toolshed: Manage installed and available tools

The Toolshed provides an interface for finding installed bundles as well as bundles available for installation from a remote server. The Toolshed can handle updating, installing and uninstalling bundles while taking care of inter-bundle dependencies.

The Toolshed interface uses pkg_resources heavily.

Each Python distribution, a ChimeraX Bundle, may contain multiple tools, commands, data formats, and specifiers, with metadata entries for each deliverable.

In addition to the normal Python package metadta, The ‘ChimeraX’ classifier entries give additional information. Depending on the values of ‘ChimeraX’ metadata fields, modules need to override methods of the BundleAPI class. Each bundle needs a ‘ChimeraX :: Bundle’ entry that consists of the following fields separated by double colons (::).

  1. ChimeraX :: Bundlestr constant

    Field identifying entry as bundle metadata.

  2. categoriesstr

    Comma-separated list of categories in which the bundle belongs.

  3. session_versionstwo comma-separated integers

    Minimum and maximum session version that the bundle can read.

  4. supersedes : str Comma-separated list of superseded bundle names.

  5. custom_initstr

    Whether bundle has initialization code that must be called when ChimeraX starts. Either ‘true’ or ‘false’. If ‘true’, the bundle must override the BundleAPI’s ‘initialize’ and ‘finish’ functions.

Bundles that provide tools need:

  1. ChimeraX :: Toolstr constant

    Field identifying entry as tool metadata.

  2. tool_namestr

    The globally unique name of the tool (also shown on title bar).

  3. categoriesstr

    Comma-separated list of categories in which the tool belongs. Should be a subset of the bundle’s categories.

  4. synopsisstr

    A short description of the tool. It is here for uninstalled tools, so that users can get more than just a name for deciding whether they want the tool or not.

Tools are created via the bundle’s ‘start_tool’ function. Bundles may provide more than one tool.

Bundles that provide commands need:

  1. ChimeraX :: Commandstr constant

    Field identifying entry as command metadata.

  2. command namestr

    The (sub)command name. Subcommand names have spaces in them.

  3. categoriesstr

    Comma-separated list of categories in which the command belongs. Should be a subset of the bundle’s categories.

  4. synopsisstr

    A short description of the command. It is here for uninstalled commands, so that users can get more than just a name for deciding whether they want the command or not.

Commands are lazily registered, so the argument specification isn’t needed until the command is first used. Bundles may provide more than one command.

Bundles that provide selectors need:

  1. ChimeraX :: Selectorstr constant

    Field identifying entry as command metadata.

  2. selector namestr

    The selector’s name.

  3. synopsisstr

    A short description of the selector. It is here for uninstalled selectors, so that users can get more than just a name for deciding whether they want the selector or not.

  4. atomicstr

    An optional boolean specifying whether the selector applies to atoms and bonds. Defaults to ‘true’ and should be set to ‘false’ if selector should not appear in Basic Actions tool, e.g., showing/hiding selected items does nothing.

Commands are lazily registered, so the argument specification isn’t needed until the command is first used. Bundles may provide more than one command.

Bundles that provide data formats need:

  1. ChimeraX :: DataFormatstr constant

    Field identifying entry as data format metadata.

  2. data_namestr

    The name of the data format.

  3. nicknamesstr

    An optional comma-separated list of alternative names. Often a short name is provided. If not provided, it defaults to the lowercase version of the data format name.

  4. categorystr

    The toolshed category.

  5. suffixesstr

    An optional comma-separated list of strings with leading periods, e.g., ‘.pdb’.

  6. mime_typesstr

    An optinal comma-separated list of strings, e.g., ‘chemical/x-pdb’.

  7. urlstr

    A string that has a URL that points to the data format’s documentation.

  8. dangerousstr

    An optional boolean and should be ‘true’ if the data format is insecure – defaults to true if a script.

  9. iconstr

    An optional string containing the filename of the icon – it defaults to the default icon for the category. The file should be ?TODO? – metadata dir? package dir?

  10. synopsis : str A short description of the data format. It is here because it needs to be part of the metadata available for uninstalled data format, so that users can get more than just a name for deciding whether they want the data format or not.

Bundles may provide more than one data format. The data format metadata includes everything needed for the Mac OS X application property list.

