From 4a9b62ac15aeec9aaacd8419f55813a0bb7d9e88 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 2 Sep 2025 11:16:23 -0500 Subject: [PATCH 1/4] Fix linting workflow --- devtools/conda-envs/lint_env.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/devtools/conda-envs/lint_env.yml b/devtools/conda-envs/lint_env.yml index 1e904d4b2..e71b20d6d 100644 --- a/devtools/conda-envs/lint_env.yml +++ b/devtools/conda-envs/lint_env.yml @@ -16,7 +16,7 @@ dependencies: - nbformat # Code example deps - openmm - - openff-toolkit-base + - openff-toolkit-base >=0.17 - openff-interchange-base - ambertools - rdkit From 667a0e8ddcf79e36437d040125f7039abf83cb1e Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 2 Sep 2025 11:28:10 -0500 Subject: [PATCH 2/4] Avoid broken Amber link --- source/install.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/install.md b/source/install.md index d0ca4f411..80442dcdd 100644 --- a/source/install.md +++ b/source/install.md @@ -273,6 +273,6 @@ Note that this will affect how Conda behaves with other environments. All OpenFF software is written in pure Python code and can be expected to function long as the relevant dependencies can be installed. As of Q3 2024, some users have reported issues with versions of AmberTools on certain Intel-based macOS platforms. OpenFF tools, for use cases that require it, work as long as the AmberTools installation functions. For those with access to Apple Silicon hardware, we recommend using the native architecture (Apple Silicon/ARM/`osx-arm64`). -Note that AmberTools can also be built locally from its own release tarball according to the [instructions Amber's website](https://ambermd.org/GetAmber.php#ambertools). +Note that AmberTools can also be built locally from its own release tarball according to instructions Amber's website. Note also that many OpenFF use cases only require AmberTools for its AM1-BCC partial charge assignment; for users with [OpenEye Licenses](https://docs.eyesopen.com/applications/common/license.html), OpenEye Toolkits' OEChem module can be used instead. From 7a177dc73c737e05b98f7ebed8c9e9e652fd8c9b Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Tue, 2 Sep 2025 11:31:48 -0500 Subject: [PATCH 3/4] Update env --- devtools/conda-envs/lint_env.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/devtools/conda-envs/lint_env.yml b/devtools/conda-envs/lint_env.yml index e71b20d6d..397f34068 100644 --- a/devtools/conda-envs/lint_env.yml +++ b/devtools/conda-envs/lint_env.yml @@ -16,8 +16,9 @@ dependencies: - nbformat # Code example deps - openmm - - openff-toolkit-base >=0.17 + - openff-toolkit-base - openff-interchange-base + - openff-nagl-models - ambertools - rdkit From 615a2ae868ecdd4fbccaaa9cbf90bca9b04796f1 Mon Sep 17 00:00:00 2001 From: Matt Thompson Date: Wed, 3 Sep 2025 00:21:40 -0500 Subject: [PATCH 4/4] Update source/install.md Co-authored-by: Josh A. Mitchell --- source/install.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/install.md b/source/install.md index 80442dcdd..3e3534582 100644 --- a/source/install.md +++ b/source/install.md @@ -273,6 +273,6 @@ Note that this will affect how Conda behaves with other environments. All OpenFF software is written in pure Python code and can be expected to function long as the relevant dependencies can be installed. As of Q3 2024, some users have reported issues with versions of AmberTools on certain Intel-based macOS platforms. OpenFF tools, for use cases that require it, work as long as the AmberTools installation functions. For those with access to Apple Silicon hardware, we recommend using the native architecture (Apple Silicon/ARM/`osx-arm64`). -Note that AmberTools can also be built locally from its own release tarball according to instructions Amber's website. +Note that AmberTools can also be built locally from its own release tarball according to instructions on Amber's website. Note also that many OpenFF use cases only require AmberTools for its AM1-BCC partial charge assignment; for users with [OpenEye Licenses](https://docs.eyesopen.com/applications/common/license.html), OpenEye Toolkits' OEChem module can be used instead.