add contributing helper doc

CONTRIBUTING.md

@@ -0,0 +1,102 @@
+# Contributing to the BluePhos Pipeline Project
+
+Thank you for your interest in contributing to the BluePhos pipeline project! As a contributor, you’ll work from your fork of the main repository. This document outlines the steps to set up your development environment, guidelines for coding, and instructions for submitting contributions.
+
+## Repository Information
+
+- **Main Repository**: [BluePhos Main Repo](https://github.com/ssec-jhu/bluephos.git)
+
+## How to Fork the Repository
+
+1. **Go to the Repository on GitHub**:
+   - Open your web browser and navigate to the main repository you want to fork. For the BluePhos pipeline, the URL is [https://github.com/ssec-jhu/bluephos.git](https://github.com/ssec-jhu/bluephos.git).
+
+2. **Click the Fork Button**:
+   - In the upper-right corner of the repository page, you’ll see a button labeled **Fork**. Click it. 
+   - GitHub will ask you to select your GitHub account or organization where you want the fork to be created.
+
+3. **Wait for the Fork to Complete**:
+   - GitHub will create a copy of the repository under your account. This new repository is your fork, and you’ll be directed to the forked repository page (e.g., `https://github.com/your-username/bluephos`).
+
+4. **Clone Your Fork Locally**:
+   - Once your fork is created, you can clone it to your local machine to start working:
+   ```bash
+   git clone https://github.com/your-username/bluephos.git
+   cd bluephos
+   ```
+
+You now have your own copy (fork) of the repository where you can make changes independently from the main repository. When you’re ready to contribute back, you can create a pull request from your fork to the main repository.
+
+## Getting Started
+
+1. **Fork the Repository**: First, create a fork of the main repository in your own GitHub account. This will allow you to freely make changes without affecting the main repository.
+
+2. **Clone Your Fork**: Clone your fork to your local machine:
+   ```bash
+   git clone https://github.com/your-username/bluephos.git
+   cd bluephos
+   ```
+
+3. **Add the Main Repository as Upstream**: To keep your fork in sync with the latest updates from the main repo, add it as a second remote named `upstream`:
+   ```bash
+   git remote add upstream https://github.com/ssec-jhu/bluephos.git
+   ```
+
+4. **Create a Branch**: Create a new branch for each feature or bug fix:
+   ```bash
+   git checkout -b feature/your-feature-name
+   ```
+
+## Making Changes
+
+- **Coding Standards**: Follow PEP 8 for Python code. Use `tox -e format` to ensure code formatting aligns with the repository’s requirements.
+- **Testing**: Ensure your changes pass all tests. Include relevant tests for any new features you add.
+- **Documentation**: Update the documentation for any significant code changes. This includes comments, docstrings, and relevant updates to the `README.md`.
+
+## Keeping Your Fork Updated
+
+Regularly pull updates from the main repository to keep your fork in sync:
+```bash
+git fetch upstream
+git merge upstream/main
+```
+
+## Submitting a Pull Request
+
+When you’re ready to contribute your changes:
+
+1. **Commit Your Changes**: Write concise and descriptive commit messages.
+   ```bash
+   git add -u # Use 'git add .' if adding new files
+   git commit -m "Description of changes"
+   ```
+
+2. **Push to Your Fork**:
+   ```bash
+   git push origin feature/your-feature-name
+   ```
+
+3. **Open a Pull Request**:
+   - Go to your forked repository on GitHub.
+   - Click on **New Pull Request**.
+   - Ensure the base repository is `ssec-jhu/bluephos` and the base branch is `main`.
+   - Provide a title and description for your pull request.
+   - Submit the pull request for review.
+
+## Code Review Process
+
+Once you submit a pull request:
+- The maintainers will review your changes and may request modifications.
+- Please address any feedback and re-submit for review.
+
+## Issues and Support
+
+If you encounter issues or have questions, feel free to open an issue on GitHub. We’ll do our best to assist.
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the same open-source license as the project.
+
+---
+
+Thank you for your contributions to the BluePhos pipeline! We’re excited to work with you.

README.md

@@ -10,6 +10,7 @@
 
 BluePhos: An automated pipeline optimizing the synthesis and analysis of blue phosphorescent materials.
 
