add links

community-engineer-update.rst

@@ -10,52 +10,61 @@ CWL Community Engineer Six Month Update
 Hello everyone. It has been a while since my last update. Here is what has been
 happening in the CWL world since I began full time work for the project.
 
-Draft 3 was released and the community has committed to releasing 1.0 of the
-standards before ISMB. I will be the release driver.
+`Draft 3 <http://www.commonwl.org>`_ was released by Peter Amstutz. The
+community has committed to releasing 1.0 of the standards before ISMB. I will
+be the release driver.
 
-I met with potential fiscal sponsor, the Software Freedom Conservancy, and
-submitted application for the CWL project to become part of their 501(c)(3).
+I met with potential fiscal sponsor, the `Software Freedom Conservancy
+<https://sfconservancy.org/>`_, and submitted an application for the CWL
+project to become part of their 501(c)(3) charity.
 
 I've been taking full advantage of my base in Europe (first Romania and now
 Belgium) to raise and enhanced the perception of CWL in the European life science
-computing community. I presented at two leading centers (SciLifeLab in
-Stockholm, Flanders ExaScience Lab in Belgium) and I participated in four
+computing community. I presented at two leading centers (`SciLifeLab
+<https://www.scilifelab.se/>`_ in Stockholm, and the `ExaScience Lab
+<http://www.exascience.com/>`_ in Belgium) and I participated in four
 ELIXIR sponsored hackathons: Amsterdam, Netherlands; Freiburg, Germany;
 Copenhagen, Denmark; and Trondheim, Norway.
 
 A CWL subgroup of academic cluster users are figuring out what changes are
 needed to support non-containerized tool execution. Non-cloud support
 for CWL will be critical for wider adoption. I have enjoyed coordinating this
-group and I was able to host a visiting Australian graduate student (Kevin
-Murray) who has gotten Docker containers to work on older platforms without
-needing to upgrade them or use ``root`` privileges.
+group and I was able to host a visiting Australian graduate student (`Kevin
+Murray <http://www.kdmurray.id.au/>`_) who has gotten `Docker containers to
+work on older platforms <https://github.com/common-workflow-language/common-workflow-language/wiki/Userspace-Container-Review>`_
+without needing to upgrade them or use ``root`` privileges.
 
 The CWL is spreading into the wider F/OSS tech world thanks to a partnership
-with the Debian-Med community, the leading community packagers of bioinformatic
-tools and workflows. In support of this partnership I applied for and received
-official status within that community (“Debian Maintainer”) and I have an
-application for full status (“Debian Developer”) in progress.
+with the `Debian-Med community <https://wiki.debian.org/DebianMed>`_, the
+leading community packagers of bioinformatic tools and workflows. In support of
+this partnership I applied for and received official status within that
+community (“Debian Maintainer”) and I have an application for full status
+(“Debian Developer”) in progress.
 
 Roman Valls Guimera and I have started a sub project to automatically produce
 CWL descriptions for those Python tools who use Python’s standard argument
-parser. This is now a Google Summer of Code project that will hopefully
-get their support for a student to work on over the summer.
+parser. This is now a `Google Summer of Code proposal
+<obf.github.io/GSoC/ideas/#automated-tool-wrapperconverter-for-cwl>`_ that will
+hopefully get their support for a student to work on over the summer.
 
 Speaking of GSoC, I agreed to co-mentor (with Stian Soiland-Reyes) another
-student's project to add CWL support to the Apache Taverna project.
+student's project to `add CWL support to the Apache Taverna project
+<https://issues.apache.org/jira/browse/TAVERNA-900>`_.
 
 New Implementations & SDKs:
-Paul Gross's Java re-implementation has already found a couple issue with the
-specifications and fixes have been incorporated. 
+`Paul Gross's CWL Java re-implementation <https://github.com/common-workflow-language/cwljava>`_
+has already found a couple issue with the specifications and fixes have been
+incorporated. 
 
-Sketched out plan for using Peter Amstutz’s “schema salad” tool to
+I have sketched out a plan for using Peter Amstutz’s “schema salad” tool to
 auto-generate code for representing the CWL object model in as many different
 languages as we care for. This is a critical first step to having autogenerated
 SDKs in multiple languages.
 
 Reference implementation improvements:
-Finished review of Peter Amstutz’s ‘cwltool’ and ‘schema salad’. I am maturing
-his work by adding Python 3 compatibility, type checking, code cleanups, and
+I finished a review of Peter Amstutz’s ‘cwltool’ and ‘schema salad’. I am maturing
+his work by adding Python 3 compatibility, `type checking
+<https://github.com/common-workflow-language/cwltool/pull/62>_`, code cleanups, and
 documentation.
 
 Other CWL impacts: