From a3d2ce2a8adf0ad816ef3d68db8de541ab2323a6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Encarnaci=C3=B3n=20Mart=C3=ADnez=20=C3=81lvarez?= Date: Mon, 7 Jan 2019 16:42:18 +0100 Subject: [PATCH 01/54] Update Task_3.md --- content_development/Task_3.md | 1 + 1 file changed, 1 insertion(+) diff --git a/content_development/Task_3.md b/content_development/Task_3.md index 5c7dcfa..2205a54 100644 --- a/content_development/Task_3.md +++ b/content_development/Task_3.md @@ -309,6 +309,7 @@ Time to take your new GitHub skills for a test-run! All content development prim * Hollie Marshall, University of Leicester * Eric D. Wilkey, Western University, Canada * José-Raúl Canay-Pazos, Universidade de Santiago de Compostela, Spain +* Encarnación Martínez Álvarez, Spain [![CC0 Public Domain Dedication](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/) From 9462a84c67f93a2e4c0c61a6f73c00eba6a197b2 Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Wed, 9 Jan 2019 17:27:05 +0100 Subject: [PATCH 02/54] Update Task_2.md --- content_development/Task_2.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/content_development/Task_2.md b/content_development/Task_2.md index 16e7246..2564282 100644 --- a/content_development/Task_2.md +++ b/content_development/Task_2.md @@ -13,6 +13,7 @@ Don't forget you can join in the discussions over at our open [**Slack channel** Estimated time to complete: 45-60 minutes. ## Table of contents +- [Foreword](#foreword) - [Set up a GitHub repository](#Setup) - [Choose your GitHub repository](#Choose) - [Login to Zenodo](#Login) @@ -31,6 +32,10 @@ Estimated time to complete: 45-60 minutes.

The workflow for Task 2. Keep this handy as you work through the task!


+## Foreword + +Although the integration of GitHub and Zenodo makes it really easier to work with these tools nowadays (January 2019), it is important to stress that there are alternatives to GitHub (Gitlab, Bitbocker,...) and alternatives to Zenodo (Other repositories might be more suited to your community, you might ask your colleagues). For instance, one can work with Gitlab and manually upload each new versions to your university repository, getting a DOI. The principles (working with a version control system online, and archiving major versions +in a repository which provides a persistent unique identifier) can be applied in different workflow. ## Set up a GitHub repository From c63ad84bf754d7021299e3da83174d739594299d Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Wed, 9 Jan 2019 17:29:44 +0100 Subject: [PATCH 03/54] Update Task_2.md typo in link --- content_development/Task_2.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content_development/Task_2.md b/content_development/Task_2.md index 2564282..1db982e 100644 --- a/content_development/Task_2.md +++ b/content_development/Task_2.md @@ -13,7 +13,7 @@ Don't forget you can join in the discussions over at our open [**Slack channel** Estimated time to complete: 45-60 minutes. ## Table of contents -- [Foreword](#foreword) +- [Foreword](#Foreword) - [Set up a GitHub repository](#Setup) - [Choose your GitHub repository](#Choose) - [Login to Zenodo](#Login) From cda6089cb8f4b85b017c224642e851d9887dc71b Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 10:19:08 +0100 Subject: [PATCH 04/54] correct type --- content_development/Task_2.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content_development/Task_2.md b/content_development/Task_2.md index 1db982e..993ec5b 100644 --- a/content_development/Task_2.md +++ b/content_development/Task_2.md @@ -34,7 +34,7 @@ Estimated time to complete: 45-60 minutes.
## Foreword -Although the integration of GitHub and Zenodo makes it really easier to work with these tools nowadays (January 2019), it is important to stress that there are alternatives to GitHub (Gitlab, Bitbocker,...) and alternatives to Zenodo (Other repositories might be more suited to your community, you might ask your colleagues). For instance, one can work with Gitlab and manually upload each new versions to your university repository, getting a DOI. The principles (working with a version control system online, and archiving major versions +Although the integration of GitHub and Zenodo makes it really easier to work with these tools nowadays (January 2019), it is important to stress that there are alternatives to GitHub (Gitlab, Bitbucket,...) and alternatives to Zenodo (Other repositories might be more suited to your community, you might ask your colleagues). For instance, one can work with Gitlab and manually upload each new versions to your university repository, getting a DOI. The principles (working with a version control system online, and archiving major versions in a repository which provides a persistent unique identifier) can be applied in different workflow. ## Set up a GitHub repository From bd6032a8a02bc3d55d46086a50063691ddf34852 Mon Sep 17 00:00:00 2001 From: Tobias Steiner Date: Thu, 10 Jan 2019 10:57:03 +0100 Subject: [PATCH 05/54] added a few new ones plus switched one from false to true --- content_development/04-quizzes.md | 71 ++++++++++++++++++++++++++++--- 1 file changed, 65 insertions(+), 6 deletions(-) diff --git a/content_development/04-quizzes.md b/content_development/04-quizzes.md index 8978897..14b6112 100644 --- a/content_development/04-quizzes.md +++ b/content_development/04-quizzes.md @@ -27,12 +27,12 @@ --- -#### Open source isn’t licensed. True or false? +#### Open source is licensed. True or false? -- [ ] True -- [X] False +- [X] True +- [ ] False -**Answer:** False. Open source licenses are essentially terms of use and not items to be purchased, as can be the case for proprietary software. There are a variety of open source licence models, where each licence model has specific terms for the use and modification of code. +**Answer:** True. Open source licenses are essentially terms of use and not items to be purchased, as can be the case for proprietary software. There are a variety of open source licence models, where each licence model has specific terms for the use and modification of code. An open source vendor can charge you for a software licence and still be open source. There is not necessarily a direct relationship between a type of license and what you have to pay to obtain it. The ‘free’ part means that you have the freedom to access the source code and change it yourself providing you abide by the terms of the license. @@ -56,10 +56,69 @@ An open source vendor can charge you for a software licence and still be open so --- +#### Who founded the Free Software Foundation? + +- [ ] Lawrence Lessig +- [X] Richard Stallman +- [ ] Bill Gates +- [ ] Linus Torvalds + +**Answer:** The Free Software Foundation (FSF) was founded by **Richard Stallman** on 4 October 1985 to support the free software movement, which promotes the universal freedom to study, distribute, create, and modify computer software, with the organization's preference for software being distributed under copyleft ("share alike") terms, such as with its own GNU General Public License. *Source:* [Wikipedia](https://en.wikipedia.org/wiki/Free_Software_Foundation) + +--- + +#### Which of the following is a free software license? + +- [X] GPL +- [ ] OSD +- [ ] OSL +- [ ] GPS + +**Answer:** The GNU General Public License (GNU GPL or GPL) is a widely used free software license, which guarantees end users the freedom to run, study, share and modify the software. *Source:* [Wikipedia](https://en.wikipedia.org/wiki/GNU_General_Public_Licensen) + +--- + +#### This type of software is distributed with a single restriction: any redistributed version of the software must be distributed with the original terms of free use, modification, and distribution. What is it? + +- [ ] libre software +- [ ] shareware +- [X] free software +- [ ] adware + +**Answer:** Free software is software that can be freely used, modified, and redistributed with only one restriction: any redistributed version of the software must be distributed with the original terms of free use, modification, and distribution (known as copyleft). The definition of free software is stipulated as part of the GNU Project and by the Free Software Foundation. Free software may be packaged and distributed for a fee; the "free" refers to the ability to reuse it, modified or unmodified, as part of another software package. As part of the ability to modify, users of free software may also have access to and study the source code. + +The concept of free software is the brainchild of Richard Stallman, head of the GNU Project. The best known example of free software is Linux, an operating system that is proposed as an alternative to Windows or other proprietary operating systems. Debian is an example of a distributor of a Linux package. + +--- + +#### What does forking entail? + +- [ ] Forking occurs when an open source program is further developed publically by the community. +- [ ] Forking is the act of stabbing your overcooked chicken until it sticks to your eating utensil. +- [ ] Forking is when a proprietary source hardware design is used as a basis to create something different. +- [X] Forking is when open source software is developed into something different. + +**Answer:** Forking, also known as software forking, is the act of taking source code from open source software or program and further developing it into something different without changing the base offering. For example, Amazon's Fire OS is a forked version of Google's Android OS. Data center administrators may fork an open source software tool to tailor it to their particular requirements, without needing to share those changes back to the entire community. + +--- + +#### OSI stands for? + +- [ ] Open Source Index +- [ ] Open Source Image +- [X] Open Source Initiative +- [ ] Open Source Instant + +**Answer:** The **Open Source Initiative (OSI)** has been celebrating its 20th Anniversary in 2018. The “open source” label was created at a strategy session held on February 3rd, 1998 in Palo Alto, California. That same month, the OSI was founded. As a global non-profit, the OSI protects and promotes open source software, development and communities, championing software freedom in society through education, collaboration, and infrastructure, stewarding the Open Source Definition (OSD), and preventing abuse of the ideals and ethos inherent to the open source movement. *Source:* [opensource.org](https://opensource.org/) + +--- + + +### ... and now for something completely different + -## ... and now for something completely different +![...and now for something completely different](https://ichef.bbci.co.uk/images/ic/640x360/p01gk35d.jpg) -!(https://ichef.bbci.co.uk/images/ic/640x360/p01gk35d.jpg) --- From de33e10c13518e96ea71a60bd1e4d459b385c77e Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 11:02:55 +0100 Subject: [PATCH 06/54] Update MAIN.md --- content_development/MAIN.md | 1 + 1 file changed, 1 insertion(+) diff --git a/content_development/MAIN.md b/content_development/MAIN.md index 598e3d9..7a5d14a 100644 --- a/content_development/MAIN.md +++ b/content_development/MAIN.md @@ -453,6 +453,7 @@ However, your Open Source journey does not stop here! This was just the beginnin - [Paola Masuzzo](https://twitter.com/pcmasuzzo), Open Source Batman, Italy. - [Ivo Grigorov](https://twitter.com/OAforClimate), Open Source Robin, Denmark. - [Rutger Vos](https://twitter.com/rvosa), Open Sourceror, Naturalis Biodiversity Center, the Netherlands. +- [Julien Colomb](https://twitter.com/j_colomb), Open Ninja, Berlin. - [Jon Tennant](https://twitter.com/protohedgehog), Dinosaur Whisperer. **Know a way this content can be improved?** From 1f245cca1284c8ef8582c117c51e04a6cb302276 Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 11:08:10 +0100 Subject: [PATCH 07/54] add continuous integration of hyperlinks checks powered via travis --- .travis.yml | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 .travis.yml diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..8bb302b --- /dev/null +++ b/.travis.yml @@ -0,0 +1,7 @@ +language: ruby +rvm: + - 2.4.1 +before_script: + - gem install awesome_bot +script: + - awesome_bot README.md From ac1ea32136d4caedd31b533c3c6f37465eaaaa34 Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 11:25:23 +0100 Subject: [PATCH 08/54] Update .travis.yml --- .travis.yml | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 8bb302b..7cc0e19 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,7 +1,9 @@ -language: ruby -rvm: - - 2.4.1 -before_script: - - gem install awesome_bot +sudo: required + +services: + - docker + script: - - awesome_bot README.md + # Link Checks + - docker run -ti --rm -v $PWD:/mnt:ro dkhamsing/awesome_bot --allow-dupe --allow-redirect --skip-save-results `find . -name "*.md"` + From 409c156b7f444afbddc6a1504fc1dcd8f365f200 Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 11:42:53 +0100 Subject: [PATCH 09/54] correct hyperlink task1 --- content_development/Task_1.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content_development/Task_1.md b/content_development/Task_1.md index ed7b4b6..2e5a8f3 100644 --- a/content_development/Task_1.md +++ b/content_development/Task_1.md @@ -96,7 +96,7 @@ Whew! Don't worry about memorising *all* of these for now. Like any new skill, f You can probably see how some of these are fairly similar to things like save, copy, paste - standard workflow operations, but adapted for a software management process. There are a [few more](https://mirrors.edge.kernel.org/pub/software/scm/git/docs/gitglossary.html) too, but this should do for getting started. -If you are interested, most of these terms come from the underlying [Git system](https://git-scm.com). Git was built to allow developers to manage different versions of source code in a distributed manner, which is great. It has lots of features and the ability to do lots of complex stuff, written by a [very clever guy](https://www.linuxfoundation.org/blog/10-years-of-git-an-interview-with-git-creator-linus-torvalds/). However, the [user interface was not designed with new users in mind](https://xkcd.com/1597/), so it can be hard to learn. +If you are interested, most of these terms come from the underlying [Git system](https://git-scm.com). Git was built to allow developers to manage different versions of source code in a distributed manner, which is great. It has lots of features and the ability to do lots of complex stuff, written by a [very clever guy](https://www.linuxfoundation.org/blog/2015/04/10-years-of-git-an-interview-with-git-creator-linus-torvalds/). However, the [user interface was not designed with new users in mind](https://xkcd.com/1597/), so it can be hard to learn.

