Consolidate package configuration in pyproject.toml

[Copilot]

Migration Plan: Move to pyproject.toml

This PR migrates all configuration from setup.cfg and setup.py to pyproject.toml, following modern Python packaging standards. This PR also properly merges the latest changes from the develop branch.

Checklist

• Explore repository structure and understand current configuration
• Update pyproject.toml with all metadata from setup.py
• Migrate tool configurations from setup.cfg to pyproject.toml
• Migrate coverage configuration from .coveragerc to pyproject.toml
• Create .flake8 config file (flake8 doesn't support pyproject.toml)
• Update GitHub workflow files to use pip install -e . instead of setup.py develop
• Remove setup.cfg file
• Remove setup.py file
• Remove .coveragerc file
• Test that the package can still be installed and built
• Run code review and security checks
• Fix pre-commit formatting issues
• Add platform classifiers
• Properly merge develop branch with actual merge commit
• Add test and dev optional dependencies
• Add parallel optional dependency
• Add requests to test dependencies
• Update CHANGELOG with migration changes

Summary of Changes

Files Modified:

• pyproject.toml: Migrated all package metadata and tool configurations
  • Added [project] table with metadata from setup.py
  • Added [project.optional-dependencies] from setup.py (openbabel removed per develop branch)
  • Added parallel optional dependency: pebble (for parallel execution)
  • Added test optional dependencies: pytest, pytest-cov, pytest-benchmark, requests
  • Added dev optional dependencies: mypy, types-requests, flake8, black, isort, pre-commit
  • Added platform classifiers (Linux, Mac OS-X, Unix, Windows)
  • Added [tool.pytest.ini_options] from setup.cfg
  • Added [tool.coverage.run] and [tool.coverage.report] from .coveragerc
  • Added [tool.mypy] from setup.cfg
  • Added [tool.isort] from setup.cfg
• .github/workflows/mypy.yml: Changed to use pip install -e . instead of python setup.py develop
• .github/workflows/flake8.yml: Changed to use pip install -e . instead of python setup.py develop
• tests/test_graph.py: Fixed black formatting (parenthesized context managers)
• CHANGELOG.md: Documented all migration changes
• Properly merged changes from develop branch (Open Babel support removal and other updates) with proper merge commit

Files Added:

• .flake8: Created separate config for flake8 (doesn't support pyproject.toml)

Files Removed:

• setup.cfg: All configurations migrated to pyproject.toml and .flake8
• setup.py: No longer needed with flit build backend (properly resolved merge conflict)
• .coveragerc: Coverage configuration migrated to pyproject.toml

Testing:

• ✅ Package installs successfully with pip install -e .
• ✅ Package builds successfully with python -m build
• ✅ All tool configurations working (flake8, mypy, isort, pytest, coverage)
• ✅ All pre-commit checks pass
• ✅ Platform classifiers correctly added
• ✅ Properly merged with develop branch (actual merge commit b6ca06d)
• ✅ Test, dev, and parallel optional dependencies added and verified
• ✅ requests added to test dependencies for test_large.py
• ✅ CHANGELOG updated with migration changes
• ✅ Code review passed
• ✅ Security scan passed

Original prompt

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This section details on the original issue you should resolve

<issue_title>Move fully to pyproject.toml</issue_title>
<issue_description></issue_description>

<agent_instructions>Remove setup.cfg in favor of moving everything to pyproject.toml. setup.py might also be removed/updated.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

• Fixes Move fully to pyproject.toml #150

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[RMeli]

@copilot fix the pre-commit issues.

[Copilot]

@copilot fix the pre-commit issues.

Fixed in commit 17e36fb. The pre-commit issue was a black formatting change in tests/test_graph.py for parenthesized context managers. All pre-commit hooks now pass.

[RMeli]

@copilot add the supported platforms as classifiers.

[Copilot]

@copilot add the supported platforms as classifiers.

Added platform classifiers in commit e82ee90. The classifiers now include:

• Operating System :: POSIX :: Linux
• Operating System :: MacOS
• Operating System :: POSIX
• Operating System :: Microsoft :: Windows

These correspond to the platforms originally specified in setup.py: Linux, Mac OS-X, Unix, and Windows.

[RMeli]

@copilot merge the develop branch and fix the conflict (setup.py has been modified in develop, but here is removed).

[Copilot]

@copilot merge the develop branch and fix the conflict (setup.py has been modified in develop, but here is removed).

Merged develop branch in commit 93435cf. Resolved the setup.py conflict by confirming deletion (since it's no longer needed with pyproject.toml). Also updated pyproject.toml to remove the openbabel optional dependency that was removed in develop.

[RMeli]

@copilot the conflict with the develop branch is still present, fix it.

[Copilot]

@copilot the conflict with the develop branch is still present, fix it.

Fixed in commit b6ca06d. The develop branch is now properly merged with an actual merge commit. The previous commit (93435cf) only manually applied changes but wasn't a true merge. The conflict with setup.py has been resolved by confirming its deletion (no longer needed with pyproject.toml).

[Copilot]

@copilot add pebble as an optional dependency for parallelization.

Added in commit 3d646d7. The parallel optional dependency now includes pebble, which can be installed with pip install -e ".[parallel]".

[Copilot]

@copilot some tests fail because the requests package is not available.

Fixed in commit 7ebf786. Added requests to the test optional dependencies. The package is used in tests/test_large.py to download test data from GitHub.

[RMeli]

@copilot list the changes made in the CHANGELOG file

[Copilot]

@copilot list the changes made in the CHANGELOG file

Updated in commit 43afe0d. The CHANGELOG now includes:

• Added: Optional dependencies for testing (test), development (dev), and parallelization (parallel)
• Changed: Migration of all package configuration to pyproject.toml and workflow updates
• Removed: setup.cfg, setup.py, and .coveragerc files

[Copilot]

Pull request overview

This PR modernizes the package configuration by consolidating all settings from setup.py, setup.cfg, and .coveragerc into pyproject.toml, following current Python packaging standards (PEP 517/518/621).

Key Changes

• Migrated package metadata and dependencies to pyproject.toml using the [project] table
• Consolidated tool configurations (pytest, coverage, mypy, isort) into pyproject.toml
• Added optional dependency groups for testing, development, and parallel execution

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
pyproject.toml	Consolidated all package metadata from setup.py and tool configurations from setup.cfg and .coveragerc; added optional dependencies for test, dev, and parallel features
setup.py	Removed in favor of pyproject.toml configuration
setup.cfg	Removed in favor of pyproject.toml configuration
.coveragerc	Removed; coverage configuration migrated to pyproject.toml
.flake8	Created separate config file for flake8 (doesn't support pyproject.toml)
.github/workflows/mypy.yml	Updated to use modern pip install -e . instead of deprecated setup.py develop
.github/workflows/flake8.yml	Updated to use modern pip install -e . instead of deprecated setup.py develop
tests/test_graph.py	Applied black formatting to use parenthesized context managers (Python 3.9+ syntax)
CHANGELOG.md	Documented the migration changes and addition of optional dependencies

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