daru 0.0.5 → 0.1.0

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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 @@
1
+ 214.80000 131.00000 131.10000 9.00000 9.70000 141.00000
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+ 214.60000 129.70000 129.70000 8.10000 9.50000 141.70000
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+ 214.80000 129.70000 129.70000 8.70000 9.60000 142.20000
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+ 214.80000 129.70000 129.60000 7.50000 10.40000 142.00000
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+ 215.00000 129.60000 129.70000 10.40000 7.70000 141.80000
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+ 215.70000 130.80000 130.50000 9.00000 10.10000 141.40000
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+ 215.50000 129.50000 129.70000 7.90000 9.60000 141.60000
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+ 214.50000 129.60000 129.20000 7.20000 10.70000 141.70000
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+ 214.90000 129.40000 129.70000 8.20000 11.00000 141.90000
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+ 215.20000 130.40000 130.30000 9.20000 10.00000 140.70000
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+ 215.30000 130.40000 130.30000 7.90000 11.70000 141.80000
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+ 215.10000 129.50000 129.60000 7.70000 10.50000 142.20000
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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