
+
10
+ after do
11
+ @r.close
12
+ end
13
+
14
+ describe Daru::Vector do
15
+ context "#to_REXP" do
16
+ it "converts to and from R data" do
17
+ a = Daru::Vector.new(100.times.map { |i| rand > 0.9 ? nil : i + rand })
18
+ rexp = a.to_REXP
19
+ expect(rexp.is_a?(Rserve::REXP::Double)).to eq(true)
20
+ expect(rexp.to_ruby).to eq(a.to_a)
21
+
22
+ @r.assign 'a', rexp
23
+ expect(@r.eval('a').to_ruby).to eq(a.to_a)
24
+ end
25
+ end
26
+ end
27
+
28
+ describe Daru::DataFrame do
29
+ context "#to_REXP" do
30
+ it "converts to and from R data" do
31
+ a = Daru::Vector.new(100.times.map { |i| rand > 0.9 ? nil : i + rand })
32
+ b = Daru::Vector.new(100.times.map { |i| rand > 0.9 ? nil : i + rand })
33
+ c = Daru::Vector.new(100.times.map { |i| rand > 0.9 ? nil : i + rand })
34
+ ds = Daru::DataFrame.new({ :a => a, :b => b, :c => c })
35
+ rexp = ds.to_REXP
36
+ expect(rexp.is_a? Rserve::REXP::GenericVector).to eq(true)
37
+
38
+ ret = rexp.to_ruby
39
+ expect(ret['a']).to eq(a.to_a)
40
+ @r.assign 'df', rexp
41
+ out_df = @r.eval('df').to_ruby
42
+
43
+ expect(out_df.attributes['class']).to eq('data.frame')
44
+ expect(out_df.attributes['names']).to eq(%w(a b c))
45
+ expect(out_df['a']).to eq(a.to_a)
46
+ end
47
+ end
48
+ end
49
+ end
50
+ rescue LoadError => e
51
+ puts "Requires rserve extension"
52
+ end
data/spec/fixtures/bank2.dat ADDED
@@ -0,0 +1,200 @@
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data/spec/fixtures/repeated_fields.csv ADDED
@@ -0,0 +1,7 @@
1
+ "id","name","age","city","a1","name","age"
2
+ 1,"Alex",20,"New York","a,b","a",3
3
+ 2,"Claude",23,"London","b,c","b",4
4
+ 3,"Peter",25,"London","a","c",5
5
+ 4,"Franz",27,"Paris",,"d",6
6
+ 5,"George","5,5","Tome","a,b,c","f",
7
+ 6,"Fernand",20,"London","c,b","f",8
data/spec/fixtures/scientific_notation.csv ADDED
@@ -0,0 +1,4 @@
1
+ x,y
2
+ 1,9.629587310436753e+127
3
+ 2,1.9341543147883677e+129
4
+ 3,3.88485279048245e+130
data/spec/io/io_spec.rb CHANGED
@@ -1,40 +1,177 @@
1
1
  require 'spec_helper.rb'
2
2
 
3
- describe Daru::DataFrame do
4
- context ".from_csv" do
5
- it "loads from a CSV file" do
6
- df = Daru::DataFrame.from_csv('spec/fixtures/matrix_test.csv',
7
- col_sep: ' ', headers: true)
3
+ describe Daru::IO do
4
+ describe Daru::DataFrame do
5
+ context ".from_csv" do
6
+ it "loads from a CSV file" do
7
+ df = Daru::DataFrame.from_csv('spec/fixtures/matrix_test.csv',
8
+ col_sep: ' ', headers: true)
8
9
 