From 75ab4f22d8ef79af162a61b6edcd8d02a355fb42 Mon Sep 17 00:00:00 2001 From: protohedgehog Date: Thu, 10 Jan 2019 13:22:45 +0100 Subject: [PATCH 10/54] Updated broken links as in #65 --- MAIN.ipynb | 0 content_development/01-plan.md | 2 +- content_development/02-design.md | 2 +- content_development/04-quizzes.md | 2 +- content_development/MAIN.md | 2 +- key_elements.md | 24 ++++++++------------ production_toolkit/MODULE_DESIGN_PROTOCOL.md | 8 +++---- 7 files changed, 18 insertions(+), 22 deletions(-) create mode 100644 MAIN.ipynb diff --git a/MAIN.ipynb b/MAIN.ipynb new file mode 100644 index 0000000..e69de29 diff --git a/content_development/01-plan.md b/content_development/01-plan.md index 5e2fbba..c0add71 100644 --- a/content_development/01-plan.md +++ b/content_development/01-plan.md @@ -77,7 +77,7 @@ - [JOSS](http://joss.theoj.org) - [Free Software Foundation](https://www.fsf.org/) - [Open Source Initiative](https://opensource.org/) - - [Digital Freedom Foundation](http://www.digitalfreedomfoundation.org/) + - [Digital Freedom Foundation](https://en.wikipedia.org/wiki/Digital_Freedom_Foundation) (note that their website seems to be broken, Jan 2019) - [Ada Initiative](https://adainitiative.org/) - Mailing lists: diff --git a/content_development/02-design.md b/content_development/02-design.md index 62c7a08..4734aa0 100644 --- a/content_development/02-design.md +++ b/content_development/02-design.md @@ -13,7 +13,7 @@ - [Choose an open source license](https://choosealicense.com/). - [The Future of Research in Free/Open Source Software Development](http://www.ics.uci.edu/~wscacchi/Papers/New/FoSER-Scacchi-2010.pdf) (Scacchi, 2010). - - [The Scientific Method in Practice: Reproducibility in the Computational Sciences](http://datascienceassn.org/sites/default/files/The%2520Scientific%2520Method%2520in%2520Practice%2520-%2520Reproducibility%2520in%2520the%2520Computational%2520Sciences.pdf) (Stodden, 2010). + - [The Scientific Method in Practice: Reproducibility in the Computational Sciences](http://datascienceassn.org/sites/default/files/The%20Scientific%20Method%20in%20Practice%20-%20Reproducibility%20in%20the%20Computational%20Sciences.pdf) (Stodden, 2010). - [The case for open computer programs](https://www.nature.com/articles/nature10836) (Ince et al., 2012). - [Code Sharing Is Associated with Research Impact in Image Processing](https://infoscience.epfl.ch/record/206184/files/Vandewalle12.pdf) (Vandewalle, 2012). - [Current issues and research trends on open-source software communities](https://www.google.com/url?q=https://idus.us.es/xmlui/bitstream/handle/11441/32245/Current%2520issues%2520and%2520research%2520trends.pdf?sequence%3D1) (Martinez-Torres and Diaz-Fernandez, 2013). diff --git a/content_development/04-quizzes.md b/content_development/04-quizzes.md index 14b6112..c79a4d8 100644 --- a/content_development/04-quizzes.md +++ b/content_development/04-quizzes.md @@ -74,7 +74,7 @@ An open source vendor can charge you for a software licence and still be open so - [ ] OSL - [ ] GPS -**Answer:** The GNU General Public License (GNU GPL or GPL) is a widely used free software license, which guarantees end users the freedom to run, study, share and modify the software. *Source:* [Wikipedia](https://en.wikipedia.org/wiki/GNU_General_Public_Licensen) +**Answer:** The GNU General Public License (GNU GPL or GPL) is a widely used free software license, which guarantees end users the freedom to run, study, share and modify the software. *Source:* [Wikipedia](https://en.wikipedia.org/wiki/GNU_General_Public_License) --- diff --git a/content_development/MAIN.md b/content_development/MAIN.md index 7a5d14a..fa63f1b 100644 --- a/content_development/MAIN.md +++ b/content_development/MAIN.md @@ -124,7 +124,7 @@ Now, this all might be a little complex to remember. However, it can be summaris ## An Open Source checklist -There are a number of existing platforms and tools that support OSS and collaboration. The [Open Science Training Handbook](https://open-science-training-handbook.gitbook.io/book/es/02opensciencebasics/03openresearchsoftwareandopensource#knowledge) provides a check-list to use for evaluating the 'openness' of existing research software, based on the Open Source Definition above: +There are a number of existing platforms and tools that support OSS and collaboration. The [Open Science Training Handbook](https://open-science-training-handbook.gitbook.io/book/) provides a check-list to use for evaluating the 'openness' of existing research software, based on the Open Source Definition above: - [ ] Is the software available to download and install? diff --git a/key_elements.md b/key_elements.md index 2e4f07f..a33e31a 100644 --- a/key_elements.md +++ b/key_elements.md @@ -21,15 +21,10 @@ ### Who to involve -- Individuals: Paola Masuzzo, Naomi Penfold, Titus Brown Rene Bernard, Daniel Katz, Neil Chue Hong, Heidi Seibold, Anna - Kostikova. -- Organisations: Sustainable Software Institute, COKO Foundation, [Free Software - Foundation](https://www.fsf.org/licensing/). -- Other: [WSSSPE community](hhttp://wssspe.researchcomputing.org.uk), - editors of software peer-reviewed journals ([Open Research Software](http://openresearchsoftware.metajnl.com), - [JOSS](http://joss.theoj.org)). -- Testimonials of scientists who just published code explaining why they went through the trouble and of scientists who already use - cloud computing. Explanations about large initiatives (e.g. TCGA) moving their data into cloud and why it has huge impact. +- Individuals: Paola Masuzzo, Naomi Penfold, Titus Brown, Rene Bernard, Daniel Katz, Neil Chue Hong, Heidi Seibold, Anna Kostikova. +- Organisations: Sustainable Software Institute, COKO Foundation, [Free Software Foundation](https://www.fsf.org/licensing/). +- Other: [WSSSPE community](hhttp://wssspe.researchcomputing.org.uk),editors of software peer-reviewed journals ([Open Research Software](http://openresearchsoftware.metajnl.com), [JOSS](http://joss.theoj.org)). +- Testimonials of scientists who just published code explaining why they went through the trouble and of scientists who already use cloud computing. Explanations about large initiatives (e.g. TCGA) moving their data into cloud and why it has huge impact. ### Key resources: @@ -37,7 +32,7 @@ - [Journal of Open Research Software](https://openresearchsoftware.metajnl.com/) and the [Journal of Open Source Software](https://joss.theoj.org/). - [InsideDNA](https://insidedna.me/), [Galaxy](https://galaxyproject.org/) - Reproducible Research environments. -- [Google Compute Engine](https://cloud.google.com/compute/) (GCE), [Amazon Web Services](https://aws.amazon.com/) (AWS) - Cloud-based software environments. +- [Google Compute Engine](https://cloud.google.com/compute/) (GCE), [Amazon Web Services](https://aws.amazon.com/) (AWS) - Cloud-based software environments. - [Software Citation Tools](https://github.com/mozillascience/software-citation-tools), Mozilla Science Lab. - [Open Science, Open Data, Open Source](https://pfern.github.io/OSODOS/gitbook/) (Fernandes and Vos, 2017). - [Choose an open source license](https://choosealicense.com/). @@ -45,11 +40,11 @@ #### Research Articles and Reports - [The Future of Research in Free/Open Source Software Development](http://www.ics.uci.edu/~wscacchi/Papers/New/FoSER-Scacchi-2010.pdf) (Scacchi, 2010). -- [The Scientific Method in Practice: Reproducibility in the Computational Sciences](http://datascienceassn.org/sites/default/files/The%2520Scientific%2520Method%2520in%2520Practice%2520-%2520Reproducibility%2520in%2520the%2520Computational%2520Sciences.pdf) (Stodden, 2010). +- [The Scientific Method in Practice: Reproducibility in the Computational Sciences](http://datascienceassn.org/sites/default/files/The%20Scientific%20Method%20in%20Practice%20-%20Reproducibility%20in%20the%20Computational%20Sciences.pdf) (Stodden, 2010). - [The case for open computer programs](https://www.nature.com/articles/nature10836) (Ince et al., 2012). -- [Code Sharing Is Associated with Research Impact in Image Processing](https://infoscience.epfl.ch/record/206184/files/Vandewalle12.pdf) (Vandewalle, 2012). -- [Current issues and research trends on open-source software communities](https://www.google.com/url?q=https://idus.us.es/xmlui/bitstream/handle/11441/32245/Current%2520issues%2520and%2520research%2520trends.pdf?sequence%3D1) (Martinez-Torres and Diaz-Fernandez, 2013). -- [Ten simple rules for reproducible computational research](http://journals.plos.org/ploscompbiol/article?id%3D10.1371/journal.pcbi.1003285) (Sandve et al., 2013). +- [Code Sharing Is Associated with Research Impact in Image Processing](https://infoscience.epfl.ch/record/206184/files/Vandewalle12.pdf) (Vandewalle, 2012). +- [Current issues and research trends on open-source software