Add fastseq source files from sctk branch

Signed-off-by: Jono Yang <jyang@nexb.com>

Author: JonoYang

.gitignore

@@ -1,5 +1,6 @@
 # Python compiled files
 *.py[cod]
+src/**/*.so
 
 # virtualenv and other misc bits
 /src/*.egg-info

README.rst

@@ -1,107 +1,4 @@
-A Simple Python Project Skeleton
-================================
+fastseq
+=======
 
-This repo attempts to standardize the structure of the Python-based project's
-repositories using modern Python packaging and configuration techniques.
-Using this `blog post`_ as inspiration, this repository serves as the base for
-all new Python projects and is mergeable in existing repositories as well.
-
-.. _blog post: https://blog.jaraco.com/a-project-skeleton-for-python-projects/
-
-
-Usage
-=====
-
-A brand new project
--------------------
-
-.. code-block:: bash
-
-    git init my-new-repo
-    cd my-new-repo
-    git pull git@github.com:nexB/skeleton
-
-    # Create the new repo on GitHub, then update your remote
-    git remote set-url origin git@github.com:nexB/your-new-repo.git
-
-From here, you can make the appropriate changes to the files for your specific project.
-
-Update an existing project
----------------------------
-
-.. code-block:: bash
-
-    cd my-existing-project
-    git remote add skeleton git@github.com:nexB/skeleton
-    git fetch skeleton
-    git merge skeleton/main --allow-unrelated-histories
-
-This is also the workflow to use when updating the skeleton files in any given repository.
-
-More usage instructions can be found in ``docs/skeleton-usage.rst``.
-
-
-Release Notes
-=============
-
-- 2025-03-31:
-
-    - Use ruff as the main code formatting tool, add ruff rules to pyproject.toml
-
-- 2025-03-29:
-
-    - Add support for beta macOS-15
-    - Add support for beta windows-2025
-
-- 2025-02-14:
-
-    - Drop support for Python 3.8, add support in CI for Python 3.13, use Python 3.12 as default
-      version.
-
-- 2025-01-17:
-
-    - Drop support for macOS-12, add support for macOS-14
-    - Add support in CI for ubuntu-24.04
-    - Add support in CI for Python 3.12
-
-- 2024-08-20:
-
-    - Update references of ownership from nexB to aboutcode-org
-
-- 2024-07-01:
-
-    - Drop support for Python 3.8
-    - Drop support for macOS-11, add support for macOS-14
-
-- 2024-02-19:
-
-    - Replace support in CI of default ubuntu-20.04 by ubuntu-22.04
-
-- 2023-10-18:
-
-    - Add dark mode support in documentation
-
-- 2023-07-18:
-
-    - Add macOS-13 job in azure-pipelines.yml
-
-- 2022-03-04:
-
-    - Synchronize configure and configure.bat scripts for sanity
-    - Update CI operating system support with latest Azure OS images
-    - Streamline utility scripts in etc/scripts/ to create, fetch and manage third-party
-      dependencies. There are now fewer scripts. See etc/scripts/README.rst for details
-
-- 2021-09-03:
-    - ``configure`` now requires pinned dependencies via the use of ``requirements.txt``
-      and ``requirements-dev.txt``
-    - ``configure`` can now accept multiple options at once
-    - Add utility scripts from scancode-toolkit/etc/release/ for use in generating project files
-    - Rename virtual environment directory from ``tmp`` to ``venv``
-    - Update README.rst with instructions for generating ``requirements.txt``
-      and ``requirements-dev.txt``, as well as collecting dependencies as wheels and generating
-      ABOUT files for them.
-
-- 2021-05-11:
-    - Adopt new configure scripts from ScanCode TK that allows correct configuration of which
-      Python version is used.
+This library is a Cython version of scancode-toolkit's ``licensedcode.seq``.

configure

@@ -117,6 +117,7 @@ create_virtualenv() {
             --no-vcs-ignore \
             $CFG_QUIET \
             "$CFG_ROOT_DIR/$VENV_DIR"
+        "$CFG_BIN_DIR/pip" install cython
     fi
 }
 

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools >= 50", "wheel", "setuptools_scm[toml] >= 6"]
+requires = ["setuptools >= 50", "wheel", "setuptools_scm[toml] >= 6", "Cython"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
@@ -68,7 +68,7 @@ include = [
   "."
 
 ]
-# ignore test data and testfiles: they should never be linted nor formatted 
+# ignore test data and testfiles: they should never be linted nor formatted
 exclude = [
 # main style
   "**/tests/data/**/*",

setup.cfg

@@ -1,12 +1,12 @@
 [metadata]
-name = skeleton
+name = fastseq
 license = Apache-2.0
 
 # description must be on ONE line https://github.com/pypa/setuptools/issues/1390
-description = skeleton
+description = "A Cython version of ScanCode-toolkit's licensedcode.seq"
 long_description = file:README.rst
 long_description_content_type = text/x-rst
-url = https://github.com/aboutcode-org/skeleton
+url = https://github.com/aboutcode-org/fastseq
 
 author = nexB. Inc. and others
 author_email = info@aboutcode.org

setup.py

@@ -1,6 +1,12 @@
 #!/usr/bin/env python
 
 import setuptools
+from Cython.Build import cythonize
+
+
+extensions = [
+    setuptools.Extension("fastseq._seq", ["src/fastseq/_seq.pyx"], language="c++"),
+]
 
 if __name__ == "__main__":
-    setuptools.setup()
+    setuptools.setup(ext_modules=cythonize(extensions))

src/README.rst

@@ -0,0 +1,10 @@
+#
+# Copyright (c) nexB Inc. and others. All rights reserved.
+# fastseq is a trademark of nexB Inc.
+# SPDX-License-Identifier: Apache-2.0
+# See http://www.apache.org/licenses/LICENSE-2.0 for the license text.
+# See https://github.com/aboutcode-org/fastseq for support or download.
+# See https://aboutcode.org for more information about nexB OSS projects.
+#
+
+from ._seq import *