willfurnass

function tau_a = shear_stress(D, Q, k_s, T, den)
    %{ Hydraulic shear stress at pipe wall (in Pa).
    %
    % Params:
    % D -- internal diameter (m)
    % Q -- flow (m^3s^-1)
    % k_s -- roughness height (m)
    % T -- temperature; defaults to 10degC)
    % den -- density defaults to 1000kg/m^3
    % 

willfurnass

--- BibTeX.js.orig	2015-07-03 07:18:37.000000000 +0100
+++ BibTeX.js	2015-08-09 14:21:08.779706944 +0100
@@ -1176,7 +1176,11 @@
 		if(!type) type = "misc";
 		
 		// create a unique citation key
-		var citekey = buildCiteKey(item, citekeys);
+		if (item.shortTitle==''){
+		    var citekey = buildCiteKey(item, citekeys);
+		} else {

willfurnass

#!/usr/bin/env python
from __future__ import print_function
from ruffus import transform, suffix, pipeline_run

# A test of using Ruffus to locally run a very simple pipeline comprised of
# tasks defined as Python functions

# Can run this from a conda environnment created using
# conda create -n drmaatest -c bioconda python=2.7 ruffus drmaa

willfurnass

#!/usr/bin/env python

# A test of whether Ruffus can be used to submit jobs to a cluster using the
# DRMAA API, sharing the DRMAA session between threads to allow multiple jobs to
# be submitted at once without burdening the head node with multiple DRMAA
# sessions.

# Can run this from a conda environnment created using
# conda create -n drmaatest -c bioconda python=2.7 ruffus drmaa

willfurnass

tmux tips

Default prefix: <ctrl>b

Session management

• tmux new -s session_name - creates a new tmux session named session_name
• tmux a - attach to first available session
• tmux attach -t session_name - attaches to an existing tmux session named session_name
• tmux switch -t session_name - switches to an existing session named session_name

willfurnass

Initialise a git repository:

cd somedir
git init

Install git subrepo if you haven't done so already:

https://github.com/ingydotnet/git-subrepo#installation

willfurnass

#!/usr/bin/tclsh

set sge_root $env(SGE_ROOT)
source "$sge_root/util/resources/jsv/jsv_include.tcl"

proc jsv_on_start {} {
    jsv_send_env
}

proc lexists name {

willfurnass

import os
from typing import Dict
import numpy as np


def export_data(data: Dict[np.ndarray],
                filename: str,
                cols_per_line: int = 8) -> None:
    """Export dictionary of 1d float arrays to a file.
 

willfurnass

Notes on setting up a Python debug environment

Used to investigate a segfault in a Python C extension within a Python package.

1. Install debug Python build using pyenv then check is available for use:

   pyenv install -g 3.8.5
   pyenv versions
   

willfurnass

import tempfile                                                                                                                                                                                                   
import os
import time

import paramiko

# Hostname of a 'submission host' in the Grid Engine cluster we want to submit a job to
hostname = 'sharc.shef.ac.uk'
# Username for logging in to the cluster via SSH
username = "te1st"