Nat  Grady

Nat Grady

1660716780

Remotes: install R Packages From GitHub, GitLab, Bitbucket, Git

remotes

Install R Packages from remote or local repositories, including GitHub, GitLab, Bitbucket, and Bioconductor

Download and install R packages stored in GitHub, GitLab, Bitbucket, Bioconductor, or plain subversion or git repositories. This package is a lightweight replacement of the install_* functions in devtools. Indeed most of the code was copied over from devtools.

Features

  • Installers:
    • Install packages with their dependencies.
    • Install from GitHub, GitLab, Bitbucket.
    • Install from git and subversion repositories.
    • Install from local files or URLs.
    • Install the dependencies of a local package tree.
    • Install specific package versions from CRAN.
  • Supports Bioconductor packages.
  • Supports the Remotes field in DESCRIPTION. See more in the dependencies vignette.
  • Supports the Additional_repositories field in DESCRIPTION.
  • Can install itself from GitHub (see below).
  • Does not depend on other R packages.
  • Does not contain compiled code, so no compiler is needed.
  • Does not need any external software (for most of the functionality at least).

Installation

Install the released version of remotes from CRAN:

install.packages("remotes")

Usage

Note that most of the examples here use GitHub. See below for other supported repository types.

To install the latest version of a package in the default branch from GitHub, you can use the user/repo form. Note that user can also be an organization:

remotes::install_github("r-lib/conflicted")

If the R package is inside a subdirectory of the root directory, then give this subdirectory as well:

# build = FALSE because of some specificities of XGBoost package
install_github("dmlc/xgboost/R-package", build = FALSE)

To install a certain branch or commit or tag, append it to the repo name, after an @:

remotes::install_github("gaborcsardi/pkgconfig@v2.0.0")

To install the latest release, append @*release to the repo name:

remotes::install_github("gaborcsardi/pkgconfig@*release")

To install a pull request, append # and the id (an integer number) of the pull request to the repo name:

remotes::install_github("r-lib/pkgconfig#7")

Dependencies

Dependencies are automatically installed from CRAN. By default, outdated dependencies are automatically upgraded. In interactive sessions you can select a subset of the dependencies to upgrade.

Dependencies on GitHub

It is also possible to install dependencies from GitHub or other supported repositories. For this you need to add a Remotes field to the DESCRIPTION file. Its format is:

Remotes: [remote::]repo_spec, [remote::]repo_spec, ...

where repo_spec is any repository specification the corresponding install_() function can handle. If remote:: is missing, github:: is assumed. Other possible values: gitlab::,bitbucket::, git::, local::, svn::, url::, version::, cran::, bioc::.

See more about the Remotes field in this vignette.

Additional repositories

remotes supports the Additional_repositories field in DESCRIPTION. This is a way to specify dependencies from non-CRAN package repositories. See the Writing R extensions manual for details.

Bioconductor packages

Bioconductor packages are automatically detected and their dependencies are installed from Bioconductor.

Currently supported remote types

  • GitHub repositories via install_github.
  • Bitbucket repositories via install_bitbucket.
  • Generic git repositories via install_git. They need either a system git installation, or the git2r R package.
  • Local directories or package archive files via install_local.
  • Remote package archive files via install_url.
  • Packages in subversion repositories via install_svn. They need a system subversion installation.
  • Specific package versions from CRAN or other CRAN-like repositories via install_version. This includes outdated and archived packages as well.
  • All dependencies of a package in a local directory via install_deps.

Download methods

  • For R older than 3.2, the curl package is required as remotes falls back to curl::curl_download in that case
  • For R newer than 3.3, default download.file() method is used. (method = "auto")
  • For in between versions,
    • method = "wininet" is used on windows OS
    • method = "libcurl" is used on other OS, if available.

See help("download.file") for informations on these methods and for setting proxies if needed.

Standalone mode

remotes will use the curl, git2r and pkgbuild packages if they are installed to provide faster implementations for some aspects of the install process. However if you are using remotes to install or update these packages (or their reverse dependencies) using them during installation may fail (particularly on Windows).

If you set the environment variable R_REMOTES_STANDALONE="true" (e.g. in R Sys.setenv(R_REMOTES_STANDALONE="true")) you can force remotes to operate in standalone mode and use only its internal R implementations. This will allow successful installation of these packages.

