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.
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.
Development Team
Know a way this content can be improved?
diff --git a/content_development/MAIN.ipynb b/content_development/MAIN.ipynb index 7edecaa..8feeea4 100644 --- a/content_development/MAIN.ipynb +++ b/content_development/MAIN.ipynb @@ -130,19 +130,19 @@ "\n", "## An Open Source checklist\n", "\n", - "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:\n", + "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:\n", "\n", - "* Is the software available to download and install?\n", + "- [ ] Is the software available to download and install?\n", "\n", - "* Can the software easily be installed on different platforms?\n", + "- [ ] Can the software easily be installed on different platforms?\n", "\n", - "* Does the software have conditions on the use?\n", + "- [ ] Does the software have conditions on the use?\n", "\n", - "* Is the source code available for inspection?\n", + "- [ ] Is the source code available for inspection?\n", "\n", - "* Is the full history of the source code available for inspection through a publicly available version history?\n", + "- [ ] Is the full history of the source code available for inspection through a publicly available version history?\n", "\n", - "* 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?\n", + "- [ ] 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?\n", "\n", "Check, check, check, done! Simples.\n", "\n", @@ -160,13 +160,13 @@ "\n", "### For individual projects\n", "\n", - "Within OSS projects, there are typically three main formal roles:\n", + "A typical open source project has the following types of formal roles:\n", "\n", - "* **Maintainer**;\n", - "* **Contributor**; and\n", - "* **Committer**.\n", - "\n", - "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](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/Task_1.md)).\n", + "- **Author**: It is the person that created the project\n", + "- **Owner**: The person/s who has administrative ownership over the organization or repository \n", + "- **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.)\n", + "- **Contributors**: The user that has already contributed to the project.\n", + "- **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.\n", "\n", "Typically, roles are made public through either the `README` file, a Contributors file, or a separate team page for the project.\n", "\n", @@ -459,6 +459,7 @@ "- [Paola Masuzzo](https://twitter.com/pcmasuzzo), Open Source Batman, Italy.\n", "- [Ivo Grigorov](https://twitter.com/OAforClimate), Open Source Robin, Denmark.\n", "- [Rutger Vos](https://twitter.com/rvosa), Open Sourceror, Naturalis Biodiversity Center, the Netherlands.\n", + "- [Julien Colomb](https://twitter.com/j_colomb), Open Ninja, Berlin.\n", "- [Jon Tennant](https://twitter.com/protohedgehog), Dinosaur Whisperer.\n", "\n", "**Know a way this content can be improved?**\n", diff --git a/content_development/MAIN.md b/content_development/MAIN.md index 598e3d9..93ee8ac 100644 --- a/content_development/MAIN.md +++ b/content_development/MAIN.md @@ -11,7 +11,7 @@ output: - [Introduction](#Introduction) - [What is Open Source Software](#What_OSS) - [Principles of Open Source Software](#Principles) - - [The Open Source community, governance, and contributions](#OS_Community) + - [The Open Source community and its governance](#OS_Community) - [Existing platforms and tools for Open Source Software](#Platforms) - [Open Source Software used in research](#Research) - [Getting Started with OSS - FAQ](#FAQ) @@ -30,7 +30,7 @@ Welcome to **Module 5** of the Open Science MOOC: **Open Research Software and O This module has been developed [in the open](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source) through collaboration by an international team of [Open Source afficianados](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/README.md#development-team-). Everything you see here has been developed in the open through interactive feedback and collaboration from the wider community. It comprises a series of videos, infographics, text-based reading, and practical tasks for you to sink you teeth into. -Don't forget you can join in the discussions over at our open [**Slack channel**](https://openmooc-ers-slackin.herokuapp.com/). Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here! +Don't forget you can join in the discussions over at our open [**Slack channel**](https://osmooc.herokuapp.com/). Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here! ### Who is this module for? @@ -84,11 +84,11 @@ Some of common advantages for developers include: - Based on open standards available to everyone. -As such, the main advantages for researchers (users) include **lower costs**, **increased transparency**, **increased security and stability**, **no vendor 'lock in' with increased user control**, and **overall higher quality**. Furthermore, sharing OSS allows researchers to receive credit for their efforts, for example through direct software citation [(Smith et al., 2016)](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Smith%20et%20al.