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AtMostafa merged 2 commits into from
Jul 18, 2026
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De conda #3

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remove conda refs
AtMostafa Jul 18, 2026
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AtMostafa Jul 18, 2026
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28 changes: 6 additions & 22 deletions README.md
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Expand Up @@ -3,22 +3,21 @@
A **lightweight** collection of functions for managing the experimental data recorded in the
BeNeuro Lab, and a CLI tool called `bnd` for easy access to this functionality.

Play around with it and raise Github issues if anything fails
Play around with it and raise Github issues if anything fails.
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## Setting up

### 1. Install `bnd`

#### Option A — uv tool (recommended)

[uv](https://docs.astral.sh/uv/) installs `bnd` in an isolated environment and makes the CLI available system-wide.

> **Upgrading from an older version?** Earlier releases were installed with pipx. Remove that
> first so the two installs don't shadow each other:
> ```shell
> pipx uninstall bnd
> ```

### 1. Install `bnd`

[uv](https://docs.astral.sh/uv/) installs `bnd` in an isolated environment and makes the CLI available system-wide.


1. Install uv if you don't have it:
```shell
# Linux / macOS
Expand Down Expand Up @@ -62,21 +61,6 @@ uv tool upgrade bnd --reinstall
`bnd` tracks a git branch rather than a pinned version, so `--reinstall` is needed to make uv
re-fetch and pick up the newest commits.

#### Option B — conda

1. Install [Miniconda](https://docs.anaconda.com/miniconda/install/#quick-command-line-install) or [Miniforge](https://github.com/conda-forge/miniforge).
2. Clone the repo and create the environment:
```shell
git clone git@github.com:BeNeuroLab/bnd.git
cd ./bnd
conda env create --file=processing_env.yml # includes scientific dependencies
conda activate bnd
pip install -e .
```
To update later:
```shell
conda env update --file=processing_env.yml
```

### 2. Set up Kilosort (separate conda env)

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8 changes: 0 additions & 8 deletions env.yml
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20 changes: 0 additions & 20 deletions processing_env.yml
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -4,7 +4,7 @@ build-backend = "hatchling.build"

[project]
name = "bnd"
version = "0.1.7"
version = "0.1.7.1"
description = "BeNeuro data pipeline CLI"
readme = "README.md"
license = "MIT"
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