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feat(lifecycle): add automatic orphaned module cleanup to update command #1059

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63b5e5a
feat(lifecycle): add automatic orphaned module cleanup to update command
AshokThangavel Feb 1, 2026
61d6e7f
docs: updated the changelog
AshokThangavel Feb 1, 2026
b72105f
Merge branch 'origin/main' into feat-remove-stale-dependencies-on-update
AshokThangavel Feb 10, 2026
b5fd4b1
Merge branch 'main' into feat-remove-stale-dependencies-on-update
AshokThangavel Mar 8, 2026
3a518a5
Merge branch 'main' into feat-remove-stale-dependencies-on-update
AshokThangavel Mar 8, 2026
6fc576e
Merge branch 'main' into feat-remove-stale-dependencies-on-update
AshokThangavel Mar 10, 2026
77d1b44
refactor: modify -keep-orphans alias and rename cleanup class
AshokThangavel Mar 10, 2026
a829109
Refactor: Modify ExistDependencies directly to identify orphans by se…
AshokThangavel Mar 10, 2026
32fed36
Merge branch 'main' into feat-remove-stale-dependencies-on-update
AshokThangavel Mar 10, 2026
95e9456
cli: removed the alias -ro from the keep-orphans
AshokThangavel Mar 13, 2026
17f0a15
refactor: updated the code based on comments
AshokThangavel Mar 13, 2026
18aa3d6
Merge branch 'main' into feat-remove-stale-dependencies-on-update
AshokThangavel Mar 19, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## [0.10.7] - Unreleased

### Added
- #1059: Add automatic orphaned module cleanup to update command

## [0.10.6] - 2026-02-24

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5 changes: 5 additions & 0 deletions src/cls/IPM/Main.cls
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Expand Up @@ -155,6 +155,10 @@ This command is an alias for `module-action module-name publish`
update HS.JSON 3.0.0
</example>

<example description="Updates the HS.JSON module from the current version to version 3.0.0 and keep the orphaned modules">
update HS.JSON 3.0.0 -keep-orphans
</example>

<!-- Parameters -->
<parameter name="module" required="true" description="Name of module on which to perform update actions" />
<parameter name="version" description="Version (or version expression) of module to update; defaults to the latest available if unspecified. Is ignored if -path is provided." />
Expand All @@ -165,6 +169,7 @@ This command is an alias for `module-action module-name publish`
<modifier name="path" aliases="p" value="true" description="Location of local tarball containing the updated version of the module. Overrides 'version' parameter if present." />
<modifier name="dev" dataAlias="DeveloperMode" dataValue="1" description="Sets the DeveloperMode flag for the module's lifecycle. Key consequences of this are that ^Sources will be configured for resources in the module, and installer methods will be called with the dev mode flag set." />
<modifier name="create-lockfile" aliases="lock" dataAlias="CreateLockFile" dataValue="1" description="Upon update, creates/updates the module's lock file." />
<modifier name="keep-orphans" aliases="ko" dataAlias="KeepOrphans" dataValue="1" description="Retains dependencies that are no longer required by the updated module. By default, these orphaned modules are automatically uninstalled." />
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nit: I don't love the alias "ko" as it has "kill" implications which is the opposite of what this does (ie. "k" by itself in Objectscript means kill, "KO" means kill in other contexts) so that could be misleading. I suggest either naming keep-orphans differently, or abbreviating it differently

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@AshokThangavel AshokThangavel Mar 10, 2026

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thank you. I agree, I've modified the alias to -ro (Retain Orphans) .

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@isc-jili isc-jili Mar 13, 2026

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Hi @AshokThangavel thank you for the change! I discussed with my team and we believe the best way is actually to remove the alias entirely. Since "ro" also has the more widely known meaning "read-only". It's okay for this command to not have an alias.

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@AshokThangavel AshokThangavel Mar 13, 2026

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Hi @isc-jili, thanks for confirming. I’ve removed the -ro alias for keep-orphans, and as suggested, there is now no alias for it. Thank you!

