Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Tell users to install the latest version of openfe #497

Merged
merged 6 commits into from
Jul 20, 2023
Merged

Tell users to install the latest version of openfe #497

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
5d76591
now we tell users to install the latest version of openfe
mikemhenry Jul 19, 2023
8a60e03
push a latest-apptainer tag
mikemhenry Jul 19, 2023
346be78
Add version for osx-arm64 too
mikemhenry Jul 19, 2023
ca6fae7
just need to update the URLs for curl
mikemhenry Jul 19, 2023
f28f3c1
updated urls for curl
mikemhenry Jul 19, 2023
4ead173
Merge branch 'main' into feat/add_version_to_docs
dwhswenson Jul 20, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions .github/workflows/docker.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -126,3 +126,4 @@ jobs:
singularity run ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif pytest --pyargs openfecli --pyargs openfe -v -n auto
echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
singularity push ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.latest-version.outputs.VERSION }}-apptainer
singularity push ../openfe_${{ steps.latest-version.outputs.VERSION }}.sif oras://${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest-apptainer
6 changes: 4 additions & 2 deletions docs/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@
#
import os
import sys
from importlib.metadata import version
from packaging.version import parse
sys.path.insert(0, os.path.abspath('../'))


Expand All @@ -22,7 +24,7 @@
project = 'OpenFE'
copyright = '2022, The OpenFE Development Team'
author = 'The OpenFE Development Team'

version = parse(version("openfe")).base_version
# -- General configuration ---------------------------------------------------

# Add any Sphinx extension module names here, as strings. They can be
Expand Down Expand Up @@ -101,4 +103,4 @@
html_static_path = ['_static']
html_css_files = [
'css/custom.css',
]
]
3 changes: 2 additions & 1 deletion docs/environment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,15 +4,16 @@ channels:
- https://conda.anaconda.org/conda-forge
dependencies:
- autodoc-pydantic
- openff-models>=0.0.5
- openff-toolkit >=0.13.0
- openff-units
- openmm
- packaging
- plugcli
- pydata-sphinx-theme
- python=3.9
- sphinx
- sphinx-click
- openff-models>=0.0.5
- tqdm
- pip:
- sphinx-design
Expand Down
39 changes: 26 additions & 13 deletions docs/installation.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -96,9 +96,11 @@ commands it suggests.
You should then close your current session and open a fresh login to ensure
that everything is properly registered.

Next we will create an environment called ``openfe_env`` with the ``openfe`` package and all required dependencies ::
Next we will create an environment called ``openfe_env`` with the ``openfe`` package and all required dependencies

$ mamba create -n openfe_env openfe
.. parsed-literal::

$ mamba create -n openfe_env openfe=\ |version|

Now we need to activate our new environment ::

Expand All @@ -109,9 +111,11 @@ Now we need to activate our new environment ::

Installing on newer Macs with Apple Silicon requires a creating an x86_64
environmment, as one of our requirements is not yet available for Apple
Silicon. Run the following modified commands::
Silicon. Run the following modified commands

.. parsed-literal::

CONDA_SUBDIR=osx-64 mamba create -n openfe_env openfe
CONDA_SUBDIR=osx-64 mamba create -n openfe_env openfe=\ |version|
mamba activate openfe_env
mamba env config vars set CONDA_SUBDIR=osx-64

Expand All @@ -135,18 +139,18 @@ Single file installers are available for x86_64 Linux and MacOS.
They are attached to our `releases on GitHub <https://github.com/OpenFreeEnergy/openfe/releases>`_ and can be downloaded with a browser or ``curl`` (or similar tool).
For example, the linux installer can be downloaded with ::

$ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/download/v0.7.4/OpenFEforge-0.7.4-Linux-x86_64.sh
$ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/latest/download/OpenFEforge-Linux-x86_64.sh

And the MacOS installer ::

$ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/download/v0.7.4/OpenFEforge-0.7.4-MacOSX-x86_64.sh
$ curl -LOJ https://github.com/OpenFreeEnergy/openfe/releases/latest/download/OpenFEforge-MacOSX-x86_64.sh

The single file installer contains all of the dependencies required for ``openfe`` and does not require internet access to use.
Both ``conda`` and ``mamba`` are also available in the environment created by the single file installer and can be used to install additional packages.
The installer can be installed in batch mode or interactively ::

$ chmod +x ./OpenFEforge-0.7.4-Linux-x86_64.sh # Make installer executable
$ ./OpenFEforge-0.7.4-Linux-x86_64.sh # Run the installer
$ chmod +x ./OpenFEforge-Linux-x86_64.sh # Make installer executable
$ ./OpenFEforge-Linux-x86_64.sh # Run the installer

Example installer output is shown below (click to expand "Installer Output")

Expand Down Expand Up @@ -334,16 +338,25 @@ Containers
We provide an official docker and apptainer (formally singularity) image.
The docker image is tagged with the version of ``openfe`` on the image and can be pulled with ::

$ docker pull ghcr.io/openfreeenergy/openfe:0.7.4
$ docker pull ghcr.io/openfreeenergy/openfe:latest

The apptainer image is pre-built and can be pulled with ::

$ singularity pull oras://ghcr.io/openfreeenergy/openfe:0.7.4-apptainer
$ singularity pull oras://ghcr.io/openfreeenergy/openfe:latest-apptainer

.. warning::

For production use, we recommend using version tags to prevent disruptions in workflows e.g.

.. parsed-literal::

$ docker pull ghcr.io/openfreeenergy/openfe:\ |version|
$ singularity pull oras://ghcr.io/openfreeenergy/openfe:\ |version|-apptainer

We recommend testing the container to ensure that it can access a GPU (if desired).
This can be done with the following command ::

$ singularity run --nv openfe_0.7.4-apptainer.sif python -m openmm.testInstallation
$ singularity run --nv openfe_latest-apptainer.sif python -m openmm.testInstallation

OpenMM Version: 8.0
Git Revision: a7800059645f4471f4b91c21e742fe5aa4513cda
Expand All @@ -367,11 +380,11 @@ Your output may produce different values for the forces, but should list the CUD

You can access the ``openfe`` CLI from the singularity image with ::

$ singularity run --nv openfe_0.7.4-apptainer.sif openfe --help
$ singularity run --nv openfe_latest-apptainer.sif openfe --help

To make sure everything is working, run the tests ::

$ singularity run --nv openfe_0.7.4-apptainer.sif pytest --pyargs openfe openfecli
$ singularity run --nv openfe_latest-apptainer.sif pytest --pyargs openfe openfecli

The test suite contains several hundred individual tests. This will take a
few minutes, and all tests should complete with status either passed,
Expand Down
Loading