Data formats that can be fetched:

# ChimeraX :: Fetch :: database_name :: format_name :: prefixes :: example_id :: is_default

Data formats that can be opened:

# ChimeraX :: Open :: format_name :: tag :: is_default

Data formats that can be saved:

# ChimeraX :: Save :: format_name :: tag :: is_default

Bundles that have other data:

# ChimeraX :: DataDir :: dir_path # ChimeraX :: IncludeDir :: dir_path # ChimeraX :: LibraryDir :: dir_path

TOOLSHED_BUNDLE_INFO_ADDED

Name of trigger fired when new bundle metadata is registered. The trigger data is a BundleInfo instance.

Type:

str

TOOLSHED_BUNDLE_INSTALLED

Name of trigger fired when a new bundle is installed. The trigger data is a BundleInfo instance.

Type:

str

TOOLSHED_BUNDLE_UNINSTALLED

Name of trigger fired when an installed bundle is removed. The trigger data is a BundleInfo instance.

Type:

str

TOOLSHED_BUNDLE_INFO_RELOADED

Name of trigger fired when bundle metadata is reloaded. The trigger data is a BundleInfo instance.

Type:

str

TOOLSHED_OUT_OF_DATE_BUNDLES

Name of trigger fired when out-of-date bundles are detected. The trigger data is None.

Type:

str

Notes

The term ‘installed’ refers to bundles whose corresponding Python module or package is installed on the local machine. The term ‘available’ refers to bundles that are listed on a remote server but have not yet been installed on the local machine.

class BundleAPI

Bases: object

API for accessing bundles

The metadata for the bundle indicates which of the methods need to be implemented.

static data_dir(bundle_info)

Supported API . Returns path to directory of bundle-specific data.

Used to get directory path to data included in the bundle.

Parameters:

bundle_info (BundleInfo instance.) –

Return type:

str or None

static executable_dir(bundle_info)

Experimental API . Returns path to directory of compiled executables.

Used to get directory path to executables at run-time.

Parameters:

bundle_info (BundleInfo instance.) –

Return type:

str or None

static finish(session, bundle_info)

Supported API . Called to deinitialize a bundle in a session.

Must be defined if the custom_init metadata field is set to ‘true’. finish is called when the bundle is unloaded.

Parameters:
static get_class(name)

Supported API . Called to get named class from bundle.

Used when restoring sessions. Instances whose class can’t be found via ‘get_class’ can not be saved in sessions. And those classes must implement the State API.

Parameters:

name (str) – Name of class in bundle.

static include_dir(bundle_info)

Experimental API . Returns path to directory of C++ header files.

Used to get directory path to C++ header files needed for compiling against libraries provided by the bundle.

Parameters:

bundle_info (BundleInfo instance.) –

Return type:

str or None

static init_manager(session, bundle_info, name, **kw)

Supported API . Called to create a manager in a bundle at startup.

Must be defined if there is a Manager tag in the bundle, unless that tag has an autostart=”false” attribute, in which case the bundle is in charge of creating the manager as needed. init_manager is called when bundles are first loaded. It is the responsibility of init_manager to make the manager locatable, e.g., assign as an attribute of session.

Parameters:

  • session (Session instance.) –

  • bundle_info (BundleInfo instance.) –

  • name (str.) – Name of manager to initialize.

  • kw (keyword arguments.) – Keyword arguments listed in the bundle_info.xml.

Returns:

The created manager.

Return type:

ProviderManager instance

static initialize(session, bundle_info)

Supported API . Called to initialize a bundle in a session.

Must be defined if the custom_init metadata field is set to ‘true’. initialize is called when the bundle is first loaded. To make ChimeraX start quickly, custom initialization is discouraged.

Parameters:
static library_dir(bundle_info)

Experimental API . Returns path to directory of compiled libraries.

Used to get directory path to libraries (shared objects, DLLs) for linking against libraries provided by the bundle.

Parameters:

bundle_info (BundleInfo instance.) –

Return type:

str or None

static register_command(*args)

Supported API . When ChimeraX starts, it registers placeholders for commands from all bundles. When a command from this bundle is actually used, ChimeraX calls this method to register the function that implements the command functionality, and then calls the command function. On subsequent uses of the command, ChimeraX will call the command function directly instead of calling this method. The API version for this method is defined by the api_version class variable and defaults to 0.

