From f336a3c65c422bab6e08a19c45e904e758d27e09 Mon Sep 17 00:00:00 2001 From: "Matthew W. Thompson" Date: Thu, 5 Oct 2023 07:11:50 -0500 Subject: [PATCH] Do not recommend conda in docs --- .github/workflows/CI.yaml | 4 ++-- CONTRIBUTING.md | 2 +- docs/getting-started/installation.md | 3 +-- docs/getting-started/quick-start.md | 6 +++--- openff/bespokefit/workflows/bespoke.py | 2 +- 5 files changed, 8 insertions(+), 9 deletions(-) diff --git a/.github/workflows/CI.yaml b/.github/workflows/CI.yaml index 1206d57d..3b64d32c 100644 --- a/.github/workflows/CI.yaml +++ b/.github/workflows/CI.yaml @@ -63,8 +63,8 @@ jobs: - name: Conda Environment Information shell: bash -l {0} run: | - conda info - conda list + mamba info + mamba list - name: Run Tests shell: bash -l {0} diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index af4a5a90..2bff58ec 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -13,7 +13,7 @@ git clone https://github.com/openforcefield/openff-bespokefit.git cd openff-bespokefit mamba env create --file devtools/conda-envs/test-env.yaml --name bespokefit-dev mamba env update --file devtools/conda-envs/docs-env.yaml --name bespokefit-dev -conda activate bespokefit-dev +mamba activate bespokefit-dev pip install -e . ``` diff --git a/docs/getting-started/installation.md b/docs/getting-started/installation.md index 4edafd68..a9b5957d 100644 --- a/docs/getting-started/installation.md +++ b/docs/getting-started/installation.md @@ -53,8 +53,7 @@ mamba install -c psi4 -c conda-forge -c defaults psi4 [Psi4]: https://psicode.org/ :::{warning} -There is an incompatibility between the AmberTools and Psi4 conda packages on Mac, and it is not possible to -create a working conda environment containing both. +There is an incompatibility between the AmberTools and Psi4 conda packages on macOS, and it is not possible to create a working conda environment containing both. ::: :::{note} diff --git a/docs/getting-started/quick-start.md b/docs/getting-started/quick-start.md index ee2f981e..15197282 100644 --- a/docs/getting-started/quick-start.md +++ b/docs/getting-started/quick-start.md @@ -12,12 +12,12 @@ field parameters trained to accurately capture the important features and phenom It produces bespoke torsion parameters that have been trained to capture as closely as possible the torsion profiles of the rotatable bonds in the target molecule, which collectively have a large impact on conformational preferences. -The recommended way to install `openff-bespokefit` is via the `conda` package manager. There are several optional +The recommended way to install `openff-bespokefit` is via the `mamba` package manager. There are several optional dependencies, and a good starting environment is: ```shell -conda create -n bespokefit -y -c conda-forge mamba python=3.9 -conda activate bespokefit +mamba create -n bespokefit -y -c conda-forge mamba python=3.9 +mamba activate bespokefit mamba install -y -c conda-forge openff-bespokefit xtb-python ambertools ``` diff --git a/openff/bespokefit/workflows/bespoke.py b/openff/bespokefit/workflows/bespoke.py index e99eb0ed..aaac55a3 100644 --- a/openff/bespokefit/workflows/bespoke.py +++ b/openff/bespokefit/workflows/bespoke.py @@ -76,7 +76,7 @@ class BespokeWorkflowFactory(ClassBase): initial_force_field: str = Field( "openff_unconstrained-2.0.0.offxml", description="The name of the unconstrained force field to use as a starting " - "point for optimization. The force field must be conda installed.", + "point for optimization. The force field must be installed with conda/mamba.", ) optimizer: Union[str, OptimizerSchema] = Field(