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updated the pull request description as well.

</command>

<command name="makedeployed">
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61 changes: 60 additions & 1 deletion src/cls/IPM/Utils/Module.cls
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Expand Up @@ -1129,11 +1129,21 @@ ClassMethod LoadNewModule(
$$$ThrowStatus($$$ERROR($$$GeneralError, msg))
}
}

set cmd = $get(params("cmd"))
set orphanCleanup = (cmd = "update") && ('$get(pParams("KeepOrphans")))
// Retrieve dependencies from the previous version and compare with the current version to find modules that are no longer required
if (orphanCleanup) {
set tModule = ##class(%IPM.Storage.Module).NameOpen(commandLineModuleName,,.tSC)
do ..GetExistingDependencies(tModule, .oldDependencies)
}
// This loads the new version of the module into storage. Overrides the module context of the currently installed module, if it exists.
set tSC = $system.OBJ.Load(pDirectory_"module.xml",$select(tVerbose:"d",1:"-d"),,.tLoadedList)
$$$ThrowOnError(tSC)

// Compare dependencies from the previous version with the latest version and collect orphaned dependencies as an array
if (orphanCleanup) {
do ..GetOrphanedDependencies(tModule,.oldDependencies, .orphanedDeps)
}
set tFirstLoaded = $order(tLoadedList(""))
if (tFirstLoaded = "") {
$$$ThrowStatus($$$ERROR($$$GeneralError,"No module definition found."))
Expand Down Expand Up @@ -1228,6 +1238,10 @@ ClassMethod LoadNewModule(
tcommit
}
$$$ThrowOnError(tSC)
// Uninstall orphaned dependencies
if (orphanCleanup) {
do ..UninstallOrphanedDependencies(.orphanedDeps, .pParams)
}
do tModule.WriteAfterInstallMessage()
} catch e {
set tSC = e.AsStatus()
Expand All @@ -1240,6 +1254,51 @@ ClassMethod LoadNewModule(
quit tSC
}

/// Uninstall orphaned dependencies identified during update.
/// Recursively removes modules not required by the main module or other local packages.
ClassMethod UninstallOrphanedDependencies(
ByRef orphanedDeps,
ByRef Params)
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nit: inconsistent capitalization of variables.
I suggest turning on the force-formatting rules found in IPM/.vscode/settings.json if working with VSCode.

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@AshokThangavel AshokThangavel Mar 13, 2026

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Fixed the capitalization of variables. Thank you!

These are the existing Force-formatting rules in the settings.json. Please let me know if anything missing

// Force formatting rules
    "intersystems.testingManager.client.relativeTestRoot": "tests/unit_tests",
    "objectscript.multilineMethodArgs": true,
    "intersystems.language-server.formatting.expandClassNames": false,
    "intersystems.language-server.formatting.commands.case": "lower",
    "intersystems.language-server.formatting.commands.length": "long",
    "intersystems.language-server.formatting.system.case": "lower",
    "intersystems.language-server.formatting.system.length": "long",

Thank you!

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Ah sorry I misremembered the rules. The rules look fine! They will not change variable capitalization so that will be up to us to catch any inconsistencies

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@AshokThangavel AshokThangavel Mar 13, 2026

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No worries. Thank you for the confirmation.

{
if '$data(orphanedDeps) {
quit
}
set dependencyModule=""
write !,"Uninstalling orphaned dependencies"
for {
set dependencyModule = $order(orphanedDeps(dependencyModule)) quit:dependencyModule=""
continue:'##class(%IPM.Storage.Module).NameExists(dependencyModule)
// Remove this module and its dependencies recursively, skipping any still in use
$$$ThrowOnError(##class(%IPM.Storage.Module).Uninstall(dependencyModule,,1,.Params))
}
}

/// Retrieves the dependency graph for the currently installed version of the module.
ClassMethod GetExistingDependencies(
Module As %IPM.Storage.Module,
Output DependencyGraph)
{
$$$ThrowOnError(Module.BuildDependencyGraph(.DependencyGraph,,,,"",,,,,,))
}

/// Compares the previous dependency graph with the current one to identify orphans.
ClassMethod GetOrphanedDependencies(
Module As %IPM.Storage.Module,
ByRef ExistDependencies,
Output OrphanedModules)
{
kill OrphanedModules
merge existDeps = ExistDependencies
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nit: inconsistent casing for vars
Also, what is the point of making a copy of ExistDependencies instead of acting directly on ExistDependencies? I don't see ExistDependencies being used after this method call.

