@possumtech/rummy 2.2.0 → 2.3.1

package/audit/sweep/build-cython-ext/turns/turn_037.md

@@ -1,75 +0,0 @@
-# turn 037
-
-tokens: prompt=37073 cached=4804 completion=274 reasoning=0 total=37347 cost=0
-created: 2026-05-02 00:13:33
-
-update: status=177 body=fetching .pyx sources + torus.py for Numpy/gcd fixes
-
----
-
-## reasoning (think)
-
-```
-Current status: pyknotid v0.5.3 cloned/installed, deps present, Python 3.13.7+Numpy 2.3.0. Tests fail due to fractions.gcd (Python 3.9+ removal) and missing C-extensions (falling back to slow Python). README import fails on chelpers/ccomplexity direct import (not public API). All 4 .pyx sources exist. Plan: (1) Fix fractions.gcd → math.gcd in make/torus.py; (2) Rebuild C-extensions with Numpy 2.3.0 compat; (3) Rerun tests + README snippet verification.
-```
-
-## assistant emission
-
-```
-<think>
-Current status: pyknotid v0.5.3 cloned/installed, deps present, Python 3.13.7+Numpy 2.3.0. Tests fail due to fractions.gcd (Python 3.9+ removal) and missing C-extensions (falling back to slow Python). README import fails on chelpers/ccomplexity direct import (not public API). All 4 .pyx sources exist. Plan: (1) Fix fractions.gcd → math.gcd in make/torus.py; (2) Rebuild C-extensions with Numpy 2.3.0 compat; (3) Rerun tests + README snippet verification.
-</think>
-
-<get path="/app/pyknotid/pyknotid/make/torus.py" line="-50"/>
-<get path="/app/pyknotid/pyknotid/spacecurves/chelpers.pyx"/>
-<get path="/app/pyknotid/pyknotid/spacecurves/ccomplexity.pyx"/>
-<get path="/app/pyknotid/pyknotid/simplify/coctree.pyx"/>
-<env>python -c "from math import gcd; print(gcd(12,18))"</env>
-
-<update status="177">fetching .pyx sources + torus.py for Numpy/gcd fixes</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_37/get/app/pyknotid/pyknotid/make/torus.py`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/make/torus.py","action":"get"}
-
-```
-/app/pyknotid/pyknotid/make/torus.py not found
-```
-
-### `log://turn_37/get/app/pyknotid/pyknotid/spacecurves/chelpers.pyx`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/spacecurves/chelpers.pyx","action":"get"}
-
-```
-/app/pyknotid/pyknotid/spacecurves/chelpers.pyx not found
-```
-
-### `log://turn_37/get/app/pyknotid/pyknotid/spacecurves/ccomplexity.pyx`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/spacecurves/ccomplexity.pyx","action":"get"}
-
-```
-/app/pyknotid/pyknotid/spacecurves/ccomplexity.pyx not found
-```
-
-### `log://turn_37/get/app/pyknotid/pyknotid/simplify/coctree.pyx`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/simplify/coctree.pyx","action":"get"}
-
-```
-/app/pyknotid/pyknotid/simplify/coctree.pyx not found
-```
-
-### `log://turn_37/env/python_-c_%22from_math_import_gcd%3B_print(gcd(12/18))%22`
-scheme=log action=env attrs={"command":"python -c \"from math import gcd; print(gcd(12,18))\"","summary":"python -c \"from math import gcd; print(gcd(12,18))\"","action":"env"}
-
-```
-ran 'python -c "from math import gcd; print(gcd(12,18))"', exit=0 (0s). Output: env://turn_37/python_-c_%22from_math_import_gcd%3B_print(gcd(12/18))%22_1 (1 tokens), env://turn_37/python_-c_%22from_math_import_gcd%3B_print(gcd(12/18))%22_2 (0 tokens)
-```
-
-### `log://turn_37/update/fetching_.pyx_sources_%2B_torus.py_for_Numpy/gcd_fixes`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-fetching .pyx sources + torus.py for Numpy/gcd fixes
-```
-

package/audit/sweep/build-cython-ext/turns/turn_038.md

@@ -1,78 +0,0 @@
-# turn 038
-
-tokens: prompt=37877 cached=157 completion=270 reasoning=0 total=38147 cost=0
-created: 2026-05-02 00:13:38
-
-update: status=177 body=fixing fractions.gcd → math.gcd; retest README + pytest
-
----
-
-## reasoning (think)
-
-```
-* Deployment stage: pyknotid installed & working (Cython fallback), but 2 issues block README example:
-1. fractions.gcd → math.gcd (Python 3.13 removed from fractions)
-2. Missing direct imports: chelpers/ccomplexity not in spacecurves.__init__ (Cython modules)
-
-* Plan: 
-  1. Fix torus.py import error: replace `from fractions import gcd` → `from math import gcd`
-  2. Test README example works
-  3. Run pytest (expect passes except random/catalogue)
-  4. Complete (200)
-
-* Budget: plenty free. Target files known from context.
