Software Publication new format migration

[Cmurilochem]

This PR closes #42.

Tasks

• [x] Move slides md file outside media/ and update figure paths.
• [x] Change slides extension from md to pmd
• [x] Add discussion.md file.
• [x] Add software_publication_pipeline.md file.
• [x] Add automating_software_publication.md file
• [x] Add exercise md file.
• [x] Add Reading material as an additional reading.md file.
• [x] Clean up main publication.md file.
• [x] Add numerical values to filenames to sort chapter order

[Cmurilochem]

@JaroCamphuijsen and @c-martinez. Could not really find dedicated guides for software publication. Available info often comes intertwined with software citation. Please, let me know of you know any besides those infos contained in Turing way and Carpentries (already included).

[c-martinez]

Hi @Cmurilochem , if I understand your question correctly, you are looking for guides that explain "Why is it important to publish software", more than "how do you make sure your software is citable (add a CFF file"?

Are the Software citation principles and CRedIT taxonomy more what you are looking for?

[Cmurilochem]

HI Carlos, this looks great. We settled on a new convention to sort the chapters by using numerical values at the start of each filename, so discussion.md should be 01.discussion.md, etc. Could you add this?

Thanks @JaroCamphuijsen. Done!

[Cmurilochem]

Hi @Cmurilochem , if I understand your question correctly, you are looking for guides that explain "Why is it important to publish software", more than "how do you make sure your software is citable (add a CFF file"?

Are the Software citation principles and CRedIT taxonomy more what you are looking for?

Thanks @c-martinez. The Software citation principles is one example that I was looking for and already helps so much! Thanks!!