1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
{-|
Module : Gargantext.Prelude
Description : Specific Prelude of the project
Copyright : (c) CNRS, 2017-Present
License : AGPL + CECILL v3
Maintainer : team@gargantext.org
Stability : experimental
Portability : POSIX
-}
{-# OPTIONS_GHC -fno-warn-orphans #-}
{-# OPTIONS_GHC -fno-warn-type-defaults #-}
module Gargantext.Prelude
( module Gargantext.Prelude
, module Protolude
, module GHC.Err.Located
, module Text.Show
, module Text.Read
, module Data.Maybe
, module Prelude
, MonadBase(..)
, Typeable
, cs
, headMay, lastMay, sortWith
, round
)
where
import Control.Monad.Base (MonadBase(..))
import Data.Set (Set)
import GHC.Exts (sortWith)
import GHC.Err.Located (undefined)
import GHC.Real (round)
import Data.Map (Map, lookup)
import Data.Maybe (isJust, fromJust, maybe)
import Data.Monoid (Monoid, mempty)
import Data.Semigroup (Semigroup, (<>))
import Data.Text (Text)
import Data.Typeable (Typeable)
import Protolude ( Bool(True, False), Int, Int64, Double, Integer
, Fractional, Num, Maybe(Just,Nothing)
, Enum, Bounded, Float
, Floating, Char, IO
, Functor(..)
, pure, (>>=), (=<<), (<*>), (<$>), (<&>), (>>)
, head, flip
, Ord, Integral, Foldable, RealFrac, Monad, filter
, reverse, map, mapM, zip, drop, take, zipWith
, sum, fromIntegral, length, fmap, foldl, foldl'
, takeWhile, sqrt, identity
, abs, min, max, maximum, minimum, return, snd, truncate
, (+), (*), (/), (-), (.), ($), (&), (**), (^), (<), (>), log
, Eq, (==), (>=), (<=), (<>), (/=), xor
, (&&), (||), not, any, all
, concatMap
, fst, snd, toS
, elem, die, mod, div, const, either
, curry, uncurry, repeat
, otherwise, when
, IO()
, compare
, on
, panic
, seq
)
import Prelude (Enum, Bounded, minBound, maxBound, putStrLn)
-- TODO import functions optimized in Utils.Count
-- import Protolude hiding (head, last, all, any, sum, product, length)
-- import Gargantext.Utils.Count
import Data.Map.Strict (insertWith)
import Data.String.Conversions (cs)
import Safe (headMay, lastMay, initMay, tailMay)
import Text.Read (Read())
import Text.Show (Show(), show)
import qualified Control.Monad as M
import qualified Data.List as L hiding (head, sum)
import qualified Data.Map as M
import qualified Data.Set as Set
import qualified Data.Vector as V
printDebug :: (Show a, MonadBase IO m) => [Char] -> a -> m ()
printDebug msg x = liftBase . putStrLn $ msg <> " " <> show x
-- printDebug _ _ = pure ()
-- | splitEvery n == chunkAlong n n
splitEvery :: Int -> [a] -> [[a]]
splitEvery _ [] = []
splitEvery n xs =
let (h,t) = L.splitAt n xs
in h : splitEvery n t
type Grain = Int
type Step = Int
-- | Function to split a range into chunks
-- if step == grain then linearity (splitEvery)
-- elif step < grain then overlapping
-- else dotted with holes
-- TODO FIX BUG if Steps*Grain /= length l
-- chunkAlong 10 10 [1..15] == [1..10]
-- BUG: what about the rest of (divMod 15 10)?
