Code for Thought

The German RSE association met for its annual conference in the north-western city of Paderborn between 20 - 22 February 2023. Ca 150 participants attended including yours truly. It was the first such conference for the German RSE community since 2019. In this episode I'd like to share some impressions and discussions I had with you.

It is also the launch for a German language version of this podcast show, which is being published as a separate episode. 

• https://zenodo.org/communities/derse23 papers for the conference can be found here
• https://de-rse23.sciencesconf.org the conference home page for deRSE23
• https://de-rse.org/de/index.html the home page for the German RSE association

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

Linting and static code analysis in general are important tools in software engineering. Making sure the code builds and works is all very well. But a consistent coding style minimises maintenance efforts and future development. In this episode I'll introduce several tools that can make your code analysis easier: 

• pylint https://www.pylint.org 
• flake8 https://flake8.pycqa.org/en/latest/index.html 
• black https://black.readthedocs.io/en/stable/index.html 
• pre-commit https://pre-commit.com 
  • pre-commit hooks https://pre-commit.com/hooks.html

Other links you may find interesting and have been mentioned in the episode

• PEP8 https://peps.python.org/pep-0008/ 
• Google Python Style Guide https://google.github.io/styleguide/pyguide.html 
• YAML file format https://yaml.org 
• Stephen C. Johnson's paper on lint https://web.archive.org/web/20220123141016/https://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.56.1841&rep=rep1&type=pdf 
• Definition of spaghetti code (yes there is one) https://en.wikipedia.org/wiki/Spaghetti_code 
• Not mentioned in the episode, but you might be interested in this linter written in Rust https://github.com/charliermarsh/ruff 

Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.
https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/
ByteSized RSE link to Imperial College

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

In 2021, the Society for Research Software Engineering in the UK launched its first mentoring pilot scheme. 20 mentor/mentee pairs registered for it.
I spoke with the organisers of the scheme, Ania Brown and Sam Mangham to give us an overview of how this project came about. For the second part of this episode, I met with Mark Turner (Newcastle University, UK) and James Graham (King's College, London, UK) who signed up for the pilot project as mentor and mentee, to find out how it all went for them.

Here is the link to the Pilot program.
https://society-rse.org/events/pilot-mentoring-programme/

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

FOSDEM, the Free and Open Source Developers' European Meeting is back as an in person event at the Université Libre in the Belgium capital, Brussels. 

This is the first time I attended this conference and, indeed, the first time for reporting from a conference for this podcast. 
It's impossible to cover all of the 788 events at FOSDEM, but I wanted to share my impressions with you.

You can view the presentations following the links on the conference website
https://www.fosdem.org/2023/ 

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

Open Access is one of the pillars of Open Science. In this episode I am talking to Jean-Claude Guedon from the University of Montreal (Canada). Jean-Claude is one of the authors of the declaration of the Budapest Open Access Initiative from 2002. He is also an expert on scientific communication and its history. 
Who better to take us through the road that led to the Open Access declaration, what has become of it and where (we hope) it will go. 

Here a few links you might look up:

• https://www.budapestopenaccessinitiative.org The site of the Budapest Open Access Initiative - which includes the declaration
• https://en.wikipedia.org/wiki/Jean-Claude_Guédon Jean-Claude's bio on Wikipedia
• https://www.frontiersin.org/articles/10.3389/frma.2018.00008/full a history on the Garfield scientific indexing
• https://www.michaeleisen.org/blog/?p=1580 Michael Eisen another co-author of the Budapest declaration. This article is from 2014 where he talks about why he forsake open access
• https://en.wikipedia.org/wiki/Stevan_Hanard Stevan Hanard is another signatory of the Budapest declaration 
• A History of Scientific Journals: publishing at the Royal Society 1665 - 2015, UCL Press A Fyfe, N Moxham, J McDougall-Waters, C Moerk Roestvik, 2022

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

In this 4th episode of our ByteSized RSE mini series, we'll talk about Continuous Integration and Deployment. Both of each play an essential part in today's software development practices and can help you in your engineering tasks. There are a number of tools available for this to get you started, and they are listed below. In addition to that, check out Martin Fowler's block post as well as the code review pyramid links. 
After a brief introduction to the topic, I will be talking to Sarah Gibson from 2i2c. Sarah and I talked about JupyterHub in an episode last year. In this episode she talks about how important Continuous Integration and Deployment are in her daily work

Tools (not an exhaustive list - there is more):

• https://github.com/features/actions GitHub actions. 
• https://about.gitlab.com/features/continuous-integration/ CI with GitLab
• https://www.jenkins.io/ Jenkins
• https://www.travis-ci.com/ Travis

Blogs and other links:

• https://martinfowler.com/articles/continuousIntegration.html Martin Fowler's blog on Continuous Integration
• https://www.morling.dev/blog/the-code-review-pyramid/ Code Review Pyramid by Gunnar Morling
• https://github.com/sgibson91 - Sarah Gibson's web-site
• https://2i2c.org/ International Interactive Computing Collaboration, the company helping you built your Jupyter Hub infrastructure.

Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.

https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/ ByteSized RSE link to Imperial College

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

For this episode I met with Nicolas Thiery from Uni Paris-Saclay in summer 2022. Nicolas is an open source activist and has been leading the Candyce project in France to promote the use of Jupyter in the classroom. 
Nicolas highlights the advantages of using open source tools like Jupyter and how the pandemic accelerated their use.
And that we need education software engineers as well as research software engineers to train people up in computing in the future.

Here a few links, mentioned in the episode:

• https://nicolas.thiery.name/ Nicolas' homepage
• https://nicolas.thiery.name/CandyceProposal/ the proposal for Candyce (in French)
• https://www.maplesoft.com/ Maple products 
• https://quantstack.net/ Quantstack cloud solutions provider 

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

This last episode of ByteSized RSE before the end of 2022 is about testing your Python code.
Testing is an essential part of software development, and a lot of what we cover in this episode applies to any programming and scripting language. 

For Python, the two big frameworks being used are unittest and PyTest. Unittest is built into Python, whereas PyTest is a module you would need to install extra.

• https://docs.python.org/3/library/unittest.html the built in unit testing framework of Python
  • https://docs.python.org/3/library/unittest.mock.html mock testing in the unittest framework
  • https://docs.python.org/3/library/unittest.html#class-and-module-fixtures fixtures for classes and modules
• https://docs.pytest.org/en/7.2.x/ the popular PyTest framework
  • Mocking can be done with monkeypatch in PyTest https://docs.pytest.org/en/7.1.x/how-to/monkeypatch.html#
  • Fixtures in PyTest: https://docs.pytest.org/en/7.2.x/reference/fixtures.html 

Books mentioned

• Working effectively with legacy code, Michael Feathers, ISBN: 9780131177055, Pearson's, 2004
• Refactoring: Improving the Design of Existing Code, Martin Fowler, ISBN: 9780134757681, 2nd edition, Addison-Wesley Professional

Byte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.

https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/ ByteSized RSE link to Imperial College

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

As time moves quickly towards the end of 2022, let's talk about ageing. While in Paris in spring 2022 I had the pleasure to meet with Michael Rera, who is a biology researcher at one of the CNRS (the French national center for scientific research) institute right in the centre of Le Marais. 
Michael has been studying ageing in fruit flies (and other organisms) and has been using the SMURF assay in his studies. SMURF, as it turns flies blue as they near their end.
Michael is also very passionate about Open Science, and he is quoting Jon Tennant, who once said: 'Open Science is just Good Science'. 

Links:

• https://www.sciencedirect.com/science/article/pii/S0092867413006454 The Hallmarks of ageing by Carlos Lopez-Otin - 2013
• https://crowdid.hypotheses.org/548 A transcript of Jon Tennant's talk on Open Science
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812435/ How to catch a SMURF, Michael Rera et al. 2018

Michael can be found on Mastodon at 
@[email protected] 

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/

In this episode, the second on the theme of nuclear fusion, I meet with Simon Pinches. Simon works at ITER at the test reactor site in Cadarache, near Aix-en-Provence in Southern France. As section leader of the modelling and simulation team, he is responsible for crucial parts of the software. Contributions to the code (e.g. IMAS) are made from a wide range of different sources and we talk about how he manages to bring and keep it all together. 

Here a few links

• https://www.iter.org ITER 
• https://www.euro-fusion.org/ European Fusion Consortium
• https://conferences.iaea.org/event/251/contributions/20713/attachments/11191/16492/IMAS%20Tutorial%20-%20Pinches.pdf Introduction to the Integrated Modelling & Analysis Suite (IMAS)
• https://indico.euro-fusion.org/event/1246/sessions/728/attachments/1988/3798/IMAS_introduction_ACH_20210920.pdf The IMAS Data Dictionary: an introduction 
• https://www.sciencedirect.com/science/article/abs/pii/S0010465597001070 IMAS Integrated Modeling and Analysis System for the solution of optimal control problems
• https://ui.adsabs.harvard.edu/abs/2020APS..DPPJ10009M/abstract 
  OMAS: A Python Library to Interface with the ITER Integrated Modeling and Analysis Suite (IMAS)
• https://arxiv.org/abs/2006.09198 The initial step towards JOREK integration in IMAS

Get in touch

Thank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören!

Contact Details/ Coordonnées / Kontakt:

• Email mailto:[email protected]
• UK RSE Slack (ukrse.slack.com): @code4thought or @piddie 
• Bluesky: https://bsky.app/profile/code4thought.bsky.social
• LinkedIn: https://www.linkedin.com/in/pweschmidt/  (personal Profile)
  • LinkedIn: https://www.linkedin.com/company/codeforthought/ (Code for Thought Profile)

This podcast is licensed under the Creative Commons Licence:  https://creativecommons.org/licenses/by-sa/4.0/