I've had this issue before and it annoyed me. It's still annoying me now!
Gantt charts are one of the types of chart that I have come to accept as a part of life that's not going away, and actually they're not all that bad. They are however difficult to draw.
I (like plenty of other people I've seen) have tried kludging together a Gantt chart in an Excel spreadsheet and it always seems to come out looking pretty horrific. I've also seen them drawn freehand in paint or Powerpoint or similar. Obviously these aren't really a proper solution, so I had a look round to try to find something that would let me manage a simple Gantt chart to plan and track my PhD progress.
Two options looked promising:
Gnome Planner - part of the gnome desktop but also usable under Windows
GanttProject - another open source cross platform piece of software
I started out with the latter and then switched to the former, but to be honest I don't find either that useful. I think the primary issue is that I'm not looking for a tool to perform PERT or CPM or do resource levelling for me. All I want is something that will accept all of my task details in a well contained format and produce a vector graphic of the chart that I can include in a LaTeX document. It's this last part where both of these tools fall down.
The output of these tools is much more of a formal report than it is a nice image. They also seem to really struggle with the multi-year duration of my work. With planner I've had to resort to taking screenshots of the window and including those in reports!
There are packages for LaTeX that support drawing of Gantt charts, but they're a bit too fiddly for the kind of quick changes that I'd like to be able to make. As Planner saves in XML format there must be a method of auto-converting to the LaTeX code...
Any solutions or alternatives out there that I'm missing?
UPDATE: In the end I went with drawing it out using one of the Latex packages. This used all the same data that the planner XML file had in it but in a different format - I was sorely tempted to put together a script to do the conversion for me but in the end I couldn't justify the time required and did it manually. I also had to meddle around a bit to get the gantt to fit on an A4 page - in the end I made it landscape and adjusted the page margins. I think the output from Latex looked a lot more professional and it would be really useful to have a conversion tool. If there is any interest in how I put the latex code together then leave a comment and I'll write a bit more about it...
18/08/2011
16/08/2011
Using a remote Bibtex file
As mentioned previously:
There are plenty of questions about this out there in internetland, mostly with the following suggestions:
- I am using version control software to backup my work
- I'm using LaTeX
- I don't like duplicating files around my system
- I'm working between both Windows and Linux
There are plenty of questions about this out there in internetland, mostly with the following suggestions:
- Move your bibtex file to within the tex installation root - I can't really do this because of 1. above.
- Use symbolic links to the original in the local folder - I can't do this becuase of 4. (windows doesn't support them)
- Give a relative filename reference e.g. '\bibiography{../literatureReview/references}'
- Adding the location as an environment variable as described here.
27/07/2011
Making a bibtex file from a folder of pdf files
The issue
As I'm going to be writing some big documents with lots of references I'd be a fool to try to manage these manually, I therefore needed to pick a reference management piece of software. After some browsing I settled on JabRef because: it's free, it's open source, it's lightweight, it's cross-platform and it handles bibtex format natively (which is what I need for it to integrate with latex). It should also link nicely into the Sciplore mind mapping software which I'm using (more about that some other time).
JabRef is basically a database management tool for references that stores its database in bibtex format. It looks like it will work rather well, but unfortunately my first stumbling block is that I already have a folder full of my references in pdf format (~200). This means that I'm immediately faced with the big task of going through and adding the details of each pdf individually. There must be a better way...
Someone else asked the same question here. The answer seemed to be that there was no easy way in JabRef, but it could be done in some other reference management software - such as Mendeley. So I could install that as well and export from there to use JabRef, that seemed like a pain though, especially as you need log in details and all sorts for Mendeley.
The solution
Somewhere else cb2Bib was suggested. This looks like an awesome piece of software, almost to the point that I could use it instead of JabRef, although I don't think it does quite the same job. It's designed as a bibtex database manager, however it is more tailored towards reference entry than editing or final use (e.g. citations) - although it can do this. Its method of adding a new reference is based on what's currently in the clipboard - thats whatever you most recently 'cut' or 'copied' in your operating system. This can either be a piece of text or a pdf file.
Files from the system can also be queued up to be added to the clipboard for addition to the bibtex database - in this manner a folders worth of pdf files can be added. Once the file is in the clipboard the software interrogates it to try to extract the right details for the bibtex reference entry. It is also able to do some other clever things like search the web and find a web reference for it that matches only one of the pieces of data it has extracted. There is also the option to manually edit the fields or to set off a whole run of files to add automatically.
My implementation
In practice the software took a little while to get used to; the buttons aren't in quite the locations I'd expect, there seem to be about 3 different windows that are independent but interrelated and the method of specifying a bibtex file and then successively saving additions to it felt a little odd (rather than running through to create a file and then saving it all at once). But once I was used to it at that level it all worked.
