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* transfer less data to gpu * add rigid uitls * add graph model hparams * add hparams * add support for loading hparam override * add optional hparam override to finetune run config * set in memory=True as default for cath and fold classification datasets * add torch geometric compile * fix scenario where only seq_pos_enc is a node feature * refactor logging to use a single logging call * remove duplicated entry * minor linting * formatting * add pre-trained inverse folding config * add EGNN pretraining config * add find graph encoder hparams * add baseline inverse folding config * add linters to toml * add pre-commit config * Add porject support for py311 * Add cpu index url for torch for CI * add cpu torch source * rollback to max python 3.10 due to lack of torchdrug support * bump graphein to 1.7.4 for PyG 2.4+ support (and backwards compatibility * add warning log * add list to track processed files in case of overwrite * addmodel attribution script * update graphein version to 1.7.5+ and add captum dependency * add some more docstrings, clean up * add attribution to cli * update gitignore * add DDP support #44 * update readme * update readme * ignore igfold dataset in overwrite test * add IGFold prediction datasets * Add igfold datamodule * fix binary graph classification config * add cdconv model * fix test fixture * update docs * linting * linting * add full model config for finetuning * linting * fix device request logging * add multihot label encoder * speed up positional encoding computation * fix device logging * add num_classes to GO datasets * lint cdconv config * add multilabel classification task configs * refactor f1_max for multilabel classif. * add auprc to classification metrics, linting * linting * set in_memory=True as default for GO datasets * clean up EC dataset * clean up GO dataset * improve instantiation test * set ec to in memory * fix GO labelling * fix metrics memory leak * add ec_Reaction sweep * Ignore local Conda env in project directory * add missing mace ca_angles hparams * add addev config * A dataset loading script for antibody_developability.py * add esm BB config * Add ESM config for all feature schemes * add ppi prediction task updates * add ppi sweep config * Update test script for masif_dataset.py * Update path for masif_site in test script * mask additional attributes in PPI site prediction * resolve sequence tokenization * refactor chain identification * fix error in error fix * Fix fix of a fix * exclude erroneous examples * fix edge cases * fix edge cases * add model io utils * standardise default features for train and finetune configs #61 * refactor to new recommended jaxtyping/beartype syntax * typechecker refactor for esm * typechecker refactor for dataset base * lint * remove merge artifact from poetry.lock * fix beartype import * fix broken lock file * fix broken poetry.lock and update jaxtyping dependency * fix broken poetry.lock and update jaxtyping dependency * use mamba in test workflow * fix pyg wheel link for torch > 2.1.0 * update tests * lint * fix test * set dummy labels on example_batch * fix zenodo url * fix zenodo url * fix beartype import name * add changelog * add attribution to toc * Update install instructions to PyTorch 2.1.2+, and sync docs with README.md line-by-line * fix malformed HTML in quickstart components * minor fixes to docs --------- Co-authored-by: Arian Jamasb <[email protected]> Co-authored-by: Jamasb <[email protected]> Co-authored-by: Jamasb <[email protected]> Co-authored-by: Jamasb <[email protected]> Co-authored-by: Alex Morehead <[email protected]> Co-authored-by: Jamasb <[email protected]>
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@@ -19,16 +19,20 @@ jobs: | |
strategy: | ||
matrix: | ||
platform: [ubuntu-latest, macos-latest, windows-latest] | ||
python-version: [3.9, "3.10", 3.11] | ||
python-version: [3.9, "3.10"] | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- name: Checkout repository | ||
uses: actions/checkout@v3 | ||
- name: Set up Python ${{ matrix.python-version }} | ||
uses: actions/setup-python@v2.3.1 | ||
- name: Setup miniconda | ||
uses: conda-incubator/setup-miniconda@v2 | ||
with: | ||
auto-update-conda: true | ||
miniforge-variant: Mambaforge | ||
channels: "conda-forge, pytorch, pyg" | ||
python-version: ${{ matrix.python-version }} | ||
use-mamba: true | ||
- id: cache-dependencies | ||
name: Cache dependencies | ||
uses: actions/[email protected] | ||
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repos: | ||
- repo: https://github.com/pre-commit/pre-commit-hooks | ||
rev: v4.5.0 | ||
hooks: | ||
- id: trailing-whitespace | ||
- id: end-of-file-fixer | ||
- id: check-yaml | ||
- id: check-added-large-files | ||
- repo: https://github.com/ambv/black | ||
rev: 23.9.1 | ||
hooks: | ||
- id: black | ||
- repo: https://github.com/jsh9/pydoclint | ||
# pydoclint version. | ||
rev: 0.3.3 | ||
hooks: | ||
- id: pydoclint | ||
args: | ||
- "--config=pyproject.toml" | ||
- repo: https://github.com/astral-sh/ruff-pre-commit | ||
# Ruff version. | ||
rev: v0.1.1 | ||
hooks: | ||
- id: ruff | ||
args: [--fix, --exit-non-zero-on-fix] |
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protein_workshop.metrics | ||
------------------------- | ||
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Stay tuned! |
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