@possumtech/rummy 2.2.0 → 2.2.1

package/audit/sweep/build-cython-ext/turns/turn_028.md

@@ -1,299 +0,0 @@
-# turn 028
-
-tokens: prompt=21213 cached=3294 completion=363 reasoning=0 total=21576 cost=0
-created: 2026-05-02 00:12:18
-
-update: status=155 body=distilling pyknotid/build-process from full setup.py + .pyx sources
-
----
-
-## reasoning (think)
-
-```
-Current stage: Distillation. Focus: unknown://pyknotid/build-process (highest priority for compilation/install).
-
-Key sources identified & promoted:
-- setup.py (2300 tokens tail visible, full content needed)
-- cinvariants.pyx (1061 tokens tail visible, full needed) 
-- pyknotid/ dir listing (confirms single .pyx: cinvariants.pyx)
-
-Plan:
-1. Promote full setup.py & cinvariants.pyx (using line="1" slices if needed to fit budget)
-2. Check other .pyx files via env (setup.py mentions chelpers/ccomplexity)
-3. Distill build-process: extract deps, Cython ext_modules config, Numpy version pins, install cmd
-4. Demote ls/cat slices after distillation
-5. Continue to next unknowns (numpy-compat after build-process)
-
-Budget ok: 1.7M free. Promote full files (~3k total < free).
-```
-
-## assistant emission
-
-```
-<think>
-Current stage: Distillation. Focus: unknown://pyknotid/build-process (highest priority for compilation/install).
-
-Key sources identified & promoted:
-- setup.py (2300 tokens tail visible, full content needed)
-- cinvariants.pyx (1061 tokens tail visible, full needed) 
-- pyknotid/ dir listing (confirms single .pyx: cinvariants.pyx)
-
-Plan:
-1. Promote full setup.py & cinvariants.pyx (using line="1" slices if needed to fit budget)
-2. Check other .pyx files via env (setup.py mentions chelpers/ccomplexity)
-3. Distill build-process: extract deps, Cython ext_modules config, Numpy version pins, install cmd
-4. Demote ls/cat slices after distillation
-5. Continue to next unknowns (numpy-compat after build-process)
-
-Budget ok: 1.7M free. Promote full files (~3k total < free).
-</think>
-
-<get path="env://turn_27/cat_/app/pyknotid/setup.py_1" line="1"/>
-<get path="env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1" line="1"/>
-<env>ls -la /app/pyknotid/pyknotid/chelpers*.pyx /app/pyknotid/pyknotid/ccomplexity*.pyx 2>/dev/null || echo "no chelpers/ccomplexity .pyx found"</env>
-<get path="env://turn_16/ls_-la_/app/pyknotid/pyknotid_1"/>
-
-<update status="155">distilling pyknotid/build-process from full setup.py + .pyx sources</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_28/get/env%3A/turn_27/cat_/app/pyknotid/setup.py_1`
-scheme=log action=get attrs={"path":"env://turn_27/cat_/app/pyknotid/setup.py_1","lineStart":1,"lineEnd":130,"totalLines":130,"action":"get"}
-
-```
-env://turn_27/cat_/app/pyknotid/setup.py_1
-[lines 1–130 / 130 total]
-from setuptools import setup, find_packages
-from distutils.extension import Extension
-
-from os.path import join, sep, dirname
-from os import walk, environ
-import glob
-import re
-
-
-package_data = {}
-
-def recursively_include(results, directory, patterns):
-    for root, subfolders, files in walk(directory):
-        for fn in files:
-            if not any([glob.fnmatch.fnmatch(fn, pattern) for pattern in patterns]):
-                continue
-            filename = join(root, fn)
-            directory = 'pyknotid'
-            if directory not in results:
-                results[directory] = []
-            results[directory].append(join(*filename.split(sep)[1:]))
-
-recursively_include(package_data, 'pyknotid',
-                    ['*.tmpl', '*.pov', '*.pyx', '*.pxd',
-                     '*.py',
-                     ])
-
-# Build cython components if possible
-try:
-    from Cython.Build import cythonize
-    import numpy
-except ImportError:
-    print('Cython or numpy could not be imported, so cythonised calculation '
-          'functions will not be built. pyknotid will use Python-only '
-          'routines instead. These are slower, but will return the '
-          'same result.')
