From fc1caf882e4c25afef267325f1836ec96a732625 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Daniel=20N=C3=BCst?= Date: Thu, 7 Nov 2024 14:23:25 +0100 Subject: [PATCH] fix some md warnings, add backlings to NL workshop pages --- .markdownlint.json | 3 +- guide/community-workflow-codechecker.md | 3 +- nl/workflow.md | 2 +- nl/workshop1.md | 6 +-- nl/workshop2.md | 69 ++++++++++--------------- nl/workshop3.md | 51 +++++++++--------- 6 files changed, 62 insertions(+), 72 deletions(-) diff --git a/.markdownlint.json b/.markdownlint.json index 339f013..ee1a93e 100644 --- a/.markdownlint.json +++ b/.markdownlint.json @@ -19,5 +19,6 @@ ] }, "MD013": false, - "MD041": false + "MD041": false, + "MD026": false } diff --git a/guide/community-workflow-codechecker.md b/guide/community-workflow-codechecker.md index dac04f8..72f8400 100644 --- a/guide/community-workflow-codechecker.md +++ b/guide/community-workflow-codechecker.md @@ -16,7 +16,7 @@ Now it's your turn. 1. Accept codechecking invitation by commenting on the issue 1. Create a repository in the CODECHECK GitHub organization, either by forking existing repository or creating new one and uploading materials 1. Create a new directory in that repository where all new files will go -1. Create a new document to write the CODECHECK certificate and *start documenting the ongoing codecheck now* +1. Create a new document to write the CODECHECK certificate and _start documenting the ongoing codecheck now_ The exact form of a codechecking procedure and form of documentation vary greatly, but there are some tools, such as [an R package](https://github.com/codecheckers/codecheck) to automate some steps, including [an Rmd template](https://github.com/codecheckers/codecheck/blob/master/inst/extdata/templates/codecheck/codecheck.Rmd); all of that is optional, as long as the final certificate contains the mandatory information 1. Open the manuscript and follow the instructions to reproduce a workflow 1. During the CODECHECK, contact the authors in case of problems; keep in mind the general [CODECHECK principles](/project/#the-codecheck-principles), especially “the codechecker records but does not fix” – unless it is a very trivial bug like pathnames; the authors can provide updated versions of code and documentation; however, the entire procedure should not be much more time-intensive than a normal peer review of a paper and not involve more than a few code revisions; the codechecker can always stop the process after a reasonable effort and close the issue as not successfully reproduced. @@ -103,4 +103,3 @@ Some further tips: ```md [![CODECHECK](https://codecheck.org.uk/img/codeworks-badge.svg)](https://doi.org/) ``` - diff --git a/nl/workflow.md b/nl/workflow.md index 6b6aa3b..3750e72 100644 --- a/nl/workflow.md +++ b/nl/workflow.md @@ -17,6 +17,6 @@ You are probably doing fine even if you digress from this documentation. 1. During the workshop, codecheckers download materials or clone the a repository 1. The workshop codecheckers create a new directory in their working environment where all new files go, and start documenting the ongoing codecheck; exact form of codechecking procedure and form of documentation vary greatly, but there are some tools, such as an R package to automate some steps, including a Rmd template; all of that is optional, as long as the final report contains the mandatory information 1. During codecheck, the workshop codecheckers can ask the authors (if present at the workshop) in case of encountered problems, keeping in mind the general Codecheck philosophy (especially “the codechecker records but does not fix” – unless it is a very trivial bug like pathnames) -1. The codecheckers summarize the process and outcome in a report and bundle it with all input and output files; this workshop codecheck bundle is then shared with the CodecheckNL project team via email or repository; the report should at least contain the information on who checked what and how; document for future self and other researchers; have a look at the available reports; most contain also optional information (compare [CODECHECK community workflow guide](/guide/community-workflow-overview)) +1. The codecheckers summarize the process and outcome in a report and bundle it with all input and output files; this workshop codecheck bundle is then shared with the CodecheckNL project team via email or repository; the report should at least contain the information on who checked what and how; document for future self and other researchers; have a look at the available reports; most contain also optional information (compare [CODECHECK community workflow guide](/guide/community-workflow-overview)) 1. The CodecheckNL project team checks the bundle and report, and together with the workshop codecheckers, revise where necessary; once ready, either the CodecheckNL project team or a corresponding codechecker upload the file on Zenodo or OSF, and [optionally] adds a pull request to original repository for the Codecheck badge 1. The CodecheckNL project team adds the new codecheck to the registry. diff --git a/nl/workshop1.md b/nl/workshop1.md index 973d0ad..a2d5b27 100644 --- a/nl/workshop1.md +++ b/nl/workshop1.md @@ -5,7 +5,9 @@ redirect_from: - /nl-workshop1/ --- -## UPDATE: We have successfully completed our first workshop! Read on... +\[[Go back to CHECK-NL main page](/nl/)\] + +## UPDATE: We have successfully completed our first workshop!

