From 33103ac3fdb6d70b4cc4eb47ad8c8ff8f288a9ff Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Tue, 5 Nov 2024 14:29:08 +0100 Subject: [PATCH 01/34] First draft developer environment Signed-off-by: Christopher Hakkaart --- docs/conf.py | 3 +- docs/developer-env.md | 289 ++++++++++++++++++++++++++++++++++++++++++ docs/index.md | 1 + docs/requirements.txt | 3 +- 4 files changed, 294 insertions(+), 2 deletions(-) create mode 100644 docs/developer-env.md diff --git a/docs/conf.py b/docs/conf.py index e1068522bf..b5a38047e0 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -34,7 +34,8 @@ 'sphinxcontrib.mermaid', 'sphinxext.rediraffe', 'sphinx_rtd_theme', - 'myst_parser' + 'myst_parser', + 'sphinx_tabs.tabs' ] myst_enable_extensions = ['colon_fence', 'deflist', 'dollarmath'] diff --git a/docs/developer-env.md b/docs/developer-env.md new file mode 100644 index 0000000000..3bc15e889e --- /dev/null +++ b/docs/developer-env.md @@ -0,0 +1,289 @@ +(developer-env)= + +# Environment setup + +Setting up a Nextflow development environment is a prerequisite for creating, testing, and optimizing data analysis pipelines. The steps below outline recommended tools for setting up an optimal Nextflow development environment. + +:::{note} +If you are using a Windows computer, you first need to install and configure the Windows Subsystem for Linux (WSL). See {ref}`wsl` for installation and configuration instructions. +::: + +## VS Code + +Installing an Integrated Development Environment (IDE) is an essential step for setting up your environment and provide a user-friendly interface for writing, editing, and managing code. + +Visual Studio Code (VS Code) is a popular lightweight IDE that is known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports macOS, Linux, and Windows, and is a good choice for both experienced and new Nextflow developers. + +````{tabs} + +```{group-tab} Windows + +To install VS Code on Windows: + +1. Visit the [VS Code](https://code.visualstudio.com/download) website. +1. Download VS Code installer for Windows. +1. Double-click the installer executable (`.exe`) file and follow the step-by-step setup installation wizard. + +``` + +```{group-tab} macOS + +To install VS Code on macOS: + +1. Visit the [VS Code](https://code.visualstudio.com/download) website. +1. Download VS Code for macOS. +1. Locate the `Visual Studio Code.app` application and move to the Applications folder to make it available in the macOS Launchpad. + +``` + +```{group-tab} Linux + +To install VS Code on Linux Debian/Ubuntu distributions: + +1. Visit the [VS Code](https://code.visualstudio.com/download) website. +1. Download VS Code Linux Debian/Ubuntu (`.deb`) distribution. +1. Open a new terminal window. +1. Navigate to the folder containing your VS Code download. +1. Run `sudo apt install ./.deb`, replacing `` with the full file name. + + :::{note} + If you're using an older Linux distribution, run `sudo dpkg -i .deb` to install VS Code and `sudo apt-get install -f` to install dependencies instead. + ::: + +See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_installation) for information about installing VS Code on other distributions. + +``` + +```` + +## Extensions + +Extensions are a key feature of IDEs and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. + +The VS Code Nextflow extension adds [Nextflow language support](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) to the editor. The Nextflow extension enhances development with: + +- Diagnostics +- Hover hints +- Code navigation +- Code completion +- Formatting +- Renaming +- Parameter schemas +- DAG previews + +See {ref}`vs-code-integration-page` for more information about the Nextflow extension. + +````{tabs} + +```{group-tab} Windows + +To install the Nextflow VS Code extension on Windows: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for Nextflow. +1. Select **Install**. + +``` + +```{group-tab} macOS + +To install the Nextflow VS Code extension on macOS: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for Nextflow. +1. Select **Install**. + +``` + +```{group-tab} Linux + +To install the Nextflow VS Code extension on Linux Debian/Ubuntu distributions: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for Nextflow. +1. Select **Install**. + +``` + +```` + +## Git + +Git provides powerful version control that helps track code changes. Git operates locally, meaning you don't need an internet connection to track changes, but it can also be used with remote platforms like GitHub, GitLab, or Bitbucket for collaborative development. + +Nextflow seamlessly integrates with Git for source code management providers for managing pipelines as version-controlled Git repositories. + +````{tabs} + +```{group-tab} Windows + +``` + +```{group-tab} macOS + +New versions of macOS already have Git installed. You can activate it through the terminal running `git version`. If Git is not installed, you can install the latest version of Git using several methods: + +To install Git on macOS with [Homebrew](https://docs.brew.sh/): + +1. Open a terminal window and run `brew install git`. + + :::{note} + You must have Homebrew installed. See [Homebrew installation](https://docs.brew.sh/Installation) for instructions. + ::: + +1. When the installation finishes, run `git version` to verify Git was installed. + +To install Git on macOS with Xcode: + +1. Open the App Store on your Mac. +1. Sign in to your Apple Account. +1. Search for Xcode. +1. Select **Install**. +1. When the installation finishes, open a new terminal window and run `git version` to verify Git was installed. + +``` + +```{group-tab} Linux + +To install Git on Linux Debian/Ubuntu distributions: + +1. Open a terminal window and run `sudo apt-get install git-all`. +1. Once complete, run `git version` to verify Git was installed. + +See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions. + +``` + +```` + +## Container engines + +Containerization enables the creation of self-contained and fully reproducible computational pipelines by bundling a script's binary dependencies into a standardized and portable format. Containers can be executed on any platform that supports a container runtime and ensures consistency across different environments. + +Nextflow supports multiple container technologies (e.g., Docker, Singularity, and Podman) allowing you to choose the one that best fits your needs. + +Configure your environment to support the container technologies you want to use. + +### Docker + +````{tabs} + +```{group-tab} Windows + +``` + +```{group-tab} macOS + +1. Visit the [Install Docker on Mac](https://docs.docker.com/desktop/install/mac-install/) page. +1. Download the installer for your chip type using the download buttons at the top of the page. +1. Double-click `Docker.dmg` to open the installer. +1. Drag the Docker icon to the **Applications** folder. +1. Double-click **Docker.app** in the **Applications** folder to start Docker. +1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. +1. From the installation window, select **Use recommended settings (Requires password)**. + + :::{note} Recommended settings lets Docker Desktop automatically set the necessary configuration settings. Advanced settings allow you to set the location of the Docker CLI tools either in the system or user directory, enable the default Docker socket, and enable privileged port mapping. See [Settings](https://docs.docker.com/desktop/settings/#advanced), for more information and how to set the location of the Docker CLI tools. + ::: + +1. Select **Finish**. If you have applied any of the previous configurations that require a password, enter your password to confirm your choice. + +``` + +```{group-tab} Linux + +To install Docker Desktop on Linux Debian/Ubuntu distributions: + +1. Set up Docker's package repository. See step one of [Install using the `apt` repository](https://docs.docker.com/engine/install/ubuntu/#install-using-the-repository). +1. Download the latest Debian/Ubuntu (`.deb`) distribution. +1. In your terminal, run `sudo apt-get install ./docker-desktop-amd64.deb` + + :::{note} + By default, Docker Desktop is installed at `/opt/docker-desktop`. + ::: + +1. Double-click **Docker Desktop** in your Applications menu to start Docker. +1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. +1. From the installation window, select **Use recommended settings (Requires password)**. Docker Desktop starts after you accept the terms. + +:::{note} +Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop. +::: + +``` + +```` + +See {ref}`container-page` for more information about supported container engines. + +## Conda + +Conda is an open-source package and environment manager that simplifies installing and configuring complex software across platforms. Nextflow supports Conda, enabling the use of Conda recipes and environment files to configure workflow dependencies. + +The preferred method for installing Conda is through Miniconda, a lightweight version of Anaconda that includes Conda and its dependencies. + +````{tabs} + +```{group-tab} Windows + +``` + +```{group-tab} macOS + +To install Conda on macOS: + +1. Visit the [Miniconda](https://docs.anaconda.com/miniconda/#miniconda) website. +1. Download the latest version of the '.pkg' Miniconda installer. +1. Double-click the '.pkg' file. +1. Follow the step-by-step setup installation instructions. +1. When the installation finishes, open a new terminal window and run `conda list` to verify Conda was installed correctly. + +See [Quick command line