%2C%202016.pdf). +As such, the main advantages for researchers (users) include **lower costs**, **increased transparency**, **increased security and stability**, **no vendor 'lock in' with increased user control**, and **overall higher quality**. Furthermore, sharing OSS allows researchers to receive credit for their efforts, for example through direct software citation ([Smith et al., 2016](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/Reading%20Material_Open%20Source%20and%20Open%20Research%20Software/Smith%20et%20al.%2C%202016.pdf)). Commonly used OSS include the [Mozilla Firefox](https://www.mozilla.org/en-US/firefox/) internet browser and the [LibreOffice](https://www.libreoffice.org/) full office suite. LibreOffice is similar to the popular Microsoft Office, including a word processor, spreadsheet manager, and slide presentation software, but is completely free and Open Source. -Some regard the OSS movement to represent a counter-movement to neoliberalism and privatisation, through defiance of regulations and norms in the construction and re-use of information, and a potential transformation of modern-day capitalism through making software abundantly available with minimal effort. See [The free/open source software movement: Resistance or change?](http://www.redalyc.org/html/742/74212712006/) by Panayiota Georgopoulou for more on this topic. +Some regard the OSS movement to represent a counter-movement to neoliberalism and privatisation, through defiance of regulations and norms in the construction and re-use of information, and a potential transformation of modern-day capitalism through making software abundantly available with minimal effort. See [The free/open source software movement: Resistance or change?](https://doi.org/10.15448/1984-7289.2009.1.5569) by Panayiota Georgopoulou for more on this topic.@@ -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? @@ -144,13 +144,17 @@ Check, check, check, done! Simples. ## The Open Source community and its governance -There are two main camps within the free software community: The **free software movement**, and the **OSS movement**. Both have differing ideologies based on user liberties and the practical applications of software. Often, the term 'FLOSS' is used to reconcile these two political camps, and means 'Free/Libre and Open Source Software'; Libre being French and Spanish for 'free' in the context of freedom. +There are two main camps within the free/libre and open source software (FLOSS) community: The **free software movement**, and the **open source software movement** (OSS). Both have differing ideologies based on user liberties and the practical applications of software. The term 'FLOSS' is used as a overaching neutral term to refer to both; libre being French and Spanish for 'free' in the context of freedom. -The core principle of re-use is what separates OSS from 'Free Software'. Free and Open Source Software (FOSS) is an inclusive term to describe software that can be classified as both free and Open Source. A good example of FOSS is the [Ubuntu Linux](https://www.ubuntu.com/) operation system. +In a similar way that people active in the open science movement are heterogeneous in their assumptions and aims, different opinions exist in the FLOSS community as well. Recalling module 1, two of the schools of thought in open science were the _Pragmatic school_ and the _Democratic school_. While the former is driven by the assumption that research could be more efficient if scientists worked together, the latter wants to set straight an unequal distribution of knowledge. They probably both end up sharing their research, but each with different intentions. -The big difference between free software and OSS is that the former must distribute updated versions under the same license as the original, whereas newer versions of OSS can be distributed under different licenses. FOSS combines the best of both worlds. +This is roughly comparable to the OSS and the free software movement: The latter evolved around 1983 to protect what they call the four essential freedoms of a program's user. These include the freedom to run, copy, distribute, study, change and improve a program. Software that respects these freedoms with an appropriate license is considered 'free'. The four freedoms are seen as vital for a society as a whole in the sense that they only enable sharing, cooperation and ultimately freedom in general. In this sense the free software movement is a social movement that creates an ethical imperative. -These definitions have now become widely adopted, both by international governments, as well as some large organisations such as the [Mozilla Foundation](https://www.mozilla.org/en-US/foundation/) and the [Wikimedia Foundation](https://wikimediafoundation.org/wiki/Home). Major organisations in the FLOSS space include the UK's [Software Sustainability Institute](https://www.software.ac.uk/), who produce valuable resources such as their recent [Software Deposit Guidance for Researchers](https://softwaresaved.github.io/software-deposit-guidance/). +The