Parameters:

  • bundle_info (BundleInfo instance.) –

  • command_info (CommandInfo instance.) –

  • logger (Logger instance.) – Version 1 of the API passes in information for both the command to be registered and the bundle where it was defined.

  • command (str) –

  • logger – Version 0 of the API only passes in the name of the command to be registered.

static register_selector(*args)

Supported API . This method is called the first time when the selector is used.

Parameters:

  • bundle_info (BundleInfo instance.) –

  • selector_info (SelectorInfo instance.) –

  • logger (chimerax.core.logger.Logger instance.) – Version 1 of the API passes in information about both the selector to be registered and the bundle where it is defined.

  • selector_name (str) –

  • logger – Version 0 of the API only passes in the name of the selector to be registered.

static run_provider(session, name, mgr, **kw)

Supported API . Called to invoke a provider in a bundle.

Must be defined if there is a Provider tag in the bundle. run_provider is called by the associated manager to perform the corresponding task.

Parameters:

  • session (Session instance.) –

  • name (str.) – Name of provider to initialize.

  • mgr (str.) – Name of manager for this provider.

  • kw (keyword arguments.) – Keyword arguments, if any, provided by the calling manager. Such keywords are specific to the manager and would be documented by the manager.

static start_tool(*args)

Supported API . This method is called when the tool is invoked, typically from the application menu. Errors should be reported via exceptions.

Parameters:

  • session (chimerax.core.session.Session instance.) –

  • bundle_info (BundleInfo instance.) –

  • tool_info (ToolInfo instance.) – Version 1 of the API passes in information for both the tool to be started and the bundle where it was defined.

  • session –

  • tool_name (str.) – Version 0 of the API only passes in the name of the tool to be started.

Returns:

The created tool.

Return type:

ToolInstance instance

class NewerVersionQuery(session)

Bases: Task

on_finish()

Experimental API . Callback method executed after task thread terminates.

This callback is executed in the UI thread after the run() method returns. By default, it does nothing.

classmethod restore_snapshot(session, data)

Experimental API . Create object using snapshot data.

run(service_name, params, blocking=False)

Experimental API . Run the task.

This method must be overridden to implement actual functionality. terminating() should be checked regularly to see whether user has requested termination.

take_snapshot(session, flags)

Experimental API . Return snapshot of current state of instance.

The semantics of the data is unknown to the caller. Returns None if should be skipped. The default implementation is for non-core classes and returns a copy of the instance dictionary (a deep copy of lists/dicts/etc., but shallow copy of named objects). Named objects are later converted to unique names.

Return type:

dict[any, any]

class ProviderManager(manager_name)

Bases: object

API for managers created by bundles

abstract add_provider(bundle_info, provider_name, **kw)

Experimental API . Callback invoked to add provider to this manager.

Parameters:
end_providers()

Experimental API . Callback invoked after all providers have been added.

class Toolshed(logger, rebuild_cache=False, check_remote=False, remote_url=None, check_available=True, session=None)

Bases: object

Toolshed keeps track of the list of bundle metadata, aka BundleInfo.

Tool metadata may be for “installed” bundles, where their code is already downloaded from the remote server and installed locally, or “available” bundles, where their code is not locally installed.

triggers

Where to register handlers for toolshed triggers

Type:

TriggerSet instance

bootstrap_bundles(session, safe_mode)

Supported API . Do custom initialization for installed bundles

After adding the Toolshed singleton to a session, allow bundles need to install themselves into the session, (For symmetry, there should be a way to uninstall all bundles before a session is discarded, but we don’t do that yet.)

bundle_info(logger, installed=True, available=False)

Supported API . Return list of bundle info.

Parameters:

  • installed (boolean) – True to include installed bundle metadata in return value; False otherwise

  • available (boolean) – True to include available bundle metadata in return value; False otherwise

Returns:

Combined list of all selected types of bundle metadata.

Return type:

list of BundleInfo instances

find_bundle(name, logger, installed=True, version=None)

Supported API . Return a BundleInfo instance with the given name.

Parameters:

  • name (str) – Name (internal or display name) of the bundle of interest.

  • logger (Logger instance) – Logging object where warning and error messages are sent.

  • installed (boolean) – True to check only for installed bundles; False otherwise.

