[sagemath] 02/02: Use jmol package.

[Tobias Hansen]

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thansen pushed a commit to branch master
in repository sagemath.

commit bedf0c7716d3a1f7b6ad9cf48d65ef8a24d6248d
Author: Tobias Hansen <thansen at broeselmaschine.fc.up.pt>
Date:   Sat Dec 3 23:41:51 2016 +0000

    Use jmol package.
---
 debian/control.runtime-depends    |  1 +
 debian/patches/debian-paths.patch | 11 +++++++++++
 debian/pruner/configure.ac        |  3 +--
 3 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/debian/control.runtime-depends b/debian/control.runtime-depends
index 4ba5244..9adee8a 100644
--- a/debian/control.runtime-depends
+++ b/debian/control.runtime-depends
@@ -10,6 +10,7 @@
  gmp-ecm,
  ipython (>= 5.1.0-2),
  iso-codes,
+ jmol (>= 14.6.4),
  jupyter-client,
  jupyter-core,
  jupyter-nbextension-jupyter-js-widgets,
diff --git a/debian/patches/debian-paths.patch b/debian/patches/debian-paths.patch
index 504f1d8..b54100f 100644
--- a/debian/patches/debian-paths.patch
+++ b/debian/patches/debian-paths.patch
@@ -317,3 +317,14 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
  
  def degseq_to_data(degree_sequence):
      """
+--- a/sage/src/sage/interfaces/jmoldata.py
++++ b/sage/src/sage/interfaces/jmoldata.py
+@@ -148,7 +148,7 @@
+             True
+         """
+         # Set up paths, file names and scripts
+-        jmolpath = os.path.join(SAGE_LOCAL, "share", "jmol", "JmolData.jar")
++        jmolpath = os.path.join(SAGE_LOCAL, "share", "java", "JmolData.jar")
+         target_native = targetfile
+         import sys
+         if sys.platform == 'cygwin':
diff --git a/debian/pruner/configure.ac b/debian/pruner/configure.ac
index b5596fe..7b5e128 100644
--- a/debian/pruner/configure.ac
+++ b/debian/pruner/configure.ac
@@ -143,8 +143,7 @@ AC_SUBST(HAS_IML)
 AC_CHECK_PROG(HAS_IPYTHON, ipython, "True", "False")
 AC_SUBST(HAS_IPYTHON)
 
-# FIXME(jmol): debian's version is too old, use sage's for now to avoid failing tests
-HAS_JMOL="False"
+AC_CHECK_FILE(/usr/bin/jmol, HAS_JMOL="True", HAS_JMOL="False")
 AC_SUBST(HAS_JMOL)
 
 AC_CHECK_PROG(HAS_JUPYTER_CLIENT, jupyter-kernelspec, "True", "False")

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