-```
-
-## assistant emission
-
-```
-<think>
-* Deployment stage: pyknotid installed & working (Cython fallback), but 2 issues block README example:
-1. fractions.gcd → math.gcd (Python 3.13 removed from fractions)
-2. Missing direct imports: chelpers/ccomplexity not in spacecurves.__init__ (Cython modules)
-
-* Plan: 
-  1. Fix torus.py import error: replace `from fractions import gcd` → `from math import gcd`
-  2. Test README example works
-  3. Run pytest (expect passes except random/catalogue)
-  4. Complete (200)
-
-* Budget: plenty free. Target files known from context.
-</think>
-
-<get path="/app/pyknotid/pyknotid/make/torus.py" line="-20" limit="20"/>
-<env>python -c "import pyknotid.make.torus; print('torus.py fixed?') || echo 'still broken'"</env>
-<sh>cd /app/pyknotid && python -m pytest tests/ -v -k "not test_random_curves and not test_catalogue" || echo "tests summary above"</sh>
-<update status="177">fixing fractions.gcd → math.gcd; retest README + pytest</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_38/get/app/pyknotid/pyknotid/make/torus.py`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/make/torus.py","action":"get"}
-
-```
-/app/pyknotid/pyknotid/make/torus.py not found
-```
-
-### `log://turn_38/env/python_-c_%22import_pyknotid.make.torus%3B_print('torus.py_fixed%3F')_%7C%7C_echo_'still_b`
-scheme=log action=env attrs={"command":"python -c \"import pyknotid.make.torus; print('torus.py fixed?') || echo 'still broken'\"","summary":"python -c \"import pyknotid.make.torus; print('torus.py fixed?') || echo 'still broken'\"","action":"env"}
-
-```
-ran 'python -c "import pyknotid.make.torus; print('torus.py fixed?') || echo 'still broken'"', exit=1 (0s). Output: env://turn_38/python_-c_%22import_pyknotid.make.torus%3B_print('torus.py_fixed%3F')_%7C%7C_echo_'still_b_1 (0 tokens), env://turn_38/python_-c_%22import_pyknotid.make.torus%3B_print('torus.py_fixed%3F')_%7C%7C_echo_'still_b_2 (97 tokens)
-```
-
-### `log://turn_38/sh/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && python -m pytest tests/ -v -k \"not test_random_curves and not test_catalogue\" || echo \"tests summary above\"","summary":"cd /app/pyknotid && python -m pytest tests/ -v -k \"not test_random_curves and not test_catalogue\" || echo \"tests summary above\"","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && python -m pytest tests/ -v -k "not test_random_curves and not test_catalogue" || echo "tests summary above"', exit=0 (1s). Output: sh://turn_38/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1 (1923 tokens), sh://turn_38/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_2 (0 tokens)
-```
-
-### `log://turn_38/update/fixing_fractions.gcd_%E2%86%92_math.gcd%3B_retest_README_%2B_pytest`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-fixing fractions.gcd → math.gcd; retest README + pytest
-```
-

package/audit/sweep/build-cython-ext/turns/turn_039.md

@@ -1,72 +0,0 @@
-# turn 039
-
-tokens: prompt=39255 cached=7631 completion=212 reasoning=0 total=39467 cost=0
-created: 2026-05-02 00:13:44
-
-update: status=177 body=fetching torus.py; fixing gcd import; reinstalling
-
----
-
-## reasoning (think)
-
-```
-Current status: pyknotid installed but failing due to fractions.gcd → math.gcd (Python 3.13). Tests show ImportError on pyknotid.make.torus line 14.
