From b51b57fcc5237a88a96e33fbbb7b769d694c8f08 Mon Sep 17 00:00:00 2001 From: walkowif <59475134+walkowif@users.noreply.github.com> Date: Tue, 9 Jan 2024 15:02:09 +0100 Subject: [PATCH] Add the feature to update `renv.lock` provided as an input (#18) --- Makefile | 4 +- README.md | 36 +- cmd/construct.go | 4 +- cmd/construct_test.go | 66 +-- cmd/download.go | 49 +- cmd/download_test.go | 15 + cmd/parse.go | 4 +- cmd/parse_test.go | 12 +- cmd/renv.go | 245 ++++++++ cmd/renv_test.go | 313 +++++++++-- cmd/root.go | 52 +- cmd/structs.go | 7 +- .../package11/subdirectory1/DESCRIPTION | 2 + .../package12/subdirectory2/DESCRIPTION | 2 + go.mod | 34 +- go.sum | 524 ++++-------------- 16 files changed, 794 insertions(+), 575 deletions(-) create mode 100644 cmd/testdata/git_updates/package11/subdirectory1/DESCRIPTION create mode 100644 cmd/testdata/git_updates/package12/subdirectory2/DESCRIPTION diff --git a/Makefile b/Makefile index 1b71ded..66edd0e 100644 --- a/Makefile +++ b/Makefile @@ -25,7 +25,7 @@ help: ## Show this help menu devdeps: ## Install development dependencies @printf "Executing target: [$@] 🎯\n" - @which -a golangci-lint > /dev/null || curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(GOPATH) v1.55.0 + @which -a golangci-lint > /dev/null || curl -sSfL https://raw.githubusercontent.com/golangci/golangci-lint/master/install.sh | sh -s -- -b $(GOPATH) v1.55.2 @which -a typex > /dev/null || go install github.com/dtgorski/typex@latest @which -a goreleaser > /dev/null || go install github.com/goreleaser/goreleaser@latest @which -a gocover-cobertura > /dev/null || go install github.com/boumenot/gocover-cobertura@latest @@ -60,7 +60,7 @@ format: ## Format source code lint: devdeps spell ## Lint source code @printf "Executing target: [$@] 🎯\n" - @golangci-lint run --fast -c .golangci.yml + @golangci-lint run -c .golangci.yml test: clean tidy devdeps spell ## Run unit tests and generate reports @printf "Executing target: [$@] 🎯\n" diff --git a/README.md b/README.md index 22cea14..c739f47 100644 --- a/README.md +++ b/README.md @@ -32,12 +32,6 @@ following command to view its capabilities: locksmith --help ``` -Example usage with multiple flags: - -```bash -locksmith --logLevel debug --exampleParameter 'exampleValue' -``` - Real-life example with multiple input packages and repositories. Please see below for [an example](#configuration-file) how to set package and repository lists more easily in a configuration file. @@ -46,7 +40,7 @@ easily in a configuration file. 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://gitlab.example.com/api/v4/projects/123456/repository/files/DESCRIPTION/raw?ref=main,https://gitlab.example.com/api/v4/projects/234567/repository/files/directory%2Fsubdirectory%2FDESCRIPTION/raw?ref=main --inputRepositoryList BioC=https://bioconductor.org/packages/release/bioc,CRAN=https://cran.rstudio.com ``` -In order to download the packages from non-public GitHub or GitLab repositories, please set the environment +In order to download the input `DESCRIPTION` files from GitHub or GitLab repositories, please set the environment variables containing the Personal Access Tokens. * For GitHub, set the `LOCKSMITH_GITHUBTOKEN` environment variable. @@ -88,6 +82,8 @@ as opposed to `inputPackageList` and `inputRepositoryList` CLI flags/YAML keys. Additionally, `inputPackageList`/`inputRepositoryList` CLI flags take precendence over `inputPackages`/`inputRepositories` YAML keys. +Please note that package repository URLs should be provided without the trailing `/`. + ## Environment variables `locksmith` reads environment variables with `LOCKSMITH_` prefix and tries to match them with CLI @@ -98,9 +94,11 @@ The order of precedence is: CLI flag → environment variable → configuration file → default value. +To check the available names of environment variables, please run `locksmith --help`. + ## Binary dependencies -For `locksmith` in order to generate an `renv.lock` with binary R packages, +If `locksmith` should generate an `renv.lock` with binary R packages, it is necessary to provide URLs to binary repositories via `inputRepositories`/`inputRepositoryList`. Examples illustrating the expected format of URLs to repositories with binary packages: @@ -120,7 +118,7 @@ Examples illustrating the expected format of URLs to repositories with binary pa where `` is e.g. `4.2`, `4.3` etc. -In all cases the URL points to a directory where the `PACKAGES` file is located. +In all cases the URL points to a directory where the `PACKAGES` file is located, without the trailing `/`. As a result, the configuration file could look like this: @@ -152,6 +150,26 @@ Simply list the types of dependencies which should not cause the `renv.lock` gen locksmith --allowIncompleteRenvLock 'Imports,Depends,Suggests,LinkingTo' ``` +## Updating existing `renv.lock` + +`locksmith` has the capability to update an existing lockfile with the newest available package versions. + +To ensure that the `input.renv.lock` has all the packages in the newest versions from the respective repositories (git, CRAN-like or BioConductor-like), and to save such updated file to `output.renv.lock`, you can run: + +```bash +locksmith --inputRenvLock input.renv.lock --outputRenvLock output.renv.lock +``` + +For git packages, a reference to the latest commit on the default branch will be saved. + +For packages which, according to the input lockfile, should be downloaded from CRAN-like or BioConductor-like repositories, a reference to the latest available package version in the respective repository will be saved. + +The packages can be updated selectively by using the `--updatePackages` flag. + +Please note that `renv` might have saved the information in the input lockfile that the package should be downloaded from `CRAN`, `RSPM` or BioConductor repository, but at the same time the definition of that repository in the `renv.lock` header (in the `Repositories` section) might be missing. For such packages `locksmith` will try to check what is the newest available package version at [CRAN](https://cloud.r-project.org). + +Please also note that `locksmith` will not verify whether the dependencies of some packages have changed - this means that the set of package names present in the lockfile will stay the same. + ## Development This project is built with the [Go programming language](https://go.dev/). diff --git a/cmd/construct.go b/cmd/construct.go index 7b945c2..d518644 100644 --- a/cmd/construct.go +++ b/cmd/construct.go @@ -35,7 +35,7 @@ func ConstructOutputPackageList(packages []PackageDescription, packagesFiles map outputPackageList = append(outputPackageList, PackageDescription{ p.Package, p.Version, p.Source, "", []Dependency{}, p.RemoteType, p.RemoteHost, p.RemoteUsername, p.RemoteRepo, p.RemoteSubdir, - p.RemoteRef, p.RemoteSha, + p.RemoteRef, p.RemoteSha, []string{}, }) } for _, p := range packages { @@ -120,7 +120,7 @@ func ResolveDependenciesRecursively(outputList *[]PackageDescription, name strin // during the processing of output package list into renv.lock file. *outputList = append(*outputList, PackageDescription{ p.Package, p.Version, "Repository", r, []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }) for _, d := range p.Dependencies { if d.DependencyType == "Depends" || d.DependencyType == "Imports" || diff --git a/cmd/construct_test.go b/cmd/construct_test.go index 188c44a..2e81532 100644 --- a/cmd/construct_test.go +++ b/cmd/construct_test.go @@ -126,7 +126,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package4", @@ -146,14 +146,14 @@ func Test_ConstructOutputPackageList(t *testing.T) { "", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package11", "0.7.8", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package14", @@ -173,28 +173,28 @@ func Test_ConstructOutputPackageList(t *testing.T) { "2.2", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package16", "2.4.5", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package6", "3.0.1", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package10", "3.0.2", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, } @@ -224,21 +224,21 @@ func Test_ConstructOutputPackageList(t *testing.T) { "", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package5", "3.2.0", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package7", "1.6.2", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package9", @@ -252,28 +252,28 @@ func Test_ConstructOutputPackageList(t *testing.T) { "3.6", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package11", "5.4.7", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package12", "1.2.3", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package15", "3.3.4.5", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, } @@ -284,7 +284,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "1.9.2", "", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, } @@ -339,7 +339,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "1.0.0", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package2", @@ -390,7 +390,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, packagesFiles, repositoryList, @@ -407,7 +407,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "GitHub", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package2", @@ -415,7 +415,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "GitHub", "", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package3", @@ -423,7 +423,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo1.example.com/ExampleRepo1", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { // package11 removed from here @@ -432,7 +432,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { // However afterwards, package4 requested package11 >= 4.5 // so it had to be retrieved from repo2. // The reference to repo1 was overwritten here. - "", "", "", "", []Dependency{}, "", "", "", "", "", "", "", + "", "", "", "", []Dependency{}, "", "", "", "", "", "", "", []string{}, }, { "package12", @@ -440,7 +440,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package4", @@ -448,7 +448,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package11", @@ -456,7 +456,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package14", @@ -464,7 +464,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo1.example.com/ExampleRepo1", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package15", @@ -472,7 +472,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package16", @@ -480,7 +480,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo1.example.com/ExampleRepo1", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package5", @@ -488,7 +488,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package6", @@ -496,7 +496,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo1.example.com/ExampleRepo1", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package7", @@ -504,7 +504,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package8", @@ -512,7 +512,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo3.example.com/ExampleRepo3", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package9", @@ -520,7 +520,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo2.example.com/ExampleRepo2", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "package10", @@ -528,7 +528,7 @@ func Test_ConstructOutputPackageList(t *testing.T) { "Repository", "https://repo1.example.com/ExampleRepo1", []Dependency{}, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, ) diff --git a/cmd/download.go b/cmd/download.go index c55c38f..90e8909 100644 --- a/cmd/download.go +++ b/cmd/download.go @@ -179,10 +179,10 @@ func ProcessDescriptionURL(descriptionURL string, } remoteType = "gitlab" packageSource = "GitLab" - shorterURL := strings.TrimPrefix(descriptionURL, "https://") - remoteHost = "https://" + strings.Split(shorterURL, "/")[0] + shorterURL := strings.TrimPrefix(descriptionURL, https) + remoteHost = https + strings.Split(shorterURL, "/")[0] remoteRef = strings.TrimPrefix(re.FindString(descriptionURL), "ref=") - projectURL := "https://" + strings.Join(strings.Split(shorterURL, "/")[0:5], "/") + projectURL := https + strings.Join(strings.Split(shorterURL, "/")[0:5], "/") descriptionPath := strings.Split(shorterURL, "/")[7] // Check whether package is stored in a subdirectory of the git repository. if strings.Contains(descriptionPath, "%2F") { @@ -218,18 +218,37 @@ func DownloadDescriptionFiles(packageDescriptionList []string, }, ) } else { - log.Warn( - "An error occurred while downloading ", packageDescriptionURL, + log.Warn("An error occurred while downloading ", packageDescriptionURL, "\nIt may have happened because the git repository is not public ", "and you didn't set the Personal Access Token.", "\nPlease make sure you provided an access token (in LOCKSMITH_GITHUBTOKEN ", - "or LOCKSMITH_GITLABTOKEN environment variable).", - ) + "or LOCKSMITH_GITLABTOKEN environment variable).") } } return inputDescriptionFiles } +// GetPackagesFileContent downloads the PACKAGES file from the repositoryURL using the downloadFileFunction +// and returns the contents, or empty string in case of error. +func GetPackagesFileContent(repositoryURL string, + downloadFileFunction func(string, map[string]string) (int, int64, string)) string { + var packagesFileURL string + if strings.Contains(repositoryURL, "/bin/windows/") || strings.Contains(repositoryURL, "/bin/macosx") { + // If we're dealing with a repository with binary Windows or macOS packages, + // we're expecting it to be in a specific format documented in the README. + packagesFileURL = repositoryURL + "/PACKAGES" + } else { + packagesFileURL = repositoryURL + "/src/contrib/PACKAGES" + } + log.Debug("Downloading ", packagesFileURL) + statusCode, _, packagesFileContent := downloadFileFunction(packagesFileURL, map[string]string{}) + if statusCode == 200 { + return packagesFileContent + } + log.Warn("An error occurred while downloading ", packagesFileURL) + return "" +} + // DownloadPackagesFiles downloads PACKAGES files from repository URLs specified in the repositoryList. // Returns a map from repository URL to the string with the contents of PACKAGES file // for that repository. @@ -237,21 +256,7 @@ func DownloadPackagesFiles(repositoryList []string, downloadFileFunction func(string, map[string]string) (int, int64, string)) map[string]string { inputPackagesFiles := make(map[string]string) for _, repository := range repositoryList { - var packagesFileURL string - if strings.Contains(repository, "/bin/windows/") || strings.Contains(repository, "/bin/macosx") { - // If we're dealing with a repository with binary Windows or macOS packages, - // we're expecting it to be in a specific format documented in the README. - packagesFileURL = repository + "/PACKAGES" - } else { - packagesFileURL = repository + "/src/contrib/PACKAGES" - } - log.Debug("Downloading ", packagesFileURL) - statusCode, _, packagesFileContent := downloadFileFunction(packagesFileURL, map[string]string{}) - if statusCode == 200 { - inputPackagesFiles[repository] = packagesFileContent - } else { - log.Warn("An error occurred while downloading ", packagesFileURL) - } + inputPackagesFiles[repository] = GetPackagesFileContent(repository, downloadFileFunction) } return inputPackagesFiles } diff --git a/cmd/download_test.go b/cmd/download_test.go index 538d477..b34c4f4 100644 --- a/cmd/download_test.go +++ b/cmd/download_test.go @@ -155,6 +155,12 @@ func mockedDownloadTextFile(url string, _ map[string]string) (int, int64, string return 200, 0, "PACKAGES contents 2" case url == "https://repo3.example.com/repo3/src/contrib/PACKAGES": return 200, 0, "PACKAGES contents 3" + case url == "https://cloud.r-project.org/bin/windows/contrib/4.3/PACKAGES": + return 200, 0, "PACKAGES content bin/windows" + case url == "https://cloud.r-project.org/src/contrib/PACKAGES": + return 200, 0, "PACKAGES content src/contrib" + case url == "https://example.com/src/contrib/PACKAGES": + return 404, 0, "Not found" } return 200, 0, "" } @@ -298,3 +304,12 @@ func Test_DownloadPackagesFiles(t *testing.T) { "https://repo3.example.com/repo3": "PACKAGES contents 3", }) } + +func Test_GetPackagesFileContent(t *testing.T) { + packagesContentBin := GetPackagesFileContent("https://cloud.r-project.org/bin/windows/contrib/4.3", mockedDownloadTextFile) + packagesContentSrc := GetPackagesFileContent("https://cloud.r-project.org", mockedDownloadTextFile) + packagesContent := GetPackagesFileContent("https://example.com", mockedDownloadTextFile) + assert.Equal(t, packagesContentBin, "PACKAGES content bin/windows") + assert.Equal(t, packagesContentSrc, "PACKAGES content src/contrib") + assert.Equal(t, packagesContent, "") +} diff --git a/cmd/parse.go b/cmd/parse.go index 515e619..6fe24ae 100644 --- a/cmd/parse.go +++ b/cmd/parse.go @@ -72,7 +72,7 @@ func ProcessPackagesFile(content string) PackagesFile { allPackages.Packages, PackageDescription{ packageName, packageMap["Version"], "", "", packageDependencies, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, ) } @@ -94,7 +94,7 @@ func ProcessDescription(description DescriptionFile, allPackages *[]PackageDescr PackageDescription{ packageMap["Package"], packageMap["Version"], description.PackageSource, "", packageDependencies, description.RemoteType, description.RemoteHost, description.RemoteUsername, description.RemoteRepo, - description.RemoteSubdir, description.RemoteRef, description.RemoteSha, + description.RemoteSubdir, description.RemoteRef, description.RemoteSha, []string{}, }, ) } diff --git a/cmd/parse_test.go b/cmd/parse_test.go index 4c9ec2d..225e343 100644 --- a/cmd/parse_test.go +++ b/cmd/parse_test.go @@ -42,7 +42,7 @@ func Test_ProcessPackagesFile(t *testing.T) { "2.15.0", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "somePackage2", @@ -68,7 +68,7 @@ func Test_ProcessPackagesFile(t *testing.T) { "", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "somePackage3", @@ -106,7 +106,7 @@ func Test_ProcessPackagesFile(t *testing.T) { "1.22", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "somePackage4", @@ -150,7 +150,7 @@ func Test_ProcessPackagesFile(t *testing.T) { "7.1.0", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, }, @@ -278,7 +278,7 @@ func Test_ParseDescriptionFileList(t *testing.T) { "", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, { "my.awesome.package.2", @@ -395,7 +395,7 @@ func Test_ParseDescriptionFileList(t *testing.T) { "1.0.0", }, }, - "", "", "", "", "", "", "", + "", "", "", "", "", "", "", []string{}, }, }, ) diff --git a/cmd/renv.go b/cmd/renv.go index 4bcd2d6..cd57b06 100644 --- a/cmd/renv.go +++ b/cmd/renv.go @@ -17,9 +17,21 @@ limitations under the License. package cmd import ( + "encoding/json" + "os" + "regexp" "sort" + "strings" + + git "github.com/go-git/go-git/v5" + githttp "github.com/go-git/go-git/v5/plumbing/transport/http" + yaml "gopkg.in/yaml.v3" ) +const GitHub = "GitHub" +const GitLab = "GitLab" +const https = "https://" + // GenerateRenvLock generates renv.lock file structure which can be then saved as a JSON file. // It uses a list of package data created by ConstructOutputPackageList, and the map of // package repositories containing the packages. @@ -60,3 +72,236 @@ func GetRepositoryKeyByValue(repositoryURL string, repositoryMap map[string]stri } return "" } + +// GetPackageRegex processes the comma-separated expression with wildcards indicating which packages +// should be updated and returns a real regex. +func GetPackageRegex(updatedPackages string) string { + splitUpdatePackages := strings.Split(updatedPackages, ",") + var allUpdateExpressions []string + // For each comma-separated wildcard expression convert "." and "*" + // characters to regexp equivalent. + for _, singleRegexp := range splitUpdatePackages { + singleRegexp = strings.ReplaceAll(singleRegexp, `.`, `\.`) + singleRegexp = strings.ReplaceAll(singleRegexp, "*", ".