Modernize packaging and project metadata (pyproject.toml, drop egg-info)

[bernalde]

Goal

Modernize packaging and project metadata so PharmaPy installs cleanly and follows current Python standards. Part of #3.

Problems today

• setup.py (PharmaPy/../setup.py): version='0.0.1' hardcoded, empty license and url, redundant py_modules=["PharmaPy"] alongside find_packages().
• No pyproject.toml (no PEP 517/518 build definition).
• Build artifacts committed to git: PharmaPy/PharmaPy.egg-info/ is tracked.
• requirements.txt is the only dependency source; no separation of runtime vs. test vs. docs deps; assimulo is a hard runtime dep (see Decouple the ODE/DAE solver behind an interface (assimulo optional, scipy fallback) #10, Relax dependency pins and enable Dependabot #9).
• No MANIFEST.in, so packaged sdists may omit data files (data/, test CSV/JSON).

Tasks

• Add pyproject.toml with [build-system] and [project] metadata (name, version, license, authors, URLs, requires-python).
• Move dependencies into [project.dependencies] and [project.optional-dependencies] (test, docs, simulation/assimulo as an extra).
• Remove PharmaPy.egg-info/ from version control and add to .gitignore.
• Add MANIFEST.in (or tool.setuptools.package-data) so data files ship in sdists/wheels.
• Real license (the repo has LICENSE.md) and project url.
• Consider dynamic/declarative versioning (single source of truth).

Acceptance criteria

• pip install -e . and python -m build both succeed and produce a wheel that imports.
• egg-info no longer tracked; git status clean after a build.
• Optional deps installable via pip install -e ".[test]", ".[docs]".

Reference

Reverted PR #106 included a pyproject.toml, setup.cfg, MANIFEST.in, and split requirements files at commit 599ffb3 — reuse selectively, keeping this PR packaging-only.

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Upstream PR

Wave 1 — isolated, high-acceptance. One focused upstream PR: pyproject.toml + remove committed egg-info + metadata. See #3.

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Reverted PR provenance

This issue is part of the selective re-introduction of useful infrastructure from the reverted upstream work:

• Implement CI/CD pipeline and enhance testing framework for PharmaPy #1 and Refactor codebase and enhance CI for quality checks #2: original fork-side CI/testing work.
• Implement CI/CD pipeline and enhance testing framework for PharmaPy CryPTSys/PharmaPy#106: upstream PR that bundled CI, packaging, tests, docs, and broad formatting.
• Revert "Implement CI/CD pipeline and enhance testing framework for PharmaPy" CryPTSys/PharmaPy#107: upstream revert of that bundled PR.

Implementation should stay small and reviewable, avoid repo-wide formatting, and preserve traceability through one focused PR per issue.