open source software movement, which splintered off in 1998, focuses on the practical advantages and does not campaign for principles. It is concerned with developing high-quality software, for which everyone's ability to obtain, modify and contribute back the source code is considered highly beneficial. + +Among multiple conclusions they arrive at, access to a program's source code is a shared one. Software thus may be considered _free_, _open source_, or both, according to agreed-on definitions by the Free Software Foundation ([FSF](https://www.gnu.org/philosophy/free-sw.html)) and the Open Source Initiative ([OSI](https://opensource.org/osd)). The FSF argues that free software is a subset of OSS, with only a [fraction](https://www.gnu.org/philosophy/free-open-overlap.html) being open source but nonfree. + +Thus, highlighting a particular license status of software in use—open source or free—is mostly about different philosophies, not about software not having the other status as well. Each movement has its share of problems explaining their term: _free_ means more than being gratis and _open source_ means more than having access to the source code. The [FSF](https://www.gnu.org/philosophy/open-source-misses-the-point.html) and the European counterpart [FSFE](https://fsfe.org/documents/whyfs.html) provide more information on this topic. ### For individual projects @@ -246,6 +250,7 @@ If that's enough for you for now great! If not for most pieces of proprietary so | STATA/SPSS | R | | MS Office | LibreOffice | | Mathematica | JupyterLab | +| Max/MSP | PureData | | Test out your new [Pull Request -PR-](https://help.github.com/articles/about-pull-requests/) Skills ... | ... by adding your own example [here](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/MAIN.md) | **Cool! But if I make the switch will I be stuck: taking ages to learn a new tool/ without support /with buggy software.** @@ -313,7 +318,7 @@ There are two ways in which contributions to a project become licensed: 1. *Explicitly*, whereby the individual contribution has a clearly indicated license independent of the main project; or 2. *Implicitly*, whereby the contribution falls under the original licensing code of the main project. -Thankfully, the process of selecting an Open Source license is relatively trivial, thanks to user-friendly tools such as [Choose A License](https://choosealicense.com/). Each of these licenses allows other users to use, copy, distribute, and build upon your work, often while ensuring that the creators are appropriately recognised for their work. Here, the key is selecting an appropriate license for your work, depending on what you want, or do not want, others to do with it. +Thankfully, the process of selecting an Open Source license is relatively trivial, thanks to user-friendly tools such as [Choose A License](https://choosealicense.com/) or [Public License Selector](https://ufal.github.io/public-license-selector/). Each of these licenses allows other users to use, copy, distribute, and build upon your work, often while ensuring that the creators are appropriately recognised for their work. Here, the key is selecting an appropriate license for your work, depending on what you want, or do not want, others to do with it.
@@ -453,6 +458,7 @@ 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?** diff --git a/content_development/MAIN.pdf b/content_development/MAIN.pdf index ef24e7e..359094b 100644 Binary files a/content_development/MAIN.pdf and b/content_development/MAIN.pdf differ diff --git a/content_development/README.md b/content_development/README.md index 7108c1a..b6149f9 100644 --- a/content_development/README.md +++ b/content_development/README.md @@ -2,23 +2,19 @@ These are the main content development files for this MOOC module. -**STATUS**: +**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).** -**LIVE! This module is now online and ready to go via [Eliademy](https://eliademy.com/app/a/courses/02d7338a7e).** +The third release for this module is now also ready, and has been published on Zenodo: -The second release for this module is now also ready, and has been published on Zenodo: - -Version 2: [](https://doi.org/10.5281/zenodo.1434288) - -Version 1: [](https://doi.org/10.5281/zenodo.1325081) +[](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: -Tennant, J. et al. (23/09/2018) Open Science MOOC: Module 5, Open Research Software and Open Source (Version 2.0) Zenodo. [http://doi.org/10.5281/zenodo.1434288](http://doi.org/10.5281/zenodo.1434288) +Jon Tennant; Simon Worthington; Tania Allard; Philipp Zumstein; Daniel S. Katz; Alexander Morley; Stephan Druskat; Julien Colomb; Arfon Smith; Ina Smith; Tobias Steiner; Rutger Vos; Konrad Förstner; Heidi Seibold; Alessandro Sarretta; Abigail Cabunoc Mayes. (2018, December 4). OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source: Third release (Version 3.0.0). Zenodo. [http://doi.org/10.5281/zenodo.1937708](http://doi.org/10.5281/zenodo.1937708). 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)) 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.
