Archive for the ‘software deployment’ Category

April 28th, 2015

I recently found myself in need of a portable install of the Jupyter notebook which made use of a portable install of R as the compute kernel. When you work in institutions that have locked-down managed Windows desktops, such portable installs can be a life-saver! This is particularly true when you are working with rapidly developing projects such as Jupyter and IRKernel.

It’s not perfect but it works for the fairly modest requirements I had for it. Here are the steps I took to get it working.

Download and install Portable Python

I downloaded Portable Python 2.7.6.1 from http://portablepython.com/ and installed into a directory called Portable Python 2.7.6.1

Update IPython and install the extra modules we need

This version of Portable Python comes with a portable IPython instance but it is too old to support alternative kernels. As such, we need to install a newer version.

Open a cmd.exe command prompt and navigate to Portable Python 2.7.6.1\App\Scripts.

Enter the command

easy_install ipython.exe

You’ll now find that you can launch the ipython.exe terminal from within this directory:

C:\Users\walkingrandomly\Desktop\Portable Python 2.7.6.1\App\Scripts>ipython
Python 2.7.6 (default, Nov 10 2013, 19:24:18) [MSC v.1500 32 bit (Intel)]
Type "copyright", "credits" or "license" for more information.

IPython 3.1.0 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object', use 'object??' for extra details.

In [1]: exit()

If you try to launch the notebook, however, you’ll get error messages. This is because we haven’t taken care of all the dependencies. Let’s do that now. Ensuring you are still in the Portable Python 2.7.6.1\App\Scripts folder, execute the following commands.

easy_install pyzmq
easy_install jinja2
easy_install tornado
easy_install jsonschema

You should now be able to launch the notebook using

ipython notebook

Install portable R and IRKernel

  • I downloaded Portable R 3.2 from http://sourceforge.net/projects/rportable/files/ and installed into a directory called R-Portable
  • Move this directory into the Portable Python directory. It needs to go inside Portable Python 2.7.6.1\App (see this discussion to learn how I discovered that this location was the correct one)
  • Launch the Portable R executable which should be at Portable Python 2.7.6.1\App\R-Portable\R-portable.exe and install the IRKernel packages by doing
install.packages(c("rzmq","repr","IRkernel","IRdisplay"), repos="http://irkernel.github.io/")

Install additional R packages

The version of Portable R I used didn’t include various necessary packages. Here’s how I fixed that.

  • Launch the Portable R executable which should be at Portable Python 2.7.6.1\App\R-Portable\R-portable.exe and install the following packages 
    install.packages('digest')
    install.packages('uuid')
    install.packages('base64enc')
    install.packages('evaluate')
    install.packages('jsonlite')

Install the R kernel file
Create the directory structure Portable Python 2.7.6.1\App\share\jupyter\kernels\R_kernel

Create a file called kernel.json that contains the following

{"argv": ["R-Portable/App/R-Portable/bin/i386/R.exe","-e","IRkernel::main()",
"--args","{connection_file}"],
 "display_name":"Portable R"
}

This file needs to go in the R_kernel directory created earlier. Note that the kernel location specified in kernel.json uses Linux style forward slashes in the path rather than the backslashes that Windows users are used to. I found that this was necessary for the kernel to work –it was ignored by the notebook otherwise.

Finishing off

Everything created so far, including R, is in the folder Portable Python 2.7.6

I created a folder called PortableJupyter and put the Portable Python 2.7.6 folder inside it. I also created the folder PortableJupyter\notebooks to allow me to carry my notebooks around with the software that runs them.

There is a bug in Portable Python 2.7.6.1 relating to scripts like IPython.exe that have been installed using easy_install. In short, they stop working if you move the directory they’re installed in – breaking portability somewhat! (Details here)

The workaround is to launch Ipython by running the script Portable Python 2.7.6.1\App\Scripts\ipython-script.py

I didn’t want to bother with that so created a shortcut in my PortableJupyter folder called Launch notebook. The target of this shortcut was the following line

%windir%\system32\cmd.exe /c "cd notebooks && "%CD%/Portable Python 2.7.6.1/App\python.exe" "%CD%/Portable Python 2.7.6.1\App\Scripts\ipython-script.py" notebook"

This starts the notebook using the default web browser and puts you in the notebooks directory.

The pay off

My folder looks like this:

PortableJupyter_folder

If I click on the Launch Notebook shortcut, I get a Jupyter session with 2 kernel options

PortableJupyter_kernels

I can choose the Portable R kernel and start using R in the notebook!

PortableJupyter_screenshot

November 12th, 2014

I follow a lot of software developers on twitter so I get to see a lot of opinions and comments about git.  Here are a few of my recent favourites

Opinions on git
I find that git is a technology that polarizes people. They either love it or they hate it…often both at the same time.

 

Git Tutorials
I find that I learn something new every time I read a different tutorial

Git tips and tricks
No matter how long you’ve used git, you can always learn a new trick or two.

July 17th, 2014

Update: September 2014 – The notes in this blog post have been uploaded to github: https://github.com/mikecroucher/Windows_Scientific_Computing. The blog post will be kept as-is for posterity reasons. For the most up to date version of the notes, see the github version.

Some time in 2013, I helped out at a Software Carpentry event at The University of Bath.  As with most software carpentry boot camps, one of the topics covered was shell scripting and the scripting language of choice was bash.  As I wandered around the room, I asked the delegates which operating system they use for the majority of their research and the most popular answer, by far, was Windows.