install](https://docs.anaconda.com/miniconda/#quick-command-line-install) for command line installation instructions. + +``` + +```{group-tab} Linux + +To install Conda on Linux Debian/Ubuntu distributions: + +1. Visit the [Miniconda](https://docs.anaconda.com/miniconda/#miniconda) website. +1. Download the latest version of the '.sh' Miniconda installer. +1. In your terminal, run `bash .sh`, replacing `` with the installer file name. +1. Follow the step-by-step setup installation prompts. +1. When the installation finishes, open a new terminal window and run `conda list` to verify Conda was installed correctly. + +``` + +```` + +(wsl)= + +# Windows Subsystem for Linux + +Developers can access the power of both Windows and Linux on a Windows machine. The Windows Subsystem for Linux (WSL) lets developers install a Linux distribution and use Linux applications, utilities, and Bash command-line tools directly on Windows without the overhead of a virtual machine or dualboot setup. The steps below outline the recommended setup. + +## Enable WSL + +Windows Subsystem for Linux (WSL) is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. + +You can enable it through the Windows Features dialog or PowerShell. + +### Windows Features dialog + +To enable WSL on Windows using Windows Features dialog: + +1. In the Windows search bar, type 'features' to bring up the Turn Windows Features on and off dialog. +1. Scroll down and check Windows Subsystem for Linux. +1. Select **OK** and restart Windows. +1. After restarting Windows, check that you have WSL enabled by opening a Command Prompt and typing 'wsl'. + +### PowerShell + +To enable WSL on Windows using Powershell: + +1. Open PowerShell or Windows Command Prompt in administrator mode by right-clicking and selecting **Run as administrator**. +1. Run `wsl --install`. +1. When prompted, restart Windows when prompted. +1. After restarting Windows, check that you have WSL enabled by opening a Command Prompt and typing 'wsl'. diff --git a/docs/index.md b/docs/index.md index 69476d91c7..35577f4bbc 100644 --- a/docs/index.md +++ b/docs/index.md @@ -48,6 +48,7 @@ P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nat overview install +developer-env your-first-script ``` diff --git a/docs/requirements.txt b/docs/requirements.txt index 06694e6ca0..3f90f2367c 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,4 +2,5 @@ myst-parser==0.18.1 sphinx==5.3.0 sphinx-rtd-theme==1.1.1 sphinxcontrib-mermaid==0.9.2 -sphinxext-rediraffe==0.2.7 \ No newline at end of file +sphinxext-rediraffe==0.2.7 +sphinx-tabs==3.4.5 \ No newline at end of file From a1dfb9f105df33daeb77357edcdb49a2b9227816 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Wed, 6 Nov 2024 10:08:14 +0100 Subject: [PATCH 02/34] Adding WSL skeleton and fixes Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 34 ++++++++++++++++++++-------------- 1 file changed, 20 insertions(+), 14 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 3bc15e889e..3b76251aee 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -136,7 +136,7 @@ To install Git on macOS with [Homebrew](https://docs.brew.sh/): 1. When the installation finishes, run `git version` to verify Git was installed. -To install Git on macOS with Xcode: +To install Git on macOS with [Xcode](https://developer.apple.com/xcode/): 1. Open the App Store on your Mac. 1. Sign in to your Apple Account. @@ -159,15 +159,15 @@ See [git-scm documentation](https://git-scm.com/downloads/linux) for more inform ```` -## Container engines +## Docker Containerization enables the creation of self-contained and fully reproducible computational pipelines by bundling a script's binary dependencies into a standardized and portable format. Containers can be executed on any platform that supports a container runtime and ensures consistency across different environments. -Nextflow supports multiple container technologies (e.g., Docker, Singularity, and Podman) allowing you to choose the one that best fits your needs. +Docker is an open-source platform that simplifies application development, deployment, and execution by packaging applications and their dependencies into containers. Docker Desktop provides a GUI for managing Docker containers. Installing Docker Desktop is a straightforward process that allows you to create, deploy, and manage applications within containers. + ````{tabs} @@ -177,7 +177,9 @@ Configure your environment to support the container technologies you want to use ```{group-tab} macOS -1. Visit the [Install Docker on Mac](https://docs.docker.com/desktop/install/mac-install/) page. +To install Docker Desktop on macOS: + +1. Visit the [Install Docker Desktop on Mac](https://docs.docker.com/desktop/install/mac-install/) page. 1. Download the installer for your chip type using the download buttons at the top of the page. 1. Double-click `Docker.dmg` to open the installer. 1. Drag the Docker icon to the **Applications** folder. @@ -208,20 +210,24 @@ To install Docker Desktop on Linux Debian/Ubuntu distributions: 1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. 1. From the installation window, select **Use recommended settings (Requires password)**. Docker Desktop starts after you accept the terms. -:::{note} -Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop. -::: + :::{note} + Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop. + ::: ``` ```` -See {ref}`container-page` for more information about supported container engines. +Nextflow supports multiple container technologies (e.g., Singularity and Podman) allowing you to choose the one that best fits your needs. See {ref}`container-page` for more information about other supported container engines. ## Conda Conda is an open-source package and environment manager that simplifies installing and configuring complex software across platforms. Nextflow supports Conda, enabling the use of Conda recipes and environment files to configure workflow dependencies. +:::{note} +Conda environments can lead to inconsistencies across systems due to dependency resolution and OS variations. +::: + The preferred method for installing Conda is through Miniconda, a lightweight version of Anaconda that includes Conda and its dependencies. ````{tabs} @@ -260,11 +266,11 @@ To install Conda on Linux Debian/Ubuntu distributions: (wsl)= -# Windows Subsystem for Linux +## Windows Subsystem for Linux Developers can access the power of both Windows and Linux on a Windows machine. The Windows Subsystem for Linux (WSL) lets developers install a Linux distribution and use Linux applications, utilities, and Bash command-line tools directly on Windows without the overhead of a virtual machine or dualboot setup. The steps below outline the recommended setup. -## Enable WSL +### Enable WSL Windows Subsystem for Linux (WSL) is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. @@ -285,5 +291,5 @@ To enable WSL on Windows using Powershell: 1. Open PowerShell or Windows Command Prompt in administrator mode by right-clicking and selecting **Run as administrator**. 1. Run `wsl --install`. -1. When prompted, restart Windows when prompted. -1. After restarting Windows, check that you have WSL enabled by opening a Command Prompt and typing 'wsl'. +1. When prompted, restart Windows. +1. After restarting Windows, open a PowerShell or Windows Command Prompt and run `wsl` to verify WSL was enabled. From 633f71b553f194805d338f8d205fd82903dbc4b5 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Thu, 7 Nov 2024 17:38:29 +0100 Subject: [PATCH 03/34] Adding dev containers section Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 207 ++++++++++++++++++++++++++++++++---------- 1 file changed, 161 insertions(+), 46 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 3b76251aee..de707de527 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -5,14 +5,16 @@ Setting up a Nextflow development environment is a prerequisite for creating, testing, and optimizing data analysis pipelines. The steps below outline recommended tools for setting up an optimal Nextflow development environment. :::{note} -If you are using a Windows computer, you first need to install and configure the Windows Subsystem for Linux (WSL). See {ref}`wsl` for installation and configuration instructions. +If you are using a Windows computer, you first need to install and configure the Windows Subsystem for Linux (WSL). See {ref}`wsl` for installation instructions. ::: +(vscode-install)= + ## VS Code Installing an Integrated Development Environment (IDE) is an essential step for setting up your environment and provide a user-friendly interface for writing, editing, and managing code. -Visual Studio Code (VS Code) is a popular lightweight IDE that is known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports macOS, Linux, and Windows, and is a good choice for both experienced and new Nextflow developers. +Visual Studio Code (VS Code) is a popular lightweight IDE that is known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports Windows, macOS, and Linux, and is a good choice for both new and experienced Nextflow developers. ````{tabs} @@ -47,7 +49,7 @@ To install VS Code on Linux Debian/Ubuntu distributions: 1. Run `sudo apt install ./.deb`, replacing `` with the full file name. :::{note} - If you're using an older Linux distribution, run `sudo dpkg -i .deb` to install VS Code and `sudo apt-get install -f` to install dependencies instead. + If you're using an older Linux distribution, run `sudo dpkg -i .deb` to install VS Code and `sudo apt-get install -f` to install dependencies. ::: See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_installation) for information about installing VS Code on other distributions. @@ -56,11 +58,14 @@ See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_install ```` -## Extensions +## Extension Extensions are a key feature of IDEs and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. -The VS Code Nextflow extension adds [Nextflow language support](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) to the editor. The Nextflow extension enhances development with: + +### Nextflow + +The VS Code [Nextflow extension](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) adds Nextflow language support to the editor. The Nextflow extension enhances development with: - Diagnostics - Hover hints @@ -110,60 +115,68 @@ To install the Nextflow VS Code extension on Linux Debian/Ubuntu distributions: ```` -## Git +(remote-development-ext)= -Git provides powerful version control that helps track code changes. Git operates locally, meaning you don't need an internet connection to track changes, but it can also be used with remote platforms like GitHub, GitLab, or Bitbucket for collaborative development. +### Remote Development extension pack -Nextflow seamlessly integrates with Git for source code management providers for managing pipelines as version-controlled Git repositories. +The [Remote Development extension pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) enables you to run WSL, SSH, or a development container for editing and debugging with the full set of VS Code features. -````{tabs} +The Remote Development extension pack includes four extensions: -```{group-tab} Windows +[Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh) - Work with source code in any location by opening folders on a remote machine/VM using SSH. +[Remote - Tunnels](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-server) - Work with source code in any location by opening folders on a remote machine/VM using a VS Code Tunnel (rather than SSH). +[Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) - Work with a separate toolchain or container based application by opening any folder mounted into or inside a container. +[WSL](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsl) - Get a Linux-powered development experience from the comfort of Windows by opening any folder in the Windows Subsystem for Linux. -``` +:::{note} +The VS Code Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, Development Containers. +::: -```{group-tab} macOS -New versions of macOS already have Git installed. You can activate it through the terminal running `git version`. If Git is not installed, you can install the latest version of Git using several methods: +````{tabs} -To install Git on macOS with [Homebrew](https://docs.brew.sh/): +```{group-tab} Windows -1. Open a terminal window and run `brew install git`. +To install the Remote Development extension pack on Windows: - :::{note} - You must have Homebrew installed. See [Homebrew installation](https://docs.brew.sh/Installation) for instructions. - ::: +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for Nextflow. +1. Select **Install**. -1. When the installation finishes, run `git version` to verify Git was installed. +``` -To install Git on macOS with [Xcode](https://developer.apple.com/xcode/): +```{group-tab} macOS -1. Open the App Store on your Mac. -1. Sign in to your Apple Account. -1. Search for Xcode. +To install the Remote Development extension pack on macOS: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for Nextflow. 1. Select **Install**. -1. When the installation finishes, open a new terminal window and run `git version` to verify Git was installed. ``` ```{group-tab} Linux -To install Git on Linux Debian/Ubuntu distributions: - -1. Open a terminal window and run `sudo apt-get install git-all`. -1. Once complete, run `git version` to verify Git was installed. +To install the Remote Development extension pack on Linux Debian/Ubuntu distributions: -See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions. +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for Nextflow. +1. Select **Install**. ``` ```` +(docker-desktop)= + ## Docker Containerization enables the creation of self-contained and fully reproducible computational pipelines by bundling a script's binary dependencies into a standardized and portable format. Containers can be executed on any platform that supports a container runtime and ensures consistency across different environments. -Docker is an open-source platform that simplifies application development, deployment, and execution by packaging applications and their dependencies into containers. Docker Desktop provides a GUI for managing Docker containers. Installing Docker Desktop is a straightforward process that allows you to create, deploy, and manage applications within containers. +Docker is an open-source platform that simplifies application development, deployment, and execution by packaging applications and their dependencies into containers. Docker Desktop provides a Graphical User Interface (GUI) for managing Docker containers. Installing Docker Desktop is a straightforward process that allows you to create, deploy, and manage applications within containers. -(wsl)= +## Git -## Windows Subsystem for Linux +Git provides powerful version control that helps track code changes. Git operates locally, meaning you don't need an internet connection to track changes, but it can also be used with remote platforms like GitHub, GitLab, or Bitbucket for collaborative development. + +Nextflow seamlessly integrates with Git for source code management providers for managing pipelines as version-controlled Git repositories. + +````{tabs} + +```{group-tab} Windows -Developers can access the power of both Windows and Linux on a Windows machine. The Windows Subsystem for Linux (WSL) lets developers install a Linux distribution and use Linux applications, utilities, and Bash command-line tools directly on Windows without the overhead of a virtual machine or dualboot setup. The steps below outline the recommended setup. +Git is already installed on most WSL distributions. You can check if it is already installed by running `git version`. -### Enable WSL +To install the latest stable Git version on Linux Debian/Ubuntu distributions: -Windows Subsystem for Linux (WSL) is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. +1. Open a terminal window and run `sudo apt-get install git-all`. +1. Once complete, run `git version` to verify Git was installed. + +See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions. + +``` + +```{group-tab} macOS -You can enable it through the Windows Features dialog or PowerShell. +Git installed is already installed on new versions of macOS. You can activate it through the terminal running `git version`. If Git is not installed, you can install the latest version of Git using several methods: +To install Git on macOS with [Homebrew](https://docs.brew.sh/): + +1. Open a terminal window and run `brew install git`. + + :::{note} + You must have Homebrew installed. See [Homebrew installation](https://docs.brew.sh/Installation) for instructions. + ::: + +1. Once complete, run `git version` to verify Git was installed. + +To install Git on macOS with [Xcode](https://developer.apple.com/xcode/): + +1. Open the App Store on your Mac. +1. Sign in to your Apple Account. +1. Search for Xcode. +1. Select **Install**. +1. Once complete, open a new terminal window and run `git version` to verify Git was installed. + +``` + +```{group-tab} Linux + +Git is already installed on most on most Linux Debian/Ubuntu distributions. + +To install the latest stable Git version on Linux Debian/Ubuntu distributions: + +1. Open a terminal window and run `sudo apt-get install git-all`. +1. Once complete, run `git version` to verify Git was installed. + +See [git-scm documentation](https://git-scm.com/downloads/linux) for more information about installing Git on other Linux distributions. + +``` + +```` + +(wsl)= + +## Windows Subsystem for Linux + +Developers can access the power of both Windows and Linux on a Windows machine. The Windows Subsystem for Linux (WSL) lets developers install a Linux distribution and use Linux applications, utilities, and Bash command-line tools directly on Windows without the overhead of a virtual machine or dual-boot setup. + +WSL is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. You can enable it through PowerShell or Windows Command Prompt. The steps below outline the recommended setup. + + ### Windows Features dialog To enable WSL on Windows using Windows Features dialog: -1. In the Windows search bar, type 'features' to bring up the Turn Windows Features on and off dialog. -1. Scroll down and check Windows Subsystem for Linux. +1. In the Windows search bar, enter 'features' to bring up the **Turn Windows Features on and off** dialog. +1. Scroll down and check **Windows Subsystem for Linux**. 1. Select **OK** and restart Windows. -1. After restarting Windows, check that you have WSL enabled by opening a Command Prompt and typing 'wsl'. +1. After restarting Windows, check that you have WSL enabled by opening a Command Prompt or PowerShell and typing `wsl`. -### PowerShell +To install Ubuntu on WSL: -To enable WSL on Windows using Powershell: +1. Go to **Start Button > Microsoft Store**. +1. Enter 'Linux' into the search field, then click **Run Linux on Windows**. +1. Select the latest Ubuntu distribution. +1. Select **Get** and wait for Windows to download and install Ubuntu. +1. When it’s finished, select **Launch**. +1. A terminal window will appear. Wait for Ubuntu to finish installing, then create a new Linux username and password when prompted. +---> + +### PowerShell or Windows Command Prompt + +To enable WSL on Windows using Powershell or Windows Command Prompt: 1. Open PowerShell or Windows Command Prompt in administrator mode by right-clicking and selecting **Run as administrator**. 