\n",
" ![](\"https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/git.png?raw=true\")
\n",
diff --git a/content_development/Task_1.md b/content_development/Task_1.md
index ed7b4b6..c9fed7d 100644
--- a/content_development/Task_1.md
+++ b/content_development/Task_1.md
@@ -8,7 +8,7 @@ output:
This task is designed for students and researchers who want to create their first Open Source project (software or non-software) on GitHub. GitHub is a place for you to come and play and experiment with new research workflows, and is really just the beginning to help set the stage for your own pathways and ideas.
-Don't forget you can join in the discussions over at our open [**Slack channel**](https://openmooc-ers-slackin.herokuapp.com/). Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here!
+Don't forget you can join in the discussions over at our open [**Slack channel**](https://osmooc.herokuapp.com/). Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here!
**PLEASE NOTE** that a screen recording for this task is also available via [YouTube](https://www.youtube.com/watch?v=AnftV9HBPSc&).
@@ -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.
diff --git a/content_development/Task_1.pdf b/content_development/Task_1.pdf
index 1585c3a..ddf6c47 100644
Binary files a/content_development/Task_1.pdf and b/content_development/Task_1.pdf differ
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!
-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_2.ipynb b/content_development/Task_2.ipynb index d43e256..072df0b 100644 --- a/content_development/Task_2.ipynb +++ b/content_development/Task_2.ipynb @@ -19,6 +19,7 @@ "Estimated time to complete: 45-60 minutes.\n", "\n", "## Table of contents\n", + "- [Foreword](#Foreword)\n", "- [Set up a GitHub repository](#Setup)\n", "- [Choose your GitHub repository](#Choose)\n", "- [Login to Zenodo](#Login)\n", @@ -37,6 +38,10 @@ "The workflow for Task 2. Keep this handy as you work through the task!
\n", "\n", "\n", + "## Foreword \n", + "\n", + "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 \n", + "in a repository which provides a persistent unique identifier) can be applied in different workflow. \n", "\n", "## Set up a GitHub repository \n", "\n", diff --git a/content_development/Task_2.md b/content_development/Task_2.md index 16e7246..afb0ecb 100644 --- a/content_development/Task_2.md +++ b/content_development/Task_2.md @@ -8,11 +8,12 @@ output: This task is designed for students and researchers who want to create and re-use GitHub-based projects/repositories in the academic literature. -Don't forget you can join in the discussions over at our open [**Slack channel**](https://openmooc-ers-slackin.herokuapp.com/). Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here! +Don't forget you can join in the discussions over at our open [**Slack channel**](https://osmooc.herokuapp.com/). 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: 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, 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_2.pdf b/content_development/Task_2.pdf index 1e6e14e..34247e5 100644 Binary files a/content_development/Task_2.pdf and b/content_development/Task_2.pdf differ 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
-
@@ -343,7 +344,7 @@
- You get to keep copies of all your work through time; @@ -390,7 +391,7 @@
Go to the repositors for this project on GitHub
Fork the repository to your own GitHub account. The URL for this should be:
https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source.git
-Head into RStudio, go to File > New Project, choose Version Control, select Git, and then paste the forkerd repository URL found in your copy of the repository. You now have your own versioned copy of this whole module. Neat. Save this somewhere on your local machine.
+Head into RStudio, go to File > New Project, choose Version Control, select Git, and then paste the forked repository URL found in your copy of the repository. You now have your own versioned copy of this whole module. Neat. Save this somewhere on your local machine.
Now, you need to tell Git that a different version of this project exists. Open up the Shell, and enter the command:
git remote add upstream https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-SourceWhat you just did was name the original branch here
upstream, just to keep things simple for now. Now, create a new branch to document your changes to this independent of the main branch. Enter the command:git checkout -b proposed-changes masterYou just created a new branch called
proposed-changeswhere you can now edit all of the content and files to your heart’s delight. Hopefully, the structure of this project is simple enough for you to navigate around. All of the raw files for the MOOC can be found in thecontent_developmentfolder, and this isTask_3.md.If you scroll to the bottom of
Task_3.md, you should see a place where you can edit in your name and affiliation. Add these in, and then go through the commit procedure detailed above. If you see anything else that needs editing too, feel free to add them in too!
