[sagenb] 01/01: Document the fact that 3D plots don't work due to JSmol

[Ximin Luo]

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infinity0 pushed a commit to branch master
in repository sagenb.

commit 64663ea47bce7a565cdb7c63ef7fabc1a56394a6
Author: Ximin Luo <infinity0 at debian.org>
Date:   Mon Dec 5 01:32:24 2016 +0100

    Document the fact that 3D plots don't work due to JSmol
---
 debian/README.Debian                     | 10 ++++++++
 debian/control                           |  2 ++
 debian/patches/debian-jmol-paths.patch   | 41 ++++++++++++++++++++++++++++++++
 debian/patches/debian-python-paths.patch | 17 +++++++++++++
 debian/patches/series                    |  2 ++
 5 files changed, 72 insertions(+)

diff --git a/debian/README.Debian b/debian/README.Debian
index f925dd3..f2d205b 100644
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -1,3 +1,13 @@
+3D Plots
+========
+
+3D plots do not work because JSmol cannot currently be packaged for Debian. See
+the README.source of the jmol package for more details on this situation.
+
+Upstream claims to support using the old Jmol applet instead of JSmol, but it
+does not work and it would be hard for us Debian folks to patch it in, see
+https://github.com/sagemath/sagenb/issues/415
+
 Secure Notebook
 ===============
 
diff --git a/debian/control b/debian/control
index 768a17b..576a2b6 100644
--- a/debian/control
+++ b/debian/control
@@ -33,6 +33,8 @@ Depends: ${python:Depends}, ${misc:Depends},
  libjs-mathjax,
  libjs-prettify,
  tinymce
+# Not working, see README.Debian
+#Recommends: jmol-applet
 Description: Standalone Sage Notebook
  The Sage Notebook is a web-based graphical user interface for
  mathematical software.
diff --git a/debian/patches/debian-jmol-paths.patch b/debian/patches/debian-jmol-paths.patch
new file mode 100644
index 0000000..05c634c
--- /dev/null
+++ b/debian/patches/debian-jmol-paths.patch
@@ -0,0 +1,41 @@
+Description: Give the correct paths to jmol-applet
+ This is just for documentation purposes; currently this is broken in upstream
+ See README.Debian for more details.
+Author: Ximin Luo <infinity0 at debian.org>
+Forwarded: not-needed
+--- a/sagenb/data/sage/js/jmol_lib.js
++++ b/sagenb/data/sage/js/jmol_lib.js
+@@ -38,11 +38,11 @@
+         deferUncover: true,                 // wait to uncover applet until script completed
+         //The paths below assume your server is set up with standard JSmol directory.  If not
+         //they will need modification for the page to work.
+-        jarPath: "/jsmol/java", //path to applet .jar files on server.
++        jarPath: "/java/jmol-applet", //path to applet .jar files on server.
+         j2sPath: "/jsmol/j2s",//path to javascript version.
+         makeLiveImg:"/jsmol/j2s/img/play_make_live.jpg",  //path to activate 3-D image.
+-        jarFile: "JmolAppletSigned0.jar",
+-        isSigned: true,
++        jarFile: "JmolApplet0.jar",
++        isSigned: false,
+         //disableJ2SLoadMonitor: true,
+         disableInitialConsole: true,
+         script: "",
+--- a/sagenb/flask_version/base.py
++++ b/sagenb/flask_version/base.py
+@@ -36,12 +36,10 @@
+         self.add_static_path('/javascript', DATA)
+         self.add_static_path('/static', DATA)
+         self.add_static_path('/java', DATA)
+-        self.add_static_path('/java/jmol', os.path.join(os.environ["SAGE_ROOT"],"local","share","jmol"))
+-        self.add_static_path('/jsmol', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol"))
+-        self.add_static_path('/jsmol/js', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","js"))
+-        self.add_static_path('/j2s', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","j2s"))
+-        self.add_static_path('/jsmol/j2s', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","j2s"))
+-        self.add_static_path('/j2s/core', os.path.join(os.environ["SAGE_ROOT"],"local","share","jsmol","j2s","core"))
++        self.add_static_path('/java/jmol', os.path.join("/usr","share","jmol"))
++        self.add_static_path('/java/jmol-applet', os.path.join("/usr","share","jmol-applet"))
++        self.add_static_path('/jsmol', os.path.join("/usr","share","jsmol"))
++        self.add_static_path('/j2s', os.path.join("/usr","share","jsmol","j2s"))
+         import mimetypes
+         mimetypes.add_type('text/plain','.jmol')
+ 
diff --git a/debian/patches/debian-python-paths.patch b/debian/patches/debian-python-paths.patch
new file mode 100644
index 0000000..defce56
--- /dev/null
+++ b/debian/patches/debian-python-paths.patch
@@ -0,0 +1,17 @@
+Description: Give the correct paths to python
+Author: Ximin Luo <infinity0 at debian.org>
+Forwarded: not-needed
+--- a/sagenb/notebook/notebook.py
++++ b/sagenb/notebook/notebook.py
+@@ -639,10 +639,9 @@
+         else:
+             import random
+             user_at_host = random.choice(server_pool)
+-            python_command = os.path.join(os.environ['SAGE_ROOT'], 'sage -python')
+             return WorksheetProcess_RemoteExpectImplementation(user_at_host=user_at_host,
+                              process_limits=process_limits,
+-                             remote_python=python_command)
++                             remote_python='python')
+ 
+ 
+     def _python_command(self):
diff --git a/debian/patches/series b/debian/patches/series
index ab0f7ee..3490384 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -9,3 +9,5 @@ disable-bgiframe.patch
 disable-farbtastic-jpicker.patch
 switch-system-jquery-vanderlee-colorpicker.patch
 debian-sage3d-java-paths.patch
+debian-python-paths.patch
+debian-jmol-paths.patch

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