This led me to wonder if we should teach using a native Windows solution rather than relying on bash?

A few years ago, this would be an insane proposition since the Windows command shell is very weak compared to bash.  PowerShell, on the other hand, is modern, powerful and installed on all modern Windows operating systems by default.

My problem was that I didn’t know PowerShell very well.  So, I took the notes for the 2013 Bath shell scripting session – https://github.com/swcarpentry/boot-camps/tree/2013-07-bath/shell – and gave myself the exercise of converting them to PowerShell.

I got close to completing this exercise last summer but various things took higher priority and so the project languished.  Rather than sit on the notes any longer, I’ve decided to just publish what I have so far in case they are useful to anyone.

You are free to use them with the following caveats

  • This is not necessarily the right way to teach PowerShell. It is an experiment in converting some classroom-tested Linux based notes to PowerShell.
  • If you use them, attribution would be nice. I am Mike Croucher, my site is www.walkingrandomly.com Details on how to contact me at http://www.walkingrandomly.com/?page_id=2055
  • I have not yet tested these notes in a classroom situation
  • These notes aren’t finished yet
  • These notes have been developed and tested on Windows 7.  Behaviour may be different using different versions of Windows.
  • These notes are given as they were left sometime in mid 2013. Some things may be out of date.
  • I was learning PowerShell as I developed these notes. As such, I fully expect them to be full of mistakes.  Corrections and improvements would be welcomed.

If anyone is interested in developing these notes into something that’s classroom-ready, contact me.

The old Windows Command Shell

The traditional Windows command shell is a program called cmd.exe which can trace its roots all the way back to the old, pre-Windows DOS prompt.

You can launch this command shell as follows

  • Hold down both the Windows button and the letter R to open the Run prompt
  • Type cmd and press Enter or click OK

Launch Cmd

  • You should see a window similar to the one below

Windows Command Prompt

The Windows command shell hasn’t changed significantly for over twenty years and is relatively feature poor compared to more modern shells. For this reason, it is recommended that you use Windows PowerShell instead. Mention of cmd.exe is only included here since, despite its deficiencies, it is still widely in use

PowerShell

To launch PowerShell:

  • Hold down both the Windows button and the letter R to open the Run prompt
  • Type powershell and press Enter or click OK

Launch PowerShell

  • You should see a window similar to the one below

PowerShell prompt

Note that although the header of the above window mentions v1.0, it could be a screenshot from either version 1.0 or version 2.0. This is a well-known bug. If you are using Windows 7 you will have version 2 at the minimum.

PowerShell versions

At the time of writing, PowerShell is at version 3. Ideally, you should at least have version 2.0 installed. To check version:

$psversiontable.psversion

Major  Minor  Build  Revision
-----  -----  -----  --------
3      0      -1     -1

If this variable does not exist, you are probably using version 1.0 and should upgrade.

Version 3.0 is available at http://blogs.technet.com/b/heyscriptingguy/archive/2013/06/02/weekend-scripter-install-powershell-3-0-on-windows-7.aspx

Comments

# This is a comment in Powershell. It is not executed

Directories

Users of Bash will feel right at home at first since PowerShell appears to have the same set of commands

pwd                         #Path to current folder
ls                          #List directory
ls *.txt                    #Wild Card
ls *_hai*
ls -R                       #Recursive folder listing
ls .                        #List current folder
ls ..                       #List Parent folder
cd ..                       #Change current folder to parent. (Move up a folder)
cd ~                        #Change current folder to your user directory.
mkdir myfolder              #Create a folder
mkdir ~/myfolder    
mv myfolder new_myfolder    #rename myfolder to new_myfolder
rm -r new_myfolder          #Delete new_myfolder if its empty

Files

cat file                    # View file
more file                   # Page through file
cat file | select -first 3  # first N lines
cat file | select -last 2   # Last N lines
cp file1 file2              # Copy
cp *.txt directory
rm file.txt                 # Delete - no recycle bin.
rm -r directory             # Recurse

Different command types in PowerShell: Aliases, Functions and Cmdlets

Many of the PowerShell ‘commands’ we’ve used so far are actually aliases to Powershell Cmdlets which have a Verb-Noun naming convention. We can discover what each command is an alias of using the get-alias cmdlet.

PS > get-alias ls

CommandType     Name                                                Definition
-----------     ----                                                ----------
Alias           ls                                                  Get-ChildItem

This shows that ls is an alias for the Cmdlet Get-ChildItem

A list of aliases for common Bash commands:

  • cat (Get-Content)
  • cd (Set-Location)
  • ls (Get-ChildItem)
  • pwd (Get-Location)

One reason why aliases were created is to make PowerShell a more familiar environment for users of other shells such as the old Windows cmd.exe or Linux’s Bash environment and also to save on typing.

You can get a list of all aliases using get-alias on its own.

PS > get-alias

Finally, here’s how you get all of the aliases for the Get-ChildItem cmdlet.

get-alias | where-object {$_.Definition -match "Get-Childitem"}

For more details on Powershell aliases, see Microsoft’s documentation at http://technet.microsoft.com/en-us/library/ee692685.aspx

What type of command is mkdir?