-Now, you want to push thee changes back to the original branch. Use the following command in your Shell:
git push origin proposed-changes
+Now, you want to push the changes back to the original branch. Use the following command in your Shell:
git push origin proposed-changesGo back to GitHub and find your fork here. Click the little green button, and create a pull request. This is essentially a review to integrate the changes made into the original branch for this MOOC project.
The owners in charge of the MOOC project will now get a notification of this, review it, and confirm it if everything went to plan! We will review it, and if it all went okay, your name will now appear for all eternity as someone who completed this advanced task.
Have a cup of tea, coffee, or wine to celebrate!
@@ -531,8 +532,14 @@ - YOUR NAME AND AFFILIATION HERE -
- YOUR NAME AND AFFILIATION HERE +
- Brendan Palmer,CRF-C, University College Cork +
- Lisa Matthias, Freie Universität Berlin +
- 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 +
- Alberto Albz Marocchino, Italy +
- Iratxe Rubio, Basque Centre for Climate Change BC3
- For the ‘Delivered’ column, a simple Yes/No Scheme should be used. +
- For the ‘Status’ column, please use one of the three symbols below. +
- For the ‘Deadline’ column, please use a traditional dating scheme: 2018/05/10. +
- For the ‘Comments’ column, insert any text as neccessary. +
Getting started
Getting Git
So, what is Git, and how is it different to GitHub? Git is a version control system, which enables you to save and track time-stamped copies of your work throughout the development process. It also works with non-code items too, like this MOOC, the majority of which was written in markdown in RStudio, and integrated with a Git/GitHub workflow.
-This is important, as all research goes through changes and sometimes we want to know what those things were. Did you delete some text that you now think is important? Version control will save that for you. Did your code used to work perfectly, but is now buggy beyond belief? Version control. It’s a great way to avoid that chaotic state where you have multiple copies of the same file, but without a stupid and annoying file naming convention. FINAL_Revised_2.2_supervisor_edits_ver1.7_scream.txt will be a thing of the past.
This is important, as all research goes through changes and sometimes we want to know what those things were. Did you delete some text that you now think is important? Version control will save that for you. Did your code work perfectly in the past, but is now buggy beyond belief? Version control. It’s a great way to avoid that chaotic state where you have multiple copies of the same file, but without a stupid and annoying file naming convention. FINAL_Revised_2.2_supervisor_edits_ver1.7_scream.txt will be a thing of the past.
GitHub is the platform that allows you to seamlessly share code from your workspace (e.g., laptop) to be hosted in an online space. So, sort of like the public interface to GitHub. The advantages of Git/GitHub are:
Step one: Download all the things
Step two: Configure Git inside RStudio
Right, that’s the easy bit done. Next, go into RStudio, and in the tabs at the top go to Go to Tools > Global Options > Git/SVN. SVN is just another version control system like Git, and we don’t need to worry about that here.
-In the place where it says Git executable, add the pathway here to the git.exe file that you just downloaded in the previous step. Make sure the boxe here that says Enable version control interface for RStudio projects is ticked. This now has tied version control to future projects in RStudio, to provide a really powerful additional dimension to collaborative or solo work.
+In the place where it says Git executable, add the pathway here to the git.exe file that you just downloaded in the previous step. Make sure the box here that says Enable version control interface for RStudio projects is ticked. This now has tied version control to future projects in RStudio, to provide a really powerful additional dimension to collaborative or solo work.
Step seven: PUSH!
Step seven: PUSH!
