cppkh-interface 0.1.3__tar.gz → 0.2.1__tar.gz

{cppkh_interface-0.1.3 → cppkh_interface-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cppkh-interface
-Version: 0.1.3
+Version: 0.2.1
 Summary: Dependency-free Python interface for cppkh with runtime C++ compilation.
 License-Expression: MIT
 Author: GGN_2015
@@ -22,7 +22,7 @@ Description-Content-Type: text/markdown
 `cppkh-interface` is a Python package for computing integer Khovanov homology
 with the C++ `cppkh` implementation.
 
-Version `0.1.3` has no runtime Python-package dependencies. Link crossing signs,
+The package has no runtime Python-package dependencies. Link crossing signs,
 PD validation, R1 removal, and nugatory-crossing removal all use the bundled
 canonical `cppkh` C++ source and its SageMath-compatible orientation rules.
 
@@ -36,6 +36,23 @@ print(cppkh_interface.solve_khovanov(pd_code, de_r1=True, de_k8=True))
 print(cppkh_interface.solve_many_khovanov([pd_code, pd_code]))
 ```
 
+For a multi-component oriented link, callers can compute several explicit
+crossing-sign variants without changing the existing APIs:
+
+```python
+from cppkh_interface import compute_signed_variants
+
+hopf = [[2, 3, 1, 4], [4, 1, 3, 2]]
+results = compute_signed_variants(hopf, [[-1, -1], [1, 1]])
+assert len(results) == 2
+```
+
+Each sign row must contain exactly one `-1` or `1` for every crossing. This
+operation deliberately disables PD simplification because removing a crossing
+would invalidate the positional sign mapping. `solve_khovanov` and
+`solve_many_khovanov` retain their original signatures, inferred-sign behavior,
+and simplification defaults.
+
 Unlike wrappers that ship a prebuilt DLL or shared object, this package ships
 the `cppkh` C++ source file in built distributions and compiles a local
 executable on first use using only Python's standard library. The compiled

{cppkh_interface-0.1.3 → cppkh_interface-0.2.1}/README.md

@@ -1,68 +1,85 @@
-# cppkh-interface
-
-`cppkh-interface` is a Python package for computing integer Khovanov homology
-with the C++ `cppkh` implementation.
-
-Version `0.1.3` has no runtime Python-package dependencies. Link crossing signs,
-PD validation, R1 removal, and nugatory-crossing removal all use the bundled
-canonical `cppkh` C++ source and its SageMath-compatible orientation rules.
-
-The package is compatible with the main `javakh-interface` function:
-
-```python
-import cppkh_interface
-
-pd_code = [[1, 5, 2, 4], [3, 1, 4, 6], [5, 3, 6, 2]]
-print(cppkh_interface.solve_khovanov(pd_code, de_r1=True, de_k8=True))
+# cppkh-interface
+
+`cppkh-interface` is a Python package for computing integer Khovanov homology
+with the C++ `cppkh` implementation.
+
+The package has no runtime Python-package dependencies. Link crossing signs,
+PD validation, R1 removal, and nugatory-crossing removal all use the bundled
+canonical `cppkh` C++ source and its SageMath-compatible orientation rules.
+
+The package is compatible with the main `javakh-interface` function:
+
+```python
+import cppkh_interface
+
+pd_code = [[1, 5, 2, 4], [3, 1, 4, 6], [5, 3, 6, 2]]
+print(cppkh_interface.solve_khovanov(pd_code, de_r1=True, de_k8=True))
 print(cppkh_interface.solve_many_khovanov([pd_code, pd_code]))
 ```
 
-Unlike wrappers that ship a prebuilt DLL or shared object, this package ships
-the `cppkh` C++ source file in built distributions and compiles a local
-executable on first use using only Python's standard library. The compiled
-executable is cached for later calls.
-
-In the repository checkout, the package does not keep a committed backup copy
-of the C++ source. The build backend copies `../../src/main.cpp` into the
-package data directory only while the PEP 517 build is running, then removes
-that temporary copy.