When I came to actually try to add all of my pre-saved pdfs however, I hit problems. Whilst automatic extraction usually managed to pull out a few nuggets of useful data, it rarely found enough for a complete entry. Hitting the button to search the web didn't seem to give much assistance. So it was time to dig a little deeper.
Probing through the website there is quite a lot of useful information on how to configure the software to do what you want. What I needed to do was look into where was being searched on the web for my articles. This is all setup in a configuration file located at:
C:\Program Files\cb2bib\data\netqinf.txt (windows)
or
/usr/share/cb2bib/data/netqinf.txt (linux) (you'll need permissions or to be root to edit)
Wading into there you can find out where is being searched and in what order. What would have been ideal for me would have been a search of the IEEE Xplore site, as that would have turned up most of my papers. Unfortunately it was not in there. Second best was google scholar, sitting at the bottom of the list of options. The documentation in the file wasn't brilliant, but with a bit of trial and error I was able to work out what was going on.
The major change I made to the file was to add this at the top of the queries list:
# QUERY INFO FOR Google Scholar
journal=
query=http://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<title>>&btnG=Search
capture_from_query=info:(.+):scholar
referenceurl_prefix=http://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=
journal=
query=http://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<excerpt>>&btnG=Search
capture_from_query=info:(.+):scholar
referenceurl_prefix=http://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=
The important changes here are the <<title>> and <<excerpt>> search strings, and the change from capture_from_query=info:(\w+):scholar in the existing scholar searches to capture_from_query=info:(.+):scholar in my search. I'm not too sure what the latter change did, but its effect was that it found the details - where previously it was often missing them!
As I'm going to be writing some big documents with lots of references I'd be a fool to try to manage these manually, I therefore needed to pick a reference management piece of software. After some browsing I settled on JabRef because: it's free, it's open source, it's lightweight, it's cross-platform and it handles bibtex format natively (which is what I need for it to integrate with latex). It should also link nicely into the Sciplore mind mapping software which I'm using (more about that some other time).
JabRef is basically a database management tool for references that stores its database in bibtex format. It looks like it will work rather well, but unfortunately my first stumbling block is that I already have a folder full of my references in pdf format (~200). This means that I'm immediately faced with the big task of going through and adding the details of each pdf individually. There must be a better way...
Someone else asked the same question here. The answer seemed to be that there was no easy way in JabRef, but it could be done in some other reference management software - such as Mendeley. So I could install that as well and export from there to use JabRef, that seemed like a pain though, especially as you need log in details and all sorts for Mendeley.
The solution
Somewhere else cb2Bib was suggested. This looks like an awesome piece of software, almost to the point that I could use it instead of JabRef, although I don't think it does quite the same job. It's designed as a bibtex database manager, however it is more tailored towards reference entry than editing or final use (e.g. citations) - although it can do this. Its method of adding a new reference is based on what's currently in the clipboard - thats whatever you most recently 'cut' or 'copied' in your operating system. This can either be a piece of text or a pdf file.
Files from the system can also be queued up to be added to the clipboard for addition to the bibtex database - in this manner a folders worth of pdf files can be added. Once the file is in the clipboard the software interrogates it to try to extract the right details for the bibtex reference entry. It is also able to do some other clever things like search the web and find a web reference for it that matches only one of the pieces of data it has extracted. There is also the option to manually edit the fields or to set off a whole run of files to add automatically.
My implementation
In practice the software took a little while to get used to; the buttons aren't in quite the locations I'd expect, there seem to be about 3 different windows that are independent but interrelated and the method of specifying a bibtex file and then successively saving additions to it felt a little odd (rather than running through to create a file and then saving it all at once). But once I was used to it at that level it all worked.
When I came to actually try to add all of my pre-saved pdfs however, I hit problems. Whilst automatic extraction usually managed to pull out a few nuggets of useful data, it rarely found enough for a complete entry. Hitting the button to search the web didn't seem to give much assistance. So it was time to dig a little deeper.
Probing through the website there is quite a lot of useful information on how to configure the software to do what you want. What I needed to do was look into where was being searched on the web for my articles. This is all setup in a configuration file located at:
C:\Program Files\cb2bib\data\netqinf.txt (windows)
or
/usr/share/cb2bib/data/netqinf.txt (linux) (you'll need permissions or to be root to edit)
Wading into there you can find out where is being searched and in what order. What would have been ideal for me would have been a search of the IEEE Xplore site, as that would have turned up most of my papers. Unfortunately it was not in there. Second best was google scholar, sitting at the bottom of the list of options. The documentation in the file wasn't brilliant, but with a bit of trial and error I was able to work out what was going on.
