Welcome!

Welcome!#

CCN Software Workshop, Jan 2025#

We are excited to see everyone at the Flatiron Center for Computational Neuroscience workshop on using open source packages to analyze and visualize neural data! You should have received an email with logistical information, including the schedule and link to the slack channel where we will be communicating the workshop. If you did not receive this email, please let us know!

Over the course of this two-day workshop, we will walk you through the notebooks included on this site in order to demonstrate how to use pynapple and NeMoS to analyze and visualize your data.

Before the workshop, please try to follow the setup instructions below to install everything on your personal laptop.

The presentations and schedule for this workshop can be found at this page.

This website#

This website contains rendered versions of the notebooks we will be working through during this workshop. During the workshop, attendees should look at the versions found under the For users section. These notebooks have some code pre-filled, as well as brief notes to help orient you. If you follow the setup instructions below, you will have editable copies of these notebooks on your laptop, and you are expected to follow along using these notebooks.

If you miss something or fall behind, you can look into the For presenters section, which includes the completed code blocks (along with some notes), so you can catch up.

After the workshop, we encourage you to return and check out the Full notebooks section, which, as the name implies, includes everything: explanatory text, code, and plots.

Setup#

Before the workshop, please try to complete the following steps. If you are unable to do so, we have an installation help session at the Flatiron Institute, 160 5th Ave, in the 3rd floor conference center, from 2 to 5pm on Wednesday, January 29. Please come by!

  1. Make sure you have git installed. It is installed by default on most Mac and Linux machines, but you may need to install it if you are on Windows. These instructions should help.

  2. Clone the github repo for this workshop:

    git clone https://github.com/flatironinstitute/ccn-software-jan-2025.git

Create a virtual environment with python 3.11#

There are many ways to set up a python virtual environment. You can use your favorite way of doing so. If you don’t have a preference or don’t know what to do, choose one of the following:

  1. Install uv by running:

    curl -LsSf https://astral.sh/uv/install.sh | sh

  2. Restart your terminal to make sure uv is available.

  3. Install python 3.11:

    uv python install 3.11

  4. Navigate to your cloned repo and create a new virtual environment:

    cd ccn-software-jan-2025
uv venv -p 3.11

  5. Activate your new virtual environment by running:

    source .venv/bin/activate

Open up powershell, then:

  1. Install uv:

    powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

  2. Install python 3.11:

    uv python install 3.11

  3. Navigate to your cloned repo and create a new virtual environment:

    cd ccn-software-jan-2025
uv venv -p 3.11

  4. Activate your new virtual environment by running:

    .venv\Scripts\activate

    Warning

    You may receive an error saying “running scripts is disabled on this system”. If so, run Set-ExecutionPolicy -Scope CurrentUser and enter Unrestricted, then press Y.

    You may have to do this every time you open powershell.

Warning

Due to recent changes to Anaconda’s Terms of Service, the Simons Foundation cannot use the defaults conda channel and it is blocked on all Flatiron Institute wireless networks. You need to specify conda-forge instead (which is community-managed and open to all). The following instructions do so, but if you follow your normal workflow, you may hit issues.

  1. Install miniforge if you do not have some version of conda or mamba installed already.

  2. Create the new virtual environment by running:

    conda create --name ccn-jan25 pip python=3.11 -c conda-forge

    Note the -c conda-forge!

  3. Activate your new environment and navigate to the cloned repo:

    conda activate ccn-jan25
cd ccn-software-jan-2025

Install dependencies and setup notebooks#

  1. Install the required dependencies. This will install pynapple and nemos, as well as jupyter and several other packages.

    uv pip install -e .

    pip install -e .

  2. Run our setup script to download data and prepare the notebooks:

    python scripts/setup.py

  3. Confirm the installation and setup completed correctly by running:

    python scripts/check_setup.py

If check_setup.py tells you setup was successful, check that you can run jupyter lab notebooks/day2/current_injection-users.ipynb and run the first few cells (up until the one containing path = workshop_utils.fetch_data("allen_478498617.nwb")). If that all works, then you’re good to go. Otherwise, please come to the installation help session on Wednesday, so everyone is ready to get started Thursday morning.

After doing the above, the data/ and notebooks/ directories within your local copy of the ccn-software-jan-2025 repository will contain the NWB files and jupyter notebooks for the workshop.