-    print('To build the cython components, install cython and numpy and rebuild '
-          'pyknotid.')
-    ext_modules = []
-    include_dirs = []
-else:
-    ext_modules = [
-            Extension("pyknotid.spacecurves.chelpers", ["pyknotid/spacecurves/chelpers.pyx"],
-                    libraries=["m"]),
-            Extension("pyknotid.spacecurves.ccomplexity", ["pyknotid/spacecurves/ccomplexity.pyx"],
-                    libraries=["m"]),
-            Extension("pyknotid.simplify.coctree", ["pyknotid/simplify/coctree.pyx"],
-                    libraries=["m"]),
-            Extension("pyknotid.cinvariants", ["pyknotid/cinvariants.pyx"],
-                    libraries=["m"]),
-            ]
-    ext_modules = cythonize(ext_modules)
-    include_dirs = [numpy.get_include()]
-
-pyknotid_init_filen = join(dirname(__file__), 'pyknotid', '__init__.py')
-version = None
-try:
-    with open(pyknotid_init_filen) as fileh:
-        lines = fileh.readlines()
-except IOError:
-    pass
-else:
-    for line in lines:
-        line = line.strip()
-        if line.startswith('__version__ = '):
-            matches = re.findall(r'["\'].+["\']', line)
-            if matches:
-                version = matches[0].strip("'").strip('"')
-                break
-if version is None:
-    raise Exception('Error: version could not be loaded from {}'.format(pyknotid_init_filen))
-
-if 'READTHEDOCS' in environ and environ['READTHEDOCS'] == 'True':
-    print('Installing for doc only')
-    install_requires=['numpy', 'peewee', 'vispy', 'sympy']
-else:
-    install_requires=['numpy', 'networkx', 'planarity',
-                      'peewee', 'vispy', 'sympy', 'appdirs',
-                      'requests', 'tqdm'],
-
-long_description = '''
-Pyknotid
-========
-
-Python (and optional Cython) modules for detecting and measuring
-knotting and linking. pyknotid can analyse space-curves, i.e. sets of
-points in three-dimensions, or can parse standard topological
-representations of knot diagrams.
-
-A graphical interface to some of these tools is available online at
-`Knot ID <http://inclem.net/knotidentifier>`__.
-
-pyknotid was developed as part of the Leverhulme Trust Research
-Programme Grant RP2013-K-009: Scientific Properties of Complex Knots
-(SPOCK), a collaboration between the University of Bristol and Durham
-University in the UK. For more information, see the `SPOCK homepage
-<http://www.maths.dur.ac.uk/spock/index.html/>`__.
-
-If you use pyknotid in your research, please `cite us
-<http://pyknotid.readthedocs.io/en/latest/sources/about.html#cite-us>`__.
-
-Questions or comments are welcome, please email alexander.taylor@bristol.ac.uk.
-
-Documentation
--------------
-
-pyknotid is documented online at `readthedocs
-<http://pyknotid.readthedocs.io/en/latest/sources/overview.html>`__.
