BibTeX hacks

Sometimes \(\LaTeX\) compilation can give fairly unhelpful error messages like these: ! Missing $ inserted. $ l.190 ... pp. 225--236, 10.1007/978-3-642-31340-0_19 18. [Online]. ? If these error message are in .bbl file, when you are using BibTeX (.bib file) for bibliography then it is possible that these error messages are result of some special characters in your .bib file. I have seen it frequently that some DOI links contain some special characters. Following are some ways to get around these issues so that resulting document is rendered correctly.

• Escape underscore (_) with a backslash (\). In the above example, the original DOI url was 10.1007/978-3-642-31340-0_19 which was resulting into errors. Escaping the underscore with backslash fixed the issue for me: 10.1007/978-3-642-31340-0\_19 (notice a backslash before _19 near the end).
• Sometimes DOI urls would contain less-than (<) and greater-than (>) character. These characters do not result into errors during compilation but would be rendered incorrectly. Escaping these characters with backslash generally does not work and often result into errors similar to that shown near the top of the post. An example (fake) DOI url is 2/3<80::AID-HBM2>3.0 which was rendering upside down question mark and exclamation marks (probably because of issues with font encoding). I found that putting < in math mode helps to resolve this issue, i.e. replace with $<$ and $>$ so that new DOI url looks like 2/3$<$80::AID-HBM2$>$3.0.
• Changing font encoding by adding following lines in \(\LaTeX\) preamble can also help to resolve above issue with < and >, as discussed here. \usepackage[T1]{fontenc} \usepackage{lmodern}
• \(\LaTeX\) provides means to describe special characters like accents or umlauts using a special notation as described in following table hot-linked from official homepage. In addition, also check out this really great answer on stackexchange about accented letters.
  
  
  

Read more ...

Useful LaTeX tricks

\(\LaTeX\) word count

It can get difficult to keep track of accurate number of words in a \(\LaTeX\) document. TeXcount is a script for counting words in text and math equations in LaTeX documents. It can also generate very detailed html output with color-coded words types. TeXcount is part of Tex live and can be installed by installing texlive-extra-utils from Ubuntu repository. TeXcount also has a web interface. $ texcount document.tex FILE: document.tex Words in text: 6462 Words in headers: 48 Words in float captions: 274 Number of headers: 19 Number of floats: 4 Number of math inlines: 204 Number of math displayed: 8 texcount -v -html document.tex > word_count.html

\(\LaTeX\) diff

Usual diff programs may not do a great job of diffing two \(\LaTeX\) documents. Following are some of the alternative ways:

• Use wdiff with colordiff, similar to this stackexchange question: wdiff -n old.tex new.tex | colordiff | less -R
• Use latexdiff to determine differences and create a new LaTeX document with markup differences between two latex files. latexdiff can be found in Ubuntu repository and detailed description of usage can be found here. An example with beautifully typeset document is given below. latexdiff draft.tex revision.tex > diff.tex
• Another alternative could be to follow a simple guideline: Always start a new sentence in a new line and do not put any line-breaks in till the sentence ends. This allows traditional diff/merge programs like meld etc to work in a much better way.

\(\LaTeX\) and git

It is useful to use a version control system, like git, with \(\LaTeX\) documents. Here are some useful tips while working with git:

• Check git + LaTeX workflow for some great tips.
• Use latexdiff (also see above) in smarter way:
  • latexdiff <(git show checksumHash:file.tex) file.tex > diff.tex
  • Git-latexdiff can also be used for more advanced operations, like documents involving multiple .texfiles.
  • Check stackexchange discussion for more solutions.

\(\LaTeX\) on blogspot.com

MathJax is awesome. It is very easy to install and get \(\LaTeX\) equations working. \[ J_\alpha(x) = \sum\limits_{m=0}^\infty \frac{(-1)^m}{m! \, \Gamma(m + \alpha + 1)}{\left({\frac{x}{2}}\right)}^{2 m + \alpha} \]

Read more ...

Git cheat sheet

Git overview: Operation and File lifecycle

Image are hotlinked from Pro Git book, written by Scott Chacon.


Some of the commands listed here may use alias and/or configuration defined in ~/.gitconfig (see near the end of the post).