The major change I made to the file was to add this at the top of the queries list:
# QUERY INFO FOR Google Scholar
journal=
query=http://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<title>>&btnG=Search
capture_from_query=info:(.+):scholar
referenceurl_prefix=http://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=
journal=
query=http://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<excerpt>>&btnG=Search
capture_from_query=info:(.+):scholar
referenceurl_prefix=http://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=
The important changes here are the <<title>> and <<excerpt>> search strings, and the change from capture_from_query=info:(\w+):scholar in the existing scholar searches to capture_from_query=info:(.+):scholar in my search. I'm not too sure what the latter change did, but its effect was that it found the details - where previously it was often missing them!
The other change I made was to untick the option "Set 'title' in double braces" box in the configuration window. After I'd made these changes it worked a lot more consistently.
Some of the time it still pulled out the wrong details if it mis-extracted the article title, however I'd named all my pdfs with the title of the paper, therefore it was simply a case of copying and pasting the filename into the title field and rerunning. It would have been really nice to be able to use the title of my pdf as part of the search but unfortunately I couldn't find a way of doing that.
The only other issue I'm having is that although cb2bib adds in the link to the pdf file, JabRef wont understand it as it uses a very slightly different bibtex format for it. The cb2bib format seems to be:
file = {location}
whereas the JabRef format seems to be:
file = {description:location:type}
There is a comment here by a Mendeley admin that suggests that there is no prescribed format for this aspect of a bibtex file, so I guess it's to be expected. I should be able to work around it with a bit of clever find/replace, but it's an annoyance.
ACTUALLY - this seems to be working under windows! It looks like a different version of JabRef has gotten around this issue.
UPDATE: After a couple of months of getting used to cb2bib and using it to produce a document I'm not really finding the need to use JabRef at all! The 'citer' facility of cb2bib is actually really good.
UPDATE: I hadn't previously gotten round to extracting from IEEE Xplore, as almost everything is on Google Scholar. However I've just tried to set it up and found that the IEEE pages use javascript buttons to produce the citation. This makes it difficult to fully automate.
If you add the following to netqinf.txt then it should search IEEE Xplore for the title, you can then manually click the "download citation" button, select BibTeX format and then copy the BibTeX citation into cb2bib:
# QUERY INFO FOR IEEEXplore
journal=
query=http://ieeexplore.ieee.org/search/searchresult.jsp?newsearch=true&queryText=<<title>>&x=35&y=7
capture_from_query=arnumber=(\d+)&contentType
referenceurl_prefix=http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_referenceurl
ACTUALLY - this seems to be working under windows! It looks like a different version of JabRef has gotten around this issue.
UPDATE: After a couple of months of getting used to cb2bib and using it to produce a document I'm not really finding the need to use JabRef at all! The 'citer' facility of cb2bib is actually really good.
UPDATE: I hadn't previously gotten round to extracting from IEEE Xplore, as almost everything is on Google Scholar. However I've just tried to set it up and found that the IEEE pages use javascript buttons to produce the citation. This makes it difficult to fully automate.
journal=
query=http://ieeexplore.ieee.org/search/searchresult.jsp?newsearch=true&queryText=<<title>>&x=35&y=7
capture_from_query=arnumber=(\d+)&contentType
referenceurl_prefix=http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_referenceurl
14/07/2011
Latex \psfragfig of figures in other folders
What I've spent part of today wrestling with...
I've detailed previously how I'm exporting Matlab plots and including them in Latex documents. This works very well for figure files in the same directory - which is kind of the way Latex is set up. Unfortunately I'd like to maintain my folder structure in a different manner, for example, I have a "results" folder and a "thesis" folder both at the same level. Within "results" I have my Matlab plotting scripts and the images that are automatically saved by them. In my "thesis" folder I have my Latex files, in which I would like to include my results images.
Ideally I would be able to simply reference the image in my Latex document but that's not quite how it worked out. Let me explain what I tried...
Using \graphicspath
This is the most obvious way of doing things as noted here, and it works fine for graphics inserted with the \includegraphics command. I was also able to reference relatively like this: \graphicspath{{../results/}} and apparently it would also look in all the subdirectories if I put a double slash on the end: \graphicspath{{../results//}}.
This would be a great solution if I were using the \includegraphics command - but I'm not. I'm using \psfragfig and it doesn't work with this command, I guess because it's not set up to?
There is also a suggestion here that this method shouldn't be used, in favour of adding the images directory within your Latex compiler setup - although I'm not sure this would be appropriate for what I was trying to do.
Using \input, \include or \import
These all do similar things, in that they allow you to bring in latex documents from elsewhere in a folder structure. Only some of them will allow relative linking via higher level directories (rather than just subdirectories). \import seemed to be what I needed (or rather the \subimport variant of it did), so I set up a .tex file containing only my \psfragfig command within the "results" folder and imported that into my document. This got the figure into the document, but it didn't do all the nice text replacement that it was supposed to. In this respect it was no better than the previous technique.