The mkdir command looks like it might be an alias as well since it doesn’t have the verb-noun naming convention of Cmdlets. Let’s try to see which Cmdlet it might be an alias of:

PS > get-alias mkdir

Get-Alias : This command cannot find a matching alias because alias with name 'mkdir' do not exist. 
At line:1 char:6
+ alias <<<<  mkdir
    + CategoryInfo          : ObjectNotFound: (mkdir:String) [Get-Alias], ItemNotFoundException
    + FullyQualifiedErrorId : ItemNotFoundException,Microsoft.PowerShell.Commands.GetAliasCommand

It turns out that mkdir isn’t an alias at all but is actually yet another PowerShell command type, a function. We can see this by using the get-command Cmdlet

PS > get-command mkdir
CommandType     Name                                                Definition
-----------     ----                                                ----------
Function        mkdir                                               ...
Application     mkdir.exe                                           C:\Program Files (x86)\Git\bin\mkdir.exe

Now we can clearly see that mkdir is a PowerShell function. The mkdir.exe is an Application which you’ll only see if you installed git for windows as I have.

Cmdlets

A Cmdlet (pronounced ‘command-let’) is a .NET class but you don’t need to worry abut what this means until you get into advanced PowerShell usage. Just think of Cmdlets as the base type of PowerShell command. They are always named according to the convention verb-noun; for example Set-Location and Get-ChildItem.

Listing all Cmdlets

The following lists all Cmdlets

Get-Command

You can pipe this list to a pager

Get-Command | more

Getting help

You can get help on any PowerShell command using the -? switch. For example

ls -?

When you do this, you’ll get help for the Get-ChildItem Cmdlet which would be confusing if you didn’t know that ls is actually an alias for Get-ChildItem

History

Up arrow browses previous commands.

By default, PowerShell version 2 remembers the last 64 commands whereas PowerShell version 3 remembers 4096. This number is controlled by the $MaximumHistoryCount variable

PS > $MaximumHistoryCount           #Display the current value
PS > $MaximumHistoryCount=150       #Change it to 150
PS > history                        #Display recent history using the alias version of the command
PS > get-history                    #Display recent history using the Cmdlet direct

Although it remembers more, PowerShell only shows the last 32 commands by default. To see a different number, use the count switch

PS > get-history -count 50

To run the Nth command in the history use Invoke-History

PS > invoke-history 7

Word count (and more) using Measure-Object

Linux has a command called wc that counts the number of lines and words in a file. Powershell has no such command but we can do something similar with the Measure-Object Cmdlet.

Say we want to count the number of lines, words and characters in the file foo.txt. The first step is to get the content of the file

get-content foo.txt                 # gets the content of foo.txt

Next, we pipe the result of the get-content Cmdlet to Measure-Object, requesting lines, words and characters

get-content foo.txt | measure-object -line -character -word

The measure-object Cmdlet can also count files

ls *.txt | measure-object           #Counts number of .txt files in the current folder

When you execute the above command, a table of results will be returned:

Count    : 3
Average  :
Sum      :
Maximum  :
Minimum  :
Property :

This is because the measure-object Cmdlet, like all PowerShell Cmdlets, actually returns an object and the above table is the textual representation of that object.

The fields in this table hint that measure-object can do a lot more than simply count things. For example, here we find some statistics concerning the file lengths found by the ls *.txt command

ls *.txt | measure-object -property length -minimum -maximum -sum -average

You may wonder exactly what type of object has been returned from measure-object and we can discover this by running the gettype() method of the returned object

(ls *.txt | measure-object).gettype()

Request just the name as follows

(ls *.txt | measure-object).gettype().Name

GenericMeasureInfo

To find out what properties an object has, pass it to the get-member Cmdlet

#Return all member types
ls *.txt | get-member

#Return only Properties
ls *.txt | get-member -membertype property

Sometimes, you’ll want to simply return the numerical value of an object’s property and you do this using the select-object Cmdlet. Here we ask for just the Count property of the GenericMeasureInfo object returned by measure-object.

#Counts the number of *.txt files and returns just the numerical result
ls *.txt | measure-object | select-object -expand Count

Searching within files

The Unix world has grep, PowerShell has Select String.  Try running the following on haiku.txt

Select-String the haiku.txt                             #Case insensitive by default, unlike grep
Select-String the haiku.txt -CaseSensitive              #Behaves more like grep
Select-String day haiku.txt -CaseSensitive
Select-String is haiku.txt -CaseSensitive
Select-String 'it is' haiku.txt -Casesensitive

There is no direct equivalent to grep’s -w switch.

grep -w is haiku.txt            #exact match

However, you can get the same behaviour using the word boundary anchors, \b

Select-String \bis\b haiku.txt -casesensitive

Grep has a -v switch that shows all lines that do not match a pattern. Select-String makes use of the -notmatch switch.

BASH: grep -v "is" haiku.txxt
PS: select-string -notmatch "is" haiku.txt -CaseSensitive

Grep has an -r switch which stands for ‘recursive’. The following will search through all files and subfolders of your current directory, looking for files that contain is

grep -r is *

Select-String has no direct equivalent to this. However, you can do the same thing by using get-childitem to get the list of files, piping the output to select-string

get-childitem * -recurse | select-string is

One difference between grep and Select-String is that the latter includes the filename and line number of each match.

grep the haiku.txt

Is not the true Tao, until
and the presence of absence:

Select-String the haiku.txt -CaseSensitive

haiku.txt:2:Is not the true Tao, until
haiku.txt:6:and the presence of absence:  

To get the grep-like output, use the following

Select-String the haiku.txt -CaseSensitive | ForEach-Object {$_.Line}

Is not the true Tao, until
and the presence of absence:

To understand how this works, you first have to know that Select-String returns an array of MatchInfo objects when there is more than one match. To demonstrate this:

$mymatches = Select-String the haiku.txt -CaseSensitive  #Put all matches in the variable 'mymatches'
$mymatches -is [Array]          #query if 'match' is an array

True

So, mymatches is an array. We can see how many elements it has using the array’s Count property

$mymatches.Count

2

The type of elements in PowerShell arrays don’t necessarily have to be the same. In this case, however, they are.

