Weekly report for the week of 2015-10-19¶
Hello! Here is the first weekly update on what I’ve been doing for the CWL covering the week of 2015-10-19, and a couple days before.
Summary: settling in and getting ready for the Festival of Genomics Workshop on November 3rd.
- Announcement of SBG Gift on Twitter & this blog. Tagged the wrong vet med school in my tweet; whoops!
- Reviewed BD2K hackathon funding opportunity, decided to skip it for the November CWL codefest; will reconsider for future workshops that have the required diversity plan.
- Renewed my membership at Cluj Cowork, where I do my work.
- Figured out how to use the UC Davis library to view paywalled articles when one is not on their network.
- Short work day due to travel logistics.
- Announced free tickets to CWL Workshop at the Festival of Genomics
- Researched how the CWL website is built; summary: schema_salad builds the raw HTML out of the README.rst and cwl-avro.yml files via a workflow specified in CWL. The process is initiated by a script that runs on the Arvados CI server. It is good that we are using our own tools (“eating our dogfood”); I will document this more as I move the automated testing and building of the website from Arvados’s servers to ones run by the project. Eventually we will want to migrate to an existing documentation system instead of building our own. Big thanks to Peter Amstutz for all his work maintaining and building the CWL website & standard!
- Noted that CWL job documents could and should include a reference to the workflow that they are intended for.
- Purchased train ticket to the Festival of Genomics.
- Started the ball rolling on a meeting at the Broad Institute on November 13th.
- Reported bug with ablog feeds: https://github.com/rtfd/readthedocs.org/issues/1771#issuecomment-149336887
- Opened a couple tracking issues, one for creating/joining a US foundation to own the CWL assets and another to create a governenace plan
- Reviewed and gave feedback on draft blog commenting policy for C. Titus Brown’s blog. It has since been published: http://ivory.idyll.org/blog/2015-site-policies.html
- Reviewed the available Code of Conduct templates and adapted one for CWL use. This Code of Conduct draft I sent for review by the leadership team. Initially I went with the Django version, but it was too unwieldy for a group our size. I received good feedback and will send out a revision next week.
- Got flights to visit TACC & Broad Institute sorted
- Noticed that we weren’t tagging the cwltool PyPI releases on the GitHub repo; wrote-up issue.
- Found and fixed a problem that prevented the installation of the SALAD from the GitHub repo (as opposed to using PyPI).
- Individual membership in GA4GH approved, spent time trying to understand its structure and how to interact with them. Sent feedback to GA4GH about issues with the signup process (password validation & broken links).
- promoted workshop & codefest on Twitter.
- followed up on blog feed issue: https://github.com/rtfd/readthedocs.org/issues/1771#issuecomment-149875488
- Put in request for video camera & microphone for the CWL codefest
- Caught up on CWL and other email backlog
- Reviewed NIH BD2K funding opportunities
- Copyedited FoG workshop materials
- initial meeting with local tech nonprofit
- reviewed mistral, a workflow engine reported by Roman Valls Guimerà. Made a quick entry on the wiki for it.
- Responded to an error with our documentation. Fixed it; thanks to Sehrish Kanwal for reporting it!
- Made CWL Build Bot user on PyPI complete with GPG signing key. Asked Peter Amstutz to make it the owner of CWL packages.
- NSF funding opportunities review
- More back and forth on the blog feed issue; finally it got fixed!
- Update on my application for the Stripe Open Source Retreat 2016: I was not selected for further review.
- Polished my notes from the week into this blogpost.
- Get Andrey Kartashov’s recently contributed workflows running for myself.
- Familiarize myself with vagrant to setup Jenkins CI server to test CWL conformance
- Refresh my backstory of the CWL slides for the Festival of Genomics workshop.
- Sketch out more technical slides for TACC/Agave presentation the week after.
- Work with Hervé Ménager to organize a CWL related workshop/codefest in Paris during the Spring.
- Start the sustainability review.
- Start an ontological comparison between the semantics of CWL tool and workflow descriptions and the other known efforts.
- Follow up on Code of Conduct
- Follow up with the Software Freedom Conservancy and NumFOCUS.