Upgrade to Pro
— share decks privately, control downloads, hide ads and more …
Speaker Deck
Features
Speaker Deck
PRO
Sign in
Sign up for free
Search
Search
Testing Research Software
Search
Nikoleta
March 14, 2017
Programming
0
310
Testing Research Software
Slides for the talk Writing tests for research software for PyCon Namibia 2017
Nikoleta
March 14, 2017
Tweet
Share
More Decks by Nikoleta
See All by Nikoleta
A trip to earth science with python as a companion
nikoletav3
0
44
Arcas: Using Python to access open research literature
nikoletav3
1
170
Optimisation of short memory strategies in the Iterated Prisoners Dilemma
nikoletav3
0
53
Arcas
nikoletav3
0
440
SSI Selection Day
nikoletav3
0
400
SWORDS-03-10-2016
nikoletav3
0
47
PyCon UK 2016
nikoletav3
0
160
Other Decks in Programming
See All in Programming
システム成長を止めない!本番無停止テーブル移行の全貌
sakawe_ee
1
220
VS Code Update for GitHub Copilot
74th
2
670
PicoRuby on Rails
makicamel
2
140
The Niche of CDK Grant オブジェクトって何者?/the-niche-of-cdk-what-isgrant-object
hassaku63
1
500
AIプログラマーDevinは PHPerの夢を見るか?
shinyasaita
1
240
AIともっと楽するE2Eテスト
myohei
8
2.9k
Git Sync を超える!OSS で実現する CDK Pull 型デプロイ / Deploying CDK with PipeCD in Pull-style
tkikuc
4
240
型で語るカタ
irof
0
530
NPOでのDevinの活用
codeforeveryone
0
870
はじめてのWeb API体験 ー 飲食店検索アプリを作ろうー
akinko_0915
0
130
High-Level Programming Languages in AI Era -Human Thought and Mind-
hayat01sh1da
PRO
0
840
『自分のデータだけ見せたい!』を叶える──Laravel × Casbin で複雑権限をスッキリ解きほぐす 25 分
akitotsukahara
2
650
Featured
See All Featured
GitHub's CSS Performance
jonrohan
1031
460k
How To Stay Up To Date on Web Technology
chriscoyier
790
250k
I Don’t Have Time: Getting Over the Fear to Launch Your Podcast
jcasabona
32
2.4k
BBQ
matthewcrist
89
9.7k
CoffeeScript is Beautiful & I Never Want to Write Plain JavaScript Again
sstephenson
161
15k
Building Adaptive Systems
keathley
43
2.7k
What’s in a name? Adding method to the madness
productmarketing
PRO
23
3.5k
ReactJS: Keep Simple. Everything can be a component!
pedronauck
667
120k
Typedesign – Prime Four
hannesfritz
42
2.7k
Embracing the Ebb and Flow
colly
86
4.7k
Fight the Zombie Pattern Library - RWD Summit 2016
marcelosomers
233
17k
How to Create Impact in a Changing Tech Landscape [PerfNow 2023]
tammyeverts
53
2.9k
Transcript
Writing tests for research software @NikoletaGlyn
None
TESTING
0, 1, 1, 2, 3, 5, 8, 13, 21, 34
...
F0 = 0 F1 = 1 Fn = Fn−1 +
Fn−2
main.py def fib(n): if n == 0: return 0 if
n == 1: return 1 return 2 * fib(n - 1)
n 2 3 4 . . . 16 17 18
Fn 1 2 3 . . . 987 1597 2584 Fn−1 1 1 2 . . . 610 987 1597 Fn Fn−1 1.000 2.000 1.500 . . . 1.618 1.618 1.618
n 2 3 4 . . . 16 17 18
Fn 1 2 3 . . . 987 1597 2584 Fn−1 1 1 2 . . . 610 987 1597 Fn Fn−1 1.000 2.000 1.500 . . . 1.618 1.618 1.618 φ 1.61803...