$mymatches[0].gettype() 
$mymatches[1].gettype()

both of these give the output

IsPublic IsSerial Name                                     BaseType
-------- -------- ----                                     --------
True     False    MatchInfo                                System.Object

If all you wanted was the name of the first object type, you’d do

$mymatches[0].gettype().name

MatchInfo

Alternatively, we could have asked for each element’s type using the For-Each-Object Cmdlet to loop over every object in the array.

$mymatches | Foreach-Object {$_.gettype().Name}

Where $_ is a special variable that effectively means ‘current object’ or ‘The object currently being considered by Foreach-Object’ if you want to be more verbose.

So, we know that we have an array of 2 MatchInfo objects in our variable mymatches. What does this mean? What properties do MatchInfo objects have? We can find out by piping one of them to the Get-Member Cmdlet.

$mymatches[0] | Get-Member

   TypeName: Microsoft.PowerShell.Commands.MatchInfo

Name         MemberType Definition
----         ---------- ----------  
Equals       Method     bool Equals(System.Object obj)
GetHashCode  Method     int GetHashCode()
GetType      Method     type GetType()
RelativePath Method     string RelativePath(string directory)
ToString     Method     string ToString(), string ToString(string directory)
Context      Property   Microsoft.PowerShell.Commands.MatchInfoContext Context {get;se
Filename     Property   System.String Filename {get;}
IgnoreCase   Property   System.Boolean IgnoreCase {get;set;}
Line         Property   System.String Line {get;set;}   
LineNumber   Property   System.Int32 LineNumber {get;set;}
Matches      Property   System.Text.RegularExpressions.Match[] Matches {get;set;}
Path         Property   System.String Path {get;set;}
Pattern      Property   System.String Pattern {get;set;}    

Now we can see that each MatchInfo object has a Line property and it’s reasonable to guess that this contains a Line containing a match. Taking a look:

$mymatches[0].Line

Is not the true Tao, until

Bringing together everything we’ve seen so far, we pull out the Line property of each element in the array as follows

$mymatches | Foreach-Object {$_.Line}

Alternatively, we can ditch the $mymatches variable and pipe in the output of Select-String directly

Select-String the haiku.txt -CaseSensitive | ForEach-Object {$_.Line}

Is not the true Tao, until
and the presence of absence:

Regular expressions

select-string 's*is' haiku.txt        # * Zero or more of preceding token
select-string 's+is' haiku.txt        # + On or more of preceding token
select-string '.nd'  haiku.txt        # . Any token followed by 'nd'
select-string 'es'   haiku.txt        # matches 'es'
select-string 'es[ht]' haiku.txt      # Exactly one of the characters listed
select-string 'es[^ht]' haiku.txt     # Matches everything except h and t
select-string 'ex[
select-string '\bis\b' haiku.txt      # \b word boundaries

Input and output redirection

> redirects output (AKA standard output). This works in both Bash and Powershell scripts. For example, in Bash we might do

#BASH
grep -r not * > found_nots.txt

Drawing on what we’ve learned so far, you might write the PowerShell version of this command as

#PS
get-childitem *.txt -recurse | select-string not > found_nots.txt

However, if you do this, you will find that the script will run forever with the hard-disk chugging like crazy. If you’ve run the above command, CTRL and C will stop it. This is because Powershell is including the output file, found_nots.txt, in its input which leads to an infinite loop. To prevent this, we must explicitly exclude the output file from the get-childitem search

get-childitem *.txt -Exclude 'found_nots.txt' -recurse | select-string not > found_nots.txt

cat found_nots.txt
ls *.txt > txt_files.txt
cat txt_files.txt

In Linux, < redirects input (AKA standard input). This does not work in PowerShell:

cat < haiku.txt
At line:1 char:5
+ cat < haiku.txt
+     ~
The '<' operator is reserved for future use.
    + CategoryInfo          : ParserError: (:) [], ParentContainsErrorRecordException
    + FullyQualifiedErrorId : RedirectionNotSupported

The above is a forced use of < since one could simply do

cat haiku.txt

Recall that cat is an alias for get-content. The use of get-content is an idiom that gets around the lack an < operator. For example, instead of

foo < input.txt

One does

get-content input.txt | foo

Error messages are output on standard error

ls idontexist.txt > output.txt  
cat output.txt                  #output.txt is empty
ls idontexist.txt 2> output.txt               # 2 is standard error
ls haiku.txt 1> output.txt                    # 1 is standard output
ls haiku.txt,test_file.txt 2>&1 > output.txt  # Combine the two streams.

Searching for files

# Find all     
UNIX: find .
PS: get-childitem .  -Recurse 
PS: get-childitem .  -Recurse | foreach-object {$_.FullName}    #To give identical output as `find`   

To save on typing, you can use the alias gci instead of get-childitem

# Directories only
UNIX: find . -type d        
PS2: gci . -recurse | where { $_.PSIsContainer }
PS3: gci -recurse -Directory 

If you have PowerShell 2, you can only use the long winded version. It’s simpler in PowerShell 3. Similarly for searching for files only.