-- TODO: chunkAlongNoRest or chunkAlongWithRest
-- default behavior: NoRest
chunkAlong :: Eq a => Grain -> Step -> [a] -> [[a]]
chunkAlong a b l = case a >= length l of
True -> [l]
False -> chunkAlong' a b l
chunkAlong' :: Eq a => Grain -> Step -> [a] -> [[a]]
chunkAlong' a b l = case a > 0 && b > 0 of
True -> chunkAlong'' a b l
False -> panic "ChunkAlong: Parameters should be > 0 and Grain > Step"
chunkAlong'' :: Eq a => Int -> Int -> [a] -> [[a]]
chunkAlong'' a b l = filter (/= []) $ only (while dropAlong)
where
only = map (take a)
while = takeWhile (\x -> length x >= a)
dropAlong = L.scanl (\x _y -> drop b x) l ([1..] :: [Integer])
-- | Optimized version (Vector)
chunkAlongV :: Int -> Int -> V.Vector a -> V.Vector (V.Vector a)
chunkAlongV a b l = only (while dropAlong)
where
only = V.map (V.take a)
while = V.takeWhile (\x -> V.length x >= a)
dropAlong = V.scanl (\x _y -> V.drop b x) l (V.fromList [1..])
-- | TODO Inverse of chunk ? unchunkAlong ?
-- unchunkAlong :: Int -> Int -> [[a]] -> [a]
-- unchunkAlong = undefined
-- splitAlong [2,3,4] ("helloworld" :: [Char]) == ["he", "llo", "worl", "d"]
splitAlong :: [Int] -> [Char] -> [[Char]]
splitAlong _ [] = [] -- No list? done
splitAlong [] xs = [xs] -- No place to split at? Return the remainder
splitAlong (x:xs) ys = take x ys : splitAlong xs (drop x ys)
-- take until our split spot, recurse with next split spot and list remainder
takeWhileM :: (Monad m) => (a -> Bool) -> [m a] -> m [a]
takeWhileM _ [] = return []
takeWhileM p (a:as) = do
v <- a
if p v
then do
vs <- takeWhileM p as
return (v:vs)
else return []
-- SUMS
-- To select the right algorithme according to the type:
-- https://github.com/mikeizbicki/ifcxt
sumSimple :: Num a => [a] -> a
sumSimple = L.foldl' (+) 0
-- | https://en.wikipedia.org/wiki/Kahan_summation_algorithm
sumKahan :: Num a => [a] -> a
sumKahan = snd . L.foldl' go (0,0)
where
go (c,t) i = ((t'-t)-y,t')
where
y = i-c
t' = t+y
-- | compute part of the dict
count2map :: (Ord k, Foldable t) => t k -> Map k Double
count2map xs = M.map (/ (fromIntegral (length xs))) (count2map' xs)
-- | insert in a dict
count2map' :: (Ord k, Foldable t) => t k -> Map k Double
count2map' xs = L.foldl' (\x y -> insertWith (+) y 1 x) M.empty xs
trunc :: (RealFrac a, Integral c, Integral b) => b -> a -> c
trunc n = truncate . (* 10^n)
trunc' :: Int -> Double -> Double
trunc' n x = fromIntegral $ truncate $ (x * 10^n)
------------------------------------------------------------------------
bool2num :: Num a => Bool -> a
bool2num True = 1
bool2num False = 0
bool2double :: Bool -> Double
bool2double = bool2num
bool2int :: Bool -> Int
bool2int = bool2num
------------------------------------------------------------------------
-- Normalizing && scaling data
scale :: [Double] -> [Double]
scale = scaleMinMax
scaleMinMax :: [Double] -> [Double]
scaleMinMax xs = map (\x -> (x - mi / (ma - mi + 1) )) xs'
where
ma = maximum xs'
mi = minimum xs'
xs' = map abs xs
scaleNormalize :: [Double] -> [Double]
scaleNormalize xs = map (\x -> (x - v / (m + 1))) xs'
where
v = variance xs'
m = mean xs'
xs' = map abs xs
normalize :: [Double] -> [Double]
normalize as = normalizeWith identity as
normalizeWith :: Fractional b => (a -> b) -> [a] -> [b]
normalizeWith extract bs = map (\x -> x/(sum bs')) bs'
where
bs' = map extract bs
-- Zip functions to add
zipFst :: ([b] -> [a]) -> [b] -> [(a, b)]
zipFst f xs = zip (f xs) xs
zipSnd :: ([a] -> [b]) -> [a] -> [(a, b)]