+
 # BluePhos Pipeline Introduction
 
 ### Overview
@@ -140,6 +141,9 @@ query_result = ddb.query('''SELECT * FROM '08ca147e-f618-11ee-b38f-eab1f408aca3-
 print(query_result.to_df())
 ```
 
+# Contributing
+
+We welcome contributions! Please see our [CONTRIBUTING.md](CONTRIBUTING.md) for guidelines on how to contribute to this project.
 
 
 

bluephos/bluephos_pipeline.py

@@ -1,23 +1,25 @@
 __doc__ = """"BluePhos Discovery Pipeline"""
 
 from pathlib import Path
-import pandas as pd
+
 import numpy as np
+import pandas as pd
 from dplutils import cli
 from dplutils.pipeline.ray import RayStreamGraphExecutor
-from bluephos.tasks.generateligandtable import GenerateLigandTableTask
-from bluephos.tasks.nn import NNTask
-from bluephos.tasks.optimizegeometries import OptimizeGeometriesTask
-from bluephos.tasks.smiles2sdf import Smiles2SDFTask
+
 from bluephos.tasks.dft import DFTTask
 from bluephos.tasks.filter_pipeline import (
+    FilterDFTInTask,
+    FilterDFTOutTask,
     FilterNNInTask,
     FilterNNOutTask,
     FilterXTBInTask,
     FilterXTBOutTask,
-    FilterDFTInTask,
-    FilterDFTOutTask,
 )
+from bluephos.tasks.generateligandtable import GenerateLigandTableTask
+from bluephos.tasks.nn import NNTask
+from bluephos.tasks.optimizegeometries import OptimizeGeometriesTask
+from bluephos.tasks.smiles2sdf import Smiles2SDFTask
 
 
 def ligand_pair_generator(halides_file, acids_file):

bluephos/modules/dft_calculators.py

@@ -1,8 +1,9 @@
+import logging
+import multiprocessing
 import os
 import subprocess
-import multiprocessing
-import logging
 from textwrap import dedent
+
 from bluephos.modules.dft_extract import extract
 
 # Constants

bluephos/modules/dft_extract.py

@@ -1,6 +1,8 @@
 import re
-import numpy as np
 from glob import iglob
+
+import numpy as np
+
 import bluephos.modules.log_config as log_config
 
 # Setup logging and get a logger instance

bluephos/tasks/dft.py

@@ -1,11 +1,13 @@
+import multiprocessing
 import os
 import tempfile
-import multiprocessing
+
 import pandas as pd
-import bluephos.modules.log_config as log_config
-from bluephos.modules.dft_calculators import OrcaCalculator, ASECalculator, remove_second_row
-from dplutils.pipeline import PipelineTask
 from dplutils import observer
+from dplutils.pipeline import PipelineTask
+
+import bluephos.modules.log_config as log_config
+from bluephos.modules.dft_calculators import ASECalculator, OrcaCalculator, remove_second_row
 
 # Setup logging and get a logger instance
 logger = log_config.setup_logging(__name__)

bluephos/tasks/generateligandtable.py

@@ -1,8 +1,9 @@
 import pandas as pd
-import bluephos.modules.log_config as log_config
 from dplutils.pipeline import PipelineTask
 from rdkit.Chem import AllChem, MolFromSmiles, MolToSmiles
 
+import bluephos.modules.log_config as log_config
+
 # Setup logging and get a logger instance
 logger = log_config.setup_logging(__name__)
 

bluephos/tasks/nn.py

@@ -1,13 +1,13 @@
 import pandas as pd
 import torch as t
 import torch.nn.functional as F
-import bluephos.modules.log_config as log_config
 from dplutils.pipeline import PipelineTask
 from torch.nn import Dropout, Linear
 from torch.nn.init import kaiming_normal_
 from torch_geometric.loader import DataLoader
 from torch_geometric.nn import GCN, Set2Set
 
+import bluephos.modules.log_config as log_config
 from bluephos.modules.sdf2feature import feature_create
 
 # Setup logging and get a logger instance

bluephos/tasks/optimizegeometries.py

@@ -1,12 +1,14 @@
-import bluephos.modules.log_config as log_config
 from time import sleep
+
 import pandas as pd
 from ase.calculators.calculator import InputError
-from dplutils.pipeline import PipelineTask
 from dplutils import observer
+from dplutils.pipeline import PipelineTask
 from rdkit import Chem
 from rdkit.Chem import AddHs, MolToXYZBlock
-from bluephos.modules.annotate_rdkit_with_ase import optimize_geometry, annotate_molecule_property
+
+import bluephos.modules.log_config as log_config
+from bluephos.modules.annotate_rdkit_with_ase import annotate_molecule_property, optimize_geometry
 from bluephos.modules.bond_length import bonds_maintained
 from bluephos.modules.isoctahedral import isoctahedral
 from bluephos.modules.octahedral_embed import octahedral_embed

bluephos/tasks/smiles2sdf.py

@@ -1,11 +1,12 @@
 from functools import reduce
+
 import pandas as pd
-import bluephos.modules.log_config as log_config
 from dplutils.pipeline import PipelineTask
 from rdkit import Chem
 from rdkit.Chem import AddHs, AllChem, MolFromSmiles
 from rdkit.Chem.rdmolops import CombineMols, Kekulize, SanitizeMol
 
+import bluephos.modules.log_config as log_config
 
 # Setup logging and get a logger instance
 logger = log_config.setup_logging(__name__)

tests/test_dft_task.py

@@ -1,8 +1,10 @@
 import os
-import pytest
-import pandas as pd
 from unittest.mock import patch
-from bluephos.tasks.dft import dft_run, remove_second_row, OrcaCalculator
+
+import pandas as pd
+import pytest
+
+from bluephos.tasks.dft import OrcaCalculator, dft_run, remove_second_row
 
 
 @pytest.fixture