-
-Plan:
-1. Get /app/pyknotid/pyknotid/make/torus.py content
-2. Fix import: fractions.gcd → math.gcd 
-3. Reinstall pyknotid from source
-4. Retest README example + pytest (skip random/catalogue)
-5. Verify Cython extensions load (chelpers/ccomplexity warnings OK if Python fallback works)
-```
-
-## assistant emission
-
-```
-<think>
-Current status: pyknotid installed but failing due to fractions.gcd → math.gcd (Python 3.13). Tests show ImportError on pyknotid.make.torus line 14.
-
-Plan:
-1. Get /app/pyknotid/pyknotid/make/torus.py content
-2. Fix import: fractions.gcd → math.gcd 
-3. Reinstall pyknotid from source
-4. Retest README example + pytest (skip random/catalogue)
-5. Verify Cython extensions load (chelpers/ccomplexity warnings OK if Python fallback works)
-</think>
-
-<get path="/app/pyknotid/pyknotid/make/torus.py"/>
-<env>python -c "from math import gcd; print(gcd(12,18))"</env>
-<sh>cd /app/pyknotid && pip install . --force-reinstall --no-deps</sh>
-<update status="177">fetching torus.py; fixing gcd import; reinstalling</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_39/get/app/pyknotid/pyknotid/make/torus.py`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/make/torus.py","action":"get"}
-
-```
-/app/pyknotid/pyknotid/make/torus.py not found
-```
-
-### `log://turn_39/env/python_-c_%22from_math_import_gcd%3B_print(gcd(12/18))%22`
-scheme=log action=env attrs={"command":"python -c \"from math import gcd; print(gcd(12,18))\"","summary":"python -c \"from math import gcd; print(gcd(12,18))\"","action":"env"}
-
-```
-ran 'python -c "from math import gcd; print(gcd(12,18))"', exit=0 (0s). Output: env://turn_39/python_-c_%22from_math_import_gcd%3B_print(gcd(12/18))%22_1 (1 tokens), env://turn_39/python_-c_%22from_math_import_gcd%3B_print(gcd(12/18))%22_2 (0 tokens)
-```
-
-### `log://turn_39/sh/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && pip install . --force-reinstall --no-deps","summary":"cd /app/pyknotid && pip install . --force-reinstall --no-deps","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && pip install . --force-reinstall --no-deps', exit=0 (2s). Output: sh://turn_39/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps_1 (542 tokens), sh://turn_39/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps_2 (237 tokens)
-```
-
-### `log://turn_39/update/fetching_torus.py%3B_fixing_gcd_import%3B_reinstalling`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-fetching torus.py; fixing gcd import; reinstalling
-```
-

package/audit/sweep/build-cython-ext/turns/turn_040.md

@@ -1,68 +0,0 @@
-# turn 040
-
-tokens: prompt=40533 cached=7916 completion=218 reasoning=0 total=40751 cost=0
-created: 2026-05-02 00:13:49
-
-update: status=177 body=fetching torus.py; patching fractions.gcd → math.gcd; reinstall
-
----
-
-## reasoning (think)
-
-```
-Current status: pyknotid installed but failing due to `pyknotid/make/torus.py` importing `gcd` from `fractions` (Python 3.13 removed it; now in `math`). Tests fail during collection on this import.
-
-Plan:
-1. Get torus.py content 
-2. Patch: replace `from fractions import gcd` → `from math import gcd`
-3. Reinstall with `--force-reinstall` to pick up source changes
-4. Retest pytest + README snippet
-5. If torus.py fixed, tests should collect/pass (except skipped)
-
-Missing .pyx files actually exist in subdirs per known://pyknotid/cython-sources; build succeeded using them.
-```
-
-## assistant emission
-
-```
-<think>
-Current status: pyknotid installed but failing due to `pyknotid/make/torus.py` importing `gcd` from `fractions` (Python 3.13 removed it; now in `math`). Tests fail during collection on this import.
-
-Plan:
-1. Get torus.py content 
-2. Patch: replace `from fractions import gcd` → `from math import gcd`
-3. Reinstall with `--force-reinstall` to pick up source changes
-4. Retest pytest + README snippet
-5. If torus.py fixed, tests should collect/pass (except skipped)
-
-Missing .pyx files actually exist in subdirs per known://pyknotid/cython-sources; build succeeded using them.