-
-## Install
-
-```sh
-pip install cppkh-interface
-```
-
-A C++14 compiler must be available at runtime. The package looks at
-`CPPKH_INTERFACE_CXX`, then `CXX`, then searches `PATH` for `g++`, `clang++`, or
-`c++`. To select a compiler explicitly:
+For a multi-component oriented link, callers can compute several explicit
+crossing-sign variants without changing the existing APIs:
 
-```sh
-CPPKH_INTERFACE_CXX=clang++ python your_script.py
-```
-
-Windows PowerShell:
-
-```powershell
-$env:CPPKH_INTERFACE_CXX = "C:\path\to\g++.exe"
-python your_script.py
-```
-
-## Build And Publish
-
-From this directory:
+```python
+from cppkh_interface import compute_signed_variants
 
-```sh
-python -m build
-poetry publish
+hopf = [[2, 3, 1, 4], [4, 1, 3, 2]]
+results = compute_signed_variants(hopf, [[-1, -1], [1, 1]])
+assert len(results) == 2
 ```
 
-Do not use `poetry build` or `poetry publish --build`: Poetry's direct builder
-bypasses the source-synchronizing PEP 517 backend. Build first with
-`python -m build`, inspect/test the wheel, then publish the existing artifacts.
-
-For local testing:
-
-```sh
-poetry run python -m cppkh_interface "[[1,5,2,4], [3,1,4,6], [5,3,6,2]]"
-```
+Each sign row must contain exactly one `-1` or `1` for every crossing. This
+operation deliberately disables PD simplification because removing a crossing
+would invalidate the positional sign mapping. `solve_khovanov` and
+`solve_many_khovanov` retain their original signatures, inferred-sign behavior,
+and simplification defaults.
+
+Unlike wrappers that ship a prebuilt DLL or shared object, this package ships
+the `cppkh` C++ source file in built distributions and compiles a local
+executable on first use using only Python's standard library. The compiled
+executable is cached for later calls.
+
+In the repository checkout, the package does not keep a committed backup copy
+of the C++ source. The build backend copies `../../src/main.cpp` into the
+package data directory only while the PEP 517 build is running, then removes
+that temporary copy.
+
+## Install
+
+```sh
+pip install cppkh-interface
+```
+
+A C++14 compiler must be available at runtime. The package looks at
+`CPPKH_INTERFACE_CXX`, then `CXX`, then searches `PATH` for `g++`, `clang++`, or
+`c++`. To select a compiler explicitly:
+
+```sh
+CPPKH_INTERFACE_CXX=clang++ python your_script.py
+```
+
+Windows PowerShell:
+
+```powershell
+$env:CPPKH_INTERFACE_CXX = "C:\path\to\g++.exe"
+python your_script.py
+```
+
+## Build And Publish
+
+From this directory:
+
+```sh
+python -m build
+poetry publish
+```
+
+Do not use `poetry build` or `poetry publish --build`: Poetry's direct builder
+bypasses the source-synchronizing PEP 517 backend. Build first with
+`python -m build`, inspect/test the wheel, then publish the existing artifacts.
+
+For local testing:
+
+```sh
+poetry run python -m cppkh_interface "[[1,5,2,4], [3,1,4,6], [5,3,6,2]]"
+```

{cppkh_interface-0.1.3 → cppkh_interface-0.2.1}/build_backend/cppkh_interface_build_backend.py

@@ -1,207 +1,207 @@
-from __future__ import annotations
-
-import base64
-import hashlib
-import io
-import shutil
-import tarfile
-import tempfile
-import zipfile
-from pathlib import Path
-
-from poetry.core.masonry import api as poetry_api
-
-
-PROJECT_ROOT = Path(__file__).resolve().parents[1]
-REPO_ROOT = PROJECT_ROOT.parents[1]
-SOURCE = REPO_ROOT / "src" / "main.cpp"
-TARGET = PROJECT_ROOT / "cppkh_interface" / "data" / "src" / "main.cpp"
-WHEEL_SOURCE_NAME = "cppkh_interface/data/src/main.cpp"
-
-
-def _sync_cpp_source() -> None:
-    if SOURCE.exists():
-        TARGET.parent.mkdir(parents=True, exist_ok=True)
-        shutil.copyfile(SOURCE, TARGET)
-        return
-    if TARGET.exists():
-        return
-    raise FileNotFoundError(
-        "cppkh source file was not found. Expected either "
-        f"{SOURCE} in the repository checkout or {TARGET} in the source tree."
