langner

"""Tools for searching Pubmed for a list of PMIDs.

The goal here is to search for many PMIDs at once, since searching
sequentially can take a long time. Using the the BioPython Entrez module
is super convenient to this end.

The results results are returned in a simple dictionary format.
"""

langner

def similar_dois(d1, d2, accuracy=1.00):
    """Determine whether DOIs are similar.

    DOIs basically need to be identical, but are case insensitive.
    """
    if not (d1 and d2):
        return False
    d1 = d1.lower().strip()
    d2 = d2.lower().strip()
    return difflib.SequenceMatcher(None, d1, d2).ratio() == accuracy

langner

def similar_pages(pages1, pages2):
    """Determine whether two pages strings are similar.

    Redundant digits in the end page should be ignored -- for example, 1660-1661 can be
    reduced to 1660-1 -- and the end page (and hyphen) can be skipped if it's a single page.
    Additionally, for some journals, WoK can also replace the end page with something else,
    for example: 241-+ instead of 241-247.e9 (supp info), or O1125-U144 (no idea what that is),
    and they have said this cannot change for technical reasons. Oh well.

    Additional exceptions:

langner

import difflib
import string

def similar_titles(t1, t2, accuracy=1.00, debug=None):
    """Determine whether two titles are similar.

    As a rule, we want titles to be identical after removing whitespace
    and punctuation. Other discrepancies should be dealt with manually by
    ensuring the titles are correct, or by replacing strings in all titles,
    in this function, before comparing them.

langner

# amavis messages
amavis\[[0-9]+\]: \([-0-9]+\) Passed (CLEAN|BAD-HEADER|SPAM|BANNED)

# avahi daemon: warnings about invalid repsonses and such
avahi-daemon\[[0-9]+\]: Invalid (query packet|legacy unicast query packet|response packet from host)
avahi-daemon\[[0-9]+\]: Received response from host [.0-9]+ with invalid source port [0-9]+ on interface         
avahi-daemon\[[0-9]+\]:( last)? message repeated [0-9]+ times
avahi-daemon\[[0-9]+\]: server.c: Packet too short or invalid while reading response record.
avahi-daemon\[[0-9]+\]: dbus-protocol.c: Too many objects for client

langner

import cclib
import numpy
import urllib

def nuclear_repulsion_energy(data):
    nre = 0.0
    for i in range(data.natom):
        ri = data.atomcoords[0][i]
        zi = data.atomnos[i]
        for j in range(i+1, data.natom):

langner

Index: postgresql-9.1-9.1.14/src/include/pg_config_manual.h
===================================================================
--- postgresql-9.1-9.1.14.orig/src/include/pg_config_manual.h   2014-10-14 16:55:38.000000000 -0400
+++ postgresql-9.1-9.1.14/src/include/pg_config_manual.h        2014-10-14 16:56:01.598940653 -0400
@@ -17,7 +17,7 @@
  *
  * Changing this requires an initdb.
  */
-#define NAMEDATALEN 64
+#define NAMEDATALEN 256

langner

#!/bin/bash

# Create work directory and empty it.
ROOTDIR="postgresql-namedatalen"
mkdir -p $ROOTDIR
cd $ROOTDIR
rm -rf *

# Get the sources and determine current version.
PKGNAME="postgresql-9.1"

langner

aptitude purge `aptitude search ~c | awk '{ print $2 }'`

langner

greek_alphabet = {
    u'\u0391': 'Alpha',
    u'\u0392': 'Beta',
    u'\u0393': 'Gamma',
    u'\u0394': 'Delta',
    u'\u0395': 'Epsilon',
    u'\u0396': 'Zeta',
    u'\u0397': 'Eta',
    u'\u0398': 'Theta',
    u'\u0399': 'Iota',