--- sd_hide_title: true --- # 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](#setup) instructions below to install everything on your personal laptop. The presentations and schedule for this workshop can be found at [this page](https://neurorse.flatironinstitute.org/workshops/jan-2025.html). ## 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! 0. 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](https://github.com/git-guides/install-git) should help. 1. Clone the github repo for this workshop: ```shell 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: :::::::{tab-set} :sync-group: category ::::::{tab-item} uv :sync: uv :::::{tab-set} :sync-group: os ::::{tab-item} Mac/Linux :sync: posix 1. Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/) by running: ```shell curl -LsSf https://astral.sh/uv/install.sh | sh ``` 2. Restart your terminal to make sure `uv` is available. 3. Install python 3.11: ```shell uv python install 3.11 ``` 4. Navigate to your cloned repo and create a new virtual environment: ```shell cd ccn-software-jan-2025 uv venv -p 3.11 ``` 5. Activate your new virtual environment by running: ```shell source .venv/bin/activate ``` :::: ::::{tab-item} Windows :sync: windows Open up `powershell`, then: 1. Install [`uv`](https://docs.astral.sh/uv/getting-started/installation/): ```powershell powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex" ``` 2. Install python 3.11: ```powershell uv python install 3.11 ``` 3. Navigate to your cloned repo and create a new virtual environment: ```powershell cd ccn-software-jan-2025 uv venv -p 3.11 ``` 4. Activate your new virtual environment by running: ```powershell .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. ::: :::: ::::: :::::: ::::::{tab-item} conda / miniforge :sync: conda :::{warning} Due to [recent changes](https://www.anaconda.com/blog/update-on-anacondas-terms-of-service-for-academia-and-research) 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](https://github.com/conda-forge/miniforge) if you do not have some version of `conda` or `mamba` installed already. 2. Create the new virtual environment by running: ```shell 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: ```shell 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. ::::{tab-set} :sync-group: category :::{tab-item} uv :sync: uv ```shell uv pip install -e . ``` ::: :::{tab-item} conda :sync: conda ```shell pip install -e . ``` ::: :::: 2. Run our setup script to download data and prepare the notebooks: ```shell python scripts/setup.py ``` 3. Confirm the installation and setup completed correctly by running: ```shell 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`: ::::::{tab-set} :sync-group: category :::::{tab-item} uv :sync: uv ::::{tab-set} :sync-group: os :::{tab-item} Mac/Linux :sync: posix ```shell cd path/to/ccn-software-jan-2025/notebooks source ../.venv/bin/activate jupyter lab ``` ::: :::{tab-item} Windows :sync: windows ```powershell cd path\to\ccn-software-jan-2025\notebooks ..\.venv\Scripts\activate jupyter lab ``` ::: ::::: :::::{tab-item} conda / miniforge :sync: conda ```shell 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](https://www.anaconda.com/blog/update-on-anacondas-terms-of-service-for-academia-and-research) 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=$(realpath ..)/.venv/share/jupyter/` to your jupyter command above: ```shell JUPYTER_DATA_DIR=$(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](https://binder.flatironinstitute.org/v2/user/wbroderick/jan2025?labpath=notebooks). 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](https://binder.flatironinstitute.org/hub/hub/home) (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](https://binder.flatironinstitute.org/hub/hub/home) 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. ```{toctree} :glob: :caption: Full notebooks :titlesonly: full/*/* ``` ```{toctree} :glob: :caption: For users (some code, some text) :titlesonly: users/*/* ``` ```{toctree} :glob: :caption: For presenter reference (all code, no text) :titlesonly: :maxdepth: 1 presenters/*/* ```