*") + allUpdateExpressions = append(allUpdateExpressions, "^"+singleRegexp+"$") + } + return strings.Join(allUpdateExpressions, "|") +} + +// GetPackageVersionFromDescription reads the DESCRIPTION file located in descriptionFilePath +// and returns the package version. +func GetPackageVersionFromDescription(descriptionFilePath string) string { + byteValue, err := os.ReadFile(descriptionFilePath) + checkError(err) + cleanedDescription := CleanDescriptionOrPackagesEntry(string(byteValue), true) + descriptionContents := make(map[string]string) + err = yaml.Unmarshal([]byte(cleanedDescription), &descriptionContents) + checkError(err) + version := descriptionContents["Version"] + return version +} + +// GetGitRepositoryURL reads the PackageDescription struct corresponding to a single package +// in the renv.lock and returns the git repository URL from which the package should be cloned. +func GetGitRepositoryURL(p PackageDescription) string { + var repoURL string + switch p.Source { + case GitHub: + repoURL = "https://github.com/" + p.RemoteUsername + "/" + p.RemoteRepo + case GitLab: + // The behavior of renv.lock is not standardized in terms of whether GitLab + // host address starts with 'https://' or not. + var remoteHost string + if strings.HasPrefix(p.RemoteHost, https) { + remoteHost = p.RemoteHost + } else { + remoteHost = https + p.RemoteHost + } + repoURL = remoteHost + "/" + p.RemoteUsername + "/" + p.RemoteRepo + } + return repoURL +} + +// GetDefaultBranchSha clones the git repository located at repoURL to gitDirectory, using Personal +// Access Tokens from LOCKSMITH_GITLABTOKEN or LOCKSMITH_GITHUBTOKEN environment variables. +// It returns the commit SHA of the HEAD of default branch and the name of the default branch, +// or empty string in case of error. +func GetDefaultBranchSha(gitDirectory string, repoURL string, + environmentCredentialsType string) (string, string) { + err := os.MkdirAll(gitDirectory, os.ModePerm) + checkError(err) + var gitCloneOptions *git.CloneOptions + switch { + case environmentCredentialsType == GitLab: + gitCloneOptions = &git.CloneOptions{ + URL: repoURL, + Auth: &githttp.BasicAuth{ + Username: "This can be any string.", + Password: os.Getenv("LOCKSMITH_GITLABTOKEN")}, + Depth: 1, + } + case environmentCredentialsType == GitHub: + gitCloneOptions = &git.CloneOptions{ + URL: repoURL, + Auth: &githttp.BasicAuth{ + Username: "This can be any string.", + Password: os.Getenv("LOCKSMITH_GITHUBTOKEN")}, + Depth: 1, + } + } + repository, err := git.PlainClone(gitDirectory, false, gitCloneOptions) + if err != nil { + log.Error("Error while cloning ", repoURL, ": ", err) + return "", "" + } + // Get SHA of repository HEAD. + ref, err := repository.Head() + checkError(err) + return ref.Hash().String(), strings.TrimPrefix(ref.Name().String(), "refs/heads/") +} + +// UpdateGitPackages iterates through the packages in renv.lock and updates the entries +// corresponding to packages stored in git repositories. Package version and latest commit SHA +// are updated in the renvLock struct. Only packages matching the updatePackageRegexp are updated. +func UpdateGitPackages(renvLock *RenvLock, updatePackageRegexp string, + getDefaultBranchShaFunction func(string, string, string) (string, string), + gitUpdatesDirectory string) { + for k, v := range renvLock.Packages { + match, err := regexp.MatchString(updatePackageRegexp, k) + checkError(err) + if !match || (v.Source != GitLab && v.Source != GitHub) { + log.Trace("Package ", k, " doesn't match updated packages regexp ", + updatePackageRegexp, " or is not a git repository.") + continue + } + log.Trace("Package ", k, " matches updated packages regexp ", + updatePackageRegexp) + // Read default branch HEAD SHA from git. + newPackageSha, defaultBranchName := getDefaultBranchShaFunction( + gitUpdatesDirectory+k, GetGitRepositoryURL(v), v.Source, + ) + var remoteSubdir string + if v.RemoteSubdir != "" { + remoteSubdir = "/" + v.RemoteSubdir + } + // Read newest package version from DESCRIPTION. + newPackageVersion := GetPackageVersionFromDescription( + gitUpdatesDirectory + k + remoteSubdir + "/DESCRIPTION") + if entry, ok := renvLock.Packages[k]; ok && newPackageSha != "" && newPackageVersion != "" { + if newPackageVersion != entry.Version && newPackageSha != entry.RemoteSha { + // Update the renv structure with new version only if the current + // default branch SHA and current package version could be retrieved + // and they are different than old ones. + log.Info("Updating package ", k, " version: ", + entry.Version, " → ", newPackageVersion, + ", SHA: ", entry.RemoteSha, " → ", newPackageSha) + entry.Version = newPackageVersion + entry.RemoteSha = newPackageSha + // Set the default branch name to ensure consistency, + // in case previously renv.lock pointed to e.g. a tag. + entry.RemoteRef = defaultBranchName + renvLock.Packages[k] = entry + } + } + } +} + +// UpdateRepositoryPackages iterates through the packages in renv.lock and updates the entries +// corresponding to packages downloaded from CRAN-like repositories. Package version is updated +// in the renvLock struct. Only packages matching the updatePackageRegexp are updated. +func UpdateRepositoryPackages(renvLock *RenvLock, updatePackageRegexp string, + packagesFiles map[string]PackagesFile) { + for k, v := range renvLock.Packages { + match, err := regexp.MatchString(updatePackageRegexp, k) + checkError(err) + if !match || v.Source == GitLab || v.Source == GitHub { + log.Trace("Package ", k, " doesn't match updated packages regexp ", + updatePackageRegexp, " or is not a git repository.") + continue + } + log.Trace("Package ", k, " matches updated packages regexp ", + updatePackageRegexp) + var repositoryPackagesFile PackagesFile + repositoryName := v.Repository + repositoryPackagesFile, ok := packagesFiles[repositoryName] + if !ok { + log.Error(`Could not retrieve PACKAGES for "`, repositoryName, `" repository `, + `(referenced by `, k, `). Attempting to use CRAN's PACKAGES as a fallback.`) + repositoryPackagesFile = packagesFiles["CRAN"] + repositoryName = "CRAN" + } + var newPackageVersion string + for _, singlePackage := range repositoryPackagesFile.Packages { + if singlePackage.Package == k { + newPackageVersion = singlePackage.Version + continue + } + } + if newPackageVersion == "" { + log.Error(`Could not find package `, k, ` in PACKAGES file for "`, repositoryName, `" repository.`) + continue + } + if entry, ok := renvLock.Packages[k]; ok { + if newPackageVersion != entry.Version { + log.Info("Updating package ", k, " version: ", + entry.Version, " → ", newPackageVersion) + entry.Version = newPackageVersion + renvLock.Packages[k] = entry + } + } + } +} + +// GetPackagesFiles downloads PACKAGES files from repositories defined in the renv.lock header. +// It returns a map from the repository name (as defined in the renv.lock header) to the PackagesFile +// struct representing repository's PACKAGES file. +func GetPackagesFiles(renvLock RenvLock) map[string]PackagesFile { + repositoryPackagesFiles := make(map[string]PackagesFile) + for _, repository := range renvLock.R.Repositories { + packagesFileContent := GetPackagesFileContent(repository.URL, DownloadTextFile) + packagesFile := ProcessPackagesFile(packagesFileContent) + repositoryPackagesFiles[repository.Name] = packagesFile + } + + // Check if the PACKAGES file from a repository named CRAN has been downloaded. + _, ok := repositoryPackagesFiles["CRAN"] + if !ok { + // If not, save CRAN's PACKAGES file to be used as a fallback, for packages which + // (according to renv.lock) should be downloaded from a repository not defined in + // the renv.lock header. + _, _, cranPackagesContent := DownloadTextFile( + "https://cloud.r-project.org/src/contrib/PACKAGES", make(map[string]string), + ) + cranPackagesFile := ProcessPackagesFile(cranPackagesContent) + repositoryPackagesFiles["CRAN"] = cranPackagesFile + } + return repositoryPackagesFiles +} + +// UpdateRenvLock reads the renv.lock from inputFileName. It then retrieves the information +// about the newest package versions from respective repositories (CRAN-like or git repositories) +// from which the packages should be downloaded according to the renv.lock. +// It returns the RenvLock struct represeting the renv.lock with updated package versions. +func UpdateRenvLock(inputFileName, updatePackages string) RenvLock { + // Read renv.lock into RenvLock struct. + var renvLock RenvLock + byteValue, err := os.ReadFile(inputFileName) + checkError(err) + err = json.Unmarshal(byteValue, &renvLock) + checkError(err) + + updatePackageRegex := GetPackageRegex(updatePackages) + + // Remove and recreate directories where temporary clones of git repositories + // used to get the newest default branch SHA will be stored. + gitUpdatesDirectory := localTempDirectory + "/git_updates/" + err = os.RemoveAll(gitUpdatesDirectory) + checkError(err) + err = os.MkdirAll(gitUpdatesDirectory, os.ModePerm) + checkError(err) + + UpdateGitPackages(&renvLock, updatePackageRegex, GetDefaultBranchSha, gitUpdatesDirectory) + repositoryPackagesFiles := GetPackagesFiles(renvLock) + UpdateRepositoryPackages(&renvLock, updatePackageRegex, repositoryPackagesFiles) + return renvLock +} diff --git a/cmd/renv_test.go b/cmd/renv_test.go index 7f971e1..0e472bd 100644 --- a/cmd/renv_test.go +++ b/cmd/renv_test.go @@ -37,6 +37,7 @@ func Test_GenerateRenvLock(t *testing.T) { "subdirectory1", "main", "aaabbb444333", + []string{}, }, { "package2", @@ -51,20 +52,10 @@ func Test_GenerateRenvLock(t *testing.T) { "subdirectory2", "v2.5.4.3", "eee888222aaa", + []string{}, }, { - "", - "", - "", - "", - []Dependency{}, - "", - "", - "", - "", - "", - "", - "", + "", "", "", "", []Dependency{}, "", "", "", "", "", "", "", []string{}, }, { "package3", @@ -72,13 +63,7 @@ func Test_GenerateRenvLock(t *testing.T) { "Repository", "https://repo1.example.com/repo1", []Dependency{}, - "", - "", - "", - "", - "", - "", - "", + "", "", "", "", "", "", "", []string{}, }, { "package4", @@ -86,13 +71,7 @@ func Test_GenerateRenvLock(t *testing.T) { "Repository", "https://repo2.example.com/repo2", []Dependency{}, - "", - "", - "", - "", - "", - "", - "", + "", "", "", "", "", "", "", []string{}, }, { "package5", @@ -100,13 +79,7 @@ func Test_GenerateRenvLock(t *testing.T) { "Repository", "https://repo3.example.com/repo3", []Dependency{}, - "", - "", - "", - "", - "", - "", - "", + "", "", "", "", "", "", "", []string{}, }, }, map[string]string{ "Repo1": "https://repo1.example.com/repo1", @@ -135,6 +108,7 @@ func Test_GenerateRenvLock(t *testing.T) { "subdirectory1", "main", "aaabbb444333", + []string{}, }, "package2": { "package2", @@ -149,6 +123,7 @@ func Test_GenerateRenvLock(t *testing.T) { "subdirectory2", "v2.5.4.3", "eee888222aaa", + []string{}, }, "package3": { "package3", @@ -156,13 +131,7 @@ func Test_GenerateRenvLock(t *testing.T) { "Repository", "Repo1", []Dependency{}, - "", - "", - "", - "", - "", - "", - "", + "", "", "", "", "", "", "", []string{}, }, "package4": { "package4", @@ -170,13 +139,7 @@ func Test_GenerateRenvLock(t *testing.T) { "Repository", "Repo2", []Dependency{}, - "", - "", - "", - "", - "", - "", - "", + "", "", "", "", "", "", "", []string{}, }, "package5": { "package5", @@ -184,14 +147,266 @@ func Test_GenerateRenvLock(t *testing.T) { "Repository", "Repo3", []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + }, + }) +} + +func Test_GetPackageRegex(t *testing.T) { + packageRegex := GetPackageRegex("package*,*some.Package,test1,my*awesome*package") + assert.Equal(t, packageRegex, `^package.*$|^.*some\.Package$|^test1$|^my.*awesome.*package$`) +} + +func Test_GetPackageVersionFromDescription(t *testing.T) { + version1 := GetPackageVersionFromDescription("testdata/DESCRIPTION1") + assert.Equal(t, version1, "0.14.0.9012") + version2 := GetPackageVersionFromDescription("testdata/DESCRIPTION2") + assert.Equal(t, version2, "0.9.1.9013") + version3 := GetPackageVersionFromDescription("testdata/NON_EXISTENT_DESCRIPTION") + assert.Equal(t, version3, "") +} + +func Test_GetGitRepositoryURL(t *testing.T) { + repoURL1 := GetGitRepositoryURL(PackageDescription{ + "", "", "GitHub", "", []Dependency{}, "", + "api.github.com", "github-org-1", "repo-name-1", "", "", "", []string{}, + }) + assert.Equal(t, repoURL1, "https://github.com/github-org-1/repo-name-1") + repoURL2 := GetGitRepositoryURL(PackageDescription{ + "", "", "GitLab", "", []Dependency{}, "", + "https://gitlab.example.com", "org1/org2", "repo-name-2", "", "", "", []string{}, + }) + assert.Equal(t, repoURL2, "https://gitlab.example.com/org1/org2/repo-name-2") + repoURL3 := GetGitRepositoryURL(PackageDescription{ + "", "", "GitLab", "", []Dependency{}, "", + "gitlab.example.com", "org3/org4", "repo-name-3", "", "", "", []string{}, + }) + assert.Equal(t, repoURL3, "https://gitlab.example.com/org3/org4/repo-name-3") +} + +func mockedGetDefaultBranchSha(_ string, repoURL string, _ string) (string, string) { + switch { + case repoURL == "https://github.com/group1/group2/package11": + return "eee111555bbbccc", "main" + case repoURL == "https://gitlab.example.com/group3/group4/package12": + return "888444dddbbbaaa", "main" + } + return "", "" +} + +func Test_UpdateGitPackages(t *testing.T) { + renvLock := RenvLock{ + RenvLockContents{ + []RenvLockRepository{ + {"Repo1", "https://repo1.example.com/repo1"}, + }, + }, + map[string]PackageDescription{ + "package11": { + "package11", + "1.0.2", + "GitHub", "", + []Dependency{}, + "github", + "api.github.com", + "group1/group2", + "package11", + "subdirectory1", + "main", + "aaabbb444333", + []string{}, + }, + "package12": { + "package12", + "2.5.4.3", + "GitLab", "", + []Dependency{}, + "gitlab", + "https://gitlab.example.com", + "group3/group4", + "package12", + "subdirectory2", + "v2.5.4.3", + "eee888222aaa", + []string{}, + }, + "package3": { + "package3", + "3.2.7.8", + "Repository", + "Repo1", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package4": { + "package4", + "3.7.0", + "GitLab", "", + []Dependency{}, + "gitlab", + "https://gitlab.example.com", + "group6/group7", + "package4", "", + "v3.7.0", + "ccceee444999", + []string{}, + }, + }, + } + UpdateGitPackages(&renvLock, "^package1.