A PhD thesis, LaTeX and me

For writing a PhD thesis in LaTeX, there are many package choices to make and a whole lot of little issues and pitfalls to handle. This starts with choosing the document class and … goes on and on. Here, I am collecting some points which took me more than a few moments, so I don’t have to go through the whole process again. And maybe my little list can help others to make their choices a little faster or avoid some of the mistakes I made.

Choosing the document class

Even though there are alternatives, for me, the main contenders for the document class were KOMA-Script class ( scrbook or scrreprt ) and memoir. In the end I chose KOMA-Script as it seems to be less bloated (i.e., memoir emulates many well established packages instead of using them directly) and there really seems to be no reason not to use it 😉 However, as you can see, I am not going into minute details as the articles mentioned above were enough to sway me.

As for the subcategory I use scrbook . It seems that from the book, report or article classes (koma-script or not) there seems to be an awful lot of features which fit a PhD thesis more than the report or article class (see this discussion). Just to name a few, such features include two-page layout or more flexible numbering with regard to front, main and back matter. Also this article explicitly states that scrbook is for dissertations.

How to handle subfigures

An interesting choice was which package to use for subfigures. I chose the subcaption package. As to why: the subfigure package seems to be old and is superseded by subfig. While the newest most flexible option seems to be a combination of the caption and the floatrow package. However, the subcaption package supposedly was a case study for the interfaces provided by the latter two packages and provides a more easy to use functionality. Indeed, the introduction of the subfigure package on CTAN specifically describes itself as “superseded […], […] and users may find the more recent subcaption package more satisfactory.” Discussions on StackExchange further support this notion. I think overall, it boils down to subfig supposedly having issues with hyperref, and subcaption being more simple than using a combination of caption and floatrow. Thus in the end subcaption seems to be the best choice.

i3: Fast switching named workspaces

i3 is a tiling window manager which allows to work nicely with named workspaces. For example, I have a messaging/social workspace, a calendar and TODO workspace, two browser workspaces, my code workspaces and so forth. However, as the number of projects I work on increases, it becomes more difficult to keep track of the different workspaces. To solve this, it would be necessary to create new named workspaces. However, to do this, the config needs to be updated which I am usually to lazy to do.

Now, the core idea to solve this is based on the i3-input directive. This lets the user type the name of the desired workspace in order to easily create, rename and move to workspaces with very specific names on the fly. However, this becomes cumbersome when workspace names are longer than two or three characters. To solve this I came up with a little Python script which allows so “shortcode” workspaces. In the following I introduce the Python script as well as the corresponding i3 config entries.

The Python script

The Python script takes three parameters “prefix”, “query”, and “postfix”. It will then pick a workspace from the list of existing i3 workspaces if the query is a prefix of that workspace name (priority 1) or if the workspace contains the query (priority 2). Also, the script supports an “index”, i.e., you can append something to query using a . which is then appended to the name chosen by the script. For example is the workspaces project and project2 exists, then the query is p.2 will choose project2. Then the script executes a command built from the prefix, the chosen workspace and the postfix: <prefix><chosen name><postfix> .

import sys
import subprocess
import json

# process input
prefix = sys.argv[1]
query_array = sys.argv[2].split(".")
query = query_array[0]
index = ""
if len(query_array) > 1:
 index = query_array[1]
postfix = sys.argv[3]

# get existing workspaces
workspaces_raw = subprocess.run(
 "i3-msg -t get_workspaces", \
 shell=True, 
 stdout=subprocess.PIPE
 ).stdout.decode("utf-8")
workspaces = json.loads(workspaces_raw)

# set default name
name = query

# pick a name if the input is a prefix of the input (priority 1)
names = [w["name"] for w in workspaces if w["name"].startswith(query)]
if len(names) > 0:
 name = sorted(names)[0] + index
 
# pick a name if the input contains the input (priority 2)
else:
 names = [w["name"] for w in workspaces if query in w["name"]]
 if len(names) > 0:
 name = sorted(names)[0] + index