Options

remotes uses the following standard R options, see ?options for their details:

download.file.method for the default download method. See ?download.file.

pkgType for the package type (source or binary, see manual) to install, download or look up dependencies for.

repos for the locations of the user's standard CRAN(-like) repositories.

It also uses some remotes specific options:

BioC_git for the URL of the default Bioconductor git mirror.

BioC_mirror for the URL of the Bioconductor mirror.

unzip for the path of the external unzip program.

Environment variables

The BITBUCKET_USER and BITBUCKET_PASSWORD environment variables are used for the default Bitbucket user name and password, in install_bitbucket()

The GITHUB_PAT environment variable is used as the default GitHub personal access token for all GitHub API queries.

The R_BIOC_MIRROR environment variable can be used to specify an alternative Bioconductor mirror. (The BioC_mirror option takes precedence over this.)

The R_BIOC_VERSION environment variable can be used to force a Bioconductor version.

The R_REMOTES_UPGRADE environment variable can be used to set a default preferred value for the upgrade = argument accepted by the various install_*() functions. For example, you can set R_REMOTES_UPGRADE="always" to upgrade dependent packages without asking the user.

Setting R_REMOTES_STANDALONE="true" forces remotes to work in standalone mode and avoid loading its optional dependencies (curl, git2 and pkgbuild currently. See "Standalone mode" above.

Setting R_REMOTES_NO_ERRORS_FROM_WARNINGS="false" will cause warning messages during calls to install.packages() to become errors. Often warning messages are caused by dependencies failing to install.

Download Details:

Author: r-lib
Source Code: https://github.com/r-lib/remotes 
License: Unknown, MIT licenses found

#r #git #github #url 

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Buddha Community

Remotes: install R Packages From GitHub, GitLab, Bitbucket, Git

CSharp REPL: A Command Line C# REPL with Syntax Highlighting

C# REPL

A cross-platform command line REPL for the rapid experimentation and exploration of C#. It supports intellisense, installing NuGet packages, and referencing local .NET projects and assemblies.

C# REPL screenshot 

(click to view animation)

C# REPL provides the following features:

  • Syntax highlighting via ANSI escape sequences
  • Intellisense with fly-out documentation
  • Nuget package installation
  • Reference local assemblies, solutions, and projects
  • Navigate to source via Source Link
  • IL disassembly (both Debug and Release mode)
  • Fast and flicker-free rendering. A "diff" algorithm is used to only render what's changed.

Installation

C# REPL is a .NET 6 global tool, and runs on Windows 10, Mac OS, and Linux. It can be installed via:

dotnet tool install -g csharprepl

If you're running on Mac OS Catalina (10.15) or later, make sure you follow any additional directions printed to the screen. You may need to update your PATH variable in order to use .NET global tools.

After installation is complete, run csharprepl to begin. C# REPL can be updated via dotnet tool update -g csharprepl.

Usage:

Run csharprepl from the command line to begin an interactive session. The default colorscheme uses the color palette defined by your terminal, but these colors can be changed using a theme.json file provided as a command line argument.

Evaluating Code

Type some C# into the prompt and press Enter to run it. The result, if any, will be printed:

> Console.WriteLine("Hello World")
Hello World

> DateTime.Now.AddDays(8)
[6/7/2021 5:13:00 PM]

To evaluate multiple lines of code, use Shift+Enter to insert a newline:

> var x = 5;
  var y = 8;
  x * y
40

Additionally, if the statement is not a "complete statement" a newline will automatically be inserted when Enter is pressed. For example, in the below code, the first line is not a syntactically complete statement, so when we press enter we'll go down to a new line:

> if (x == 5)
  | // caret position, after we press Enter on Line 1

Finally, pressing Ctrl+Enter will show a "detailed view" of the result. For example, for the DateTime.Now expression below, on the first line we pressed Enter, and on the second line we pressed Ctrl+Enter to view more detailed output:

> DateTime.Now // Pressing Enter shows a reasonable representation
[5/30/2021 5:13:00 PM]

