Python

Updated: May 21, 2020

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For beginners to python, there are a variety of options. See our page on Training and Finding Help for additional details on in-person and other training opportunities. In addition to that, there are some publicly accessible resources available to assist in getting started learning and using Python for scientific research computing.

Accessing Python

There are many ways to use python beyond a local installation on your computer from Python.org. These methods depend more on the type of computing you will need to use and in what way you want to interact with your code and it’s output.

Via the local HPC cluster

SciComp maintains a current list of the various builds of Python available on rhino and gizmo for use by researchers. Each build has different modules installed and versions of Python itself, thus identifying if an existing Python build matches your needs is a first step to using Python on gizmo. Specific information about which Python Modules are available, including more information about packages installed in them can be found on our dedicated Python Module page. If you do not see the software you are looking for, email scicomp to request it or add your own GitHub issue in the easybuild-life-sciences repo. Either way, please be specific about the source and version of the software you are interested in.

Writing Python Code: Common IDEs

Visual Studio Code

This original content can still be found in it’s original repo written by a member of the Fred Hutch, this is an adaptation of that content.

Setup

  1. Install Visual Studio Code
  2. Add the following four key extensions (Code Runner 0.9.16, Python, R, markdownlint).
    • Do this by clicking on the four box icon on the left sidebar.
    • Search for the extensions by name and install
  3. Ensure you have a python >= 3.6 environment available.

Shortcuts for Mac

  • ⌘ is the Command () key.
  • ⌃ is the Control key.
  • ⌥ is the Option (alt) key.
  • ⇧ is the Shift key.
  • ⇪ is the Caps Lock key.
  • Select Panes with ⌘1,⌘2, … #n. If n is greater than the number of open panes, this will create a new pane.
  • Select Tabs within Panes with ⌃1,⌃2, … ⌃n. Get to the 2nd tab in the leftmost pane [⌘1], then [⌃2].
  • Select Explorer Pane with ⌘0. Once you are in the explorer you can use up and down keys to select files.

  • Reveal File Paths Instantly Click on the file panel Use the keyboard shortcut [⌥⌘C], and bam!, the full path is copied to your clipboard (e.g., /Users/kmayerbl/active/demo_vsc/README.md)

  • Reveal Paths with Clicks Instantly get to where your code lives on your machine. Save time by right-clicking on a folder or file, and select [Reveal in Finder] or [Open in Terminal]. Need the path just click [Copy Path].

  • Save one or Save all by Group

Take a look at the icon on the browser panel. You can, with one-click, save all the files or all the files in a group.

  • Preview your README.md

VSC offers a live rendering of your markdown. To view it, right-click on your markdown file and select [Open Preview].

  • Run Script or Only Part of Script With ⌃⌥N

You can run a segment of a script by selecting the part you care about and hitting [⌃⌥N]. The results show up in the OUTPUT table.

  • Identify Problems and Their Quick Fixes

Code linters help you find possible syntactical and stylistic problems quickly. Issues detected by the built-in VSCode linter are reported in the Problems tab of the Here are two examples.

  • No-trailing-spaces (see one line above)
  • No-bare URLs (see in the first block)

Get to the problems quickly with this shortcut [⇧⌘ M].

Problems and Their Fixes

Here you can see tests that are failing, and “lint” that’s piling up in your code. One of the things, I like about VSCode is that you can auto-correct simple problems like those above without even having to search through the code.

Script Debugging

When we run python hi.py we see an error. Suppose we want to see where that error emerges.

Traceback (most recent call last):
  File "greetings/hi.py", line 51, in <module>
    assert sentance_case_to_be_degbugged("Camel") == "Camel"
AssertionError
  • Breakpoints fn + F9, or using the mouse by clicking in the left margin in the editor.
  • Click the Bug with the play icon
  • We can start at the source of the error and move inwards

The breakpoint is placed on line 51 at the source of the error:

error1

“Step Into” the error (that is, go to the function being called) by clicking on the downward blue arrow. Then, step line by line through the problematic function and check whether state of all variables meet your expectations.

error2 1

Develop a Specific Unit Test

A great thing about VSCode is how it organizes your test. You can even run them one by one.