-'''
-
-setup(
-    name='pyknotid',
-    version=version,
-    description=('Tools for identifying and analysing knots, in space-curves '
-                 'or standard topological representations'),
-    long_description=long_description,
-    author='Alexander Taylor',
-    author_email='alexander.taylor@bristol.ac.uk',
-    install_requires=install_requires,
-    ext_modules=ext_modules,
-    include_dirs=include_dirs,
-    packages=find_packages(),
-    package_data=package_data,
-    entry_points={
-        'console_scripts': [
-            'analyse-knot-file = pyknotid.cli.analyse_knot_file:main',
-            'plot-knot = pyknotid.cli.plot_knot:main']
-        }
-)
-
-```
-
-### `log://turn_28/get/env%3A/turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1`
-scheme=log action=get attrs={"path":"env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1","lineStart":1,"lineEnd":72,"totalLines":72,"action":"get"}
-
-```
-env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1
-[lines 1–72 / 72 total]
-
-import numpy as n
-cimport numpy as n
-cimport cython
-
-from pyknotid.utils import vprint
-
-cdef long crude_modulus(long val, long modulo):
-    if val < 0:
-        return val + modulo
-    return val
-    
-
-@cython.wraparound(False)
-@cython.boundscheck(False)
-cpdef vassiliev_degree_3(long [:, :] arrows):
-    cdef long num_arrows = len(arrows)
-    cdef long num_crossings = len(arrows) * 2
-
-    cdef long a1s, a1e, a2s, a2e, a3s, a3e
-    cdef long [:] arrow1, arrow2, arrow3
-    cdef long i1, i2, i3
-    cdef long sign1, sign2, sign3
-
-    cdef set used_sets = set()
-    cdef long representations_sum_1 = 0
-    cdef long representations_sum_2 = 0
-    cdef tuple ordered_indices
-    for i1 in range(num_arrows):
-        arrow1 = arrows[i1]
-        a1s = arrow1[0]
-        a1e = arrow1[1]
-        sign1 = arrow1[2]
-
-        a1e = crude_modulus(a1e - a1s, num_crossings)
-
-        for i2 in range(num_arrows):
-            arrow2 = arrows[i2]
-            a2s = arrow2[0]
-            a2e = arrow2[1]
-            sign2 = arrow2[2]
-
-            a2s = crude_modulus(a2s - a1s, num_crossings)
-            a2e = crude_modulus(a2e - a1s, num_crossings)
-
-            for i3 in range(num_arrows):
-                arrow3 = arrows[i3]
-                a3s = arrow3[0]
-                a3e = arrow3[1]
-                sign3 = arrow3[2]
-
-                a3s = crude_modulus(a3s - a1s, num_crossings)
-                a3e = crude_modulus(a3e - a1s, num_crossings)
-
-                ordered_indices = tuple(sorted((i1, i2, i3)))
-                if ordered_indices in used_sets:
-                    continue
-
-                if (a2s < a1e and a3e < a1e and a3e > a2s and
-                    a3s > a1e and a2e > a3s):
-                    representations_sum_1 += sign1 * sign2 * sign3
-                    used_sets.add(ordered_indices)
-                if (a2e < a1e and a3s < a1e and a3s > a2e and
-                    a2s > a1e and a3e > a2s):
-                    representations_sum_2 += sign1 * sign2 * sign3
-                    used_sets.add(ordered_indices)
-
-                    
-    return representations_sum_1 / 2. + representations_sum_2
-
-    
-
-```
-
-### `log://turn_28/env/ls_-la_/app/pyknotid/pyknotid/chelpers*.pyx_/app/pyknotid/pyknotid/ccomplexity*.`
-scheme=log action=env attrs={"command":"ls -la /app/pyknotid/pyknotid/chelpers*.pyx /app/pyknotid/pyknotid/ccomplexity*.pyx 2>/dev/null || echo \"no chelpers/ccomplexity .pyx found\"","summary":"ls -la /app/pyknotid/pyknotid/chelpers*.pyx /app/pyknotid/pyknotid/ccomplexity*.pyx 2>/dev/null || echo \"no chelpers/ccomplexity .pyx found\"","action":"env"}