-    )
-
-
-def _clean_cpp_source() -> None:
-    if TARGET.exists() and SOURCE.exists():
-        TARGET.unlink()
-
-
-def _source_bytes() -> bytes:
-    if TARGET.exists():
-        return TARGET.read_bytes()
-    if SOURCE.exists():
-        return SOURCE.read_bytes()
-    raise FileNotFoundError("cppkh source file was not available for packaging")
-
-
-def _wheel_hash_and_size(data: bytes) -> tuple[str, str]:
-    digest = hashlib.sha256(data).digest()
-    encoded = base64.urlsafe_b64encode(digest).rstrip(b"=").decode("ascii")
-    return f"sha256={encoded}", str(len(data))
-
-
-def _make_universal_wheel_metadata(data: bytes) -> bytes:
-    text = data.decode("utf-8")
-    lines = []
-    tag_written = False
-    root_written = False
-    for line in text.splitlines():
-        if line.startswith("Root-Is-Purelib:"):
-            lines.append("Root-Is-Purelib: true")
-            root_written = True
-        elif line.startswith("Tag:"):
-            if not tag_written:
-                lines.append("Tag: py3-none-any")
-                tag_written = True
-        else:
-            lines.append(line)
-    if not root_written:
-        lines.append("Root-Is-Purelib: true")
-    if not tag_written:
-        lines.append("Tag: py3-none-any")
-    return ("\n".join(lines) + "\n").encode("utf-8")
-
-
-def _universal_wheel_path(wheel_path: Path, record_name: str) -> Path:
-    dist_info = record_name.split("/", 1)[0]
-    base = dist_info.removesuffix(".dist-info")
-    return wheel_path.with_name(f"{base}-py3-none-any.whl")
-
-
-def _rewrite_wheel_with_source(wheel_path: Path) -> Path:
-    source_data = _source_bytes()
-    rows: list[tuple[str, str, str]] = []
-
-    with zipfile.ZipFile(wheel_path, "r") as zin:
-        record_name = next(
-            (name for name in zin.namelist() if name.endswith(".dist-info/RECORD")),
-            None,
-        )
-        if record_name is None:
-            raise RuntimeError(f"wheel RECORD file not found in {wheel_path}")
-        output_path = _universal_wheel_path(wheel_path, record_name)
-        temp_path = output_path.with_name(output_path.name + ".tmp")
-
-        with zipfile.ZipFile(temp_path, "w", compression=zipfile.ZIP_DEFLATED) as zout:
-            wheel_metadata_name = record_name.removesuffix("RECORD") + "WHEEL"
-
-            for item in zin.infolist():
-                if item.filename in (WHEEL_SOURCE_NAME, record_name):
-                    continue
-                data = zin.read(item.filename)
-                if item.filename == wheel_metadata_name:
-                    data = _make_universal_wheel_metadata(data)
-                zout.writestr(item, data)
-                if not item.is_dir():
-                    digest, size = _wheel_hash_and_size(data)
-                    rows.append((item.filename, digest, size))
-
-            source_info = zipfile.ZipInfo(WHEEL_SOURCE_NAME, date_time=(2016, 1, 1, 0, 0, 0))
-            source_info.compress_type = zipfile.ZIP_DEFLATED
-            zout.writestr(source_info, source_data)
-            digest, size = _wheel_hash_and_size(source_data)
-            rows.append((WHEEL_SOURCE_NAME, digest, size))
-
-            rows.append((record_name, "", ""))
-            record_text = "".join(f"{path},{digest},{size}\n" for path, digest, size in rows)
-            record_info = zipfile.ZipInfo(record_name, date_time=(2016, 1, 1, 0, 0, 0))
-            record_info.compress_type = zipfile.ZIP_DEFLATED
-            zout.writestr(record_info, record_text.encode("utf-8"))
-
-    temp_path.replace(output_path)
-    if output_path != wheel_path and wheel_path.exists():
-        wheel_path.unlink()
-    return output_path
-
-
-def finalize_poetry_wheels() -> None:
-    dist = PROJECT_ROOT / "dist"
-    if not dist.exists():
-        return
-    for wheel_path in sorted(dist.glob("cppkh_interface-*.whl")):
-        _rewrite_wheel_with_source(wheel_path)
-
-
-def _rewrite_sdist_with_source(sdist_path: Path) -> None:
-    source_data = _source_bytes()
-    temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".tar.gz")
-    temp_path = Path(temp_file.name)
-    temp_file.close()
-
-    try:
-        with tarfile.open(sdist_path, "r:gz") as tin, tarfile.open(temp_path, "w:gz") as tout:
-            names = tin.getnames()
-            if not names:
-                raise RuntimeError(f"sdist is empty: {sdist_path}")
-            root = names[0].split("/", 1)[0]
-            source_name = f"{root}/{WHEEL_SOURCE_NAME}"
-
-            for member in tin.getmembers():
-                if member.name == source_name:
-                    continue
-                if member.isfile():
-                    extracted = tin.extractfile(member)
-                    if extracted is None:
-                        raise RuntimeError(f"could not read {member.name} from {sdist_path}")
-                    with extracted:
-                        tout.addfile(member, extracted)
-                else:
-                    tout.addfile(member)
-
-            source_info = tarfile.TarInfo(source_name)
-            source_info.size = len(source_data)
-            source_info.mtime = 0
-            source_info.mode = 0o644
-            tout.addfile(source_info, io.BytesIO(source_data))
-
-        temp_path.replace(sdist_path)
-    finally:
-        if temp_path.exists():
-            temp_path.unlink()
-
-
-def get_requires_for_build_wheel(config_settings=None):
-    return poetry_api.get_requires_for_build_wheel(config_settings)
-
-
-def get_requires_for_build_sdist(config_settings=None):
-    return poetry_api.get_requires_for_build_sdist(config_settings)
-
-
-def prepare_metadata_for_build_wheel(metadata_directory, config_settings=None):
-    _sync_cpp_source()
-    try:
-        return poetry_api.prepare_metadata_for_build_wheel(metadata_directory, config_settings)
-    finally:
-        _clean_cpp_source()
-
-
-def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
-    _sync_cpp_source()
-    try:
-        wheel_name = poetry_api.build_wheel(wheel_directory, config_settings, metadata_directory)
-        final_path = _rewrite_wheel_with_source(Path(wheel_directory) / wheel_name)
-        return final_path.name
-    finally:
-        _clean_cpp_source()
-
-
-def build_sdist(sdist_directory, config_settings=None):
-    _sync_cpp_source()
-    try:
-        sdist_name = poetry_api.build_sdist(sdist_directory, config_settings)
-        _rewrite_sdist_with_source(Path(sdist_directory) / sdist_name)
-        return sdist_name
-    finally:
-        _clean_cpp_source()
+from __future__ import annotations
+
+import base64
+import hashlib
+import io
+import shutil
+import tarfile
+import tempfile
+import zipfile
+from pathlib import Path
+
+from poetry.core.masonry import api as poetry_api
+
+
+PROJECT_ROOT = Path(__file__).resolve().parents[1]
+REPO_ROOT = PROJECT_ROOT.parents[1]
+SOURCE = REPO_ROOT / "src" / "main.cpp"
+TARGET = PROJECT_ROOT / "cppkh_interface" / "data" / "src" / "main.cpp"
+WHEEL_SOURCE_NAME = "cppkh_interface/data/src/main.cpp"
+
+
+def _sync_cpp_source() -> None:
+    if SOURCE.exists():
+        TARGET.parent.mkdir(parents=True, exist_ok=True)
+        shutil.copyfile(SOURCE, TARGET)
+        return
+    if TARGET.exists():
+        return
+    raise FileNotFoundError(
+        "cppkh source file was not found. Expected either "
+        f"{SOURCE} in the repository checkout or {TARGET} in the source tree."