zipSnd f xs = zip xs (f xs)
-- | maximumWith
maximumWith :: (Ord a1, Foldable t) => (a2 -> a1) -> t a2 -> a2
maximumWith f = L.maximumBy (compare `on` f)
-- | To get all combinations of a list with no
-- repetition and apply a function to the resulting list of pairs
listToCombi :: forall a b. (a -> b) -> [a] -> [(b,b)]
listToCombi f l = [ (f x, f y) | (x:rest) <- L.tails l, y <- rest ]
------------------------------------------------------------------------
-- Empty List Sugar Error Handling
-- TODO add Garg Monad Errors
listSafe1 :: Text -> ([a] -> Maybe a)
-> Text -> [a] -> a
listSafe1 s f e xs = maybe (panic $ h <> e) identity (f xs)
where
h = "[ERR][Gargantext] Empty list for " <> s <> " in "
head' :: Text -> [a] -> a
head' = listSafe1 "head" headMay
last' :: Text -> [a] -> a
last' = listSafe1 "last" lastMay
------------------------------------------------------------------------
listSafeN :: Text -> ([a] -> Maybe [a])
-> Text -> [a] -> [a]
listSafeN s f e xs = maybe (panic $ h <> e) identity (f xs)
where
h = "[ERR][Gargantext] Empty list for " <> s <> " in "
tail' :: Text -> [a] -> [a]
tail' = listSafeN "tail" tailMay
init' :: Text -> [a] -> [a]
init' = listSafeN "init" initMay
------------------------------------------------------------------------
--- Some Statistics sugar functions
-- Exponential Average
eavg :: [Double] -> Double
eavg (x:xs) = a*x + (1-a)*(eavg xs)
where a = 0.70
eavg [] = 0
-- Simple Average
mean :: Fractional a => [a] -> a
mean xs = sum xs / fromIntegral (length xs)
sumMaybe :: Num a => [Maybe a] -> Maybe a
sumMaybe = fmap sum . M.sequence
variance :: Floating a => [a] -> a
variance xs = sum ys / (fromIntegral (length xs) - 1)
where
m = mean xs
ys = map (\x -> (x - m) ** 2) xs
deviation :: Floating a => [a] -> a
deviation = sqrt . variance
movingAverage :: (Eq b, Fractional b) => Int -> [b] -> [b]
movingAverage steps xs = map mean $ chunkAlong steps 1 xs
-----------------------------------------------------------------------
-----------------------------------------------------------------------
--- Map in Map = Map2
-- To avoid Map (a,a) b
type Map2 a b = Map a (Map a b)
lookup2 :: Ord a
=> a
-> a
-> Map2 a b
-> Maybe b
lookup2 a b m = do
m' <- lookup a m
lookup b m'
-----------------------------------------------------------------------
foldM' :: (Monad m) => (a -> b -> m a) -> a -> [b] -> m a
foldM' _ z [] = return z
foldM' f z (x:xs) = do
z' <- f z x
z' `seq` foldM' f z' xs
-----------------------------------------------------------------------
-- | Instance for basic numerals
-- See the difference between Double and (Int Or Integer)
instance Monoid Double where
mempty = 1
instance Semigroup Double where
(<>) a b = a * b
-----------
instance Monoid Int where
mempty = 0
instance Semigroup Int where
(<>) a b = a + b
----
instance Monoid Integer where
mempty = 0
instance Semigroup Integer where
(<>) a b = a + b
------------------------------------------------------------------------
hasDuplicates :: Ord a => [a] -> Bool
hasDuplicates = hasDuplicatesWith Set.empty
hasDuplicatesWith :: Ord a => Set a -> [a] -> Bool
hasDuplicatesWith _seen [] =
False -- base case: empty lists never contain duplicates
hasDuplicatesWith seen (x:xs) =
-- If we have seen the current item before, we can short-circuit; otherwise,
-- we'll add it the the set of previously seen items and process the rest of the
-- list against that.
x `Set.member` seen || hasDuplicatesWith (Set.insert x seen) xs