tests

Also here is an easter egg if you like doctests:

pytest --doctest-modules -v

Magic Sauce and Git Interface

The Peak function is Some Serious Magic beans. Sometimes you don’t want to search for where a variable or function is defined. VSCode has a peak function that lets you examine externally referenced objects, and even edit them, directly from where an object is referenced. Let’s look at what the French hello should be:

peak

SSH Extension for remote development

If you’ve ever had to access and work on files through a remote connection you’ve probably found yourself at the mercy of the development tools provided on the remote server you’re accessing. Luckily VSCode has a well-supported extension which can allow you to enjoy the same development experience on a remote server that you would if you were developing locally. Follow the step-by-step instructions on setting up the Visual Studio Code Remote - SSH to get set up to run VSCode when connected to a remote server.

The Visual Studio Code Remote - WSL extension is a related extension which allows you to use VSCode with the Windows Subsystem for Linux. This can greatly simplify using Linux toolchains and utilities from within a Windows environment.

Merge Conflicts example

Let’s look at resolving a merge conflict. A merge conflict often arises when two users commit changes to the same file. For instance, on GitHub, I wrote:

I think we should think global!

But on my laptop, I wrote:

I think we should start local!

When I tried to, push the second commit, my push was rejected:

Fail to Push

So I pulled the version on GitHub that was one commit ahead, revealing a conflict without an auto-resolution. Git cannot merge two versions of the same file, if they have different content on the same line! How would git know which was correct?

Merge Conlict

Fortunately, VSCode makes it easy to review the confict and pick the winner (or keep both, by appending a version as new lines of code).

Resolve Merge Conflict

After resolving the conflict, remember to commit and push the resolution.

settings.json

JSON file with all your user-specific settings. How to get to it? (see the common settings wheel at the lower left)

where is settngs dot json

PyCharm

This original content can still be found in it’s original repo written by a member of the Fred Hutch, this is an adaptation of that content.

PyCharm is an incredibly powerful IDE created by JetBrains. It comes in a free, open-source community edition, and a paid-for subscription edition.

Key shortcuts:

  • ⌘k will bring up a commit dialog box, listing all the files that have been modified. You can uncheck the checkbox next to each file that you don’t want included in the commit. A diff viewer will be present for each file changed, allowing you to see how the file changed for this commit.

  • fn+⇧+k will bring up the push menu, and will include a list of all the commits which will be pushed as a result of this action, as well as the ability to view the diffs that will be applied to each changed file.

  • ⌘b will take you to the closest (scope-wise) definition of a variable you have high-lighted, whether that’s in the current function or deep in some third-party library in your virtual environment. I find this one to be invaluable when trying to trace back clues as to why an object isn’t behaving the way I think it should, and overall better understand how those objects work.

  • ⌥⇧E will allow you to execute any highlighted code in an IPython console which will automatically appear. The console will contain the state of any state from previous code executions in that console, but can be easily reset using the ‘return’ button along the Python Console toolbar. This is super handy for testing small snippets of code while you’re developing.

  • ⇧⌘I will open up a small peek window with a view of the definition of an object or class you have highlighted. This is in contrast to ⌘b, which will take you directly to the module and location of the declaration of the highlighted object.

peek_image

All these hotkeys and tons more can be configured iin the Preferences > Keymap menu. If you’re a hotkey ninja (which I am not), you can get set up to keep your hand off the mouse almost completely. There are vim and emacs keymap plugins which will allow you to use your vim/emacs setups in PyCharm as well.

Object inspection, completion

When working with objects that may have lots of methods on them, it can be easy to forget what methods are available. By simply typing a variable which has been prior been assigned a type (through just assigning it a value, Py3 method signature type hints, or in-line type hints) and typing the ‘.’ operator, a list of all properties and methods of that variable will appear in a drop-down. Furthermore, once you’ve selected a method and are beginning to feed it parameters, you can type ⌘p from within the method parentheses to list all the parameters the function takes. If you’d like to know more about how the function itself works, you can jump to its definition by highlighting it and typing ⌘b

Setting the python environment

By associating your project with a python interpreter (whether it’s a global installation, or some conda/venv/pipenv install) your IDE will be better able to perform proper syntax highlighting and will also be able to do cool things like run tests and execute scripts or selected code blocks. You can even create multiple run / test configurations with different versions of Python in case you’d like to test across any differences between versions.
To set a python environment, open the Preferences pane by selecting PyCharm > Preferences from the toolbar (or ⌘, for shortcut). Then from the Project drop-down select Project Interpreter. From here you can create a new conda/pipenv/venv environment for this project (generally good practice) or select an existing interpreter on your computer. To create a new environment, or link an existing interpreter to PyCharm select ‘Add’ from the menu that appears when you click the gear next to the Python Interpreter drop-down menu.
add_interpreter

From the next pane you can create a new conda/pipenv/venv or link PyCharm to an existing interpreter / environment by browsing directly to its location on your computer, which makes it available to select in the Project Interpreter drop-down menu on the previous page.

