Code for Thought

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' homepagehttps://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 touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 Pythonhttps://docs.python.org/3/library/unittest.mock.html mock testing in the unittest frameworkhttps://docs.python.org/3/library/unittest.html#class-and-module-fixtures fixtures for classes and moduleshttps://docs.pytest.org/en/7.2.x/ the popular PyTest frameworkMocking 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 mentionedWorking effectively with legacy code, Michael Feathers, ISBN: 9780131177055, Pearson's, 2004Refactoring: Improving the Design of Existing Code, Martin Fowler, ISBN: 9780134757681, 2nd edition, Addison-Wesley ProfessionalByte-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 CollegeGet in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 - 2013https://crowdid.hypotheses.org/548 A transcript of Jon Tennant's talk on Open Sciencehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5812435/ How to catch a SMURF, Michael Rera et al. 2018Michael can be found on Mastodon at @Michael__Rera@drosophila.social Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 linkshttps://www.iter.org ITER https://www.euro-fusion.org/ European Fusion Consortiumhttps://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 problemshttps://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 IMASGet in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 part of the Software Sustainability Institute's Research Software Camp on supporting mental health, SSI Research Associate and accredited mindfulness teacher Anita Banerji delivers this 10 minute meditation.Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 part of the Software Sustainability Institute's Research Software Camp on supporting mental health, SSI Research Associate and accredited mindfulness teacher Anita Banerji delivers this short breathing space mindfulness exercise.Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 part of the Software Sustainability Institute's Research Software Camp on supporting mental health, SSI Research Associate and accredited mindfulness teacher Anita Banerji delivers this self-compassion meditation.Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 of ByteSized we look at code reviews and GitHub. Code reviews have a long tradition (see the link to Michael Fagan's paper from 1976 below). Modern code management tools like GitHub, GitLab and others provide features to integrate code reviews with your overall development and deployment workflow.In this episode we look specifically at GitHub and how you can use the mechanism of 'pull requests' to start a conversation and review with your colleagues.In my conversation with Thibault Lestang from Imperial, we discuss what to look out for when doing a code review with your colleagues. And the fact that reviews are still useful, even if you are not using Github. Linkshttps://ieeexplore.ieee.org/document/5388086 Michael Fagan's paper on code inspectionshttps://git-scm.com/ The GIT versioning system book. Has a chapter on branchinghttps://github.com/features/code-review GitHub pages on code reviewsByte-sized RSE is presented in collaboration with the UNIVERSE-HPC project.https://www.imperial.ac.uk/computational-methods/rse/events/byte-sized-rse/ Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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/

Bastian Greshake-Tzovaras and I were accepted as Fellows of the Software Sustainability Institute around the same time. Bastian, trained in biology, has done a lot of work on "citizen science" and the Open Humans platform. The latter of which we discuss in a bit more detail as well as two projects Bastian has been working on.Linkshttps://www.openhumans.org Open Humans Platformhttps://academic.oup.com/gigascience/article/8/6/giz076/5523201 Journal article on open humans platformGet in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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 we speak to Shoaib Sufi and Rachael Ainsworth from the Software Sustainability Institute’s Community team about their Event Organisation Guide and some upcoming SSI events.The Event Organisation Guide brings together years of experience of the SSI in organising events. It covers different stages of the event organisation process from idea through feasibility, sign off, running your event project and closing down. The guide can be tailored to your needs, giving hints and tips on varied subjects such as venue, catering, budget, agenda, publicity and more. Read the Event Organisation Guide on Read the Docs.If you’d like to raise any issues, offer suggestions or get involved, you can use the GitHub project associated with the guide. Read how SSI Communications Manager Selina Aragon used the guide to plan the first Research Software Camp in this blog post and find out more about our upcoming Research Software Camp on supporting mental health in research.Read Shoaib’s blog post on Behind the scenes: SSI Event Organisation Guide which explores the how and why of the guide.Find out more about Collaborations Workshop 2023 (CW23). Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org 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/