On the day of the workshop, we will run through the notebooks in the order they’re listed on this website. To open them, navigate to the notebooks/ directory, activate your virtual environment and start jupyter lab:

cd path/to/ccn-software-jan-2025/notebooks
source ../.venv/bin/activate
jupyter lab

cd path\to\ccn-software-jan-2025\notebooks
..\.venv\Scripts\activate
jupyter lab

cd path/to/ccn-software-jan-2025/notebooks
conda activate ccn-jan25
jupyter lab

Troubleshooting#

  • If you are on Mac and get an error related to ruamel.yaml (or clang) when running pip install -e ., we think this can be fixed by updating your Xcode Command Line Tools.

  • On Windows, you may receive an error saying “running scripts is disabled on this system” when trying to activate the virtual environment. If so, run Set-ExecutionPolicy -Scope CurrentUser and enter Unrestricted, then press Y. (You may have to do this every time you open powershell.)

  • When creating the conda environment, you may get errors related to accessing the defaults channel. Due to recent changes to Anaconda’s Terms of Service, the Simons Foundation cannot use the defaults conda channel and it is blocked on all Flatiron Institute wireless networks. You need to specify conda-forge instead (which is community-managed and open to all). (The instructions above should do so.)

  • If you have multiple jupyter installs on your path (because e.g., because you have an existing jupyter installation in a conda environment and you then used uv to setup the virtual environment for this workshop), jupyter can get confused. (You can check if this is the case by running which -a jupyter on Mac / Linux.) To avoid this problem, either make sure you only have one virtual environment active (e.g., by running conda deactivate) or prepend JUPYTER_DATA_DIR=$(realpath ..)/.venv/share/jupyter/ to your jupyter command above:

    JUPYTER_DATA_DIR=$(realpath ..)/.venv/share/jupyter/ jupyter lab

    (On Windows, replace $(realpath ..) with the path to the ccn-software-jan-2025 directory.)

  • We have noticed jupyter notebooks behaving a bit odd in Safari — if you are running/editing jupyter in Safari and the behavior seems off (scrolling not smooth, lag between creation and display of cells), try a different browser. We’ve had better luck with Firefox or using the arrow keys to navigate between cells.

  • On Windows + conda: if after installing conda the path are not correctly set, you may encounter this error message:

    conda : The term 'conda' is not recognized as the name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try again.

    In this case, you can try the following steps:

    • Locate the path to the condabin folder. The path should look like: some-folder-path\Miniforge3\condabin.

      The following powershell command could be useful (note that i am starting form C: as a root, but you can change that):

      Get-ChildItem -Path C:\ -Directory -Recurse -Filter "condabin" -ErrorAction SilentlyContinue | Select-Object -ExpandProperty FullName

    • Temporarily add conda to the paths:

      $env:Path += ";some-folder-path\Miniforge3\condabin"

    • Initialize conda:

      conda init powershell

    • Restart the powershell and check that conda is in the path. Run for example conda --version.

  • If you see sys:1: DeprecationWarning: Call to deprecated function (or staticmethod) _destroy. when running python scripts/setup.py, we don’t think this is actually a problem. As long as check_setup.py says everything looks good, you’re fine!

  • If you get an issue during the creation of the conda environment, try making sure the ~/.condarc file looks like the following (that file might not be created; create it if needed):

    channels:
- conda-forge
ssl_verify: false
channel_priority: true

  • If you see an error that mentions SSL verification and are using conda, add the following line to your ~/.condarc: ssl_verify: false. Then restart your terminal and run the command again. (If you are using uv, I’m not sure how to set this configuration option.)

  • On an ARM-based (newer) Mac using conda, during check_setup.py, if you get This version of jaxlib was built using AVX instructions, uninstall using pip and install using conda: pip uninstall jax jaxlib; conda install -c conda-forge jax jaxlib.

    • If not using conda, not sure how to avoid this issue, you may have to switch.

Binder#

A binder instance (a virtual environment running on Flatiron’s cluster) is provided in case we cannot get your installation working. To access it, click the “launch binder” button in the top left of this site or click here.

You must login with the email address you provided when registering for the workshop. If you get a 403 Forbidden error or would like to use a different email, send Billy Broderick a message on the workshop slack.

Some usage notes:

  • You are only allowed to have a single binder instance running at a time, so if you get the “already have an instance running error”, go to the binderhub page (or click on “check your currently running servers” on the right of the page) to join your running instance.

  • If you lose connection halfway through the workshop, go to the binderhub page to join your running instance rather than restarting the image.

  • This is important because if you restart the image, you will lose all data and progress.

  • The binder will be shutdown automatically after 1 day of inactivity or 7 days of total usage. Data will not persist after the binder instance shuts down, so please download any notebooks you want to keep.

  • I will destroy this instance in 2 weeks. You can download your notebooks to keep them after the fact.

Full notebooks

For users (some code, some text)

For presenter reference (all code, no text)