1. Run `wsl --install`. + + :::{note} + This command will enable the features necessary to run WSL and install the Ubuntu distribution. + ::: + 1. When prompted, restart Windows. -1. After restarting Windows, open a PowerShell or Windows Command Prompt and run `wsl` to verify WSL was enabled. +1. After restarting Windows, open the Ubuntu distribution using the **Start** menu and create a new Linux **User Name** and **Password** when prompted. + + :::{note} + The **User Name** and **Password** is specific to each Linux distribution that you install and has no bearing on your Windows user name. + ::: + +See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for additional instructions for setting up a WSL development environment. + +## Development Containers + +Development Containers (Dev Containers), are Docker containers that are specifically configured to provide a fully featured development environment. It can be used to run an application, to separate tools, libraries, or runtimes needed for working with a codebase. Dev Containers can be run locally or remotely, in a private or public cloud, in a variety of supporting tools and editors. + +VS code and Docker are required to create and manage your Dev Containers. See {ref}`vscode-install` and {ref}`docker-desktop` for installation instructions. + +### Development Containers Extension + +The VS Code Dev Containers extension lets you use a container as a full-featured development environment. It allows you to open any folder inside (or mounted into) a container and take advantage of VS Code's full feature set. A `devcontainer.json` file in your project tells VS Code how to access or create a development container with a defined tool and runtime stack and can be used to run an application or to separate tools, libraries, or runtimes. + +The Dev Containers extension is included as a part of the [Remote Development extension pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack). See {ref}`remote-development-ext`) for installation instructions. + +### Create a Dev Container + + + +See [Create a Dev Container](https://code.visualstudio.com/docs/devcontainers/create-dev-container) for more information. + +:::{note} +Dev Containers can also be used by GitHub Codespaces in VS Code or the browser. See [GitHub Codespaces](https://code.visualstudio.com/docs/remote/codespaces) for more information. +::: \ No newline at end of file From ef32325ee71be62892f4e33860cb47dbe98d3c45 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 13:09:36 +0100 Subject: [PATCH 04/34] Finish draft Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 93 ++++++++++++++++++++++++++++++++++++------- docs/vscode.md | 1 + 2 files changed, 79 insertions(+), 15 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index de707de527..ff74e971ab 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -34,7 +34,7 @@ To install VS Code on macOS: 1. Visit the [VS Code](https://code.visualstudio.com/download) website. 1. Download VS Code for macOS. -1. Locate the `Visual Studio Code.app` application and move to the Applications folder to make it available in the macOS Launchpad. +1. Drag the `Visual Studio Code.app` application to the Applications folder to make it available in the macOS Launchpad. ``` @@ -58,9 +58,9 @@ See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_install ```` -## Extension +## Extensions -Extensions are a key feature of IDEs and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. +Extensions are a key feature of IDE's and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. ### Nextflow @@ -76,7 +76,7 @@ The VS Code [Nextflow extension](https://marketplace.visualstudio.com/items?item - Parameter schemas - DAG previews -See {ref}`vs-code-integration-page` for more information about the Nextflow extension. +See {ref}`vs-code-page` for more information about the Nextflow extension. ````{tabs} @@ -117,7 +117,7 @@ To install the Nextflow VS Code extension on Linux Debian/Ubuntu distributions: (remote-development-ext)= -### Remote Development extension pack +### Remote Development The [Remote Development extension pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) enables you to run WSL, SSH, or a development container for editing and debugging with the full set of VS Code features. @@ -129,7 +129,7 @@ The Remote Development extension pack includes four extensions: [WSL](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsl) - Get a Linux-powered development experience from the comfort of Windows by opening any folder in the Windows Subsystem for Linux. :::{note} -The VS Code Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, Development Containers. +The VS Code Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, or Development Containers. ::: @@ -186,6 +186,28 @@ Configure your environment to support the container technologies you want to use ```{group-tab} Windows +To install Docker Desktop on Windows: + +1. Visit the [Install Docker Desktop on Windows](https://docs.docker.com/desktop/setup/install/windows-install/) page. +1. Download the installer using the download button at the top of the page, or from the release notes. +1. Double-click Docker Desktop `Installer.exe` to run the installer. By default, Docker Desktop is installed at `C:\Program Files\Docker\Docker`. +1. When prompted, ensure the Use WSL 2 instead of Hyper-V option on the Configuration page is selected, or not, depending on your choice of backend. + + :::{note} + You won't be able to select which backend to use if your system only supports one of the two options. + ::: + +1. Follow the instructions on the installation wizard to authorize the installer and proceed with the install. +1. When the installation is complete, select **Close**. +1. Start Docker Desktop. +1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. + + :::{note} + Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop. + ::: + +1. Docker Desktop starts after you accept the terms. + ``` ```{group-tab} macOS @@ -347,7 +369,7 @@ Developers can access the power of both Windows and Linux on a Windows machine. WSL is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. You can enable it through PowerShell or Windows Command Prompt. The steps below outline the recommended setup. - + ### PowerShell or Windows Command Prompt +---> To enable WSL on Windows using Powershell or Windows Command Prompt: From 493b2e923fe6ce036e15dabb17b066f7a4b75338 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 13:21:57 +0100 Subject: [PATCH 06/34] Improve clarity Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index a220951867..2b8f9f2c1b 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -466,7 +466,7 @@ To create a dev container with an existing image: A Dockerfile may also live in the `.devcontainer` folder. You can replace the image property in `devcontainer.json` with dockerfile and create a custom container image. See [Create a Dev Container](https://code.visualstudio.com/docs/devcontainers/create-dev-container) for more information. ::: -1. Enter **Dev Containers: Reopen in Container** in the VS Code Command Palette and reopen your project. You should now see the name of the container ("Nextflow Dev Container" in the above example) in the bottom left corner of VS Code. +1. Enter **Dev Containers: Reopen in Container** in the VS Code Command Palette and reopen your project. You should now see the name of the container ("Nextflow Dev Container" if using the above example) in the bottom left corner of VS Code. :::{note} Dev Containers can also be used by GitHub Codespaces in VS Code or the browser. See [GitHub Codespaces](https://code.visualstudio.com/docs/remote/codespaces) for more information. From 9a5a1fd4c809b05fa9379200d0d62c78bbdf088c Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 13:37:11 +0100 Subject: [PATCH 07/34] Improve clarity again Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 2b8f9f2c1b..218074a866 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -423,9 +423,9 @@ The Dev Containers extension is included as a part of the [Remote Development ex ### Create and run a dev container -A `devcontainer.json` file in your project directory tells VS Code how to access, create, and configure a development container. It can be used to run an application or to separate tools, libraries, or runtimes. +A `devcontainer.json` file in your project directory instructs VS Code how to access, create, and configure a development container. It can be used to run an application or to separate tools, libraries, or runtimes. -You can alter your configuration to do things such as: +The `devcontainer.json` can be used to: - Install additional tools in the container. - Automatically install extensions. @@ -437,7 +437,7 @@ You can alter your configuration to do things such as: To create a dev container with an existing image: 1. Create a Dev Container `.json` under `.devcontainer/devcontainer.json` in the root of your project. -1. Add an image with the required tooling, and customizations, to the `.json` file. For example: +1. Add an image with the Nextflow tooling, and VS Code customizations, to the `.json` file. For example: ```json { @@ -463,7 +463,7 @@ To