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Refactor code (#4)
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@walkowif
walkowif authored Oct 27, 2023
1 parent f35ade0 commit 980c6f6
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11 changes: 9 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@

`locksmith` is a utility to generate `renv.lock` file containing all dependencies of given set of R packages.

Given the input list of R packages or git repositories containing the R packages, as well as a list of R package repositories (e.g. in a package manager, CRAN, BioConductor etc.), `locksmith` will try to determine the list of all dependencies and their versions required to make the input list of packages work. It will then save the result in an `renv.lock`-compatible file.
Given the input list of git repositories containing the R packages, as well as a list of R package repositories (e.g. in a package manager, CRAN, BioConductor etc.), `locksmith` will try to determine the list of all dependencies and their versions required to make the input list of packages work. It will then save the result in an `renv.lock`-compatible file.

## Installing

Expand All @@ -27,9 +27,16 @@ locksmith --logLevel debug --exampleParameter 'exampleValue'
Real-life example with multiple input packages and repositories.

```bash
locksmith --inputPackageList https://raw.githubusercontent.com/insightsengineering/formatters/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rtables/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda.2022/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/nestcolor/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/tern/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rlistings/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/citril/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda.test/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/citril.metadata/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/chevron/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/dunlin/main/DESCRIPTION --inputRepositoryList https://bioconductor.org/packages/release/bioc,https://cran.rstudio.com/
locksmith --inputPackageList https://raw.githubusercontent.com/insightsengineering/formatters/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rtables/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/scda.2022/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/nestcolor/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/tern/main/DESCRIPTION,https://raw.githubusercontent.com/insightsengineering/rlistings/main/DESCRIPTION --inputRepositoryList BioC=https://bioconductor.org/packages/release/bioc,CRAN=https://cran.rstudio.com/
```

In order to download the packages from GitHub or GitLab repositories, please set the environment variables containing the Personal Access Tokens.

* For GitHub, set the `LOCKSMITH_GITHUBTOKEN` environment variable.
* For GitLab, set the `LOCKSMITH_GITLABTOKEN` environment variable.

By default `locksmith` will save the resulting output file to `renv.lock`.

## Configuration file

If you'd like to set the above options in a configuration file, by default `locksmith` checks `~/.locksmith`, `~/.locksmith.yaml` and `~/.locksmith.yml` files.
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78 changes: 47 additions & 31 deletions cmd/construct.go
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Original file line number Diff line number Diff line change
Expand Up @@ -20,9 +20,13 @@ import (
"strings"
)

func constructOutputPackageList(packages []PackageDescription, packagesFiles map[string]PackagesFile,
// ConstructOutputPackageList generates a list of all packages and their dependencies
// which should be included in the output renv.lock file,
// based on the list of package descriptions, and information contained in the PACKAGES files.
func ConstructOutputPackageList(packages []PackageDescription, packagesFiles map[string]PackagesFile,
repositoryList []string) []PackageDescription {
var outputPackageList []PackageDescription
var fatalErrors string
// Add all input packages to output list, as the packages should be downloaded from git repositories.
for _, p := range packages {
outputPackageList = append(outputPackageList, PackageDescription{
Expand All @@ -33,28 +37,32 @@ func constructOutputPackageList(packages []PackageDescription, packagesFiles map
}
for _, p := range packages {
for _, d := range p.Dependencies {
skipDependency := false
if d.DependencyType == "Depends" || d.DependencyType == "Imports" ||
d.DependencyType == "Suggests" || d.DependencyType == "LinkingTo" {
if checkIfSkipDependency("", p.Package, d.DependencyName,
if !CheckIfSkipDependency("", p.Package, d.DependencyName,
d.VersionOperator, d.VersionValue, &outputPackageList) {
skipDependency = true
}
if !skipDependency {
log.Info(p.Package, " → ", d.DependencyName)
resolveDependenciesRecursively(
log.Info(p.Package, " → ", d.DependencyName, " (", d.DependencyType, ")")
ResolveDependenciesRecursively(
&outputPackageList, d.DependencyName, d.VersionOperator,
d.VersionValue, repositoryList, packagesFiles, 1,
d.VersionValue, repositoryList, packagesFiles, 1, &fatalErrors,
)
}
}
}
}
if fatalErrors != "" {
log.Fatal(fatalErrors)
}
return outputPackageList
}