communities](https://www.google.com/url?q=https://idus.us.es/xmlui/bitstream/handle/11441/32245/Current%2520issues%2520and%2520research%2520trends.pdf?sequence%3D1) (Martinez-Torres and Diaz-Fernandez, 2013). +- [Ten simple rules for reproducible computational research](http://journals.plos.org/ploscompbiol/article?id%3D10.1371/journal.pcbi.1003285) (Sandve et al., 2013). - [Practices in source code sharing in astrophysics](https://arxiv.org/abs/1304.6780) (Shamir et al., 2013). - [A systematic literature review on the barriers faced by newcomers to open source software projects](http://igor.pro.br/publica/papers/IST_SysReview_PrePrint.pdf) (Steinmacher et al., 2014). - [Knowledge sharing in open source software communities: motivations and management](https://pdfs.semanticscholar.org/f2a2/c5129cf5656af7acc7ffaf84c9c9bafe72c5.pdf) (Iskoujina and Roberts, 2015). @@ -85,3 +80,4 @@ - Document everything done by creating a README file. - Make sure to select an appropriate license for your repo. - Archive your versioned code in Zenodo. +- Integrate Git with RStudio diff --git a/production_toolkit/MODULE_DESIGN_PROTOCOL.md b/production_toolkit/MODULE_DESIGN_PROTOCOL.md index c55df42..63d3d55 100644 --- a/production_toolkit/MODULE_DESIGN_PROTOCOL.md +++ b/production_toolkit/MODULE_DESIGN_PROTOCOL.md @@ -8,8 +8,8 @@ This is a collaborative, team-based effort. Each module has its own repo on GitH 2. [Open Collaboration](https://github.com/OpenScienceMOOC/Module-2-Collaborative-Platforms) 3. [Reproducible Research and Data Analysis](https://github.com/OpenScienceMOOC/Module-3-Reproducible-Research-and-Data-Analysis) 4. [Open Research Data](https://github.com/OpenScienceMOOC/Module-4-Open-Research-Data) -5. [Open Research Software and Open Source](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Ope) -6. [Open Access to Research Papers](https://github.com/OpenScienceMOOC/Module-6-Open-Access-to-Resea) +5. [Open Research Software and Open Source](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/) +6. [Open Access to Research Papers](https://github.com/OpenScienceMOOC/Module-6-Open-Access-to-Research-Papers) 7. [Open Evaluation](https://github.com/OpenScienceMOOC/Module-7-Open-Evaluation) 8. [Public Engagement with Science](https://github.com/OpenScienceMOOC/Module-8-Public-Engagement-with-Science) 9. [Open Educational Resources](https://github.com/OpenScienceMOOC/Module-9-Open-Educational-Resources) @@ -27,14 +27,14 @@ This is a collaborative, team-based effort. Each module has its own repo on GitH 2. Expectations of what each will contribute and receive from taking part. 3. An explanation of time scales and commitments. 4. An exploration of the MOOC module, the design and development protocol, the knowledge that will be included, and what the challenges to be addressed are. - 5. The core learning outcomes and mission objectives for the module. These are all defined in the [Proposed Modules](https://opensciencemooc.eu/proposed-modules/) section of the companion website for the MOOC. + 5. The core learning outcomes and mission objectives for the module. These are all defined in the [Modules](https://opensciencemooc.eu/modules/) section of the companion website for the MOOC. 3. Setting a timeline and action plan for development. 4. Acquiring team information. Each team member will be required to provide: 1. A profile picture. 2. A short bio. 3. Twitter handle (where appropriate). 4. Personal website (where appropriate). -5. Publicising the team to the MOOC companion website, [here](https://opensciencemooc.eu/about-us/production-team/). +5. Publicising the team to the MOOC companion website, [here](https://opensciencemooc.eu/people/#production). ## The development process From df69666a4563e76b0b1c802ae0f47057e5ed4692 Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 13:32:00 +0100 Subject: [PATCH 11/54] add badge saying if all hyperlinks are working --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index dcf82b4..e3e550c 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,5 @@ +All hyperlinks work?: [![Build Status](https://travis-ci.org/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source.svg?branch=master)](https://travis-ci.org/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) + # Module 5: Open Research Software and Open Source ## Table of Contents From 2df9ab70fa15016c4ba180e422bf2b2ed16a206b Mon Sep 17 00:00:00 2001 From: Jon Tennant Date: Thu, 10 Jan 2019 12:39:26 +0000 Subject: [PATCH 12/54] Update README.md Edited link to Eliademy --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e3e550c..8a20ed2 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ Welcome to Module 5 of the Open Science MOOC! Here you can find important inform **STATUS**: LIVE -This module us now LIVE on [Eliademy](https://eliademy.com/app/a/courses/02d7338a7e). +This module us now LIVE on [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). The second release for this module is now also ready, and has been published on Zenodo: From 5761a8ee4ea7e400ab87391a9c58433f22c10276 Mon Sep 17 00:00:00 2001 From: Julien Colomb Date: Thu, 10 Jan 2019 13:53:17 +0100 Subject: [PATCH 13/54] correct hyperlink OpenScienceMOOC last to correct --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index b7888d6..962c8b6 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -17,7 +17,7 @@ If you want to contribute, please firstly join our open [Slack channel](https:// If you have questions about the project, please [email us](info@opensciencemooc.eu) directly. -Stay tuned on what's happening on Twitter with [@OpenSci_MOOC](https://twitter.com/OpenSci_MOOC). +Stay tuned on what's happening on Twitter with [@OpenSci_MOOC](https://twitter.com/OpenScienceMOOC). For partnerships, please see [here](https://opensciencemooc.github.io/site/About/). From f45ba1f36607c230589334b1947f6f04a84d4182 Mon Sep 17 00:00:00 2001 From: johave Date: Fri, 11 Jan 2019 19:24:01 +0100 Subject: [PATCH 14/54] Update 04-quizzes.md --- content_development/04-quizzes.md | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/content_development/04-quizzes.md b/content_development/04-quizzes.md index c79a4d8..b11da43 100644 --- a/content_development/04-quizzes.md +++ b/content_development/04-quizzes.md @@ -9,25 +9,27 @@ ## Questions -#### Contrary to proprietary software, Open Source means that anybody can change a OS project, just like on Wikipedia... that's just plain dangerous. True or false? +#### Contrary to proprietary software, Open Source means that anybody can change a OS project, just like on Wikipedia... that's just plain dangerous. True or false? - [ ] True - [X] False -**Answer:** This is a common misunderstanding. Wikipedia is a great way to understand collaborative innovation, but it's not a great euphemism for open source software. First, most open source projects are managed by "benevolent dictators" who have total control over what goes into their project. Contributors offer changes to these maintainers, and after some careful review they'll permit the change to be made. Second, open source software must perform the task it was designed to do. If it doesn't, the community discovers that pretty quickly. On Wikipedia, there's a chance that misinformation could stay in an entry for days before someone corrects it. Finally, it's important to understand the social and political aspect of open source projects. Open source contributors trade on their reputations. If you submit a bunch of good ideas, your stock goes up in the project's community. That's your reward: you solved your problem, and you get accolades from your friends in the community. Likewise, the maintainers don't want to be associated with bad software that's buggy or not useful to anyone. So because people want problems solved, and want to be respected by their peers, open source projects police their changes very carefully. (Source: [opensource.com](https://opensource.com/open-source-myths)) +**Answer:** This is a common misunderstanding. Wikipedia is a great way to understand collaborative innovation, but it's not a great euphemism for open source software. First, most open source projects are managed by "benevolent dictators" who have total control over what goes into their project. Contributors offer changes to these maintainers, and after some careful review they'll permit the change to be made. Second, open source software must perform the task it was designed to do. If it doesn't, the community discovers that pretty quickly. The Wikipedia community also has gatekeepers (what's their name again? see https://en.wikipedia.org/wiki/Wikipedia:Quality_control and https://en.wikipedia.org/wiki/Wikipedia:Editorial_oversight_and_control, remember Wikipedia is also open source) and quality assessment ppl who make sure Wikipedia entries are of high and growing quality. Different communities have different approaches of building content. +It's important to understand the social and