Running code through the IDE

Once you have a python interpreter associated with your project you should be able to right-click on any .py file selected from the project navigator and select Run. Any output from your project will appear in a terminal window which should appear when the file is run. You can customize Run configurations for each executable file, providing things like command-line arguments, environment variables and further environment setup by selecting Run > Edit Configurations from the top toolbar,

Debugging support

A file can be run with a debugger attached that will stop the program at any breakpoints you’ve placed by selecting a file, and selecting Run > Debug… from the top toolbar, or right-clicking on the file from the project navigator and clicking Debug ‘file.py’. Breakpoints can be placed on any line of code by clicking in the gutter next to the line number, or using the shortcut ⌘F8. Once you’ve entered the debugger and have stopped at a line a powerful array of tools are available to do things like execute a single line, step over lines, inspect / watch variable values, and explore variable attributes or execute arbitrary code in the breakpoint context.

Testing

PyCharm’s testing abilities really help make this project shine. From within the Preferences menu you have can select Tools > Python Integrated Tools. From here you can choose your favorite test runner (mine happens to be pytest)), which will tell PyCharm what tool to use when detecting and running tests in your project.

Test Suite

By going to the Test Configurations menu under the Run menu dropdown you can make custom test run configurations for particular modules or scripts, with different test runners or runtime parameters and environment setups.

Test debugging

While debugging doesn’t always have to occur during a unittest, they often go hand in hand. Say you’ve got a test that is failing and you just don’t know why. Don’t you which you could freeze the test right in the middle, inspect the variables and see which one contains the erroneous value that is making the test puke?

To drop a breakpoint into a test, simply click on the gutter to the left of the line you want to stop at. This will place a red dot where the code will stop when we attach a debugger. Now when you go to click the ‘play’ button on the test, right-click and select ‘Debug test_stuff.py’. This will attach a debugger to the test runner, which will stop the code every time it sees one of the red dots in the gutter. When the test stops you’ll have a few windows pop up in the bottom of the IDE, one containing the current stack frames, and on containing any locally-defined variables and their value.
You can also add variables to a watch list from this window, so that if the test traverses many functions you can keep track of the value of an interesting variable. Collections and objects in the Variables window will give you the ability to drill-down through their attributes as well if you would like to further interrogate them.

File ran with debugger

This picture shows the debugger stopping the program prior to executing the line 13 assert rand > 2 and the debugger context which appears at the bottom of the screen, containing the current call stack, a list of all variables found in the context of the breakpoint which allows you to easily explore the attributes and values of nested objects, and a similar watch context for following a particular variables value across different scopes.

Refactoring

Remember when you thought raccoon would be a funny name for a variable? And then that raccoon persisted throughout the project, leaving its trail everywhere and leaving you and your teammates to try to figure out what a raccoon object is in the context of bioinformatics? PyCharm makes refactoring of variable / object names extremely easy. Simply highlight the variable or object you want to rename, click >Refactor, then click > Rename. PyCharm will then search for any reference to that variable and present you with a list of all the places throughout the entire project that the highlighted variable occurs. If you’d like to rename all of them it’s as easy as clicking ‘Do Refactor’. I’ve found this incredibly useful for changing object names to be more clear about their purpose, without having to hunt through scores of modules to determine where they occur.

Find Usages

Sometimes you find a seemingly important variable or method that might need to be changed, but have no idea where it’s being used or how it’s being used. By highlighting the object, right-clicking and clicking Find Usages… a small pop-up window will show where that varible is referenced throughout the entire project. This is particularly helpful for when you’re cleaning up cruft and want to know if you can delete something. ‘No Usages Found’? Deleted.

