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9 changes: 5 additions & 4 deletions conf.py
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Expand Up @@ -35,6 +35,7 @@
# to refer to the author. Default is ``{}``.
blog_authors = {
'Michael R. Crusoe': ('Michael R. Crusoe', None),
'me': ('Michael R. Crusoe', None),
}


Expand All @@ -51,14 +52,14 @@
# links of these locations. Similar to :confval:`blog_authors`, dictionary
# keys should be used in ``post`` directive to refer to the locations.
# Default is ``{}``.
#blog_locations = {
# 'Earth': ('The Blue Planet', 'http://en.wikipedia.org/wiki/Earth),
#}
blog_locations = {
'Cluj': ('Cluj-Napoca, Romania', 'http://clujcowork.ro/'),
}


# -- Blog Post Related --------------------------------------------------------

# post_date_format = '%b %d, %Y'
post_date_format = '%Y-%m-%d'


# Number of paragraphs (default is ``1``) that will be displayed as an excerpt
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3 changes: 0 additions & 3 deletions index.rst
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@@ -1,9 +1,6 @@
Updates from @mr-c's CWL work
=============================


Here is a list of most recent posts:

.. postlist:: 5
:excerpts:

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113 changes: 62 additions & 51 deletions week-of-20151019-update.rst
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@@ -1,3 +1,8 @@
.. post:: 2015-10-26
:tags: weekly-update
:author: me
:location: Cluj

****************************************
Weekly report for the week of 2015-10-19
****************************************
Expand All @@ -13,12 +18,12 @@ 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
- 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.
- Renewed my membership at `Cluj Cowork <http://clujcowork.ro/>`_, where I do
my work.

Friday 2015-10-16
-----------------
Expand All @@ -30,60 +35,66 @@ Friday 2015-10-16
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)
- `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)
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 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](https://github.com/common-workflow-language/common-workflow-language/issues/148).
- `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).
- 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
- 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.
This `Code of Conduct draft
<https://github.com/mr-c/common-workflow-language/tree/CoC>`_ 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](https://github.com/common-workflow-language/schema_salad/issues/2).
- Found and
[fixed](https://github.com/common-workflow-language/schema_salad/pull/3) a
`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
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
Expand All @@ -94,24 +105,24 @@ Thursday 2015-10-22

- copyedited FoG workshop materials
- initial meeting with local tech nonprofit
- reviewed `mistral`, a workflow engine reported by
[Roman Valls Guimerà](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)
- reviewed `mistral`, a workflow engine reported by `Roman Valls Guimerà
<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 [Sehrish Kanwal](https://github.com/skanwal) for
- Responded to `an error with our documentation
<https://github.com/common-workflow-language/common-workflow-language/issues/149>`_.
Fixed it; thanks to `Sehrish Kanwal <https://github.com/skanwal>`_ 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](https://github.com/common-workflow-language/cwltool/issues/4).
- Made CWL Build Bot user on PyPI complete with GPG signing key. `Asked Peter
Amstutz 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)!
- 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.

Expand All @@ -123,8 +134,8 @@ Saturday 2015-10-24
To do
-----

- Get [Andrey Kartashov's recently contributed
workflows](https://github.com/common-workflow-language/schema_salad/issues/4)
- Get `Andrey Kartashov'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
Expand All @@ -134,8 +145,8 @@ To do
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).
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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