This container will help you to convert Jupyter notebooks to html pages.
Before using, make sure you have the latest version of Singularity installed.
The easiest thing is to pull the container from Singularity Hub where it's already built.
singularity pull --name latex.simg shub://vsoch/singularity-nbconvert:latex
Progress |===================================| 100.0%
Done. Container is at: /tmp/singularity/latex.simg
The container is a file sitting in your present working directory! To convert from Jupyter notebook (extension .ipynb) to pdf. It's primary function (called a runscript) is to perform a conversion, and that looks like this:
singularity run latex.simg --to pdf test_notebook.ipynb
[NbConvertApp] Converting notebook test_notebook.ipynb to pdf
[NbConvertApp] Support files will be in test_notebook_files/
[NbConvertApp] Making directory test_notebook_files
[NbConvertApp] Writing 17358 bytes to notebook.tex
[NbConvertApp] Building PDF
[NbConvertApp] Running xelatex 3 times: [u'xelatex', u'notebook.tex']
[NbConvertApp] Running bibtex 1 time: [u'bibtex', u'notebook']
[NbConvertApp] WARNING | bibtex had problems, most likely because there were no citations
[NbConvertApp] PDF successfully created
[NbConvertApp] Writing 52431 bytes to test_notebook.pdf
The call above can have any custom arguments that you would give to jupyter nbconvert. It doesn't necessarily have to convert to --pdf, and you can add other options. E.g., to see help:
singularity run latex --help
The above command targets the nbconvert executable directly (via Jupyter), but you can also execute a custom command, the container has all of the dependencies like jupyter, nbconvert, etc. installed. For example, here I am listing the contents of the conda installation bin:
singularity exec latex ls /opt/conda/bin
2to3 infotocap pip tabs
activate jsonschema pydoc tclsh
c_rehash jupyter pygmentize tclsh8.6
captoinfo jupyter-kernelspec python tic
chardetect jupyter-migrate python-config toe
clear jupyter-nbconvert python2 tput
conda jupyter-run python2-config tset
conda-env jupyter-troubleshoot python2.7 wheel
deactivate jupyter-trust python2.7-config wish
easy_install ncursesw6-config reset wish8.6
easy_install-2.7 openssl smtpd.py
idle pandoc sqlite3
infocmp pandoc-citeproc sqlite3_analyzer
Development with Singularity is easiest when you build a "sandbox," which is like building into a folder.
sudo singularity build --sandbox latex/ Singularity.latex
You can build the image with Singularity 2.4 with the following command:
sudo singularity build --writable latex.simg Singularity.latex
When it's time for a "production" build (squash fs image):
sudo singularity build latex.simg Singularity.latex