> DateTime.Now // Pressing Ctrl+Enter shows a detailed representation
[5/30/2021 5:13:00 PM] {
  Date: [5/30/2021 12:00:00 AM],
  Day: 30,
  DayOfWeek: Sunday,
  DayOfYear: 150,
  Hour: 17,
  InternalKind: 9223372036854775808,
  InternalTicks: 637579915804530992,
  Kind: Local,
  Millisecond: 453,
  Minute: 13,
  Month: 5,
  Second: 0,
  Ticks: 637579915804530992,
  TimeOfDay: [17:13:00.4530992],
  Year: 2021,
  _dateData: 9860951952659306800
}

A note on semicolons: C# expressions do not require semicolons, but statements do. If a statement is missing a required semicolon, a newline will be added instead of trying to run the syntatically incomplete statement; simply type the semicolon to complete the statement.

> var now = DateTime.Now; // assignment statement, semicolon required

> DateTime.Now.AddDays(8) // expression, we don't need a semicolon
[6/7/2021 5:03:05 PM]

Keyboard Shortcuts

  • Basic Usage
    • Ctrl+C - Cancel current line
    • Ctrl+L - Clear screen
    • Enter - Evaluate the current line if it's a syntactically complete statement; otherwise add a newline
    • Control+Enter - Evaluate the current line, and return a more detailed representation of the result
    • Shift+Enter - Insert a new line (this does not currently work on Linux or Mac OS; Hopefully this will work in .NET 7)
    • Ctrl+Shift+C - Copy current line to clipboard
    • Ctrl+V, Shift+Insert, and Ctrl+Shift+V - Paste text to prompt. Automatically trims leading indent
  • Code Actions
    • F1 - Opens the MSDN documentation for the class/method under the caret (example)
    • F9 - Shows the IL (intermediate language) for the current statement in Debug mode.
    • Ctrl+F9 - Shows the IL for the current statement with Release mode optimizations.
    • F12 - Opens the source code in the browser for the class/method under the caret, if the assembly supports Source Link.
  • Autocompletion
    • Ctrl+Space - Open autocomplete menu. If there's a single option, pressing Ctrl+Space again will select the option
    • Enter, Right Arrow, Tab - Select active autocompletion option
    • Escape - closes autocomplete menu
  • Text Navigation
    • Home and End - Navigate to beginning of a single line and end of a single line, respectively
    • Ctrl+Home and Ctrl+End - Navigate to beginning of line and end across multiple lines in a multiline prompt, respectively
    • Arrows - Navigate characters within text
    • Ctrl+Arrows - Navigate words within text
    • Ctrl+Backspace - Delete previous word
    • Ctrl+Delete - Delete next word

Adding References

Use the #r command to add assembly or nuget references.

  • For assembly references, run #r "AssemblyName" or #r "path/to/assembly.dll"
  • For project references, run #r "path/to/project.csproj". Solution files (.sln) can also be referenced.
  • For nuget references, run #r "nuget: PackageName" to install the latest version of a package, or #r "nuget: PackageName, 13.0.5" to install a specific version (13.0.5 in this case).

Installing nuget packages

To run ASP.NET applications inside the REPL, start the csharprepl application with the --framework parameter, specifying the Microsoft.AspNetCore.App shared framework. Then, use the above #r command to reference the application DLL. See the Command Line Configuration section below for more details.

csharprepl --framework  Microsoft.AspNetCore.App

Command Line Configuration

The C# REPL supports multiple configuration flags to control startup, behavior, and appearance:

csharprepl [OPTIONS] [response-file.rsp] [script-file.csx] [-- <additional-arguments>]

Supported options are:

  • OPTIONS:
    • -r <dll> or --reference <dll>: Reference an assembly, project file, or nuget package. Can be specified multiple times. Uses the same syntax as #r statements inside the REPL. For example, csharprepl -r "nuget:Newtonsoft.Json" "path/to/myproj.csproj"
      • When an assembly or project is referenced, assemblies in the containing directory will be added to the assembly search path. This means that you don't need to manually add references to all of your assembly's dependencies (e.g. other references and nuget packages). Referencing the main entry assembly is enough.
    • -u <namespace> or --using <namespace>: Add a using statement. Can be specified multiple times.
    • -f <framework> or --framework <framework>: Reference a shared framework. The available shared frameworks depends on the local .NET installation, and can be useful when running an ASP.NET application from the REPL. Example frameworks are:
      • Microsoft.NETCore.App (default)
      • Microsoft.AspNetCore.All
      • Microsoft.AspNetCore.App
      • Microsoft.WindowsDesktop.App
    • -t <theme.json> or --theme <theme.json>: Read a theme file for syntax highlighting. This theme file associates C# syntax classifications with colors. The color values can be full RGB, or ANSI color names (defined in your terminal's theme). The NO_COLOR standard is supported.
    • --trace: Produce a trace file in the current directory that logs CSharpRepl internals. Useful for CSharpRepl bug reports.
    • -v or --version: Show version number and exit.
    • -h or --help: Show help and exit.
  • response-file.rsp: A filepath of an .rsp file, containing any of the above command line options.
  • script-file.csx: A filepath of a .csx file, containing lines of C# to evaluate before starting the REPL. Arguments to this script can be passed as <additional-arguments>, after a double hyphen (--), and will be available in a global args variable.

If you have dotnet-suggest enabled, all options can be tab-completed, including values provided to --framework and .NET namespaces provided to --using.

Integrating with other software

C# REPL is a standalone software application, but it can be useful to integrate it with other developer tools:

Windows Terminal

To add C# REPL as a menu entry in Windows Terminal, add the following profile to Windows Terminal's settings.json configuration file (under the JSON property profiles.list):

{
    "name": "C# REPL",
    "commandline": "csharprepl"
},

To get the exact colors shown in the screenshots in this README, install the Windows Terminal Dracula theme.

Visual Studio Code

To use the C# REPL with Visual Studio Code, simply run the csharprepl command in the Visual Studio Code terminal. To send commands to the REPL, use the built-in Terminal: Run Selected Text In Active Terminal command from the Command Palette (workbench.action.terminal.runSelectedText).

Visual Studio Code screenshot

Windows OS

To add the C# REPL to the Windows Start Menu for quick access, you can run the following PowerShell command, which will start C# REPL in Windows Terminal:

$shell = New-Object -ComObject WScript.Shell
$shortcut = $shell.CreateShortcut("$env:appdata\Microsoft\Windows\Start Menu\Programs\csharprepl.lnk")
$shortcut.TargetPath = "wt.exe"
$shortcut.Arguments = "-w 0 nt csharprepl.exe"
$shortcut.Save()

You may also wish to add a shorter alias for C# REPL, which can be done by creating a .cmd file somewhere on your path. For example, put the following contents in C:\Users\username\.dotnet\tools\csr.cmd:

wt -w 0 nt csharprepl

This will allow you to launch C# REPL by running csr from anywhere that accepts Windows commands, like the Window Run dialog.

Comparison with other REPLs

This project is far from being the first REPL for C#. Here are some other projects; if this project doesn't suit you, another one might!

Visual Studio's C# Interactive pane is full-featured (it has syntax highlighting and intellisense) and is part of Visual Studio. This deep integration with Visual Studio is both a benefit from a workflow perspective, and a drawback as it's not cross-platform. As far as I know, the C# Interactive pane does not support NuGet packages or navigating to documentation/source code. Subjectively, it does not follow typical command line keybindings, so can feel a bit foreign.

csi.exe ships with C# and is a command line REPL. It's great because it's a cross platform REPL that comes out of the box, but it doesn't support syntax highlighting or autocompletion.

dotnet script allows you to run C# scripts from the command line. It has a REPL built-in, but the predominant focus seems to be as a script runner. It's a great tool, though, and has a strong community following.

dotnet interactive is a tool from Microsoft that creates a Jupyter notebook for C#, runnable through Visual Studio Code. It also provides a general framework useful for running REPLs.

Download Details:
Author: waf
Source Code: https://github.com/waf/CSharpRepl
License: MPL-2.0 License

#dotnet  #aspdotnet  #csharp 

Nat  Grady

Nat Grady

1660716780

Remotes: install R Packages From GitHub, GitLab, Bitbucket, Git

remotes

Install R Packages from remote or local repositories, including GitHub, GitLab, Bitbucket, and Bioconductor

Download and install R packages stored in GitHub, GitLab, Bitbucket, Bioconductor, or plain subversion or git repositories. This package is a lightweight replacement of the install_* functions in devtools. Indeed most of the code was copied over from devtools.