  • version (str) – None to find any version; specific string to check for one particular version.

find_bundle_for_class(cls)

Supported API . Find bundle that has given class

find_bundle_for_command(cmd)

Supported API . Find bundle registering given command

cmd must be the full command name, not an abbreviation.

find_bundle_for_tool(name, prefix_okay=False)

Supported API . Find named tool and its bundle

Return the bundle it is in and its true name.

Parameters:

  • name (str) – Name or prefix of the tool of interest.

  • prefix_okay (boolean) – Whether name only needs to be a prefix of a tool name or must be an exact match.

import_bundle(bundle_name, logger, install='ask', session=None)

Supported API . Return the module for the bundle with the given name.

Parameters:

  • bundle_name (str) – Name (internal or display name) of the bundle of interest.

  • logger (Logger instance) – Logging object where warning and error messages are sent.

  • install (str) – Action to take if bundle is uninstalled but available. “ask” (default) means to ask user, if session is not None; “never” means not to install; and “always” means always install.

  • session (chimerax.core.session.Session instance.) – Session that is requesting the module. Defaults to None.

Raises:

ImportError – Raised if a module for the bundle cannot be found.

install_bundle(bundle, logger, *, per_user=True, reinstall=False, session=None, no_deps=False)

Supported API . Install the bundle by retrieving it from the remote shed.

Parameters:

  • bundle (string or BundleInfo instance or sequence of them) – If string, path to wheel installer. If instance, should be from the available bundle list.

  • per_user (boolean) – True to install bundle only for the current user (default); False to install for everyone.

  • reinstall (boolean) – True to force reinstall package.

  • logger (Logger instance) – Logging object where warning and error messages are sent.

Raises:

ToolshedInstalledError – Raised if the bundle is already installed.

Notes

A TOOLSHED_BUNDLE_INSTALLED trigger is fired after installation.

reload(logger, *, session=None, reread_cache=True, rebuild_cache=False, check_remote=False, report=False, _session=None)

Supported API . Discard and reread bundle info.

Parameters:

  • logger (Logger instance) – A logging object where warning and error messages are sent.

  • rebuild_cache (boolean) – True to ignore local cache of installed bundle information and rebuild it by scanning Python directories; False otherwise.

  • check_remote (boolean) – True to check remote server for updated information; False to ignore remote server

uninstall_bundle(bundle, logger, *, session=None, force_remove=False)

Supported API . Uninstall bundle by removing the corresponding Python distribution.

Parameters:

  • bundle (string or BundleInfo instance or sequence of them) – If string, path to wheel installer. If instance, should be from the available bundle list.

  • logger (Logger instance) – Logging object where warning and error messages are sent.

Raises:

ToolshedInstalledError – Raised if the bundle is not installed.

Notes

A TOOLSHED_BUNDLE_UNINSTALLED trigger is fired after package removal.

exception ToolshedError

Bases: Exception

Generic Toolshed error.

exception ToolshedInitializationError

Bases: ToolshedError

Initialization error.

This exception derives from ToolshedError and is usually raised when doing manager, provider or custom initialization.

exception ToolshedInstalledError

Bases: ToolshedError

Bundle-already-installed error.

This exception derives from ToolshedError and is usually raised when trying to install a bundle that is already installed or to uninstall a bundle that is not installed yet.

exception ToolshedUnavailableError

Bases: ToolshedError

Bundle-not-found error.

This exception derives from ToolshedError and is usually raised when no Python distribution can be found for a bundle.

get_toolshed()

Supported API . Return current toolshed.

Returns:

  • Toolshed instance – The toolshed singleton.

  • The toolshed singleton will be None if py:func:init hasn’t been called yet.

init(*args, debug=None, **kw)

Supported API . Initialize toolshed.

The toolshed instance is a singleton across all sessions. The first call creates the instance and all subsequent calls return the same instance. The toolshed debugging state is updated at each call.

Parameters:

  • debug (boolean) – If true, debugging messages are sent to standard output. Default value is false.

  • arguments (other) – All other arguments are passed to the Toolshed initializer.

class ToolInfo(name, categories, synopsis=None)

Bases: object

Metadata about a tool

name

Tool name.

Type:

str

categories

Menu categories that tool should be in.

Type:

list of str

synopsis

One line description.