List of participants who completed the ADVANCED version of this task
-
-
\n",
" This is to provide a structured check list to track content development. Status traffic light scheme: Green: All looks good Green Orange: Issues that can impact launch date Orange Red: Launch date in danger Red![](\"https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source/blob/master/content_development/images/git_svn.png?raw=true\")
\n",
@@ -262,7 +264,7 @@
"\n",
"2. Fork the repository to your own GitHub account. The URL for this should be: `https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source.git`\n",
"\n",
- "3. Head into RStudio, go to **File > New Project**, choose *Version Control*, select *Git*, and then paste the forkerd repository URL found in your copy of the repository. You now have your own versioned copy of this whole module. Neat. Save this somewhere on your local machine.\n",
+ "3. Head into RStudio, go to **File > New Project**, choose *Version Control*, select *Git*, and then paste the forked repository URL found in your copy of the repository. You now have your own versioned copy of this whole module. Neat. Save this somewhere on your local machine.\n",
"\n",
"4. Now, you need to tell Git that a different version of this project exists. Open up the *Shell*, and enter the command: `git remote add upstream https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source`\n",
"\n",
@@ -272,7 +274,7 @@
"\n",
"7. If you scroll to the bottom of `Task_3.md`, you should see a place where you can edit in your name and affiliation. Add these in, and then go through the commit procedure detailed above. If you see anything else that needs editing too, feel free to add them in too!\n",
"\n",
- "8. Now, you want to push thee changes back to the original branch. Use the following command in your *Shell*: `git push origin proposed-changes`\n",
+ "8. Now, you want to push the changes back to the original branch. Use the following command in your *Shell*: `git push origin proposed-changes`\n",
"\n",
"9. Go back to GitHub and find your fork here. Click the little green button, and create a pull request. This is essentially a review to integrate the changes made into the original branch for this MOOC project.\n",
"\n",
@@ -308,9 +310,14 @@
"\n",
"## List of participants who completed the ADVANCED version of this task\n",
"\n",
- "* YOUR NAME AND AFFILIATION HERE\n",
- "* YOUR NAME AND AFFILIATION HERE\n",
- "\n",
+ "* Brendan Palmer,CRF-C, University College Cork\n",
+ "* Lisa Matthias, Freie Universität Berlin\n",
+ "* Hollie Marshall, University of Leicester \n",
+ "* Eric D. Wilkey, Western University, Canada\n",
+ "* José-Raúl Canay-Pazos, Universidade de Santiago de Compostela, Spain\n",
+ "* Encarnación Martínez Álvarez, Spain\n",
+ "* Alberto Albz Marocchino, Italy\n",
+ "* Iratxe Rubio, Basque Centre for Climate Change BC3\n",
"\n",
"[](https://creativecommons.org/publicdomain/zero/1.0/)"
]
diff --git a/content_development/Task_3.md b/content_development/Task_3.md
index 5c7dcfa..6452616 100644
--- a/content_development/Task_3.md
+++ b/content_development/Task_3.md
@@ -8,7 +8,7 @@ output:
This task is designed for students and researchers who want to implement a system of version control within a standard R-based workflow. This can be applied to a range of software development, data analysis and project management tasks. Your future research self will thank your for the convenience.
-Don't forget you can join in the discussions over at our open [**Slack channel**](https://openmooc-ers-slackin.herokuapp.com/). Please do introduce yourself at #module5opensource, and tell us a bit about who you are, your background, and how you ended up here!
+Don't forget you can join in the discussions over at our open [**Slack channel**](https://osmooc.herokuapp.com/). 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
@@ -227,7 +227,7 @@ Select the `README` file in the Git window, which should show up automatically i
Here, you have a chance to review your changes, and write a nice commit message. Type in something brief, but informative about the changes that you have made in this version or snapshot of your work. You want this to be enough information so that if you or someone else looks back on it, you'll know why you made this commit and the changes associated with it. These are like safety nets for your project in case you need to fall back for some reason.
-> **Pro-tip**: Here, you will see a list of all the changes you have made since your last commit. Older removed lines are in red, and newly added lines are in green. Double check these to make sure that the edits you have made are the ones you intended to make. This is really helpful for spotting typos, stray edits, and any other little mistakes you might have accidentially introduced. Safety first.
+> **Pro-tip**: Here, you will see a list of all the changes you have made since your last commit. Older removed lines are in red, and newly added lines are in green. Double check these to make sure that the edits you have made are the ones you intended to make. This is really helpful for spotting typos, stray edits, and any other little mistakes you might have accidentally introduced. Safety first.
**Note** If you are colour-blind and can't see which lines have been added or removed, you can use the line numbers in the two columns on the left of the window as a guide. Here, the number in the first column identifies the older version, and the number in the second column identifies the new version.
