Merge pull request #1 from AltinLab/rewrite

Reformat repo for readability

Author: ljwoods2

.dvc/.gitignore

@@ -0,0 +1,2 @@
+/config.local
+/cache

.dvc/config

@@ -0,0 +1,4 @@
+[core]
+    remote = origin
+['remote "origin"']
+    url = /tgen_labs/altin/dvc/tcrtrifold-experiments/

.dvcignore

@@ -0,0 +1,4 @@
+# Add patterns of files dvc should ignore, which could improve
+# the performance. Learn more at
+# https://dvc.org/doc/user-guide/dvcignore
+**/inference

.github/copilot-instructions.md

@@ -0,0 +1,26 @@
+This is a Python and Nextflow repository for predicting whether TCRs (T-cell receptors) bind to p:MHCs (peptide:MHC complexes) using AlphaFold3. Please follow these guidelines when contributing:
+
+## Code Standards
+
+### Required Before Each Commit
+- Run `black .` from the cloned project root (using the `tcrtrifold-experiments` conda environment) before committing any changes to ensure proper code formatting
+- This will run black on all Python files to maintain consistent style
+
+### Development Flow
+- Test: `./scripts/test/<script_name>.sh`
+
+## Repository Structure
+- `data/`: Parquet files, AF3 inference outputs, and other data associated with triads (TCRs in complex with p:MHCs) and p:MHC complexes alone, organized on a per-dataset basis.
+- `envs/`: Conda environments for different purposes in this repo. `env_runner.yaml` is the primary package code containing the package described by 'pyproject.toml' and its dependencies, often used by nextflow pipelines kicked off using the `nf-core` environment.
+- `notebooks/`: Jupyter notebooks for analyzing results and making figures
+- `results/`: Persistent storage for outputs of jupyter notebooks
+- `scripts/`: Primary entrypoint for interacting with this repo. Contains slurm scripts (which should be run as bash scripts in the runner environment) that kick off the nextflow pipelines.
+- `src/tcrtrifold/`: The python package code used by the pipelines in this repo, organized using the "src" layout.
+- `workflows/`: Nextflow pipelines and their associated Python scripts for running AlphaFold3, formatting data, and extracting features.
+
+## Key Guidelines
+1. Follow Python best practices and idiomatic patterns
+2. Use Numpy-style docstrings for Python methods and classes
+3. Maintain existing code structure and organization
+4. If issues are ambiguous, ask clarifying questions before attempting to solve them
+5. While other datasets are present in this repo, `data/test` is the dataset intended to be used by the runner environment. Pipelines should be written in a way that works on test data but is generic enough to be run on other datasets.

.github/workflows/copilot-setup-steps.yml

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+name: "Copilot Setup Steps"
+
+# Automatically run the setup steps when they are changed to allow for easy validation, and
+# allow manual testing through the repository's "Actions" tab
+on:
+  workflow_dispatch:
+  push:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+  pull_request:
+    paths:
+      - .github/workflows/copilot-setup-steps.yml
+
+jobs:
+
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      # More info on options: https://github.com/conda-incubator/setup-miniconda
+      - name: Install conda dependencies for main env
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+            activate-environment: ""
+            auto-activate-base: true
+            show-channel-urls: true
+            auto-update-conda: true
+            conda-remove-defaults: true
+
+      - name: Create all conda envs
+        shell: bash -l {0}
+        run: |
+          conda env create -f envs/env_runner.yaml
+          conda env create -f envs/nf-core.yaml

.gitignore

@@ -111,12 +111,15 @@ ENV/
 # poetry
 poetry.lock
 
-
 # AF3 inference
 **/inference
 **/.nextflow
 **/*.log*
-# notebooks
-**/.ipynb
+
 # scratch
-tmp/
+tmp
+
+# data
+data/*
+!data/test
+!data/*.dvc

data/cresta.dvc

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+outs:
+- md5: 2db2e84f3866767c326302937466581d.dir
+  size: 2654157
+  nfiles: 12
+  hash: md5
+  path: cresta