# Files only
UNIX: find . -type f          
PS2: get-childitem -recurse | where { ! $_.PSIsContainer }
PS3: gci -recurse -File

With the Unix find command, you can specify the maximum and minimum search depths. There is no direct equivalent in PowerShell although you could write a function that will do this. Such a function can be found at http://windows-powershell-scripts.blogspot.co.uk/2009/08/unix-linux-find-equivalent-in.html although I have not tested this!

# Maximum depth of tree
UNIX: find . -maxdepth 2
PS : No direct equivalent
# Minimum depth of tree
UNIX: find . -mindepth 3 
PS : No direct equivalent

You can also filter by name. Confusingly, PowerShell offers two ways of doing this. More details on the differences between these can be found at http://tfl09.blogspot.co.uk/2012/02/get-childitem-and-theinclude-and-filter.html

One key difference between find and get-childitem is that the latter is case-insenstive whereas find is case sensitive.

# Find by name
UNIX: find . -name '*.txt' 
PS: gci -recurse -include *.txt
PS: gci -recurse -filter *.txt

#Find empty files
UNIX: find . -empty    
PS: gci -recurse | where ($_.Length -eq 0) | Select FullName 

#Create empty file
UNIX: touch emptyfile.txt
PS: new-item emptyfile.txt -type file

Command Substituion

In bash, you can execute a command using backticks and the result is substituted in place. i.e.

#bash
foo `bar`

The backticks are used as escape characters in PowerShell so you do the following instead

#PS
foo $(bar)

In both cases, the command bar is executed and result is substituted into the call to foo.

Power of the pipe

| is a pipe. Use the pipe to connect the output of one command to the input of another:

Count text files

ls -filter *.txt | measure

ls outputs a list of files, measure inputs a list of files.

echo "Number of .txt files:"; ls -filter *.txt | measure | select -expand count

; equivalent to running two commands on separate lines.

Question: what does this do?

ls -name | select-string s | measure

Answer: counts the number of files with s in their name.

history | select-string 'echo'

Power of well-defined modular components with well-defined interfaces,

  • Bolt together to create powerful computational and data processing workflows.
  • Good design principle applicable to programming – Python modules, C libraries, Java classes – modularity and reuse.
  • “little pieces loosely joined” – history + select-string = function to search for a command.

Variables

get-variable                            # See all variables
$MYFILE="data.txt"                      # Need quotes around strings
echo $MYFILE
echo "My file name is $MYFILE"
$num = 1                                #Numbers don't need quotes
$num = $num+1                           #Simple Arithmetic
$TEXT_FILES=get-childitem               Save output of get-childitem
echo $TEXT_FILES

Variables only persist for the duration of the current PowerShell Session

Environment variables

Windows environment variables don’t show up when you execute get-variable; to list them all you do

#PS
get-childitem env:                  #Show all Windows Environment variables 
echo $env:PATH                      #Show the contents of PATH
$env:Path = $env:Path + ";C:\YourApp\bin\"  #temporarily add a folder to PATH

This modification to PATH will only last as long as the current session. It is possible to permanently modify the system PATH but this should only be done with extreme care and is not covered here.

PowerShell Profile

The PowerShell profile is a script that is executed whenever you launch a new session. Every user has their own profile. The location of your PowerShell profile is defined by the variable $profile

$profile

Open it with

notepad $profile

Add something to it such as

echo "Welcome to PowerShell.  This is a message from your profile"

Restart PowerShell and you should see the message. You can use this profile to customise your PowerShell sessions. For example, if you have installed NotePad++, you might find adding the following function to your PowerShell Profile to be useful.

# Launch notepad++ using the npp command
function npp($file)
{
if ($file -eq $null)
    {
        & "C:\Program Files (x86)\Notepad++\notepad++.exe";
    }
    else
    {
        & "C:\Program Files (x86)\Notepad++\notepad++.exe" $file;
    }
}

With this function in your profile, you can open Notepad++ with the command npp or npp(filename.txt)

Conditionals

$num = 1
if($num -eq 1)
{
  write-host 'num equals 1'
}

$word="hello"
if($word -eq "hello")
{
  write-host 'The same'
}

By default, string tests are case insensitive

$word="hello"
if($word -eq "HELLO")
{
  write-host 'The same'
}

To force them to be case sensitive, add a c to the operator:

$word="hello"
if($word -ceq "HELLO")
{
  write-host 'The Same. This won't be printed'
}

You can similarly be explicitly case insensitive by adding an i. Although this is the the same behaviour as the undecorated operators and so might seem unnecessary, it shows your intent to the reader.

    $word="hello"
    if($word -ieq "HELLO")
    {
      write-host 'The same'
    }
Comparison Operators
-eq Equal to
-lt Less than
-gt Greater than
-ge Greater than or equal to
-le Less than or equal to
-ne Not equal to
Logical operators
-not    Not
!       Not
-or     Or
-and    And

Loops

PowerShell has several looping constructs. Here, I only consider two.

for

Allows you to run a block of code a set number of times.

for ($i=1; $i -le 5; $i=$i+1)
{
   Write-Host $i
}

foreach

Do something with every element of a collection

foreach($item in $(ls *.txt)) {echo $item.Name}

foreach vs foreach-object

TODO

Shell scripts

  • Save retyping.
  • PowerShell scripts have the extension .ps1
  • PowerShell scripts must be created with plain text editors such as Notepad or Notepad++. NEVER use Microsoft Word!