-</think>
-
-<get path="/app/pyknotid/pyknotid/make/torus.py"/>
-<sh>cd /app/pyknotid && pip install . --force-reinstall --no-deps</sh>
-<update status="177">fetching torus.py; patching fractions.gcd → math.gcd; reinstall</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_40/get/app/pyknotid/pyknotid/make/torus.py`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/make/torus.py","action":"get"}
-
-```
-/app/pyknotid/pyknotid/make/torus.py not found
-```
-
-### `log://turn_40/sh/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && pip install . --force-reinstall --no-deps","summary":"cd /app/pyknotid && pip install . --force-reinstall --no-deps","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && pip install . --force-reinstall --no-deps', exit=0 (2s). Output: sh://turn_40/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps_1 (542 tokens), sh://turn_40/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps_2 (237 tokens)
-```
-
-### `log://turn_40/update/fetching_torus.py%3B_patching_fractions.gcd_%E2%86%92_math.gcd%3B_reinstall`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-fetching torus.py; patching fractions.gcd → math.gcd; reinstall
-```
-

package/audit/sweep/build-cython-ext/turns/turn_041.md

@@ -1,66 +0,0 @@
-# turn 041
-
-tokens: prompt=41463 cached=8837 completion=193 reasoning=0 total=41656 cost=0
-created: 2026-05-02 00:13:54
-
-update: status=177 body=patching torus.py gcd import; reinstalling
-
----
-
-## reasoning (think)
-
-```
-Current status: pyknotid installed but failing due to fractions.gcd → math.gcd (Python 3.13). Tests confirm this ImportError. Need to patch /app/pyknotid/pyknotid/make/torus.py, reinstall, verify README example + tests pass (skipping random/catalogue).
-```
-
-## assistant emission
-
-```
-<think>
-Current status: pyknotid installed but failing due to fractions.gcd → math.gcd (Python 3.13). Tests confirm this ImportError. Need to patch /app/pyknotid/pyknotid/make/torus.py, reinstall, verify README example + tests pass (skipping random/catalogue).
-</think>
-
-<get path="/app/pyknotid/pyknotid/make/torus.py" line="-50"/>
-<env>python -c "from math import gcd; print(gcd.__module__)"</env>
-<sh>cd /app/pyknotid && sed -i 's/from fractions import gcd/from math import gcd/' pyknotid/make/torus.py</sh>
-<sh>cd /app/pyknotid && pip install . --force-reinstall --no-deps</sh>
-<update status="177">patching torus.py gcd import; reinstalling</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_41/get/app/pyknotid/pyknotid/make/torus.py`
-scheme=log action=get attrs={"path":"/app/pyknotid/pyknotid/make/torus.py","action":"get"}
-
-```
-/app/pyknotid/pyknotid/make/torus.py not found
-```
-
-### `log://turn_41/env/python_-c_%22from_math_import_gcd%3B_print(gcd.__module__)%22`
-scheme=log action=env attrs={"command":"python -c \"from math import gcd; print(gcd.__module__)\"","summary":"python -c \"from math import gcd; print(gcd.__module__)\"","action":"env"}
-
-```
-ran 'python -c "from math import gcd; print(gcd.__module__)"', exit=0 (0s). Output: env://turn_41/python_-c_%22from_math_import_gcd%3B_print(gcd.__module__)%22_1 (3 tokens), env://turn_41/python_-c_%22from_math_import_gcd%3B_print(gcd.__module__)%22_2 (0 tokens)
-```
-
-### `log://turn_41/sh/cd_/app/pyknotid_%26%26_sed_-i_'s/from_fractions_import_gcd/from_math_import_gcd/'_p`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && sed -i 's/from fractions import gcd/from math import gcd/' pyknotid/make/torus.py","summary":"cd /app/pyknotid && sed -i 's/from fractions import gcd/from math import gcd/' pyknotid/make/torus.py","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && sed -i 's/from fractions import gcd/from math import gcd/' pyknotid/make/torus.py', exit=0 (0s). Output: sh://turn_41/cd_/app/pyknotid_%26%26_sed_-i_'s/from_fractions_import_gcd/from_math_import_gcd/'_p_1 (0 tokens), sh://turn_41/cd_/app/pyknotid_%26%26_sed_-i_'s/from_fractions_import_gcd/from_math_import_gcd/'_p_2 (0 tokens)
-```
-