-
-```
-ran 'ls -la /app/pyknotid/pyknotid/chelpers*.pyx /app/pyknotid/pyknotid/ccomplexity*.pyx 2>/dev/null || echo "no chelpers/ccomplexity .pyx found"', exit=0 (0s). Output: env://turn_28/ls_-la_/app/pyknotid/pyknotid/chelpers*.pyx_/app/pyknotid/pyknotid/ccomplexity*._1 (18 tokens), env://turn_28/ls_-la_/app/pyknotid/pyknotid/chelpers*.pyx_/app/pyknotid/pyknotid/ccomplexity*._2 (0 tokens)
-```
-
-### `log://turn_28/get/env%3A/turn_16/ls_-la_/app/pyknotid/pyknotid_1`
-scheme=log action=get attrs={"path":"env://turn_16/ls_-la_/app/pyknotid/pyknotid_1","action":"get"}
-
-```
-env://turn_16/ls_-la_/app/pyknotid/pyknotid_1 promoted
-```
-
-### `log://turn_28/update/distilling_pyknotid/build-process_from_full_setup.py_%2B_.pyx_sources`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilling pyknotid/build-process from full setup.py + .pyx sources
-```
-

package/audit/sweep/build-cython-ext/turns/turn_029.md

@@ -1,370 +0,0 @@
-# turn 029
-
-tokens: prompt=23965 cached=4314 completion=823 reasoning=0 total=24788 cost=0
-created: 2026-05-02 00:12:23
-
-update: status=155 body=distilled build-process; checking missing .pyx dirs
-
----
-
-## reasoning (think)
-
-```
-* Current stage: Distillation - resolving unknown://pyknotid/build-process using promoted setup.py + cinvariants.pyx
-* Key discoveries: setup.py defines 4 Cython exts (chelpers, ccomplexity, coctree, cinvariants); only cinvariants.pyx exists in root, others missing from v0.5.3
-* Distill build-process: cd /app/pyknotid; pip install . (requires Cython, numpy); expect missing .pyx errors for chelpers/ccomplexity/coctree
-* Next: Distill into known://pyknotid/build-process; check other .pyx locations; plan fixes for missing sources
-* Budget ok: setup.py (2359) + cinvariants (1135) already promoted
-* Continue distillation after setting known entry
-```
-
-## assistant emission
-
-```
-<think>
-* Current stage: Distillation - resolving unknown://pyknotid/build-process using promoted setup.py + cinvariants.pyx
-* Key discoveries: setup.py defines 4 Cython exts (chelpers, ccomplexity, coctree, cinvariants); only cinvariants.pyx exists in root, others missing from v0.5.3
-* Distill build-process: cd /app/pyknotid; pip install . (requires Cython, numpy); expect missing .pyx errors for chelpers/ccomplexity/coctree
-* Next: Distill into known://pyknotid/build-process; check other .pyx locations; plan fixes for missing sources
-* Budget ok: setup.py (2359) + cinvariants (1135) already promoted
-* Continue distillation after setting known entry
-</think>
-
-<get path="env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1" line="1" limit="72"/>
-<get path="env://turn_27/cat_/app/pyknotid/setup.py_1" line="1" limit="130"/>
-
-<set path="known://pyknotid/build-process" visibility="visible" summary="pyknotid,build,install,cython,extensions,setup.py,deps,steps">
-# Related
-[prompt](prompt://1) 
-[unknown resolved](unknown://pyknotid/build-process)
-[setup.py full](env://turn_27/cat_/app/pyknotid/setup.py_1)
-[cinvariants.pyx full](env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1)
-[pyknotid/ ls](env://turn_16/ls_-la_/app/pyknotid/pyknotid_1)
-[repo structure](known://pyknotid/repo-structure)
-
-# Pyknotid Build Process (v0.5.3)
-
-## Install Steps
-ʼ``
-cd /app/pyknotid
-pip install .  # or python setup.py build_ext --inplace; pip install -e .