Here is a very simple script

notepad protein_filter.ps1                  #Open the file

#A simple protein filter
$DATE = get-date
echo "Processing date: $DATE"

foreach($item in get-childitem *.pdb)
{
   echo $item.Name
}

echo "Processing complete"

To run this just type the filename:

protein_filter.ps1

If you get an error message, it may be because your execution policy is set not to run scripts locally. Change this with the command

Set-ExecutionPolicy RemoteSigned            #Allow local scripts to run.  Needs to be run with admin privileges
protein_filter.ps1                          #Run the script

Download files via command-line

Primary Care Trust Prescribing Data – April 2011 onwards

$file="prim-care-trus-pres-data-apr-jun-2011-dat.csv"
$path="$pwd\$file"   #Path needs to be fully qualified. This puts it in the current folder
$url = "http://www.ic.nhs.uk/catalogue/PUB02342/$file"
$client = new-object System.Net.WebClient
$client.DownloadFile( $url, $path )

Permissions

Windows file permissions are rather more complicated than those of Linux but most users won’t need to worry about them in day to day use.

The call operator

It is sometimes convenient to construct strings that contain the full path to a PowerShell script we want to execute. For example:

$fullpath = "$pwd\myscript.ps1"

To actually run the script pointed to by this variable, you need to use the call operator &

& $fullpath                 #Runs myscript.ps1

You also need to do this if you try to call any script where the path contains spaces

"C:\Program Files\myscript.ps1"             #Will just display the string literal
& "C:\Program Files\myscript.ps1"           #Runs the script

Background Jobs

Consider the script counter.ps1

param($step=1)
#counter.ps1: A simple, long running job to demonstrate background jobs

$i=1

while ( $i -lt 200000 )
{
    echo $i
    $i=$i+$step
}

This counts up to 200000 in user-defined steps.

./counter.ps1   > 1step.txt                 #Counts in steps of 1
./counter.ps1 -step 2 > 2step.txt           #Counts in steps of 2

The script takes quite a while to complete and you cannot do anything else in your PowerShell session while it is working. Using the start-job Cmdlet, we can run counter.ps1 in the background

start-job -scriptblock { C:\Users\walkingrandomly\Dropbox\SSI_Windows\dir_full_of_files\some_directory\counter.ps1 >  C:\Users\walkingrandomly\Dropbox\SSI_Windows\dir_full_of_files\some_directory\outcount1.txt }

Note that you have to use the full path to both the counter.ps1 script and the output file. You can see the status of the job with get-job

get-job

Id              Name            State      HasMoreData     Location             Command
--              ----            -----      -----------     --------             -------
1              Job1             Running    True            localhost             C:\Users\walkingrando...

Eventually, your job will complete

get-job

Id              Name            State      HasMoreData     Location             Command
--              ----            -----      -----------     --------             -------
1               Job1            Completed  False           localhost             C:\Users\walkingrando...

ls outcount*                    #Ensure that output file has been created
remove-job 1                    #remove remnants of job 1 from the queue
get-job                         #Check that queue is empty

You can run as many simultaneous jobs as you like but it is best not to run too many or your computer will grind to a halt.

Here’s an example that runs 5 counter.ps1 jobs concurrently

#parallel_counters.ps1
#Runs 5 instances of counter.ps1 in parallel

$scriptname     = "counter.ps1"
$outputfileBase = "outfile"
$outputfileExt  = ".txt"

$scriptPath = "$pwd\$scriptname"

for ($i=1; $i -le 5; $i++)
{
  $outputfilePath = "$pwd\$outputfileBase" + $i + $outputfileExt
  $command = "$scriptPath -step $i `> $outputfilePath"
  $myScriptBlock = [scriptblock]::Create($command)
  start-job -scriptblock $myScriptBlock
}

Run this as a demonstration

parallel_counters.ps1
get-job                             #Keep running until all have completed
ls outfile*
more outfile5.txt
more outfile2.txt
$myjob=get-job 2                    #Get info on job Id 2 and store in variable $myjob
$myjob.Command                      #Look at the command that comprised job 2
remove-job *                        #Remove all job remnants from the queue
get-job                             #Should be empty

TODO: Dealing with output, recieve-job

Secure Shell

There is no equivalent to the Linux commands ssh and sftp in PowerShell. The following free programs are recommended

Packaging

There are no direct PowerShell equivalents to zip, unzip, tar etc. There are write-zip, write-tar and write-gzip cmdlets in the third party, free PowerShell Community Extensions but I have not investigated them yet.

Transcripts

Start-transcript Initializes a transcript file which records all subsequent input/Output. Use the following syntax:

Start-Transcript [[-path] FilePath] [-force] [-noClobber] [-append]

Stop-transcript Stops recording and finalizes the transcript.

start-transcript -path ./diary.txt
ls
echo "Hello dear diary"
stop-transcript
cat diary.txt
  • Record commands typed, commands with lots of outputs, trial-and-error when building software.
  • Send exact copy of command and error message to support.
  • Turn into blog or tutorial.

Shell power

(Bentley, Knuth, McIlroy 1986) Programming pearls: a literate program Communications of the ACM, 29(6), pp471-483, June 1986. DOI: [10.1145/5948.315654].

