diff --git a/README.md b/README.md index df3b624..09ec9b1 100644 --- a/README.md +++ b/README.md @@ -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. ## 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 @@ -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) diff --git a/env.yml b/env.yml deleted file mode 100644 index 757b524..0000000 --- a/env.yml +++ /dev/null @@ -1,8 +0,0 @@ -name: bnd -dependencies: - - pip - - python=3.10 - - pytest - - typer - - pip: - - -e ./ \ No newline at end of file diff --git a/processing_env.yml b/processing_env.yml deleted file mode 100644 index 7ec16b4..0000000 --- a/processing_env.yml +++ /dev/null @@ -1,20 +0,0 @@ -name: bnd -channels: - - conda-forge - - pytorch - - nvidia - - defaults -dependencies: - - pip - - python=3.10 - - pytest - - typer - - pynwb - - numpy - - pandas - - scipy - - spikeinterface - - pip: - - ndx_pose - - neuroconv~=0.6.0 - - -e . \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index e04d139..7712001 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -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"