create a dev container with an existing image: ``` :::{note} - A Dockerfile may also live in the `.devcontainer` folder. You can replace the image property in `devcontainer.json` with dockerfile and create a custom container image. See [Create a Dev Container](https://code.visualstudio.com/docs/devcontainers/create-dev-container) for more information. + Instead of using a prebuilt image, a custom Dockerfile may also live in the `.devcontainer` folder. You can replace the image property in `devcontainer.json` with dockerfile and utilize the custom container. See [Create a Dev Container](https://code.visualstudio.com/docs/devcontainers/create-dev-container) for more information. ::: 1. Enter **Dev Containers: Reopen in Container** in the VS Code Command Palette and reopen your project. You should now see the name of the container ("Nextflow Dev Container" if using the above example) in the bottom left corner of VS Code. From 72cb41d56129854002550fff118f00d9cffe6847 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 14:11:21 +0100 Subject: [PATCH 08/34] Fix bullet points Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 218074a866..6ab6464b23 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -123,10 +123,10 @@ The [Remote Development extension pack](https://marketplace.visualstudio.com/ite The Remote Development extension pack includes four extensions: -[Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh) - Work with source code in any location by opening folders on a remote machine/VM using SSH. -[Remote - Tunnels](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-server) - Work with source code in any location by opening folders on a remote machine/VM using a VS Code Tunnel (rather than SSH). -[Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) - Work with a separate toolchain or container based application by opening any folder mounted into or inside a container. -[WSL](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsl) - Get a Linux-powered development experience from the comfort of Windows by opening any folder in the Windows Subsystem for Linux. +- [Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh) - Work with source code in any location by opening folders on a remote machine/VM using SSH. +- [Remote - Tunnels](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-server) - Work with source code in any location by opening folders on a remote machine/VM using a VS Code Tunnel (rather than SSH). +- [Dev Containers](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-containers) - Work with a separate toolchain or container based application by opening any folder mounted into or inside a container. +- [WSL](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-wsl) - Get a Linux-powered development experience from the comfort of Windows by opening any folder in the Windows Subsystem for Linux. :::{note} The VS Code Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, or Development Containers. From 57e002426a428603ff91473fd379d7c5f8beaf66 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 14:14:23 +0100 Subject: [PATCH 09/34] Try new phrasing Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 6ab6464b23..43783d177e 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -436,8 +436,8 @@ The `devcontainer.json` can be used to: To create a dev container with an existing image: -1. Create a Dev Container `.json` under `.devcontainer/devcontainer.json` in the root of your project. -1. Add an image with the Nextflow tooling, and VS Code customizations, to the `.json` file. For example: +1. Create `.devcontainer/devcontainer.json` in the root of your project. +1. Add an image with the Nextflow tooling and VS Code customizations to the `.json` file. For example: ```json { From d75d3bb8febee3b516eb669110aa29000b6dfdfe Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 14:15:47 +0100 Subject: [PATCH 10/34] Try new phrasing Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 43783d177e..8b8bd2d9a9 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -437,7 +437,7 @@ The `devcontainer.json` can be used to: To create a dev container with an existing image: 1. Create `.devcontainer/devcontainer.json` in the root of your project. -1. Add an image with the Nextflow tooling and VS Code customizations to the `.json` file. For example: +1. Add an image with the Nextflow tooling and VS Code customizations to the `devcontainer.json`. For example: ```json { From ba8175d82c04a2769b87f700b45ac7fb800613d3 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Fri, 8 Nov 2024 15:46:17 +0100 Subject: [PATCH 11/34] Incorporate comments from draft review Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 81 +++++++++++++++++++++++++++++++++++++------ 1 file changed, 70 insertions(+), 11 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 8b8bd2d9a9..6e320d91ab 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -4,6 +4,8 @@ Setting up a Nextflow development environment is a prerequisite for creating, testing, and optimizing data analysis pipelines. The steps below outline recommended tools for setting up an optimal Nextflow development environment. +Nextflow must be installed separately. See {ref}`install-page` for Nextflow installation instructions. + :::{note} If you are using a Windows computer, you first need to install and configure the Windows Subsystem for Linux (WSL). See {ref}`wsl` for installation instructions. ::: @@ -58,7 +60,7 @@ See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_install ```` -## Extensions +## VS Code Extensions Extensions are a key feature of IDE's and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. @@ -86,7 +88,7 @@ To install the Nextflow VS Code extension on Windows: 1. Open VS Code. 1. Open the VS Code Extensions view in the left-hand menu. -1. Search for Nextflow. +1. Search for **Nextflow**. 1. Select **Install**. ``` @@ -97,7 +99,7 @@ To install the Nextflow VS Code extension on macOS: 1. Open VS Code. 1. Open the VS Code Extensions view in the left-hand menu. -1. Search for Nextflow. +1. Search for **Nextflow**. 1. Select **Install**. ``` @@ -108,7 +110,65 @@ To install the Nextflow VS Code extension on Linux Debian/Ubuntu distributions: 1. Open VS Code. 1. Open the VS Code Extensions view in the left-hand menu. -1. Search for Nextflow. +1. Search for **Nextflow**. +1. Select **Install**. + +``` + +```` + + + +### nf-core + +The [nf-core extensionpack](https://marketplace.visualstudio.com/items?itemName=nf-core.nf-core-extensionpack) adds a selection of tools that help develop with nf-core, a community effort to collect a curated set of analysis pipelines built using Nextflow. + +The nf-core extension pack includes 12 extensions: + +- [Apptainer/Singularity](https://marketplace.visualstudio.com/items?itemName=onnovalkering.vscode-singularity) - Provides syntax highlighting for Apptainer/Singularity definition files +- [Code Spell Checker](https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker) - A basic spell checker that works well with camelCase code. +- [Docker](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-docker) - Makes it easy to create, manage, and debug containerized applications +- [EditorConfig](https://marketplace.visualstudio.com/items?itemName=EditorConfig.EditorConfig) - Support for EditorConfig project files for code standardisation. +- [indent-rainbow](https://marketplace.visualstudio.com/items?itemName=oderwat.indent-rainbow) - Highlight indentation level, especially if inconsistent +- [Nextflow](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) - Nextflow language support +- [Prettier](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode) - Code formatter using prettier +- [Rainbow CSV](https://marketplace.visualstudio.com/items?itemName=mechatroner.rainbow-csv) - Highlight columns in csv files in different colors +- [Ruff](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff) - An extremely fast Python linter and code formatter, written in Rust. +- [Todo Tree](https://marketplace.visualstudio.com/items?itemName=Gruntfuggly.todo-tree) - Show TODO, FIXME, etc. comment tags in a tree view +- [YAML](https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml) - YAML Language Support by Red Hat, with built-in Kubernetes syntax support +- [Markdown Extended](https://marketplace.visualstudio.com/items?itemName=jebbs.markdown-extended) - Gives nice markdown previews, including admonitions + +````{tabs} + +```{group-tab} Windows + +To install the nf-core extension pack on Windows: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for **nf-core-extensionpack**. +1. Select **Install**. + +``` + +```{group-tab} macOS + +To install the nf-core extension pack on macOS: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for **nf-core-extensionpack**. +1. Select **Install**. + +``` + +```{group-tab} Linux + +To install the nf-core extension pack on Linux Debian/Ubuntu distributions: + +1. Open VS Code. +1. Open the VS Code Extensions view in the left-hand menu. +1. Search for **nf-core-extensionpack**. 1. Select **Install**. ``` @@ -132,7 +192,6 @@ The Remote Development extension pack includes four extensions: The VS Code Remote Development extension pack is required if you are developing using remote servers, Windows Subsystem for Linux, or Development Containers. ::: - ````{tabs} ```{group-tab} Windows @@ -141,7 +200,7 @@ To install the Remote Development extension pack on Windows: 1. Open VS Code. 1. Open the VS Code Extensions view in the left-hand menu. -1. Search for Nextflow. +1. Search for **Remote Development**. 