Right-clicking an object opens a menu which contains the ‘Find Usages…’ button:
find usages example

After clicking the ‘Find Usages’ button, a pane will open listing all the usages of that object found throughout the project, presented in a tree-like fashion. Double-clicking on any of these usages will take you directly to that location in the code. found_usages_example

Customized lint-hinting

PyCharm comes with a huge number of different of type and style hints to conform to PEP-8 and avoid some logic errors, particularly if you use the Python 3 type declarations in your code. Missing parentheses, brackets, bad indentation, unused variable detection, unreachable code, possibly uninitialized variables being used all can be reported with varying levels of severity. Which hints to receive, as well as their presentation attributes, can be set in the Preferences menu under the Editor tab.

VCS integrations

While many of you are command-line git ninjas, I find myself pulling my hair out paging through merge conflicts or diffing various commits from a history. The VCS integration in PyCharm makes it easy to see what branches you’re working on, whether any of those branches contain changes others don’t, and contains a beautiful diff viewer comparing files, whether it be do resolve a merge conflict, or while comparing a file to how it may have looked 6 months ago.

Files which have been modified since the last commit will be highlighted in blue, making it obvious what files you’ve touched.

Diff window comparing two conflicting files and showing the file resulting from how you merge the conflict.
Merge Conflict differ

You also have the ability to look through the git revision history of any module or folder by selecting the folder / module, right-clicking and selecting ‘Git > Show history…’

Show History

This allows you to see the various concurrent branches of development for the file, as well as a diff viewer showing the commit diff at each commit. This can be super handy when trying to find where a problem was introduced, or if you need to roll back to a specific commit before your last merge.

Installing plugins
From the top toolbar, select PyCharm > Preferences > Plugins. There are a myriad of plugins to help smooth out your development experience, such as database connectors, AWS log and CLI plugins, Docker management tools, various language support plugins, hotkey keymap setups, color schemes and more.

Jupyter Notebook extension

PyCharm is capable of running Jupyter Notebooks. This is far from my area of expertise, but the community edition of PyCharm does appear to support it. A very basic jupyter notebook file is included in this project repo to show that it can be done. The kernel running the Jupyter Notebook can be configured similarly to how a test runner is configured. Go to the Run window drop-down, click > Edit Configurations.. and select an item from the drop-down below Jupter Notebooks on the left side of the window that appears.

README writing

When writing any markdown file (ending with .md), PyCharm automatically picks it up as a markdown file and gives you the option to view the rendered markdown side-by-side with your markdown file as you create it.

Extensions

There are lots of various plugins for PyCharm that can be accessed through the Preferences tab, for various things like vim keyboard mappings, SQL highlighting and completion, bash completion, ticketing-service integrations, etc.

I’ve played with the youtrack extension before, and it was pretty neat once I got it up and running. It allowed me to create branches from within PyCharm linked to an issue listed on youtrack, and then commits I made to that branch would show up as links in the youtrack ticket. I could also close the ticket after merging the feature back in. They have a number of other issue tracker integrations, including JIRA, Trello, and GitLab.

There are also various tools to enable easier development in cloud applications.

Other languages

PyCharm attempts to provide basic code highlighting and completion (like closing tags in HTML) in various languages, including HTML, SQL, and Docker. The professional version provides better syntax highlighting for things like Django and Jinja2 templates (and I think some light-weight javascript highlighting?), but I didn’t really find them worth it when I did my 30-day free trial of the professional version. There are many active community plugin projects for supporting tons of various languages.

Jupyter Notebooks

This original content can still be found in it’s original repo written by a member of the Fred Hutch, this is an adaptation of that content.

Here are some reasons to take a look at Jupyter, a linearly executed IDE, with come caveats.

Preliminaries

First, it’s good to know there’s two distinct products associated with Jupyter. The earliest and first product developed by the Jupyter team is called Jupyter Notebook. This is the one you will see discussed and screenshoted the most when surfing the web. The second and latest product developed by the Jupyter team and the one we’ll discuss in further detail below is JupyterLab.

So let’s get started with JupyterLab, oh and I’ll just say at the top that I do not think JupyterLab can currently replace a more engineering focused IDE application like Atom, VSCode or PyCharm but it is heading in that direction with its extensions and it does presently make a very good light-weight, browser-based analytical tool for teaching, data wrangling, modeling, scripting, cloud computing and various other analytic needs outside of engineering.