Features

  • Installers:
    • Install packages with their dependencies.
    • Install from GitHub, GitLab, Bitbucket.
    • Install from git and subversion repositories.
    • Install from local files or URLs.
    • Install the dependencies of a local package tree.
    • Install specific package versions from CRAN.
  • Supports Bioconductor packages.
  • Supports the Remotes field in DESCRIPTION. See more in the dependencies vignette.
  • Supports the Additional_repositories field in DESCRIPTION.
  • Can install itself from GitHub (see below).
  • Does not depend on other R packages.
  • Does not contain compiled code, so no compiler is needed.
  • Does not need any external software (for most of the functionality at least).

Installation

Install the released version of remotes from CRAN:

install.packages("remotes")

Usage

Note that most of the examples here use GitHub. See below for other supported repository types.

To install the latest version of a package in the default branch from GitHub, you can use the user/repo form. Note that user can also be an organization:

remotes::install_github("r-lib/conflicted")

If the R package is inside a subdirectory of the root directory, then give this subdirectory as well:

# build = FALSE because of some specificities of XGBoost package
install_github("dmlc/xgboost/R-package", build = FALSE)

To install a certain branch or commit or tag, append it to the repo name, after an @:

remotes::install_github("gaborcsardi/pkgconfig@v2.0.0")

To install the latest release, append @*release to the repo name:

remotes::install_github("gaborcsardi/pkgconfig@*release")

To install a pull request, append # and the id (an integer number) of the pull request to the repo name:

remotes::install_github("r-lib/pkgconfig#7")

Dependencies

Dependencies are automatically installed from CRAN. By default, outdated dependencies are automatically upgraded. In interactive sessions you can select a subset of the dependencies to upgrade.

Dependencies on GitHub

It is also possible to install dependencies from GitHub or other supported repositories. For this you need to add a Remotes field to the DESCRIPTION file. Its format is:

Remotes: [remote::]repo_spec, [remote::]repo_spec, ...

where repo_spec is any repository specification the corresponding install_() function can handle. If remote:: is missing, github:: is assumed. Other possible values: gitlab::,bitbucket::, git::, local::, svn::, url::, version::, cran::, bioc::.

See more about the Remotes field in this vignette.

Additional repositories

remotes supports the Additional_repositories field in DESCRIPTION. This is a way to specify dependencies from non-CRAN package repositories. See the Writing R extensions manual for details.

Bioconductor packages

Bioconductor packages are automatically detected and their dependencies are installed from Bioconductor.

Currently supported remote types

  • GitHub repositories via install_github.
  • Bitbucket repositories via install_bitbucket.
  • Generic git repositories via install_git. They need either a system git installation, or the git2r R package.
  • Local directories or package archive files via install_local.
  • Remote package archive files via install_url.
  • Packages in subversion repositories via install_svn. They need a system subversion installation.
  • Specific package versions from CRAN or other CRAN-like repositories via install_version. This includes outdated and archived packages as well.
  • All dependencies of a package in a local directory via install_deps.

Download methods

  • For R older than 3.2, the curl package is required as remotes falls back to curl::curl_download in that case
  • For R newer than 3.3, default download.file() method is used. (method = "auto")
  • For in between versions,
    • method = "wininet" is used on windows OS
    • method = "libcurl" is used on other OS, if available.

See help("download.file") for informations on these methods and for setting proxies if needed.

Standalone mode

remotes will use the curl, git2r and pkgbuild packages if they are installed to provide faster implementations for some aspects of the install process. However if you are using remotes to install or update these packages (or their reverse dependencies) using them during installation may fail (particularly on Windows).

If you set the environment variable R_REMOTES_STANDALONE="true" (e.g. in R Sys.setenv(R_REMOTES_STANDALONE="true")) you can force remotes to operate in standalone mode and use only its internal R implementations. This will allow successful installation of these packages.

Options

remotes uses the following standard R options, see ?options for their details:

download.file.method for the default download method. See ?download.file.

pkgType for the package type (source or binary, see manual) to install, download or look up dependencies for.

repos for the locations of the user's standard CRAN(-like) repositories.

It also uses some remotes specific options:

BioC_git for the URL of the default Bioconductor git mirror.

BioC_mirror for the URL of the Bioconductor mirror.

unzip for the path of the external unzip program.

