Sphinx sources for the diffpy.org web page.
This repository contains 3 branches:
source sphinx sources for the web pagemaster sources compiled to HTML format that are published via GitHub pagesarchive converted subversion repository for the old diffpy.org sourcesPlease, see the Wiki for more information and tips about this project.
When adding a new publication to the list of references used within the website, add the citation text of the publication to the documentation only once as a named snippet in abbreviations.txt. For example:
.. |citeJuhasJac18| replace::
P. Juhás, J. N. Louwen, L. van Eijck, E. T. C. Vogt, S. J. L. Billinge,
`PDFgetN3: atomic pair distribution functions from
neutron powder diffraction data using ad hoc corrections
<https://doi.org/10.1107/S1600576718010002>`__,
*J. Appl. Crystallogr.*, **51**, 1492--1497 (2018)
|downloadJuhasJac18|Here, |citeJuhasJac18| is the name that can be used elsewhere in the documentation and the Sphinx documentation generator will replace all instances of this tag with the indented text following the replace:: directive.
Important: After defining the publication's tag as described above, make sure to add the publication to the list of publications maintained in publications.rst. Make sure that you add the reference to the proper section and do so in descending reverse chronological order (i.e., the newest citations should appear at the top of their respective sections).
Note: In this example, the citation is for a publication which describes a product of the DiffPy-CMI project (namely, PDFgetN3). For publications which describe a component of DiffPy-CMI, we provide a link to download the publication directly from the diffpy.org website. Here, the link is provided via the |downloadJuhasJac18| tag which is the identifier for another snippet within abbreviations.txt following the definition of |citeJuhasJac18|, seen here as:
.. |downloadJuhasJac18| image:: /images/pdficon_small.png
:target: /doc/pdfgetx/Juhas-jac-2018.pdfFurthermore, note that since the initial use of |downloadJuhasJac18| occurs within the indented text of the definition of |citeJuhasJac18|, the link to |downloadJuhasJac18| will appear everywhere |citeJuhasJac18| does.
Lastly, make sure that the linked publication has been included within this project's files, placed in an appropriate directory (typically, the parent directory of the project that the paper relates to). In the above example, the publication covers the PDFgetN3 feature of the pdfgetx package, thus it is placed within pdfgetx's documentation directory and referenced accordingly with the line
:target: /doc/pdfgetx/Juhas-jac-2018.pdfAdding references to publications that do not describe the release/use of a product within the DiffPy-CMI project (e.g., papers which use some component of DiffPy-CMI), we simply provide the usual citation text (with appropriate DOI link). To add a citation of this type, refer to the information in Reference Section, but disregard everything starting at, and following, the Note.
For releasing an updated version of a project, first follow the release procedure outlined in the group wiki for packaging and deploying your project.
In what follows, pdfgetx v2.1.1 was chosen to show example commands for the steps outlined.
After following the steps necessary for releasing your project, grab the set of documentation that will be provided with the deliverable upon user's request (typically, this would be something like the files hosted by GitHub on the GitHub releases page). Create a new directory for the updated version's documentation to live in
diffpy.github.io (source)$ mkdir static_root/doc/pdfgetx/2.1.1Copy the updated documentation to this directory
diffpy.github.io (source)$ tar --directory=static_root/doc/pdfgetx/2.1.1/ \
--strip-components=4 \
-vxzf ~/Downloads/diffpy.pdfgetx-2.1.1.tar.gz \
diffpy.pdfgetx-2.1.1/doc/manual/_build/PDFgetXNS3_manual.pdf
diffpy.github.io (source)$ tar --directory=static_root/doc/pdfgetx/2.1.1/ \
--strip-components=5 \
--exclude=objects.inv \
--exclude=.buildinfo \
-vxzf ~/Downloads/diffpy.pdfgetx-2.1.1.tar.gz \
diffpy.pdfgetx-2.1.1/doc/manual/_build/html/
diffpy.github.io (source)$ cp ~/Downloads/pdfgetxn3-examples.zip \
static_root/doc/pdfgetx/2.1.1/Make sure to include all relevant files (e.g., PDFgetXNS3_manual.pdf and pdfgetxn3-examples.zip), exclude any files we don't want to provide to the user (e.g., objects.inv and .buildinfo from diffpy.pdfgetx-2.1.1.tar.gz)
Finally, edit the landing page of your project (in the source branch) to properly document and provide the updated version of your project. Once the preceding steps are complete, see the instructions of the Publishing Changes section for publishing these changes.
For adding a new project to the website, see one of the existing projects (e.g., pdfgetx) as reference.
You will need to create a directory for the project to live in within (e.g., /static_root/doc/pdfgetx), then write a landing page for the project (e.g., /products/pdfgetx.rst) which will provide any necessary information or files needed for a user to use the project. Once this is complete, see Publishing New Version of Existing Project for steps on publishing the project.
In order to test and/or publish changes, activate a conda environment that has a working installation of Sphinx (or make sure you have the necessary packages installed at a system level). If unsure how to achieve this, see the Install Sphinx section of the projecct release wiki.
Make sure you have an active installation of Sphinx as per Publishing Changes, run the set of Sphinx validation command(s) to check that the static files that Sphinx will create to be served on the website are written properly:
diffpy.github.io (source)$ make linkcheck SPHINXOPTS="-W"NOTE: the "-W" flag forces warnings to be treated as errors. If you believe there is a falsely reported warning that should be ignored that is preventing the test from passing, rerun the above command with the SPHINXOPTS="-W" portion omitted.
Additionally, one can visually/user-experience validate that the changes are what is expected by running:
diffpy.github.io (source)$ make htmlThen opening /_build/html/index.html which will open a local instance of the website with the proposed changes in place.
In order to update the contents of diffpy.org, create a new branch off of source in your local fork of this repo and make whatever changes you need to. Once the desired edits are complete, follow the steps outlined in Testing Changes to verify the site won't break as a result of these changes. Finally, after verifying that the changes won't break things, push your changes to your fork and open a pull-request to submit the changes back into this repo.
First, follow the steps outlines in Testing Changes to verify that the changes won't mess things up (too bad). Note that these tests, as they currently exist, are not extensive and it's quite possible that something indeed may appear incorrectly on the website (hence the manual review portion). After reviewing the changes, have Sphinx generate the static files to be hosted on the website:
diffpy.github.io (source)$ make htmlPrepare the changes to be published:
diffpy.github.io (source)$ make publish-prepareFinally, publish the changes:
diffpy.github.io (source)$ make publish-push