Type:

str

class BundleInfo(name, installed, version=None, api_package_name=None, categories=(), synopsis=None, description='Unknown', session_versions=range(1, 2), custom_init=False, data_dir=None, include_dir=None, library_dir=None, executable_dir=None, managers=None, providers=None, inits=None, packages=None, supersedes=None)

Bases: object

Supported API. Metadata about a bundle, whether installed or available.

A BundleInfo instance stores the properties about a bundle and can create a tool instance.

commands

list of CommandInfo List of commands registered for this bundle.

tools

list of ToolInfo List of tools registered for this bundle.

installed

boolean True if this bundle is installed locally; False otherwise.

session_versions

range Given as the minimum and maximum session versions that this bundle can read.

session_write_version

integer The session version that bundle data is written in. Defaults to maximum of ‘session_versions’.

custom_init

boolean Whether bundle has custom initialization code

cache_data()

Supported API . Return state data that can be used to recreate the instance.

Returns:

List and dictionary suitable for passing to BundleInfo.

Return type:

2-tuple of (list, dict)

data_dir()

Supported API .

Returns:

Path (relative to the bundle root) of the bundle’s data directory.

dependents(logger)

Supported API . Return set of bundles that directly depends on this one.

Parameters:

logger (Logger instance) – Where to log error messages.

Returns:

Dependent bundles.

Return type:

set of BundleInfo instances

deregister(logger)

Supported API . Deregister bundle commands, tools, data formats, selectors, etc.

Parameters:

logger (Logger instance) – Where to log error messages.

distribution()

Supported API . Return distribution information.

Returns:

Distribution name and version.

Return type:

2-tuple of (str, str).

executable_dir()

Supported API . Returns: Path (relative to bundle root) of the bundle’s directory of executables.

finish(session)

Supported API . Deinitialize bundle by calling custom finish code if needed.

This method is only called when a bundle is explicitly unloaded. In particular, it is not called when ChimeraX exits normally.

classmethod from_cache_data(data)

Supported API . Class method for reconstructing instance from cache data. :rtype: instance of BundleInfo

get_class(class_name, logger)

Supported API . Return bundle’s class with given name.

get_module(force_import=True)

Supported API . Return module that has bundle’s code

include_dir()

Supported API .

Returns: Path (relative to bundle root) of the bundle’s directory of compilation include files.

init_manager(session, name, **kw)

Supported API . Initialize bundle manager if needed.

initialize(session)

Supported API . Initialize bundle by calling custom initialization code if needed.

library_dir()

Supported API .

Returns: Path (relative to bundle root) of the bundle’s directory of link libraries.

property name

Supported API.

Returns: Internal name of the bundle.

newer_than(bi)

Supported API . Return whether this BundleInfo instance is newer than given one

Parameters:

bi (BundleInfo instance) – The instance to compare against

Returns:

True if this instance is newer; False if ‘bi’ is newer.

Return type:

Boolean

register(logger)

Supported API . Register bundle commands, tools, data formats, selectors, etc.

Parameters:

logger (Logger instance) – Where to log error messages.

run_provider(session, name, mgr, **kw)

Supported API . Called by manager to invoke bundle provider.

property short_name

Supported API.

Returns:

A short name for the bundle. Typically the same as ‘name’ with ‘ChimeraX-’ omitted.

start_tool(session, tool_name, *args, **kw)

Supported API . Create and return a tool instance.

Parameters:

  • session (Session instance) – The session in which the tool will run.

  • args (any) – Positional arguments to pass to tool instance initializer.

  • kw (any) – Keyword arguments to pass to tool instance initializer.

Returns:

The registered running tool instance.

Return type:

ToolInstance instance

Raises:

ToolshedError – If the tool is not installed or cannot be started.

property synopsis

Supported API.

Returns:

Bundle synopsis; a short description of this bundle.

unload(logger)

Supported API . Unload bundle modules (as best as we can).

property version

Supported API.

Returns:

Bundle version (which is actually the same as the distribution version, so all bundles from the same distribution share the same version).

class CommandInfo(name, categories, synopsis=None)

Bases: ToolInfo

Metadata about a command

class SelectorInfo(name, synopsis=None, atomic=True)

Bases: ToolInfo

Metadata about a selector

name

Tool name.

Type:

str

synopsis

One line description.

Type:

str

atomic

Whether selector applies to atoms and bonds.

Type:

boolean