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cwl-website's Introduction

Common Workflow Language Website

The main repo for the CWL Website.

GitHub: https://github.com/common-workflow-language/cwl-website/

Table of Contents

Repositories

The main website's files are in the /content/ directory, and built with Jekyll.

The CWL Specification is hosted separately from this repo, but built via the /site/ directory and ./website.sh script found here.

Getting Started

For setup and development instructions, see CWL Website Instructions - Setup & Development

Contributing

Contributing to New Issues:

  1. Create a new GitHub Issue
  2. In your terminal, from the main branch, create a new local branch by running git checkout -b branch-name-here
  3. Edit & Commit your changes, mentioning the Issue number in your commit, e.g. git commit file-names-here -m "Fix XYZ from #99"
  4. Push the changes via git push origin branch-name-here
  5. Find the branch on the GitHub repo (the url looks like https://github.com/common-workflow-language/cwl-website/tree/branch-name-here) and click "Compare and Pull Request"
  6. The reviewers will either suggest additional revisions, or approve the pull request.

Existing Issues: To contribute to an existing issue and branch: Checkout the existing branch via git checkout remote-branch-name-here (don't add the -b). Then follow steps 3-6 above.

Reporting a Vulnerability

See the Security Policy page.

User Gallery Nomination

To suggest a new entry for the CWL User Gallery, create a new Issue, via the: User Gallery Nomination issue template

Editing the Main Site

Setup Instructions: CWL Website Instructions - Setup & Development

Editing Guidelines: Editing the CWL Website

The root directory contains the following important files and directories:

  • /content/ - directory for the main website
  • /site/ - directory for the docs. Not the main site
  • README.md - general readme for the repo.
  • website.sh - script that builds the website (both the main site and the docs)

Note: All edits and updates should be made in /content/ unless there is a specific reason to do otherwise.

cwl-website's People

Contributors

alexiswl avatar awz avatar bpmweel avatar cure avatar dependabot[bot] avatar dleehr avatar fienne avatar fmigneault avatar geoffjentry avatar glassofwhiskey avatar hubentu avatar illusional avatar imgbot[bot] avatar imgbotapp avatar kinow avatar ksebby avatar lgtm-com[bot] avatar longr avatar lunacodes avatar melibleq avatar mr-c avatar sarthakpati avatar skanwal avatar stain avatar swzcuroverse avatar tetron avatar tom-tan avatar wilke avatar zimmera avatar

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cwl-website's Issues

Update and/or Merge README files

The main./README.md and /content/README.md have redundant, but mismatched content. To-Dos need to be cleaned up and/or moved to GitHub Issues.

Staging site needs to parse _config_staging.yml

The add-jekyll-site branch needs to parse both _config.yml and _config_staging.yml, in order for the staging site to properly function as a staging site. I didn't want to touch the Jenkins build config, but the respective terminal command would be bundle exec jekyll build --config "_config.yml,_config_staging.yml".

This is largely why #54 (incorrect nav links issue) came up.

@tetron @mr-c

linkchecker errors

LinkChecker 10.0.1
Copyright (C) 2000-2016 Bastian Kleineidam, 2010-2021 LinkChecker Authors
LinkChecker comes with ABSOLUTELY NO WARRANTY!
This is free software, and you are welcome to redistribute it under
certain conditions. Look at the file `LICENSE' within this distribution.
Get the newest version at https://linkchecker.github.io/linkchecker/
Write comments and bugs to https://github.com/linkchecker/linkchecker/issues

Start checking at 2022-03-02 17:57:42+000

URL        `Common%20Workflow%20Language_files/openstand-128x128-blue.png'
Name       `Open Stand badge - the modern paradigm for standards'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/specification/index.html, line 87, col 244
Real URL   file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/specification/Common%20Workflow%20Language_files/openstand-128x128-blue.png
Check time 0.000 seconds
Result     Error: URLError: <urlopen error [Errno 2] No such file or directory: '/var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/specification/Common Workflow Language_files/openstand-128x128-blue.png'>

URL        `https://umccr.github.io/'
Name       `University of Melbourne Center for Cancer Research'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/contributors/index.html, line 105, col 7
Real URL   https://umccr.github.io/
Check time 0.288 seconds
Size       5KB
Result     Error: 404 Not Found

URL        `https://agaveapi.co/'
Name       `Agave Platform'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/contributors/index.html, line 107, col 136
Real URL   https://agaveapi.co/
Check time 0.035 seconds
Result     Error: ConnectionError: HTTPSConnectionPool(host='agaveapi.co', port=443): Max retries exceeded with url: / (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f28c04df3a0>: Failed to establish a new connection: [Errno ...

