{"id":20081098,"url":"https://github.com/trangdata/vscode-notes","last_synced_at":"2026-03-06T11:30:58.687Z","repository":{"id":95113118,"uuid":"536599029","full_name":"trangdata/vscode-notes","owner":"trangdata","description":null,"archived":false,"fork":false,"pushed_at":"2022-09-26T12:01:12.000Z","size":3,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-02T13:27:54.078Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/trangdata.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-09-14T13:47:42.000Z","updated_at":"2024-09-10T16:41:53.000Z","dependencies_parsed_at":"2023-05-26T18:15:29.278Z","dependency_job_id":null,"html_url":"https://github.com/trangdata/vscode-notes","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/trangdata/vscode-notes","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fvscode-notes","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fvscode-notes/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fvscode-notes/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fvscode-notes/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/trangdata","download_url":"https://codeload.github.com/trangdata/vscode-notes/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/trangdata%2Fvscode-notes/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30173694,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-06T07:56:45.623Z","status":"ssl_error","status_checked_at":"2026-03-06T07:55:55.621Z","response_time":250,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-13T15:33:24.611Z","updated_at":"2026-03-06T11:30:58.657Z","avatar_url":"https://github.com/trangdata.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Some notes on vscode, aws ec2, ssh, git, python, r\n\n## Local setup\n\n- Install [VSCode](https://code.visualstudio.com/download)\n\n- In `/Users/let20/.ssh/config`:\n\n``` shell\nHost TODO\n  # Only if needed, uncomment below, set a different username than your local user\n  # User \u003cUSER\u003e\n\n  # Enable agent forwarding such that local SSH keys are available on the VM.\n  # This can be helpful for things like SSH GitHub authentication.\n  ForwardAgent yes\n\n  # Will forward port 8888 from the dev VM to local port 8890, which is useful\n  # for access to Jupyter Lab\n  LocalForward 8890 127.0.0.1:8888\n```\n\n## Server setup\nWhether you ssh in from VSCode or Terminal, on the AWS server, (_e.g._, RCE v2):\n\nInstall [Miniforge 3](https://github.com/conda-forge/miniforge):\n\n```\nwget \"https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh\"\nbash Miniforge3-$(uname)-$(uname -m).sh\n```\n\nBy doing so, you're setting the default channel to `conda-forge`,\nso you can install [programs](https://anaconda.org/conda-forge/python) simply with\n\n```\nconda install python\nconda install r-base\nconda install r-languageserver\nconda install r-dplyr\nconda install r-seurat\nconda install -c bioconda bioconductor-ensdb.hsapiens.v86\n```\n\n_Notes_: some packages may not be available on conda-forge, in which case you will need to find a different way to install them (_e.g._, `pip`, `install.packages`)\n\nFor a more reproducible workflow, create a new environment with all the necessary packages (with versions) specified in [`environment.yml`](environment.yml):\n```\nconda env create -f environment.yml\nconda activate myenv\n```\n\n## Helpful VSCode extensions\n- [Remote - SSH](https://marketplace.visualstudio.com/items?itemName=ms-vscode-remote.remote-ssh)\n- [GitLens](https://marketplace.visualstudio.com/items?itemName=eamodio.gitlens)\n- [Jupyter](https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter)\n- [Python](https://marketplace.visualstudio.com/items?itemName=ms-python.python)\n- [vscode-R](https://marketplace.visualstudio.com/items?itemName=REditorSupport.r)\n- [Docker](https://marketplace.visualstudio.com/items?itemName=ms-azuretools.vscode-docker)\n\n\n## VSCode for R\nPrimary extensions:\n- [vscode-R](https://marketplace.visualstudio.com/items?itemName=REditorSupport.r): R Extension for Visual Studio Code\n- [languageserver](https://github.com/REditorSupport/languageserver): An implementation of the Language Server Protocol for R\n- [radian](https://github.com/randy3k/radian): A 21 century R console (Terminal -\u003e Configure terminal settings -\u003e rterm -\u003e `/home/let20/miniforge3/bin/radian`)\n    - smarter about running what lines (within a function, for loops, etc.)\n    - syntax highlighting/coloring \n    - when arrow \"up\" to previous function, up by the entire execution, not just one line at a time\n    - autocomplete files\n\n## VSCode basics (demo)\n- Command Palette: `Cmd Shift P`.\nFrom here, you can go to Remote SSH, Settings, R Addins, Python: Select Interpreter, Convert to .py, Preview markdown, etc.\n- Edit shortcuts\n- Git\n- add Terminals\n\n## RStudio vs VSCode\n\n### RStudio\nThings just work out of the box. Minimal customization required.\n- Shortcuts: for pipes, finding in scope, create new function\n- Ctrl+.: not just files but also functions\n- View object by Cmd+Click\n- View() especially large dataframe is easy, filter...\n- R Workspace/Environment has a lot more information about objects\n- help page now has \"Run examples\" button\n- fuzzy search completion\n- snippets?\n\n### VSCode\n- better git integration\n- better multi language support\n- function hover\n\n## aws commands\n\n```\n# set up keys\naws configure set aws_access_key_id your_access_key --profile riku\naws configure set aws_secret_access_key you_secret_key --profile riku\n\n# example: copy a local file to the researchanalytics bucket\naws s3 --profile riku cp test-trang.txt s3://celgene-rnd-riku-researchanalytics/Evotec/Supplementary/\n```\n\nTODO\n\naws s3 R package\n\n## Additional readings\n\n- https://code.visualstudio.com/docs/editor/workspaces\n- https://code.visualstudio.com/docs/languages/r\n- RenKun's [video](https://youtu.be/9xXBDU2z_8Y) and accompanying [blogpost](https://renkun.me/2019/12/11/writing-r-in-vscode-a-fresh-start/) on his complete setup\n- https://schiff.co.nz/blog/r-and-vscode/\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrangdata%2Fvscode-notes","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftrangdata%2Fvscode-notes","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftrangdata%2Fvscode-notes/lists"}