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VS Code

VS Code is a free, open source, cross-platform, modern editor for code and text documents. It is developed by Microsoft.

It has Git support built in. A large ecosystem of extensions provide support for many programming languages, file formats, and editing tasks. Of particular use in the MOAD group are:

  • the Python extension that includes support for conda environments and the ability to edit Jupyter notebooks directly in VS Code
  • the Remote - SSH extension that enables you to use all of the features of VS Code on directories and files located on remote machines including the Waterhole machines, salish, and the Alliance HPC clusters.

Remote - SSH Extension Notes

  • The Remote - SSH extension page has brief documentation and a link to a tutorial on how to use the extension.

  • If you use the Remote - SSH extension you should increase the connection timeout setting because salish and some of the Waterhole workstations take >30 seconds to establish ssh connections. You can change that setting by using the menu to open the settings view: :guilabel:`File > Preferences > Settings` and using the search bar at the top of the view to find remote ssh connect timeout. Changing the value from the default of 15 seconds to 45 seconds should ensure successful connections to salish and the Waterhole workstations that are slow to connect.

  • Extensions that you want to use on the remote machine have to be installed have to be installed there. When you have a Remote - SSH session running, the Extensions sidebar shows extensions that you have installed locally in a :guilabel:`LOCAL - INSTALLED` list. If an extension can be installed for remote use a button like :guilabel:`Install in SSH: salish` should be available to trigger the remote installation.

    Extensions installed on the remote host show in a list with a name like :guilabel:`SSH: SALISH - INSTALLED`.

    So, to use Python and Jupyter in Remote - SSH connected to salish you will need to click the :guilabel:`Install in SSH: salish` in the Python extension tile in the Extensions sidebar. If you have the Python extension installed locally, you should be able to find its tile in the :guilabel:`LOCAL - INSTALLED` list. Otherwise, look for it in the :guilabel:`RECOMMENDED` list, or use the search box at the top of the Extension sidebar to find it.

Recommended Extensions

All of these extensions can be installed from the Extensions sidebar. The links included below are so that you can confirm that you are installing the recommended one because there are many, many extensions with very similar names.

Microsoft's Python Extension

Includes Jupyter support and many other features

https://marketplace.visualstudio.com/items?itemName=ms-python.python

Microsoft's Jupyter Notebook Renderers

Renderers for various image/graph formats output in Jupyter notebooks

https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter-renderers

Microsoft's Remote SSH Extension

Uses :program:`ssh` to open any directory/folder on a remote machine so that its files can be edited in VS Code.

Includes an editing mode for :program:`ssh` configuration files.

https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh

GitLens

Enhanced Git functionality and repository visualization

https://marketplace.visualstudio.com/items?itemName=eamodio.gitlens

Code Spell Checker

A basic spell checker that works well with code and documents

https://marketplace.visualstudio.com/items?itemName=streetsidesoftware.code-spell-checker

Clipboard

A clipboard that remembers your last 200 copy/cut fragments

https://marketplace.visualstudio.com/items?itemName=Digoro.Clipboard

Modern Fortran

Syntax highlighting, etc. for Fortran

https://marketplace.visualstudio.com/items?itemName=fortran-lang.linter-gfortran

Rainbow CSV

Highlight in colour the columns of CSV and similar file types, and other helpers for working with those types of files

https://marketplace.visualstudio.com/items?itemName=mechatroner.rainbow-csv

reStructuredText Syntax highlighting

Syntax highlighting and document symbols for reStructuredText

https://marketplace.visualstudio.com/items?itemName=trond-snekvik.simple-rst

vscode-pdf

Display PDF files in VS Code

https://marketplace.visualstudio.com/items?itemName=tomoki1207.pdf

Fortran Language Server (fortls)

The fortls package provides a lot of higher level, IDE functionality to the Modern Fortran extension. Among other things, it does background compilation of files you are editing to provide in-editor compiler errors and warnings.

To set up fortls in Remote - SSH sessions on nibi, salish, etc.:

  1. Use the Extensions sidebar to ensure that the Modern Fortran extension is enabled on the remote machine

  2. In a terminal session on the remote machine, create a conda environment called fortls with the fortls package and its dependencies installed in it:

    $ conda create -n fortls fortls

  3. Confirm the path of that new fortls environment by looking at the output of :command:`conda env list`. You should see a line like:

    fortls                   /home/dlatorne/miniforge3/envs/fortls

    with your userid instead of Doug's.

  4. In the VS Code settings, search for fortls. Select the remote settings for the machine you are on; e.g. Remote [SSH: nibi]. Change the value of the Fortran > Fortls: Path setting to the fortls environment path with :file:`/bin/fortls` appended; e.g. :file:`/home/dlatorne/miniforge3/envs/fortls/bin/fortls`

The language server compiles the code in the files you are editing to provide you with compiler errors and warnings and other features as you type. That results in the creation of .mod files beside your Fortran source code files; i.e. if you are editing :file:`bdydta.F90`, a :file:`bdydta.mod` will be created. .mod files are compiler product files that should not be committed to version control. Please just ignore them!

For namelist files you may have to explicitly tell VS Code to use the Fortran language mode because our naming convention is different to what the extension and language server expect. Near the right side of the bottom bar of the editor, find the language mode selector. For namelist it will probably say Plain Text, or occasionally HSLS. Click the selector and choose Fortran (FortranFreeForm).