Commit c9082250 authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
Browse files

fix image paths

parent 49d106fb
......@@ -56,7 +56,7 @@ Calendar invitations will be sent to all Ambassadors containing details of the b
| Call | Date | Time | Topic |
|---|---|---|---|
| 1 | Wednesday 3 November 2021 | 09:30 - 11:00 | intro and why open science |
| 1 | Wednesday 3 November 2021 | 09:30 - 11:00 | intro to the programme |
| 2 | Wednesday 10 November 2021 | 09:30 - 11:00 | git and gitlab |
| 3 | Wednesday 17 November 2021 | 09:30 - 11:00 | tools demos and questions (meet the developers) |
| 4 | Wednesday 24 November 2021 | 09:30 - 11:00 | policy, incentives, training, monitoring |
......
......@@ -28,7 +28,7 @@ The aims for the hack day were to:
The day was structured around “lightning pitches” from the infrastructure developers to advertise where they would benefit from community engagement, followed by training in how to use GitHub to make contributions (submitting a pull request to [an external repository](https://cassgvp.github.io/git-for-collaborative-documentation)), and then three hours of dedicated time to work with the tools developers to make contributions and build ideas for future interactions. Summary attendance and engagement figures from the hack day are provided in below.
![hack day 1 attendance](../../img/img-hackday-1-pies.png){:height="100%" width="100%"}
![hack day 1 attendance](../../../img/img-hackday-1-pies.png){:height="100%" width="100%"}
## What did we achieve?
......
......@@ -18,7 +18,7 @@ Below is a live copy of the [Open Research Calendar](https://openresearchcalenda
Visit [@OpenResearchCal](https://twitter.com/OpenResearchCal) on twitter to find out how to add your events.
![open-research-calendar](../../img/img-orc.png)
![open-research-calendar](../../../img/img-orc.png)
<div class="span3">
......
......@@ -16,7 +16,7 @@ How to set up and use Atom for writing markdown
---
![logo-atom](../../img/logo-atom-200.png)
![logo-atom](../../../img/logo-atom-200.png)
Atom is my fave editor for all types of "code". Python, bash, markdown, html... I've not tried with LaTeX, but I wouldn't be surprised if it can handle that. My guess is it probably can't handle MATLAB, but that's cool.
......
......@@ -67,8 +67,8 @@ Everything you have added will be uploaded ("pushed") to your repository.
At this point (especially if it is a big load of changes I'm uploading) I'll often skip excitedly over to my online repository and have a look at my commit and the file changes. It's almost as if I don't trust the magic!?! 😉
![gif-basic-git](../../img/gifs/basic-git.gif)
![gif-basic-git](../../../img/gifs/basic-git.gif)
Give it a few minutes to let the changes take effect, then go back and refresh your Pages site. Boom! Updated content.
![gif-basic-git-show-changes](../../img/gifs/basic-git-show-change.gif)
![gif-basic-git-show-changes](../../../img/gifs/basic-git-show-change.gif)
......@@ -31,7 +31,7 @@ Once you have found the documentation you want to contribute to, you need to loc
When you have found the GitHub repository, you need to "fork" it, to create a copy in your own GitHub account.
![gif-fork-repo](../../img/gifs/fork-repo.gif)
![gif-fork-repo](../../../img/gifs/fork-repo.gif)
## 2. Clone your online copy to your local computer
......@@ -41,7 +41,7 @@ Get the https address of the repository you want to clone via the "code" button,
`git clone [https-address]`
![gif-fork-repo-clone](../../img/gifs/fork-repo-clone.gif)
![gif-fork-repo-clone](../../../img/gifs/fork-repo-clone.gif)
## 3. Create a branch
......@@ -51,7 +51,7 @@ Create your branch by entering the command below, replacing `[your-branch-name]`
`git checkout -b [your-branch-name]`
![gif-create-branch](../../img/gifs/create-branch.gif)
![gif-create-branch](../../../img/gifs/create-branch.gif)
## 4. Make and push your changes
......@@ -67,13 +67,13 @@ Finally, add, commit and save the changes as described in the earlier [git basic
Notice the git gave me a helpful error which told me that it din't know where to push my changes - there was not "upstream branch" - and very kindly told me what commands I need to enter to set the upstream to be this branch on my copy of the repository. Thanks, Git.
![gif-make-edits-to-forked-repo](../../img/gifs/make-edits-to-forked-repo.gif)
![gif-make-edits-to-forked-repo](../../../img/gifs/make-edits-to-forked-repo.gif)
## 5. Submit your pull request master
Once your changes have been pushed, GitHub online will tell you that your copy and your branch are "ahead of" (have more changes than) the original repository. You can compare the changes and submit your pull request if you are happy with them!