func resolveDependenciesRecursively(outputList *[]PackageDescription, name string, versionOperator string,
versionValue string, repositoryList []string, packagesFiles map[string]PackagesFile, recursionLevel int) {
// ResolveDependenciesRecursively checks dependencies of the package, and their required versions.
// Checks if the required version is already included in the output package list
// (later used to generate the renv.lock), or if the dependency should be downloaded from a package repository.
// Repeats the process recursively for all dependencies not yet processed.
func ResolveDependenciesRecursively(outputList *[]PackageDescription, name string, versionOperator string,
versionValue string, repositoryList []string, packagesFiles map[string]PackagesFile, recursionLevel int,
fatalErrors *string) {
var indentation string
for i := 0; i < recursionLevel; i++ {
indentation += " "
Expand All @@ -67,14 +75,14 @@ func resolveDependenciesRecursively(outputList *[]PackageDescription, name strin
log.Warn(indentation, name, " not found in top repository.")
}
// Check if package in the repository is available in sufficient version.
if !checkIfVersionSufficient(p.Version, versionOperator, versionValue) {
// Try to retrieve the package from the next repository.
if !CheckIfVersionSufficient(p.Version, versionOperator, versionValue) {
log.Warn(
indentation, p.Package, " in repository ", r,
" is available in version ", p.Version,
" which is insufficient according to requirement ",
versionOperator, " ", versionValue,
)
// Try to retrieve the package from the next repository.
continue
}
// Add package to the output list.
Expand All @@ -87,12 +95,15 @@ func resolveDependenciesRecursively(outputList *[]PackageDescription, name strin
for _, d := range p.Dependencies {
if d.DependencyType == "Depends" || d.DependencyType == "Imports" ||
d.DependencyType == "LinkingTo" {
if !checkIfSkipDependency(indentation, p.Package, d.DependencyName,
if !CheckIfSkipDependency(indentation, p.Package, d.DependencyName,
d.VersionOperator, d.VersionValue, outputList) {
log.Info(indentation, p.Package, " → ", d.DependencyName)
resolveDependenciesRecursively(
outputList, d.DependencyName, d.VersionOperator,
d.VersionValue, repositoryList, packagesFiles, recursionLevel+1,
log.Info(
indentation, p.Package, " → ", d.DependencyName,
" (", d.DependencyType, ")",
)
ResolveDependenciesRecursively(
outputList, d.DependencyName, d.VersionOperator, d.VersionValue,
repositoryList, packagesFiles, recursionLevel+1, fatalErrors,
)
}
}
Expand All @@ -106,13 +117,13 @@ func resolveDependenciesRecursively(outputList *[]PackageDescription, name strin
if versionOperator != "" && versionValue != "" {
versionConstraint = " in version " + versionOperator + " " + versionValue
}
log.Fatal(
indentation, "Could not find package ", name, versionConstraint,
" in any of the repositories.",
)
*fatalErrors += "Could not find package " + name + versionConstraint + " in any of the repositories.\n"
}

func checkIfBasePackage(name string) bool {
// CheckIfBasePackage checks whether the package should be treated as a base R package
// (included in every R installation) or if it should be treated as a dependency
// to be downloaded from a package repository.
func CheckIfBasePackage(name string) bool {
var basePackages = []string{
"base", "compiler", "datasets", "graphics", "grDevices", "grid",
"methods", "parallel", "splines", "stats", "stats4", "tcltk", "tools",
Expand All @@ -121,10 +132,13 @@ func checkIfBasePackage(name string) bool {
return stringInSlice(name, basePackages)
}

func checkIfSkipDependency(indentation string, packageName string, dependencyName string,
// CheckIfSkipDependency checks if processing of the package (dependency) should be skipped.
// Dependency should be skipped if it is a base R package, or has already been added to output
// package list (later used to generate the renv.lock).
func CheckIfSkipDependency(indentation string, packageName string, dependencyName string,
versionOperator string, versionValue string, outputList *[]PackageDescription) bool {
if checkIfBasePackage(dependencyName) {
log.Debug(indentation, "Skipping package ", dependencyName, " as it is a base R package.")
if CheckIfBasePackage(dependencyName) {
log.Trace(indentation, "Skipping package ", dependencyName, " as it is a base R package.")
return true
}
// Go through the list of dependencies added to the output list previously, to check
Expand All @@ -133,24 +147,24 @@ func checkIfSkipDependency(indentation string, packageName string, dependencyNam
for i := 0; i < len(*outputList); i++ {
if dependencyName == (*outputList)[i].Package {
// Dependency found on the output list.
if checkIfVersionSufficient((*outputList)[i].Version, versionOperator, versionValue) {
if CheckIfVersionSufficient((*outputList)[i].Version, versionOperator, versionValue) {
var requirementMessage string
if versionOperator != "" && versionValue != "" {
requirementMessage = " according to the requirement " + versionOperator + " " + versionValue
} else {
requirementMessage = " since no required version has been specified."
}
log.Debug(
indentation, "Output list already contains dependency ", dependencyName, " version ",
indentation, "Output list already contains ", dependencyName, " version ",
(*outputList)[i].Version, " which is sufficient for ", packageName,
requirementMessage,
)
return true
}
log.Warn(
indentation,
"Output list already contains dependency ", dependencyName, " version ",
(*outputList)[i].Version, " but it is insufficient as ", packageName,
"Output list already contains ", dependencyName, " but the version ",
(*outputList)[i].Version, " is insufficient as ", packageName,
" requires ", dependencyName, " ", versionOperator, " ", versionValue,
)
// Overwrite the information about the previous version of the dependency on the output list.
Expand All @@ -172,7 +186,9 @@ func splitVersion(r rune) bool {
return r == '.' || r == '-'
}

func checkIfVersionSufficient(availableVersionValue string, versionOperator string,
// CheckIfVersionSufficient checks if availableVersionValue fulfills the requirement
// expressed by versionOperator ('>=' or '>') and requiredVersionValue.
func CheckIfVersionSufficient(availableVersionValue string, versionOperator string,
requiredVersionValue string) bool {
// Check if there are any version requirements at all.
if versionOperator == "" && requiredVersionValue == "" {
Expand Down
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