From aae7ae06b709372e16ccb018dd037ebd8ca3ce42 Mon Sep 17 00:00:00 2001 From: Jerome Kelleher Date: Thu, 5 Feb 2026 14:36:31 +0000 Subject: [PATCH] Remove unmaintained docker definition Remove unmaintained container instructions --- containers/docker-minimal | 12 ---- docs/development.md | 20 ------- docs/installation.md | 113 +------------------------------------- 3 files changed, 1 insertion(+), 144 deletions(-) delete mode 100644 containers/docker-minimal diff --git a/containers/docker-minimal b/containers/docker-minimal deleted file mode 100644 index 2e8d258c4..000000000 --- a/containers/docker-minimal +++ /dev/null @@ -1,12 +0,0 @@ -#maintainer Ariella Gladstein -#organization tskit-dev -#application "Msprime: a population genetics simulator of ancestry and DNA sequence evolution" - -# TODO change this to a minimal Python image -FROM jupyter/scipy-notebook:latest - -# Set the working directory to /app -WORKDIR /app - -# Install latest msprime release -RUN pip install --pre msprime diff --git a/docs/development.md b/docs/development.md index aa568b6b9..28d1aefae 100644 --- a/docs/development.md +++ b/docs/development.md @@ -795,26 +795,6 @@ Note the following tips: - There is a script: `benchmarks/check_asv.sh` that can be used to benchmark recent commits. -## Containerization - -To run msprime in a container, see the -{ref}`installation instructions `. - -You can use `docker` to locally build an image, but it requires root access: - -```{code-block} bash - -$ sudo docker build -t tskit/msprime . - -``` - -[podman]() can build and run images without root privilege. - -```{code-block} bash - -$ podman build -t tskit/msprime . - -``` ## Troubleshooting - If `make` is giving you strange errors, or if tests are failing for diff --git a/docs/installation.md b/docs/installation.md index 91c79659a..e0e24f716 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -2,12 +2,10 @@ # Installation -There are three options for installing `msprime`: +There are two main options for installing `msprime`: 1. {ref}`sec_installation_conda`: the recommended options for most users 2. {ref}`sec_installation_pip`: more flexibility and control for advanced users -3. {ref}`sec_installation_container`: to use - `msprime` inside an extremely isolated environment (sec_installation_conda)= @@ -233,112 +231,3 @@ With GSL installed, install from source by doing: python3 -m pip install msprime --no-binary msprime ``` -(sec_installation_container)= - -## Via Container - -An [open container]() image (aka docker image) is built on -[Dockerhub]() for each release of -msprime. Each image is [tagged]() -with the corresponding release. For example, for msprime release 0.7.5, the -corresponding image tag is `tskit/msprime:0.7.5`. - -To run a container, you can use [docker](), -[Singularity](), -[podman]() or similar tools supporting docker images. - -### docker - -`docker` requires root privilege to run a container: - -```{code-block} bash - -$ sudo docker run -it tskit/msprime: mspms 10 1 -T - -``` - -### podman - -podman can run an msprime container without root privilege: - -```{code-block} bash - -$ podman run -it docker.io/tskit/msprime: mspms 10 1 -T - -``` - -### Singularity - -A docker image can also be converted to a Singularity container and -then run without root privilege: - -```{code-block} bash - -$ singularity pull docker://tskit/msprime: msprime-.simg -$ singularity exec msprime-.simg mspms 10 1 -T - -``` - -::::::{note} - -It is possible that your current environment may conflict with the environment in the singularity container. -There are two workarounds: - -1. Ignore your home with the conflicting environment with `--contain` or `-H -e` - -```{code-block} bash - -$ singularity shell --contain msprime-release-0.7.3.simg -Singularity: Invoking an interactive shell within container... - -Singularity msprime-release-0.7.3.simg:~> python3 -Python 3.6.8 (default, Jan 14 2019, 11:02:34) -[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux -Type "help", "copyright", "credits" or "license" for more information. ->>> import msprime ->>> - -``` - -or use a different path as your home that does not have a conflicting environment - -```{code-block} bash - -$ singularity shell -H -e msprime-release-0.7.3.simg -Singularity: Invoking an interactive shell within container... - -Singularity msprime-release-0.7.3.simg:~/cnn_classify_demography> python3 -Python 3.6.8 (default, Jan 14 2019, 11:02:34) -[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux -Type "help", "copyright", "credits" or "license" for more information. ->>> import msprime ->>> - -``` - -2. In python get rid of your local path - -```{code-block} bash - -$ singularity shell msprime-release-0.7.3.simg -Singularity: Invoking an interactive shell within container... - -Singularity msprime-release-0.7.3.simg:~> python3 -Python 3.6.8 (default, Jan 14 2019, 11:02:34) -[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]] on linux -Type "help", "copyright", "credits" or "license" for more information. ->>> import sys ->>> for _path in sys.path: -... if ".local" in _path: -... sys.path.remove(_path) -... ->>> import msprime ->>> - -``` - -:::::: - -For more information on Singularity, see - -