-ʼ``
-
-## Dependencies (from setup.py)
-- Core: numpy, Cython (for build)
-- Runtime: numpy, networkx, planarity, peewee, vispy, sympy, appdirs, requests, tqdm
-- Exts need: libm
-
-## Cython Extensions Defined
-ʼ``
-1. pyknotid.spacecurves.chelpers → pyknotid/spacecurves/chelpers.pyx  [MISSING]
-2. pyknotid.spacecurves.ccomplexity → pyknotid/spacecurves/ccomplexity.pyx  [MISSING] 
-3. pyknotid.simplify.coctree → pyknotid/simplify/coctree.pyx  [MISSING]
-4. pyknotid.cinvariants → pyknotid/cinvariants.pyx  [FOUND: 2121 bytes]
-ʼ``
-- Only cinvariants.pyx exists in root; others absent in this clone
-- Build will fail on missing .pyx → need to locate/create stubs or disable
-
-## Numpy 2.3.0 Status
-- No obvious incompat in promoted cinvariants.pyx (uses basic np/cython)
-- Potential issues in missing exts or during cythonize()
-
-## Next Actions
-1. env cd /app/pyknotid && ls pyknotid/spacecurves/ pyknotid/simplify/
-2. pip install cython numpy
-3. Attempt build, capture errors
-</set>
-
-<set path="unknown://pyknotid/build-process" visibility="summarized"/>
-
-<env>cd /app/pyknotid && ls -la pyknotid/spacecurves/ pyknotid/simplify/ 2>/dev/null || echo "dirs missing"</env>
-
-<update status="155">distilled build-process; checking missing .pyx dirs</update>
-```
-
-## actions (chronological log entries)
-
-### `log://turn_29/get/env%3A/turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1`
-scheme=log action=get attrs={"path":"env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1","lineStart":1,"lineEnd":72,"totalLines":72,"action":"get"}
-
-```
-env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1
-[lines 1–72 / 72 total]
-
-import numpy as n
-cimport numpy as n
-cimport cython
-
-from pyknotid.utils import vprint
-
-cdef long crude_modulus(long val, long modulo):
-    if val < 0:
-        return val + modulo
-    return val
-    
-
-@cython.wraparound(False)
-@cython.boundscheck(False)
-cpdef vassiliev_degree_3(long [:, :] arrows):
-    cdef long num_arrows = len(arrows)
-    cdef long num_crossings = len(arrows) * 2
-
-    cdef long a1s, a1e, a2s, a2e, a3s, a3e
-    cdef long [:] arrow1, arrow2, arrow3
-    cdef long i1, i2, i3
-    cdef long sign1, sign2, sign3
-
-    cdef set used_sets = set()
-    cdef long representations_sum_1 = 0
-    cdef long representations_sum_2 = 0
-    cdef tuple ordered_indices
-    for i1 in range(num_arrows):
-        arrow1 = arrows[i1]
-        a1s = arrow1[0]
-        a1e = arrow1[1]
-        sign1 = arrow1[2]
-
-        a1e = crude_modulus(a1e - a1s, num_crossings)
-
-        for i2 in range(num_arrows):
-            arrow2 = arrows[i2]
-            a2s = arrow2[0]
-            a2e = arrow2[1]
-            sign2 = arrow2[2]
-
-            a2s = crude_modulus(a2s - a1s, num_crossings)
-            a2e = crude_modulus(a2e - a1s, num_crossings)
-
-            for i3 in range(num_arrows):
-                arrow3 = arrows[i3]
-                a3s = arrow3[0]
-                a3e = arrow3[1]
-                sign3 = arrow3[2]
-
-                a3s = crude_modulus(a3s - a1s, num_crossings)
-                a3e = crude_modulus(a3e - a1s, num_crossings)
-
-                ordered_indices = tuple(sorted((i1, i2, i3)))
-                if ordered_indices in used_sets:
-                    continue
-
-                if (a2s < a1e and a3e < a1e and a3e > a2s and
-                    a3s > a1e and a2e > a3s):
-                    representations_sum_1 += sign1 * sign2 * sign3
-                    used_sets.add(ordered_indices)
-                if (a2e < a1e and a3s < a1e and a3s > a2e and
-                    a2s > a1e and a3e > a2s):
-                    representations_sum_2 += sign1 * sign2 * sign3
-                    used_sets.add(ordered_indices)
-
-                    
-    return representations_sum_1 / 2. + representations_sum_2
-
-    
-
-```
-
-### `log://turn_29/get/env%3A/turn_27/cat_/app/pyknotid/setup.py_1`
-scheme=log action=get attrs={"path":"env://turn_27/cat_/app/pyknotid/setup.py_1","lineStart":1,"lineEnd":130,"totalLines":130,"action":"get"}
-
-```
-env://turn_27/cat_/app/pyknotid/setup.py_1
-[lines 1–130 / 130 total]
-from setuptools import setup, find_packages
-from distutils.extension import Extension
-
-from os.path import join, sep, dirname
-from os import walk, environ
-import glob
-import re
-
-
-package_data = {}
-
-def recursively_include(results, directory, patterns):
-    for root, subfolders, files in walk(directory):
-        for fn in files:
-            if not any([glob.fnmatch.fnmatch(fn, pattern) for pattern in patterns]):
-                continue
-            filename = join(root, fn)
-            directory = 'pyknotid'
-            if directory not in results:
-                results[directory] = []
-            results[directory].append(join(*filename.split(sep)[1:]))
-
-recursively_include(package_data, 'pyknotid',
-                    ['*.tmpl', '*.pov', '*.pyx', '*.pxd',
-                     '*.py',
-                     ])
-
-# Build cython components if possible
-try:
-    from Cython.Build import cythonize
-    import numpy
-except ImportError:
-    print('Cython or numpy could not be imported, so cythonised calculation '
-          'functions will not be built. pyknotid will use Python-only '
-          'routines instead. These are slower, but will return the '
-          'same result.')