# print chosen name
print(name)

# setup the command
cmd = "i3-msg '%s%s%s'" % (prefix, name, postfix)
print(cmd)

# run the command
subprocess.run(cmd, shell=True)

import sys

import subprocess

import json

# process input

prefix = sys.argv[1]

query_array = sys.argv[2].split(".")

query = query_array[0]

index = ""

if len(query_array) > 1:

index = query_array[1]

postfix = sys.argv[3]

# get existing workspaces

workspaces_raw = subprocess.run(

"i3-msg -t get_workspaces", \

shell=True,

stdout=subprocess.PIPE

).stdout.decode("utf-8")

workspaces = json.loads(workspaces_raw)

# set default name

name = query

# pick a name if the input is a prefix of the input (priority 1)

names = [w["name"] for w in workspaces if w["name"].startswith(query)]

if len(names) > 0:

name = sorted(names)[0] + index

# pick a name if the input contains the input (priority 2)

else:

names = [w["name"] for w in workspaces if query in w["name"]]

if len(names) > 0:

name = sorted(names)[0] + index

# print chosen name

print(name)

# setup the command

cmd = "i3-msg '%s%s%s'" % (prefix, name, postfix)

print(cmd)

# run the command

subprocess.run(cmd, shell=True)

The i3 config

The Python script introduced above is then used in the i3 config as follows:

# rename workspace
bindsym $mod+m exec i3-input -P "Switch to: " -F "exec python3 ~/.config/i3/find_workspace.py 'workspace ' %s ''"
bindsym $mod+Shift+m exec i3-input -P "Move to: " -F "exec python3 ~/.config/i3/find_workspace.py 'move container to workspace ' %s ''"
bindsym $mod+Control+m exec i3-input -P "Rename: " -F "rename workspace to %s"

# rename workspace

bindsym $mod+m exec i3-input -P "Switch to: " -F "exec python3 ~/.config/i3/find_workspace.py 'workspace ' %s ''"

bindsym $mod+Shift+m exec i3-input -P "Move to: " -F "exec python3 ~/.config/i3/find_workspace.py 'move container to workspace ' %s ''"

bindsym $mod+Control+m exec i3-input -P "Rename: " -F "rename workspace to %s"

This allows to rename a workspace using MOD+Ctrl+m . For example using the name project2 . Then using MOD+m and typing p or p.2 will take you to that workspace. Similarly, MOD+Shift+m and typing p or p.2 will move the active container to the project workspace.

Conclusion

This made my life a lot easier since now it is possible to quickly create, rename, and move to arbitrarily named workspaces. I hope this helps a few people making their lives easier 😉 Finally, let me know if you have alternative or better solutions!

BibSonomy Scholar: A Chrome browser extension for BibSonomy

A while ago I was working on a Chrome browser extension for integrating BibSonomy, a social bookmarking and publication management platform, with the Google Chrome browser. The idea was to directly manage publication on the Google Scholar page without the cumbersome process of getting the BibTex, opening BibSonomy, pasting the BibTex, downloading the PDF, uploading the PDF … you get my point.

Google Scholar

Anyways, the extensions now directly integrates with Google Scholar allowing to manage publications without ever leaving the current page. This includes marking already posted publications, directly posting and deleting publications, automatic upload of PDFs, etc.. Here is a little screenshot:

Managing Bookmarks

After a while, I came across the issue of choosing a new laptop, having a million tabs open, clicking through them again and again, trying to remember which laptop an which page was the one I was interested in and why. So I thought that adding tags to URLs for a better categorization of my reviewed laptops and leaving notes on each page would be a tremendous help. While I know that Firefox supports tagging of bookmarks and I guess that there are quite a few browser extensions to support leaving notes, I did not want to get started with yet another system for managing things. So, since BibSonomy actually supports adding tags and descriptions for bookmarks, I added a “Quick Bookmark Button” to the BibSonomy Scholar extension.