1. Select **Install**. ``` @@ -152,7 +211,7 @@ To install the Remote Development extension pack on macOS: 1. Open VS Code. 1. Open the VS Code Extensions view in the left-hand menu. -1. Search for Nextflow. +1. Search for **Remote Development**. 1. Select **Install**. ``` @@ -163,7 +222,7 @@ To install the Remote Development extension pack on Linux Debian/Ubuntu distribu 1. Open VS Code. 1. Open the VS Code Extensions view in the left-hand menu. -1. Search for Nextflow. +1. Search for **Remote Development**. 1. Select **Install**. ``` @@ -324,8 +383,6 @@ See [git-scm documentation](https://git-scm.com/downloads/linux) for more inform ```{group-tab} macOS -Git installed is already installed on new versions of macOS. You can activate it through the terminal running `git version`. If Git is not installed, you can install the latest version of Git using several methods: - To install Git on macOS with [Homebrew](https://docs.brew.sh/): 1. Open a terminal window and run `brew install git`. @@ -409,9 +466,10 @@ To enable WSL on Windows using Powershell or Windows Command Prompt: See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more information. + From 9cb8f7b0ec7ed28306024d4ef3554d1b88704021 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 12:23:40 +0100 Subject: [PATCH 12/34] Uncomment dev containers and add Gitpod note Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 6e320d91ab..bcdebfc8c6 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -466,7 +466,6 @@ To enable WSL on Windows using Powershell or Windows Command Prompt: See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more information. - From fdd9ca2a43665bd2a91157045d0b073b45bd3d7c Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:46:22 +0100 Subject: [PATCH 13/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index bcdebfc8c6..54b3ba3127 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -470,7 +470,7 @@ See [Set up a WSL development environment](https://learn.microsoft.com/en-us/win [Development Containers](https://containers.dev/) (Dev Containers), are Docker containers that are specifically configured to provide a fully featured development environment. They can be used to run an application, to separate tools, libraries, or runtimes needed for working with a codebase. Dev Containers can be run locally or remotely, in a private or public cloud, and in a variety of supporting tools and editors. -VS code and Docker are required to create and manage your Dev Containers. See {ref}`vscode-install` and {ref}`docker-desktop` for installation instructions. +VS Code and Docker are required to create and manage your Dev Containers. See {ref}`vscode-install` and {ref}`docker-desktop` for installation instructions. ### Development Containers extension From 73b66a737640eee2c9e9abedcadad2c838cd1852 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:46:46 +0100 Subject: [PATCH 14/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 54b3ba3127..64b4731db4 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -458,7 +458,7 @@ To enable WSL on Windows using Powershell or Windows Command Prompt: ::: 1. When prompted, restart Windows. -1. After restarting Windows, open the Ubuntu distribution using the **Start** menu and create a new Linux **User Name** and **Password** when prompted. +1. After restarting Windows, open the Ubuntu distribution and create a new Linux **User Name** and **Password** when prompted. :::{note} The **User Name** and **Password** is specific to each Linux distribution that you install and has no bearing on your Windows user name. From c4d733e61350d626e338da346c728a6230b4a786 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:46:58 +0100 Subject: [PATCH 15/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 64b4731db4..f9d9486a35 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -7,7 +7,7 @@ Setting up a Nextflow development environment is a prerequisite for creating, te Nextflow must be installed separately. See {ref}`install-page` for Nextflow installation instructions. :::{note} -If you are using a Windows computer, you first need to install and configure the Windows Subsystem for Linux (WSL). See {ref}`wsl` for installation instructions. +If you are using a Windows computer, first install and configure the Windows Subsystem for Linux (WSL). See {ref}`wsl` for installation instructions. ::: (vscode-install)= From a7cc66763ed28fb1a7e135e726915d3b11ddc975 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:47:15 +0100 Subject: [PATCH 16/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index f9d9486a35..43273913b7 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -14,7 +14,7 @@ If you are using a Windows computer, first install and configure the Windows Sub ## VS Code -Installing an Integrated Development Environment (IDE) is an essential step for setting up your environment and provide a user-friendly interface for writing, editing, and managing code. +An Integrated Development Environment (IDE) provides a user-friendly interface for writing, editing, and managing code. Installing one is an essential step for setting up your environment. Visual Studio Code (VS Code) is a popular lightweight IDE that is known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports Windows, macOS, and Linux, and is a good choice for both new and experienced Nextflow developers. From f3b10be669e6c3ca253a0043eec2995f375d6d30 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:47:27 +0100 Subject: [PATCH 17/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 43273913b7..8ed98a050b 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -405,7 +405,7 @@ To install Git on macOS with [Xcode](https://developer.apple.com/xcode/): ```{group-tab} Linux -Git is already installed on most on most Linux Debian/Ubuntu distributions. +Git is already installed on most Linux Debian/Ubuntu distributions. To install the latest stable Git version on Linux Debian/Ubuntu distributions: From 6686425fc0992e4f4faf144955942147f25670e7 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:48:01 +0100 Subject: [PATCH 18/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 8ed98a050b..e55c11aa4f 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -450,7 +450,7 @@ To install Ubuntu on WSL: To enable WSL on Windows using Powershell or Windows Command Prompt: -1. Open PowerShell or Windows Command Prompt in administrator mode by right-clicking and selecting **Run as administrator**. +1. Right-click and select **Run as administrator** to use PowerShell or Windows Command Prompt in administrator mode. 1. Run `wsl --install`. :::{note} From 55db7ab676157c4ddc15a3af0eb54c2ca9de0617 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:48:10 +0100 Subject: [PATCH 19/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index e55c11aa4f..26e1d12205 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -16,7 +16,7 @@ If you are using a Windows computer, first install and configure the Windows Sub An Integrated Development Environment (IDE) provides a user-friendly interface for writing, editing, and managing code. Installing one is an essential step for setting up your environment. -Visual Studio Code (VS Code) is a popular lightweight IDE that is known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports Windows, macOS, and Linux, and is a good choice for both new and experienced Nextflow developers. +Visual Studio Code (VS Code) is a popular lightweight IDE known for its versatility and extensibility. It offers features like syntax highlighting, intelligent code completion, and integrated debugging tools for various programming languages. VS Code supports Windows, macOS, and Linux, and is a good choice for both new and experienced Nextflow developers. ````{tabs} From 9f9147ecda3c0097ad1071ef58515a1ca5d2c4e1 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:48:20 +0100 Subject: [PATCH 20/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 26e1d12205..360b1a2009 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -62,7 +62,7 @@ See [Linux installation](https://code.visualstudio.com/docs/setup/linux#_install ## VS Code Extensions -Extensions are a key feature of IDE's and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. +Extensions are a key feature of IDEs and allow you to customize your development environment by adding support for various programming languages, tools, and features. The [VS Code Marketplace](https://marketplace.visualstudio.com/vscode) offers thousands of extensions that can enhance your productivity and tailor the editor to your specific needs. ### Nextflow From 2a7ebc26b7ddc01ceda5dea1181f5c8fb326b64a Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:48:58 +0100 Subject: [PATCH 21/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 360b1a2009..8fd1d6036c 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -434,7 +434,7 @@ To enable WSL on Windows using Windows Features dialog: 1. In the Windows search bar, enter 'features' to bring up the **Turn Windows Features on and off** dialog. 1. Scroll down and check **Windows Subsystem for Linux**. 1. Select **OK** and restart Windows. -1. After restarting Windows, check that you have WSL enabled by opening a Command Prompt or PowerShell and typing `wsl`. +1. After restarting Windows, open a PowerShell or Command Prompt and type `wsl` to confirm that you have WSL enabled. To install Ubuntu on WSL: From 177f2a9dc5d5ebe5bb80c963751d8b2bb4bb453b Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:49:33 +0100 Subject: [PATCH 22/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 8fd1d6036c..52aaf0466b 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -45,7 +45,7 @@ To install VS Code on macOS: To install VS Code on Linux Debian/Ubuntu distributions: 1. Visit the [VS Code](https://code.visualstudio.com/download) website. -1. Download VS Code Linux Debian/Ubuntu (`.deb`) distribution. +1. Download the VS Code Linux Debian/Ubuntu (`.deb`) distribution. 