Constava Analyze module in parallel processes and extra changes

.gitignore

@@ -61,3 +61,6 @@ build/
 conformine_training_dataset/
 constava/data/*.pkl
 datagen/
+
+# Python
+__pycache__

CITATION.cff

@@ -0,0 +1,47 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Bickel"
+  given-names: "David"
+  orcid: "https://orcid.org/0000-0001-6431-3442"
+- family-names: "Gavalda-Garcia"
+  given-names: "Jose"
+  orcid: "https://orcid.org/0000-0003-0332-8338"
+- family-names: "Díaz"
+  given-names: "Adrián"
+  orcid: "https://orcid.org/0000-0003-0165-1318"
+title: "Bio2Byte/constava"
+version: 1.1.0
+doi: 10.5281/zenodo.12699038
+date-released: 2024-07-09
+url: "https://github.com/Bio2Byte/constava"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Gavalda-Garcia"
+    given-names: "Jose"
+    orcid: "https://orcid.org/0000-0001-6431-3442"
+  - family-names: "Bickel"
+    given-names: "David"
+    orcid: "https://orcid.org/0000-0003-0332-8338"
+  - family-names: "Roca-Martinez"
+    given-names: "Joel"
+    orcid: "https://orcid.org/0000-0002-4313-3845"
+  - family-names: "Raimondi"
+    given-names: "Daniele"
+    orcid: "https://orcid.org/0000-0003-1157-1899"
+  - family-names: "Orlando"
+    given-names: "Gabriele"
+    orcid: "https://orcid.org/0000-0002-5935-5258"
+  - family-names: "Vranken"
+    given-names: "Wim"
+    orcid: "https://orcid.org/0000-0001-7470-4324"
+  doi: "10.1093/nargab/lqae082"
+  journal: "NAR Genomics and Bioinformatics"
+  month: 7
+  start: lqae082
+  end: lqae082
+  title: "Data-driven probabilistic definition of the low energy conformational states of protein residues"
+  issue: 3
+  volume: 6
+  year: 2024

CODE_OF_CONDUCT.md

@@ -0,0 +1,14 @@
+# Code of Conduct
+
+**We pledge to make our Constava community welcoming, safe, and equitable for all.**
+
+## Expected standards
+
+We agree to behave mindfully toward each other and act in ways that center 
+our shared values, including:
+
+1. Respecting the **purpose of our community**, our activities, and our ways of gathering.
+2. Engaging **kindly and honestly** with others.
+3. Respecting **different viewpoints** and experiences.
+4. **Taking responsibility** for our actions and contributions.
+5. Gracefully giving and accepting **constructive feedback**.

CONTRIBUTING.md

@@ -0,0 +1,80 @@
+# Contributing to Constava
+
+Contributions of all kinds are welcome: bug reports, documentation improvements, feature requests, and code changes.
+
+Please read the guidelines below to make the contribution process smooth for everyone.
+
+---
+
+## How to Contribute
+
+### Reporting Bugs
+
+If you find a bug, please open an issue and include:
+- A clear and descriptive title
+- Steps to reproduce the issue
+- Expected and actual behavior
+- Your environment (OS, Python version, Constava version)
+
+If possible, include a minimal example or traceback.
+
+### Suggesting Enhancements
+
+Feature requests and improvements are welcome.  
+When opening an issue, try to explain:
+- The problem you are trying to solve
+- Why the current behavior is insufficient
+- Any alternative solutions you have considered
+
+### Development Setup
+
+1. Fork the repository and clone your fork.
+2. Create a virtual environment.
+3. Install dependencies:
+   ```bash
+   pip install -r requirements.txt
+   pip install -e .
+   ```
+
+4.	Run the test suite to ensure everything works:
+    ```bash
+    constava test
+    ```
+
+### Making Changes
+
+1. Create a new branch for your changes.
+1. Keep commits focused and atomic.
+1. Write or update tests when changing behavior.
+1. Update documentation if your change affects public APIs or CLI usage.
+
+
+### Code Style
+
+1. Follow standard Python conventions (PEP 8).
+1. Keep code readable and well-documented.
+1. Avoid unnecessary complexity; clarity beats cleverness.
+
+### Testing
+
+All changes should pass the test suite before submission:
+
+```bash
+constava test
+```
+
+Pull requests that break tests will not be merged.
+
+
+### Submitting a Pull Request
+
+1. Open a pull request against the default branch.
+1. Clearly describe what the PR does and why it is needed.
+1. Link related issues where applicable.
+1. Be prepared to revise your PR based on review feedback.
+
+
+## Code of Conduct
+
+This project follows a Code of Conduct.
+By participating, you are expected to uphold it in all interactions.

MANIFEST.in

@@ -1,2 +1,31 @@
-include constava/data/*
-include requirements.txt
+recursive-include constava/internal-data *
+
+include requirements.txt
+include LICENSE
+include authors.md
+include CITATION.cff
+include CONTRIBUTING.md
+include CODE_OF_CONDUCT.md
+
+global-exclude .DS_Store
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude __pycache__
+global-exclude *.log
+global-exclude *.tmp
+global-exclude *.swp
+global-exclude *.bak
+global-exclude *.orig
+
+global-exclude *.egg-info
+global-exclude .pytest_cache
+global-exclude .coverage
+global-exclude htmlcov
+global-exclude .ruff_cache
+global-exclude .mypy_cache
+global-exclude .tox
+
+global-exclude dist
+global-exclude build
+global-exclude .idea
+global-exclude .vscode

Makefile

@@ -3,13 +3,15 @@ PACKAGE_NAME = constava
 .PHONY: build install uninstall publish clean
 
 build:
-	python3 setup.py sdist bdist_wheel
+# 	python3 setup.py sdist bdist_wheel
+	python3 -m build
 
 install:
-	pip install dist/$(PACKAGE_NAME)-*.tar.gz
+	python3 -m pip install dist/$(PACKAGE_NAME)-*.tar.gz
 
+.PHONY: test
 test:
-	python -m $(PACKAGE_NAME) test
+	constava test
 
 uninstall:
 	-pip uninstall -y $(PACKAGE_NAME)
@@ -18,4 +20,4 @@ publish:
 	twine upload dist/*
 
 clean:
-	rm -rf dist build $(PACKAGE_NAME).egg-info
+	rm -rf dist build $(PACKAGE_NAME).egg-info