![gif-pull-request](../../img/gifs/pull-request.gif)
![gif-pull-request](../../../img/gifs/pull-request.gif)
Note that depending on how long it has been between you forking the original repository and submitting your pull request, you may have become out of sync with the original if there has been more work done on it. Follow the instructions [here from "7. Sync your forked master branch"](https://www.freecodecamp.org/news/how-to-make-your-first-pull-request-on-github-3/) to get yourself back in sync before submitting your pull request.
......@@ -81,7 +81,7 @@ Note that depending on how long it has been between you forking the original rep
If you're feeling excited by all this wonderful collaboration, jump back into the original repository you cloned from, and check that the pull request is there. You can even write something nice to the repository owners, if you're feeling friendly.
![gif-pull-request-confirmed](../../img/gifs/pull-request-confirm.gif)
![gif-pull-request-confirmed](../../../img/gifs/pull-request-confirm.gif)
Your pull request will now be reviewed by the repository owners, and you will get an email if/when it has been accepted. Now you have left a comment, you will also be notified when there are additional comments added to your thread.
......
......@@ -30,7 +30,7 @@ Coming soon
Below is a list of numbers. For your first contribution to someone else's documentation, I would like you to write your name, your pronouns, today's date, and your GitHub profile link against one of these numbers. If you don't know your profile link, click your profile icon (top right side) and open 'Your Profile' in a new tab. You can use the URL of that page to build your GitHub profile link. Use the link format: `[Link text here](LINK URL HERE)`. If you want to get jazzy, you can do something more complicated, like add a picture or some formatting! I invite you to freestyle or keep it functional as you wish.
Use the procedure described earlier to [fork, clone, branch, edit, push, and submit a pull request](3-2-fork-their-repo.md) to update the lines below.
Use the procedure described earlier to [fork, clone, branch, edit, push, and submit a pull request](../3-2-fork-their-repo.md) to update the lines below.
We're going to assume we're in a "class" setting right now, and I'm expecting your pull requests to come in. I'll accept them as soon as I can! If we're not in an active tutorial, I'll still aim to get to them as soon as I can, but please accept my apologies if it is not instantaneous. Often collaboration is asynchronous!
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......@@ -28,7 +28,7 @@ Next git it a name, description, and add a README file. I've chosen not to add a
Click "Create Repository" Ta-da! You have a repository! 🎉
![gif-make-repo](../../img/gifs/create-repo.gif)
![gif-make-repo](../../../img/gifs/create-repo.gif)
## 2. Update your README.md
......@@ -50,7 +50,7 @@ To get a quick outline of the README structure (and to differentiate it from the
To save your changes, describe what you did in the commit message, then press "commit"
![gif-update-readme](../../img/gifs/update-readme.gif)
![gif-update-readme](../../../img/gifs/update-readme.gif)
## 3. Create a LICENSE.md
......@@ -60,7 +60,7 @@ To get the license file in place, I'm going to use the "add file" function and a
To save your changes, describe what you did in the commit message, then press "commit"
![gif-add-license](../../img/gifs/add-license.gif)
![gif-add-license](../../../img/gifs/add-license.gif)
## 4. Create a CONTRIBUTING.md
......@@ -70,6 +70,6 @@ To get the contributing file in place, I'm going to use the "add file" function
To save your changes, describe what you did in the commit message, then press "commit"
![gif-add-contributing](../../img/gifs/add-contributing.gif)
![gif-add-contributing](../../../img/gifs/add-contributing.gif)
Have a look at our [what to include in a repository](../analysis/repo-include.md) guide for a more complete description of these files.
......@@ -32,7 +32,7 @@ Click "Select Theme" to return to your setting page. You will now see that the U
Woohoo! You have a website! 🎉
![gif-make-pages](../../img/gifs/make-pages.gif)
![gif-make-pages](../../../img/gifs/make-pages.gif)
## 2. Change your theme
......@@ -42,11 +42,11 @@ If you chose to use a theme other than one GitHub already supports, you can use
To change your theme, update the "_config" file which was created automatically by GitHub when you created your pages site. Edit this file in GitHub directly to include the "remote_theme" tag (as described on the [remote themes blog](https://github.blog/2017-11-29-use-any-theme-with-github-pages/)), and the name of the developer and theme you have chosen (the name of their repository).
![gif-update-theme](../../img/gifs/update-theme.gif)
![gif-update-theme](../../../img/gifs/update-theme.gif)
While you're here, it's a good idea to add the URL of your pages site to the "About" description on your GitHub repository. This is useful to help people find your pages site if they land on your repository first. Remember, your GitHub repository and your Pages site both exist as separate entities (at separate URLs), with the content repeated on both but "rendered" differently at each URL.