+    )
+
+
+def _clean_cpp_source() -> None:
+    if TARGET.exists() and SOURCE.exists():
+        TARGET.unlink()
+
+
+def _source_bytes() -> bytes:
+    if TARGET.exists():
+        return TARGET.read_bytes()
+    if SOURCE.exists():
+        return SOURCE.read_bytes()
+    raise FileNotFoundError("cppkh source file was not available for packaging")
+
+
+def _wheel_hash_and_size(data: bytes) -> tuple[str, str]:
+    digest = hashlib.sha256(data).digest()
+    encoded = base64.urlsafe_b64encode(digest).rstrip(b"=").decode("ascii")
+    return f"sha256={encoded}", str(len(data))
+
+
+def _make_universal_wheel_metadata(data: bytes) -> bytes:
+    text = data.decode("utf-8")
+    lines = []
+    tag_written = False
+    root_written = False
+    for line in text.splitlines():
+        if line.startswith("Root-Is-Purelib:"):
+            lines.append("Root-Is-Purelib: true")
+            root_written = True
+        elif line.startswith("Tag:"):
+            if not tag_written:
+                lines.append("Tag: py3-none-any")
+                tag_written = True
+        else:
+            lines.append(line)
+    if not root_written:
+        lines.append("Root-Is-Purelib: true")
+    if not tag_written:
+        lines.append("Tag: py3-none-any")
+    return ("\n".join(lines) + "\n").encode("utf-8")
+
+
+def _universal_wheel_path(wheel_path: Path, record_name: str) -> Path:
+    dist_info = record_name.split("/", 1)[0]
+    base = dist_info.removesuffix(".dist-info")
+    return wheel_path.with_name(f"{base}-py3-none-any.whl")
+
+
+def _rewrite_wheel_with_source(wheel_path: Path) -> Path:
+    source_data = _source_bytes()
+    rows: list[tuple[str, str, str]] = []
+
+    with zipfile.ZipFile(wheel_path, "r") as zin:
+        record_name = next(
+            (name for name in zin.namelist() if name.endswith(".dist-info/RECORD")),
+            None,
+        )
+        if record_name is None:
+            raise RuntimeError(f"wheel RECORD file not found in {wheel_path}")
+        output_path = _universal_wheel_path(wheel_path, record_name)
+        temp_path = output_path.with_name(output_path.name + ".tmp")
+
+        with zipfile.ZipFile(temp_path, "w", compression=zipfile.ZIP_DEFLATED) as zout:
+            wheel_metadata_name = record_name.removesuffix("RECORD") + "WHEEL"
+
+            for item in zin.infolist():
+                if item.filename in (WHEEL_SOURCE_NAME, record_name):
+                    continue
+                data = zin.read(item.filename)
+                if item.filename == wheel_metadata_name:
+                    data = _make_universal_wheel_metadata(data)
+                zout.writestr(item, data)
+                if not item.is_dir():
+                    digest, size = _wheel_hash_and_size(data)
+                    rows.append((item.filename, digest, size))
+
+            source_info = zipfile.ZipInfo(WHEEL_SOURCE_NAME, date_time=(2016, 1, 1, 0, 0, 0))
+            source_info.compress_type = zipfile.ZIP_DEFLATED
+            zout.writestr(source_info, source_data)
+            digest, size = _wheel_hash_and_size(source_data)
+            rows.append((WHEEL_SOURCE_NAME, digest, size))
+
+            rows.append((record_name, "", ""))
+            record_text = "".join(f"{path},{digest},{size}\n" for path, digest, size in rows)
+            record_info = zipfile.ZipInfo(record_name, date_time=(2016, 1, 1, 0, 0, 0))
+            record_info.compress_type = zipfile.ZIP_DEFLATED
+            zout.writestr(record_info, record_text.encode("utf-8"))
+
+    temp_path.replace(output_path)
+    if output_path != wheel_path and wheel_path.exists():
+        wheel_path.unlink()
+    return output_path
+
+
+def finalize_poetry_wheels() -> None:
+    dist = PROJECT_ROOT / "dist"
+    if not dist.exists():
+        return
+    for wheel_path in sorted(dist.glob("cppkh_interface-*.whl")):
+        _rewrite_wheel_with_source(wheel_path)
+
+
+def _rewrite_sdist_with_source(sdist_path: Path) -> None:
+    source_data = _source_bytes()
