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Add GitHub Actions workflow for testing and deployment #2

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@kasinadhsarma kasinadhsarma commented Oct 30, 2024 •
edited by coderabbitai bot
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Add detailed project description, setup instructions, contribution guidelines, and usage of OpenMM and PDB for protein development to README.md.

Add GitHub Actions workflow for CI/CD in .github/workflows/main.yml.

  • Define jobs for setting up the environment, installing dependencies, linting, and running tests.

Add data preprocessing module in src/data_preprocessing.py.

  • Implement functions for cleaning, normalizing, transforming, and preprocessing protein data.
  • Include functions for parsing PDB files and creating simulations.

Add model training module in src/model_training.py.

  • Implement functions for building, training, and evaluating a 3D model for protein folding.

Add NLP processing module in src/nlp_processing.py.

  • Implement functions for cleaning, tokenizing, removing stopwords, and embedding text.

Add virtual screening module in src/virtual_screening.py.

  • Implement functions for selecting, docking, and scoring potential drug compounds.

Add main script in src/main.py.

  • Integrate data preprocessing, model training, NLP processing, and virtual screening.

Add unit tests for data preprocessing, model training, NLP processing, and virtual screening in tests/.

For more details, open the Copilot Workspace session.

Summary by CodeRabbit

Release Notes

  • New Features

    • Introduced a continuous integration (CI) workflow for automated testing and code quality checks.
    • Enhanced the README with project descriptions, setup instructions, and contribution guidelines.
    • Added functionality for data preprocessing, model training, natural language processing, and virtual screening of drug compounds.

  • Bug Fixes

    • Implemented tests to validate data preprocessing, model training, NLP processing, and virtual screening functionalities.

  • Documentation

    • Expanded README to include detailed usage information and guidelines for contributors.

  • Tests

    • Added comprehensive test suites for data preprocessing, model training, NLP processing, and virtual screening.

@kasinadhsarma
Add GitHub Actions workflow for testing and deployment
93e3a2f 
Add detailed project description, setup instructions, contribution guidelines, and usage of OpenMM and PDB for protein development to `README.md`.

Add GitHub Actions workflow for CI/CD in `.github/workflows/main.yml`.
* Define jobs for setting up the environment, installing dependencies, linting, and running tests.

Add data preprocessing module in `src/data_preprocessing.py`.
* Implement functions for cleaning, normalizing, transforming, and preprocessing protein data.
* Include functions for parsing PDB files and creating simulations.

Add model training module in `src/model_training.py`.
* Implement functions for building, training, and evaluating a 3D model for protein folding.

Add NLP processing module in `src/nlp_processing.py`.
* Implement functions for cleaning, tokenizing, removing stopwords, and embedding text.

Add virtual screening module in `src/virtual_screening.py`.
* Implement functions for selecting, docking, and scoring potential drug compounds.

Add main script in `src/main.py`.
* Integrate data preprocessing, model training, NLP processing, and virtual screening.

Add unit tests for data preprocessing, model training, NLP processing, and virtual screening in `tests/`.

---

For more details, open the [Copilot Workspace session](https://copilot-workspace.githubnext.com/VishwamAI/ProtienFlex?shareId=XXXX-XXXX-XXXX-XXXX).
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coderabbitai bot commented Oct 30, 2024 •
edited
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Walkthrough

The changes introduce a new continuous integration (CI) workflow in GitHub Actions and several new Python modules for processing protein data, model training, natural language processing, and virtual screening. The README.md file has been significantly updated to provide comprehensive project details, setup instructions, and contribution guidelines. New test suites have been added to validate the functionalities of the newly introduced modules, ensuring robustness and correctness in data preprocessing, model training, NLP tasks, and virtual screening.

Changes

File Change Summary
.github/workflows/main.yml New GitHub Actions CI workflow added, defining a build job with steps for code checkout, Python setup, dependency installation, linting, and testing.
README.md Significant updates including project description, goals, setup instructions, contribution guidelines, and usage information for OpenMM and PDB.
src/data_preprocessing.py New file added with functions for cleaning, normalizing, transforming protein data, and handling PDB files.
src/main.py New main function added to orchestrate protein data processing, model training, and virtual screening.
src/model_training.py New file added with functions for building, training, and evaluating a 3D convolutional neural network model.
src/nlp_processing.py New file added with functions for text cleaning, tokenization, stopword removal, and embedding generation.
src/virtual_screening.py New file added with functions for virtual screening of drug compounds using molecular docking techniques.
tests/test_data_preprocessing.py New test suite added to validate data preprocessing functions.
tests/test_model_training.py New test suite added to validate model training functionalities.
tests/test_nlp_processing.py New test suite added to validate NLP processing functions.
tests/test_virtual_screening.py New test suite added to validate virtual screening functionalities.

Poem

🐰 In the meadow where proteins play,
New workflows spring up every day.
With tests to check and docs so bright,
Our code now dances in the light!
Hopping forward, we cheer and say,
"Onward, dear project, lead the way!" 🌼

Note

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@kasinadhsarma
Remove unused imports and add blank lines before function definitions
81078a8 
* **src/data_preprocessing.py**
  - Remove unused import 'pandas as pd'
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines

* **src/model_training.py**
  - Remove unused import 'numpy as np'
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines

* **src/nlp_processing.py**
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines
  - Import 'stopwords' and 'np'

* **src/virtual_screening.py**
  - Remove unused imports from 'rdkit'
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines

* **src/main.py**
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines
  - Import 'Chem' and 'Descriptors' from 'rdkit'

* **tests/test_data_preprocessing.py**
  - Add two blank lines before each function definition
  - Shorten lines longer than 79 characters

* **tests/test_model_training.py**
  - Add two blank lines before each function definition
  - Shorten lines longer than 79 characters

* **tests/test_nlp_processing.py**
  - Add two blank lines before each function definition
  - Shorten lines longer than 79 characters
  - Fix invalid escape sequences
  - Import 'stopwords' and 'np'

* **tests/test_virtual_screening.py**
  - Add two blank lines before each function definition
  - Remove trailing whitespace from lines
  - Shorten lines longer than 79 characters
@kasinadhsarma
Remove unused imports and add blank lines before function definitions
7ea0448 
* **src/data_preprocessing.py**
  - Remove unused import 'pandas as pd'
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines

* **src/model_training.py**
  - Remove unused import 'numpy as np'
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines

* **src/nlp_processing.py**
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines
  - Import 'stopwords' and 'np'

* **src/virtual_screening.py**
  - Remove unused imports from 'rdkit'
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines

* **src/main.py**
  - Add two blank lines before each function definition
  - Remove trailing whitespace from blank lines
  - Import 'Chem' and 'Descriptors' from 'rdkit'

* **tests/test_data_preprocessing.py**
  - Add two blank lines before each function definition
  - Shorten lines longer than 79 characters

* **tests/test_model_training.py**
  - Add two blank lines before each function definition
  - Shorten lines longer than 79 characters

* **tests/test_nlp_processing.py**
  - Add two blank lines before each function definition
  - Shorten lines longer than 79 characters
  - Fix invalid escape sequences
  - Import 'stopwords' and 'np'

* **tests/test_virtual_screening.py**
  - Add two blank lines before each function definition
  - Remove trailing whitespace from lines
  - Shorten lines longer than 79 characters
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