1. Open a new terminal window. 1. Navigate to the folder containing your VS Code download. 1. Run `sudo apt install ./.deb`, replacing `` with the full file name. From 73040744643447202738ac63a81a6998cb2a8458 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:50:12 +0100 Subject: [PATCH 23/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 52aaf0466b..6d7483cf56 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -26,7 +26,7 @@ To install VS Code on Windows: 1. Visit the [VS Code](https://code.visualstudio.com/download) website. 1. Download VS Code installer for Windows. -1. Double-click the installer executable (`.exe`) file and follow the step-by-step setup installation wizard. +1. Double-click the installer executable (`.exe`) file and follow the set up steps. ``` From 1a8e1e5b743f97c25f7cbaf48cf00b8fb8da1c9d Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:50:28 +0100 Subject: [PATCH 24/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 6d7483cf56..fd056c4d92 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -25,7 +25,7 @@ Visual Studio Code (VS Code) is a popular lightweight IDE known for its versatil To install VS Code on Windows: 1. Visit the [VS Code](https://code.visualstudio.com/download) website. -1. Download VS Code installer for Windows. +1. Download VS Code for Windows. 1. Double-click the installer executable (`.exe`) file and follow the set up steps. ``` From e6349f15f362e95974242df43c0b8c892d8ca02b Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:51:08 +0100 Subject: [PATCH 25/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index fd056c4d92..5177a950aa 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -36,7 +36,7 @@ To install VS Code on macOS: 1. Visit the [VS Code](https://code.visualstudio.com/download) website. 1. Download VS Code for macOS. -1. Drag the `Visual Studio Code.app` application to the Applications folder to make it available in the macOS Launchpad. +1. Drag the `Visual Studio Code.app` application to the Applications folder to add it to the macOS Launchpad. ``` From b3c00c5301234eb7e56fdcfd2b5dfdbb3311682c Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:51:42 +0100 Subject: [PATCH 26/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 5177a950aa..e645dff1bd 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -47,7 +47,7 @@ To install VS Code on Linux Debian/Ubuntu distributions: 1. Visit the [VS Code](https://code.visualstudio.com/download) website. 1. Download the VS Code Linux Debian/Ubuntu (`.deb`) distribution. 1. Open a new terminal window. -1. Navigate to the folder containing your VS Code download. +1. Navigate to the folder where you downloaded VS Code. 1. Run `sudo apt install ./.deb`, replacing `` with the full file name. :::{note} From d046d2f46f89165a75c9d4f5c937abedace02842 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:51:57 +0100 Subject: [PATCH 27/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index e645dff1bd..3335d80b91 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -468,7 +468,7 @@ See [Set up a WSL development environment](https://learn.microsoft.com/en-us/win ## Development Containers -[Development Containers](https://containers.dev/) (Dev Containers), are Docker containers that are specifically configured to provide a fully featured development environment. They can be used to run an application, to separate tools, libraries, or runtimes needed for working with a codebase. Dev Containers can be run locally or remotely, in a private or public cloud, and in a variety of supporting tools and editors. +[Development Containers](https://containers.dev/) (Dev Containers), are Docker containers that are specifically configured to provide a full-featured development environment. They can be used to run an application, to separate tools, libraries, or runtimes needed for working with a codebase. Dev Containers can be run locally or remotely, in a private or public cloud, and in a variety of supporting tools and editors. VS Code and Docker are required to create and manage your Dev Containers. See {ref}`vscode-install` and {ref}`docker-desktop` for installation instructions. From e4832f7c1d1ed4953aa3d3b13a13673f6f06063c Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:52:56 +0100 Subject: [PATCH 28/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 3335d80b91..53e9bb51ba 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -87,7 +87,7 @@ See {ref}`vs-code-page` for more information about the Nextflow extension. To install the Nextflow VS Code extension on Windows: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **Nextflow**. 1. Select **Install**. From 2dd42b9c963e013a436f54199b160327fef6e750 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:53:45 +0100 Subject: [PATCH 29/34] Update docs/developer-env.md Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 53e9bb51ba..aac4957c26 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -98,7 +98,7 @@ To install the Nextflow VS Code extension on Windows: To install the Nextflow VS Code extension on macOS: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **Nextflow**. 1. Select **Install**. From 461a157dcb4d30838c4eb34a0982b57b5b2905b8 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Mon, 11 Nov 2024 20:57:30 +0100 Subject: [PATCH 30/34] Apply suggestions from code review Co-authored-by: Justine Geffen Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 62 +++++++++++++++++++++---------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index aac4957c26..dfc49df894 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -109,7 +109,7 @@ To install the Nextflow VS Code extension on macOS: To install the Nextflow VS Code extension on Linux Debian/Ubuntu distributions: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **Nextflow**. 1. Select **Install**. @@ -125,18 +125,18 @@ The [nf-core extensionpack](https://marketplace.visualstudio.com/items?itemName= The nf-core extension pack includes 12 extensions: -- [Apptainer/Singularity](https://marketplace.visualstudio.com/items?itemName=onnovalkering.vscode-singularity) - Provides syntax highlighting for Apptainer/Singularity definition files +- [Apptainer/Singularity](https://marketplace.visualstudio.com/items?itemName=onnovalkering.vscode-singularity) - Provides syntax highlighting for Apptainer/Singularity definition files. - [Code Spell Checker](https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker) - A basic spell checker that works well with camelCase code. -- [Docker](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-docker) - Makes it easy to create, manage, and debug containerized applications +- [Docker](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-docker) - Makes it easy to create, manage, and debug containerized applications. - [EditorConfig](https://marketplace.visualstudio.com/items?itemName=EditorConfig.EditorConfig) - Support for EditorConfig project files for code standardisation. -- [indent-rainbow](https://marketplace.visualstudio.com/items?itemName=oderwat.indent-rainbow) - Highlight indentation level, especially if inconsistent -- [Nextflow](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) - Nextflow language support -- [Prettier](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode) - Code formatter using prettier -- [Rainbow CSV](https://marketplace.visualstudio.com/items?itemName=mechatroner.rainbow-csv) - Highlight columns in csv files in different colors +- [indent-rainbow](https://marketplace.visualstudio.com/items?itemName=oderwat.indent-rainbow) - Highlight indentation levels, especially if they're inconsistent. +- [Nextflow](https://marketplace.visualstudio.com/items?itemName=nextflow.nextflow) - Nextflow language support. +- [Prettier](https://marketplace.visualstudio.com/items?itemName=esbenp.prettier-vscode) - Code formatter using Prettier. +- [Rainbow CSV](https://marketplace.visualstudio.com/items?itemName=mechatroner.rainbow-csv) - Highlight columns in .CSV files in different colors. - [Ruff](https://marketplace.visualstudio.com/items?itemName=charliermarsh.ruff) - An extremely fast Python linter and code formatter, written in Rust. -- [Todo Tree](https://marketplace.visualstudio.com/items?itemName=Gruntfuggly.todo-tree) - Show TODO, FIXME, etc. comment tags in a tree view -- [YAML](https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml) - YAML Language Support by Red Hat, with built-in Kubernetes syntax support -- [Markdown Extended](https://marketplace.visualstudio.com/items?itemName=jebbs.markdown-extended) - Gives nice markdown previews, including admonitions +- [Todo Tree](https://marketplace.visualstudio.com/items?itemName=Gruntfuggly.todo-tree) - Show TODO, FIXME, etc. comment tags in a tree view. +- [YAML](https://marketplace.visualstudio.com/items?itemName=redhat.vscode-yaml) - YAML Language Support by Red Hat, with built-in Kubernetes syntax support. +- [Markdown Extended](https://marketplace.visualstudio.com/items?itemName=jebbs.markdown-extended) - Gives Markdown previews, including admonitions. ````{tabs} @@ -145,7 +145,7 @@ The nf-core extension pack includes 12 extensions: To install the nf-core extension pack on Windows: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **nf-core-extensionpack**. 