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‎.dockerignore

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# ignore the checkpoints directory
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checkpoints/
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# ignore the data directory
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data/
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# ignore the logs directory
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logs/
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# ignore the git directory
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.git
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# ignore generated YAML files
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scripts/nautilus/data_transfer_pod_pvc.yaml
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scripts/nautilus/gpu_job.yaml
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scripts/nautilus/hm_gpu_job.yaml
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scripts/nautilus/persistent_storage.yaml

‎.env.example

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# example of file for storing private and user specific environment variables, like keys or system paths
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# rename it to ".env" (excluded from version control by default)
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# .env is loaded by train.py automatically
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# hydra allows you to reference variables in .yaml configs with special syntax: ${oc.env:MY_VAR}
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MY_VAR="/home/user/my/system/path"

‎.github/PULL_REQUEST_TEMPLATE.md

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## What does this PR do?
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<!--
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Please include a summary of the change and which issue is fixed.
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Please also include relevant motivation and context.
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List any dependencies that are required for this change.
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List all the breaking changes introduced by this pull request.
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-->
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Fixes #\<issue_number>
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## Before submitting
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- [ ] Did you make sure **title is self-explanatory** and **the description concisely explains the PR**?
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- [ ] Did you make sure your **PR does only one thing**, instead of bundling different changes together?
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- [ ] Did you list all the **breaking changes** introduced by this pull request?
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## Did you have fun?
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Make sure you had fun coding 🙃

‎.github/workflows/code-quality-main.yaml

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# Same as `code-quality-pr.yaml` but triggered on commit to main branch
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# and runs on all files (instead of only the changed ones)
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name: Code Quality Main
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on:
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push:
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branches: [main]
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jobs:
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code-quality:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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- name: Run pre-commits
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uses: pre-commit/[email protected]

‎.github/workflows/code-quality-pr.yaml

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# This workflow finds which files were changed, prints them,
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# and runs `pre-commit` on those files.
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# Inspired by the sktime library:
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# https://github.com/alan-turing-institute/sktime/blob/main/.github/workflows/test.yml
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name: Code Quality PR
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on:
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pull_request:
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branches: [main, "release/*"]
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jobs:
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code-quality:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v2
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- name: Find modified files
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id: file_changes
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uses: trilom/[email protected]
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with:
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output: " "
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- name: List modified files
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run: echo '${{ steps.file_changes.outputs.files}}'
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- name: Run pre-commits
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uses: pre-commit/[email protected]
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with:
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extra_args: --files ${{ steps.file_changes.outputs.files}}

‎.github/workflows/test.yml

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name: Tests
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main, "release/*"]
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jobs:
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run_tests:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest", "macos-latest"]
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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timeout-minutes: 10
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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conda install -y -c conda-forge mamba
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mamba env create -f environment.yaml
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conda activate bio-diffusion
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python -m pip install --upgrade pip
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pip install -e .
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pip install pytest
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pip install sh
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- name: List dependencies
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run: |
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python -m pip list
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- name: Run pytest
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run: |
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pytest -v
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run_tests_windows:
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["windows-latest"]
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python-version: ["3.7", "3.8", "3.9", "3.10"]
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timeout-minutes: 10
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v3
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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conda install -y -c conda-forge mamba
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mamba env create -f environment.yaml
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conda activate bio-diffusion
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python -m pip install --upgrade pip
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pip install -e .
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pip install pytest
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- name: List dependencies
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run: |
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python -m pip list
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- name: Run pytest
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run: |
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pytest -v
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# upload code coverage report
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code-coverage:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v2
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- name: Set up Python 3.10
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uses: actions/setup-python@v2
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with:
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python-version: "3.10"
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- name: Install dependencies
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run: |
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conda install -y -c conda-forge mamba
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mamba env create -f environment.yaml
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conda activate bio-diffusion
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python -m pip install --upgrade pip
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pip install -e .
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pip install pytest
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pip install pytest-cov[toml]
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pip install sh
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- name: Run tests and collect coverage
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run: pytest --cov src # NEEDS TO BE UPDATED WHEN CHANGING THE NAME OF "src" FOLDER
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v3

‎.gitignore

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*.sage.py
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# Environments
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.env
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.venv
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env/
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venv/
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# Pyre type checker
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.pyre/
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### VisualStudioCode
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.vscode/*
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!.vscode/settings.json
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!.vscode/tasks.json
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!.vscode/launch.json
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!.vscode/extensions.json
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*.code-workspace
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**/.vscode
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# JetBrains
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.idea/
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# Data & Models
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*.h5
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*.tar
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*.tar.gz
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# Bio-Diffusion
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.env
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.autoenv
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.hydra
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*.dot
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*.pdf
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fit-perf_logs.txt
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*.sdf
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checkpoints/GEOM/*
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checkpoints/QM9/*
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configs/local/*.yaml
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scripts/*_grid_search_runs.json
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scripts/*_grid_search_scripts*/gpu_job_*.yaml
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scripts/*_grid_search_scripts*/train_*.bash
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scripts/*_grid_search_scripts*/*.out
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scripts/*_grid_search_scripts*/*.done
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scripts/local/*.bash
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scripts/nautilus/data_transfer_pod_pvc.yaml
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scripts/nautilus/gpu_job.yaml
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scripts/nautilus/hm_gpu_job.yaml
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scripts/nautilus/persistent_storage.yaml
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bio-diffusion/
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logs/
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data/EDM/GEOM
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data/EDM/QM9
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# NFS
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.nfs*
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# Git
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.git-credentials

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