After some experimentation it seems that \psfragfig only looks locally to the master document for the .tex files that it uses to include text with the figures.
Using \write18
So it appeared that the only way I was going to get the \psfragfig command to work properly was by having both the "figure.eps" file and the "figure.tex" file local to the master document. I'm not keen on the unnecessary duplication involved in this, so at the very least I decided to make it automatic. I therefore set it up so that these two files are automatically copied to the local directory during compile. This means that I always have the most up to date version of them in my document, and everything stays nice and automatic.
I think the only way to copy a file around between directories from within a Latex document is by issuing a system level command using \write18. This is usually disabled by default in Latex as it has the possibility of really mucking things up in your system if you were compiling 3rd party code. Therefore I had to compile my code with the extra argument '--shell-escape' as detailed here.
So I want to use the Latex \write18 command to execute a DOS copy command, that's fine; but there is also the tricky issue of needing to use backslashes for the path in the DOS copy command - these are obviously reserved in Latex. Therefore I had to use the technique outlined here to get around this.
So finally I managed to put together a Latex command that works, and it looks like this:
\def\psfragfigremote{\begingroup\catcode 92 12 \execB}
\def\execB#1#2%
So after including that in my header I can reference figures in other directories in my document like so:
\psfragfigremote{..\results\}{figure}
This copies both figure.eps and figure.tex (generated from Matlab with the matlabfrag command) from the results folder into the current folder and then includes them in the document.
It works fairly well, but not the first time it is run. I'm not sure why this is, possibly it hasn't finished copying the .tex file before starting to execute the next command. Therefore two compiles may be necessary to get all the labels sorted out.
I'm sure there must be a better way of doing this, possibly modifying the \graphicspath and \psfragfig commands so that they play well together would be a neater solution, but this works ok for now.
I hope this is of use to someone. Any improvements or suggestions then please comment.
UPDATE: Replacing the \write18 commands with:
\write18{robocopy #1 . #2.tex #2.eps}%
and removing the star after \psfragfig will only copy the files if they have changed, speeding up processing significantly.
I've detailed previously how I'm exporting Matlab plots and including them in Latex documents. This works very well for figure files in the same directory - which is kind of the way Latex is set up. Unfortunately I'd like to maintain my folder structure in a different manner, for example, I have a "results" folder and a "thesis" folder both at the same level. Within "results" I have my Matlab plotting scripts and the images that are automatically saved by them. In my "thesis" folder I have my Latex files, in which I would like to include my results images.
Ideally I would be able to simply reference the image in my Latex document but that's not quite how it worked out. Let me explain what I tried...
Using \graphicspath
This is the most obvious way of doing things as noted here, and it works fine for graphics inserted with the \includegraphics command. I was also able to reference relatively like this: \graphicspath{{../results/}} and apparently it would also look in all the subdirectories if I put a double slash on the end: \graphicspath{{../results//}}.
This would be a great solution if I were using the \includegraphics command - but I'm not. I'm using \psfragfig and it doesn't work with this command, I guess because it's not set up to?
There is also a suggestion here that this method shouldn't be used, in favour of adding the images directory within your Latex compiler setup - although I'm not sure this would be appropriate for what I was trying to do.
Using \input, \include or \import
These all do similar things, in that they allow you to bring in latex documents from elsewhere in a folder structure. Only some of them will allow relative linking via higher level directories (rather than just subdirectories). \import seemed to be what I needed (or rather the \subimport variant of it did), so I set up a .tex file containing only my \psfragfig command within the "results" folder and imported that into my document. This got the figure into the document, but it didn't do all the nice text replacement that it was supposed to. In this respect it was no better than the previous technique.
After some experimentation it seems that \psfragfig only looks locally to the master document for the .tex files that it uses to include text with the figures.
Using \write18
So it appeared that the only way I was going to get the \psfragfig command to work properly was by having both the "figure.eps" file and the "figure.tex" file local to the master document. I'm not keen on the unnecessary duplication involved in this, so at the very least I decided to make it automatic. I therefore set it up so that these two files are automatically copied to the local directory during compile. This means that I always have the most up to date version of them in my document, and everything stays nice and automatic.
I think the only way to copy a file around between directories from within a Latex document is by issuing a system level command using \write18. This is usually disabled by default in Latex as it has the possibility of really mucking things up in your system if you were compiling 3rd party code. Therefore I had to compile my code with the extra argument '--shell-escape' as detailed here.
So I want to use the Latex \write18 command to execute a DOS copy command, that's fine; but there is also the tricky issue of needing to use backslashes for the path in the DOS copy command - these are obviously reserved in Latex. Therefore I had to use the technique outlined here to get around this.
