<commit_before>****************************************
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](http://bd2kcc.org/files/hackathons.pdf), 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](http://clujcowork.ro/), 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](https://groups.google.com/d/msg/common-workflow-language/hAMs0nu2k_o/h3eXXbwkDQAJ)
- Researched how the CWL website is built; summary:
  [schema_salad](https://github.com/common-workflow-language/schema_salad)
  builds the raw HTML out of the
  [README.rst](https://github.com/common-workflow-language/common-workflow-language/blob/master/README.md)
  and
  [cwl-avro.yml](https://github.com/common-workflow-language/common-workflow-language/blob/master/draft-3/cwl-avro.yml)
  files via a worklow 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](https://github.com/common-workflow-language/schema_salad/issues/4)
  instead of building our own. Big thanks to <NAME> 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](https://github.com/common-workflow-language/common-workflow-language/issues/148).
- Purchased train ticket to the Festival of Genomics.
- Started the ball rolling on [a meeting at the Broad Institute on November 13th](https://groups.google.com/d/msg/ga4gh-dwg-containers-workflows/55TTWIFTk6M/584NcQaVDQAJ).
- 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](https://github.com/common-workflow-language/common-workflow-language/issues/147)
  and another [to create a governenace
  plan](https://github.com/common-workflow-language/common-workflow-language/issues/146)
- Reviewed and [gave feedback](https://github.com/ctb/titus-blog/pull/9) 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](https://github.com/mr-c/common-workflow-language/tree/CoC)
  I seny 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](https://github.com/common-workflow-language/schema_salad/issues/2).
- Found and
  [fixed](https://github.com/common-workflow-language/schema_salad/pull/3) 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](https://twitter.com/biocrusoe/status/656789421421961216) &
  [codefest](https://twitter.com/biocrusoe/status/656791781510676480) 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
  [<NAME>](https://github.com/brainstorm). Made a quick entry on the
  [wiki](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems#mistral)
  for it.
- Responded to [an error with our
  documentation](https://github.com/common-workflow-language/common-workflow-language/issues/149).
  Fixed it; thanks to [<NAME>](https://github.com/skanwal) for
  reporting it!
- Made CWL Build Bot user on PyPI complete with GPG signing key. [Asked <NAME> to make it the owner of CWL
  packages](https://github.com/common-workflow-language/cwltool/issues/4).

Friday 2015-10-23
-----------------

- NSF funding opportunities review
- More back and forth on the blog feed issue; finally [it got
  fixed](https://github.com/abakan/ablog/issues/54#issuecomment-150762739)!
- Learned that I was not selected for the Stripe Open Source Retreat 2016.

Saturday 2015-10-24
-------------------

- Polished my notes from the week into this blogpost.

To do
-----

- Get [<NAME>'s recently contributed
  workflows](https://github.com/common-workflow-language/schema_salad/issues/4)
  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.

<commit_msg>update todo<commit_after>****************************************
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](http://bd2kcc.org/files/hackathons.pdf), 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](http://clujcowork.ro/), 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](https://groups.google.com/d/msg/common-workflow-language/hAMs0nu2k_o/h3eXXbwkDQAJ)
- Researched how the CWL website is built; summary:
  [schema_salad](https://github.com/common-workflow-language/schema_salad)
  builds the raw HTML out of the
  [README.rst](https://github.com/common-workflow-language/common-workflow-language/blob/master/README.md)
  and
  [cwl-avro.yml](https://github.com/common-workflow-language/common-workflow-language/blob/master/draft-3/cwl-avro.yml)
  files via a worklow 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](https://github.com/common-workflow-language/schema_salad/issues/4)
  instead of building our own. Big thanks to <NAME> 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](https://github.com/common-workflow-language/common-workflow-language/issues/148).
- Purchased train ticket to the Festival of Genomics.
- Started the ball rolling on [a meeting at the Broad Institute on November 13th](https://groups.google.com/d/msg/ga4gh-dwg-containers-workflows/55TTWIFTk6M/584NcQaVDQAJ).
- 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](https://github.com/common-workflow-language/common-workflow-language/issues/147)
  and another [to create a governenace
  plan](https://github.com/common-workflow-language/common-workflow-language/issues/146)
- Reviewed and [gave feedback](https://github.com/ctb/titus-blog/pull/9) on draft blog commenting policy for <NAME>'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](https://github.com/mr-c/common-workflow-language/tree/CoC)
  I seny 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](https://github.com/common-workflow-language/schema_salad/issues/2).
- Found and
  [fixed](https://github.com/common-workflow-language/schema_salad/pull/3) 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](https://twitter.com/biocrusoe/status/656789421421961216) &
  [codefest](https://twitter.com/biocrusoe/status/656791781510676480) 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
  [<NAME>](https://github.com/brainstorm). Made a quick entry on the
  [wiki](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems#mistral)
  for it.
- Responded to [an error with our
  documentation](https://github.com/common-workflow-language/common-workflow-language/issues/149).
  Fixed it; thanks to [<NAME>](https://github.com/skanwal) for
  reporting it!
- Made CWL Build Bot user on PyPI complete with GPG signing key. [Asked <NAME> to make it the owner of CWL
  packages](https://github.com/common-workflow-language/cwltool/issues/4).

Friday 2015-10-23
-----------------

- NSF funding opportunities review
- More back and forth on the blog feed issue; finally [it got
  fixed](https://github.com/abakan/ablog/issues/54#issuecomment-150762739)!
- 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 [<NAME>'s recently contributed
  workflows](https://github.com/common-workflow-language/schema_salad/issues/4)
  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 <NAME> to organize a CWL related workshop/codefest in Paris
  during the Spring.
- Start the sustainability review.
- Start an ontological comparision between the semantics of CWL tool and
  workflow descriptions and [the other known
  efforts](https://github.com/common-workflow-language/common-workflow-language/wiki/Existing-Workflow-systems).
- Follow up on Code of Conduct
- Follow up with the Software Freedom Conservancy and NumFOCUS.

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