From 2790e72382831268a8a0be0d4e05419516eaa332 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 16:05:03 -0700 Subject: [PATCH 1/5] bump rc releases to v1.7.0 --- abfe_tutorial/abfe_tutorial.ipynb | 2 +- ahfe_tutorial/ahfe_tutorial.ipynb | 2 +- openmm_septop/septop_tutorial.ipynb | 2 +- .../PlottingFreeEnergiesUsingCinnabar.ipynb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/abfe_tutorial/abfe_tutorial.ipynb b/abfe_tutorial/abfe_tutorial.ipynb index ec866bd..f75972b 100644 --- a/abfe_tutorial/abfe_tutorial.ipynb +++ b/abfe_tutorial/abfe_tutorial.ipynb @@ -47,7 +47,7 @@ "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " !pip install -q condacolab\n", " import condacolab\n", - " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0a0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")" ] }, { diff --git a/ahfe_tutorial/ahfe_tutorial.ipynb b/ahfe_tutorial/ahfe_tutorial.ipynb index d5af938..29086c7 100644 --- a/ahfe_tutorial/ahfe_tutorial.ipynb +++ b/ahfe_tutorial/ahfe_tutorial.ipynb @@ -47,7 +47,7 @@ "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " !pip install -q condacolab\n", " import condacolab\n", - " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")" ] }, { diff --git a/openmm_septop/septop_tutorial.ipynb b/openmm_septop/septop_tutorial.ipynb index 5fa0dbc..653cf6d 100644 --- a/openmm_septop/septop_tutorial.ipynb +++ b/openmm_septop/septop_tutorial.ipynb @@ -49,7 +49,7 @@ "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " !pip install -q condacolab\n", " import condacolab\n", - " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0a0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")" ] }, { diff --git a/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb b/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb index 0ade1da..22ced8b 100644 --- a/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb +++ b/plotting_rbfes_with_cinnabar/PlottingFreeEnergiesUsingCinnabar.ipynb @@ -33,7 +33,7 @@ "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " !pip install -q condacolab\n", " import condacolab\n", - " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/ExampleNotebooks/releases/download/april-2025/OpenFEforge-1.5.0.dev0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")" ] }, { From 9399bb4e795285d0c3624578c30e2c1e494ff311 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 16:09:30 -0700 Subject: [PATCH 2/5] bump CI to use python 3.12 --- .github/workflows/CI.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 0669a21..f76042e 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -29,10 +29,8 @@ jobs: strategy: fail-fast: false matrix: - # Note: we temporarily pin to macos-12 to avoid compatibility issues - # between AT22+ and macos-13+ runners os: ["ubuntu-latest", "macos-latest"] - python-version: ["3.10"] + python-version: ["3.12"] steps: - uses: actions/checkout@v2.4.0 From d098e679aa6deda982420666cfc6a17767c2231e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 16:12:35 -0700 Subject: [PATCH 3/5] update README --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4d455ae..5b8947e 100644 --- a/README.md +++ b/README.md @@ -6,9 +6,9 @@ # OpenFE Notebooks Collection of notebooks for the Open FreeEnergy project. -These can be ran in the browser via the Binder links. +These can be run in the browser via the Colab links. -| Binder link | Description | +| Colab link | Description | | --- | --- | | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/OpenFreeEnergy/ExampleNotebooks/blob/main/showcase/openfe_showcase.ipynb) | Start here. This notebook demonstrates how a free energy calculation can be defined, executed and analyzed using the `openfe` package. | From a4754b494ff12a8b3a8cfc233f4064822a31a653 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 16:39:36 -0700 Subject: [PATCH 4/5] bump binder env version for testing --- .binder/environment.yml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.binder/environment.yml b/.binder/environment.yml index 9ed9164..5580eb1 100644 --- a/.binder/environment.yml +++ b/.binder/environment.yml @@ -1,6 +1,5 @@ name: openfe-notebooks channels: - - jaimergp/label/unsupported-cudatoolkit-shim - conda-forge dependencies: - MDAnalysis @@ -27,6 +26,6 @@ dependencies: - python - rdkit - typing_extensions - - gufe>=1.4.1 - - openfe~=1.2 + - gufe>=1.7.0 + - openfe>=1.7.0 - py3dmol From 691c04ba87f06f7718572b4e617f8946c21aeb61 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 23 Oct 2025 17:17:41 -0700 Subject: [PATCH 5/5] updates to t4lysozyme rbfe example --- openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb b/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb index 489d6d2..5cd47fd 100644 --- a/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb +++ b/openmm_rbfe/OpenFE_showcase_1_RBFE_of_T4lysozyme.ipynb @@ -44,7 +44,7 @@ "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " !pip install -q condacolab\n", " import condacolab\n", - " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.0.0/OpenFEforge-1.0.0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.7.0/OpenFEforge-1.7.0-Linux-x86_64.sh\")" ] }, { @@ -885,6 +885,7 @@ "\n", "rbfe_settings.simulation_settings.equilibration_length = 10 * unit.picosecond\n", "rbfe_settings.simulation_settings.production_length = 50 * unit.picosecond\n", + "rbfe_settings.engine_settings.gpu_device_index = None # default is to require CUDA, None allows for falling back to OpenCL or CPU\n", "\n", "pprint(rbfe_settings.simulation_settings.dict())" ]