From 16cec5d2d4f51b9832228cbbe3588e358fdd87b1 Mon Sep 17 00:00:00 2001 From: "Kevin R. Thornton" Date: Mon, 3 Apr 2023 08:58:21 -0700 Subject: [PATCH] Fixes to docs on user environments. (#1149) Closes #1148 --- doc/pages/userenv.md | 54 +------------------------------------------- 1 file changed, 1 insertion(+), 53 deletions(-) diff --git a/doc/pages/userenv.md b/doc/pages/userenv.md index 5b6ef3d990..44f4cd0da8 100644 --- a/doc/pages/userenv.md +++ b/doc/pages/userenv.md @@ -10,7 +10,7 @@ mkdir ~/venvs python3 -m venv ~/venvs/fwdpy11 source activate ~/venvs/fwdpy11/bin/activate python -m pip install --upgrade pip -pip install fwpdy11 +python -m pip install fwpdy11 ``` :::{note} @@ -64,55 +64,3 @@ channels: ``` ::: - -### Working in "environments" - -:::{note} - -The stability of conda installation into environments is a moving target. -We will try to keep this up to date. - -::: - -Many users prefer to set up different environments for different projects. -Doing so requires some care. -Currently, `conda-forge`, the channel from which `bioconda` pulls dependencies, builds for Python versions not supported by `bioconda`. -Thus, building an environment like this will often lead to failure: - -```{code-block} bash - -conda create -n myenv -y - -``` - -The problem here is that installing dependencies that are *not* from `bioconda` is likely to pull in Python 3.9, leaving you unable to install `bioconda` packages. -(Currently, `bioconda` only supports up to Python 3.8.) - -Unfortunately, creating a new environment based on Python 3.8 will also lead to failure: - -```{code-block} bash - -conda create -n myenv python=3.8 -y - -``` - -The problem here is that the Python 3.8 build will be upgraded compared to what came with `miniconda`. -For reasons that we are unable to understand, this upgrade leads to run-time problems in some instances. - -Thus, the safest thing to do is to clone your `base`: - -```{code-block} bash - -conda create -n myenv --clone base - -``` - -Now, `myenv` is an exact copy of `base`, and you can `conda install fwdpy11` successfully. -This solution is safest if you never install anything into `base`, leaving it as it was when you installed `miniconda`. - -:::{warning} - -When working in environments, never `conda update`! -Updating is likely to do *bad things* to dependencies that you won't notice until you run something. - -:::