Delft workshop participants @@ -48,7 +50,6 @@ If you cannot make this workshop, there will be further opportunities later in the year as we plan three more workshops around the Netherlands. - ### What do I get if I submit my code? A codechecker will work with you during the session to check whether @@ -66,7 +67,6 @@ reproducibility of your work. By participating, you contribute towards making science more open and transparent AND increase the visibility of your own research! - ### Sounds good! What should I do? Are you interested in submitting code or data for this event, and helping to diff --git a/nl/workshop2.md b/nl/workshop2.md index 3689379..ec0d3da 100644 --- a/nl/workshop2.md +++ b/nl/workshop2.md @@ -5,81 +5,68 @@ redirect_from: - /nl-workshop2/ --- +\[[Go back to CHECK-NL main page](/nl/)\] + ## Update from UTwente: Small is beautiful (and reproducible) -On the stormy morning of 26th September, despite disrupted train schedules, a small but determined group of codecheckers assembled at the Faculty of Geosciences and Earth Observation at the University of Twente for the second codecheck workshop of our project. The trains may not have run that day, but the code sure did! +On the stormy morning of 26th September, despite disrupted train schedules, a small but determined group of codecheckers assembled at the Faculty of Geosciences and Earth Observation at the University of Twente for the second codecheck workshop of our project. The trains may not have run that day, but the code sure did! -We began our morning with a round of introductions, and an intro to the project by Frank Ostermann, our PI. Shortly after, Stephen Eglen, one of the founders of codecheck, joined us virtually to introduce the concept and logistics of codecheck, and how it aligns with the goals of reproducibility in science. Following Stephen, Frank took over again to run us through a practical application of codecheck, drawing on examples from codechecks he has done as part of reproducibility reviews at previous [AGILE conferences](https://reproducible-agile.github.io/). +We began our morning with a round of introductions, and an intro to the project by Frank Ostermann, our PI. Shortly after, Stephen Eglen, one of the founders of codecheck, joined us virtually to introduce the concept and logistics of codecheck, and how it aligns with the goals of reproducibility in science. Following Stephen, Frank took over again to run us through a practical application of codecheck, drawing on examples from codechecks he has done as part of reproducibility reviews at previous [AGILE conferences](https://reproducible-agile.github.io/). -We took a break for an excellent warm lunch in the faculty canteen -- much needed in the gloomy weather -- and then delved straight into breakout groups for the afternoon. Four authors joined us with their submissions, which the breakout groups began to codecheck. Three were finished on the spot, and a fourth was begun and we agreed to complete it after the session. And voila! Completed codecheck certificates from the workshop are already available, [have a look](https://osf.io/m7tze/)! +We took a break for an excellent warm lunch in the faculty canteen -- much needed in the gloomy weather -- and then delved straight into breakout groups for the afternoon. Four authors joined us with their submissions, which the breakout groups began to codecheck. Three were finished on the spot, and a fourth was begun and we agreed to complete it after the session. And voila! Completed codecheck certificates from the workshop are already available, [have a look](https://osf.io/m7tze/)! -We wrapped up the day with an interesting reflection session. Along with the authors and codecheckers, we were also joined by Prof. Dr Alfred Stein, editor of the Journal of Spatial Statistics, and (virtually) Daniel Nuest, another founder of Codecheck. One of our goals in this project is to explore ways in which the codecheck workflow can be incorporated into journal submission processes, and a lively discussion followed on what codecheck can add to the review process, where in the review workflow codecheck could fit, and who would conduct them. As always, issues of reward and recognition were central to our discussions