9
- expect(df.vectors).to eq([:image_resolution, :mls, :true_transform].to_index)
10
- expect(df.vector[:image_resolution].first).to eq(6.55779)
11
- expect(df.vector[:true_transform].first).to eq("-0.2362347,0.6308649,0.7390552,0,0.6523478,-0.4607318,0.6018043,0,0.7201635,0.6242881,-0.3027024,4262.65,0,0,0,1")
10
+ expect(df.vectors).to eq([:image_resolution, :mls, :true_transform].to_index)
11
+ expect(df.vector[:image_resolution].first).to eq(6.55779)
12
+ expect(df.vector[:true_transform].first).to eq("-0.2362347,0.6308649,0.7390552,0,0.6523478,-0.4607318,0.6018043,0,0.7201635,0.6242881,-0.3027024,4262.65,0,0,0,1")
13
+ end
14
+
15
+ it "works properly for repeated headers", focus: true do
16
+ df = Daru::DataFrame.from_csv('spec/fixtures/repeated_fields.csv')
17
+ expect(df.vectors.to_a).to eq([:a1, :age_1, :age_2, :city, :id, :name_1, :name_2])
18
+
19
+ age = Daru::Vector.new([3, 4, 5, 6, nil, 8])
20
+ expect(df[:age_2]).to eq(age)
21
+ end
22
+
23
+ it "accepts scientific notation as float" do
24
+ ds = Daru::DataFrame.from_csv('spec/fixtures/scientific_notation.csv')
25
+ expect(ds.vectors.to_a).to eq([:x, :y])
26
+ y = [9.629587310436753e+127, 1.9341543147883677e+129, 3.88485279048245e+130]
27
+ y.zip(ds[:y]).each do |y_expected, y_ds|
28
+ expect(y_ds).to be_within(0.001).of(y_expected)
29
+ end
30
+ end
31
+ end
32
+
33
+ context "#write_csv" do
34
+ it "writes DataFrame to a CSV file" do
35
+ df = Daru::DataFrame.new({
36
+ a: [1,2,3,4,5],
37
+ b: [11,22,33,44,55],
38
+ c: ['a', 'g', 4, 5,'addadf'],
39
+ d: [nil, 23, 4,'a','ff']})
40
+ t = Tempfile.new('data.csv')
41
+ df.write_csv t.path
42
+
43
+ expect(Daru::DataFrame.from_csv(t.path)).to eq(df)
44
+ end
45
+ end
46
+
47
+ context ".from_excel" do
48
+ before do
49
+ id = Daru::Vector.new([1, 2, 3, 4, 5, 6])
50
+ name = Daru::Vector.new(%w(Alex Claude Peter Franz George Fernand))
51
+ age = Daru::Vector.new( [20, 23, 25, nil, 5.5, nil])
52
+ city = Daru::Vector.new(['New York', 'London', 'London', 'Paris', 'Tome', nil])
53
+ a1 = Daru::Vector.new(['a,b', 'b,c', 'a', nil, 'a,b,c', nil])
54
+ @expected = Daru::DataFrame.new({
55
+ :id => id, :name => name, :age => age, :city => city, :a1 => a1
56
+ }, order: [:id, :name, :age, :city, :a1])
57
+ end
58
+
59
+ it "loads DataFrame from an Excel Spreadsheet" do
60
+ df = Daru::DataFrame.from_excel 'spec/fixtures/test_xls.xls'
61
+
62
+ expect(df.nrows).to eq(6)
63
+ expect(df.vectors.to_a).to eq([:id, :name, :age, :city, :a1])
64
+ expect(df[:age][5]).to eq(nil)
65
+ expect(@expected).to eq(df)
66
+ end
67
+ end
68
+
69
+ context "#write_excel" do
70
+ before do
71
+ a = Daru::Vector.new(100.times.map { rand(100) })
72
+ b = Daru::Vector.new((['b'] * 100))
73
+ @expected = Daru::DataFrame.new({ :b => b, :a => a })
74
+
75
+ tempfile = Tempfile.new('test_write.xls')
76
+
77
+ @expected.write_excel tempfile.path
78
+ @df = Daru::DataFrame.from_excel tempfile.path
79
+ end
80
+
81
+ it "correctly writes DataFrame to an Excel Spreadsheet" do
82
+ expect(@expected).to eq(@df)
83
+ end
84
+ end
85
+
86
+ context ".from_sql" do
87
+ it "loads data from an SQL database" do
88
+ # TODO: write these tests
89
+ end
90
+ end
91
+
92
+ context "#write_sql" do
93
+ it "writes the DataFrame to an SQL database" do
94
+ # TODO: write these tests
95
+ end
96
+ end
97
+
98
+ context ".from_plaintext" do
99
+ it "reads data from plain text files" do
100
+ df = Daru::DataFrame.from_plaintext 'spec/fixtures/bank2.dat', [:v1,:v2,:v3,:v4,:v5,:v6]
101
+
102
+ expect(df.vectors.to_a).to eq([:v1,:v2,:v3,:v4,:v5,:v6])
103
+ end
12
104
  end
13
- end
14
105
 
