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Dev Log

2026-02-26 10:43:13 +0100

  • Ran: pip install -e .
  • Result: build isolation failed while installing build deps (no network), error: No matching distribution found for setuptools>=64.
  • Changes made earlier in this session:
    • Added pyproject.toml with build-system requirements (setuptools, wheel, Cython).
    • Updated setup.py:
      • Read version from PanPA/version.py without importing the package.
      • Fixed Python version message and python_requires.
      • Use requirements.txt for install_requires.
      • Use repo-root paths for README/requirements.

2026-02-26 10:43:31 +0100

  • Ran: PIP_NO_BUILD_ISOLATION=1 pip install -e .
  • Result: still attempted build dependency install and failed (no network), error: No matching distribution found for setuptools>=64.

2026-02-26 10:45:18 +0100

  • Ran: pip install -e . --no-build-isolation
  • Result: metadata generation failed; read_version() regex didn’t match.
  • Change: fixed version regex in setup.py to allow whitespace (single-escaped \s).

2026-02-26 10:45:56 +0100

  • Ran: pip install -e . --no-build-isolation
  • Result: Cython compile error in PanPA/_main.pyx (no suitable method found for a.replace).
  • Change: cast C++ string to Python bytes before .replace() in two loops.

2026-02-26 10:46:19 +0100

  • Ran: pip install -e . --no-build-isolation
  • Result: build succeeded, install failed due to sandbox permissions: Operation not permitted: '/Users/fawaz/.local/lib'.

2026-02-26 10:47:19 +0100

  • Ran (escalated): pip install -e . --no-build-isolation
  • Result: success. Editable install completed.

2026-02-26 10:53:36 +0100

  • Start: implement shipping generated C++ sources and optional Cython build; add --version CLI flag.

2026-02-26 10:54:19 +0100

  • Ran: cython -3 --cplus over PanPA/*.pyx
  • Result: Cython errors in graph_edit_distance.pyx and graph_smith_waterman.pyx (int vs double due to /).
  • Change: replaced / with // for integer division at those lines.

2026-02-26 10:54:51 +0100

  • Ran: cython -3 --cplus -o ... over PanPA/*.pyx after fixes.
  • Result: generated .cpp files (one warning about const qualifier in reverse_complement_fast.pyx).
  • Changes:
    • setup.py: optional Cython build; fall back to pre-generated .cpp sources when Cython isn't available.
    • MANIFEST.in: include .pyx/.cpp sources in sdist.
    • PanPA/main.py: add --version flag.

2026-02-26 10:55:10 +0100

  • Change: pyproject.toml build-system no longer requires Cython (since we ship generated .cpp).

2026-02-26 10:59:16 +0100

  • Fix for build error in reverse_complement_fast:
    • PanPA/reverse_complement_fast.pyx: make seq_pointer const char *.
    • Regenerated PanPA/reverse_complement_fast.cpp with Cython.

2026-02-26 10:59:34 +0100

  • Ran: pip install -e .
  • Result: build isolation failed (offline) while trying to install setuptools>=64.

2026-02-26 11:00:28 +0100

  • Fix: setup.py now passes relative source paths to Extension(...) to avoid absolute-path error during build.

2026-02-26 11:02:23 +0100

  • Ran (escalated): pip install -e . --no-build-isolation
  • Result: success.

2026-02-26 11:04:13 +0100

  • Added scripts/regen_cython.sh to regenerate .cpp from .pyx using Cython.
  • Set executable bit on scripts/regen_cython.sh.

2026-02-26 11:51:25 +0100

  • Updated docs in README.md to reflect Python 3.6–3.11 support, no Cython required for install, offline build-isolation note, and --version usage.
  • Updated environment.yml to current toolchain (python<=3.11, setuptools, wheel, pip, cython).

2026-02-26 11:53:46 +0100

  • Updated .gitignore to stop ignoring generated PanPA/*.cpp so they can be committed.

2026-02-26 11:57:19 +0100

  • Removed legacy PanPA/reverse_complement_fast.c to avoid confusion (we ship C++ now).
  • Updated .gitignore to ignore PanPA/reverse_complement_fast.c going forward.

2026-02-26 12:16:29 +0100

  • Updated Python upper bound to <3.14:
    • setup.py: version guard + python_requires.
    • README.md: support statement updated to 3.6–3.13.
    • environment.yml: python constraint to <3.14.

2026-02-26 12:19:27 +0100

  • setup.py: default to pre-generated .cpp sources; only use Cython when PANPA_USE_CYTHON=1.
  • This avoids Cython-generated absolute source paths breaking wheel builds.

2026-02-26 12:23:10 +0100

  • setup.py: resolve ROOT, use os.path.relpath for extension sources to guarantee relative paths in wheel builds.
  • Removed legacy tests_require to avoid setuptools warning.
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