Code for Thought

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 declarationhttps://en.wikipedia.org/wiki/Jean-Claude_Guédon Jean-Claude's bio on Wikipediahttps://www.frontiersin.org/articles/10.3389/frma.2018.00008/full a history on the Garfield scientific indexinghttps://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 accesshttps://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, 2022Get in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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 workTools (not an exhaustive list - there is more):https://github.com/features/actions GitHub actions. https://about.gitlab.com/features/continuous-integration/ CI with GitLabhttps://www.jenkins.io/ Jenkinshttps://www.travis-ci.com/ TravisBlogs and other links:https://martinfowler.com/articles/continuousIntegration.html Martin Fowler's blog on Continuous Integrationhttps://www.morling.dev/blog/the-code-review-pyramid/ Code Review Pyramid by Gunnar Morlinghttps://github.com/sgibson91 - Sarah Gibson's web-sitehttps://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 CollegeGet in touchThank you for listening! Merci de votre écoute! Vielen Dank für´s Zuhören! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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' 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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! If you're like to support this show, you can leave a little tip at https://en.tipeee.com/code-for-thought-podcast/ Contact Details/ Coordonnées / Kontakt: Email mailto:peter@code4thought.org UK RSE Slack (ukrse.slack.com): @code4thought or @piddie US RSE Slack (usrse.slack.com): @Peter Schmidt Mastodon: https://fosstodon.org/@code4thought or @code4thought@fosstodon.org 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/