-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* align_ct_on_T1_2 * flake8 * added "align_ct_on_T1_2" by default * segment_skull
- Loading branch information
1 parent
f3e8ccc
commit 39b769c
Showing
11 changed files
with
125 additions
and
80 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,2 +1,4 @@ | ||
|
|
||
| include workflows/params*.json | ||
|
|
||
| include skullTo3d/_version.py |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| [build-system] | ||
| requires = [ | ||
| "setuptools", "wheel" | ||
| ] | ||
| build-backend = "setuptools.build_meta" | ||
|
|
||
| [project] | ||
| dynamic = ['version'] | ||
| name = "skullTo3d" | ||
| maintainers = [{name = "SkullTo3d developers" }] | ||
| authors= [{name = "Macatools team"}] | ||
| description= "Pipeline for skull extraction for macaque/marmoset " | ||
| readme = {content-type = "text/markdown", file = "README.md"} | ||
| requires-python = ">= 3.10" | ||
| license = {text = "BSD-3-Clause"} | ||
|
|
||
| dependencies = [ | ||
| "macapype", | ||
| "matplotlib" | ||
| ] | ||
|
|
||
| [project.optional-dependencies] | ||
| # Dependencies for building the documentation | ||
| doc_deps = [ | ||
| "sphinx", | ||
| "sphinx-gallery", | ||
| "sphinx_bootstrap_theme", | ||
| "numpydoc", | ||
| "sphinxcontrib-fulltoc" | ||
| ] | ||
|
|
||
| # Dependencies for test | ||
| test_deps = [ | ||
| "pytest", | ||
| "pytest-cov", | ||
| "codecov", | ||
| ] | ||
| flake_deps = [ | ||
| "flake8" | ||
| ] | ||
|
|
||
| # real calls | ||
| test=["skullTo3d[test_deps, flake_deps]"] | ||
| doc=["skullTo3d[flake_deps, test_deps, doc_deps]"] | ||
|
|
||
| [project.scripts] | ||
| segment_skull = "workflows.segment_skull:main" | ||
|
|
||
| [tool.setuptools.packages] | ||
| find = {} # Scanning implicit namespaces is active by default |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,59 +1,28 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
|
|
||
| from setuptools import setup | ||
| import re | ||
| from setuptools import find_packages, setup | ||
|
|
||
| test_deps = ['codecov', 'pytest', 'pytest-cov'] | ||
|
|
||
| flake_deps = ['flake8'] | ||
|
|
||
| doc_deps = ['sphinx', | ||
| 'sphinx-gallery', | ||
| 'sphinx_bootstrap_theme', | ||
| 'numpydoc', | ||
| 'sphinxcontrib-fulltoc', | ||
| 'matplotlib'] | ||
|
|
||
| # requirements | ||
| with open('requirements.txt') as f: | ||
| requirements = f.read().splitlines() | ||
|
|
||
| # version | ||
| verstr = "unknown" | ||
| try: | ||
| verstrline = open('skullTo3d/_version.py', "rt").read() | ||
| except EnvironmentError: | ||
| pass # Okay, there is no version file. | ||
| def _get_version(): | ||
|
|
||
| else: | ||
| VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]" | ||
| mo = re.search(VSRE, verstrline, re.M) | ||
| if mo: | ||
| verstr = mo.group(1) | ||
| verstr = "unknown" | ||
| try: | ||
| verstrline = open('skullTo3d/_version.py', "rt").read() | ||
| except EnvironmentError: | ||
| pass # Okay, there is no version file. | ||
| else: | ||
| raise RuntimeError("unable to find version in yourpackage/_version.py") | ||
|
|
||
| print("Will not build conda module") | ||
|
|
||
| print("*******************************************************") | ||
| print(find_packages()) | ||
| print("*******************************************************") | ||
|
|
||
| setup( | ||
| name="skullTo3d", | ||
| version=verstr, | ||
| packages=find_packages(), | ||
| author="macatools team", | ||
| description="Pipeline for skull extraction for macaque/marmoset", | ||
| long_description=open('README.md').read(), | ||
| long_description_content_type='text/markdown', | ||
| license='BSD 3', | ||
| entry_points={ | ||
| 'console_scripts': ['segment_petra = workflows.segment_petra:main']}, | ||
| extras_require={ | ||
| 'test': test_deps + flake_deps, | ||
| 'doc': flake_deps + test_deps + doc_deps | ||
| }, | ||
| install_requires=requirements, | ||
| include_package_data=True) | ||
| VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]" | ||
| mo = re.search(VSRE, verstrline, re.M) | ||
| if mo: | ||
| verstr = mo.group(1) | ||
| else: | ||
| raise RuntimeError( | ||
| "unable to find version in yourpackage/_version.py") | ||
| return verstr | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| setup( | ||
| version=_get_version() | ||
| ) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -177,6 +177,9 @@ | |
| }, | ||
| "skull_ct_pipe": | ||
| { | ||
| "align_ct_on_T1_2": | ||
| { | ||
| }, | ||
| "ct_skull_auto_mask": | ||
| { | ||
| "kmeans": true, | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes.