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gitpod config to be used for tutorials #1093

Merged
merged 23 commits into from
Mar 19, 2022
Merged

gitpod config to be used for tutorials #1093

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660952a
added gitpod exercise and gitpod button 01
Mar 17, 2022
6e57ce8
test nfcore image
Mar 17, 2022
b7b1c64
reverted gitpod yml in favour of branching out for exercises
Mar 17, 2022
c800df4
deleted exercises from main branch so it can open exercise branch lat…
Mar 17, 2022
54a5120
added exercise and modified .gitpod yaml
Mar 17, 2022
0f494e1
fixed exercise code
Mar 17, 2022
43f8962
added second exercise gitpod
Mar 17, 2022
5357084
fixed name of file
Mar 17, 2022
eb03d4d
second exercise
Mar 17, 2022
c131c61
viralrecon params fix
Mar 17, 2022
27bbefa
testing opening preview
Mar 17, 2022
2730d10
opening automatically the page with the tutorial on nfcore website
Mar 17, 2022
c3a347f
by opening web page we don't need code files anymore
Mar 17, 2022
e399b5b
added vscode settings in attempt to open browser straight away
Mar 17, 2022
bb68e0f
changing extensions in vscode
lescai Mar 17, 2022
59588bf
added vscode settings hoping would change opening behaviour
lescai Mar 17, 2022
29585c8
resolved
Mar 17, 2022
e5bc0df
deleting everything that's not used for gitpod config
Mar 17, 2022
55a317c
fixed conflicts with upstream
Mar 18, 2022
d7f1f7c
trying to capture url variable in config
Mar 18, 2022
9494a96
trying to parse url
Mar 18, 2022
2ee0533
fixing gp preview command
Mar 18, 2022
dc1f7ea
does not seem to accept string with variable
Mar 18, 2022
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60 changes: 0 additions & 60 deletions .github/CONTRIBUTING.md
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29 changes: 0 additions & 29 deletions .github/ISSUE_TEMPLATE/bug_report.md
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8 changes: 0 additions & 8 deletions .github/ISSUE_TEMPLATE/config.yml
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17 changes: 0 additions & 17 deletions .github/ISSUE_TEMPLATE/feature_request.md
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14 changes: 0 additions & 14 deletions .github/markdownlint.yml
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22 changes: 0 additions & 22 deletions .github/workflows/broken_link.yml
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23 changes: 0 additions & 23 deletions .github/workflows/markdown.yml
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56 changes: 0 additions & 56 deletions .github/workflows/web-deploy.yml
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25 changes: 0 additions & 25 deletions .github/workflows/yaml.yml
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43 changes: 0 additions & 43 deletions .gitignore
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44 changes: 16 additions & 28 deletions .gitpod.yml
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Original file line number Diff line number Diff line change
@@ -1,31 +1,19 @@
---
# based on https://github.com/gitpod-io/template-docker-compose
image: nfcore/gitpod:latest

tasks:
- init: docker-compose pull
- command: chmod a+x /workspace/nf-co.re && docker-compose up
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level

ports:
- port: 8888
onOpen: open-preview

vscode:
extensions:
- ms-azuretools.vscode-docker
- esbenp.prettier-vscode
github:
prebuilds:
# enable for the default branch (defaults to true)
master: true
# enable for all branches in this repo (defaults to false)
branches: false
# enable for pull requests coming from this repo (defaults to true)
pullRequests: true
# enable for pull requests coming from forks (defaults to false)
pullRequestsFromForks: true
# add a check to pull requests (defaults to true)
addCheck: true
# add a "Review in Gitpod" button as a comment to pull requests (defaults to false)
addComment: false
# add a "Review in Gitpod" button to the pull request's description (defaults to false)
addBadge: true
- port: 8080
onOpen: ignore
tasks:
- init: git checkout gitpod_exercises
- command: |
parsed=`echo $url | tr -s "[" "/" | tr -s "+" "."`
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So this parses the string

https://gitpod.io/#url=nf-co+re[usage[tutorials[nf_core_usage_tutorial/https://github.com/nf-core/nf-co.re/blob/gitpod_config_training/

Parts of the URL:

https://gitpod.io/#                                              // Gitpod prefix
url=nf-co+re[usage[tutorials[nf_core_usage_tutorial              // Value pair, separate by commas
https://github.com/nf-core/nf-co.re/blob/gitpod_config_training/ // Repo + branch to open

Does URL encoding work (it says the values are URL encoded)? https://www.urlencoder.org/

https://carpentries-incubator.github.io/workflows-nextflow/01-getting-started-with-nextflow/index.html

becomes

https%3A%2F%2Fcarpentries-incubator.github.io%2Fworkflows-nextflow%2F01-getting-started-with-nextflow%2Findex.html

How can I test this? I tried editing the other page https://github.com/nf-core/nf-co.re/pull/1094/files
but then I can't get to the button in the preview browser.

We may just be over complicating things here though.
What would be nice is just:
teaching_view

So a preview panel with the website (using gp preview URL and it's navigable)
And then as large a terminal as possible. I moved the terminal position to the right to have them side by side.
( Menu > View > Appearance > Panel position > right ).
Then they can do all their work in an exercises folder and not have to worry about all the other distractions along the side.

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I was too focused on carpentries material before and forgot we have two use cases here.

For the nf-core training material we want buttons on each page as they are standalone training guides, so we should definitely see if URL encoding is sufficient to open the correct URL with gp preview.

The Carpentries Workshop though just needs to start from the setup page and can have a simpler link.

newurl="https://$parsed"
gp preview $newurl
4 changes: 4 additions & 0 deletions .vscode/settings.json
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@@ -0,0 +1,4 @@
{
"settings": "",
"workbench.startupEditor": "none"
}
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