Description

This PR updates installation guidance and packaging configuration to fix confusing/outdated instructions. These were the edits I performed locally to successfully install PharmaPy

Changes

• Updated setup.py
  • Removed py_modules=["PharmaPy"] so editable install resolves the package correctly.
  • Removed unused Extension import.
• Updated install_instructions.txt
  • Replaced deprecated python setup.py develop with pip install -e ..
  • Added -y for conda requirements install.
  • Corrected test instructions to run from tests/integration:
    • cd tests/integration
    • python reactor_tests.py
  • Added an explicit import smoke test:
    • python -c "import PharmaPy; print('PharmaPy import OK')"
• Updated .gitignore
  • Added common Python cache/build artifacts and local env/package metadata paths.

Motivation

• Previous install steps were outdated and could fail or confuse users.
• Packaging metadata conflicted with package discovery in editable installs.
• Test command path in instructions did not match repo layout.

Validation

• Created a clean conda env (pharma-py) and installed dependencies from requirements.txt.
• Installed PharmaPy in editable mode.
• Verified import works outside repo root.
• Ran integration test successfully from tests/integration (reactor_tests.py, 2 tests passing).