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@AshokThangavel AshokThangavel Mar 10, 2026 •
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I've updated the code.
Thank you!

set sc = Module.BuildDependencyGraph(.dependencyGraph,,,,"",,,,,,)
$$$ThrowOnError(sc)
set module=""
for {
set module = $order(dependencyGraph(module)) quit:module=""
kill existDeps(module)
}
merge OrphanedModules = existDeps
}

/// Load dependencies of a module in a synchronous manner, one at a time, in the correct order.
/// This method builds a dependency graph (optionally with phases) and installs missing dependencies.
ClassMethod LoadDependencies(
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229 changes: 229 additions & 0 deletions tests/integration_tests/Test/PM/Integration/OrphanCleanup.cls
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@@ -0,0 +1,229 @@
Class Test.PM.Integration.OrphanCleanup Extends Test.PM.Integration.Base
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nit: We already have an existing Update test suite in Test.PM.Integration.Update. I suggest either adding to that suite, or naming this test suite to be explicitly update related (eg. UpdateOrphanCleanup.cls)

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Thank you. I've updated the class name to Test.PM.Integration.UpdateOrphanCleanup

{

Method TestRemoveOrphanedModOnUpdate() As %Status
{
#define NormalizeDir(%dir) ##class(%File).NormalizeDirectory(%dir)
#define NormalizeFilename(%file,%dir) ##class(%File).NormalizeFilename(%file,%dir)

do $$$LogMessage("Verify and uninstall the demo-module1 if it was installed.")
set isExist = ##class(%IPM.Storage.Module).NameExists("demo-module1")
if isExist{
set status = ..RunCommand("uninstall demo-module1 -r")
do $$$AssertStatusOK(status, "Uninstalled the demo-module1 successfully")
}
set testRoot = $$$NormalizeDir($get(^UnitTestRoot))
set moduleDir = $$$NormalizeDir(##class(%File).GetDirectory(testRoot)_"/_data/demo-module/")

set v1ModuleDir = $$$NormalizeDir(moduleDir_"/v1.0.0")
set v2ModuleDir = $$$NormalizeDir(moduleDir_"/v2.0.0")
set v3ModuleDir = $$$NormalizeDir(moduleDir_"/v3.0.0")

do ..CreateDirectory(v1ModuleDir)
set moduleFile = $$$NormalizeFilename("module.xml",v1ModuleDir)
set status = ..CreateModuleFile(moduleFile, "DemoModuleV1")
do $$$AssertStatusOK(status, "demo-module1 version 1.0.0 Module.xml created")

do $$$LogMessage("Load demo-module version 1.0.0")
set status = ..RunCommand("load "_v1ModuleDir)
do $$$AssertStatusOK(status, "demo-module1 version 1.0.0 laoded successfully")

set moduleObj = ##class(%IPM.Storage.Module).NameOpen("demo-module1")
set depsCount = moduleObj.Dependencies.Count()
for i=1:1:depsCount{
set depsName = moduleObj.Dependencies.GetAt(i)
do $$$LogMessage("Module "_depsName.Name_" installed successfully")
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nit: in the log make it explicit that these installed modules are dependencies of module1

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updated the code!

}
if depsCount = 3 {
do $$$LogMessage("All 3 modules are loaded successfully")
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nit: "All 3 dependency modules ..."

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Fixed the message. Thank you!

