.. post:: 2015-10-26 :tags: weekly-update :author: me :location: Cluj **************************************** 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. Thursday 2015-10-15 ------------------- - 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. Friday 2015-10-16 ----------------- - 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. Monday 2015-10-19 ----------------- - `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 Tuesday 2015-10-20 ------------------ - 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). Wednesday 2015-10-21 -------------------- - 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 Thursday 2015-10-22 ------------------- - 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 `_. Friday 2015-10-23 ----------------- - 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. Saturday 2015-10-24 ------------------- - Polished my notes from the week into this blogpost. To do ----- - 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.