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feat(install): install dependencies by id and explain unknown module names - #144
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Dependency entries had only a display name, such as "Flow Registration", which is too long to type and can contain spaces. The manifest schema now has an optional "id": a short, lowercase, kebab-case identifier for a community toolbox that is unique across manifests. readManifest returns it in the Id field. Every community toolbox in the core manifest and in the two-photon module manifest gets an id, for example "flowreg", "normcorre", "suite2p" and "catalog". A test checks that the core ids are present, unique and match the pattern in the schema. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
The installCheck for Flow Registration was "OF_Options", but the
class in the flow_registration toolbox is defined as OF_options. On
macOS, which ignores case in file names, which("OF_Options") still
finds OF_options.m. On a case-sensitive file system the check does
not find the file, so NANSEN would report Flow Registration as
missing even when it is installed.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
AddonManager.installMissingAddons prints a summary of failed installs only when the caller requests no outputs or passes ShowSummary. nansen_install requested the number of installed add-ons, so failed downloads and setup steps were never reported. When every missing add-on failed, that number was zero and nansen_install printed "All dependencies are installed". nansen_install now passes ShowSummary=true and prints that message only when no add-on needed to be installed (NumAttempted is zero). Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
nansen_install("flowreg") installs only the community toolboxes with
the given ids, plus MatBox, and adds them to the path. It skips the
core installation check. Update=true updates the named toolboxes that
are installed and installs the missing ones. The ids come from the
core manifest and from the dependencies.nansen.json file of each
module on the MATLAB search path.
nansen_install(Modules=...) accepts a module's package name, the name
in its module.nansen.json file, or the last part of its package name.
Module names and dependency ids are checked before anything is
downloaded. An unknown module name lists the modules on the path and
explains that modules are found in +nansen/+module folders on the
path. An unknown id lists the available ids by module, and a module
name given as an id points to Modules=.
New functions in nansen.internal.dependencies:
- listModules finds modules with what() and dir(), so it works
before community toolboxes such as recursiveDir are installed
- resolveModuleNames and resolveDependencyIds convert user input and
raise the errors above
- assertInstalled throws an error with the nansen_install command
for a dependency that is not on the path, for code to call before
it uses an optional toolbox
AddonManager.installMissingAddons, updateAddons and
getManagedAddonsForModules take an AddonNames filter.
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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Summary
nansen_install(Modules="some_name")raised a warning for an unknown module and then installed only the core dependencies, without saying which module names exist. There was no way to install a single dependency. This PR adds ids to the dependency manifests, a targeted install by id, and error messages that list what is available.Changes
idfield: a short, lowercase, kebab-case identifier for a community toolbox, unique across manifests.readManifestreturns it asId. Every community toolbox incode/dependencies.nansen.jsonand in the two-photon module manifest has an id, for exampleflowreg,normcorre,suite2pandcatalog.nansen_install("flowreg")installs only the named community toolboxes plus MatBox and adds them to the path. It accepts a string array of ids.Update=trueupdates the named toolboxes that are installed and installs the missing ones. The core installation check (verifyInstallation) is skipped for this call.nansen_install(Modules=...)accepts the package name (nansen.module.ophys.twophoton), the name inmodule.nansen.json("Two Photon Imaging") or the short name (twophoton). The last two are matched without regard to letter case.NANSEN:Dependencies:UnknownModulewith a table of the modules on the path and a note that NANSEN finds modules in+nansen/+modulefolders on the MATLAB search path. An unknown id throwsNANSEN:Dependencies:UnknownDependencywith the available ids grouped by module. A module name passed as an id points toModules=.nansen.internal.dependencies.assertInstalled("flowreg")throwsNANSEN:Dependencies:NotInstalledwith the commandnansen_install("flowreg")when theinstallCheckof the toolbox is not on the path. Code that needs an optional toolbox can call it before using the toolbox.nansen.internal.dependencies:listModules,resolveModuleNames,resolveDependencyIdsandassertInstalled.listModulesuseswhatanddir, so it works before community toolboxes such asrecursiveDirare installed.AddonManager.installMissingAddons,updateAddonsandgetManagedAddonsForModulestake anAddonNamesfilter.nansen_install()requested an output frominstallMissingAddons, which suppresses its failure summary, so failed installs were not reported. When every missing add-on failed, it printed "All dependencies are installed". It now passesShowSummary=trueand prints that message only when no add-on needed to be installed.installCheckwasOF_Options, but the class isOF_options. The check matched only on file systems that ignore case.DependencyLookupTestcreates fixture modules in a temporary folder on the path and covers the lookups, the error messages and the checks innansen_install.TestDependencyManagementchecks the core ids against the pattern in the schema.AddonManagerTestcovers theAddonNamesfilter.Notes
code/modules/+nansen/+module/+ophys/+twophoton/dependencies.nansen.jsonin WP8: remove the two-photon module from NANSEN and require it from its own repository #137. Rebasing the stack onto this PR gives a modify/delete conflict on that file; keep the deletion.OF_optionsfix. The fourassertAddonInstalledmethods there (flowreg, normcorre, suite2p, extract) can then callnansen.internal.dependencies.assertInstalledwith their id.🤖 Generated with Claude Code