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Update install instructions
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docs/installation.rst

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@@ -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::
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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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