@@ -254,7 +254,7 @@ Close that window down, and the next one. Go to your project on GitHub, refresh,
Alright, so you just pushed some content to your first repo, awesome! Now let's put it into practice for a real project. Like, the one you are participating in right now. Let's try this out:
-1. Go to the repositors for this project on [GitHub](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source)
+1. Go to the repository for this project on [GitHub](https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source)
2. Fork the repository to your own GitHub account. The URL for this should be: `https://github.com/OpenScienceMOOC/Module-5-Open-Research-Software-and-Open-Source.git`
@@ -309,6 +309,17 @@ 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
+* Alberto Albz Marocchino, Italy
+* Iratxe Rubio, Basque Centre for Climate Change BC3
+* Gabriele Orlandi, Paris School of Advanced Studies in Social Sciences (EHESS), France
+* Hande Sodacı, Turkey
+* Luke W. Johnston, Aarhus University, Denmark
+* Philippe Joly, WZB and HU-Berlin
+* Paul Griffiths, NCAS and U. Cambridge
+* Harin Lee, Goldsmiths, University of London
+* Luis Camacho, Catholic University, Perú
+* Tom Cridford, Imperial College London
+* Nithiya Streethran, University of Stavanger
[](https://creativecommons.org/publicdomain/zero/1.0/)
diff --git a/content_development/Task_3.pdf b/content_development/Task_3.pdf
index 66c3810..7bc9282 100644
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diff --git a/content_development/tex2pdf.10300/297659baecdb0d0acef9d2f8fd1575986c7998dd.svg b/content_development/tex2pdf.10300/297659baecdb0d0acef9d2f8fd1575986c7998dd.svg
deleted file mode 100644
index a4e508f..0000000
--- a/content_development/tex2pdf.10300/297659baecdb0d0acef9d2f8fd1575986c7998dd.svg
+++ /dev/null
@@ -1,35 +0,0 @@
-
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diff --git a/content_development/tex2pdf.10300/input.aux b/content_development/tex2pdf.10300/input.aux
deleted file mode 100644
index 4ddce3a..0000000
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+++ /dev/null
@@ -1,36 +0,0 @@
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-\@writefile{toc}{\contentsline {section}{Task 2: How to make your code citable using GitHub and Zenodo}{1}{section*.1}}
-\newlabel{task-2-how-to-make-your-code-citable-using-github-and-zenodo}{{}{1}{Task 2: How to make your code citable using GitHub and Zenodo}{section*.1}{}}
-\@writefile{toc}{\contentsline {subsection}{Table of contents}{1}{section*.2}}
-\newlabel{table-of-contents}{{}{1}{Table of contents}{section*.2}{}}
-\@writefile{toc}{\contentsline {subsection}{Set up a GitHub repository }{1}{section*.3}}
-\newlabel{set-up-a-github-repository}{{}{1}{Set up a GitHub repository}{section*.3}{}}
-\@writefile{toc}{\contentsline {subsection}{Choose your GitHub repository }{1}{section*.4}}
-\newlabel{choose-your-github-repository}{{}{1}{Choose your GitHub repository}{section*.4}{}}
-\@writefile{toc}{\contentsline {subsection}{Login to Zenodo }{1}{section*.5}}
-\newlabel{login-to-zenodo}{{}{1}{Login to Zenodo}{section*.5}{}}
-\@writefile{toc}{\contentsline {subsection}{Authorise GitHub to connect with Zenodo }{2}{section*.6}}
-\newlabel{authorise-github-to-connect-with-zenodo}{{}{2}{Authorise GitHub to connect with Zenodo}{section*.6}{}}
-\@writefile{toc}{\contentsline {subsection}{Select the repository to archive }{2}{section*.7}}
-\newlabel{select-the-repository-to-archive}{{}{2}{Select the repository to archive}{section*.7}{}}
-\@writefile{toc}{\contentsline {subsection}{Check repository settings }{2}{section*.8}}
-\newlabel{check-repository-settings}{{}{2}{Check repository settings}{section*.8}{}}
-\@writefile{toc}{\contentsline {subsection}{Create a new release }{2}{section*.9}}
-\newlabel{create-a-new-release}{{}{2}{Create a new release}{section*.9}{}}
diff --git a/content_development/tex2pdf.10300/input.log b/content_development/tex2pdf.10300/input.log
deleted file mode 100644
index 115723f..0000000
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+11 May 2018
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+MOOC planning template
+How to use this template
+
+
+
+
+
+
+
+
+
+
+
+Design Phase
+Delivered
+Status badge
+Deadline
+Comments
+
+
+Initiate and plan
+
+
+
+
+
+
+Kick off
+Yep
+2018/05/10
+Sprint success!