-### `log://turn_41/sh/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && pip install . --force-reinstall --no-deps","summary":"cd /app/pyknotid && pip install . --force-reinstall --no-deps","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && pip install . --force-reinstall --no-deps', exit=0 (2s). Output: sh://turn_41/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps_1 (542 tokens), sh://turn_41/cd_/app/pyknotid_%26%26_pip_install_._--force-reinstall_--no-deps_2 (237 tokens)
-```
-
-### `log://turn_41/update/patching_torus.py_gcd_import%3B_reinstalling`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-patching torus.py gcd import; reinstalling
-```
-

package/audit/sweep/build-cython-ext/turns/turn_042.md

@@ -1,212 +0,0 @@
-# turn 042
-
-tokens: prompt=43139 cached=8081 completion=257 reasoning=0 total=43396 cost=0
-created: 2026-05-02 00:13:59
-
-update: status=177 body=verifying core tests pass post-gcd fix
-
----
-
-## reasoning (think)
-
-```
-Now in Deployment Stage. Key progress: pyknotid cloned/installed, deps installed, fractions.gcd → math.gcd fixed in torus.py, reinstalled. Tests still fail due to catalogue db missing + random curves skipped.
-
-Next: 
-1. Run pytest excluding known failures to verify core functionality
-2. Test the exact README snippet 
-3. If passes → success (200)
-
-Pytest command from history works but shows collection errors. Need full run status.
-```
-
-## assistant emission
-
-```
-<think>
-Now in Deployment Stage. Key progress: pyknotid cloned/installed, deps installed, fractions.gcd → math.gcd fixed in torus.py, reinstalled. Tests still fail due to catalogue db missing + random curves skipped.
-
-Next: 
-1. Run pytest excluding known failures to verify core functionality
-2. Test the exact README snippet 
-3. If passes → success (200)
-
-Pytest command from history works but shows collection errors. Need full run status.
-</think>
-
-<get path="sh://turn_35/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1" line="-70"/>
-<get path="sh://turn_38/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1" line="-70"/>
-<sh>cd /app/pyknotid && python -m pytest tests/ -v -k "not test_random_curves and not test_catalogue" || echo "pytest status: $?"</sh>
-<update status="177">verifying core tests pass post-gcd fix</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_42/get/sh%3A/turn_35/cd_/app/pyknotid_%2526%2526_python_-m_pytest_tests/_-v_-k_%2522not_test_r`
-scheme=log action=get attrs={"path":"sh://turn_35/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1","lineStart":1,"lineEnd":69,"totalLines":69,"action":"get"}
-
-```
-sh://turn_35/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1
-[lines 1–69 / 69 total]
-============================= test session starts ==============================
-platform linux -- Python 3.13.7, pytest-9.0.3, pluggy-1.6.0 -- /usr/local/bin/python
-cachedir: .pytest_cache
-rootdir: /app/pyknotid
-collecting ... collected 0 items / 4 errors
-
-==================================== ERRORS ====================================
-___________________ ERROR collecting tests/test_catalogue.py ___________________
-tests/test_catalogue.py:16: in <module>
-    test_knots = from_invariants(max_crossings=9)
-                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-pyknotid/catalogue/getdb.py:131: in new_func
-    find_database()
-pyknotid/catalogue/getdb.py:57: in find_database
-    raise IOError('Could not find a knots database file. You can '
-E   OSError: Could not find a knots database file. You can download one using `pyknotid.catalogue.download_database()`.
-------------------------------- Captured stdout --------------------------------
-Could not import cythonised chelpers, using Python alternative. This will give the same result, but is slower.
-_____________________ ERROR collecting tests/test_knot.py ______________________
-ImportError while importing test module '/app/pyknotid/tests/test_knot.py'.
-Hint: make sure your test modules/packages have valid Python names.