-    print('To build the cython components, install cython and numpy and rebuild '
-          'pyknotid.')
-    ext_modules = []
-    include_dirs = []
-else:
-    ext_modules = [
-            Extension("pyknotid.spacecurves.chelpers", ["pyknotid/spacecurves/chelpers.pyx"],
-                    libraries=["m"]),
-            Extension("pyknotid.spacecurves.ccomplexity", ["pyknotid/spacecurves/ccomplexity.pyx"],
-                    libraries=["m"]),
-            Extension("pyknotid.simplify.coctree", ["pyknotid/simplify/coctree.pyx"],
-                    libraries=["m"]),
-            Extension("pyknotid.cinvariants", ["pyknotid/cinvariants.pyx"],
-                    libraries=["m"]),
-            ]
-    ext_modules = cythonize(ext_modules)
-    include_dirs = [numpy.get_include()]
-
-pyknotid_init_filen = join(dirname(__file__), 'pyknotid', '__init__.py')
-version = None
-try:
-    with open(pyknotid_init_filen) as fileh:
-        lines = fileh.readlines()
-except IOError:
-    pass
-else:
-    for line in lines:
-        line = line.strip()
-        if line.startswith('__version__ = '):
-            matches = re.findall(r'["\'].+["\']', line)
-            if matches:
-                version = matches[0].strip("'").strip('"')
-                break
-if version is None:
-    raise Exception('Error: version could not be loaded from {}'.format(pyknotid_init_filen))
-
-if 'READTHEDOCS' in environ and environ['READTHEDOCS'] == 'True':
-    print('Installing for doc only')
-    install_requires=['numpy', 'peewee', 'vispy', 'sympy']
-else:
-    install_requires=['numpy', 'networkx', 'planarity',
-                      'peewee', 'vispy', 'sympy', 'appdirs',
-                      'requests', 'tqdm'],
-
-long_description = '''
-Pyknotid
-========
-
-Python (and optional Cython) modules for detecting and measuring
-knotting and linking. pyknotid can analyse space-curves, i.e. sets of
-points in three-dimensions, or can parse standard topological
-representations of knot diagrams.
-
-A graphical interface to some of these tools is available online at
-`Knot ID <http://inclem.net/knotidentifier>`__.
-
-pyknotid was developed as part of the Leverhulme Trust Research
-Programme Grant RP2013-K-009: Scientific Properties of Complex Knots
-(SPOCK), a collaboration between the University of Bristol and Durham
-University in the UK. For more information, see the `SPOCK homepage
-<http://www.maths.dur.ac.uk/spock/index.html/>`__.
-
-If you use pyknotid in your research, please `cite us
-<http://pyknotid.readthedocs.io/en/latest/sources/about.html#cite-us>`__.
-
-Questions or comments are welcome, please email alexander.taylor@bristol.ac.uk.
-
-Documentation
--------------
-
-pyknotid is documented online at `readthedocs
-<http://pyknotid.readthedocs.io/en/latest/sources/overview.html>`__.