*$", mockedGetDefaultBranchSha, "testdata/git_updates/") + assert.Equal(t, renvLock.Packages["package11"].Version, "1.0.4") + assert.Equal(t, renvLock.Packages["package12"].Version, "2.6.1.1") + assert.Equal(t, renvLock.Packages["package4"].Version, "3.7.0") + assert.Equal(t, renvLock.Packages["package11"].RemoteSha, "eee111555bbbccc") + assert.Equal(t, renvLock.Packages["package12"].RemoteSha, "888444dddbbbaaa") + assert.Equal(t, renvLock.Packages["package4"].RemoteSha, "ccceee444999") + assert.Equal(t, renvLock.Packages["package11"].RemoteRef, "main") + assert.Equal(t, renvLock.Packages["package12"].RemoteRef, "main") + assert.Equal(t, renvLock.Packages["package4"].RemoteRef, "v3.7.0") +} + +func Test_UpdateRepositoryPackages(t *testing.T) { + renvLock := RenvLock{ + RenvLockContents{ + []RenvLockRepository{ + {"Repo1", "https://repo1.example.com/ExampleRepo1"}, + {"Repo2", "https://repo2.example.com/ExampleRepo2"}, + {"Repo3", "https://repo3.example.com/ExampleRepo3"}, + }, + }, + map[string]PackageDescription{ + "package13": { + "package13", + "1.1.0", + "Repository", + "Repo1", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package14": { + "package14", + "3.7.0", + "GitLab", "", + []Dependency{}, + "gitlab", + "https://gitlab.example.com", + "group6/group7", + "package4", "", - "", + "v3.7.0", + "ccceee444999", + []string{}, + }, + "package15": { + "package15", + "2.4.7", + "Repository", + "Repo2", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package16": { + "package16", + "0.0.5", + "Repository", + "Repo3", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package17": { + "package17", + "1.1.1", + "Repository", + "Repo1", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package18": { + "package18", + "2.3.2", + "Repository", + "Repo2", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package19": { + "package19", + "4.1.1", + "Repository", + "NonExistentRepository", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + "package21": { + "package21", + "3.8.1", + "Repository", + "Repo1", + []Dependency{}, + "", "", "", "", "", "", "", []string{}, }, }, - }) + } + packagesFiles := make(map[string]PackagesFile) + packagesFiles["Repo1"] = PackagesFile{ + []PackageDescription{ + { + "package13", + "2.2.0", + "", "", []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + { + "package21", + "3.9.3", + "", "", []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + }, + } + packagesFiles["Repo2"] = PackagesFile{ + []PackageDescription{ + { + "package15", + "3.2.1", + "", "", []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + }, + } + packagesFiles["Repo3"] = PackagesFile{ + []PackageDescription{ + { + "package16", + "1.2.3", + "", "", []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + }, + } + packagesFiles["CRAN"] = PackagesFile{ + []PackageDescription{ + { + "package19", + "5.2.3", + "", "", []Dependency{}, + "", "", "", "", "", "", "", []string{}, + }, + }, + } + UpdateRepositoryPackages(&renvLock, "^package1.*$", packagesFiles) + assert.Equal(t, renvLock.Packages["package13"].Version, "2.2.0") + assert.Equal(t, renvLock.Packages["package14"].Version, "3.7.0") + assert.Equal(t, renvLock.Packages["package15"].Version, "3.2.1") + assert.Equal(t, renvLock.Packages["package16"].Version, "1.2.3") + assert.Equal(t, renvLock.Packages["package17"].Version, "1.1.1") + assert.Equal(t, renvLock.Packages["package18"].Version, "2.3.2") + assert.Equal(t, renvLock.Packages["package19"].Version, "5.2.3") + assert.Equal(t, renvLock.Packages["package21"].Version, "3.8.1") } diff --git a/cmd/root.go b/cmd/root.go index 90169a9..d88299a 100644 --- a/cmd/root.go +++ b/cmd/root.go @@ -20,6 +20,7 @@ package cmd import ( "fmt" "os" + "runtime" "github.com/jamiealquiza/envy" "github.com/sirupsen/logrus" @@ -32,8 +33,10 @@ var cfgFile string var logLevel string var gitHubToken string var gitLabToken string +var inputRenvLock string var outputRenvLock string var allowIncompleteRenvLock string +var updatePackages string // In case the lists are provided as arrays in YAML configuration file: var inputPackages []string @@ -44,6 +47,8 @@ var inputRepositories []string var inputPackageList string var inputRepositoryList string +var localTempDirectory string + var log = logrus.New() func setLogLevel() { @@ -93,17 +98,30 @@ in an renv.lock-compatible file.`, fmt.Println("inputRepositoryList =", inputRepositoryList) fmt.Println("inputPackages =", inputPackages) fmt.Println("inputRepositories =", inputRepositories) + fmt.Println("inputRenvLock =", inputRenvLock) fmt.Println("outputRenvLock =", outputRenvLock) fmt.Println("allowIncompleteRenvLock =", allowIncompleteRenvLock) - - packageDescriptionList, repositoryList, repositoryMap, allowedMissingDependencyTypes := ParseInput() - inputDescriptionFiles := DownloadDescriptionFiles(packageDescriptionList, DownloadTextFile) - inputPackages := ParseDescriptionFileList(inputDescriptionFiles) - repositoryPackagesFiles := DownloadPackagesFiles(repositoryList, DownloadTextFile) - packagesFiles := ParsePackagesFiles(repositoryPackagesFiles) - outputPackageList := ConstructOutputPackageList(inputPackages, packagesFiles, repositoryList, allowedMissingDependencyTypes) - renvLock := GenerateRenvLock(outputPackageList, repositoryMap) - writeJSON(outputRenvLock, renvLock) + fmt.Println("updatePackages =", updatePackages) + + if runtime.GOOS == "windows" { + localTempDirectory = os.Getenv("TMP") + `\tmp\locksmith` + } else { + localTempDirectory = "/tmp/locksmith" + } + + if inputRenvLock != "" { + renvLock := UpdateRenvLock(inputRenvLock, updatePackages) + writeJSON(outputRenvLock, renvLock) + } else { + packageDescriptionList, repositoryList, repositoryMap, allowedMissingDependencyTypes := ParseInput() + inputDescriptionFiles := DownloadDescriptionFiles(packageDescriptionList, DownloadTextFile) + inputPackages := ParseDescriptionFileList(inputDescriptionFiles) + repositoryPackagesFiles := DownloadPackagesFiles(repositoryList, DownloadTextFile) + packagesFiles := ParsePackagesFiles(repositoryPackagesFiles) + outputPackageList := ConstructOutputPackageList(inputPackages, packagesFiles, repositoryList, allowedMissingDependencyTypes) + renvLock := GenerateRenvLock(outputPackageList, repositoryMap) + writeJSON(outputRenvLock, renvLock) + } }, } rootCmd.PersistentFlags().StringVarP(&cfgFile, "config", "c", "", @@ -118,12 +136,19 @@ in an renv.lock-compatible file.`, "Token to download non-public files from GitHub.") rootCmd.PersistentFlags().StringVarP(&gitLabToken, "gitLabToken", "g", "", "Token to download non-public files from GitLab.") + rootCmd.PersistentFlags().StringVarP(&inputRenvLock, "inputRenvLock", "n", "input.renv.lock", + "Lockfile which should be read and updated to include the newest versions of the packages.") rootCmd.PersistentFlags().StringVarP(&outputRenvLock, "outputRenvLock", "o", "renv.lock", "File name to save the output renv.lock file.") rootCmd.PersistentFlags().StringVarP(&allowIncompleteRenvLock, "allowIncompleteRenvLock", "i", "", "Locksmith will fail if any of dependencies of input packages cannot be found in the repositories. "+ "However, it will not fail for comma-separated dependency types listed in this argument, e.g.: "+ "'Imports,Depends,Suggests,LinkingTo'") + rootCmd.PersistentFlags().StringVarP(&updatePackages, "updatePackages", "u", "*", + "Expression with wildcards indicating which packages from the inputRenvLock should be updated to the newest version. "+ + "The expression follows the pattern: \"expression1,expression2,...\" where \"expressionN\" can be: "+ + "literal package name and/or * symbol(s) meaning any set of characters. Example: "+ + `'package*,*abc,a*b,someOtherPackage'. By default all packages are updated.