URL        `https://www.embl-abr.org.au/'
Name       `EMBL Australia Bioinformatics Resource'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/contributors/index.html, line 113, col 7
Real URL   https://www.embl-abr.org.au/
Check time 0.040 seconds
Result     Error: ConnectionError: HTTPSConnectionPool(host='www.embl-abr.org.au', port=443): Max retries exceeded with url: / (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f28c04f71f0>: Failed to establish a new connection:...

URL        `https://www.ibm.com/spectrum-computing'
Name       `IBM Spectrum Computing'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/contributors/index.html, line 114, col 7
Real URL   https://www.ibm.com/spectrum-computing
Check time 0.146 seconds
Size       2KB
Result     Error: 404 Not Found

URL        `mailto:[email protected]'
Name       `[email protected]'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/contributors/index.html, line 148, col 21
Real URL   mailto:[email protected]
Check time 0.061 seconds
Warning    [mail-no-mx-host] No MX mail host for biodatomics.com
           found.
Result     Valid: Valid mail address syntax

URL        `../CWL-Logo-Header.png'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/v1.1/SchemaSalad.html, line 89, col 55
Real URL   file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/CWL-Logo-Header.png
Check time 0.000 seconds
Result     Error: URLError: <urlopen error [Errno 2] No such file or directory: '/var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/CWL-Logo-Header.png'>

URL        `https://fonts.gstatic.com'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/gallery/index.html, line 27, col 5
Real URL   https://fonts.gstatic.com
Check time 0.105 seconds
Size       1KB
Result     Error: 404 Not Found

URL        `https://fonts.googleapis.com'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/gallery/index.html, line 26, col 71
Real URL   https://fonts.googleapis.com
Check time 0.161 seconds
Result     Error: 404 Not Found

URL        `Common%20Workflow%20Language_files/openstand-128x128-blue.png'
Name       `Open Stand badge'
Parent URL file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/about/index.html, line 115, col 174
Real URL   file:///var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/about/Common%20Workflow%20Language_files/openstand-128x128-blue.png
Check time 0.000 seconds
Result     Error: URLError: <urlopen error [Errno 2] No such file or directory: '/var/lib/cwl/stgbcd235e1-bd1c-48b9-8638-733e0c696f53/about/Common Workflow Language_files/openstand-128x128-blue.png'>

Statistics:
Downloaded: 2.19MB.
Content types: 77 image, 282 text, 1 video, 0 audio, 92 application, 27 mail and 113 other.
URL lengths: min=15, max=413, avg=64.

That's it. 592 links in 658 URLs checked. 1 warning found. 9 errors found.
Stopped checking at 2022-03-02 17:58:39+000 (57 seconds)

New website changes based on feedback

@tetron had some changes that he suggested that I thought would be good to incorporate into the draft before we get feedback from the larger group. Maybe @lunacodes can do these?

This is the list, I believe. @tetron can verify :)

  • * Convert both the banner and the boxes on the main page to be clickable links (the whole graphic) instead of having it have a blue hyperlink inside. The banner should link to the discourse post about the conference: https://cwl.discourse.group/t/2022-cwl-conference-feb-28-mar-4-2022/519
  • * Reorder the gallery entries to put the bioinformatics users first, then the geospatial, hydrology, radio astronomy and general. Basically this is to keep the most compelling stories first
  • * Rename Users Gallery to User Gallery
  • * Make Features a Single Page -- if it looks too large, we could consider adding a left-nav. Based on what Luna thinks looks best.
  • * Move the Background Section from Community to the Features Page. Instead of naming it about - call it "Benefits of Workflows and Standards"
  • * Move the list of Contributors to the About section in their own page. I believe this is where we landed Peter, but if this is wrong let me know.
  • * Put a maximum width on the text, at least for the text-heavy pages like "Getting Started" or now it would be in Features or About, I believe (added based on Peter's suggestion below)

Additional bug that I added -

  • * I can't seem the link to BOSC to work in the timeline, so the hyperlink just needs to be fixed. Sorry about that.

