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need clarification on question about CLI
This commit is contained in:
David W.H. Swenson
2022-10-30 22:48:40 -05:00
committed by Richard Gowers
parent 48b802e0f1
commit 610ecdab2f
1 changed files with 14 additions and 11 deletions
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docs/installation.rst
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@@ -12,7 +12,7 @@ Installing ``openfe``
---------------------
When you install ``openfe`` through any of the methods described below, you
will install both the core library and the command line interface.
will install both the core library and the command line interface (CLI).
Installation with ``conda`` (recommended)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -23,15 +23,17 @@ OpenMM and ambertools, which are needed by ``openfe``.
Conda can be installed either with the `full Anaconda distribution
<https://www.anaconda.com/products/individual>`_, or with
the `smaller-footprint miniconda
<https://docs.conda.io/en/latest/miniconda.html>`_. We also recommend
`mamba
<https://mamba.readthedocs.io/en/latest/installation.html#installation>`_ as
a more perfomant variant of ``conda``.
<https://docs.conda.io/en/latest/miniconda.html>`_.
You can get ``openfe`` from the ``conda-forge`` channel. To install the most
recent release, use the command ::
recent release in its own environment, use the commands ::
$ conda install -c conda-forge openfe
$ conda create -n openfe -c conda-forge openfe
$ conda activate openfe
That creates a separate environment for ``openfe`` that won't interfere with
other things you have installed. You will need to activate the ``openfe``
environment before using it in a new shell.
With that, you should be ready to use ``openfe``!
@@ -84,7 +86,7 @@ optional packages.
* **perses tools**: To use perses, you need to install perses and OpenEye,
and you need a valid OpenEye license. To install both packages, use::
$ conda install -c conda-forge -c openeye perses openeye
$ conda install -c conda-forge -c openeye perses openeye-toolkits
Testing your installation
-------------------------
@@ -97,7 +99,8 @@ start to troubleshooting any installation problems. The test suite requires
Then you can run the test suite (from any directory) with the command::
$ py.test --pyargs openfe openfecli
$ pytest --pyargs openfe openfecli
The test suite contains several hundred individual tests. All should
complete with status either passed, skipped, or xfailed (expected fail).
The test suite contains several hundred individual tests. This will take a
few minutes, and all tests should complete with status either passed,
skipped, or xfailed (expected fail).