about codecheck. Have an idea about this? Join us at the next codecheck session in [Rotterdam](https://codecheckRotterdam.eventbrite.com)! +We wrapped up the day with an interesting reflection session. Along with the authors and codecheckers, we were also joined by Prof. Dr Alfred Stein, editor of the Journal of Spatial Statistics, and (virtually) Daniel Nuest, another founder of Codecheck. One of our goals in this project is to explore ways in which the codecheck workflow can be incorporated into journal submission processes, and a lively discussion followed on what codecheck can add to the review process, where in the review workflow codecheck could fit, and who would conduct them. As always, issues of reward and recognition were central to our discussions about codecheck. Have an idea about this? Join us at the next codecheck session in [Rotterdam](https://codecheckRotterdam.eventbrite.com)! --------------------------------------------------------------------------------------------------- -## CALL FOR PAPERS/PREPRINTS/CODE: Are you a researcher in geosciences/environmental sciences interested in reproducible code and Open Science? We have the perfect opportunity for you!  - -As part of our NWO project [CHECK-NL](https://codecheck.org.uk/nl), **we are looking for researchers from the field of geosciences/environmental sciences based at a Dutch knowledge institution or university who would like their papers or projects to be “codechecked” during a live, one-day code-checking workshop on 26 September 2024** at the University of Twente.  A codecheck is a light-touch independent peer review to check that your code and data can generate the computational results in your paper or project (see more details [here](https://codecheck.org.uk/process/)).  - - +## CALL FOR PAPERS/PREPRINTS/CODE: Are you a researcher in geosciences/environmental sciences interested in reproducible code and Open Science? We have the perfect opportunity for you! -You can participate as a codechecker (i.e., a person reviewing code), or by submitting your own work to be checked (or both if you are up for it!). *Curious to know how it works? Read about our first [workshop in Delft](https://codecheck.org.uk/nl-workshop1/).* +As part of our NWO project [CHECK-NL](https://codecheck.org.uk/nl), **we are looking for researchers from the field of geosciences/environmental sciences based at a Dutch knowledge institution or university who would like their papers or projects to be “codechecked” during a live, one-day code-checking workshop on 26 September 2024** at the University of Twente.  A codecheck is a light-touch independent peer review to check that your code and data can generate the computational results in your paper or project (see more details [here](https://codecheck.org.uk/process/)). - +You can participate as a codechecker (i.e., a person reviewing code), or by submitting your own work to be checked (or both if you are up for it!). *Curious to know how it works? Read about our first [workshop in Delft](https://codecheck.org.uk/nl-workshop1/).* Anyone is welcome to participate at the workshop. Participation is free of cost and includes lunch. We have limited funding (on a first come, first served basis) for reimbursing train tickets for PhD (non-AiO) students. PhD candidates who participate in the workshop can reach out to us about getting credits for participation, provided their supervisors and institutions/departments also agree. - - - -## What do I get if I submit my paper or pre-print?   -A codechecker will work with you during the session to check whether your code and data can be run by others to generate the same or similar results.   +## What do I get if I submit my paper or pre-print?   -The codechecker will work with you to resolve any issues found during the code check, and make your code as reproducible as possible!   +A codechecker will work with you during the session to check whether your code and data can be run by others to generate the same or similar results.   -Upon completion, your paper will receive a codecheck certificate that confirms your results could be reproduced.  This can be shared, for instance with potential journal editors, to enhance the visibility and reproducibility of your work.    +The codechecker will work with you to resolve any issues found during the code check, and make your code as reproducible as possible!   -By participating, you contribute towards making science more open and transparent AND increase the visibility of your own research!   +Upon completion, your paper will receive a codecheck certificate that confirms your results could be reproduced.  This can be shared, for instance with potential journal editors, to enhance the visibility and reproducibility of your work. - -## Sounds good! What should I do?   +By participating, you contribute towards making science more open and transparent AND increase the visibility of your own research!   -Are you interested in participating in this event, and help contribute to promoting code reproducibility? Send an email to codechecknl@gmail.com **by 9 September 2024** with a *brief description of your paper/project, and links to your code and data*. This could be code related to:   +## Sounds good! What should I do?   -- A paper that you have recently published   +Are you interested in participating in this event, and help contribute to promoting code reproducibility? Send an email to  **by 9 September 2024** with a *brief description of your paper/project, and links to your code and data*. This could be code related to:   -- A preprint that is publicly available   +- A paper that you have recently published   -- Code and results files that have been or will be deposited in a repository, preferably  GitHub or GitLab   +- A preprint that is publicly available   -In each case, the code and data underlying the paper should be openly available, or you plan to make them available once the paper is published.  +- Code and results files that have been or will be deposited in a repository, preferably  GitHub or GitLab   +In each case, the code and data underlying the paper should be openly available, or you plan to make them available once the paper is published. +**Selected papers/projects will be notified in early September 2024. All authors are invited to register join the workshop.**   -**Selected papers/projects will be notified in early September 2024. All authors are invited to register join the workshop.**   +## What if I want to volunteer to be a codechecker instead? - - -## What if I want to volunteer to be a codechecker instead?  - - If you are interested in learning more about the codecheck process and becoming a codechecker, please register on our [eventbrite page](https://www.eventbrite.nl/e/codecheck-workshop-for-the-geosciences-and-environmental-sciences-tickets-945474348227?aff=oddtdtcreator) to volunteer to become a codechecker at the workshop on 26th September. The event will be held in person at the University of Twente. -### Why would I volunteer your time to code check other people's work?  +### Why would I volunteer your time to code check other people's work? -- Learn how others ensure reproducibility of their work   +- Learn how others ensure reproducibility of their work   - Gaining hands-on experience in peer reviewing code - Learn to make your own code more reproducible -- Contributing to more transparent science  - -  +- Contributing to more transparent science -*Interested but still have questions? Ask us!*  +*Interested but still have questions? Ask us!* -Write to us at codechecknl@gmail.com, we are happy to answer any questions!  +Write to us at , we are happy to answer any questions! -For questions related to the NWO project CHECK-NL, please contact Frank Ostermann (f.o.ostermann@utwente.nl) -  +For questions related to the NWO project CHECK-NL, please contact Frank Ostermann () diff --git a/nl/workshop3.md b/nl/workshop3.md index 3b55fde..8c2cdbd 100644 --- a/nl/workshop3.md +++ b/nl/workshop3.md @@ -5,44 +5,47 @@ redirect_from: - /nl-workshop3/ --- +\[[Go back to CHECK-NL main page](/nl/)\] + ## CALL FOR PAPERS/PRE-PRINTS/CODE: YOU can help increase reproducibility in the social sciences! **Are you from the social/behavioural sciences and interested in reproducible code and open science? We have the perfect opportunity for you!** - -As part of our NWO project [CHECK-NL](https://codecheck.org.uk/nl), **we are looking for researchers from the social and behavioural sciences at a Dutch knowledge institution or university who would like their papers or projects to be “codechecked” during a live, one-day code-checking workshop on 28 November 2024.** A [codecheck](https://codecheck.org.uk/process/) is a light-touch independent peer review to check that your code and data can generate the computational results in your paper or project.  -You can participate (a) by submitting your own work to be checked, (b) as a codechecker (that is, a person reviewing code as a participant in the workshop), or (c) both, if you are up for it! Read on to see how… +As part of our NWO project [CHECK-NL](https://codecheck.org.uk/nl), **we are looking for researchers from the social and behavioural sciences at a Dutch knowledge institution or university who would like their papers or projects to be “codechecked” during a live, one-day code-checking workshop on 28 November 2024.