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Python setup & napari installation

Python setup & napari installation#

Tip

If you have any issues with installation, please feel free to write us a message on the napari zulip and we will try to help you get unstuck.

Note

Make sure you review the instructions below and verify that they are still correct before using them in your workshop.

Installing Python using conda#

In this tutorial, we will install Python via miniforge, a distribution of Python based in the conda package manager. If you already have anaconda, miniconda, or miniforge installed, those will work as well and you can skip to the next section.

  1. In your web browser, navigate to the miniforge page.

  2. Scroll down to the “Miniforge3” header of the “Downloads” section. Click the link to download the appropriate version for your operating system. Note that even if you have a new Apple computer with an M1 processor, you should download the OS X x86_64 version.

    • Windows: Miniforge3-Windows-x86_64

    • Mac with Intel processor: Miniforge3-MacOSX-x86_64

    • Mac with M1 (“Apple silicon”): Miniforge3-MacOSX-x86_64

    • Linux with an Intel processor: Miniforge3-Linux-x86_64

  3. Once you have downloaded miniforge installer, run it to install Python.

    • Windows

      1. Find the file you downloaded (Miniforge3-Windows-x86_64.exe) and double click to execute it. Follow the instructions to complete the installation.

      2. Once the installation has completed, you can verify it was correctly installed by searching for the “miniforge prompt” in your Start menu.

    • Mac OS

      1. Open your Terminal (you can search for it in spotlight - cmd + space)

      2. Navigate to the folder you downloaded the installer to. For example, if the file was downloaded to your Downloads folder, you would enter:

        cd ~/Downloads

      3. Execute the installer with the command below. You can use your arrow keys to scroll up and down to read it/agree to it.

        bash Miniforge3-MacOSX-x86_64.sh -b

      4. To verify that your installation worked, close your Terminal window and open a new one. You should see (base) to the left of your prompt.

      5. Finally, initialize miniforge with the command below. This makes sure that your terminal is set up correctly for your python installation.

        conda init

    • Linux

      1. Open your terminal application

      2. Navigate to the folder you downloaded the installer to. For example, if the file was downloaded to your Downloads folder, you would enter:

        cd ~/Downloads

      3. Execute the installer with the command below. You can use your arrow keys to scroll up and down to read it/agree to it.

         bash Miniforge3-Linux-x86_64.sh -b

      4. To verify that your installation worked, close your Terminal window and open a new one. You should see (base) to the left of your prompt.

      5. Finally, initialize miniforge with the command below. This makes sure that your terminal is set up correctly for your python installation.

        conda init

Setting up your environment#

  1. Open your terminal.

    • Windows: Open the “miniforge prompt” from your start menu

    • Mac OS: Open Terminal (you can search for it in spotlight - cmd + space)

    • Linux: Open your terminal application

  2. We use an environment to encapsulate the Python tools used for this workshop. This ensures that the requirements for this workshop do not interfere with your other Python projects. To create the environment (named napari-tutorial) and install Python 3.9 in it, enter the following command:

    conda create -n napari-tutorial python=3.9

  3. Once the environment setup has finished, activate the environment:

    conda activate napari-tutorial

    If you successfully activated the environment, you should now see (napari-tutorial) to the left of your command prompt.

  4. Install the workshop dependencies with the commands below.

    If you’re on an M1 Mac:

    conda install -c conda-forge notebook napari
python -m pip install cookiecutter magicgui
python -m pip install stardist-napari

    Other systems:

    conda install -c conda-forge notebook
python -m pip install cookiecutter magicgui "napari[all]"
python -m pip install stardist-napari

  5. If you are on a Mac, please install this one additional dependency.

    conda install -c conda-forge python.app

  6. Test that your notebook installation is working. We will be using notebooks for interactive analysis. Enter the command below and it should launch the jupyter notebook application in a web browser. Once you’ve confirmed it launches, close the web browser and press ctrl+c in the terminal window to stop the notebook server.

    jupyter notebook

  7. Test your napari installation. Enter the command below and an empty napari viewer should open. You can close the window after it opens. Please note that it takes a bit of extra time to launch napari the first time.

    napari

Errors launching?

Sometimes, napari installation can fail on an M1 Mac due to mismatching dependencies on pip.

If you get an error at step 4 above, or can’t launch napari after installation, you should try to delete your napari-tutorial environment, and follow the installation instructions below.

  1. Delete your napari-tutorial environment

    conda activate base
conda env remove -n napari-tutorial

  2. Create your environment and install napari from conda-forge

    conda create -y -n napari-tutorial python=3.9 napari

  3. Then, after creation:

    conda activate napari-tutorial
conda install -c conda-forge notebook
pip install cookiecutter magicgui
pip install stardist-napari
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