political aspect of open source projects. Open source contributors trade on their reputations. If you submit a bunch of good ideas, your stock goes up in the project's community. That's your reward: you solved your problem, and you get accolades from your friends in the community. Likewise, the maintainers don't want to be associated with bad software that's buggy or not useful to anyone. So because people want problems solved, and want to be respected by their peers, open source projects police their changes very carefully. (Source: [opensource.com](https://opensource.com/open-source-myths)) --- -#### Open source can't be secure if anybody can openly find flaws and use them for exploits. True or false? +#### Open Source can't be secure if anybody can openly find flaws and use them for exploits. True or false? - [ ] True - [X] False -**Answer:** It's actually the other way around: open source is secure because anyone can find the flaws. If you ask security experts like Bruce Schneier, the National Security Agency, or any locksmith, they'll tell you that keeping your inner workings a secret is a great way to guarantee a security problem. The reason is simple: one developer isn't as a smart as all the developers. As Linux creator Linus Torvalds once said, "A thousand eyes make all bugs shallow." In other words, open source subjects you to the collective scrutiny of the community -- since they have as much to lose from your security problems as you do. Everyone works together to make things more secure. (Source: [opensource.com](https://opensource.com/open-source-myths)) +**Answer:** It's actually the other way around: open source is secure because anyone can find the flaws. If you ask security experts like Bruce Schneier, the (which country?) National Security Agency, or any locksmith, they'll tell you that keeping your inner workings a secret is a great way to guarantee a security problem. The reason is simple: one developer isn't as smart as all the developers. As Linux creator Linus Torvalds once said, "A thousand eyes make all bugs shallow." In other words, open source subjects you to the collective scrutiny of the community -- since they have as much to lose from your security problems as you do. Everyone works together to make things more secure. (Source: [opensource.com](https://opensource.com/open-source-myths)) --- -#### Open source is licensed. True or false? +#### Open Source is licensed by default (?). True or false? +I feel the question can be a bit misleading. Rather ask: Anyone can use Open Source code and content without mentioning the original copyright holders / copyright doies not apply. - [X] True - [ ] False @@ -38,7 +40,7 @@ An open source vendor can charge you for a software licence and still be open so --- -#### Open source has to be free of charge? +#### Open source has to be free of charge. - [ ] True - [X] False @@ -47,7 +49,7 @@ An open source vendor can charge you for a software licence and still be open so --- -#### Big Software Companies Don’t Use Open Source - true or false? +#### Big software companies don’t use Open Source - true or false? - [ ] True - [X] False From 7b25577b22266015f34dea10082c1c5a8470cddd Mon Sep 17 00:00:00 2001 From: Alberto Marocchino Date: Sat, 12 Jan 2019 00:34:01 +0100 Subject: [PATCH 15/54] update task3 with my name, Alberto --- content_development/Task_3.md | 1 + 1 file changed, 1 insertion(+) diff --git a/content_development/Task_3.md b/content_development/Task_3.md index 2205a54..e6f3b0f 100644 --- a/content_development/Task_3.md +++ b/content_development/Task_3.md @@ -310,6 +310,7 @@ Time to take your new GitHub skills for a test-run! All content development prim * Eric D. Wilkey, Western University, Canada * José-Raúl Canay-Pazos, Universidade de Santiago de Compostela, Spain * Encarnación Martínez Álvarez, Spain +* Alberto Albz Marocchino, Italy [![CC0 Public Domain Dedication](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/) From 2af7aba8575f99b0862ff5f3ac4eb48ea3c61422 Mon Sep 17 00:00:00 2001 From: protohedgehog Date: Thu, 17 Jan 2019 15:57:04 +0100 Subject: [PATCH 16/54] Updated new Slack links --- CONTRIBUTING.md | 6 +++--- README.md | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 962c8b6..4d3cd1e 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -7,19 +7,19 @@ These are the main contributing guidelines for the development of this MOOC, and * Invited experts as part of a core development team, led by one or two managers for each module. * Open participation, where anyone can contribute using the standard processes on GitHub. -Feedback and contributions of any form are welcomed. Feel free also to [contact us](https://opensciencemooc.github.io/site/Contact/) to discuss anything further. +Feedback and contributions of any form are welcomed. Feel free also to [contact us](https://opensciencemooc.eu/contact/) to discuss anything further. At the present, development is in early stages, as this is an entirely crowd-sourced and volunteer-led project. We are focusing inititally on [Module 5, Open Research Software and Open Source](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) to run as a pilot for testing and receiving feedback. After this, the [protocol](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/tree/master/production_toolkit) and content will be revised, and then applied accordingly to the development of the remaining modules. ## Contact us -If you want to contribute, please firstly join our open [Slack channel](https://openmooc-ers-slackin.herokuapp.com/). Secondly, please add yourself to the [Development team](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) on GitHub. Thirdly, please [add yourself](https://github.com/OpenScienceMOOC/site#how-to-add-a-person-to-be-listedrendered-on-the-website) to the main MOOC website. +If you want to contribute, please firstly join our open [Slack channel](https://osmooc.herokuapp.com/). Secondly, please add yourself to the [Development team](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) on GitHub. Thirdly, please [add yourself](https://github.com/OpenScienceMOOC/site#how-to-add-a-person-to-be-listedrendered-on-the-website) to the main MOOC website. If you have questions about the project, please [email us](info@opensciencemooc.eu) directly. Stay tuned on what's happening on Twitter with [@OpenSci_MOOC](https://twitter.com/OpenScienceMOOC). -For partnerships, please see [here](https://opensciencemooc.github.io/site/About/). +For partnerships, please see [here](https://opensciencemooc.eu/about/). ## Getting started diff --git a/README.md b/README.md index 8a20ed2..1b90a17 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,7 @@ Tennant, J. et al. (23/09/2018) Open Science MOOC: Module 5, Open Research Softw - [**Production Toolkit**](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/tree/master/production_toolkit) - This is where the basic protocols and outline for the module development are kept. It includes a tracking scheme as the content development progresses. -Don't forget to join us in our open [Slack group](https://openmooc-ers-slackin.herokuapp.com/)! The channel for this module is #module5opensource. You can also sign up to our mailing list [here](https://opensciencemooc.eu/contact/). To join the development team for the Open Science MOOC, anyone can openly add themselves [here](https://open-science-mooc-invite.herokuapp.com/). +Don't forget to join us in our open [Slack group](https://osmooc.herokuapp.com/)! The channel for this module is #module5opensource. You can also sign up to our mailing list [here](https://opensciencemooc.eu/contact/). To join the development team for the Open Science MOOC, anyone can openly add themselves [here](https://open-science-mooc-invite.herokuapp.com/). ## Rationale From 57469fc468878a9744418a66a25bfef77cecdef2 Mon Sep 17 00:00:00 2001 From: irrubio Date: Fri, 18 Jan 2019 17:30:45 +0100 Subject: [PATCH 17/54] New script --- Proposed_changes_TRIAL.R | 1 + 1 file changed, 1 insertion(+) create mode 100644 Proposed_changes_TRIAL.R diff --git a/Proposed_changes_TRIAL.R b/Proposed_changes_TRIAL.R new file mode 100644 index 0000000..21ac9bb --- /dev/null +++ b/Proposed_changes_TRIAL.R @@ -0,0 +1 @@ +#TRIAL \ No newline at end of file From cbe0ac3021827ea6febb53e7019d4103d4aad146 Mon Sep 17 00:00:00 2001 From: irrubio Date: Fri, 18 Jan 2019 17:45:46 +0100 Subject: [PATCH 18/54] Delete Proposed_changes_TRIAL.R --- Proposed_changes_TRIAL.R | 1 - 1 file changed, 1 deletion(-) delete mode 100644 Proposed_changes_TRIAL.R diff --git a/Proposed_changes_TRIAL.R b/Proposed_changes_TRIAL.R deleted file mode 100644 index 21ac9bb..0000000 --- a/Proposed_changes_TRIAL.R +++ /dev/null @@ -1 +0,0 @@ -#TRIAL \ No newline at end of file From 58bc5597fe1c99202a5a9d26d26adb636765f23a Mon Sep 17 00:00:00 2001 From: irrubio Date: Fri, 18 Jan 2019 17:54:19 +0100 Subject: [PATCH 19/54] Update Task_3.md --- content_development/Task_3.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content_development/Task_3.md b/content_development/Task_3.md index e6f3b0f..cfe59dd 100644 --- a/content_development/Task_3.md +++ b/content_development/Task_3.md @@ -311,6 +311,6 @@ Time to take your new GitHub skills for a test-run! All content development prim * José-Raúl Canay-Pazos, Universidade de Santiago de Compostela, Spain * Encarnación Martínez Álvarez, Spain * Alberto Albz Marocchino, Italy - +* Iratxe Rubio, Basque Centre for Climate Change BC3 [![CC0 Public Domain Dedication](https://img.shields.io/badge/License-CC0%201.0-lightgrey.svg)](https://creativecommons.org/publicdomain/zero/1.0/) From 97ab5ffab1b0e9a8693df827bba1e1683e832787 Mon Sep 17 00:00:00 2001 From: Jon Tennant Date: Tue, 22 Jan 2019 21:40:06 +0100 Subject: [PATCH 20/54] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1b90a17..8abe4d0 100644 --- a/README.md +++ b/README.md @@ -17,7 +17,7 @@ Welcome to Module 5 of the Open Science MOOC! Here you can find important inform **STATUS**: LIVE -This module us now LIVE on [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). +This module us now LIVE on [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). Check out the latest video online here: https://www.youtube.com/watch?v=1fwGliIyAZs The second release for this module is now also ready, and has been published on Zenodo: From 0dae690fba384abc0b4372fb41bccb3997a6d1ff Mon Sep 17 00:00:00 2001 From: protohedgehog Date: Wed, 23 Jan 2019 17:37:40 +0100 Subject: [PATCH 21/54] Minor edits, added readme file to reading list --- MAIN.ipynb | 0 README.md | 13 +++++-------- .../README.md | 3 +++ key_elements.md | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) delete mode 100644 MAIN.ipynb create mode 100644 Reading Material_Open Source and Open Research Software/README.md diff --git a/MAIN.ipynb b/MAIN.ipynb deleted file mode 100644 index e69de29..0000000 diff --git a/README.md b/README.md index 8abe4d0..514533d 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,3 @@ -All hyperlinks work?: [![Build Status](https://travis-ci.org/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source.svg?branch=master)](https://travis-ci.org/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) - # Module 5: Open Research Software and Open Source ## Table of Contents @@ -17,13 +15,9 @@ Welcome to Module 5 of the Open Science MOOC! Here you can find important inform **STATUS**: LIVE -This module us now LIVE on [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). Check out the latest video online here: https://www.youtube.com/watch?v=1fwGliIyAZs - -The second release for this module is now also ready, and has been published on Zenodo: +This module us now LIVE on [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). Check out the latest [video online here](https://www.youtube.com/watch?v=1fwGliIyAZs). -Ver. 1: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1325081.svg)](https://doi.org/10.5281/zenodo.1325081) - -Ver. 2: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1434288.svg)](https://doi.org/10.5281/zenodo.1434288) +The second release for this module is now also ready, and has been published on Zenodo: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1434288.svg)](https://doi.org/10.5281/zenodo.1434288) To cite this work, please use the following: @@ -59,6 +53,7 @@ Software and technology underpin modern science. There is an increasing demand f - [Paola Masuzzo](https://twitter.com/pcmasuzzo), Open Source Batman, Italy. - [Ivo Grigorov](https://twitter.com/OAforClimate), Open Source Robin, Denmark. - [Jon Tennant](https://twitter.com/protohedgehog), Rogue scientist, World. +- [Julien Colomb](https://twitter.com/j_colomb), Open Science Ninja, Berlin, Germany ## Key documents @@ -79,3 +74,5 @@ MOOC content license: [![CC0 Public Domain Dedication](https://img.shields.io/ba ### Code and software Software associated with the MOOCs, or any code snippets contained in the MOOCs, carry the following default license: [![License:MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT). If needed a different [OSI approved software license](https://opensource.org/licenses) may be chosen. + +All hyperlinks work?: [![Build Status](https://travis-ci.org/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source.svg?branch=master)](https://travis-ci.org/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) diff --git a/Reading Material_Open Source and Open Research Software/README.md b/Reading Material_Open Source and Open Research Software/README.md new file mode 100644 index 0000000..28b52d7 --- /dev/null +++ b/Reading Material_Open Source and Open Research Software/README.md @@ -0,0 +1,3 @@ +## Reading Material + +This is where the core additional reading materials for this module of the MOOC are kept. \ No newline at end of file diff --git a/key_elements.md b/key_elements.md index a33e31a..5556255 100644 --- a/key_elements.md +++ b/key_elements.md @@ -31,7 +31,7 @@ #### Tools - [Journal of Open Research Software](https://openresearchsoftware.metajnl.com/) and the [Journal of Open Source Software](https://joss.theoj.org/). -- [InsideDNA](https://insidedna.me/), [Galaxy](https://galaxyproject.org/) - Reproducible Research environments. +- [InsideDNA](https://insidedna.me/), [Galaxy](https://galaxyproject.org/) - Reproducible Research environments. - [Google Compute Engine](https://cloud.google.com/compute/) (GCE), [Amazon Web Services](https://aws.amazon.com/) (AWS) - Cloud-based software environments. - [Software Citation Tools](https://github.com/mozillascience/software-citation-tools), Mozilla Science Lab. - [Open Science, Open Data, Open Source](https://pfern.github.io/OSODOS/gitbook/) (Fernandes and Vos, 2017). @@ -45,7 +45,7 @@ - [Code Sharing Is Associated with Research Impact in Image Processing](https://infoscience.epfl.ch/record/206184/files/Vandewalle12.pdf) (Vandewalle, 2012). - [Current issues and research trends on open-source software communities](https://www.google.com/url?q=https://idus.us.es/xmlui/bitstream/handle/11441/32245/Current%2520issues%2520and%2520research%2520trends.pdf?sequence%3D1) (Martinez-Torres and Diaz-Fernandez, 2013). - [Ten simple rules for reproducible computational research](http://journals.plos.org/ploscompbiol/article?id%3D10.1371/journal.pcbi.1003285) (Sandve et al., 2013). -- [Practices in source code sharing in astrophysics](https://arxiv.org/abs/1304.6780) (Shamir et al., 2013). +- [Practices in source code sharing in astrophysics](https://arxiv.org/abs/1304.6780) (Shamir et al., 2013). - [A systematic literature review on the barriers faced by newcomers to open source software projects](http://igor.pro.br/publica/papers/IST_SysReview_PrePrint.pdf) (Steinmacher et al., 2014). - [Knowledge sharing in open source software communities: motivations and management](https://pdfs.semanticscholar.org/f2a2/c5129cf5656af7acc7ffaf84c9c9bafe72c5.pdf) (Iskoujina and Roberts, 2015). - [An open source pharma roadmap](http://journals.plos.org/plosmedicine/article?id%3D10.1371/journal.pmed.1002276) (Balasegaram et al., 2017). From ab196c6d2aa475189844952f3abe76e5d8ac9217 Mon Sep 17 00:00:00 2001 From: protohedgehog Date: Wed, 23 Jan 2019 17:55:30 +0100 Subject: [PATCH 22/54] Updated planning template to reflect latest changes --- .../README.md | 2 +- .../MOOC_planning_template.html | 774 ++++++++++++++++++ production_toolkit/MOOC_planning_template.md | 48 +- production_toolkit/README.md | 3 +- .../Video_management_protocol.md | 19 +- 5 files changed, 807 insertions(+), 39 deletions(-) create mode 100644 production_toolkit/MOOC_planning_template.html diff --git a/Reading Material_Open Source and Open Research Software/README.md b/Reading Material_Open Source and Open Research Software/README.md index 28b52d7..8e1d036 100644 --- a/Reading Material_Open Source and Open Research Software/README.md +++ b/Reading Material_Open Source and Open Research Software/README.md @@ -1,3 +1,3 @@ ## Reading Material -This is where the core additional reading materials for this module of the MOOC are kept. \ No newline at end of file +This is where the core additional reading materials for this module of the MOOC are kept. All articles here are Open Access, and thus can be freely read, shared, and re-used. You can also find links to them within the [live module for this MOOC](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html). \ No newline at end of file diff --git a/production_toolkit/MOOC_planning_template.html b/production_toolkit/MOOC_planning_template.html new file mode 100644 index 0000000..1df8de8 --- /dev/null +++ b/production_toolkit/MOOC_planning_template.html @@ -0,0 +1,774 @@ + + + + + + + + + + + + + + + +Mooc planning template + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + + + + + + + + + + + +
+

