From 02076a3af54f182dd654eb066893c361975aeacf Mon Sep 17 00:00:00 2001 From: Clarence Mah Date: Wed, 3 May 2023 01:48:44 +0000 Subject: [PATCH] bump version --- docs/source/installation.md | 39 +++++++++++++++++++++---------------- pyproject.toml | 2 +- 2 files changed, 23 insertions(+), 18 deletions(-) diff --git a/docs/source/installation.md b/docs/source/installation.md index a71b25c..a138e6e 100644 --- a/docs/source/installation.md +++ b/docs/source/installation.md @@ -1,8 +1,9 @@ -# {octicon}`terminal` Installation -Bento requires Python version 3.8 or 3.9. Only Python 3.8 is supported for Windows. +# {octicon}`terminal` Installation +Bento requires Python version 3.8 or 3.9. ## Setup a virtual environment + We highly recommend using a virtual environment to install Bento to avoid conflicting dependencies with other packages. If you are unfamiliar with virtual environments, we recommend using [Miniconda](https://docs.conda.io/en/latest/miniconda.html). To setup a virtual environment with `Miniconda`, run the following. This will create and activate a new environment called `bento` with Python 3.8. @@ -18,6 +19,7 @@ conda config --env --add channels conda-forge conda activate bento ``` + ## 2. Dependencies Bento makes use of several packages for spatial analyses that require addtional non-Python dependencies. @@ -37,35 +39,38 @@ conda install -c conda-forge pandoc All that's left is the package itself. Install with pip: ```bash -pip install bento-tools==2.0.0a0 +pip install bento-tools ``` --- + ## Development + The package and its dependencies are built using [Poetry](https://python-poetry.org/). 1. Install [Poetry](https://python-poetry.org/). 2. Clone the `bento-tools` GitHub repository. 3. Use poetry to manage dependencies and pip to install the package in editable mode. - ```bash - cd bento-tools - poetry install - pip install -e . - ``` + ```bash + cd bento-tools + poetry install + pip install -e . + ``` - For updating documentation locally, install extra dependencies and launch a live server to preview doc builds: + For updating documentation locally, install extra dependencies and launch a live server to preview doc builds: - First install pandoc (see [dependencies](#Dependencies) section for more details). + First install pandoc (see [dependencies](#Dependencies) section for more details). - ```bash - poetry install --extras "docs" - pip install -e .\[docs\] - cd docs - make livehtml # See output for URL - ``` + ```bash + poetry install --extras "docs" + pip install -e .\[docs\] + cd docs + make livehtml # See output for URL + ``` --- + ## GPU Support (Optional) -Bento currently only uses GPUs to accelerate tensor decomposition (via [Tensorly](https://tensorly.org/stable/index.html)) GPU support can be enabled by installing PyTorch. We recommend the [PyTorch installation instructions](https://pytorch.org/get-started/locally/) for more details as installation varies by platform. +Bento currently only uses GPUs to accelerate tensor decomposition (via [Tensorly](https://tensorly.org/stable/index.html)) GPU support can be enabled by installing PyTorch. We recommend the [PyTorch installation instructions](https://pytorch.org/get-started/locally/) for more details as installation varies by platform. diff --git a/pyproject.toml b/pyproject.toml index 0cc2917..229a0f9 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -6,7 +6,7 @@ include = [ "bento/models/**/*", "bento/tools/gene_sets/*", ] -version = "2.0.0a0" +version = "2.0.0" description = "A toolkit for subcellular analysis of spatial transcriptomics data" authors = ["Clarence Mah "] license = "BSD-2-Clause"