So finally I managed to put together a Latex command that works, and it looks like this:
\def\psfragfigremote{\begingroup\catcode 92 12 \execB}
\def\execB#1#2%
{\immediate
\write18{copy #1#2.eps}%
\write18{copy #1#2.tex}%
\psfragfig*{#2}
\endgroup
}
So after including that in my header I can reference figures in other directories in my document like so:
\psfragfigremote{..\results\}{figure}
This copies both figure.eps and figure.tex (generated from Matlab with the matlabfrag command) from the results folder into the current folder and then includes them in the document.
It works fairly well, but not the first time it is run. I'm not sure why this is, possibly it hasn't finished copying the .tex file before starting to execute the next command. Therefore two compiles may be necessary to get all the labels sorted out.
I'm sure there must be a better way of doing this, possibly modifying the \graphicspath and \psfragfig commands so that they play well together would be a neater solution, but this works ok for now.
I hope this is of use to someone. Any improvements or suggestions then please comment.
UPDATE: Replacing the \write18 commands with:
\write18{robocopy #1 . #2.tex #2.eps}%
and removing the star after \psfragfig will only copy the files if they have changed, speeding up processing significantly.
11/07/2011
Google Chrome Extensions
A quick post to note down some of the extensions I'm using for Google Chrome. I switched over to Chrome as my browser of choice around a year ago (from Firefox) and I'm still very much enjoying the experience. The extensions I use are probably what make that experience good, so I thought I would give some kudos to them.
AdBlock - Blocks adverts that I don't want to see, brilliant
Add to Amazon Wish List - Allows me to keep track of stuff I'd like to buy
Backspace As Back/Forward for Linux - Does what it says most of the time, but doesn't seem to work 100% of the time - better than nothing.
Better Gmail (unofficial) - Cleans up my gmail inbox a bit
Context Menu Search - This is awesome, it allows me to highlight text and search for it in the websites I usually use. I use it most for Google Maps and internet shopping (Amazon, eBay and Google Products).
Facebook - Lets me keep on top of that all important social networking.
Google Calendar Checker - Counts down the time to my next event and lets me go straight to my calendar with one click.
Google Calendar ebay reminder - I had to hack this one a bit to make it work, but it adds a link to ebay auction pages allowing me to add the auction end as an event in my calendar.
Mail Checker Plus - An icon showing how many unread messages I have and a quick link to my inbox.
Use HTTPS - Keeps my browsing secure
KB SSL Enforcer - More security stuff
Shareaholic - Lets me email a link to the current page, or makes a shortened URL for it.
As you can see from this list, most of them just cut down the number of buttons I need to press to get stuff done - what can I say, I'm lazy!
Anything else that I might find useful?
AdBlock - Blocks adverts that I don't want to see, brilliant
Add to Amazon Wish List - Allows me to keep track of stuff I'd like to buy
Backspace As Back/Forward for Linux - Does what it says most of the time, but doesn't seem to work 100% of the time - better than nothing.
Better Gmail (unofficial) - Cleans up my gmail inbox a bit
Context Menu Search - This is awesome, it allows me to highlight text and search for it in the websites I usually use. I use it most for Google Maps and internet shopping (Amazon, eBay and Google Products).
Facebook - Lets me keep on top of that all important social networking.
Google Calendar Checker - Counts down the time to my next event and lets me go straight to my calendar with one click.
Google Calendar ebay reminder - I had to hack this one a bit to make it work, but it adds a link to ebay auction pages allowing me to add the auction end as an event in my calendar.
Mail Checker Plus - An icon showing how many unread messages I have and a quick link to my inbox.
Use HTTPS - Keeps my browsing secure
KB SSL Enforcer - More security stuff
Shareaholic - Lets me email a link to the current page, or makes a shortened URL for it.
As you can see from this list, most of them just cut down the number of buttons I need to press to get stuff done - what can I say, I'm lazy!
Anything else that I might find useful?
07/06/2011
Portable Version Control
Background
I've mentioned previously that I'm version controlling my work using distributed version control software - specifically Bazaar. I explained that part of the reason I'm doing this is because I work at a number of different locations, and I need to be able to manage various different versions of my work and keep them all in sync.
One of the locations I work at is a Laptop provided by my sponsor. Unfortunately their corporate system does not allow the installation of unauthorised software and Bazaar is not on their approved list. I did briefly look into using subversion (as it was used elsewhere in the company and linking between this and Bazaar is possible) however it looked like it was going to be too much hassle to justify getting it installed. I've therefore decided to attempt to run my version control purely from my flash memory. This will not only allow me to version control my work on my sponsors laptop, but also on any other machine I decide to use.