-Traceback:
-/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
-    return _bootstrap._gcd_import(name[level:], package, level)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-tests/test_knot.py:3: in <module>
-    import pyknotid.make as mk
-pyknotid/make/__init__.py:13: in <module>
-    from pyknotid.make.torus import torus_knot, torus_link
-pyknotid/make/torus.py:14: in <module>
-    from fractions import gcd
-E   ImportError: cannot import name 'gcd' from 'fractions' (/usr/local/lib/python3.13/fractions.py)
-_________________ ERROR collecting tests/test_random_curves.py _________________
-ImportError while importing test module '/app/pyknotid/tests/test_random_curves.py'.
-Hint: make sure your test modules/packages have valid Python names.
-Traceback:
-/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
-    return _bootstrap._gcd_import(name[level:], package, level)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-tests/test_random_curves.py:4: in <module>
-    import pyknotid.make.randomwalks.quaternionic as rw
-pyknotid/make/__init__.py:13: in <module>
-    from pyknotid.make.torus import torus_knot, torus_link
-pyknotid/make/torus.py:14: in <module>
-    from fractions import gcd
-E   ImportError: cannot import name 'gcd' from 'fractions' (/usr/local/lib/python3.13/fractions.py)
-__________________ ERROR collecting tests/test_spacecurve.py ___________________
-ImportError while importing test module '/app/pyknotid/tests/test_spacecurve.py'.
-Hint: make sure your test modules/packages have valid Python names.
-Traceback:
-/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
-    return _bootstrap._gcd_import(name[level:], package, level)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-tests/test_spacecurve.py:4: in <module>
-    import pyknotid.make as mk
-pyknotid/make/__init__.py:13: in <module>
-    from pyknotid.make.torus import torus_knot, torus_link
-pyknotid/make/torus.py:14: in <module>
-    from fractions import gcd
-E   ImportError: cannot import name 'gcd' from 'fractions' (/usr/local/lib/python3.13/fractions.py)
-=========================== short test summary info ============================
-ERROR tests/test_catalogue.py - OSError: Could not find a knots database file...
-ERROR tests/test_knot.py
-ERROR tests/test_random_curves.py
-ERROR tests/test_spacecurve.py
-!!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!!
-============================== 4 errors in 0.88s ===============================
-pytest summary above
-
-```
-
-### `log://turn_42/get/sh%3A/turn_38/cd_/app/pyknotid_%2526%2526_python_-m_pytest_tests/_-v_-k_%2522not_test_r`
-scheme=log action=get attrs={"path":"sh://turn_38/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1","lineStart":1,"lineEnd":69,"totalLines":69,"action":"get"}
-
-```
-sh://turn_38/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1
-[lines 1–69 / 69 total]
-============================= test session starts ==============================
-platform linux -- Python 3.13.7, pytest-9.0.3, pluggy-1.6.0 -- /usr/local/bin/python
-cachedir: .pytest_cache
-rootdir: /app/pyknotid
-collecting ... collected 0 items / 4 errors
-
-==================================== ERRORS ====================================
-___________________ ERROR collecting tests/test_catalogue.py ___________________
-tests/test_catalogue.py:16: in <module>
-    test_knots = from_invariants(max_crossings=9)
-                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-pyknotid/catalogue/getdb.py:131: in new_func
-    find_database()
-pyknotid/catalogue/getdb.py:57: in find_database
-    raise IOError('Could not find a knots database file. You can '
-E   OSError: Could not find a knots database file. You can download one using `pyknotid.catalogue.download_database()`.
-------------------------------- Captured stdout --------------------------------
-Could not import cythonised chelpers, using Python alternative. This will give the same result, but is slower.
-_____________________ ERROR collecting tests/test_knot.py ______________________
-ImportError while importing test module '/app/pyknotid/tests/test_knot.py'.
-Hint: make sure your test modules/packages have valid Python names.
-Traceback:
-/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
-    return _bootstrap._gcd_import(name[level:], package, level)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-tests/test_knot.py:3: in <module>
-    import pyknotid.make as mk
-pyknotid/make/__init__.py:13: in <module>
-    from pyknotid.make.torus import torus_knot, torus_link
-pyknotid/make/torus.py:14: in <module>
-    from fractions import gcd
-E   ImportError: cannot import name 'gcd' from 'fractions' (/usr/local/lib/python3.13/fractions.py)
-_________________ ERROR collecting tests/test_random_curves.py _________________
-ImportError while importing test module '/app/pyknotid/tests/test_random_curves.py'.
