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  • Vim text editor (Joakim)
    • lots of keystroke shortcuts, syntax highlighting options. Very little mousing.
    • Comparable functionality to emacs
    • Tabs, multiple files at the same time
    • Ctags to index and find functions in your directory tree
    • Fugitive to integrate with git
    • Vim diff, Configure status line at the bottom, Autocomplete
  • Screen (Joakim)
    • Multiple shell sessions at the same time (Ctrl-A C)
    • Sessions will stay active even if computer disconnects (Ctrl-A D)
    • Can split vertically (Ctrl-A |, not available on all versions)
    • Comparable to tmux.
    • Screen User's Manual
    • Quick reference
  • Custom something to be able to show images in terminal (Joakim)
  • Readline (Joakim)
    • Shortcuts in terminal and across applications
    • .inputrc
    • Access history of commands issued
  • Zsh (Nils)
    • Zsh Summary
    • Shell (alternative to bash)
    • Globbing expressions - recursive pattern matching to find files, more powerful than find
    • Can find files based on file name, type, permissions
    • Spaceship zsh to customize prompts and make shortcuts, tab complete
    • git integration, has nice icon which indicate status of repo, and branch indication
    • Oh my zsh
    • Nice alias “git l” for generating graphical (ascii art) version of git history. Better than git log
    • Likely gonna be the default in the next Mac OS release (licensing reasons)
  • Vi plugin managers (Nils)
    • Language server protocol
  • Tmux (Dylan)
    • Similar to **screens **for detached sessions and working remotely
    • Split horizontally/vertically
    • List of active sessions
    • Can notify you when process completes
  • Window manager (Dylan)
    • Google “tiling window manager”
    • Tiling for application windows
    • **Xmonad. **Need to setup config in Haskell.
    • Divvy. Option for Mac. $14 purchase.
    • Magnet. $5 option for Mac.
  • Vim (Ruth)
    • More ergonomic keyboard shortcuts compared to emacs.
    • jonathansick/sickvim - for the config files - or dfm/dotfiles
    • Some specific keyboard bindings for latex files
    • Overleaf has vim keyboard bindings
  • **Iterm2 **(Ruth)
    • Window manager for terminal windows
  • API documentation (Ruth)
    • Docstring format from a google template.
    • Google style guide for Python: https://google.github.io/styleguide/pyguide.html
    • Astropy using the numpy doc template
    • Any pros and cons of numpy vs astropy/numpy template?
      • No real difference, just aesthetic.
  • Readthedocs (Ruth)
    • Auto generate documentation based on docstrings
    • Best practice for formatting docstrings
  • Travis (Ruth)
    • For automatic running of tests via github
  • Pycharm (Nikolai)
    • Editor for Python, but with many, many bells and whistles.
    • Compared to Spyder.
    • Documentation screen built in access to docstrings
    • Autocomplete functions and arguments
    • Very visual
    • Can autopopulate docstrings based on defined parameters and defined template
    • Lots of git integration and visual feedback, auto displays the diff
    • Lots of feedback on PEP and best practices
    • Change variables throughout
    • Profiling
    • Professional version has more things. ask for license from SCC. or use .edu email address to qualify for edu version.
    • Can execute parts of the code with # %%
    • Interact with variables and output via SciView
    • Easy to manage different conda/pip environments
  • More** PyCharm** (Tiberiu)
    • Integrates with unittest
    • Click to run all the tests
    • Also works with pytest.
    • Debugger, add breakpoints, run line by line
    • Run with Coverage to give graphical feedback on what is tested and not tested
    • Can also create and edit Jupyter notebooks. Split screen interaction.
    • Can also interact with markup languages (md, html) with a split screen interaction with code on one side and rendered version on the other.
  • Jupyter Addons (Tiberiu)
  • Black (Tiberiu)
    • Code formatter - linter
    • Reformats code
    • Made a custom shortcut to run black on code to reformat code
    • Can integrate with git so it does it everytime you commit
  • JupyterLab (Tiberiu)
    • Nicer interface than Jupyter
    • Jupyterlab_code_formatter repo
  • R in Jupyter notebook (Danxun)
    • DESeq2 R package
    • lots of work on the cluster and send up an environment with all necessary packages
    • R kernel does support tab completion and access to data frame properties
  • VSCode (Jeremy)
    • MD file in the repo with lots of notes
    • Sublime Text 3 is an alternative, and Pycharm
    • VSCode is very different than VSStudio
    • Lightweight text editor with extensions
    • Developed by Microsoft but open source
    • File explorer, split screen options
    • Extension marketplace. Choose based on number of downloads and stars
    • Github integration and history browsing with GitLens extension
    • Recommend Pyright extension for Python static typing
    • Similar to Atom, but takes up lots of memory. Anecdotal is that VSCode is less resource intensive
    • All of these have Vim emulator
  • TensorBoard (Charlie)
    • IDE for Tensorflow (machine learning package)
    • Histograms of gradients to help identify trends of the model over time
  • Cortex: Manuscripts from github repo (Rodrigo)
    • Reproducible papers
    • Links to scripts/commits which generate the figure
    • Figures live as scripts
    • Every commit triggers a build and force pushes pdf to a new branch