Merge remote-tracking branch 'upstream/main' into openeye-decorators

openforcefield · Nov 7, 2023 · a7b610b · a7b610b
2 parents 1fe98ec + 6050dba
commit a7b610b
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diff --git 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
+          micromamba info
+          micromamba list
 
       - name: Run Tests
         shell: bash -l {0}

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
   - id: check-yaml
   - id: debug-statements
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 23.9.1
   hooks:
   - id: black
     files: ^openff
@@ -17,7 +17,7 @@ repos:
   - id: isort
     files: ^openff
 - repo: https://github.com/PyCQA/flake8
-  rev: 6.0.0
+  rev: 6.1.0
   hooks:
   - id: flake8
     files: ^openff
diff --git 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/devtools/conda-envs/docs-env.yaml b/devtools/conda-envs/docs-env.yaml
@@ -21,7 +21,7 @@ dependencies:
   - openff-toolkit-base >=0.11.3
   - openff-forcefields
   - openff-interchange
-  - openff-qcsubmit ==0.5.0
+  - openff-qcsubmit <0.50
   - openmm >=7.6.0
 
     # Optional

diff --git a/devtools/conda-envs/no_openeye.yaml b/devtools/conda-envs/no_openeye.yaml
@@ -22,8 +22,15 @@ dependencies:
   - rdkit >=22
   - ambertools >=22
   - openff-utilities
+<<<<<<< HEAD
   - openff-toolkit-base
   - openff-qcsubmit ==0.5.0
+=======
+  - openff-toolkit-base >=0.11
+  - openff-forcefields
+  - openff-interchange
+  - openff-qcsubmit <0.50
+>>>>>>> upstream/main
   - openmm >=7.6.0
 
     # Optional

diff --git a/devtools/conda-envs/test-env.yaml b/devtools/conda-envs/test-env.yaml
@@ -22,9 +22,11 @@ dependencies:
   - click-option-group
   - rdkit
   - openff-utilities
-  - openff-toolkit-base
-  - openff-interchange-base
-  - openff-qcsubmit ==0.5.0
+  - openff-toolkit-base >=0.11
+  - openff-forcefields
+  - openff-interchange
+  - openff-units
+  - openff-qcsubmit <0.50
   - openmm >=7.6.0
 
     # Optional

diff --git 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 are some incompatibilities between the AmberTools and Psi4 conda packages on macOS, and it may not be 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
@@ -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 
 ```