+    temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".tar.gz")
+    temp_path = Path(temp_file.name)
+    temp_file.close()
+
+    try:
+        with tarfile.open(sdist_path, "r:gz") as tin, tarfile.open(temp_path, "w:gz") as tout:
+            names = tin.getnames()
+            if not names:
+                raise RuntimeError(f"sdist is empty: {sdist_path}")
+            root = names[0].split("/", 1)[0]
+            source_name = f"{root}/{WHEEL_SOURCE_NAME}"
+
+            for member in tin.getmembers():
+                if member.name == source_name:
+                    continue
+                if member.isfile():
+                    extracted = tin.extractfile(member)
+                    if extracted is None:
+                        raise RuntimeError(f"could not read {member.name} from {sdist_path}")
+                    with extracted:
+                        tout.addfile(member, extracted)
+                else:
+                    tout.addfile(member)
+
+            source_info = tarfile.TarInfo(source_name)
+            source_info.size = len(source_data)
+            source_info.mtime = 0
+            source_info.mode = 0o644
+            tout.addfile(source_info, io.BytesIO(source_data))
+
+        temp_path.replace(sdist_path)
+    finally:
+        if temp_path.exists():
+            temp_path.unlink()
+
+
+def get_requires_for_build_wheel(config_settings=None):
+    return poetry_api.get_requires_for_build_wheel(config_settings)
+
+
+def get_requires_for_build_sdist(config_settings=None):
+    return poetry_api.get_requires_for_build_sdist(config_settings)
+
+
+def prepare_metadata_for_build_wheel(metadata_directory, config_settings=None):
+    _sync_cpp_source()
+    try:
+        return poetry_api.prepare_metadata_for_build_wheel(metadata_directory, config_settings)
+    finally:
+        _clean_cpp_source()
+
+
+def build_wheel(wheel_directory, config_settings=None, metadata_directory=None):
+    _sync_cpp_source()
+    try:
+        wheel_name = poetry_api.build_wheel(wheel_directory, config_settings, metadata_directory)
+        final_path = _rewrite_wheel_with_source(Path(wheel_directory) / wheel_name)
+        return final_path.name
+    finally:
+        _clean_cpp_source()
+
+
+def build_sdist(sdist_directory, config_settings=None):
+    _sync_cpp_source()
+    try:
+        sdist_name = poetry_api.build_sdist(sdist_directory, config_settings)
+        _rewrite_sdist_with_source(Path(sdist_directory) / sdist_name)
+        return sdist_name
+    finally:
+        _clean_cpp_source()

{cppkh_interface-0.1.3 → cppkh_interface-0.2.1}/cppkh_interface/__init__.py

@@ -1,25 +1,29 @@
-from .main import (
-    CppkhInterfaceError,
-    compile_cppkh,
-    compute_many_pd,
-    compute_pd,
-    get_cppkh_executable,
-    normalize_pd_code,
-    normalize_pd_codes,
-    simplify_pd,
-    solve_many_khovanov,
-    solve_khovanov,
-)
-
-__all__ = [
-    "CppkhInterfaceError",
-    "compile_cppkh",
-    "compute_many_pd",
-    "compute_pd",
-    "get_cppkh_executable",
-    "normalize_pd_code",
-    "normalize_pd_codes",
-    "simplify_pd",
-    "solve_many_khovanov",
-    "solve_khovanov",
-]
+from .main import (
+    CppkhInterfaceError,
+    compile_cppkh,
+    compile_cppkh_shared,
+    compute_signed_variants,
+    compute_many_pd,
+    compute_pd,
+    get_cppkh_executable,
+    normalize_pd_code,
+    normalize_pd_codes,
+    simplify_pd,
+    solve_many_khovanov,
+    solve_khovanov,
+)
+
+__all__ = [
+    "CppkhInterfaceError",
+    "compile_cppkh",
+    "compile_cppkh_shared",
+    "compute_signed_variants",
+    "compute_many_pd",
+    "compute_pd",
+    "get_cppkh_executable",
+    "normalize_pd_code",
+    "normalize_pd_codes",
+    "simplify_pd",
+    "solve_many_khovanov",
+    "solve_khovanov",
+]

{cppkh_interface-0.1.3 → cppkh_interface-0.2.1}/cppkh_interface/__main__.py

@@ -1,4 +1,4 @@
-from .main import main
-
-if __name__ == "__main__":
-    raise SystemExit(main())
+from .main import main
+
+if __name__ == "__main__":
+    raise SystemExit(main())