Similar to the usual bookmark button in Chrome, this “Quick Bookmark Button” indicates whether the currently viewed URL has already been bookmarked. It also supports posting, deleting and updating bookmarks by clicking on the button or using a keyboard shortcut (CTRL+B). Furthermore, for leaving notes, it renders Markdown directly in the posting dialog. Here is a screenshot:

Conclusion

Overall, I think that the BibSonomy Scholar extension can be quite helpful and allows for a very “integrated” experience of BibSonomy. Of course I see many things which can still be improved and even more features which would be nice to implement. For example, all publications and bookmarks posted are public for now. Especially for bookmarks, this might not always be the desired option. Concerning additional features, I think it would be nice to handle pages from publishers containing publications differently than regular bookmarks, i.e., indicating if the corresponding publication has already been posted, or directly posting this publication instead of a bookmark. There are many more ideas floating around. I hope to find the time to add them at some point.

Finally, if you want to try out the extension have a look in the chrome web store and let me know about your experience with the extension. Also do not hesitate to post bug reports or feature requests or contribute yourself. The extension is open source and can be forked on Bitbucket. I will be happy to accept push request.

Hello world!

Welcome to my Blog! This is my first post where I try out some plug-ins before starting to write away.

Crayon Syntax Highlighter

This is Crayon Syntax Highlighter:

vim hallo.txt
export test=5
$test

vim hallo.txt

export test=5

$test

WP LaTeX

And this is WP LaTeX:
$e^{\i \pi} + 1 = 0$

BibSonomy/PUMA CSL

I also use BibSonomy, so I tried to install the corresponding plug-in in order to list some publications and research articles. This turned out to be a little cumbersome since it does not seem to be compatible with PHP7. When I try to activate the plug-in, I get two errors:

// error 1
Warning: Declaration of CurlHttpRequestProxy::send() should be compatible with CurlHttpRequest::send($fork = true, $sleep = 5) in WP_DIR/wp-content/plugins/bibsonomy-csl/lib/bibsonomy/CurlHttpRequestProxy.php on line 0 

// error 2
Fatal error: Uncaught Error: Class 'DOMDocument' not found in WP_DIR/wp-content/plugins/bibsonomy-csl/BibsonomyCsl.php:323 Stack trace: #0 WP_DIR/wp-includes/plugin.php(525): BibsonomyCsl->jal_install_data('') #1 WP_DIR/wp-admin/plugins.php(166): do_action('activate_bibson...') #2 {main} thrown in WP_DIR/wp-content/plugins/bibsonomy-csl/BibsonomyCsl.php on line 323

// error 1

Warning: Declaration of CurlHttpRequestProxy::send() should be compatible with CurlHttpRequest::send($fork = true, $sleep = 5) in WP_DIR/wp-content/plugins/bibsonomy-csl/lib/bibsonomy/CurlHttpRequestProxy.php on line 0

// error 2

Fatal error: Uncaught Error: Class 'DOMDocument' not found in WP_DIR/wp-content/plugins/bibsonomy-csl/BibsonomyCsl.php:323 Stack trace: #0 WP_DIR/wp-includes/plugin.php(525): BibsonomyCsl->jal_install_data('') #1 WP_DIR/wp-admin/plugins.php(166): do_action('activate_bibson...') #2 {main} thrown in WP_DIR/wp-content/plugins/bibsonomy-csl/BibsonomyCsl.php on line 323

The first error we can solve by modifying the file CurlHttpRequestProxy.php , i.e., we replace

public function send() {
    $this->curl();
}

public function send() {

$this->curl();

}

public function send($fork = true, $sleep = 5) {
    $this->curl($fork, $sleep);
}

public function send($fork = true, $sleep = 5) {

$this->curl($fork, $sleep);

}

The second error I was able to “fix” by installing the package php-xml :

apt-get install php-xml
service apache2 reload

1 2	apt-get install php-xml service apache2 reload

After this, the BibSonomy plug-in worked for me.