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Remove unmaintained docker definition
Remove unmaintained container instructions
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containers/docker-minimal

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docs/development.md

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@@ -795,26 +795,6 @@ Note the following tips:
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- There is a script: `benchmarks/check_asv.sh` that can be used to benchmark recent commits.
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## Containerization
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To run msprime in a container, see the
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{ref}`installation instructions <sec_installation_container>`.
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You can use `docker` to locally build an image, but it requires root access:
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```{code-block} bash
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$ sudo docker build -t tskit/msprime .
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```
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[podman](<https://podman.io/>) can build and run images without root privilege.
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```{code-block} bash
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$ podman build -t tskit/msprime .
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```
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## Troubleshooting
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- If `make` is giving you strange errors, or if tests are failing for

docs/installation.md

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# Installation
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There are three options for installing `msprime`:
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There are two main options for installing `msprime`:
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1. {ref}`sec_installation_conda`: the recommended options for most users
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2. {ref}`sec_installation_pip`: more flexibility and control for advanced users
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3. {ref}`sec_installation_container`: to use
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`msprime` inside an extremely isolated environment
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(sec_installation_conda)=
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python3 -m pip install msprime --no-binary msprime
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```
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(sec_installation_container)=
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## Via Container
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An [open container](<https://opencontainers.org/>) image (aka docker image) is built on
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[Dockerhub](<https://hub.docker.com/r/tskit/msprime>) for each release of
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msprime. Each image is [tagged](<https://hub.docker.com/r/tskit/msprime/tags>)
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with the corresponding release. For example, for msprime release 0.7.5, the
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corresponding image tag is `tskit/msprime:0.7.5`.
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To run a container, you can use [docker](<https://www.docker.com/>),
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[Singularity](<https://sylabs.io/singularity/>),
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[podman](<https://podman.io/>) or similar tools supporting docker images.
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### docker
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`docker` requires root privilege to run a container:
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```{code-block} bash
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$ sudo docker run -it tskit/msprime:<release> mspms 10 1 -T
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```
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### podman
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podman can run an msprime container without root privilege:
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```{code-block} bash
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$ podman run -it docker.io/tskit/msprime:<release> mspms 10 1 -T
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```
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### Singularity
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A docker image can also be converted to a Singularity container and
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then run without root privilege:
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```{code-block} bash
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$ singularity pull docker://tskit/msprime:<release> msprime-<release>.simg
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$ singularity exec msprime-<release>.simg mspms 10 1 -T
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```
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::::::{note}
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It is possible that your current environment may conflict with the environment in the singularity container.
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There are two workarounds:
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1. Ignore your home with the conflicting environment with `--contain` or `-H </new/path/to/home> -e`
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```{code-block} bash
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$ singularity shell --contain msprime-release-0.7.3.simg
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Singularity: Invoking an interactive shell within container...
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Singularity msprime-release-0.7.3.simg:~> python3
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Python 3.6.8 (default, Jan 14 2019, 11:02:34)
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[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
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Type "help", "copyright", "credits" or "license" for more information.
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>>> import msprime
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>>>
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```
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or use a different path as your home that does not have a conflicting environment
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```{code-block} bash
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$ singularity shell -H </new/path/to/home> -e msprime-release-0.7.3.simg
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Singularity: Invoking an interactive shell within container...
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Singularity msprime-release-0.7.3.simg:~/cnn_classify_demography> python3
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Python 3.6.8 (default, Jan 14 2019, 11:02:34)
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[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
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Type "help", "copyright", "credits" or "license" for more information.
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>>> import msprime
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>>>
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```
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2. In python get rid of your local path
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```{code-block} bash
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$ singularity shell msprime-release-0.7.3.simg
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Singularity: Invoking an interactive shell within container...
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Singularity msprime-release-0.7.3.simg:~> python3
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Python 3.6.8 (default, Jan 14 2019, 11:02:34)
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[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux
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Type "help", "copyright", "credits" or "license" for more information.
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>>> import sys
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>>> for _path in sys.path:
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... if ".local" in _path:
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... sys.path.remove(_path)
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...
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>>> import msprime
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>>>
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```
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::::::
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For more information on Singularity, see <https://www.sylabs.io/guides/3.6/user-guide/>
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