Refactor code structure and update CI workflows

[js2264]

Refactor the code structure by organizing files into src/hicstuff and updating the pyproject.toml. Use rich-click for CLI. Remove branch restrictions in the CI workflow and adjust aligner parameters in tests. Enhance linting and fix pytest errors to improve code quality. Update Dockerfile dependencies and CI workflows for better integration with GitHub Container Registry.

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Pull request overview

Refactors the project into a modern src/-based Python package with a new rich-click CLI entrypoint, and updates packaging/CI/Docker to use pyproject.toml + uv + Ruff.

Changes:

• Migrate packaging from setup.py/requirements.txt to pyproject.toml (src/ layout) and add Ruff/pre-commit tooling.
• Replace the legacy docopt-based CLI with a rich-click-based CLI and update CLI tests accordingly.
• Revamp CI workflows (lint/test/publish) and Docker build/install flow to match the new packaging approach.

Reviewed changes

Copilot reviewed 42 out of 44 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
tests/test_pipeline.py	Updates pipeline tests and aligner parametrization.
tests/test_io.py	Test cleanup/formatting changes; fixes temp file closing calls.
tests/test_hicstuff.py	Import ordering/formatting changes and minor test adjustments.
tests/test_filter.py	Formatting/cleanup of filter tests.
tests/test_doctests.py	Minor import formatting.
tests/test_distance_law.py	Updates tests to new internal distance-law helper names and formatting.
tests/test_digest.py	Formatting and minor cleanup of digest tests.
tests/test_commands.py	Rewrites CLI tests to use click.testing.CliRunner against the new hicstuff.cli:cli.
src/hicstuff/view.py	Formatting/cleanup and fixes FASTA reordering logic to sort records properly.
src/hicstuff/stats.py	New stats module for parsing pipeline logs and emitting text/JSON summaries.
src/hicstuff/pipeline.py	Refactors imports/formatting and updates logging/IO patterns.
src/hicstuff/log.py	Minor import reordering/cleanup.
src/hicstuff/iteralign.py	Refactors/renames internal helpers and simplifies subprocess/logging code.
src/hicstuff/io.py	Refactors imports, improves error handling, and adjusts defaults for mutable args.
src/hicstuff/hicstuff.py	Refactors formatting and adjusts several utility implementations.
src/hicstuff/filter.py	Refactors formatting and narrows exception handling around plotting.
src/hicstuff/distance_law.py	Refactors formatting, makes several helpers “private”, and fixes NaN handling.
src/hicstuff/digest.py	Refactors formatting and improves error reporting on fragment ID/position inconsistencies.
src/hicstuff/cutsite.py	Refactors formatting and simplifies string building.
src/hicstuff/cli.py	New rich-click CLI implementation replacing legacy docopt entrypoint.
src/hicstuff/init.py	Adds runtime version discovery via importlib.metadata and updates author metadata.
setup.py	Removed legacy setuptools entrypoint/build configuration.
setup.cfg	Removed legacy wheel build config.
requirements.txt	Removed legacy dependency list in favor of pyproject.toml.
README.md	Updates docs to new CLI help output, install workflow (uv), and CI badge/workflows.
pyproject.toml	Adds PEP 621 project metadata, dependencies, scripts, Ruff/pytest/coverage configuration.
MANIFEST.in	Removed legacy manifest configuration.
Makefile	Removed legacy build/test helper targets.
hicstuff/version.py	Removed generated version file (version now resolved from package metadata).
hicstuff/stats.py	Removed legacy stats module (replaced by src/hicstuff/stats.py).
hicstuff/main.py	Removed docopt-based CLI entrypoint.
environment.yml	Removed conda env file (CI/Docker now install deps differently).
Dockerfile	Updates installation to use uv and installs system tools via micromamba.
doc/notebooks/demo_api.ipynb	Formatting and minor code snippet updates.
doc/conf.py	Removes legacy encoding header.
.pylintrc	Removed legacy pylint configuration (migrating to Ruff).
.pre-commit-config.yaml	Adds pre-commit hooks for Ruff + basic hygiene checks.
.github/workflows/pypi-publish.yml	Removed legacy Twine-based publish workflow.
.github/workflows/publish.yml	New publish workflow for PyPI (uv) + GHCR Docker builds.
.github/workflows/ci.yml	New CI workflow using Ruff + pytest across a Python version matrix.
.github/workflows/build.yml	Removed legacy micromamba-based CI workflow.
.appveyor.yml	Removed legacy Windows CI config.

Comments suppressed due to low confidence (6)

src/hicstuff/pipeline.py:246

• The mapped-read percentage calculation is off by a factor of 100 due to multiplying by 100 twice. This will log incorrect mapping rates (e.g., 5000% instead of 50%). Compute the percent once (e.g., 100 * mapped / total) and format it directly.
  src/hicstuff/io.py:151
• save_sparse_matrix() uses dtype is int to pick the integer format, but s_mat.dtype is typically a NumPy dtype (e.g., dtype('int64')), so this condition will almost always be false and integer matrices will be saved with float formatting. Use a NumPy-safe check (e.g., np.issubdtype(dtype, np.integer)) to select the integer format.
  src/hicstuff/hicstuff.py:1829
• corrcoef_sparse() currently ignores the B parameter: the vstack((A, B)) result is not assigned, so the correlation is always computed on A only. Also A.copy() is called without using the copy. Restore the previous behavior by assigning the stacked matrix to the variable used for downstream computations.
  src/hicstuff/hicstuff.py:2046
• split_matrix() calls len(chunk), but chunk from itertools.groupby() is an iterator, so len(chunk) raises TypeError at runtime. Convert the chunk to a list first (or consume it while counting) and use its length for slicing.
  src/hicstuff/hicstuff.py:1410
• max_intra_distance = max(len(contigs == u) ...) is incorrect: contigs == u produces a boolean array and len(...) returns the total length of contigs for every u, so max_intra_distance becomes n regardless of contig sizes. This breaks the intra/inter distance split logic; use a count of elements per contig (e.g., np.sum(contigs == u)).
  src/hicstuff/distance_law.py:917
• plot_ps_slope() builds a colormap iterator and advances it with next(cols), but the resulting color is never applied to the plotted lines. Either pass the extracted color into loglog/semilogx (so the rainbow mapping is used) or remove the unused iterator to avoid misleading dead code.

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