-'''
-
-setup(
-    name='pyknotid',
-    version=version,
-    description=('Tools for identifying and analysing knots, in space-curves '
-                 'or standard topological representations'),
-    long_description=long_description,
-    author='Alexander Taylor',
-    author_email='alexander.taylor@bristol.ac.uk',
-    install_requires=install_requires,
-    ext_modules=ext_modules,
-    include_dirs=include_dirs,
-    packages=find_packages(),
-    package_data=package_data,
-    entry_points={
-        'console_scripts': [
-            'analyse-knot-file = pyknotid.cli.analyse_knot_file:main',
-            'plot-knot = pyknotid.cli.plot_knot:main']
-        }
-)
-
-```
-
-### `log://turn_29/set/known%3A/pyknotid/build-process`
-scheme=log action=set attrs={"path":"known://pyknotid/build-process","patch":"===================================================================\n--- known://pyknotid/build-process\told\t\n+++ known://pyknotid/build-process\tnew\t\n@@ -0,0 +1,39 @@\n+# Related\n+[prompt](prompt://1) \n+[unknown resolved](unknown://pyknotid/build-process)\n+[setup.py full](env://turn_27/cat_/app/pyknotid/setup.py_1)\n+[cinvariants.pyx full](env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1)\n+[pyknotid/ ls](env://turn_16/ls_-la_/app/pyknotid/pyknotid_1)\n+[repo structure](known://pyknotid/repo-structure)\n+\n+# Pyknotid Build Process (v0.5.3)\n+\n+## Install Steps\n+```\n+cd /app/pyknotid\n+pip install .  # or python setup.py build_ext --inplace; pip install -e .\n+```\n+\n+## Dependencies (from setup.py)\n+- Core: numpy, Cython (for build)\n+- Runtime: numpy, networkx, planarity, peewee, vispy, sympy, appdirs, requests, tqdm\n+- Exts need: libm\n+\n+## Cython Extensions Defined\n+```\n+1. pyknotid.spacecurves.chelpers → pyknotid/spacecurves/chelpers.pyx  [MISSING]\n+2. pyknotid.spacecurves.ccomplexity → pyknotid/spacecurves/ccomplexity.pyx  [MISSING] \n+3. pyknotid.simplify.coctree → pyknotid/simplify/coctree.pyx  [MISSING]\n+4. pyknotid.cinvariants → pyknotid/cinvariants.pyx  [FOUND: 2121 bytes]\n+```\n+- Only cinvariants.pyx exists in root; others absent in this clone\n+- Build will fail on missing .pyx → need to locate/create stubs or disable\n+\n+## Numpy 2.3.0 Status\n+- No obvious incompat in promoted cinvariants.pyx (uses basic np/cython)\n+- Potential issues in missing exts or during cythonize()\n+\n+## Next Actions\n+1. env cd /app/pyknotid && ls pyknotid/spacecurves/ pyknotid/simplify/\n+2. pip install cython numpy\n+3. Attempt build, capture errors\n\\n","merge":"<<<<<<< SEARCH\n=======\n# Related\n[prompt](prompt://1) \n[unknown resolved](unknown://pyknotid/build-process)\n[setup.py full](env://turn_27/cat_/app/pyknotid/setup.py_1)\n[cinvariants.pyx full](env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1)\n[pyknotid/ ls](env://turn_16/ls_-la_/app/pyknotid/pyknotid_1)\n[repo structure](known://pyknotid/repo-structure)\n\n# Pyknotid Build Process (v0.5.3)\n\n## Install Steps\n```\ncd /app/pyknotid\npip install .  # or python setup.py build_ext --inplace; pip install -e .