[ARVADOS] updated: 1.3.0-270-g099399979

[Git user]

Summary of changes:
 build/run-library.sh                    | 5 +++++
 doc/admin/upgrading.html.textile.liquid | 8 ++++++++
 sdk/cwl/fpm-info.sh                     | 2 ++
 3 files changed, 15 insertions(+)

       via  09939997947db0390e62e4b450fef43896d318aa (commit)
      from  bdbf7c4ee346fd1615f882255b3606d8d5360710 (commit)

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commit 09939997947db0390e62e4b450fef43896d318aa
Author: Ward Vandewege <wvandewege at veritasgenetics.com>
Date:   Tue Feb 5 17:14:05 2019 -0500

    Make the python-arvados-cwl-runner package expose the cwltool executable, make
    it conflict with the python-cwltool (and cwltool) packages, and add a note to
    the upgrade documentation to that effect. Also document the Centos7 specific
    upgrade from python33 to rh-python35 as part of story 9945.
    
    refs #9945
    
    Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <wvandewege at veritasgenetics.com>

diff --git a/build/run-library.sh b/build/run-library.sh
index 9df62adee..e6b086a5a 100755
--- a/build/run-library.sh
+++ b/build/run-library.sh
@@ -602,6 +602,11 @@ fpm_build_virtualenv () {
     COMMAND_ARR+=("usr/share/$python/dist/$PYTHON_PKG/data/lib/security/libpam_arvados.py=/usr/data/lib/security/")
   fi
 
+  # the python-arvados-cwl-runner package comes with cwltool, expose that version
+  if [[ -e "$WORKSPACE/$PKG_DIR/dist/build/usr/share/python2.7/dist/python-arvados-cwl-runner/bin/cwltool" ]]; then
+    COMMAND_ARR+=("usr/share/python2.7/dist/python-arvados-cwl-runner/bin/cwltool=/usr/bin/")
+  fi
+
   COMMAND_ARR+=(".")
 
   FPM_RESULTS=$("${COMMAND_ARR[@]}")
diff --git a/doc/admin/upgrading.html.textile.liquid b/doc/admin/upgrading.html.textile.liquid
index f94ecdc87..eda25d5cc 100644
--- a/doc/admin/upgrading.html.textile.liquid
+++ b/doc/admin/upgrading.html.textile.liquid
@@ -56,6 +56,14 @@ Or alternatively, by updating the shebang line at the start of the script to:
 </pre>
 </notextile>
 
+h4. python-arvados-cwl-runner deb/rpm package now conflicts with python-cwltool deb/rpm package
+
+As part of story "#9945":https://dev.arvados.org/issues/9945, the distribution packaging (deb/rpm) of our Python packages has changed. The python-arvados-cwl-runner package now includes a version of cwltool. If present, the python-cwltool and cwltool distribution packages will need to be uninstalled before the python-arvados-cwl-runner deb or rpm package can be installed.
+
+h4. Centos7 Python 3 dependency upgraded to rh-python35
+
+As part of story "#9945":https://dev.arvados.org/issues/9945, the Python 3 dependency for Centos7 Arvados packages was upgraded from SCL python33 to rh-python35.
+
 h4. Centos7 package for libpam-arvados depends on the python-pam package, which is available from EPEL
 
 As part of story "#9945":https://dev.arvados.org/issues/9945, it was discovered that the Centos7 package for libpam-arvados was missing a dependency on the python-pam package, which is available from the EPEL repository. The dependency has been added to the libpam-arvados package. This means that going forward, the EPEL repository will need to be enabled to install libpam-arvados on Centos7.
diff --git a/sdk/cwl/fpm-info.sh b/sdk/cwl/fpm-info.sh
index fa8f43e6e..5c47532db 100644
--- a/sdk/cwl/fpm-info.sh
+++ b/sdk/cwl/fpm-info.sh
@@ -10,3 +10,5 @@ case "$TARGET" in
         fpm_depends+=(libcurl3-gnutls libpython2.7)
         ;;
 esac
+
+fpm_args+=(--conflicts=python-cwltool --conflicts=cwltool)

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