![gif-update-about](../../img/gifs/update-about.gif)
![gif-update-about](../../../img/gifs/update-about.gif)
......@@ -66,7 +66,7 @@ git clone [https address for your repo]
Boom! You have a local copy of your code 💃.
![gif-clone-repo](../../img/gifs/clone-repo.gif)
![gif-clone-repo](../../../img/gifs/clone-repo.gif)
Now dig into the "how to" guide of your chosen theme to learn what you can add to make your pages site 💯.
......@@ -76,11 +76,11 @@ In the below I've edited my repo in atom. I've added a few pages, and the front
Once you've made a few changes, simply [add, commit and push](2-4-git-basics.md) them to your repo!
![gif-add-pages](../../img/gifs/add-pages.gif)
![gif-add-pages](../../../img/gifs/add-pages.gif)
It takes a little while for your pushed changes to appear on your site (especially if they are more complex things than adding/removing words). Be patient ⏳. Wait for them to arrive and see what you have created!
![gif-check-render](../../img/gifs/check-render.gif)
![gif-check-render](../../../img/gifs/check-render.gif)
## 4. Tweak your theme and content as you wish!
......
......@@ -16,7 +16,7 @@ Find out about the principles guiding this project
This project is being developed with the guiding principle of "Open Leadership". The Open Leadership framework was developed by Mozilla to support open source community projects. It describes a set of tools and practices which have been used in creating this repository along with exercises which have helped design effective paths to contribution. These principles were passed to the Open WIN Community Coordinator through participation in the [Open Life Science](https://openlifesci.org) program.
![Mozilla Open Leadership structure](../img/img-open-leadership.png)
![Mozilla Open Leadership structure](../../img/img-open-leadership.png)
# Mozilla Open Leadership Framework
......@@ -53,11 +53,11 @@ We are working open as this is an effective way to develop a user focused and in
The open canvas is designed to help define project goals, strategy and resource needs to create a minimum viable product (MVP). The images below describe the sections for the open canvas and the model we have drafted for the future [Open WIN Ambassadors](ambassadors.md) program.
![Open canvas section descriptions](../img/mozilla-framework/open-canvas-instruc.png)
![Open canvas section descriptions](../../img/mozilla-framework/open-canvas-instruc.png)
<!-- <img src="/img/mozilla-framework/open-canvas-instructpng" alt="Open canvas section descriptions" width="100%" height="50%"> -->
![Open canvas for WIN Open Ambassadors Program](../img/mozilla-framework/open-canvas-ambas.png)
![Open canvas for WIN Open Ambassadors Program](../../img/mozilla-framework/open-canvas-ambas.png)
<!-- <img src="/img/mozilla-framework/open-canvas-ambasspng" alt="Open canvas for WIN Open Ambassadors Program" width="100%" height="50%"> -->
......
......@@ -30,17 +30,17 @@ Coming soon
<br>
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/acquisition/#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/acquisition/#for-external-researchers)
[![For WIN members](../../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/acquisition/#for-win-members) [![For external researchers](../../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/acquisition/#for-external-researchers)
## For WIN members
### Benefits
#### Version control ![version-control](../../img/icon-version-control.png)
#### Version control ![version-control](../../../img/icon-version-control.png)
The acquisition database is version controlled, so WIN members are invited to upload their protocols during pilotting to keep track of optimisation and final versions. Comments and notes can be added to each entry to you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data](data.md) server
#### Citable research output ![doi](../../img/icon-doi.png)
#### Citable research output ![doi](../../../img/icon-doi.png)
Versions (with minor and major edits) can be assigned a digital object identified (DOI) using the [Oxford Research Archive (ORA) Data repository](https://deposit.ora.ox.ac.uk) using the stable link provided by the acquisition database. Once a DOI has been created, your acquisition protocol becomes a citable object which you can add to your list of research outputs.
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../../img/icon-reproduce.png)
Depositing your acquisition protocol in the database is as simple as uploading the sequence pdf available from the scanner console, or alternatively you can upload the .exar file used by our [Siemens scanners](https://www.win.ox.ac.uk/about/facilities). All sequence detail is captured from either document, and parsed into a unified machine readable and searchable format. You can upload a single sequence, or all sequences used in a single imaging session (a protocol) together.
## For external researchers
......
......@@ -35,17 +35,17 @@ Coming soon
<br>
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/analysis/#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/analysis/#for-external-researchers)
[![For WIN members](../../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/analysis/#for-win-members) [![For external researchers](../../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/analysis/#for-external-researchers)
## For WIN members
### Benefits
#### Version control ![version-control](../../img/icon-version-control.png)
#### Version control ![version-control](../../../img/icon-version-control.png)
WIN members will be encouraged to develop their analysis pipelines into standalone scripts and store these on the [WIN GitLab instance](https://git.fmrib.ox.ac.uk). We will support our members in using git to version control their code, and employ best practice in ensuring their pipelines are robust and accurate. Find out more about [using GitLab](gitlab.md)
#### Citable research output ![doi](../../img/icon-doi.png)
#### Citable research output ![doi](../../../img/icon-doi.png)
Versions of analysis code can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading them from GitLab. Once a DOI has been created, your analysis code becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository](gitlab/4-2-you-doi.md).