\n```\n\n## Dependencies (from setup.py)\n- Core: numpy, Cython (for build)\n- Runtime: numpy, networkx, planarity, peewee, vispy, sympy, appdirs, requests, tqdm\n- Exts need: libm\n\n## Cython Extensions Defined\n```\n1. pyknotid.spacecurves.chelpers → pyknotid/spacecurves/chelpers.pyx  [MISSING]\n2. pyknotid.spacecurves.ccomplexity → pyknotid/spacecurves/ccomplexity.pyx  [MISSING] \n3. pyknotid.simplify.coctree → pyknotid/simplify/coctree.pyx  [MISSING]\n4. pyknotid.cinvariants → pyknotid/cinvariants.pyx  [FOUND: 2121 bytes]\n```\n- Only cinvariants.pyx exists in root; others absent in this clone\n- Build will fail on missing .pyx → need to locate/create stubs or disable\n\n## Numpy 2.3.0 Status\n- No obvious incompat in promoted cinvariants.pyx (uses basic np/cython)\n- Potential issues in missing exts or during cythonize()\n\n## Next Actions\n1. env cd /app/pyknotid && ls pyknotid/spacecurves/ pyknotid/simplify/\n2. pip install cython numpy\n3. Attempt build, capture errors\n>>>>>>> REPLACE","beforeTokens":0,"afterTokens":727,"summary":"pyknotid,build,install,cython,extensions,setup.py,deps,steps","action":"set"}
-
-```
-# Related
-[prompt](prompt://1) 
-[unknown resolved](unknown://pyknotid/build-process)
-[setup.py full](env://turn_27/cat_/app/pyknotid/setup.py_1)
-[cinvariants.pyx full](env://turn_27/cat_/app/pyknotid/pyknotid/cinvariants.pyx_1)
-[pyknotid/ ls](env://turn_16/ls_-la_/app/pyknotid/pyknotid_1)
-[repo structure](known://pyknotid/repo-structure)
-
-# Pyknotid Build Process (v0.5.3)
-
-## Install Steps
-ʼ``
-cd /app/pyknotid
-pip install .  # or python setup.py build_ext --inplace; pip install -e .
-ʼ``
-
-## Dependencies (from setup.py)
-- Core: numpy, Cython (for build)
-- Runtime: numpy, networkx, planarity, peewee, vispy, sympy, appdirs, requests, tqdm
-- Exts need: libm
-
-## Cython Extensions Defined
-ʼ``
-1. pyknotid.spacecurves.chelpers → pyknotid/spacecurves/chelpers.pyx  [MISSING]
-2. pyknotid.spacecurves.ccomplexity → pyknotid/spacecurves/ccomplexity.pyx  [MISSING] 
-3. pyknotid.simplify.coctree → pyknotid/simplify/coctree.pyx  [MISSING]
-4. pyknotid.cinvariants → pyknotid/cinvariants.pyx  [FOUND: 2121 bytes]
-ʼ``
-- Only cinvariants.pyx exists in root; others absent in this clone
-- Build will fail on missing .pyx → need to locate/create stubs or disable
-
-## Numpy 2.3.0 Status
-- No obvious incompat in promoted cinvariants.pyx (uses basic np/cython)
-- Potential issues in missing exts or during cythonize()
-
-## Next Actions
-1. env cd /app/pyknotid && ls pyknotid/spacecurves/ pyknotid/simplify/
-2. pip install cython numpy
-3. Attempt build, capture errors
-```
-
-### `log://turn_29/set/unknown%3A/pyknotid/build-process`
-scheme=log action=set attrs={}
-
-```
-unknown://pyknotid/build-process set to summarized
-```
-
-### `log://turn_29/env/cd_/app/pyknotid_%26%26_ls_-la_pyknotid/spacecurves/_pyknotid/simplify/_2%3E/dev/null_`
-scheme=log action=env attrs={"command":"cd /app/pyknotid && ls -la pyknotid/spacecurves/ pyknotid/simplify/ 2>/dev/null || echo \"dirs missing\"","summary":"cd /app/pyknotid && ls -la pyknotid/spacecurves/ pyknotid/simplify/ 2>/dev/null || echo \"dirs missing\"","action":"env"}
-
-```
-ran 'cd /app/pyknotid && ls -la pyknotid/spacecurves/ pyknotid/simplify/ 2>/dev/null || echo "dirs missing"', exit=0 (0s). Output: env://turn_29/cd_/app/pyknotid_%26%26_ls_-la_pyknotid/spacecurves/_pyknotid/simplify/_2%3E/dev/null__1 (634 tokens), env://turn_29/cd_/app/pyknotid_%26%26_ls_-la_pyknotid/spacecurves/_pyknotid/simplify/_2%3E/dev/null__2 (0 tokens)
-```
-
-### `log://turn_29/update/distilled_build-process%3B_checking_missing_.pyx_dirs`
-scheme=log action=update attrs={"status":155,"action":"update"}
-
-```
-distilled build-process; checking missing .pyx dirs
-```
-