MOOC planning template

+
+

How to use this template

+

This is to provide a structured check list to track content development.

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  • For the ‘Delivered’ column, a simple Yes/No Scheme should be used.
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  • For the ‘Status’ column, please use one of the three symbols below.
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  • For the ‘Deadline’ column, please use a traditional dating scheme: 2018/05/10.
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  • For the ‘Comments’ column, insert any text as neccessary.
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+

Status traffic light scheme:

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Green: All looks good

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+Green +

Green

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Orange: Issues that can impact launch date

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+Orange +

Orange

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Red: Launch date in danger

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+Red +

Red

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+ +++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Design PhaseDeliveredStatus badgeDeadlineComments
Initiate and plan
Kick offYepGreen2018/05/10Sprint success!
Define target groupYepGreen2018/05/31Sprint success!
Refine learning objectives/outcomesYepGreen2018/05/31Sprint success!
Design course outlineYepGreen2018/05/31Sprint success!
Design project plan and timelineYepGreen2018/06/31
Identify promotion channelsYepGreen2018/06/31
Design and scripting
Identify key resourcesYepGreen2018/06/31Sprint success!
Design learner activitiesYepGreen2018/06/313/3 completed
Find existing key resourcesYepGreen2018/06/31Sprint success!
Write audio/video scriptsIn prepGreen2018/08/316/6 completed
Review all learning resourcesIn prep2018/11/31
Finalise all scriptsIn prep2018/11/31
Copyright strategyYepGreen2018/08/31
Recording and editing
Record on location/in studio
Edit all audio/visual material
Internal reviewing
Cross-check and review contentIn prepGreen2018/08/31Continuous process
Checks from Steering CommitteeIn prepGreen2018/08/31Continuous process
External testing and review
All reviewing conducted via GitHubIn prepGreen2018/08/31Continuous process
Existing channels from communications strategy
Internal reviewing and finalisation
Cross-review and check content
Final checks from Steering Committee
Implementation
Agreement on platformIn prepGreen2018/08/31
Module logo designedYepGreen2018/08/31
Module description and introductionYesGreen2018/07/31
Team member and guest lecturer agreementsYesGreen2018/07/31
Team member and guest lecturer profilesYesGreen2018/07/31
Course readings acquiredYesGreen2018/07/31
Port content to selected platform
All content deposited in ZenodoYepGreen2018/08/31Second release completed
Promotion
Content and communication calendar/strategy/timelineIn progressGreen
Identify relevant channels (mailing lists, social media and hashtags, organisations, individuals, websites, conferences)YesGreen2018/07/31
Images for use in social mediaYepGreen2018/07/31
Course title marketing checkYesGreen2018/07/31
Launch
Publicity startYesGreenDec 2018
Open and free for all, continuous, self-paced learning, 100% onlineYesGreenDec 2018Continuous, self-paced
Soft launchYesGreenDec 2018
Course launchYesGreen
Monitoring of learner experiences and reactionsIn progressJan 2019
Prepare to provide additional information if requiredPending
Reviewing and optimisation
Collate and review learner feedback at regular intervalsIn prep
Track any new information during course durationIn prep
Prepare evaluation reportPending
Evaluation meetingPending
Optimise content where relevantPending
+
+
+ + + + +
+ + + + + + + + diff --git a/production_toolkit/MOOC_planning_template.md b/production_toolkit/MOOC_planning_template.md index dda3c9e..c4473f5 100644 --- a/production_toolkit/MOOC_planning_template.md +++ b/production_toolkit/MOOC_planning_template.md @@ -42,28 +42,28 @@ Red: Launch date in danger | Define target group | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/05/31 | Sprint success! | | Refine learning objectives/outcomes | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/05/31 | Sprint success! | | Design course outline | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/05/31 | Sprint success! | -| Design project plan and timeline | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | | -| Identify promotion channels | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | | +| Design project plan and timeline | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | Seems to have been largely successful | +| Identify promotion channels | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | Comms strategy has been used widely | | **Design and scripting** | | | | | | Identify key resources | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | Sprint success! | | Design learner activities | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | 3/3 completed | | Find existing key resources | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/06/31 | Sprint success! | -| Write audio/video scripts | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | 2/6 completed | -| Review all learning resources | In prep | | | 2018/11/31 | -| Finalise all scripts | In prep | | | 2018/11/31 | -| Copyright strategy | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | | 2018/08/31 | +| Write audio/video scripts | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | 6/6 completed | +| Review all learning resources | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/11/31 | Continuous process | +| Finalise all scripts | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/11/31 | Worked like a charm | +| Copyright strategy | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | Done, vids all released without issue | | **Recording and editing** | | | | | -| Record on location/in studio | | | | | -| Edit all audio/visual material | | | | | +| Record on location/in studio | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2019/01/22 | Slight delay, but all good | +| Edit all audio/visual material | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2019/01/22 | OpenShot video editor works fine, or WeVideo | | **Internal reviewing** | | | | | | Cross-check and review content | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | Continuous process | | Checks from Steering Committee | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | Continuous process | | **External testing and review** | | | | | | All reviewing conducted via GitHub | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | Continuous process | -| Existing channels from communications strategy | | | | | +| Existing channels from communications strategy | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2019/01/23 | Seems to be going well at time of writing | | **Internal reviewing and finalisation** | | | | | -| Cross-review and check content | | | | | -| Final checks from Steering Committee | | | | | +| Cross-review and check content | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | | | +| Final checks from Steering Committee | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | | | | **Implementation** | | | | | | Agreement on platform | In prep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | | | Module logo designed | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | | @@ -71,23 +71,23 @@ Red: Launch date in danger | Team member and guest lecturer agreements | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/07/31 | | | Team member and guest lecturer profiles | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/07/31 | | | Course readings acquired | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/07/31 | | -| Port content to selected platform | | | | | +| Port content to selected platform | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | Jan 2019 | Eliademy seems 100% suitable for this project | | All content deposited in Zenodo | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/08/31 | Second release completed | | **Promotion** | | | | | -| Content and communication calendar/strategy/timeline | | | | | +| Content and communication calendar/strategy/timeline | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | Jan 2019 | Continuous processes | | Identify relevant channels (mailing lists, social media and hashtags, organisations, individuals, websites, conferences) | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/07/31 | | | Images for use in social media | Yep | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/07/31 | | | Course title marketing check | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | 2018/07/31 | | | **Launch** | | | | | -| Publicity start | | | | | -| Open and free for all, continuous, self-paced learning, 100% online | | | | | -| Soft launch | | | | | -| Course launch | | | | | -| Monitoring of learner experiences and reactions | | | | | -| Prepare to provide additional information if required | | | | | +| Publicity start | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | Dec 2018 | | +| Open and free for all, continuous, self-paced learning, 100% online | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | Dec 2018 | Continuous, self-paced | +| Soft launch | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | | Dec 2018 | +| Course launch | Yes | ![Green](https://img.shields.io/badge/Status-text-green.svg) | | | +| Monitoring of learner experiences and reactions | In progress | | | Jan 2019 | +| Prepare to provide additional information if required | Pending | | | | | **Reviewing and optimisation** | | | | | -| Collate