Incidentally it's worth mentioning that I'm storing all my work on the flash memory (micro-sd) card of my phone. I upgraded to an 8 Gb card which should be plenty (at least initially). I always carry my phone anyway so all I need to retrieve my work at any time or location is a USB cable (or bluetooth if I'm desperate!). I don't treat this as a working copy, but I backup to it regularly and use it to transfer versions between machines. In version control terminology this means I have a 'branch' on each machine I work at and another 'branch' on my phone. I 'push' or 'pull' changes between the phone branch and the local copy branch to backup/transfer the work.
Bazaar is coded using the Python programming language. This is a pretty modern and, by most accounts, a pretty handy programming language; however it's not something that I'm particularly familiar with. The main benefit to me is that there is a variant of it available called Portable Python which is designed to run from a USB storage device (like my phone). This means that it is possible for me to install Portable Python on my phone, and then run Bazaar from that.
I was quite surprised not to be able to find any instructions for this setup on the net anywhere, as it seems like quite a handy proposition (certainly for someone in my situation). The only references that I could find to it were suggestions of using it here, and here. I'm far from an expert on this type of thing but I've sort of got it working - so I thought I'd publish the steps I took incase anyone has any feedback, or it is of use to someone else.
Unfortunately portable python is only windows based; however this is where I'm most likely to need it. (there's also a chance that it will work under linux through wine, but I haven't really experimented with that yet.)
Python Installation
The current version of Python is 3.2, however I don't think any of the Bazaar source is built on that version, so I went with 2.6 (I'm not sure if I could have gotten away with a newer version or not?). I downloaded Portable Python from here and copied it to a "python" folder on my phone. I then ran the installer and told it to install to the same folder on the phone.
Bazaar Installation
I tried installing Bazaar from some executables, unfortunately these complained that it needed python 2.6 in the registry, and gave me no option for manually specifying a python path. So instead I downloaded a tarball of the Bazaar source from here which I extracted to the Python "App" directory. I then opened a command prompt, navigated to the python "App" directory, and ran:
python bzr-2.4b3\setup.py install
(actually I was still using Linux at this point and instead ran SPE-Portable.exe under wine and then ran setup.py through that - I'm pretty sure it had the same effect though)
This ran for a while and terminated without any errors. Within the bazaar directory a "build" folder had now appeared.
From the command prompt I was then able to run :
python bzr-2.4b3\bzr status C:\test
where C:\test was a directory under version control. This gave the correct response, but it also gave me this warning that some extensions couldn't be loaded. I don't think this is a problem, so I ignored it (the link gives a method for turning off the warning if you're bothered about it).
Bazaar Explorer Installation
I wasn't keen on typing everything through the command line, so I looked into getting bazaar explorer running. The official instructions for this are here.
So I changed to the plugins directory of bazaar:
cd F:\python\PortablePython_1.1_py2.6.1\App\bzr-2.4b3\bzrlib\plugins
and ran bzr with the command to download from launchpad:
F:\python\PortablePython_1.1_py2.6.1\App\python F:\python\PortablePython_1.1_py2.6.1\App\bzr-2.4b3\bzr branch lp:bzr-explorer explorer
This warned me that I hadn't given a launchpad ID, but I don't think that matters as I'm not intending on writing anything back to launchpad. Then it went about downloading and building explorer. This process took a little while.
I then tried to run it, but there were a few dependencies that needed fulfilling. Firstly it told me I needed QBzr. So, still in the plugins directory, I ran:
F:\python\PortablePython_1.1_py2.6.1\App\python F:\python\PortablePython_1.1_py2.6.1\App\bzr-2.4b3\bzr branch lp:qbzr
this then went through the same process as with explorer.
On the next try it requested qt libraries (ERROR: No modeule names PyQt4). Some googling reveals this, which suggests installing it in a "non-portable" install and then copying selected files across. (I did try a proper install before this but got nowhere*). I downloaded "PyQt-Py2.6-gpl-4.5.4-1.exe" from here, and installed to C:\Python26. This created a folder in C:\Python26\Lib called "site-packages", I copied the contents of this to the Lib\site-packages folder of my portable python install.
I then tried running:
python bzr-2.4b3\bzr explorer
and up it popped!
Unfortunately a lot of the buttons bring up a deprecation warning for commands in plugins\explorer\lib\app_suite.py. This is something I haven't been able to fix yet. My guess is that it's due to a new version of explorer being used with an older version of Bazaar, but that's just a guess. If anyone can help with it then I'd love to hear from you!
It's still useful as a GUI for inspecting the changes and looking at differences; however any major commands need to be made from the command prompt.
Also this all took a while working from the phone flash card, next time I might consider doing it locally on the hard drive and then copying it across.
Please let me know if you know of any better methods for getting this working, or where I've gone wrong with getting explorer working. Hope this is of interest to someone.
I've also just come across another (easier looking) solution here.