Environment variables

The BITBUCKET_USER and BITBUCKET_PASSWORD environment variables are used for the default Bitbucket user name and password, in install_bitbucket()

The GITHUB_PAT environment variable is used as the default GitHub personal access token for all GitHub API queries.

The R_BIOC_MIRROR environment variable can be used to specify an alternative Bioconductor mirror. (The BioC_mirror option takes precedence over this.)

The R_BIOC_VERSION environment variable can be used to force a Bioconductor version.

The R_REMOTES_UPGRADE environment variable can be used to set a default preferred value for the upgrade = argument accepted by the various install_*() functions. For example, you can set R_REMOTES_UPGRADE="always" to upgrade dependent packages without asking the user.

Setting R_REMOTES_STANDALONE="true" forces remotes to work in standalone mode and avoid loading its optional dependencies (curl, git2 and pkgbuild currently. See "Standalone mode" above.

Setting R_REMOTES_NO_ERRORS_FROM_WARNINGS="false" will cause warning messages during calls to install.packages() to become errors. Often warning messages are caused by dependencies failing to install.

Download Details:

Author: r-lib
Source Code: https://github.com/r-lib/remotes 
License: Unknown, MIT licenses found

#r #git #github #url 

How to Install Pyenv on Ubuntu 18.04

What is Pyenv?
Pyenv is a fantastic tool for installing and managing multiple Python versions. It enables a developer to quickly gain access to newer versions of Python and keeps the system clean and free of unnecessary package bloat. It also offers the ability to quickly switch from one version of Python to another, as well as specify the version of Python a given project uses and can automatically switch to that version. This tutorial covers how to install pyenv on Ubuntu 18.04.

#tutorials #apt #debian #environment #git #github #linux #package #package management #package manager #personal package archive #ppa #pyenv #python #python 3 #python support #python-pip #repository #smb #software #source install #ubuntu #ubuntu 18.04 #venv #virtualenv #web application development

How To Rename Your Git Repositories From "Master" to "Main"

Until recently, almost every Git repository had a default branch named “master”. But thankfully, as part of a movement to make the tech industry more inclusive and open, many software teams and open source projects are moving away from this unhealthy naming.

There has been quite some debate about a good replacement. And while “default” and “primary” had been interesting candidates, most of the Git community seems to agree that “main” should be a good successor for the outdated “master”.

Many Git hosting platforms like GitHub, GitLab, or Bitbucket will soon make changes on their end (or, depending on when exactly you read this post, they might already have done so). In the near future, if you create a new Git repository on any of these platforms, you will find “main” to be the new default branch.

But what about your current, existing projects? That’s exactly what we’ll be talking about in this post: how you can rename “master” to “main” in your existing Git repositories!

Step 1: Rename Your Local master Branch

The first step is to rename the local “master” branch in your local repositories. You can do that easily with the following command:

$ git branch -m master main

Let’s make sure this has worked:

$ git branch * main

Perfect! Our local branch has been renamed, but we now have to do the same on the remote side of things.

#git #github #gitlab #bitbucket #hackernoon-top-story #rename-git-repositories #make-tech-inclusive #rename-git-repo-master-to-main

Jolie  Reichert

Jolie Reichert

1591607040

How to migrate GitLab/Bitbucket to GitHub in a simple way

These changes are so competitive to other code hosting services like Bitbucket or GitLab. Many teams are going to relocate their projects to GitHub as I think.
If you share the same idea and look for a simple way to migrate a repo from Bitbucket or GitLab, the followings are several simple steps to accomplish this.
Inside your GitHub team page, create an empty private repo with the same name of Bitbucket/GitLab repo that you want to transfer.
Copy your newly created repo link, either in HTTPS or SSH. For example, git@github.com:team-name/repo-name.git (SSH type)
Inside your local project folder, change the remote URL under.git/config ‘s file to your copied GitHub’s one. The content looks similar as follows. [remote “origin”]
url = git@github.com:team-name/repo-name.git
fetch = +refs/heads/:refs/remotes/origin/
Do a git push: git push -all . It will push all codes and commit history on your newly GitHub repository.
Done. After that, when we push new commits, it will push to GitHub only.
The Bitbucket/GitLab repo now can be archived to ‘Read-only’ mode.

#github #git #bitbucket #gitlab