and review learner feedback at regular intervals | | | | | -| Track any new information during course duration | | | | | -| Prepare evaluation report | | | | | -| Evaluation meeting | | | | | -| Optimise content where relevant | | | | | +| Collate and review learner feedback at regular intervals | In prep | | | | +| Track any new information during course duration | In prep | | | | +| Prepare evaluation report | Pending | | | | +| Evaluation meeting | Pending | | | | +| Optimise content where relevant | Pending | | | | diff --git a/production_toolkit/README.md b/production_toolkit/README.md index 016912d..c9c2653 100644 --- a/production_toolkit/README.md +++ b/production_toolkit/README.md @@ -1,10 +1,11 @@ # Production files -This repo is aimed to provide the production files for content development and management for each MOOC module. Each MOOC repo has its own copy of these files, which can be customised for each module as needed. +This folder is aimed to provide the production files for content development and management for each MOOC module. Each MOOC repo has its own copy of these files, which can be customised for each module as needed. Please see the [contributing guidelines](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/CONTRIBUTING.md) for how to use these files. ## Table of contents + - [MOOC planning template](MOOC_planning_template.md) - [Module design protocol](MODULE_DESIGN_PROTOCOL.md) - [Writing a script](Writing_a_script.md) diff --git a/production_toolkit/Video_management_protocol.md b/production_toolkit/Video_management_protocol.md index c3b9e51..e740419 100644 --- a/production_toolkit/Video_management_protocol.md +++ b/production_toolkit/Video_management_protocol.md @@ -1,12 +1,7 @@ Video management protocol ========================= -Videos can be powerful tools for communication in education. They can -range from lecture formats, to more informal chats and live -demonstrations. Videos are designed to be engaging and deliver content -in a more digestible way to help your learners achieve their objectives. -They can also be used to help convey complex topics in a more insightful -manner. +Videos can be powerful tools for communication in education. They can range from lecture formats, to more informal chats and live demonstrations. Videos are designed to be engaging and deliver content in a more digestible way to help your learners achieve their objectives. They can also be used to help convey complex topics in a more insightful manner. Preparation ----------- @@ -85,16 +80,14 @@ that even then there might be some restrictions that apply: If you would like to use your own content, please add a simple statement in the readme file (or a separate file) for each project repo stating: -*I/we grant the Open Science MOOC the right to re-use the content that -I/we provide for the project. Specifically, I/we give permission to:* +I/we grant the Open Science MOOC the right to re-use the content that +I/we provide for the project. Specifically, I/we give permission to: -- *Use the material for educational purposes for the project* +- Use the material for educational purposes for the project -- *Publish the educational videos to the MOOC platform, and share any - relevant ones on social media* +- Publish the educational videos to the MOOC platform, and share any relevant ones on social media -- *Release the content under a Creative Commons CC BY 4.0 - International license* +- Release the content under a Creative Commons CC BY 4.0 International license Tips for presenters ------------------- From 95b20479001659407bdc44dd54cacc10b5aba643 Mon Sep 17 00:00:00 2001 From: protohedgehog Date: Wed, 23 Jan 2019 20:17:05 +0100 Subject: [PATCH 23/54] minor updates --- content_development/README.md | 12 ++++-------- 1 file changed, 4 insertions(+), 8 deletions(-) diff --git a/content_development/README.md b/content_development/README.md index 7108c1a..6569dcc 100644 --- a/content_development/README.md +++ b/content_development/README.md @@ -2,15 +2,11 @@ These are the main content development files for this MOOC module. -**STATUS**: - -**LIVE! This module is now online and ready to go via [Eliademy](https://eliademy.com/app/a/courses/02d7338a7e).** +**STATUS**: **LIVE! This module is now online and ready to go via [Eliademy](https://eliademy.com/catalog/oer/module-5-open-research-software-and-open-source.html).** The second release for this module is now also ready, and has been published on Zenodo: -Version 2: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1434288.svg)](https://doi.org/10.5281/zenodo.1434288) - -Version 1: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1325081.svg)](https://doi.org/10.5281/zenodo.1325081) +[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1434288.svg)](https://doi.org/10.5281/zenodo.1434288) and an introductory video has also been [published](https://www.youtube.com/watch?v=1fwGliIyAZs). To cite this work, please use the following reference: @@ -18,7 +14,7 @@ Tennant, J. et al. (23/09/2018) Open Science MOOC: Module 5, Open Research Softw Please refer to the [contributing guidelines](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/CONTRIBUTING.md) before making changes here. -Anyone can join our [open Slack channel](https://openmooc-ers-slackin.herokuapp.com/) and [team on GitHub](https://open-science-mooc-invite.herokuapp.com/) for the whole MOOC project. +Anyone can join our [open Slack channel](https://osmooc.herokuapp.com/) and [open team on GitHub](https://open-science-mooc-invite.herokuapp.com/) for the whole MOOC project. ## Core content @@ -34,7 +30,7 @@ For notedown: ### In markdown format -- [**MAIN CONTENT**](MAIN.md) - The main content for this Module. +- [**MAIN CONTENT**](MAIN.md) - The main content for this Module. ([YouTube video](https://www.youtube.com/watch?v=BHrOEmKk5zM)) - [**TASK 1**](Task_1.md) - How to set up your first repository on GitHub. ([YouTube video](https://www.youtube.com/watch?v=AnftV9HBPSc&t=4s)) - [**TASK 2**](Task_2.md) - How to make your code citable using GitHub and Zenodo. ([YouTube video](https://www.youtube.com/watch?v=pjsbBQYOOaE&t=4s)) - [**TASK 3**](Task_3.md) - How to integrate Git with RStudio. ([YouTube video](https://www.youtube.com/watch?v=Q-6jfjSAspA)) From aa2c07d23971a5ed3f1c7c43e0890d1694fc6120 Mon Sep 17 00:00:00 2001 From: protohedgehog Date: Wed, 23 Jan 2019 20:22:10 +0100 Subject: [PATCH 24/54] Updated HTML versions, deleted redundant PDF chaff --- content_development/02-design.md | 6 +- content_development/03-recording.md | 3 +- content_development/MAIN.html | 26 +- content_development/Task_1.html | 2 +- content_development/Task_2.html | 4 +- content_development/Task_3.html | 19 +- ...7659baecdb0d0acef9d2f8fd1575986c7998dd.svg | 35 - content_development/tex2pdf.10300/input.aux | 36 - content_development/tex2pdf.10300/input.log | 693 ------------------ ...7659baecdb0d0acef9d2f8fd1575986c7998dd.svg | 35 - content_development/tex2pdf.15144/input.aux | 36 - content_development/tex2pdf.15144/input.log | 693 ------------------ 12 files changed, 35 insertions(+), 1553 deletions(-) delete mode 100644 content_development/tex2pdf.10300/297659baecdb0d0acef9d2f8fd1575986c7998dd.svg delete mode 100644 content_development/tex2pdf.10300/input.aux delete mode 100644 content_development/tex2pdf.10300/input.log delete mode 100644 content_development/tex2pdf.15144/297659baecdb0d0acef9d2f8fd1575986c7998dd.svg delete mode 100644 content_development/tex2pdf.15144/input.aux delete mode 100644 content_development/tex2pdf.15144/input.log diff --git a/content_development/02-design.md b/content_development/02-design.md index 4734aa0..e8db8e0 100644 --- a/content_development/02-design.md +++ b/content_development/02-design.md @@ -28,13 +28,13 @@ - [Perspectives on Reproducibility and Sustainability of Open-Source Scientific Software from Seven Years of the Dedalus Project](https://arxiv.org/abs/1801.08200) (Oishi et al., 2018). - [Good enough practices in scientific computing](https://doi.org/10.1371/journal.pcbi.1005510) (Wilson et al. ,2017). - 2. Design learner activities with clear instructions + 2. Design learner activities with clear instructions (completed) - Task 1: Create your first GitHub project - Task 2: Integrate a GitHub project with Zenodo - Task 3: Integrating Git and R Studio 3. Find resources (video, illustrations, screencasts, podcasts, assignments, quizzes, presentations) - - In preparation; requires new content to be produced + - Completed (including 2 quizzes) 4. Write concise, engaging video (and audio) scripts - Completed @@ -43,7 +43,7 @@ - In preparation 6. Finalise all scripts - - Pending (2/6) + - Completed 7. Copyright strategy - Completed \ No newline at end of file diff --git a/content_development/03-recording.md b/content_development/03-recording.md index d5adab2..1098ba0 100644 --- a/content_development/03-recording.md +++ b/content_development/03-recording.md @@ -17,5 +17,4 @@ See [Script](script_intro.md) for details. -For further information, please see the [video management protocol](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/production_toolkit/Video_management_protocol.md) and the information on how to [write a script](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/production_toolkit/Writing_a_script.md). - +For further information, please see the [video management protocol](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/production_toolkit/Video_management_protocol.md) and the information on how to [write a script](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/production_toolkit/Writing_a_script.md). \ No newline at end of file diff --git a/content_development/MAIN.html b/content_development/MAIN.html index c04a9e7..927fdaf 100644 --- a/content_development/MAIN.html +++ b/content_development/MAIN.html @@ -401,14 +401,14 @@

