@@ -35,9 +35,9 @@ To work with the latest version `on GitHub`_: clone the repository and `cd` into
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its root directory. To install using symbolic links (stay up to date with your
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cloned version after you update with `git pull `) call::
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- flit install -s # from an activated venv or conda env
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+ flit install -s --deps=develop # from an activated venv or conda env
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# or
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- flit install -s --python path/to/venv/bin/python
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+ flit install -s --deps=develop -- python path/to/venv/bin/python
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If you intend to do development work, there are some extra dependencies you'll want.
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These can be install with `scanpy ` via::
@@ -52,21 +52,19 @@ If you want to let conda_ handle the installations of dependencies, do::
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beni pyproject.toml > environment.yml
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conda env create -f environment.yml
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conda activate scanpy
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- flit install -s
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+ flit install -s --deps=develop
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On Windows, you might have to use `flit install --pth-file `
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if you are not able to give yourself the `create symbolic links `_ privilege.
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- Be aware that a `conda bug `_ might prevent `conda list ` from working then.
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.. _create symbolic links : https://docs.microsoft.com/en-us/windows/security/threat-protection/security-policy-settings/create-symbolic-links
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- .. _conda bug : https://github.com/conda/conda/issues/9074
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Docker
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~~~~~~
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- If you're using Docker _, you can use the minimal ` fastgenomics /scanpy `_ image from the Docker Hub.
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+ If you're using Docker _, you can use e.g. the image ` gcfntnu /scanpy `_ from Docker Hub.
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.. _Docker : https://en.wikipedia.org/wiki/Docker_(software)
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- .. _ fastgenomics /scanpy : https://hub.docker.com/r/fastgenomics /scanpy
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+ .. _ gcfntnu /scanpy : https://hub.docker.com/r/gcfntnu /scanpy
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.. _bioconda : https://bioconda.github.io/
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Troubleshooting
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