Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Test on MacOS and remove progress bar from example #159

Open
wants to merge 8 commits into
base: main
Choose a base branch
from
Open

Test on MacOS and remove progress bar from example #159

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
8 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
102 changes: 50 additions & 52 deletions .github/workflows/examples-ci.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,65 +28,63 @@ jobs:
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-12, ubuntu-latest]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

macos-12 is being removed next month 😞

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Is macos-latest appropriate?

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Yeah I think so, it's no longer intel but AmberTools doesn't work on macOS-13. Thanks so much for looking at this!

python-version: ["3.11", "3.12"]
pydantic-version: ["2"]
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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@v1
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: conda 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: conda 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
conda info
conda 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
51 changes: 44 additions & 7 deletions examples/train-gnn-to-electric-field/train-gnn-to-electric-field.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -551,7 +551,13 @@
{
"cell_type": "markdown",
"id": "79cb1d56-3d70-4307-93f0-0d5956fdb32e",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"source": [
"### Training the model\n",
"\n",
Expand All @@ -562,7 +568,13 @@
"cell_type": "code",
"execution_count": 13,
"id": "5bfcbce1-8323-4403-a607-89292681375b",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [],
"source": [
"import pytorch_lightning as pl\n",
Expand All @@ -573,12 +585,18 @@
"cell_type": "code",
"execution_count": null,
"id": "c8cb0a08-eea6-41e4-9fd6-158204e26e79",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [],
"source": [
"trainer = pl.Trainer(\n",
" max_epochs=100,\n",
" callbacks=[TQDMProgressBar()], # add progress bar\n",
" # callbacks=[TQDMProgressBar()], # add progress bar\n",
" accelerator=\"cpu\"\n",
")"
]
Expand All @@ -587,7 +605,13 @@
"cell_type": "code",
"execution_count": null,
"id": "f8846142-77f2-4d60-a74e-c3bc3c3ed3ee",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [],
"source": [
"datamodule = training_model.create_data_module(verbose=False)"
Expand All @@ -597,7 +621,13 @@
"cell_type": "code",
"execution_count": 14,
"id": "4e0174d7-a57b-49d9-89a3-5c756adc0d8c",
"metadata": {},
"metadata": {
"editable": true,
"slideshow": {
"slide_type": ""
},
"tags": []
},
"outputs": [
{
"name": "stderr",
Expand Down Expand Up @@ -2154,7 +2184,14 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.4"
"version": "3.12.7"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
Expand Down
Loading