# Python 3 Support and Python 2 End of Life (EOL) As stated in [Sunsetting Python 2](https://www.python.org/doc/sunset-python-2/), the Python core development team supports only Python 3.x, having sunset Python 2.x support on January 1, 2020. This FAQ explains Python 3.x and Python 2.x support on the DNAnexus Platform. DNAnexus provides Python 3 app execution environment ("Python 3 AEE") based on Ubuntu 16.04 that includes the following: * The stock Ubuntu `python2.7` interpreter, available at `/usr/bin/python` * The stock Ubuntu `python3.5.2` interpreter, available at `/usr/bin/python3` * `dx` command-line client based on `python3` interpreter * `dxpy` Python module installations that work with both `python2.7` and `python3.5.2` interpreters An app with `dxapp.json` containing `"runSpec": {"release": "16.04", "version": "1", "interpreter": "python3" ...}` is executed in "Python3 AEE" using `python3.5.2` interpreter. An app with `dxapp.json` containing `"runSpec": {"release": "16.04", "version": "1", "interpreter": "bash" ...}` is executed in "Python3 AEE" using bash interpreter and the `dx` commands invoke `python3.5.2` installation of dx-toolkit. For reference, Ubuntu 16.04 apps without `"version":"1"` in `dxapp.json` are executed in the legacy "Python 2 AEE" that includes: * The dx-toolkit package (including the `dx` command-line client and the `dxpy` Python module), configured in a way that requires Python 2. * The stock Ubuntu `python2.7` interpreter, available at `/usr/bin/python`. * The stock Ubuntu `python3.5.2` interpreter, available at `/usr/bin/python3`. ## Does the `dxpy` Python module work with Python 2 and Python 3? The `dxpy` module works with both Python 2 and Python 3. For historical reasons, the default installation of `dxpy` in the existing "Python 2 AEE" is `python2.7`-specific. "Python 3 AEE" removes this constraint. You can continue using `pip3` to install a `python3`-compatible version of the `dxpy` module outside of the DNAnexus execution environment. This applies to installations on your laptop or other local environments. ## Do apps that use Python 2 work after January 1, 2020? Apps that do not rely on installing `python2.7` packages using `pip` at runtime (either through `pip` dependencies in `dxapp.json` or through `pip install` commands in the shell script) should continue running on the platform. An app that installs `python2.7` packages at runtime *may* stop working if it depends on the latest version of a package that has dropped `python2.7` support, such as numpy or pandas. For such packages, you must specify in your app's dependencies a specific version of the library that does support `python2.7` to ensure your app continues working with `python2.7`. For example, if your `dxapp.json` specifies the numpy package without a version, that is, via `"execDepends": [ {"name": "numpy", "package_manager": "pip"]`, the execution fails trying to install the latest version of numpy with the error message `RuntimeError: Python version >= 3.5 required`. You can address the problem by specifying an earlier version of numpy, that is, via `"execDepends": [ {"name": "numpy", "package_manager": "pip", "version":"1.16"}]`. ## What are the potential security implications of using Python 2 after January 1, 2020? Any security vulnerabilities discovered in Python 2 after January 1, 2020, are not going to be patched. The DNAnexus execution environment isolates the execution of apps in a secure Linux container, and mitigates the impact of potential Python 2 security vulnerabilities. Given the lack of support after Python 2 goes End-of-Life (EOL), significant security vulnerabilities may cause the DNAnexus Platform to disable execution of Python 2 or have you assume full liability for execution of Python 2 customer code. ## How long is the DNAnexus Support for the "Python 2 AEE"? DNAnexus stopped updating the "Python 2 AEE" on March 1, 2021. Starting March 1, 2021: * DNAnexus deprecated and stopped updating the "Python 2 AEE". The platform no longer accepts new applets or apps with the "Python 2 AEE" option specified in `dxapp.json`, or with the `interpreter` option set to `python2.7`. * The `dx-toolkit` package (including the `dx` command-line client and the `dxpy` Python module) removed support for Python 2. Previously published versions of `dxpy` that had Python 2 support remain available via `pip`. * For reproducibility, existing apps or applets that rely on the "Python 2 AEE" continue to run and use the last version of `dxpy` that was compatible with Python 2. ## How can an app that uses Python 2 be migrated to Python 3? After introducing the new "Python 3 AEE" option in `dxapp.json`, rebuild the app with that option specified. This also applies to bash apps that don't call Python code explicitly but rely on the `dx` command-line client. If `dxapp.json` has the `interpreter` option set to `python2.7`, change it to `python3`. If your app includes any Python code, make sure it is compatible with Python 3. For more information about porting Python 2 code to Python 3, consult the [Python porting guide](https://docs.python.org/3/howto/pyporting.html). If your app depends on other resources, assets, or packages that use Python, ensure that these dependencies have also been updated. Other alternatives for removing Python 2 dependencies from your app include the following: * Re-implement your app in a higher-level [WDL](https://github.com/dnanexus/dxWDL) workflow description language. * Encapsulate your app execution environment and app dependencies in a Docker container for advanced use cases such as interpreting your app using Python 3.8 or running on Ubuntu 18.04, and use `docker` command supported by Ubuntu 16.04 AEE. * Contact the [DNAnexus Professional Services](https://www.dnanexus.com/professional-services) for assistance with the transition.