Thanks @lunacodes.

clarify the type of workflows CWL is for

"CWL is for dataflow style batch analysis, where the units of processing are command line programs. " On the https://www.commonwl.org/ page if you added that as the second sentence (after "The Common Workflow Language (CWL) is an open standard...") I think that would make it clear. Something similar could go into the spec with more info, though once you get to a spec you usually know why you are there. But maybe a Scope Statement/Section - "What it is" and "What it isn't" (e.g., "explicitly not for business process modeling") would be helpful there to bound change requests.

https://gitter.im/common-workflow-language/common-workflow-language?at=5f96dc6c57fe0a4f30359951

https://gitter.im/common-workflow-language/common-workflow-language?at=5f96099beb82301c1a4c348a

Minor edits on the new draft of the website

These are minor edits - and do not need to prevent the website from going live, but I just wanted to list them here for @lunacodes.

  • For the development tools page:
    ** you probably don't need the extra development tools header. https://deploy-preview-75--cwl-website.netlify.app/tools/
    ** capitalize every description in the unless it is lowercase because of the tool name, e.g. cwltool
  • For the implementations page:
    ** Local is sometimes capitalized and sometimes not -- I would personally suggest lowercase
  • For the repos page:
    ** Remove any periods after entries so they are all consistent.
  • For the projects page:
    ** Capitalize all entries and remove periods
  • For the gallery page:
    ** Some of the entries are missing periods at the end.

Most of these were my fault , but if you could help clean them up - that would really be helpful.

These are more suggestions than minor edits to consider:

  • Center the logos on the bottom row in the minor users gallery on the main page -- they look a little odd to me justified to the left. No sure if that is just me though.

SEO for website?

@lunacodes looks like when I google cwl, cwl workflow or common workflow language - we don't really get hits on the main website - we get mostly links to the standards or the user guide. The standards have a link back to the main page but the user guide doesn't. Any ideas on how to make the website show up better in google searches? Thanks! Also is it possible to make a link back to the main page from the User Guide @tetron ?

Website Refresh to Reflect Personas and Other General Updates

Do a general refresh of the main website to reflect persona work in these repos:
https://github.com/common-workflow-language/for_novices
https://github.com/common-workflow-language/for_novices

includes content, look, organization and navigation

This work can be funded by the EOSS CZI grant that Curii received.
I will work on this and then will work on a plan (early and often) of getting feedback :)

I will put links and ideas in conversation below.

Python CWLGen + CWLUtils

I noticed CWL-utils is in the utility section on the website, but it might be useful to also add it to the generators section as we generate pretty decent parsers + codegen.

Also, Python CWLGen has been deprecated (and archived), should we remove this from the list, or mark it deprecated in some way.

invalid HTML on the front page

On the front page, using Firefox "view source" it is highlighting invalid HTML:

line 69: there is a dangling </nav> but there is no opening <nav>

the features grid has nested anchors (a <a> inside another <a>)
this seems to be due to using <h3> for the box titles, it is inserting <a href="#open-and-free" class="heading__anchor-symbol">§</a>
it probably shouldn't use <h3>, just a div with the appropriate styling.

Add Custom Video Player & Twitter Feed

Add Custom Video Player & Twitter Feed

Implement custom video player and Twitter feed, in order to avoid YouTube and Twitter's automatic tracking

  • Replace embedded YouTube player with a custom video player
  • Add subtitles and captions for video
  • Create custom Twitter Feed

Documenting the CWL Technical Team

  • Need to create a new section under https://www.commonwl.org/governance/ named "CWL Technical Team"
    The team is initially responsible for approving new versions of the CWL standards before that proposal goes to the CWL Leadership Team for the final vote.
  • Collect ORCIDs as well

Confirmed members who have consented to being listed:

Yet to confirm: @johnbradley @michael-kotliar @pr80ik @audrium

GitHub Team: https://github.com/orgs/common-workflow-language/teams/tech_team
Matrix Room: https://matrix.to/#/#cwltool-dev:matrix.org

Convert CWL website to Jekyll

Convert commonwl.org to run off Jekyll, in order to facilitate a more straightforward future editing process. This will only affect the main site, and not the user documentation, at present.

  • Rewrite site to utilize RWD (Responsive Web Design)
  • Evaluate the site's WCAG Web Accesibility Guidelines compliance and implement any necessary fixes
  • Evaluate site performance and implement any necessary improvements
  • Incorporate new content
  • Add Top Nav Menu and Site Footer
  • Setup long-term staging/testing solution
  • Incorporate custom Twitter feed
  • Fill in SEO info in _config.yml

Format off for Community Page

The meeting details on the new community page are not formatted by like the rest of the page.

