From 00f268b6b2a1644afca01faacdd1b87f68998429 Mon Sep 17 00:00:00 2001 From: Simon Mages <3968483+simonwm@users.noreply.github.com> Date: Sat, 18 Feb 2023 17:21:39 -0500 Subject: [PATCH] updated installation docs, updated reference to Nat Biotech --- README.md | 28 ++++++++++++++++++++++++++-- docsource/references.rst | 6 +++--- environment.yml | 5 +---- 3 files changed, 30 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 9cab85d..6447bbd 100644 --- a/README.md +++ b/README.md @@ -1,9 +1,11 @@ # TACCO: Transfer of Annotations to Cells and their COmbinations -TACCO is a python framework for working with categorical and compositional annotations for high-dimensional observations, in particular for transferring annotations from single cell to spatial transcriptomics data. TACCO comes with an extensive ever expanding [documentation](https://simonwm.github.io/tacco/) and a set of [example notebooks](https://github.com/simonwm/tacco_examples). If TACCO is useful for your research, you can cite [bioRxiv (2022)](https://doi.org/10.1101/2022.10.02.508471). +TACCO is a python framework for working with categorical and compositional annotations for high-dimensional observations, in particular for transferring annotations from single cell to spatial transcriptomics data. TACCO comes with an extensive ever expanding [documentation](https://simonwm.github.io/tacco/) and a set of [example notebooks](https://github.com/simonwm/tacco_examples). If TACCO is useful for your research, you can cite [Nat Biotechnol (2023)](https://doi.org/10.1038/s41587-023-01657-3). ## How to install TACCO +### Clean + The simplest way to install TACCO is to create a clean environment with `conda` using the `environment.yml` file from the TACCO repository: ``` @@ -11,12 +13,34 @@ conda env create -f "https://raw.githubusercontent.com/simonwm/tacco/master/envi ``` (For older versions of `conda` one needs to download the `environment.yml` and use the local file for installation.) -To install TACCO in an already existing environment, one can use `pip` to directly install the latest release from github: +### Conda + +To install TACCO in an already existing environment, use `conda` to install from the `conda-forge` channel: + +``` +conda install -c conda-forge tacco +``` + +### Pip + +It is also possible to install from pypi via `pip`: + +``` +pip install tacco +``` + +This is however not recommended. Unlike `conda`, `pip` cannot treat python itself as a package, so if you start with the wrong python version, you will run into errors with dependencies (e.g. at the time of writing, `mkl-service` is not available for python 3.10 and `numba` not for 3.11). + +### Github + +To access the most recent pre-release versions it is also possible to pip-install directly from github: ``` pip install tacco@git+https://github.com/simonwm/tacco.git ``` +Obviously, this is not recomended for production environments. + ## How to use TACCO TACCO features a fast and straightforward API for the compositional annotation of one dataset, given as an anndata object `adata`, with a categorically annotated second dataset, given as an anndata object `reference`. The annotation is wrapped in a single function call diff --git a/docsource/references.rst b/docsource/references.rst index 01b3e7a..4ee5920 100644 --- a/docsource/references.rst +++ b/docsource/references.rst @@ -29,9 +29,9 @@ References *GOATOOLS: A Python library for Gene Ontology analyses*, `Scientific Reports `__. -.. [Mages23] Mages *et al.* (2022), - *TACCO: Unified annotation transfer and decomposition of cell identities for single-cell and spatial omics*, - `BioRxiv `__. +.. [Mages23] Mages *et al.* (2023), + *TACCO unifies annotation transfer and decomposition of cell identities for single-cell and spatial omics*, + `Nature Biotechnology `__. .. [Nitzan19] Nitzan *et al.* (2019), *Gene expression cartography*, diff --git a/environment.yml b/environment.yml index 65a9158..73f8a9c 100644 --- a/environment.yml +++ b/environment.yml @@ -22,8 +22,5 @@ dependencies: - scikit-learn - threadpoolctl - pyamg - - pip # for pip installing tacco - - git # for pip installing tacco from github - - pip: - - git+https://github.com/simonwm/tacco.git + - tacco