`) // Add version command. rootCmd.AddCommand(extension.NewVersionCobraCmd()) @@ -173,13 +198,8 @@ func Execute() { func initializeConfig() { for _, v := range []string{ - "logLevel", - "inputPackageList", - "inputRepositoryList", - "gitHubToken", - "gitLabToken", - "outputRenvLock", - "allowIncompleteRenvLock", + "logLevel", "inputPackageList", "inputRepositoryList", "gitHubToken", "gitLabToken", + "inputRenvLock", "outputRenvLock", "allowIncompleteRenvLock", "updatePackages", } { // If the flag has not been set in newRootCommand() and it has been set in initConfig(). // In other words: if it's not been provided in command line, but has been diff --git a/cmd/structs.go b/cmd/structs.go index 14be0f6..5925d39 100644 --- a/cmd/structs.go +++ b/cmd/structs.go @@ -79,8 +79,8 @@ type PackageDescription struct { // of the package repository, in case Source is 'Repository'. Repository string `json:"Repository,omitempty"` // Dependencies contains the list of package dependencies. - Dependencies []Dependency `json:"Requirements,omitempty"` - // When processing packages stored in package repositories, the fields below are empty. + Dependencies []Dependency `json:"Dependencies,omitempty"` + // When processing packages stored in package repositories, the Remote* fields below are empty. // These fields are documented in the DescriptionFile struct. RemoteType string `json:"RemoteType,omitempty"` RemoteHost string `json:"RemoteHost,omitempty"` @@ -89,6 +89,9 @@ type PackageDescription struct { RemoteSubdir string `json:"RemoteSubdir,omitempty"` RemoteRef string `json:"RemoteRef,omitempty"` RemoteSha string `json:"RemoteSha,omitempty"` + // Requirements field is not used, except to be able to unmarshal renv.lock JSON in which + // this field is present. + Requirements []string `json:"Requirements,omitempty"` } type Dependency struct { diff --git a/cmd/testdata/git_updates/package11/subdirectory1/DESCRIPTION b/cmd/testdata/git_updates/package11/subdirectory1/DESCRIPTION new file mode 100644 index 0000000..c2c704c --- /dev/null +++ b/cmd/testdata/git_updates/package11/subdirectory1/DESCRIPTION @@ -0,0 +1,2 @@ +Package: package11 +Version: 1.0.4 diff --git a/cmd/testdata/git_updates/package12/subdirectory2/DESCRIPTION b/cmd/testdata/git_updates/package12/subdirectory2/DESCRIPTION new file mode 100644 index 0000000..9d03fa7 --- /dev/null +++ b/cmd/testdata/git_updates/package12/subdirectory2/DESCRIPTION @@ -0,0 +1,2 @@ +Package: package12 +Version: 2.6.1.1 diff --git a/go.mod b/go.mod index 9edebcb..b697577 100644 --- a/go.mod +++ b/go.mod @@ -3,33 +3,45 @@ module github.com/insightsengineering/locksmith go 1.21 require ( + github.com/go-git/go-git/v5 v5.11.0 github.com/jamiealquiza/envy v1.1.0 github.com/sirupsen/logrus v1.9.3 - github.com/spf13/cobra v1.7.0 - github.com/spf13/viper v1.17.0 + github.com/spf13/cobra v1.8.0 + github.com/spf13/viper v1.18.2 github.com/stretchr/testify v1.8.4 go.szostok.io/version v1.2.0 gopkg.in/yaml.v3 v3.0.1 ) require ( + dario.cat/mergo v1.0.0 // indirect github.com/Masterminds/goutils v1.1.1 // indirect github.com/Masterminds/semver/v3 v3.2.0 // indirect github.com/Masterminds/sprig/v3 v3.2.3 // indirect + github.com/Microsoft/go-winio v0.6.1 // indirect + github.com/ProtonMail/go-crypto v0.0.0-20230828082145-3c4c8a2d2371 // indirect github.com/araddon/dateparse v0.0.0-20210429162001-6b43995a97de // indirect github.com/aymanbagabas/go-osc52/v2 v2.0.1 // indirect + github.com/cloudflare/circl v1.3.3 // indirect + github.com/cyphar/filepath-securejoin v0.2.4 // indirect github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc // indirect github.com/dustin/go-humanize v1.0.1 // indirect + github.com/emirpasic/gods v1.18.1 // indirect github.com/fatih/color v1.14.1 // indirect - github.com/fsnotify/fsnotify v1.6.0 // indirect + github.com/fsnotify/fsnotify v1.7.0 // indirect + github.com/go-git/gcfg v1.5.1-0.20230307220236-3a3c6141e376 // indirect + github.com/go-git/go-billy/v5 v5.5.0 // indirect github.com/goccy/go-yaml v1.11.0 // indirect - github.com/google/uuid v1.1.2 // indirect + github.com/golang/groupcache v0.0.0-20210331224755-41bb18bfe9da // indirect + github.com/google/uuid v1.4.0 // indirect github.com/hashicorp/go-version v1.6.0 // indirect github.com/hashicorp/hcl v1.0.0 // indirect github.com/hokaccha/go-prettyjson v0.0.0-20211117102719-0474bc63780f // indirect github.com/huandu/xstrings v1.3.3 // indirect github.com/imdario/mergo v0.3.11 // indirect github.com/inconshreveable/mousetrap v1.1.0 // indirect + github.com/jbenet/go-context v0.0.0-20150711004518-d14ea06fba99 // indirect + github.com/kevinburke/ssh_config v1.2.0 // indirect github.com/lucasb-eyer/go-colorful v1.2.0 // indirect github.com/magiconair/properties v1.8.7 // indirect github.com/mattn/go-colorable v0.1.13 // indirect @@ -40,22 +52,30 @@ require ( github.com/mitchellh/reflectwalk v1.0.0 // indirect github.com/muesli/termenv v0.15.1 // indirect github.com/pelletier/go-toml/v2 v2.1.0 // indirect + github.com/pjbgf/sha1cd v0.3.0 // indirect github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 // indirect github.com/rivo/uniseg v0.2.0 // indirect - github.com/sagikazarmark/locafero v0.3.0 // indirect + github.com/sagikazarmark/locafero v0.4.0 // indirect github.com/sagikazarmark/slog-shim v0.1.0 // indirect + github.com/sergi/go-diff v1.1.0 // indirect github.com/shopspring/decimal v1.2.0 // indirect + github.com/skeema/knownhosts v1.2.1 // indirect github.com/sourcegraph/conc v0.3.0 // indirect - github.com/spf13/afero v1.10.0 // indirect - github.com/spf13/cast v1.5.1 // indirect + github.com/spf13/afero v1.11.0 // indirect + github.com/spf13/cast v1.6.0 // indirect github.com/spf13/pflag v1.0.5 // indirect github.com/subosito/gotenv v1.6.0 // indirect + github.com/xanzy/ssh-agent v0.3.3 // indirect go.uber.org/atomic v1.9.0 // indirect go.uber.org/multierr v1.9.0 // indirect golang.org/x/crypto v0.17.0 // indirect golang.org/x/exp v0.0.0-20230905200255-921286631fa9 // indirect + golang.org/x/mod v0.12.0 // indirect + golang.org/x/net v0.19.0 // indirect golang.org/x/sys v0.15.0 // indirect golang.org/x/text v0.14.0 // indirect + golang.org/x/tools v0.13.0 // indirect golang.org/x/xerrors v0.0.0-20220907171357-04be3eba64a2 // indirect gopkg.in/ini.v1 v1.67.0 // indirect + gopkg.in/warnings.v0 v0.1.2 // indirect ) diff --git a/go.sum b/go.sum index 7cbf1b4..388af94 100644 --- a/go.sum +++ b/go.sum @@ -1,165 +1,83 @@ -cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= -cloud.google.com/go v0.34.