tylerjereddy

import numpy as np
import pytest
import hypothesis
from hypothesis import given, settings
from hypothesis import strategies as st
from hypothesis.extra import numpy as hynp

@settings(max_examples=5)
@given(st.floats(min_value=0, max_value=1, width=64),
       st.integers(np.finfo(np.double).minexp, np.finfo(np.double).maxexp - 1)

tylerjereddy

import subprocess

trials = 20
pass_counts = 0
fail_counts = 0

for i in range(trials):
    print("trial number:", i)
    try:
        o = subprocess.check_output('python runtests.py -t "numpy/testing/tests/test_utils.py" -- -n 4', shell=True)

tylerjereddy

import MDAnalysis
import numpy as np
from scipy.spatial.distance import euclidean

u = MDAnalysis.Universe('split_rhombic_small.gro')
residue = u.atoms.residues[0]
residue_centroid_no_pbc = residue.atoms.centroid(pbc=False)
residue_centroid = residue.atoms.centroid(pbc=True)
head_centroid_distance = euclidean(residue.atoms.positions[0],
        residue_centroid)

tylerjereddy

'''Module to assess and adjust URLs / links in MDA project documentation after recent move to github.'''
import os
import subprocess

for dirname, dirnames, filenames in os.walk('/Users/treddy/python_modules/MDAnalysis/MDA_dev/mdanalysis/'):
    # print path to all filenames.
    #for filename in filenames:
        #print os.path.join(dirname, filename)

    #print all lines from .py files with OLD HOMEPAGE URLs in them:

tylerjereddy

#if you don't have the Julia PyCall library you can install it with Pkg.add("PyCall") as the first line in this code
using PyCall
@pyimport MDAnalysis
#careful with dotted imports--need simpler module name representation for usage in Julia
@pyimport MDAnalysis.tests.datafiles as MDT 

#can now use MDAnalysis seamlessly and leverage some of the powerful features of the Julia numerical computing language
u = MDAnalysis.Universe(MDT.GRO,MDT.XTC) #although this works very naturally, many MDA methods currently require pycall invocation

all_atom_selection = pycall(u["selectAtoms"],PyAny,"all") #double quotes only for the "all" string--single quotes are character literals in Julia