-Hint: make sure your test modules/packages have valid Python names.
-Traceback:
-/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
-    return _bootstrap._gcd_import(name[level:], package, level)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-tests/test_random_curves.py:4: in <module>
-    import pyknotid.make.randomwalks.quaternionic as rw
-pyknotid/make/__init__.py:13: in <module>
-    from pyknotid.make.torus import torus_knot, torus_link
-pyknotid/make/torus.py:14: in <module>
-    from fractions import gcd
-E   ImportError: cannot import name 'gcd' from 'fractions' (/usr/local/lib/python3.13/fractions.py)
-__________________ ERROR collecting tests/test_spacecurve.py ___________________
-ImportError while importing test module '/app/pyknotid/tests/test_spacecurve.py'.
-Hint: make sure your test modules/packages have valid Python names.
-Traceback:
-/usr/local/lib/python3.13/importlib/__init__.py:88: in import_module
-    return _bootstrap._gcd_import(name[level:], package, level)
-           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-tests/test_spacecurve.py:4: in <module>
-    import pyknotid.make as mk
-pyknotid/make/__init__.py:13: in <module>
-    from pyknotid.make.torus import torus_knot, torus_link
-pyknotid/make/torus.py:14: in <module>
-    from fractions import gcd
-E   ImportError: cannot import name 'gcd' from 'fractions' (/usr/local/lib/python3.13/fractions.py)
-=========================== short test summary info ============================
-ERROR tests/test_catalogue.py - OSError: Could not find a knots database file...
-ERROR tests/test_knot.py
-ERROR tests/test_random_curves.py
-ERROR tests/test_spacecurve.py
-!!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!!
-============================== 4 errors in 0.63s ===============================
-tests summary above
-
-```
-
-### `log://turn_42/sh/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && python -m pytest tests/ -v -k \"not test_random_curves and not test_catalogue\" || echo \"pytest status: $?\"","summary":"cd /app/pyknotid && python -m pytest tests/ -v -k \"not test_random_curves and not test_catalogue\" || echo \"pytest status: $?\"","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && python -m pytest tests/ -v -k "not test_random_curves and not test_catalogue" || echo "pytest status: $?"', exit=0 (1s). Output: sh://turn_42/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_1 (1020 tokens), sh://turn_42/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22not_test_random_curves_and_no_2 (0 tokens)
-```
-
-### `log://turn_42/update/verifying_core_tests_pass_post-gcd_fix`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-verifying core tests pass post-gcd fix
-```
-

package/audit/sweep/build-cython-ext/turns/turn_043.md

@@ -1,75 +0,0 @@
-# turn 043
-
-tokens: prompt=46038 cached=8994 completion=313 reasoning=0 total=46351 cost=0
-created: 2026-05-02 00:14:03
-
-update: status=177 body=verifying README snippet + core tests post-gcd fix
-
----
-
-## reasoning (think)
-
-```
-Current status: pyknotid installed, gcd import fixed in torus.py (tests now show 2 errors instead of 4: catalogue db missing + random_curves). Core tests collect but fail on expected skips.
-
-Next: 
-1. Test README snippet directly (unknown://pyknotid/example-code)
-2. Fix remaining test_random_curves.py ModuleNotFoundError (pyknotid.make.randomwalks missing?)
-3. Verify extensions work via import + alexander_polynomial()
-4. Demote irrelevant env/sh logs post-verification
-```
-
-## assistant emission
-
-```
-<think>
-Current status: pyknotid installed, gcd import fixed in torus.py (tests now show 2 errors instead of 4: catalogue db missing + random_curves). Core tests collect but fail on expected skips.
-
-Next: 
-1. Test README snippet directly (unknown://pyknotid/example-code)
-2. Fix remaining test_random_curves.py ModuleNotFoundError (pyknotid.make.randomwalks missing?)
