From ee8c384899d8a6a73148e3735c5579c1bdeec2bb Mon Sep 17 00:00:00 2001 From: Philipp A Date: Thu, 14 Jan 2021 12:23:10 +0100 Subject: [PATCH] Update install instructions --- docs/installation.rst | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/docs/installation.rst b/docs/installation.rst index b51f9012eb..ba029cedac 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -35,9 +35,9 @@ To work with the latest version `on GitHub`_: clone the repository and `cd` into its root directory. To install using symbolic links (stay up to date with your cloned version after you update with `git pull`) call:: - flit install -s # from an activated venv or conda env + flit install -s --deps=develop # from an activated venv or conda env # or - flit install -s --python path/to/venv/bin/python + flit install -s --deps=develop --python path/to/venv/bin/python If you intend to do development work, there are some extra dependencies you'll want. These can be install with `scanpy` via:: @@ -52,21 +52,19 @@ If you want to let conda_ handle the installations of dependencies, do:: beni pyproject.toml > environment.yml conda env create -f environment.yml conda activate scanpy - flit install -s + flit install -s --deps=develop On Windows, you might have to use `flit install --pth-file` if you are not able to give yourself the `create symbolic links`_ privilege. -Be aware that a `conda bug`_ might prevent `conda list` from working then. .. _create symbolic links: https://docs.microsoft.com/en-us/windows/security/threat-protection/security-policy-settings/create-symbolic-links -.. _conda bug: https://github.com/conda/conda/issues/9074 Docker ~~~~~~ -If you're using Docker_, you can use the minimal `fastgenomics/scanpy`_ image from the Docker Hub. +If you're using Docker_, you can use e.g. the image `gcfntnu/scanpy`_ from Docker Hub. .. _Docker: https://en.wikipedia.org/wiki/Docker_(software) -.. _fastgenomics/scanpy: https://hub.docker.com/r/fastgenomics/scanpy +.. _gcfntnu/scanpy: https://hub.docker.com/r/gcfntnu/scanpy .. _bioconda: https://bioconda.github.io/ Troubleshooting