}

do $$$LogMessage("Update the demo-module1 to version 2.0.0")
do ..CreateDirectory(v2ModuleDir)
set v2moduleFile = $$$NormalizeFilename("module.xml",v2ModuleDir)
set status = ..CreateModuleFile(v2moduleFile, "DemoModuleV2")
do $$$AssertStatusOK(status, "demo-module1 version 2.0.0 Module.xml created")
;
do $$$LogMessage("update the demo-module to version 2.0.0 without -keep-orphans flag. So orphaed modules will be removed from the package manager")
set status = ..RunCommand("update demo-module1 -p "_v2ModuleDir)
do $$$AssertStatusOK(status, "demo-module1 version 2.0.0 updated successfully")

set moduleObj = ##class(%IPM.Storage.Module).NameOpen("demo-module1")
set depsCount = moduleObj.Dependencies.Count()

for i=1:1:depsCount{
set depsName = moduleObj.Dependencies.GetAt(i)
do $$$LogMessage("Module "_depsName.Name_" exist")
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nit: "Dependency module ..."

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Fixed the message.

}
if depsCount = 2 {
do $$$LogMessage("Only 2 modules are exist after update the module")
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nit: "Only 2 dependency modules exist after updating module1"

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updated the message. Thank you!

}
do $$$LogMessage("Check the irisjwt module was uninstalled")
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nit: "Check that the irisjwt module, which is no longer a dependency of module1 version 2.0.0, ..."

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@AshokThangavel AshokThangavel Mar 10, 2026

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Fixed. Additionally, following the CONTRIBUTING.md guidelines, I have replaced the existing dependency test modules with smaller, purpose-built modules. This prevents conflicts or errors during the installation

Thank You!

set isExist = ##class(%IPM.Storage.Module).NameExists("irisjwt")
do $$$AssertTrue('isExist," The orphaed irisjwt module was uninstalled successfully")

//
do $$$LogMessage("update the demo-module to version 3.0.0 with -keep-orphans flag. So No orphaed modules removed from the package manager")
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nit: typos in "No orphaed"

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updated the code

do ..CreateDirectory(v3ModuleDir)
set v3moduleFile = $$$NormalizeFilename("module.xml",v3ModuleDir)
set status = ..CreateModuleFile(v3moduleFile, "DemoModuleV3")
do $$$AssertStatusOK(status, "demo-module1 version 2.0.0 Module.xml created")
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nit: Should be 3.0.0 here

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Thank you. Fixed the code


set status = ..RunCommand("update demo-module1 -p "_v3ModuleDir_" -keep-orphans")
do $$$AssertStatusOK(status, "demo-module1 version updated to 3.0.0 successfully")
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nit: Add "Dependencies should be kept due to -keep-orphans flag"

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@AshokThangavel AshokThangavel Mar 10, 2026

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modified the code!


set moduleObj = ##class(%IPM.Storage.Module).NameOpen("demo-module1")
set depsCount = moduleObj.Dependencies.Count()
do $$$LogMessage("Dependency module count is "_depsCount)

for i=1:1:depsCount{
set depsName = moduleObj.Dependencies.GetAt(i)
do $$$LogMessage("Module "_depsName.Name_" exist")
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nit: "Dependency module ..."

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fixed!

}
set isExist = ##class(%IPM.Storage.Module).NameExists("LocalizationLab")
do $$$AssertTrue(isExist," The orphaed LocalizationLab module still exist")
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nit: The orphaned dependency module LocalizationLab still exists"

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Updated the logic. I have replaced the existing dependency test modules with smaller, purpose-built modules. Thank you!

}

Method RunCommand(Command) As %Status
{
do $$$LogMessage("executing command "_Command)
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nit: Capitalize "Executing"

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fixed the Capitalize "Executing"

set status = ##class(%IPM.Main).Shell(Command)
return status
}

Method CreateDirectory(Directory)
{
if '##class(%File).DirectoryExists(Directory) {
set status = ##class(%File).CreateDirectoryChain(Directory)
do $$$AssertStatusOK(status," Directory"_Directory_" not exist. So created the directory")
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nit: "Directory "Directory" does not exist. So created the directory."

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modified the code.