. |-- main.py |-- golden.py
golden.py import main for n in range(10, 100000): golden_ratio =
fib(n) / fib(n - 1) print(golden_ratio)
golden.py import main for n in range(10, 100000): golden_ratio =
fib(n) / fib(n - 1) print(golden_ratio) 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 ...
golden.py import main for n in range(10, 100000): golden_ratio =
fib(n) / fib(n - 1) print(golden_ratio) 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 ... Glynatsi 2017, “SOLVES THE FIBONACCI MYSTERY”
WRITE REVIEW PUBLISH
20% OF GENETIC RESEARCH IS WRONG Gene name errors are
widespread in the scientific literature by Mark Ziemann, Yotam Eren and Assam El-Osta
INDUSTRY
INDUSTRY AMAZON
. |-- main.py |-- golden.py |-- test_main.py
test main.py import unittest import main class TestExample(unittest.TestCase): def test_initial(self):
self.assertEqual(fib(0), 0) self.assertEqual(fib(1), 1) def test_fib(self): self.assertEqual(fib(2), 1) self.assertEqual(fib(3), 2)
test main.py import unittest import main class TestExample(unittest.TestCase): def test_initial(self):
self.assertEqual(fib(0), 0) self.assertEqual(fib(1), 1) def test_fib(self): self.assertEqual(fib(2), 1) self.assertEqual(fib(3), 2) python -m unittest test_main.py
test main.py import unittest import main class TestExample(unittest.TestCase): def test_initial(self):
self.assertEqual(fib(0), 0) self.assertEqual(fib(1), 1) def test_fib(self): self.assertEqual(fib(2), 1) self.assertEqual(fib(3), 2) python -m unittest test_main.py self.assertEqual(fib(2), 1) AssertionError: 2 != 1 ----------------------------- Ran 2 tests in 0.000s FAILED (failures=1)
main.py def fib(n): if n == 0: return 0 if
n == 1: return 1 return 2 * fib(n - 1)
main.py def fib(n): if n == 0: return 0 if
n == 1: return 1 return fib(n - 1) + fib(n - 2)
main.py def fib(n): if n == 0: return 0 if
n == 1: return 1 return fib(n - 1) + fib(n - 2) python -m unittest test_main.py ------------------------------- Ran 2 tests in 0.000s OK
main.py def fib(n): if n == 0: return 0 if
n == 1: return 1 return fib(n - 1) + fib(n - 2) python -m unittest test_main.py ------------------------------- Ran 2 tests in 0.000s OK Glynatsi 2017, “TRYING TO RECLAIM REPUTATION”
Doc Testing
main.py import unittest def fib(n): """Returns the n th fibonacci
number. For example: >>> fib(5) 5 >>> fib(6) 8 >>> fib(5) + fib(6) 13 >>> fib(7) 10 """ if n == 0: return 0 elif n == 1: return 1 else: return fib(n - 1) + fib(n - 2)
python -m doctest main.py Failed example: fib(7) Expected: 10 Got:
13 **************************** 1 items had failures: 1 of 4 in main.fib ***Test Failed*** 1 failures.
main.py import unittest def fib(n): """Returns the n th fibonacci
number. For example: >>> fib(5) 5 >>> fib(6) 8 >>> fib(5) + fib(6) 13 >>> fib(7) 13 """ if n == 0: return 0 elif n == 1: return 1 else: return fib(n - 1) + fib(n - 2)
Property Based Testing
from hypothesis import given from hypothesis.strategies import integers class TestFib(unittest.TestCase):
@given(k=integers(min_value=2)) def test_fib(self, k): self.assertTrue(fib(k), fib(k - 1) + fib(k - 2)) https://github.com/HypothesisWorks @DRMacIver
It’s impossible to conduct research without software, say 7 out
of 10 UK researchers Simon Hettrick uk/blog/2016-09-12-its-impossible-conduct-research-without-out-10-uk- researchers
USE 92%
IMPOSSIBLE 69%
DEVELOP 56%
TRAINING 79%
USE 92% IMPOSSIBLE 69% DEVELOP 56% TRAINING 79%
Axelrod : https://github.com/Axelrod-Python/Axelrod Arcas: https://github.com/Nikoleta-v3/Arcas Ciw: https://github.com/CiwPython/Ciw Pandas: https://github.com/pandas-dev/pandas Skleanr:
http://scikit-learn.org/stable/ Numpy: https://github.com/numpy/numpy cryptography: https://github.com/pyca/cryptography fastnumbers: https://github.com/SethMMorton/fastnumbers yacluster: https://github.com/KrzysiekJ/yacluster binaryornot: https://github.com/audreyr/binaryornot . . .
None
@NikoletaGlyn https://github.com/Nikoleta-v3 @SoftwateSaved @PhoenixCUni