15
- context "JSON" do
16
- it "loads parsed JSON" do
17
- require 'json'
106
+ context "JSON" do
107
+ it "loads parsed JSON" do
108
+ require 'json'
18
109
 
19
- json = File.read 'spec/fixtures/countries.json'
20
- df = Daru::DataFrame.new JSON.parse(json)
110
+ json = File.read 'spec/fixtures/countries.json'
111
+ df = Daru::DataFrame.new JSON.parse(json)
21
112
 
22
- expect(df.vectors).to eq([
23
- :name, :nativeName, :tld, :cca2, :ccn3, :cca3, :currency, :callingCode,
24
- :capital, :altSpellings, :relevance, :region, :subregion, :language,
25
- :languageCodes, :translations, :latlng, :demonym, :borders, :area].to_index)
113
+ expect(df.vectors).to eq([
114
+ :name, :nativeName, :tld, :cca2, :ccn3, :cca3, :currency, :callingCode,
115
+ :capital, :altSpellings, :relevance, :region, :subregion, :language,
116
+ :languageCodes, :translations, :latlng, :demonym, :borders, :area].to_index)
26
117
 
27
- expect(df.row[0][:name]).to eq("Afghanistan")
118
+ expect(df.row[0][:name]).to eq("Afghanistan")
119
+ end
120
+ end
121
+
122
+ context "Marshalling" do
123
+ it "" do
124
+ vector = Daru::Vector.new (0..100).collect { |_n| rand(100) }
125
+ dataframe = Daru::Vector.new({a: vector, b: vector, c: vector})
126
+ expect(Marshal.load(Marshal.dump(dataframe))).to eq(dataframe)
127
+ end
128
+ end
129
+
130
+ context "#save" do
131
+ before do
132
+ @data_frame = Daru::DataFrame.new({b: [11,12,13,14,15], a: [1,2,3,4,5],
133
+ c: [11,22,33,44,55]},
134
+ order: [:a, :b, :c],
135
+ index: [:one, :two, :three, :four, :five])
136
+ end
137
+
138
+ it "saves df to a file" do
139
+ outfile = Tempfile.new('dataframe.df')
140
+ @data_frame.save(outfile.path)
141
+ a = Daru::IO.load(outfile.path)
142
+ expect(a).to eq(@data_frame)
143
+ end
28
144
  end
29
145
  end
30
146
 
31
- context "#inspect" do
32
- it "prints DataFrame pretty" do
147
+ describe Daru::Vector do
148
+ context "Marshalling" do
149
+ it "" do
150
+ vector = Daru::Vector.new (0..100).collect { |_n| rand(100) }
151
+ expect(Marshal.load(Marshal.dump(vector))).to eq(vector)
152
+ end
153
+ end
33
154
 
155
+ context "#save" do
156
+ ALL_DTYPES.each do |dtype|
157
+ it "saves to a file and returns the same Vector of type #{dtype}" do
158
+ vector = Daru::Vector.new(
159
+ [5, 5, 5, 5, 5, 6, 6, 7, 8, 9, 10, 1, 2, 3, 4, 11, -99, -99],
160
+ dtype: dtype)
161
+ outfile = Tempfile.new('vector.vec')
162
+ vector.save(outfile.path)
163
+ expect(Daru::IO.load(outfile.path)).to eq(vector)
164
+ end
165
+ end
34
166
  end
35
167
  end
36
168
 
37
- context "#to_csv" do
38
- # TODO
169
+ describe Daru::Index do
170
+ context "Marshalling" do
171
+ it "" do
172
+ i = Daru::Index.new([:a, :b, :c, :d, :e], [8,6,4,3,5])
173
+ expect(Marshal.load(Marshal.dump(i))).to eq(i)
174
+ end
175
+ end
39
176
  end
40
- end
177
+ end