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Update test environments #467

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merged 5 commits into from
Sep 8, 2022
Merged

Update test environments #467

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9535daf
Update test environments
mattwthompson Aug 31, 2022
121f0df
Try constraining jobqueue
mattwthompson Aug 31, 2022
b4a73e6
Update for behavior changes in dask-jobqueue 0.8.0
mattwthompson Sep 8, 2022
03f18d3
Run `pre-commit autoupdate`
mattwthompson Sep 8, 2022
359b027
Switch to micromamba
mattwthompson Sep 8, 2022
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15 changes: 4 additions & 11 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,26 +39,19 @@ jobs:
- uses: actions/checkout@v3.0.2

- name: Setup Conda Environment
uses: conda-incubator/setup-miniconda@v2.1.1
uses: mamba-org/provision-with-micromamba@main
with:

python-version: ${{ matrix.python-version }}
environment-file: devtools/conda-envs/test_env.yaml

activate-environment: test

auto-update-conda: true
auto-activate-base: false

show-channel-urls: true
extra-specs: |
python=${{ matrix.python-version }}

- name: Install OpenEye
if: matrix.openeye
shell: bash -l {0}
run: |
echo "${SECRET_OE_LICENSE}" > ${OE_LICENSE}

conda install -c openeye openeye-toolkits
micromamba install -c openeye openeye-toolkits
python -c "from openeye import oechem; assert oechem.OEChemIsLicensed()"
env:
SECRET_OE_LICENSE: ${{ secrets.OE_LICENSE }}
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ ci:
autoupdate_schedule: "monthly"
repos:
- repo: https://github.com/psf/black
rev: 22.3.0
rev: 22.8.0
hooks:
- id: black
files: (^openff|^integration-tests)
Expand All @@ -12,7 +12,7 @@ repos:
- id: isort
files: (^openff|^integration-tests)
- repo: https://github.com/PyCQA/flake8
rev: 4.0.1
rev: 5.0.4
hooks:
- id: flake8
files: (^openff|^integration-tests)
13 changes: 2 additions & 11 deletions devtools/conda-envs/docs_env.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,5 @@
name: evaluator
channels:
- conda-forge/label/openff-toolkit_rc
- conda-forge/label/openff-interchange_rc
- conda-forge
dependencies:
# Base depends
Expand All @@ -10,25 +8,18 @@ dependencies:
- pip

# Standard dependencies
- openff-toolkit >=0.11.0rc3
- smirnoff99frosst
- numpy
- pandas
- openmm >=7.6
- networkx
- openff-toolkit >=0.11.0
- packmol
- pymbar >=3.0.5,<4.0.0
- mdtraj >=1.9.3
- dask >=2.7.0
- distributed >=2.7.0
- dask-jobqueue >=0.7.0
- dask-jobqueue >=0.7.0,<=0.8.0
- uncertainties
- openmmtools
- yank >=0.25.2
- pyyaml
- requests
- rdkit
- cmiles
- python-dateutil
- pydantic <2.0.0a0
- paprika
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16 changes: 3 additions & 13 deletions devtools/conda-envs/test_env.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
name: evaluator-test-env
channels:
- conda-forge/label/openff-toolkit_rc
- conda-forge/label/openff-interchange_rc
- jaimergp/label/unsupported-cudatoolkit-shim
- conda-forge
dependencies:
# Base depends
Expand All @@ -17,25 +16,16 @@ dependencies:
- coverage >=4.4

# Standard dependencies
- openff-toolkit >=0.11.0rc3
- smirnoff99frosst
- numpy
- pandas
- openmm >=7.6
- networkx
- packmol
- openff-toolkit >=0.11.0
- pymbar >=4.0.0
- mdtraj >=1.9.3
- dask >=2.7.0
- distributed >=2.7.0
- dask-jobqueue >=0.7.0
- dask-jobqueue >=0.8.0
- uncertainties
- openmmtools
- yank >=0.25.2
- pyyaml
- requests
- rdkit
- cmiles
- python-dateutil
- pydantic <2.0.0a0
- paprika
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4 changes: 2 additions & 2 deletions openff/evaluator/backends/dask.py
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Expand Up @@ -335,7 +335,7 @@ def _get_env_extra(self):
The extra commands to run.
"""
env_extra = dask.config.get(
f"jobqueue.{self._cluster_type}.env-extra", default=[]
f"jobqueue.{self._cluster_type}.job-script-prologue", default=[]
)

if self._setup_script_commands is not None:
Expand All @@ -353,7 +353,7 @@ def _get_job_extra(self):
The extra header options to add.
"""
job_extra = dask.config.get(
f"jobqueue.{self._cluster_type}.job-extra", default=[]
f"jobqueue.{self._cluster_type}.job-extra-directives", default=[]
)

if self._extra_script_options is not None:
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