  1. First let’s install JupyterLab. The latest version is 2.0.1 and that’s important because some of the add-ons and extensions may not work with this or other versions.
  2. By default JupyterLab installs python but to install all the other cools stuff* you’ll need:

    *Caveat here - some of these extensions/add-on are not as frequently updated as the core JupyterLab product and may not be available with the latest version of JupyterLab so be mindful when installing them.

Shortcuts for Mac

  • ⌘ is the Command () key.
  • ⌃ is the Control key.
  • ⌥ is the Option (alt) key.
  • ⇧ is the Shift key.
  • ⇪ is the Caps Lock key.

The shortcuts I use most when operating in Jupyterlab are the following:

  • Shift + Return - will run the cell selected
  • Return - will allow you to enter into the cell to edit the code
  • Esc - while escape will take you out of the cell while keeping it selected. You can then use the arrow keys to navigate down to another cell or..
  • A - hitting A after hitting Esc so you are no longer in a cell will create a new cell above where you are now
  • B - B will create a cell below the one you are in now and..
  • DD - hitting D twice will delete the cell selected
  • M - hitting M when a cell is selected will turn that cell from a code to a markdown cell
  • Y - Y will turn the markdown cell back into a coded one
  • R - R will turn the cell into a raw format

It also auto-saves checkpoints so I don’t worry too much about saving but use ⌘+S for good measures every now and again. Jupyterlab also has a text editor which has keyboard maps to popular text editors like vim, emacs or Sublime Text which you can select and edit under Settings. And if you just need a cheat sheet BOOM!

Preview your README.md

Jupyterlab offers live rendering of your markdown. To set it up, locate the markdown file you want to edit in Jupyter’s file browser; right-click on the markdown file and select Open With > Markdown Preview. This will open up the file as a rendered markdown. You can then double-click on the same file again in the explorer and it’ll open in Jupyter’s Text Editor at which point you can grab and move/split the tabs to your preference for live editing of markdown.

Run Script or Only Part of Script With ⌃⌥N

You can run a segment of a script by selecting the part you care about and hitting [⌃⌥N]. The results show up in the OUTPUT table. Take the segment of code you want to run and drop it into a new cell and Shift+Return. Seems manual but this ability to take parts of code and iterate and interact with them by dropping them into a new cell to run is what some find beatiful about Jupyter. It is like an inline console which speaking of if you want to create a new console just select File > New and you can create a new console, or a new notebook (in either a python, R, Julia or other kernel), a terminal instance, a new text file, or a markdown.

Identifying Problems and Their Quick Fixes

Linters help you find problems quickly and this guy built a good one based on the flake8 python library for linting. The only problem is that currently it doesn’t work with JupyterLab 2.0 yet that doesn’t mean it won’t in the future ; )

Debugging

So having a debugger in your IDE that you can insert breakpoints, step in, cycle thru your lines, and step out is nice. Once again we have a great extension here that provides that in Jupyterlab. Unfortunately, after many attempts at getting the debugger switch to show up in the UI and then trying to get it to operate I had to give up on it but in version 1 it worked as a good debugger should so hopefully this will be operating smoothly in Jupyterlab 2.0 soon.

Magic Sauce

Ok, so the “magic beans” here with Jupyterlab is that you have a very light and functional, once all the extensions are updated to play nicely with Jupyterlab 2.0, web-based IDE which outside of hard core engineering can be of use to you especially with the rise of cloud-computing; oh it has a dark theme now! Settings > JupyterLab Theme.

Git extension for JupyterLab

“There’s an extension for that”…seriously! Yet, it’s not as nice as the github integration for VSCode or PyCharm but then again JupyterLab is new and the extensions I believe are community-driven so they haven’t had the time or resources to flush it out like the others may have. There’s also one specifically for diffing and merging of notebooks.

Settings

You can set system and all your user-specific settings by going to Settings > Advance Setting Editor.

the .ipynb file

This IS the ipython notebook file or your JupyterLab file with code and markdown in it and note you can only access these from the directory you execute jupyterlab in so either pwd to make sure or have a set location of where you save the files because you’ll only be able to open .ipynb files in either the start-up directory or it’s sub-folders.