Principles of Open Source Software

An Open Source checklist

-

There are a number of existing platforms and tools that support OSS and collaboration. The Open Science Training Handbook provides a check-list to use for evaluating the ‘openness’ of existing research software, based on the Open Source Definition above:

+

There are a number of existing platforms and tools that support OSS and collaboration. The Open Science Training Handbook provides a check-list to use for evaluating the ‘openness’ of existing research software, based on the Open Source Definition above:

    -
  • Is the software available to download and install?

  • -
  • Can the software easily be installed on different platforms?

  • -
  • Does the software have conditions on the use?

  • -
  • Is the source code available for inspection?

  • -
  • Is the full history of the source code available for inspection through a publicly available version history?

  • -
  • Are the dependencies of the software (hardware and software) described properly? Do these dependencies require only a reasonably minimal amount of effort to obtain and use?

  • +
  • [ ] Is the software available to download and install?

  • +
  • [ ] Can the software easily be installed on different platforms?

  • +
  • [ ] Does the software have conditions on the use?

  • +
  • [ ] Is the source code available for inspection?

  • +
  • [ ] Is the full history of the source code available for inspection through a publicly available version history?

  • +
  • [ ] Are the dependencies of the software (hardware and software) described properly? Do these dependencies require only a reasonably minimal amount of effort to obtain and use?

Check, check, check, done! Simples.


@@ -421,13 +421,14 @@

The Open Source community and its governance

These definitions have now become widely adopted, both by international governments, as well as some large organisations such as the Mozilla Foundation and the Wikimedia Foundation. Major organisations in the FLOSS space include the UK’s Software Sustainability Institute, who produce valuable resources such as their recent Software Deposit Guidance for Researchers.

For individual projects

-

Within OSS projects, there are typically three main formal roles:

+

A typical open source project has the following types of formal roles:

    -
  • Maintainer;
  • -
  • Contributor; and
  • -
  • Committer.
  • +
  • Author: It is the person that created the project
  • +
  • Owner: The person/s who has administrative ownership over the organization or repository
  • +
  • Maintainers: Contributors who are responsible for driving the vision and managing the organizational aspects of the project. (They may also be authors or owners of the project.)
  • +
  • Contributors: The user that has already contributed to the project.
  • +
  • Community Members: People who use the project. They might be active in conversations, create new issues or express their opinion on the future project improvements.
-

A maintainer is a user with ‘commit’ access to implement suggested changes to the project. They have responsibility for the direction and improvement of the project. A contributor is someone who directly adds value to the project through issue resolution, code writing, or even external activities such as communications and event organisation. A committer is someone who can make ‘commits’ to the project (see Task 1).

Typically, roles are made public through either the README file, a Contributors file, or a separate team page for the project.


@@ -683,6 +684,7 @@

Development Team

  • Paola Masuzzo, Open Source Batman, Italy.
  • Ivo Grigorov, Open Source Robin, Denmark.
  • Rutger Vos, Open Sourceror, Naturalis Biodiversity Center, the Netherlands.
  • +
  • Julien Colomb, Open Ninja, Berlin.
  • Jon Tennant, Dinosaur Whisperer.
  • Know a way this content can be improved?

    diff --git a/content_development/Task_1.html b/content_development/Task_1.html index 4fe846d..4116c52 100644 --- a/content_development/Task_1.html +++ b/content_development/Task_1.html @@ -395,7 +395,7 @@

    The GitHub language

    Whew! Don’t worry about memorising all of these for now. Like any new skill, familiarity comes with experience.

    You can probably see how some of these are fairly similar to things like save, copy, paste - standard workflow operations, but adapted for a software management process. There are a few more too, but this should do for getting started.

    -

    If you are interested, most of these terms come from the underlying Git system. Git was built to allow developers to manage different versions of source code in a distributed manner, which is great. It has lots of features and the ability to do lots of complex stuff, written by a very clever guy. However, the user interface was not designed with new users in mind, so it can be hard to learn.

    +

    If you are interested, most of these terms come from the underlying Git system. Git was built to allow developers to manage different versions of source code in a distributed manner, which is great. It has lots of features and the ability to do lots of complex stuff, written by a very clever guy. However, the user interface was not designed with new users in mind, so it can be hard to learn.

    diff --git a/content_development/Task_2.html b/content_development/Task_2.html index e6bbb28..723a66b 100644 --- a/content_development/Task_2.html +++ b/content_development/Task_2.html @@ -317,6 +317,7 @@

    Task 2: How to make your code citable using GitHub and Zenodo

    Table of contents

      +
    • Foreword
    • Set up a GitHub repository
    • Choose your GitHub repository
    • Login to Zenodo
    • @@ -334,7 +335,8 @@

      Table of contents

      The workflow for Task 2. Keep this handy as you work through the task!

      -


      +


      ## Foreword

      +

      Although the integration of GitHub and Zenodo makes it really easier to work with these tools nowadays (January 2019), it is important to stress that there are alternatives to GitHub (Gitlab, Bitbucket,…) and alternatives to Zenodo (Other repositories might be more suited to your community, you might ask your colleagues). For instance, one can work with Gitlab and manually upload each new versions to your university repository, getting a DOI. The principles (working with a version control system online, and archiving major versions in a repository which provides a persistent unique identifier) can be applied in different workflow.

    Set up a GitHub repository

    diff --git a/content_development/Task_3.html b/content_development/Task_3.html index 882929c..9282ff9 100644 --- a/content_development/Task_3.html +++ b/content_development/Task_3.html @@ -315,6 +315,7 @@

    Task 3: How to integrate Git with R Studio

    Don’t forget you can join in the discussions over at our open Slack channel. Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here!

    Estimated time to complete: 30 minutes

    Estimate time saving once complete: Virtually infinite

    +

    NOTE A video guide version of this task is now available on YouTube.

    Table of contents