In general: Perhaps we don't need this on the community page but a link to a new page since it swallows up the rest of the resources of which the page was intended. We already have a mention of the weekly chat in the bullet points, so it is extra confusing. Perhaps that should link to a nicely formatted page about the meetings if people are interested.

To look like the rest of the page/general guidelines:
(1) Follow look and feel of rest of site

  • Titles should be in all caps --> Agenda and Notes not Agenda and notes (and/if/but not caps)
  • If you have a list of items --> Use the bullets
  • We use numbers no where else on the site
  • Periods only needed at end of sentences (https://w3id.org/cwl/meeting_minutes.)
  • Hyperlinks should be given context (https://w3id.org/cwl/meeting_minutes.) and alt text instead of the direct link.
  • Avoid long hyperlinks if possible: EMEA-Americas: weekly every Wednesday at 16:00 UTC from March-November and 17:00 UTC from November-March
  • You should try to not have have section headers just start mid-page, for a good example to do this correctly see here: https://www.commonwl.org/features
  • Balance new sections with existing format and content: Code of conduct already lives here: https://www.commonwl.org/code-of-conduct/ -- link to it perhaps in the list of bullet points above instead of having a new section for it.
  • Consider making a new page when a topic seems to overwhelm the content of the page and/or is not of interest to all participants or very detailed on one topic
  • Avoid hyperlinks when you can just put the detail easily on the page -- aka EMEA (Europe, the Middle East and Africa) is way more informative than linking to a wikipedia article. Same with APAC.

(2) Make things are new person/user friendly as possible: No explanation made about what the Weekly Meeting is, why one would attend or any context. Again, lots of work to make things as user-friendly in mind so we should keep doing this.

In general, we should have a review process since a bunch of work was made to make the website look good , organized, be approachable and consistent. Otherwise, I fear we will lose the headway we made quickly with the reformat.

Suggested fixes for the website

Hi everyone. These are some things that I can't suggest directly as code changes.

Also, some standards are needed:

  • Decide whether to use the Oxford/Serial Comma or not
  • What to do with the word "analys/ze"?
  • In tables (ecosystem, projects) maybe always start paragraphs with a capital letter?

Please also see a compilation of my suggestions in this review: #75 (review)

Links hrefs to anchors need to use _relative_url

Link hrefs to anchors need to use _relative_url so they work properly, regardless of environment (staging, production, local, etc).

e.g.: [CWL leadership team]({{ site.url }}/#Leadership_Team) should be [CWL leadership team]({{ "#Leadership_Team" | relative_url }})

CWL Leadership Team: missing text from old website

Here is the old text, that should replace (alphabetical) under https://www.commonwl.org/cwl-staging/#CWL_Leadership_Team

CWL is a member project of the Software Freedom Conservancy. In general, discussions about CWL should happen on open forums but you can also contact the CWL leadership team & Conservancy directly via [email protected]. This address should be CC'ed regarding all activities that involve activities of Common Workflow Language that related to things other than software development and documentation, and particularly any activities that expect to make use of Software Freedom Conservancy's non-profit status.

To contact just the CWL leadership team, please email [email protected].

The CWL leadership team consists of the following people, listed in alphabetical order by their last name:

User Gallery Nomination: WorkflowHub

User or Project name.
WorkflowHub

Section to list under
Cross-Domain

Link (URL) to website
https://www.workflowhub.eu

Description
WorkflowHub is a registry for describing, sharing and publishing scientific computational workflows.

The registry supports any workflow in its native repository.

WorkflowHub aims to facilitate discovery and re-use of workflows in an accessible and interoperable way. This is achieved through extensive use of open standards and tools, including Common Workflow Language (CWL), RO-Crate, BioSchemas and TRS, in accordance with the FAIR principles.

Logo or small graphic
https://workflowhub.eu/assets/logos/workflowhub-902d467e74d8797a4a2ac8313621208a1a2b215329e568e07b620baa03ed910b.svg

social icon hover text

           <title>Matrix (protocol) logo</title>

This title shows up as a hover text for this icon on Firefox (non-mobile), but none of the other icons have a hover text.

If there is to be a hover text, I would prefer it said "CWL Matrix Space"

YouTube: "CWL YouTube Channel"
Twitter: "CWL Twitter Account"
GitHub: "CWL GitHub Organization"
Discourse: "CWL Discourse Forum"

Originally posted by @mr-c in #116 (comment)

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