Dr. Drang, More shell, less egg, December 4th, 2011.

Common words problem: read a text file, identify the N most frequently-occurring words, print out a sorted list of the words with their frequencies.

10 plus pages of Pascal … or … 1 line of shell

#BASH version
$ nano words.sh
tr -cs A-Za-z '\n' | tr A-Z a-z | sort | uniq -c | sort -rn | sed ${1}q
$ chmod +x words.sh
$ nano words.sh < README.md
$ nano words.sh < README.md 10

The PowerShell version is more complicated but still very short compared to the 10 pages of Pascal

#count_words.ps1
Param([string]$filename,[int]$num)
$text=get-content $filename
$split = foreach($line in $text) {$line.tolower() -split "\W"}
$split | where-object{-not [string]::IsNullorEmpty($_)} |  group -noelement | sort Count -Descending | select -first $num

count_words.sh README.md 10

“A wise engineering solution would produce, or better, exploit-reusable parts.” – Doug McIlroy

Links

October 24th, 2013

One of my favourite parts of my job at The University of Manchester is the code optimisation service that my team provides to researchers there.  We take code written in languages such as  MATLAB, Python, Mathematica and R and attempt (usually successfully) to make them go faster.  It’s sort of a cross between training and consultancy, is a lot of fun and we can help a relatively large number of people in a short time.  It also turns out to be very useful to the researchers as some of my recent testimonials demonstrate.

Other researchers,however, need something more.  They already have a nice piece of code with several users and a selection of papers.  They also have a bucket-load of ideas about how to  turn this nice code into something amazing.  They have all this good stuff and yet they find that they are struggling to get their code to the next level.  What these people need is some quality time with a team of research software engineers.

Enter the Software Sustainability Institute (SSI), an organisation that I have been fortunate enough to have a fellowship with throughout 2013.  These guys are software-development ninjas, have extensive experience with working with academic researchers and, right now, they have an open call for projects.  It’s free to apply and, if your application is successful, all of their services will be provided for free.  If you’d like an idea of the sort of projects they work on, take a look at the extensive list of past projects.

So, if you are a UK-based researcher who has a software problem, and no one else can help, maybe you can hire* the SSI team.

*for free!

Links

August 12th, 2013

Right now it’s packaging season (not the official term!) at my university–a time of year when IT staff have to battle with silent installers, SCCM, MSI creation and Adminstudio in order to create the student desktop image for the next academic year.  Packaging season makes me grouchy, it makes me work late and it makes me massively over-react to every minor installation issue caused by software vendors. Right now, however, I am not grouchy because of packaging season..I am grouchy because of concurrent network licensing (or floating licensing if you are Wikipedia).

I like network licenses…they make many aspects of my job easier but they the way they are implemented by some software vendors causes them to be a pain.  Over the years, I’ve bothered many a support-desk with my network license tails of woe and thought that I would collate them all together in one blog post.

The more of these things your software does, the more pain you cause me and my colleagues.

1. You don’t use standard FlexLM/FlexNet. 

Like it or loathe it, FlexLM is used by the vast majority of software vendors out there. We run license servers that host dozens of FlexLM based applications and we have got the administration of these down to a fine art.  In fact, we’ve replaced the vast majority of the process with a script. If an application uses FlexLM, system administration and license monitoring is bordering on the trivial for us now.  The further you stray away from FlexLM, the more difficult our job becomes.

One thing guaranteed to ruin my day is a call from a vendor I’ve worked with for years who says ‘Great news Mike, we’re ditching FlexLM for our own, in house license system.’  Fabulous! Rather than use our lovely, generic, one-size fits all scripts, we are going to have to do a load of extra work and testing just for you.  I look forward to all the new and interesting bugs your system will generate.

2. You don’t support redundant license servers.

The idea behind redundant license servers is this:  Instead of your application relying on just one machine, it relies on three; only two of which have to be operational at any one time.  This gives us resiliency and resiliency is a good thing when you are teaching a lab with 120 students in it.

I’ll keep this simple.  If you don’t support redundant license servers, it means that you don’t believe that your software is important. It tells me that you are just playing at being a big, grown up piece of software but you don’t really think anyone will take you seriously.

3. You support redundant license servers but can’t select them via the installer.

At install time, there is no option to give three severs. The user can only give one. You then expect the user to copy a pre-prepared license file that has details of all three servers as a post-installation step.

What usually happens here is that users give the primary license server, find that the application will launch and stop reading the installation instructions.  At some point in the future, we take down the primary license server for maintenance and the vast majority of self-serve installations break!

4. You use the LM_LICENSE_FILE environment variable

The problem is, so does everyone else. We end up with a situation where the LM_LICENSE_FILE variable is pointing at several license servers and some client applications really don’t like that. Be a good FlexLM citizen and use a vendor specific environment variable.  For example, MATLAB uses MLM_LICENSE_FILE and I could give them a big hug just for that!

5. You ‘helpfully’ tell the user when the license is about to expire.

I’ve moaned about this before. 1000 users panicking and emailing the helpdesk…lovely!  Bonus points are awarded if you don’t allow any supported way of switching these warnings off.

6. Your new license doesn’t support old clients.

This should speak for itself and happens more than I’d like.  We can’t upgrade the entire estate instantaneously and even if we could, we probably wouldn’t want to.  Some users, for one reason or another, cling to old versions of your software like grim death. They don’t care that there is a new shiny version available, all they know is that I broke their application and they hate me for it.

