Revise tutorials for new data format and bundle APIs

[Conrad Huang]

Need to document APIs referenced in tutorials and annotate methods as to whether they are part of the public API

[pett]

Milestone renamed

[Conrad Huang]

ChimeraX 0.6 APIs will include those used in tutorials

APIs used in tutorials (so far)

:py:class:`chimerax.core.atomic.Atom`
:py:class:`chimerax.core.atomic.AtomicStructure`
:py:class:`chimerax.core.atomic.Bond`
:py:class:`chimerax.core.atomic.Collection`
:py:class:`chimerax.core.atomic.Residue`
:py:class:`chimerax.core.commands`
:py:class:`chimerax.core.commands.cli.CmdDesc`
:py:class:`chimerax.core.commands.ModelsArg`
:py:class:`chimerax.core.commands.register`
:py:class:`chimerax.core.commands.register_selector`
:py:func:`chimerax.core.commands.cli.register`
:py:func:`chimerax.core.commands.run`
:py:class:`chimerax.core.logger.Logger`
:py:class:`chimerax.core.models.Model`
:py:class:`chimerax.core.objects.Objects`
:py:class:`chimerax.core.session.Session`
:py:class:`chimerax.core.toolshed.BundleAPI`
:py:class:`chimerax.core.toolshed.BundleInfo`
:py:class:`chimerax.core.toolshed.CommandInfo`
:py:class:`chimerax.core.toolshed.SelectorInfo`
:py:class:`chimerax.core.toolshed.ToolInfo`
:py:class:`~chimerax.core.toolshed.BundleAPI.fetch_from_database`
:py:class:`~chimerax.core.toolshed.BundleAPI.finish`
:py:class:`~chimerax.core.toolshed.BundleAPI.get_class`
:py:class:`~chimerax.core.toolshed.BundleAPI.initialize`
:py:class:`~chimerax.core.toolshed.BundleAPI.open_file`
:py:class:`~chimerax.core.toolshed.BundleAPI.register_command`
:py:class:`~chimerax.core.toolshed.BundleAPI.register_selector`
:py:class:`~chimerax.core.toolshed.BundleAPI.save_file`
:py:class:`~chimerax.core.toolshed.BundleAPI.start_tool`
:py:class:`chimerax.core.ui.HtmlToolInstance`
:py:class:`chimerax.core.ui.widgets.HtmlView.
:py:func:`chimerax.core.io.open_filename`

Source code will also need to be updated so that supported API functions, methods and attributes are annotated with the string "Supported API" at the beginning of their doc-strings. The first time an API entry is proposed, it should be labeled with "Supported API: proposed x.y" where x.y is the ChimeraX version in which this entry is officially supported. When ChimeraX x.y is released, the doc-string must be changed to "Supported API: added x.y". Once an API has been "added", it can never go back to being "proposed". Instead, keywords added after the initial API should be annotated with "proposed: x.y" during development and "added: x.y" when committed/released.

[pett]

Marked supported APIs for chimerax.core.atomic.Atom. I'm assuming that "chimerax.core.atomic.Atom" doesn't imply chimerax.core.atomic.Atoms, which I did not mark up (but which could probably be deduced from the Atom API markup).

[Conrad Huang]

More verification and editing needed.

[Conrad Huang]

Toolshed classes now have "Supported API" notation. More classes need to be examined.

[Conrad Huang]

Classes listed on ​Developer index page

(*) = has at least one Supported API markup.

• Atom (*)
  • CyAtom (*)
• AtomicStructure
  • Structure
    • StructureData (*)
    • Model
• Atoms
  • Collection
• Bond (*)
• Camera
• Chain
  • StructureSeq
    • Sequence
• Command
• Drawing
• Grid_Data
• Lighting
• Log (*)
• Material
• Model
  • Drawing
• MolecularSurface
  • Surface
    • Model
• Place
• Residue
  • CyResidue (*)
• Session
  • ConfigFile
• Settings
• ToolInfo (*)
• ToolInstance
  • State
• Toolshed (*)
• TriggerSet
• View
• Volume
  • Model

Base classes not listed on Developer index page

• Collection
• CyAtom (*)
• CyResidue (*)
• ConfigFile
• Sequence
• State
• Structure
• StructureData (*)
• StructureSeq
• Surface

Some classes not listed on Developer index page

• CommandInfo, FormatInfo, BundleInfo
  • Accessible from "toolshed" link.
  • Has Supported API markup.

• Bonds, Residues, Models
  • Other subclasses of Collection.

[Conrad Huang]

Ticket retargeted after milestone closed

[Conrad Huang]

The API used in tutorials were documented a while back. With the changes in the file format/open/save handling introduced in 0.93, Eric will be revising the tutorials to use the new supported bundle and io APIs.

[pett]

The new open/save APIs were documented before the RC1 release.