​Change set for a pure Python bundle upgraded from old layout to new layout.

​Change set for a bundle with C++ code upgraded from old layout to new layout. Ignore the changes in apps, which is a one-time change for all bundles.

Conrad: Working my way down. Updated and tested bundles are in black and crossed out. Updated but untested are in blue. Skipped (too scary) are in red. Not updated are in black.

Old School

(no src subdir)

• oculus (TomG) [not part of distribution]

Slightly Behind the Times

(src subdir, no bundle_info.xml)

• cytoscape (Scooter) [no longer in distribution]
• stringdb (Scooter) [no longer in distribution]
• toolshed (Conrad) [no longer used]

Trendsetters

(bundle_info.xml)

• add_missing_atoms (TomG)
• alignments (Eric) -- custom init now needed in bundle info
• align_algs (Eric) -- subdirectory support_cpp still uses old-style Makefile because it installs a non-Python C/C++ library and some include files. So far this is the only instance outside of the core.
• blastprotein (Conrad)
• bogus (Conrad)
• bundle_builder (Conrad) -- must use setup.py.in because the dev command depends on this bundle
• cage_builder (TomG)
• cellpack (TomG)
• chem_group (Eric) not updated, sel amide crashes
• cmd_line (Eric)
• color_globe (TomG)
• contacts (TomG)
• crosslinks (TomG)
• exp_cmd (Conrad)
• file_history (TomG)
• hbonds (Eric) -- bundle testing procedure needs improvement
• help_viewer (Greg)
• ihm (TomG)
• label (TomG)
• list_info (Conrad)
• log (Eric)
• map_series_gui (TomG)
• match_maker (Eric)
• mav (Eric)
• md_crds (Eric)
• mlp (TomG)
• mmtf (Greg)
• mmtf-python (Greg) [Replaced by mmtf]
• model_panel (Eric)
• model_series (TomG)
• mol2 (Eric) updated but save test.mol2 crashes
• morph (TomG)
• mouse_modes (TomG)
• movie (TomG)
• remote_control (TomG) no XMLRPC test case for remotecontrol
• residue_fit (TomG)
• rest_server (Conrad)
• shell (Eric)
• shortcuts (TomG)
• sideview (Greg)
• sim_matrices (Eric)
• smooth_lines (TomG)
• spacenavigator (TomG)
• stl (Greg)
• storm (TomG)
• struts (TomG)
• test (TomG)
• tug (TomG)
• vive (TomG)
• volume_viewer (TomG)
• vtk (TomG)