Using Jupyter Notebooks at Fred Hutch

Jupyter Notebooks are web interfaces to interpreter shells such as Python and R. They allow the user to write code in small, executable chunks that can be interspersed with blocks of markdown. They are particularly well suited to exploring data and generating narrative-style presentations of analyses. They are most used by data scientists who would like to experiment with their code and easily generate charts and graphs. At Fred Hutch there are at least 4 ways how you can use Jupyter Notebooks, including the latest incarnation called ‘Jupyter Lab’. You can find more information about Jupyter and related technologies here at the Project Jupyter site.

Jupyter Notebook on your computer

Install the software on your own computer install Jupyter and run locally.

Jupyter on Rhino
For instructions on how to connect to rhino see this page.

After you have connected to rhino, just load a Python distribution maintained by SciComp and run Jupyter lab:

    petersen@rhino1:~$ ml Python/3.6.7-foss-2016b-fh2
    petersen@rhino1:~$ jupyter lab --ip=$(hostname) --port=$(fhfreeport) --no-browser

    ... or simply use the 'jupyterlab' wrapper script:
    petersen@rhino1:~$ jupyterlab

Then connect to the URL, copying the link given by the previous command, which looks as follows:

       Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://rhino1:11112/?token=0eee692be6c81c1061db

Jupyter on Gizmo

From Rhino execute the grabjupyter command and a node will be allocated on Gizmo after you selected the CPUs and number of days you need the node. For more information on working with gizmo, see the dedicated page here

Jupyter on Jupyterhub

SciComp maintains an installation of Jupyterhub. Login with your Hutch Net Id. (Jupyterhub does not have the latest Python packages)

Please note that only the first method (running Jupyter from your local machine) allows you to install your own python packages as administrator of your machine. The other 3 methods require you to either request a package from Scientific Computing or install the package in your home directory with the –user option (e.g. pip3 install --upgrade --user mypkg) or to create a virtual Python environment, for example:

    petersen@rhino1:~$ ml Python/3.6.7-foss-2016b-fh2
    petersen@rhino1:~$ python3 -m venv ~/mypython
    petersen@rhino1:~$ source ~/mypython/bin/activate
    (mypython) petersen@rhino1:~$ jupyter lab
    (mypython) petersen@rhino1:~$ deactivate
    petersen@rhino1:~$

Conclusions

Jupyterlab built upon the success of Jupyter notebook as a light-weight, browser based linearly executed IDE, but now has an updated front-end making it seem more similar to RStudio and Spyder. It comes with a much quicker backend running in your browser than Jupyter notebook and with the help of some extensions which you can theoretically load by enabling the Extension Manager in Settings you can add linting, debugging, version control and many more (fasta render anyone?).

The downside though is that version 2 was a major release for them and they are now at 2.0.1 which was released in March 6, 2020 so the project is very new which means the extensions which add a lot of features to flush out the product also need to stay update-to-date with the current code base but that can create problems. There’s guides for that, “JupyterLab 1.x to 2.x Extension Migration Guide”, but it’ll be great when everything is playing nice and you have a powerful browser-based, light-weight IDE at your finger tips.

Let’s hope the synergy of the versioning of the core product and the community of extensions improves. Until then there’s nothing stopping a python or R user from doing all their engineering in Atom, PyCharm, RStudio, or VSCode and then the rest of their coding/management in Jupyterlab since it is browser-based. Hopefully, this tutorial has heightened your interest.

More IDEs to explore

The three IDEs described in detail on this page were chosen due to developers at the Hutch having positive experiences with them that they wanted to share. There are many more well supported IDEs out there, and what works best for you will take a matter of experimentation to find what works best for the type of work you do. A few more common IDEs that are worth looking into are:

  • Atom: a highly extensible text editor with native support for a number of languages, and a wide array of community-developed packages to support other languages. Atom has a thriving community which is constantly developing a lot of really interesting plugins and extensions.
  • Spyder: has elements of Jupyter Notebook where specific parts of a script can be executed independently, with the state of any affected variables carrying over in a session to any subsequent executions. Very handy for rapid prototyping and analysis-driven programming.
  • Sublime Text: lightweight language-agnostic text editor with a rich plugin ecosystem and ability to customize for when you want more horsepower. Has syntax highlighting for a ton of languages

Updated: May 21, 2020

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