removed transonic

.github/workflows/publish_from_sanpy.yml

@@ -17,7 +17,6 @@ jobs:
           fail-fast: false
           matrix:
             python-version:
-            - ["3.8", "cp38"]
             - ["3.9", "cp39"]
             - ["3.10", "cp310"]
             - ["3.11", "cp311"]
@@ -55,7 +54,10 @@ jobs:
         strategy:
           fail-fast: false
           matrix:
-            python-version: ["3.8", "3.9", "3.10", "3.11"]
+            python-version:
+            - ["3.9", "cp39"]
+            - ["3.10", "cp310"]
+            - ["3.11", "cp311"]
         steps:
         - uses: actions/checkout@v3
         - name: Set up Python ${{ matrix.python-version }}
@@ -83,7 +85,10 @@ jobs:
         strategy:
           fail-fast: false
           matrix:
-            python-version: ["3.8", "3.9", "3.10", "3.11"]
+            python-version:
+            - ["3.9", "cp39"]
+            - ["3.10", "cp310"]
+            - ["3.11", "cp311"]
         steps:
         - uses: actions/checkout@v3
         - name: Set up Python cudmore ${{ matrix.python-version }}

MANIFEST.in

@@ -1,2 +1,2 @@
 include brightest_path_lib/cost/reciprocal_transonic.py
-include brightest_path_lib/heuristic/euclidean_transonic.py
+include brightest_path_lib/heuristic/euclidean_transonic.py

README.md

@@ -22,12 +22,16 @@ Contributions are very welcome. Tests can be run with `pytest`, please ensure th
 
 To contribute to this package, first checkout the code. Then create a new virtual environment:
 
-    cd brightest-path-lib
-    python -m venv brightest-venv
-    source brightest-venv/bin/activate
-
+ - With venv
+    python -m venv brightest-env
+    source brightest-env/bin/activate
+ - With conda
+    conda create -y -n brightest-env python=3.9
+    conda activate brightest-env
+
 Now install the package with the testing dependencies:
 
+    cd brightest-path-lib
     pip install -e '.[test]'
 
 To run the tests:

brightest_path_lib/__init__.py

@@ -1,3 +1,5 @@
+DO_TRANSONIC = False
+
 # __version__ = "1.0.27"
 # from ._version import __version__
 from ._myVersion import __version__

brightest_path_lib/cost/__init__.py

@@ -1,3 +1,8 @@
 from .cost import Cost
 from .reciprocal import Reciprocal
-from .reciprocal_transonic import ReciprocalTransonic
+
+DO_TRANSONIC = False
+if DO_TRANSONIC:
+    from .reciprocal_transonic import ReciprocalTransonic
+else:
+    from .reciprocal import Reciprocal as ReciprocalTransonic

brightest_path_lib/heuristic/__init__.py

@@ -1,3 +1,13 @@
 from .heuristic import Heuristic
 from .euclidean import Euclidean
-from .euclidean_transonic import EuclideanTransonic
+
+# 20240527, making a version to not use transonic
+# was this
+# from .euclidean_transonic import EuclideanTransonic
+from .euclidean import Euclidean as EuclideanTransonic
+
+DO_TRANSONIC = False
+if DO_TRANSONIC:
+    from .reciprocal_transonic import EuclideanTransonic
+else:
+    from .euclidean import Euclidean as EuclideanTransonic

docs/index.md

@@ -27,7 +27,7 @@ With its efficient implementation and intuitive API, this library is a valuable
 - It supports both grayscale and color images and can handle images of arbitrary sizes.
 - The library also provides support for users to know which points in the image are being considered for the brightest path in real-time so that they display them on the original image.
 