* The copying method sounded like it might be a bit flaky, and I saw some sites indicating that it could be done in a more "conventional" manner, so I got the files for it from here. I also needed "SIP" (I tried it without but it said no). SIP can be obtained from the same place here, and extracted to the python/App directory. I then changed to the python directory and ran:
I've mentioned previously that I'm version controlling my work using distributed version control software - specifically Bazaar. I explained that part of the reason I'm doing this is because I work at a number of different locations, and I need to be able to manage various different versions of my work and keep them all in sync.
One of the locations I work at is a Laptop provided by my sponsor. Unfortunately their corporate system does not allow the installation of unauthorised software and Bazaar is not on their approved list. I did briefly look into using subversion (as it was used elsewhere in the company and linking between this and Bazaar is possible) however it looked like it was going to be too much hassle to justify getting it installed. I've therefore decided to attempt to run my version control purely from my flash memory. This will not only allow me to version control my work on my sponsors laptop, but also on any other machine I decide to use.
Incidentally it's worth mentioning that I'm storing all my work on the flash memory (micro-sd) card of my phone. I upgraded to an 8 Gb card which should be plenty (at least initially). I always carry my phone anyway so all I need to retrieve my work at any time or location is a USB cable (or bluetooth if I'm desperate!). I don't treat this as a working copy, but I backup to it regularly and use it to transfer versions between machines. In version control terminology this means I have a 'branch' on each machine I work at and another 'branch' on my phone. I 'push' or 'pull' changes between the phone branch and the local copy branch to backup/transfer the work.
Bazaar is coded using the Python programming language. This is a pretty modern and, by most accounts, a pretty handy programming language; however it's not something that I'm particularly familiar with. The main benefit to me is that there is a variant of it available called Portable Python which is designed to run from a USB storage device (like my phone). This means that it is possible for me to install Portable Python on my phone, and then run Bazaar from that.
I was quite surprised not to be able to find any instructions for this setup on the net anywhere, as it seems like quite a handy proposition (certainly for someone in my situation). The only references that I could find to it were suggestions of using it here, and here. I'm far from an expert on this type of thing but I've sort of got it working - so I thought I'd publish the steps I took incase anyone has any feedback, or it is of use to someone else.
Unfortunately portable python is only windows based; however this is where I'm most likely to need it. (there's also a chance that it will work under linux through wine, but I haven't really experimented with that yet.)
Python Installation
The current version of Python is 3.2, however I don't think any of the Bazaar source is built on that version, so I went with 2.6 (I'm not sure if I could have gotten away with a newer version or not?). I downloaded Portable Python from here and copied it to a "python" folder on my phone. I then ran the installer and told it to install to the same folder on the phone.
Bazaar Installation
I tried installing Bazaar from some executables, unfortunately these complained that it needed python 2.6 in the registry, and gave me no option for manually specifying a python path. So instead I downloaded a tarball of the Bazaar source from here which I extracted to the Python "App" directory. I then opened a command prompt, navigated to the python "App" directory, and ran:
python bzr-2.4b3\setup.py install
(actually I was still using Linux at this point and instead ran SPE-Portable.exe under wine and then ran setup.py through that - I'm pretty sure it had the same effect though)
This ran for a while and terminated without any errors. Within the bazaar directory a "build" folder had now appeared.
From the command prompt I was then able to run :
python bzr-2.4b3\bzr status C:\test
where C:\test was a directory under version control. This gave the correct response, but it also gave me this warning that some extensions couldn't be loaded. I don't think this is a problem, so I ignored it (the link gives a method for turning off the warning if you're bothered about it).
Bazaar Explorer Installation
I wasn't keen on typing everything through the command line, so I looked into getting bazaar explorer running. The official instructions for this are here.
So I changed to the plugins directory of bazaar:
cd F:\python\PortablePython_1.1_py2.6.1\App\bzr-2.4b3\bzrlib\plugins
and ran bzr with the command to download from launchpad:
F:\python\PortablePython_1.1_py2.6.1\App\python F:\python\PortablePython_1.1_py2.6.1\App\bzr-2.4b3\bzr branch lp:bzr-explorer explorer
This warned me that I hadn't given a launchpad ID, but I don't think that matters as I'm not intending on writing anything back to launchpad. Then it went about downloading and building explorer. This process took a little while.
I then tried to run it, but there were a few dependencies that needed fulfilling. Firstly it told me I needed QBzr. So, still in the plugins directory, I ran:
F:\python\PortablePython_1.1_py2.6.1\App\python F:\python\PortablePython_1.1_py2.6.1\App\bzr-2.4b3\bzr branch lp:qbzr
this then went through the same process as with explorer.