When we discover that old versions of your application will stop working, it also delays roll out of the new version since we have to do a lot of user-communications and ensure that nothing mission-critical will stop working.  This makes power-users of your application hate me because they want the new shiny version.

7. You don’t have a silent installer.

Strictly speaking not a network license moan but closely related.  We use network licensing because we deploy your software to lots of machines.  When I say ‘lots’ I mean thousands.  It turns out, however, that you don’t support scripted installation (sometimes called ‘silent installation’ or ‘unattended installation’).  This means that your software is a lot more difficult to deploy than your competitor!  I’m now a big fan of your competitor!

8. You have a silent installer but it’s a bad one.

If I install manually, via point and click, I can configure every aspect of your application.  Your silent installer, on the other hand, is just a /S switch that does a default install…no configuration possible.  Bonus points for ‘silent’ installers that include pop-up dialogue boxes that can’t be switched off.

While on the topic of silent installation, can I just ask that you directly support deployment by SCCM on Windows please?  It will help with next year’s packaging season big time!

Cheers,

Mike

February 19th, 2013

From time to time I find myself having to write or modify windows batch files.  Sometimes it might be better to use PowerShell, VBScript or Python but other times a simple batch script will do fine.  As I’ve been writing these scripts, I’ve kept notes on how to do things for future reference.  Here’s a summary of these notes.  They were written for my own personal use and I put them here for my own convenience but if you find them useful, or have any comments or corrections, that’s great.

These notes were made for Windows 7 and may contain mistakes, please let me know if you spot any.  If you use any of the information here, we agree that its not my fault if you break your Windows installation.  No warranty and all that.

These notes are not meant to be a tutorial.

Comments

Comments in windows batch files start with REM. Some people use :: which is technically a label. Apparently using :: can result in faster script execution (See here and here). I’ve never checked.

REM This is a comment
:: This is a comment too...but different. Might be faster.

If statements

If "%foo%"=="bar" (
REM Do stuff
REM Do more stuff
)
else (
REM Do different stuff
)

Check for existence of file

if exist {insert file name here} (
    rem file exists
) else (
    rem file doesn't exist
)

Or on a single line (if only a single action needs to occur):

if exist {insert file name here} {action}

for example, the following opens notepad for autoexec.bat, if the file exists:

if exist c:\autoexec.bat notepad c:\autoexec.bat

Echoing and piping output
To get a newline in echoed output, chain commands together with &&

echo hello && echo world

gives

hello
world

To pipe output to a file use > or >> The construct 2>&1 ensures that you get both standard output and standard error in your file

REM > Clobbers log.txt, overwriting anything you already have in it
"C:\SomeProgram.exe" > C:\log.txt 2>&1

REM >> concatenates output of SomeProgram.exe to log.txt
"C:\SomeProgram.exe" >> C:\log.txt 2>&1

Environment Variables

set and setx

  • set – sets variable immediately in the current context only.  So, variable will be lost when you close cmd.exe.
  • setx – sets variable permanently but won’t be valid until you start a new context (i.e. open a new cmd.exe)

List all environment variables defined in current session using the set command

set

To check if the environment variable FOO is defined

if defined FOO (
 echo "FOO is defined and is set to %FOO%"
)

To permanently set the system windows environment variable FOO, use setx /m

setx FOO /m "someValue"

To permanently unset the windows environment variable FOO, set it to an empty value

setx FOO ""

A reboot may be necessary. Strictly speaking this does not remove the variable since it will still be in the registry and will still be visible from Control Panel->System->Advanced System Settings->Environment variables. However, the variable will not be listed when you perform a set command and defined FOO will return false.  To remove all trace of the variable, delete it from the registry.

Environment variables in the registry

On Windows 7:

  •  System environment variables are at HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\Environment
  •  User environment variables are at HKEY_CURRENT_USER\Environment

If you change environment variables using the registry, you will need to reboot for them to take effect.

Pausing
This command will pause for 10 seconds

TIMEOUT /T 10

Killing an application

This command will kill the notepad.exe window with the title Readme.txt

taskkill /f /im notepad.exe /fi "WINDOWTITLE eq Readme.txt"

Time stamping

The variable %time% expands to the current time which leads you to do something like the following to create time stamps between the execution of commands.

echo %time%
timeout /t 1
echo %time%

This works fine unless your code is in a block (i.e. surrounded by brackets), as it might be if it is part of an if-statement for example:

(
echo %time%
timeout /t 1
echo %time%
)

If you do this, the echoed time will be identical in both cases because the %time% entries get parsed at the beginning of the code block. This is almost certainly not what you want.

Setlocal EnableDelayedExpansion
(
echo !time!
timeout /t 1
echo !time!
)

Now we get the type of behaviour we expect.

Where is this script?

Sometimes your script will need to know where it is.  Say test.bat is at C:\Users\mike\Desktop\test.bat and contains the following

set whereAmI=%~dp0

When you run test.bat, the variable whereAmI will contain C:\Users\mike\Desktop\

Details on %dp0 can be found at StackOverflow.

Variable substrings
This came from StackOverflow’s Hidden features of Windows batch files which is a great resource.  They’ve tightened up on what constitutes a ‘valid question’ these days and so great Q+A such as this won’t be appearing there in future.

> set str=0123456789
> echo %str:~0,5%
01234
> echo %str:~-5,5%
56789
> echo %str:~3,-3%
3456
TOP