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../../img/icon-reproduce.png)
Alongside your analysis code, WIN members will be supported in implementing a "[wrapper](https://techterms.com/definition/wrapper)" script which can:
1. access data stored on the WIN [Open Data](data.md) servers;
2. access your GitLab code repository;
......
......@@ -36,7 +36,7 @@ The Data Usage Agreement and de-identification process is being developed with t
#### Quality control
WIN members will also be encouraged to run and share the results of predefined quality control algorithms, so anyone accessing the data can have a ready measure of image quality.
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-external-researchers)
[![For WIN members](../../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-win-members) [![For external researchers](../../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/data/#for-external-researchers)
Coming soon
{: .label .label-yellow }
......@@ -52,15 +52,15 @@ Note while the XNAT system is in development, we suggest you use the below wordi
> "Data will be made available on the WIN Open Data server. This is currently in development. Register here to find out when materials are available for download: [https://web.maillist.ox.ac.uk/ox/subscribe/win-open-data](https://web.maillist.ox.ac.uk/ox/subscribe/win-open-data)"
### Benefits
#### Version control ![version-control](../../img/icon-version-control.png)
#### Version control ![version-control](../../../img/icon-version-control.png)
Coming soon
{: .label .label-yellow }
#### Citable research output ![doi](../../img/icon-doi.png)
#### Citable research output ![doi](../../../img/icon-doi.png)
Coming soon
{: .label .label-yellow }
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../../img/icon-reproduce.png)
Coming soon
{: .label .label-yellow }
......
......@@ -22,17 +22,17 @@ The Open Tasks working group aims to encourage and incentivise researchers desig
<br>
[![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-win-members) [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-external-researchers)
[![For WIN members](../../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-win-members) [![For external researchers](../../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-external-researchers)
## For WIN members
### Benefits
#### Version control ![version-control](../../img/icon-version-control.png)
#### Version control ![version-control](../../../img/icon-version-control.png)
The [WIN Open Tasks repository](https://git.fmrib.ox.ac.uk/open-science) is maintained in the WIN GitLab server. WIN members are invited to deposit their task code and materials when they are using a stable version, by cloning from their own GitLab or GitHub repository. This implies that WIN members will be using a git process when developing their task, and as such their development journey will be version controlled. Find out more about [using GitLab](gitlab.md)
#### Citable research output ![doi](../../img/icon-doi.png)
#### Citable research output ![doi](../../../img/icon-doi.png)
Versions of task materials can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading individual task repositories from GitLab. Once a DOI has been created, your task material becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository](gitlab/4-2-you-doi.md).
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
#### Reproducible methods detail ![reproduce](../../../img/icon-reproduce.png)
WIN members will be supported in developing the necessary and sufficient documentation and running environments to enable others to launch, maintain and adapting their tasks. This facilitates effective re-use and modification of tasks within a research group, and with external collaborators.
......@@ -57,7 +57,7 @@ Yes! We think the [Pavlovia](https://pavlovia.org) system for task sharing is a
### How do I add my task to the WIN Open Tasks repository and/or to the OPEN_WIN Pavlovia repository?
Once you've been added as a member of the WIN Open Tasks reposistory and/or the OPEN_WIN Pavlovia repository (see above), you can add your repositories to these groups! In WIN GitLab, go to your repository, and then click on "Members", then "Invite Group", and choose "open-science" in your group to invite. In PsychoPy, go to [Pavlovia GitLab](https://gitlab.pavlovia.org/), and then click on "Settings", "Members", "Invite Group", and choose "OPEN_WIN" as the group. We recommend that you add the repository to the group with 'reporter' permissions. See below for an example of how to do this:
![Pavlovia example](../../img/pavlovia_OPENWIN_walkthrough.png)
![Pavlovia example](../../../img/pavlovia_OPENWIN_walkthrough.png)
### Who should I ask for further advice about sharing my tasks?
......
......@@ -53,7 +53,7 @@ To comment on the issues you will need a GitHub login. If you haven’t got one,
## Do I have to write something?
No. If you don't feel like writing out something, you are very welcome to add a quick emoji to something someone else has written. Feedback on other people's feedback is also really helpful!
![github-issue-emoji](../img/img-github-issue-emoji.png)
![github-issue-emoji](../../img/img-github-issue-emoji.png)
If you are able to write something, you are welcome to add just a few words, sentences, or paragraphs if you'd like. Whatever works for you is great.
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