On the next try it requested qt libraries (ERROR: No modeule names PyQt4). Some googling reveals this, which suggests installing it in a "non-portable" install and then copying selected files across. (I did try a proper install before this but got nowhere*). I downloaded "PyQt-Py2.6-gpl-4.5.4-1.exe" from here, and installed to C:\Python26. This created a folder in C:\Python26\Lib called "site-packages", I copied the contents of this to the Lib\site-packages folder of my portable python install.
I then tried running:
python bzr-2.4b3\bzr explorer
and up it popped!
Unfortunately a lot of the buttons bring up a deprecation warning for commands in plugins\explorer\lib\app_suite.py. This is something I haven't been able to fix yet. My guess is that it's due to a new version of explorer being used with an older version of Bazaar, but that's just a guess. If anyone can help with it then I'd love to hear from you!
It's still useful as a GUI for inspecting the changes and looking at differences; however any major commands need to be made from the command prompt.
Also this all took a while working from the phone flash card, next time I might consider doing it locally on the hard drive and then copying it across.
Please let me know if you know of any better methods for getting this working, or where I've gone wrong with getting explorer working. Hope this is of interest to someone.
I've also just come across another (easier looking) solution here.
* The copying method sounded like it might be a bit flaky, and I saw some sites indicating that it could be done in a more "conventional" manner, so I got the files for it from here. I also needed "SIP" (I tried it without but it said no). SIP can be obtained from the same place here, and extracted to the python/App directory. I then changed to the python directory and ran:
python sip-4.12.3\configure.py
after this had created a sip module Makefile it errored with unable to open siplib\siplib.sbf - not sure what this means, so I then tried:
python PyQt-win-gpl-4.8.4\configure.py
this said: "make sure you have a working qt v4 qmake on your path". I was a bit lost then so I gave up and tried the technique of copying across!
03/06/2011
Simulink to eps
I've mentioned previously that I've developed a process to export plots from Matlab and include them as (eps format) figures in a Latex document. Well today I spent a load of time trying to get a similar method working for exporting Simulink model diagrams from Matlab. This hasn't proved quite as easy, but I think I'm there now.
My main issue was that Simulink doesn't allow you to print in the same way as a normal Matlab figure does. The "print" command can be used, but it works in a very specific way. It is fairly easy to use this command to print in eps format (see my previous posting for why this is a good thing); however it doesn't allow you the same freedom to setup the page. More specifically it will only allow you to use a pre-defined page size (A4, US legal, etc). It rescales and centres the figure to fill the page, but, unless the model is the exact same aspect ratio as a pre-set paper type, you end up with white borders at either the top/bottom or left/right.
EDIT: This seems to have been corrected in newer versions of Matlab now!
I've tried all sorts to get round this, including calling Ghostscript from within matlab to post-process the eps file. This should work as it ought to be able to find the right "bounding-box" for the figure and resize the page accordingly. However I had no luck with this - it would either not trim it down at all, or over-trim it removing some of the image.
I also tried exporting in a few other formats (namely normal postscript and pdf) and then converting with Ghostscript. This worked a little better and I was able to get the right bounding box through a process of:
So an alternative process I finally came up with is:
There's nothing very clever in the code, but if anyone wants a copy of my function I'll happily forward it to them. Hope this helps somebody!
EDIT: Code for my function is available here.
My main issue was that Simulink doesn't allow you to print in the same way as a normal Matlab figure does. The "print" command can be used, but it works in a very specific way. It is fairly easy to use this command to print in eps format (see my previous posting for why this is a good thing); however it doesn't allow you the same freedom to setup the page. More specifically it will only allow you to use a pre-defined page size (A4, US legal, etc). It rescales and centres the figure to fill the page, but, unless the model is the exact same aspect ratio as a pre-set paper type, you end up with white borders at either the top/bottom or left/right.
EDIT: This seems to have been corrected in newer versions of Matlab now!
I've tried all sorts to get round this, including calling Ghostscript from within matlab to post-process the eps file. This should work as it ought to be able to find the right "bounding-box" for the figure and resize the page accordingly. However I had no luck with this - it would either not trim it down at all, or over-trim it removing some of the image.
I also tried exporting in a few other formats (namely normal postscript and pdf) and then converting with Ghostscript. This worked a little better and I was able to get the right bounding box through a process of:
- Simulink export to pdf,
- Ghostscript convert pdf-to-eps,
- Ghostscript convert eps-to-eps.
So an alternative process I finally came up with is:
- Find out the ratio of the figure (I did this by exporting as a raster image and then reading back in - I'm not very happy with this technique as it's pretty dirty, but at least it works)
- Simulink export to eps, with the model at the very bottom of the page
- Automatically edit the resulting eps file to adjust its bounding box information
There's nothing very clever in the code, but if anyone wants a copy of my function I'll happily forward it to them. Hope this helps somebody!
EDIT: Code for my function is available here.
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