** A [codecheck](https://codecheck.org.uk/process/) is a light-touch independent peer review to check that your code and data can generate the computational results in your paper or project. + +You can participate (a) by submitting your own work to be checked, (b) as a codechecker (that is, a person reviewing code as a participant in the workshop), or (c) both, if you are up for it! Read on to see how… + +## What do I get if I submit my code? + +- A codechecker will work with you during the session to check whether your code and data can be run by others to generate the same or similar results. +- The codechecker will work with you to resolve any issues found during the code check, and make your code as reproducible as possible! +- Upon completion, your paper will receive a codecheck certificate that confirms your results could be reproduced.  This can be shared, for instance, with potential journal editors, to enhance the visibility and reproducibility of your work. +By participating, you contribute towards making science more open and transparent AND increase the visibility of your own research! -## What do I get if I submit my code?  +## Sounds good! What should I do? -- A codechecker will work with you during the session to check whether your code and data can be run by others to generate the same or similar results.  -- The codechecker will work with you to resolve any issues found during the code check, and make your code as reproducible as possible!  -- Upon completion, your paper will receive a codecheck certificate that confirms your results could be reproduced.  This can be shared, for instance, with potential journal editors, to enhance the visibility and reproducibility of your work.   -By participating, you contribute towards making science more open and transparent AND increase the visibility of your own research!  +Are you interested in participating in this event, and contribute to promoting code reproducibility? Send an email to  **by 11 November 2024** with **a brief description of your paper/project, and links to your code and data**. This could be code related to: -## Sounds good! What should I do?  +- A paper that you have recently published +- A preprint that is publicly available +- Code and results files that have been or will be deposited in a repository, preferably GitHub or GitLab -Are you interested in participating in this event, and contribute to promoting code reproducibility? Send an email to codechecknl@gmail.com **by 11 November 2024** with **a brief description of your paper/project, and links to your code and data**. This could be code related to:  -- A paper that you have recently published  -- A preprint that is publicly available  -- Code and results files that have been or will be deposited in a repository, preferably GitHub or GitLab  +In each case, the code and data underlying the paper should be openly available, or you plan to make them available once the paper is published. -In each case, the code and data underlying the paper should be openly available, or you plan to make them available once the paper is published. +**Selected papers/projects will be notified in mid November 2024**. All authors are invited to join the workshop. -**Selected papers/projects will be notified in mid November 2024**. All authors are invited to join the workshop. +## What if I want to participate as a codechecker instead? -## What if I want to participate as a codechecker instead? +You can register to participate in the workshop on our [eventbrite page](https://www.eventbrite.nl/e/codecheck-workshop-for-the-social-sciences-tickets-1024618099317?aff=oddtdtcreator), and volunteer to become a codechecker on 28th November. The event will be held in person on the EUR campus (see event page for details). -You can register to participate in the workshop on our [eventbrite page](https://www.eventbrite.nl/e/codecheck-workshop-for-the-social-sciences-tickets-1024618099317?aff=oddtdtcreator), and volunteer to become a codechecker on 28th November. The event will be held in person on the EUR campus (see event page for details). +### Why would I volunteer my time to codecheck other people's work? -### Why would I volunteer my time to codecheck other people's work? -- You will learn how others ensure reproducibility of their work (and pick up tips for yourself) -- You will gain hands-on experience in peer reviewing code -- You will be contributing to more transparent science +- You will learn how others ensure reproducibility of their work (and pick up tips for yourself) +- You will gain hands-on experience in peer reviewing code +- You will be contributing to more transparent science *PhD candiates at the Erasmus Graduate School for Social Sciences and the Humanities are eligible for 1.5 ECTS credit for participating in the workshop, see [this page](https://www.eur.nl/en/egsh/course/code-check-your-research) for more information.* -Interested but still have questions? Ask us! -Write to us at codechecknl@gmail.com, we are happy to answer any questions! - +Interested but still have questions? Ask us! +Write to us at , we are happy to answer any questions!