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= -cloud.google.com/go v0.38.0/go.mod h1:990N+gfupTy94rShfmMCWGDn0LpTmnzTp2qbd1dvSRU= -cloud.google.com/go v0.44.1/go.mod h1:iSa0KzasP4Uvy3f1mN/7PiObzGgflwredwwASm/v6AU= -cloud.google.com/go v0.44.2/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY= -cloud.google.com/go v0.44.3/go.mod h1:60680Gw3Yr4ikxnPRS/oxxkBccT6SA1yMk63TGekxKY= -cloud.google.com/go v0.45.1/go.mod h1:RpBamKRgapWJb87xiFSdk4g1CME7QZg3uwTez+TSTjc= -cloud.google.com/go v0.46.3/go.mod h1:a6bKKbmY7er1mI7TEI4lsAkts/mkhTSZK8w33B4RAg0= -cloud.google.com/go v0.50.0/go.mod h1:r9sluTvynVuxRIOHXQEHMFffphuXHOMZMycpNR5e6To= -cloud.google.com/go v0.52.0/go.mod h1:pXajvRH/6o3+F9jDHZWQ5PbGhn+o8w9qiu/CffaVdO4= -cloud.google.com/go v0.53.0/go.mod h1:fp/UouUEsRkN6ryDKNW/Upv/JBKnv6WDthjR6+vze6M= -cloud.google.com/go v0.54.0/go.mod h1:1rq2OEkV3YMf6n/9ZvGWI3GWw0VoqH/1x2nd8Is/bPc= -cloud.google.com/go v0.56.0/go.mod h1:jr7tqZxxKOVYizybht9+26Z/gUq7tiRzu+ACVAMbKVk= -cloud.google.com/go v0.57.0/go.mod h1:oXiQ6Rzq3RAkkY7N6t3TcE6jE+CIBBbA36lwQ1JyzZs= -cloud.google.com/go v0.62.0/go.mod h1:jmCYTdRCQuc1PHIIJ/maLInMho30T/Y0M4hTdTShOYc= -cloud.google.com/go v0.65.0/go.mod h1:O5N8zS7uWy9vkA9vayVHs65eM1ubvY4h553ofrNHObY= -cloud.google.com/go v0.72.0/go.mod h1:M+5Vjvlc2wnp6tjzE102Dw08nGShTscUx2nZMufOKPI= -cloud.google.com/go v0.74.0/go.mod h1:VV1xSbzvo+9QJOxLDaJfTjx5e+MePCpCWwvftOeQmWk= -cloud.google.com/go v0.75.0/go.mod h1:VGuuCn7PG0dwsd5XPVm2Mm3wlh3EL55/79EKB6hlPTY= -cloud.google.com/go/bigquery v1.0.1/go.mod h1:i/xbL2UlR5RvWAURpBYZTtm/cXjCha9lbfbpx4poX+o= -cloud.google.com/go/bigquery v1.3.0/go.mod h1:PjpwJnslEMmckchkHFfq+HTD2DmtT67aNFKH1/VBDHE= -cloud.google.com/go/bigquery v1.4.0/go.mod h1:S8dzgnTigyfTmLBfrtrhyYhwRxG72rYxvftPBK2Dvzc= -cloud.google.com/go/bigquery v1.5.0/go.mod h1:snEHRnqQbz117VIFhE8bmtwIDY80NLUZUMb4Nv6dBIg= -cloud.google.com/go/bigquery v1.7.0/go.mod h1://okPTzCYNXSlb24MZs83e2Do+h+VXtc4gLoIoXIAPc= -cloud.google.com/go/bigquery v1.8.0/go.mod h1:J5hqkt3O0uAFnINi6JXValWIb1v0goeZM77hZzJN/fQ= -cloud.google.com/go/datastore v1.0.0/go.mod h1:LXYbyblFSglQ5pkeyhO+Qmw7ukd3C+pD7TKLgZqpHYE= -cloud.google.com/go/datastore v1.1.0/go.mod h1:umbIZjpQpHh4hmRpGhH4tLFup+FVzqBi1b3c64qFpCk= -cloud.google.com/go/pubsub v1.0.1/go.mod h1:R0Gpsv3s54REJCy4fxDixWD93lHJMoZTyQ2kNxGRt3I= -cloud.google.com/go/pubsub v1.1.0/go.mod h1:EwwdRX2sKPjnvnqCa270oGRyludottCI76h+R3AArQw= -cloud.google.com/go/pubsub v1.2.0/go.mod h1:jhfEVHT8odbXTkndysNHCcx0awwzvfOlguIAii9o8iA= -cloud.google.com/go/pubsub v1.3.1/go.mod h1:i+ucay31+CNRpDW4Lu78I4xXG+O1r/MAHgjpRVR+TSU= -cloud.google.com/go/storage v1.0.0/go.mod h1:IhtSnM/ZTZV8YYJWCY8RULGVqBDmpoyjwiyrjsg+URw= -cloud.google.com/go/storage v1.5.0/go.mod h1:tpKbwo567HUNpVclU5sGELwQWBDZ8gh0ZeosJ0Rtdos= -cloud.google.com/go/storage v1.6.0/go.mod h1:N7U0C8pVQ/+NIKOBQyamJIeKQKkZ+mxpohlUTyfDhBk= -cloud.google.com/go/storage v1.8.0/go.mod h1:Wv1Oy7z6Yz3DshWRJFhqM/UCfaWIRTdp0RXyy7KQOVs= -cloud.google.com/go/storage v1.10.0/go.mod h1:FLPqc6j+Ki4BU591ie1oL6qBQGu2Bl/tZ9ullr3+Kg0= -cloud.google.com/go/storage v1.14.0/go.mod h1:GrKmX003DSIwi9o29oFT7YDnHYwZoctc3fOKtUw0Xmo= -dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU= -github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= -github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo= +dario.cat/mergo v1.0.0 h1:AGCNq9Evsj31mOgNPcLyXc+4PNABt905YmuqPYYpBWk= +dario.cat/mergo v1.0.0/go.mod h1:uNxQE+84aUszobStD9th8a29P2fMDhsBdgRYvZOxGmk= github.com/Masterminds/goutils v1.1.1 h1:5nUrii3FMTL5diU80unEVvNevw1nH4+ZV4DSLVJLSYI= github.com/Masterminds/goutils v1.1.1/go.mod h1:8cTjp+g8YejhMuvIA5y2vz3BpJxksy863GQaJW2MFNU= github.com/Masterminds/semver/v3 v3.2.0 h1:3MEsd0SM6jqZojhjLWWeBY+Kcjy9i6MQAeY7YgDP83g= github.com/Masterminds/semver/v3 v3.2.0/go.mod h1:qvl/7zhW3nngYb5+80sSMF+FG2BjYrf8m9wsX0PNOMQ= github.com/Masterminds/sprig/v3 v3.2.3 h1:eL2fZNezLomi0uOLqjQoN6BfsDD+fyLtgbJMAj9n6YA= github.com/Masterminds/sprig/v3 v3.2.3/go.mod h1:rXcFaZ2zZbLRJv/xSysmlgIM1u11eBaRMhvYXJNkGuM= +github.com/Microsoft/go-winio v0.5.2/go.mod h1:WpS1mjBmmwHBEWmogvA2mj8546UReBk4v8QkMxJ6pZY= +github.com/Microsoft/go-winio v0.6.1 h1:9/kr64B9VUZrLm5YYwbGtUJnMgqWVOdUAXu6Migciow= +github.com/Microsoft/go-winio v0.6.1/go.mod h1:LRdKpFKfdobln8UmuiYcKPot9D2v6svN5+sAH+4kjUM= +github.com/ProtonMail/go-crypto v0.0.0-20230828082145-3c4c8a2d2371 h1:kkhsdkhsCvIsutKu5zLMgWtgh9YxGCNAw8Ad8hjwfYg= +github.com/ProtonMail/go-crypto v0.0.0-20230828082145-3c4c8a2d2371/go.mod h1:EjAoLdwvbIOoOQr3ihjnSoLZRtE8azugULFRteWMNc0= +github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be h1:9AeTilPcZAjCFIImctFaOjnTIavg87rW78vTPkQqLI8= +github.com/anmitsu/go-shlex v0.0.0-20200514113438-38f4b401e2be/go.mod h1:ySMOLuWl6zY27l47sB3qLNK6tF2fkHG55UZxx8oIVo4= github.com/araddon/dateparse v0.0.0-20210429162001-6b43995a97de h1:FxWPpzIjnTlhPwqqXc4/vE0f7GvRjuAsbW+HOIe8KnA= github.com/araddon/dateparse v0.0.0-20210429162001-6b43995a97de/go.mod h1:DCaWoUhZrYW9p1lxo/cm8EmUOOzAPSEZNGF2DK1dJgw= +github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5 h1:0CwZNZbxp69SHPdPJAN/hZIm0C4OItdklCFmMRWYpio= +github.com/armon/go-socks5 v0.0.0-20160902184237-e75332964ef5/go.mod h1:wHh0iHkYZB8zMSxRWpUBQtwG5a7fFgvEO+odwuTv2gs= github.com/aymanbagabas/go-osc52/v2 v2.0.1 h1:HwpRHbFMcZLEVr42D4p7XBqjyuxQH5SMiErDT4WkJ2k= github.com/aymanbagabas/go-osc52/v2 v2.0.1/go.mod h1:uYgXzlJ7ZpABp8OJ+exZzJJhRNQ2ASbcXHWsFqH8hp8= -github.com/census-instrumentation/opencensus-proto v0.2.1/go.mod h1:f6KPmirojxKA12rnyqOA5BBL4O983OfeGPqjHWSTneU= -github.com/chzyer/logex v1.1.10/go.mod h1:+Ywpsq7O8HXn0nuIou7OrIPyXbp3wmkHB+jjWRnGsAI= -github.com/chzyer/readline v0.0.0-20180603132655-2972be24d48e/go.mod h1:nSuG5e5PlCu98SY8svDHJxuZscDgtXS6KTTbou5AhLI= -github.com/chzyer/test v0.0.0-20180213035817-a1ea475d72b1/go.mod h1:Q3SI9o4m/ZMnBNeIyt5eFwwo7qiLfzFZmjNmxjkiQlU= -github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= -github.com/cncf/udpa/go v0.0.0-20191209042840-269d4d468f6f/go.mod h1:M8M6+tZqaGXZJjfX53e64911xZQV5JYwmTeXPW+k8Sc= -github.com/cncf/udpa/go v0.0.0-20200629203442-efcf912fb354/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk= -github.com/cncf/udpa/go v0.0.0-20201120205902-5459f2c99403/go.mod h1:WmhPx2Nbnhtbo57+VJT5O0JRkEi1Wbu0z5j0R8u5Hbk= -github.com/cpuguy83/go-md2man/v2 v2.0.2/go.mod h1:tgQtvFlXSQOSOSIRvRPT7W67SCa46tRHOmNcaadrF8o= +github.com/bwesterb/go-ristretto v1.2.3/go.mod h1:fUIoIZaG73pV5biE2Blr2xEzDoMj7NFEuV9ekS419A0= +github.com/cloudflare/circl v1.3.3 h1:fE/Qz0QdIGqeWfnwq0RE0R7MI51s0M2E4Ga9kq5AEMs= +github.com/cloudflare/circl v1.3.3/go.mod h1:5XYMA4rFBvNIrhs50XuiBJ15vF2pZn4nnUKZrLbUZFA= +github.com/cpuguy83/go-md2man/v2 v2.0.3/go.mod h1:tgQtvFlXSQOSOSIRvRPT7W67SCa46tRHOmNcaadrF8o= +github.com/cyphar/filepath-securejoin v0.2.4 h1:Ugdm7cg7i6ZK6x3xDF1oEu1nfkyfH53EtKeQYTC3kyg= +github.com/cyphar/filepath-securejoin v0.2.4/go.mod h1:aPGpWjXOXUn2NCNjFvBE6aRxGGx79pTxQpKOJNYHHl4= github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc h1:U9qPSI2PIWSS1VwoXQT9A3Wy9MM3WgvqSxFWenqJduM= github.com/davecgh/go-spew v1.1.2-0.20180830191138-d8f796af33cc/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/dustin/go-humanize v1.0.1 h1:GzkhY7T5VNhEkwH0PVJgjz+fX1rhBrR7pRT3mDkpeCY= github.com/dustin/go-humanize v1.0.1/go.mod 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