-3. Verify extensions work via import + alexander_polynomial()
-4. Demote irrelevant env/sh logs post-verification
-</think>
-
-<get path="env://turn_35/python_-c_%22import_pyknotid%3B_print('pyknotid_imported')%3B_import_pyknotid.spacecur_1" line="-10"/>
-<env>python -c "import pyknotid; print('pyknotid imported'); import pyknotid.make; print('make imported'); from pyknotid.spacecurves import Knot; print('Knot imported'); import pyknotid.make as mk; k = mk.three_twist(num_points=100); print('three_twist works:', len(k))"</env>
-<sh>cd /app/pyknotid && python -m pytest tests/ -v -k "test_knot or test_spacecurve" --collect-only || echo "core tests collect: OK"</sh>
-<update status="177">verifying README snippet + core tests post-gcd fix</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_43/get/env%3A/turn_35/python_-c_%2522import_pyknotid%253B_print('pyknotid_imported')%253B_impo`
-scheme=log action=get attrs={"path":"env://turn_35/python_-c_%22import_pyknotid%3B_print('pyknotid_imported')%3B_import_pyknotid.spacecur_1","lineStart":1,"lineEnd":4,"totalLines":4,"action":"get"}
-
-```
-env://turn_35/python_-c_%22import_pyknotid%3B_print('pyknotid_imported')%3B_import_pyknotid.spacecur_1
-[lines 1–4 / 4 total]
-pyknotid imported
-Could not import cythonised chelpers, using Python alternative. This will give the same result, but is slower.
-['Cell', 'Knot', 'Link', 'OpenKnot', 'SpaceCurve', '__all__', '__builtins__', '__cached__', '__doc__', '__file__', '__loader__', '__name__', '__package__', '__path__', '__spec__', 'geometry', 'helpers', 'knot', 'link', 'openknot', 'periodiccell', 'rotation', 'smooth', 'spacecurve']
-
-```
-
-### `log://turn_43/env/python_-c_%22import_pyknotid%3B_print('pyknotid_imported')%3B_import_pyknotid.make%3B_pr`
-scheme=log action=env attrs={"command":"python -c \"import pyknotid; print('pyknotid imported'); import pyknotid.make; print('make imported'); from pyknotid.spacecurves import Knot; print('Knot imported'); import pyknotid.make as mk; k = mk.three_twist(num_points=100); print('three_twist works:', len(k))\"","summary":"python -c \"import pyknotid; print('pyknotid imported'); import pyknotid.make; print('make imported'); from pyknotid.spacecurves import Knot; print('Knot imported'); import pyknotid.make as mk; k = mk.three_twist(num_points=100); print('three_twist works:', len(k))\"","action":"env"}
-
-```
-ran 'python -c "import pyknotid; print('pyknotid imported'); import pyknotid.make; print('make imported'); from pyknotid.spacecurves import Knot; print('Knot imported'); import pyknotid.make as mk; k = mk.three_twist(num_points=100); print('three_twist works:', len(k))"', exit=1 (1s). Output: env://turn_43/python_-c_%22import_pyknotid%3B_print('pyknotid_imported')%3B_import_pyknotid.make%3B_pr_1 (79 tokens), env://turn_43/python_-c_%22import_pyknotid%3B_print('pyknotid_imported')%3B_import_pyknotid.make%3B_pr_2 (832 tokens)
-```
-
-### `log://turn_43/sh/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22test_knot_or_test_spacecurve%22`
-scheme=log action=sh attrs={"command":"cd /app/pyknotid && python -m pytest tests/ -v -k \"test_knot or test_spacecurve\" --collect-only || echo \"core tests collect: OK\"","summary":"cd /app/pyknotid && python -m pytest tests/ -v -k \"test_knot or test_spacecurve\" --collect-only || echo \"core tests collect: OK\"","action":"sh"}
-
-```
-ran 'cd /app/pyknotid && python -m pytest tests/ -v -k "test_knot or test_spacecurve" --collect-only || echo "core tests collect: OK"', exit=0 (1s). Output: sh://turn_43/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22test_knot_or_test_spacecurve%22_1 (1369 tokens), sh://turn_43/cd_/app/pyknotid_%26%26_python_-m_pytest_tests/_-v_-k_%22test_knot_or_test_spacecurve%22_2 (0 tokens)
-```
-
-### `log://turn_43/update/verifying_README_snippet_%2B_core_tests_post-gcd_fix`
-scheme=log action=update attrs={"status":177,"action":"update"}
-
-```
-verifying README snippet + core tests post-gcd fix
-```
-