-## Napi Plugin
+## Napari Plugin
 
 We have also created a [Napari Tracing Plugin](https://github.com/mapmanager/napari-tracing) to provide an intuititive graphical-user-interface that uses the `brightest-path-lib`` package. We are using this to trace neuronal dendrites and axons.
 

pyproject.toml

@@ -1,4 +1,6 @@
 [build-system]
+# as this 20240527, removing transonic
+#requires = ["setuptools", "wheel", "numpy"]
 requires = ["setuptools", "wheel", "numpy", "transonic"]
 #requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel", "numpy", "transonic"]
 build-backend = "setuptools.build_meta"

setup.py

@@ -1,75 +1,19 @@
 import os
-from pathlib import Path
-from setuptools import setup, find_packages
 import sys
-from transonic.dist import ParallelBuildExt, make_backend_files, init_transonic_extensions
-
-here = Path(__file__).parent.absolute()
-sys.path.insert(0, ".")
-
-__version__ = "1.0.55"
-# from .brightest_path_lib._myVersion import __version__
-
-TRANSONIC_BACKEND = "pythran"
-
-build_dependencies_backends = {
-    "pythran": ["pythran"],
-    "cython": ["cython"],
-    "python": [],
-    "numba": ["numba"],
-}
-
-# setup_requires = ['setuptools_scm']
-setup_requires = []
-setup_requires.extend(build_dependencies_backends[TRANSONIC_BACKEND])
-
-def transonize():
-    paths = [
-        "brightest_path_lib/cost/reciprocal_transonic.py",
-        "brightest_path_lib/heuristic/euclidean_transonic.py"
-    ]
-    make_backend_files([here / path for path in paths], backend=TRANSONIC_BACKEND)
-
-def create_pythran_extensions():
-    import numpy as np
-
-    extensions = init_transonic_extensions(
-        # "brightest-path-lib",
-        "brightest_path_lib",
-        backend=TRANSONIC_BACKEND,
-        include_dirs=np.get_include(),
-        compile_args=("-O3", f"-march=native", "-DUSE_XSIMD"),
-        # compile_args=("-O2", "-DUSE_XSIMD"),
-    )
-    return extensions
+from setuptools import setup, find_packages
 
-def create_extensions():
-    transonize()
-    return create_pythran_extensions()
+VERSION = "1.0.56"
 
 packages = find_packages(exclude=["tests"])
 print(f"found packages: {packages}")
 
+setup_requires = ['numpy']
+
 # load the readme
 _thisPath = os.path.abspath(os.path.dirname(__file__))
 with open(os.path.abspath(_thisPath+"/README.md")) as f:
     long_description = f.read()
 
-# def myversion():
-#     from setuptools_scm.version import SEMVER_MINOR, guess_next_simple_semver, release_branch_semver_version
-
-#     def my_release_branch_semver_version(version):
-#         v = release_branch_semver_version(version)
-#         if v == version.format_next_version(guess_next_simple_semver, retain=SEMVER_MINOR):
-#             # return version.format_next_version(guess_next_simple_semver, fmt="{guessed}")  # , retain=SEMVER_MINOR)
-#             return version.format_next_version(guess_next_simple_semver, fmt="{guessed}", retain=SEMVER_MINOR)
-#         return v
-
-#     return {
-#         'version_scheme': my_release_branch_semver_version,
-#         'local_scheme': 'no-local-version',
-#     }
-
 setup(
     name="brightest-path-lib",
     description="A library of path-finding algorithms to find the brightest path between points in an image.",
@@ -83,16 +27,15 @@ def create_extensions():
         "Changelog": "https://github.com/mapmanager/brightest-path-lib/releases",
     },
     license="GNU General Public License, Version 3",
-    # version=VERSION,
-    version=__version__,
+    version=VERSION,
     #packages=["brightest_path_lib"],
     #packages=find_packages(),
     packages=packages,
-    # use_scm_version=myversion,  #True,
     setup_requires=setup_requires,
     install_requires=["numpy", "transonic"],
     extras_require={
         'dev': [
+            'jupyter',
             'mkdocs',
             'mkdocs-material',
             'mkdocs-jupyter',
@@ -106,7 +49,5 @@ def create_extensions():
             "pooch"
         ]
     },
-    python_requires=">=3.8",  # transonic requires >= 3.9
-    cmdclass={"build_ext": ParallelBuildExt},
-    ext_modules=create_extensions(),
-)
+    python_requires=">=3.9",
+)