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Test on MacOS and remove progress bar from example #159

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Test on MacOS and remove progress bar from example #159

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38d4665
Test on MacOS and remove progress bar from example
Yoshanuikabundi Nov 12, 2024
69abd32
Undo formatting changes
Yoshanuikabundi Nov 12, 2024
45e4de1
Disable progress bar in electric field example
Yoshanuikabundi Nov 12, 2024
17a88d2
Use macos-latest instead of macos-12
Yoshanuikabundi Nov 12, 2024
691ebff
conda -> micromamba in examples CI
Yoshanuikabundi Nov 12, 2024
2d183de
Update setup-micromamba to v2
Yoshanuikabundi Nov 12, 2024
75adaca
Remove defaults channel from examples environment
Yoshanuikabundi Nov 12, 2024
8870d78
try telling pytorch not to use mps
lilyminium Nov 12, 2024
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103 changes: 51 additions & 52 deletions .github/workflows/examples-ci.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -22,71 +22,70 @@ defaults:

env:
OE_LICENSE: ${{ github.workspace }}/oe_license.txt
PYTORCH_ENABLE_MPS_FALLBACK: 0

jobs:
example_tests:
name: Examples CI (${{ matrix.os }}, py-${{ matrix.python-version }}, rdkit=${{ matrix.include-rdkit }}, openeye=${{ matrix.include-openeye }}, dgl=${{ matrix.include-dgl }}), pydantic=${{ matrix.pydantic-version }}
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
python-version: ["3.11", "3.12"]
pydantic-version: ["2"]
include-rdkit: [true]
include-openeye: [false]
include-dgl: [true]

fail-fast: false
matrix:
os: [macOS-latest, ubuntu-latest]
python-version: ["3.11", "3.12"]
pydantic-version: ["2"]
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Sorry to be a bit of a nitpicker, but this could also go away (and below)

include-rdkit: [true]
include-openeye: [false]
include-dgl: [true]

steps:
- uses: actions/checkout@v4
- uses: actions/checkout@v4

- name: Build information
run: |
uname -a
df -h
ulimit -a

- name: Build information
run: |
uname -a
df -h
ulimit -a
- name: Install environment
uses: mamba-org/setup-micromamba@v2
with:
environment-file: devtools/conda-envs/examples_env.yaml
create-args: >-
python=${{ matrix.python-version }}
pydantic=${{ matrix.pydantic-version }}

- name: Install environment
uses: mamba-org/setup-micromamba@v1
with:
environment-file: devtools/conda-envs/examples_env.yaml
create-args: >-
python=${{ matrix.python-version }}
pydantic=${{ matrix.pydantic-version }}
- name: Install package
run: |
python -m pip install . --no-deps

- name: Install package
run: |
python -m pip install . --no-deps
- uses: ./.github/actions/include-openeye
if: matrix.include-openeye == true
with:
openeye-license-text: ${{ secrets.OE_LICENSE }}
openeye-license-file: ${{ env.OE_LICENSE }}

- uses: ./.github/actions/include-openeye
if: matrix.include-openeye == true
with:
openeye-license-text: ${{ secrets.OE_LICENSE }}
openeye-license-file: ${{ env.OE_LICENSE }}
- name: Uninstall OpenEye
if: matrix.include-openeye == false
run: micromamba remove --force openeye-toolkits --yes || echo "openeye not installed"


- name: Uninstall OpenEye
if: matrix.include-openeye == false
run: conda remove --force openeye-toolkits --yes || echo "openeye not installed"
- name: Uninstall RDKit
if: matrix.include-rdkit == false
run: micromamba remove --force rdkit --yes || echo "rdkit not installed"

- name: Uninstall RDKit
if: matrix.include-rdkit == false
run: conda remove --force rdkit --yes || echo "rdkit not installed"

- name: Python information
run: |
which python
conda info
conda list
- name: Python information
run: |
which python
micromamba info
micromamba list

- name: Check toolkit installations
shell: bash -l -c "python -u {0}"
run: |
from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}'
assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}'
- name: Check toolkit installations
shell: bash -l -c "python -u {0}"
run: |
from openff.toolkit.utils.toolkits import OPENEYE_AVAILABLE, RDKIT_AVAILABLE
assert str(OPENEYE_AVAILABLE).lower() == '${{ matrix.include-openeye }}'
assert str(RDKIT_AVAILABLE).lower() == '${{ matrix.include-rdkit }}'

- name: Run example notebooks
run: |
python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --nbval-cell-timeout=50000 --dist loadscope examples
- name: Run example notebooks
run: |
python -m pytest -r fE -v -x --tb=short -nauto --nbval-lax --dist loadscope examples
2 changes: 0 additions & 2 deletions devtools/conda-envs/examples_env.yaml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
name: openff-nagl-test
channels:
- conda-forge
- defaults
dependencies:
# Base depends
- python
Expand Down Expand Up @@ -42,7 +41,6 @@ dependencies:
# compatibility
- apsw >=3.42


# CI
- nbval
- pytest
Expand Down
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