+
+
+Define target group
+Yep
+2018/05/31
+Sprint success!
+
+
+Refine learning objectives/outcomes
+Yep
+2018/05/31
+Sprint success!
+
+
+Design course outline
+Yep
+2018/05/31
+Sprint success!
+
+
+Design project plan and timeline
+Yep
+2018/06/31
+
+
+
+Identify promotion channels
+Yep
+2018/06/31
+
+
+
+Design and scripting
+
+
+
+
+
+
+Identify key resources
+Yep
+2018/06/31
+Sprint success!
+
+
+Design learner activities
+Yep
+2018/06/31
+3/3 completed
+
+
+Find existing key resources
+Yep
+2018/06/31
+Sprint success!
+
+
+Write audio/video scripts
+In prep
+2018/08/31
+6/6 completed
+
+
+Review all learning resources
+In prep
+
+
+ 2018/11/31
+
+
+Finalise all scripts
+In prep
+
+
+ 2018/11/31
+
+
+Copyright strategy
+Yep
+
+ 2018/08/31
+
+
+Recording and editing
+
+
+
+
+
+
+Record on location/in studio
+
+
+
+
+
+
+Edit all audio/visual material
+
+
+
+
+
+
+Internal reviewing
+
+
+
+
+
+
+Cross-check and review content
+In prep
+2018/08/31
+Continuous process
+
+
+Checks from Steering Committee
+In prep
+2018/08/31
+Continuous process
+
+
+External testing and review
+
+
+
+
+
+
+All reviewing conducted via GitHub
+In prep
+2018/08/31
+Continuous process
+
+
+Existing channels from communications strategy
+
+
+
+
+
+
+Internal reviewing and finalisation
+
+
+
+
+
+
+Cross-review and check content
+
+
+
+
+
+
+Final checks from Steering Committee
+
+
+
+
+
+
+Implementation
+
+
+
+
+
+
+Agreement on platform
+In prep
+2018/08/31
+
+
+
+Module logo designed
+Yep
+2018/08/31
+
+
+
+Module description and introduction
+Yes
+2018/07/31
+
+
+
+Team member and guest lecturer agreements
+Yes
+2018/07/31
+
+
+
+Team member and guest lecturer profiles
+Yes
+2018/07/31
+
+
+
+Course readings acquired
+Yes
+2018/07/31
+
+
+
+Port content to selected platform
+
+
+
+
+
+
+All content deposited in Zenodo
+Yep
+2018/08/31
+Second release completed
+
+
+Promotion
+
+
+
+
+
+
+Content and communication calendar/strategy/timeline
+In progress
+
+
+
+
+Identify relevant channels (mailing lists, social media and hashtags, organisations, individuals, websites, conferences)
+Yes
+2018/07/31
+
+
+
+Images for use in social media
+Yep
+2018/07/31
+
+
+
+Course title marketing check
+Yes
+2018/07/31
+
+
+
+Launch
+
+
+
+
+
+
+Publicity start
+Yes
+Dec 2018
+
+
+
+Open and free for all, continuous, self-paced learning, 100% online
+Yes
+Dec 2018
+Continuous, self-paced
+
+
+Soft launch
+Yes
+
+ Dec 2018
+
+
+Course launch
+Yes
+
+
+
+
+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
+In prep
+
+
+
+
+
+Track any new information during course duration
+In prep
+
+
+
+
+
+Prepare evaluation report
+Pending
+
+
+
+
+
+Evaluation meeting
+Pending
+
+
+
+
+
+
+Optimise content where relevant
+Pending
+
+
+
+