}
else {
do $$$LogMessage("Directory "_Directory_" is already exist")
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nit: "Directory "Directory" already exists."

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fixed. Thank you!

}
}

Method CreateModuleFile(
ModuleFile As %String = "",
moduleXdata As %String = "")
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nit: Inconsistent capitalization of variables

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Corrected the Parameter variables Inconsistency. Thank you!

{
if ModuleFile=""||(moduleXdata="") {
quit 0
}
if '##class(%File).Exists(ModuleFile) {
do $$$LogMessage(ModuleFile_" not exist. So creating the xml")
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nit: does not exist

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added the changes!

}
set fileStream = ##class(%Stream.FileCharacter).%New()
set fileStream.Filename = ModuleFile
set v1ModFile = ##class(%Dictionary.XDataDefinition).%OpenId($classname()_"||"_moduleXdata)
do fileStream.CopyFrom(v1ModFile.Data)
set status = fileStream.%Save()
do $$$AssertStatusOK(status, "Module.xml created on "_ModuleFile)
return status
}

XData DemoModuleV1 [ MimeType = application/xml ]
{
<?xml version="1.0" encoding="UTF-8"?>
<Export generator="Cache" version="25">
<Document name="demo-module1.ZPM">
<Module>
<Name>demo-module1</Name>
<Version>1.0.0</Version>
<Description>description</Description>
<Keywords>keywords</Keywords>
<Author>
<Person>your name</Person>
<Organization>your organization</Organization>
<CopyrightDate>2020</CopyrightDate>
<License>MIT</License>
<Notes>notes</Notes>
</Author>
<Dependencies>
<ModuleReference>
<Name>objectscript-math</Name>
<Version>0.0.5</Version>
</ModuleReference>
<ModuleReference>
<Name>LocalizationLab</Name>
<Version>1.0.0</Version>
</ModuleReference>
<ModuleReference>
<Name>irisjwt</Name>
<Version>1.0.0</Version>
</ModuleReference>
</Dependencies>
<Packaging>module</Packaging>
<Default Name="count" Value="7"/>
<SourcesRoot>src</SourcesRoot>
</Module>
</Document>
</Export>
}

XData DemoModuleV2 [ MimeType = application/xml ]
{
<?xml version="1.0" encoding="UTF-8"?>
<Export generator="Cache" version="25">
<Document name="demo-module1.ZPM">
<Module>
<Name>demo-module1</Name>
<Version>2.0.0</Version>
<Description>description</Description>
<Keywords>keywords</Keywords>
<Author>
<Person>your name</Person>
<Organization>your organization</Organization>
<CopyrightDate>2020</CopyrightDate>
<License>MIT</License>
<Notes>notes</Notes>
</Author>
<Dependencies>
<ModuleReference>
<Name>objectscript-math</Name>
<Version>0.0.5</Version>
</ModuleReference>
<ModuleReference>
<Name>LocalizationLab</Name>
<Version>1.0.0</Version>
</ModuleReference>
</Dependencies>
<Packaging>module</Packaging>
<Default Name="count" Value="7"/>
<SourcesRoot>src</SourcesRoot>
</Module>
</Document>
</Export>
}

XData DemoModuleV3 [ MimeType = application/xml ]
{
<?xml version="1.0" encoding="UTF-8"?>
<Export generator="Cache" version="25">
<Document name="demo-module1.ZPM">
<Module>
<Name>demo-module1</Name>
<Version>3.0.0</Version>
<Description>description</Description>
<Keywords>keywords</Keywords>
<Author>
<Person>your name</Person>
<Organization>your organization</Organization>
<CopyrightDate>2020</CopyrightDate>
<License>MIT</License>
<Notes>notes</Notes>
</Author>
<Dependencies>
<ModuleReference>
<Name>objectscript-math</Name>
<Version>0.0.5</Version>
</ModuleReference>
</Dependencies>
<Packaging>module</Packaging>
<Default Name="count" Value="7"/>
<SourcesRoot>src</SourcesRoot>
</Module>
</Document>
</Export>
}

}