General operations

• Help with git: git --help # List available git commands git help <command> # More details about a specific command git <command> --help # More details about a specific command
• Display status of (local) repository: git status git st # Abbreviated using ~/.gitconfig git status -sb # Shorter output git status -uno # Hide details of untracked files
• Adding files to staging area: git add --dry-run <file1> <file2...fileN> # Dry run. No change in repository git add -n <file1> <file2...fileN> # Abbreviated flag for dry run git add <file1> <file2...fileN> # Add files to staging area git add *.m *.txt # Also supports wildcards
• Commit changes with message: git commit -m 'message' # Commit ONLY staged files git commit -a -m 'message' # Commit ALL changes, including unstaged files git ci 'message' # Abbreviated using ~/.gitconfig

Compare and inspect

• Changes in working directory: git diff --color # Colored diff git diff --stat # Show diffstat git diff --ignore-all-space # Ignore all whitespace git diff -w # Abbreviated --ignore-all-space git diff --ignore-space-changes # Ignore change in amount of whitespace git diff -b # Abbreviated --ignore-space-changes git diff -w --color-words # Colored word diff (rather than line diff) ignoring whitespace git diff --cached # Show changes in staged files git diff --staged # Same as --cached
• Inspect changes:
  (gitk is a tcl/tk based gui; Beginner tutorial) gitk --all # Browse all branches in local repository git log --oneline --graph # Inspect repository with summary of changes git log --oneline --graph --stat # Inspect repository with diffstats git whatchanged --oneline --graph # Similar to git log git lg # Abbreviated using ~/.gitconfig git show <commit> # Shows details of changes in commit
• Inspect changes beyond file renames:
  (Take care with renames: NEVER commit renames and modifications in the same commit. Check these as well.) git log --oneline --follow <filename> # Summary of changes git log --follow -p <filename> # Detailed changes gitk <filename> # Detailed changes using gitk

Branching

• Pro Git book has an excellent chapter on Branching and Merging.
• When typing in the name of a branch in following commands, try using TAB for auto-completion. It works most of the times.
• git branch # List local branches git branch -a # List all local and remote branches git checkout <branch_name> # Switch to other existing branch git checkout -b <branch_name> # Create a branch and switch to it git branch -d <branch name> # Delete a branch
• Compare branches: (order of branches matter) git diff <branch1>..<branch2> git diff --stat <branch1>..<branch2> # Generate diffstat git diff --name-status <branch1>..<branch2> # Short diff with only name and status git diff <branch1> <branch2> <filename> # Show differences only for a file git difftool <branch1> <branch2> <filename> # Use (external) diff tool
• Compare directories (branches/commits): (requires git version >=1.7.10) git difftool --dir-diff <commit1>..<commit2> git difftool --dir-diff <commit1> git difftool --dir-diff <branch1> git difftool --dir-diff <branch1>..<branch2>
• Remote branches & its management
  A very good and detailed description of remote branch management can be found in Pro Git book. # Pushing to remote git push origin localBranch # Pushes localBranch to origin git push -u origin localBranch # Pushes/sets association of localBranch to origin git push origin localBranch:remoteBranchName # Pushes localBranch to origin/remoteBranchName git push -u origin localBranch:remoteBranchName # Similar effect to -u above # Tracking or defining association. Also see this. git branch -u origin/remoteBranchName # Associates current branch to origin/remoteBranchName git branch -u origin/remoteBranchName localBranch # Associates localBranch to origin/remoteBranchName # Checking out from remote git fetch origin && git checkout remoteBranchName # Checkout origin/remoteBranchName git checkout -b localBranch origin/remoteBranchName # Checkout origin/remoteBranchName to localBranch git pull # Works after checking out or associating. # Deleting remote branch git push origin :remoteBranchName # Deletes origin/remoteBranchName git push origin --delete remoteBranchName # Deletes origin/remoteBranchName # Prune stale branch. See git remote branch deleted but still appears in 'branch -a' git remote prune origin # Removes all stale branches git fetch -p # Fetches from origin and prunes all stale branches # Show details of branch tracking information git remote -v show origin git branch -vv -a

Merge conflicts

Good read about three-way merge in git: Painless Merge... and Three way git... Here is a summary:

• Use git mergetool with meld. See ~/.gitconfig below. Mergetool would go through the conflicting files and create various new files with different file extensions so that it can use following command with meld (see git source code for more details). meld --output $MERGED $LOCAL $BASE $REMOTE
• $LOCAL: Contents of the file on the current branch. This is presented in Left-most column in meld.
• $REMOTE: Contents of the file to be merged. Right-most column in meld.
• $BASE: Common base of the merge OR half-finished merge where things started to fail. It is shown in middle column in meld. This is column which you would want to edit.
• $MERGED: File to which meld would write the merge resolution. It is not shown in meld. However, when $BASE is saved after editing, the output is written to $MERGED. Usually, $MERGED does not have any special extension like above files.
• Mergetool creates *.orig backup files while resolving merges. These are safe to remove once a file has been merged.