1. Select **Install**. @@ -156,7 +156,7 @@ To install the nf-core extension pack on Windows: To install the nf-core extension pack on macOS: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **nf-core-extensionpack**. 1. Select **Install**. @@ -167,7 +167,7 @@ To install the nf-core extension pack on macOS: To install the nf-core extension pack on Linux Debian/Ubuntu distributions: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **nf-core-extensionpack**. 1. Select **Install**. @@ -181,7 +181,7 @@ To install the nf-core extension pack on Linux Debian/Ubuntu distributions: The [Remote Development extension pack](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.vscode-remote-extensionpack) enables you to run WSL, SSH, or a development container for editing and debugging with the full set of VS Code features. -The Remote Development extension pack includes four extensions: +The Remote Development extension pack contains 4 extensions: - [Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh) - Work with source code in any location by opening folders on a remote machine/VM using SSH. - [Remote - Tunnels](https://marketplace.visualstudio.com/items?itemName=ms-vscode.remote-server) - Work with source code in any location by opening folders on a remote machine/VM using a VS Code Tunnel (rather than SSH). @@ -199,7 +199,7 @@ The VS Code Remote Development extension pack is required if you are developing To install the Remote Development extension pack on Windows: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **Remote Development**. 1. Select **Install**. @@ -210,7 +210,7 @@ To install the Remote Development extension pack on Windows: To install the Remote Development extension pack on macOS: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **Remote Development**. 1. Select **Install**. @@ -221,7 +221,7 @@ To install the Remote Development extension pack on macOS: To install the Remote Development extension pack on Linux Debian/Ubuntu distributions: 1. Open VS Code. -1. Open the VS Code Extensions view in the left-hand menu. +1. Open the **Extensions** view in the left-hand menu. 1. Search for **Remote Development**. 1. Select **Install**. @@ -247,10 +247,10 @@ Configure your environment to support the container technologies you want to use To install Docker Desktop on Windows: -1. Visit the [Install Docker Desktop on Windows](https://docs.docker.com/desktop/setup/install/windows-install/) page. -1. Download the installer using the download button at the top of the page, or from the release notes. +1. Go to [Install Docker Desktop on Windows](https://docs.docker.com/desktop/setup/install/windows-install/). +1. Download the installer. 1. Double-click Docker Desktop `Installer.exe` to run the installer. By default, Docker Desktop is installed at `C:\Program Files\Docker\Docker`. -1. When prompted, ensure the Use WSL 2 instead of Hyper-V option on the Configuration page is selected, or not, depending on your choice of backend. +1. Depending on your choice of backend, select the **Use WSL 2 instead of Hyper-V** option on the Configuration page. :::{note} You won't be able to select which backend to use if your system only supports one of the two options. @@ -259,7 +259,7 @@ To install Docker Desktop on Windows: 1. Follow the instructions on the installation wizard to authorize the installer and proceed with the install. 1. When the installation is complete, select **Close**. 1. Start Docker Desktop. -1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. +1. Review the Docker Subscription Service Agreement and select **Accept** to continue. :::{note} Docker Desktop won't run if you do not agree to the terms. You can choose to accept the terms at a later date by opening Docker Desktop. @@ -273,15 +273,15 @@ To install Docker Desktop on Windows: To install Docker Desktop on macOS: -1. Visit the [Install Docker Desktop on Mac](https://docs.docker.com/desktop/install/mac-install/) page. -1. Download the installer for your chip type using the download buttons at the top of the page. +1. Go to [Install Docker Desktop on Mac](https://docs.docker.com/desktop/install/mac-install/). +1. Download the installer for your chip type. 1. Double-click `Docker.dmg` to open the installer. -1. Drag the Docker icon to the **Applications** folder to make it available in the macOS Launchpad. +1. Drag the Docker icon to the **Applications** folder to add it to the macOS Launchpad. 1. Double-click **Docker.app** in the **Applications** folder to start Docker. 1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. 1. From the installation window, select **Use recommended settings (Requires password)**. - :::{note} Recommended settings lets Docker Desktop automatically set the necessary configuration settings. Advanced settings allow you to set the location of the Docker CLI tools either in the system or user directory, enable the default Docker socket, and enable privileged port mapping. See [Settings](https://docs.docker.com/desktop/settings/#advanced), for more information and how to set the location of the Docker CLI tools. + :::{note} The **recommended settings** allow Docker Desktop to automatically set the necessary configuration settings. Advanced settings allow you to set the location of the Docker CLI tools either in the system or user directory, enable the default Docker socket, and enable privileged port mapping. See [Settings](https://docs.docker.com/desktop/settings/#advanced), for more information and how to set the location of the Docker CLI tools. ::: 1. Select **Finish**. If you have applied any of the previous configurations that require a password, enter your password to confirm your choice. @@ -301,7 +301,7 @@ To install Docker Desktop on Linux Debian/Ubuntu distributions: ::: 1. Double-click **Docker Desktop** in your Applications menu to start Docker. -1. Review the Docker Subscription Service Agreement and, if you agree, select **Accept** to continue. +1. Review the Docker Subscription Service Agreement and select **Accept** to continue. 1. From the installation window, select **Use recommended settings (Requires password)**. Docker Desktop starts after you accept the terms. :::{note} @@ -312,12 +312,12 @@ To install Docker Desktop on Linux Debian/Ubuntu distributions: ```` -Nextflow supports multiple container technologies (e.g., Singularity and Podman) allowing you to choose the one that best fits your needs. See {ref}`container-page` for more information about other supported container engines. +Nextflow supports multiple container technologies (e.g., Singularity and Podman) so you can choose the one that best fits your needs. See {ref}`container-page` for more information about other supported container engines. - ````{tabs} ```{group-tab} Windows @@ -422,7 +325,7 @@ See [git-scm documentation](https://git-scm.com/downloads/linux) for more inform ```` -(wsl)= +(devenv-wsl)= ## Windows Subsystem for Linux @@ -430,28 +333,6 @@ Developers can access the power of both Windows and Linux on a Windows machine. WSL is an optional feature on Windows 10 version 2004 and higher (Build 19041 and higher) or Windows 11. You can enable it through PowerShell or Windows Command Prompt. The steps below outline the recommended setup. - - To enable WSL on Windows using Powershell or Windows Command Prompt: 1. Right-click and select **Run as administrator** to use PowerShell or Windows Command Prompt in administrator mode. @@ -470,17 +351,18 @@ To enable WSL on Windows using Powershell or Windows Command Prompt: See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more information. + \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index e2990f7dac..731b2bd30e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -48,7 +48,6 @@ P. Di Tommaso, et al. Nextflow enables reproducible computational workflows. Nat overview install -developer-env your-first-script ``` @@ -140,6 +139,7 @@ developer/plugins :caption: Tutorials :maxdepth: 1 +developer-env flux metrics ``` From 9eb86500c2c2e66f09aa4c742b4abec8d7488f31 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Thu, 5 Dec 2024 12:24:23 +0100 Subject: [PATCH 34/34] Remove commented text Signed-off-by: Christopher Hakkaart --- docs/developer-env.md | 113 +----------------------------------------- 1 file changed, 1 insertion(+), 112 deletions(-) diff --git a/docs/developer-env.md b/docs/developer-env.md index 32db673a53..83c01189d2 100644 --- a/docs/developer-env.md +++ b/docs/developer-env.md @@ -222,52 +222,6 @@ To install Docker Desktop on Linux Debian/Ubuntu distributions: Nextflow supports multiple container technologies (e.g., Singularity and Podman) so you can choose the one that best fits your needs. See {ref}`container-page` for more information about other supported container engines. - - ## Git Git provides powerful version control that helps track code changes. Git operates locally, meaning you don't need an internet connection to track changes, but it can also be used with remote platforms like GitHub, GitLab, or Bitbucket for collaborative development. @@ -349,69 +303,4 @@ To enable WSL on Windows using Powershell or Windows Command Prompt: The **User Name** and **Password** is specific to each Linux distribution that you install and has no bearing on your Windows user name. ::: -See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more information. - - \ No newline at end of file +See [Set up a WSL development environment](https://learn.microsoft.com/en-us/windows/wsl/setup/environment) for more about installing WSL.