Tagging

• Create/Delete tags (Also see Pro Git book) git tag -a v1.4 -m 'my version 1.4' # Creates annotated tag to current commit git tag -a v1.4 -m 'my version 1.4 <checksum> # Adds tag to an older commit git tag -d <tag_name> # Deletes a tag
• List tags git tag -l # Lists tags in alphabetical order git tag # Lists tags in alphabetical order git tag -l -n1 # Lists tags along with annotation git tag -l <pattern> # Lists tags in matching a pattern git tag -l v13* # Lists tags starting with v13 git log --tags --simplify-by-decoration --pretty="%d" # Lists tags in chronological order git tl # Abbreviated by ~/.gitconfig git show <tag_name> # Show details of a tags
• Remote tags git ls-remote --tags origin # List all tags on origin git push origin <tag_name> # Push a tag to origin git push origin --tags # Push all tags to origin git push origin :refs/tags/<tag_name> # Delete a tag on origin

Others:

• Revert changes (excellent examples in git-reset documentation) git reset # Undo all add. Retains all changes in working tree git reset --hard # Undo add all. Discards all changes in working tree git reset HEAD <file_name> # Undo add one file. Retains all changes in working tree git reset --soft HEAD^ # Undo last commit. Retains all changes in working tree uncommitted (un-stage) all changes including files and folders:

~/.gitconfig

git difftool falls back to git mergetool config variables when the difftool equivalents have not been defined. If a merge resolution program is not specified, git mergetool will use the configuration variable merge.tool. [core] editor = emacs autocrlf = input [merge] tool = meld [alias] ci = commit -a -m st = status -sb rb = rebase lg = log --graph --all --format=format:'%C(auto)%h (%cd)%C(reset)%C(bold red)%d%C(reset) %C(bold green)%s%C(reset) %C(bold white)- %cn%C(reset)' --abbrev-commit --date=short df = diff -w --color-words dft = difftool -y tl = log --tags --simplify-by-decoration --format=format:'%C(auto)%h (%cd) -%C(reset)%C(bold red)%d%C(reset) %C(bold white)- %cn%C(reset)' --date=short --author-date-order [color] ui = true [color "status"] added = yellow changed = red untracked = cyan [push] default = current

Other great Git references:

• Pro Git book is a great reference to learn Git. Many of above commands are derived it.
• git ready provides tonnes of great git tips for all level of users.
• Visual Git Reference is another (short) reference to get idea and basics of Git.
• Git immersion is a full length Git tutorial starting from very basic.
• GitRef provides a quick reference to Git's syntax.
• Andrew Peterson's interactive Git cheat sheet.
• Another very extensive cheat sheet.

Read more ...

Dropbox Bug?

UPDATE: This is an expected behavior of dropbox. See relevant discussion at Dropbox Forums.

It seems that there is a dropbox bug which may affect the recovery of deleted files and folders in this specific situation. I will try to document and elaborate my observations in this post. In short, dropbox seems to be not able to recover a deleted folder if a new file with exact same name is replaced at the exact same location as the deleted folder. I am a free user of dropbox and I am not sure whether this is one of the free features. I found this particular problem 7-8 months back & I could recover the files from my personal backup, which is separate and independent from dropbox.

Here are the steps to reproduce the results. (I did backup all the data, so nothing was lost in reality. This is just a demonstration.) Here, I am going to delete a folder named 'Image Fun' from my dropbox which has some more files and folders in it. The goal is to check, if I can recover those files and folders inside the folder Image Fun.

1. Make sure Dropbox is running. (I am using Linux Mint 13)
2. Delete the folder Image Fun, with some files and folders.
3. Create a file with name Image Fun (no extensions) somewhere outside the Dropbox folder and then copy the file to the location of original Image Fun folder.
4. Log on to dropbox.com website and hit "Show deleted files". I can not see any folder which has been deleted & has name Image Fun. Though, I can see the file I created with the exact same name (among normal files, not deleted files).
5. Navigate to "Events" link on the left on dropbox website. This is the part where it gets interesting. I could see the notification which says that I deleted Image Fun and other 45 files in that folder. See the screenshot below. Now when I click on Image Fun, I am taken to home page where it highlighted the new Image Fun file.


6. Clicking on "output" link in events page (output was a folder inside the delete folder) showed a message in red saying "The folder /Image Fun/output is deleted" (screenshot below).


7. When I clicked on "45 more files" in the events page, it showed me a page where all the files were listed, but I could not click on any of them in order to recover. 


8. But, when I clicked on link "a1.jpg" in events page (where it said "You deleted a1.jpg and 45 more files"), I was taken to a page where I can actually see the older version of that particular file - a1.jpg. Clicking on version 0 shows the correct original file. 

9. You must have noticed the "Restore" button on a1.jpg link (above screenshot). When I clicked on it, something unexpected happened. The file which I created, with name Image Fun, was actually removed with the folder Image Fun and a1.jpg was restored in the folder. Now I could navigate to the folder and even see deleted files. This could be one way to recover the file. But I would count it as very unreliable method. It relies on finding and clicking on one particular file's deleted link and then recovering it. That particular link may actually get lost if many other files in other locations were also deleted. Events page after the recovery looks like this:

Hopefully, this will help to fix or address the issue I mentioned. It is probably an expected behavior. See relevant discussion at Dropbox Forums.

Read more ...