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Commit d9ee2beb authored by André Anjos's avatar André Anjos :speech_balloon:
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[root] Homogenize package and buildout requirements (closes #1)

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README.rst
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...@@ -18,7 +18,8 @@ ...@@ -18,7 +18,8 @@
Binary Segmentation Benchmark Package for Bob Binary Segmentation Benchmark Package for Bob
=============================================== ===============================================
This package is part of the signal-processing and machine learning toolbox Bob_. This package is part of the signal-processing and machine learning toolbox
Bob_. It implements training and inference for binary segmentation tasks.
Installation Installation
...@@ -40,4 +41,4 @@ development `mailing list`_. ...@@ -40,4 +41,4 @@ development `mailing list`_.
.. Place your references here: .. Place your references here:
.. _bob: https://www.idiap.ch/software/bob .. _bob: https://www.idiap.ch/software/bob
.. _installation: https://www.idiap.ch/software/bob/install .. _installation: https://www.idiap.ch/software/bob/install
.. _mailing list: https://www.idiap.ch/software/bob/discuss .. _mailing list: https://www.idiap.ch/software/bob/discuss
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buildout.cfg
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...@@ -11,4 +11,4 @@ verbose = true ...@@ -11,4 +11,4 @@ verbose = true
[scripts] [scripts]
recipe = bob.buildout:scripts recipe = bob.buildout:scripts
dependent-scripts = true dependent-scripts = true
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develop.cfg
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...@@ -3,17 +3,47 @@ ...@@ -3,17 +3,47 @@
[buildout] [buildout]
parts = scripts parts = scripts
develop = .
eggs = bob.ip.binseg eggs = bob.ip.binseg
bob.db.drive
bob.db.stare
bob.db.chasedb1
bob.db.hrf
bob.db.drionsdb
bob.db.rimoner3
bob.db.drishtigs1
bob.db.refuge
bob.db.iostar
extensions = bob.buildout extensions = bob.buildout
bob.blitz mr.developer
bob.core auto-checkout = *
develop = src/bob.ip.binseg
src/bob.db.drive
src/bob.db.stare
src/bob.db.chasedb1
src/bob.db.hrf
src/bob.db.drionsdb
src/bob.db.rimoner3
src/bob.db.drishtigs1
src/bob.db.refuge
src/bob.db.iostar
.
; options for bob.buildout extension ; options for bob.buildout extension
debug = true debug = true
verbose = true verbose = true
newest = false newest = false
[sources]
bob.db.drive = git git@gitlab.idiap.ch:bob/bob.db.drive
bob.db.stare = git git@gitlab.idiap.ch:bob/bob.db.stare
bob.db.chasedb1 = git git@gitlab.idiap.ch:bob/bob.db.chasedb1
bob.db.hrf = git git@gitlab.idiap.ch:bob/bob.db.hrf
bob.db.drionsdb = git git@gitlab.idiap.ch:bob/bob.db.drionsdb
bob.db.rimoner3 = git git@gitlab.idiap.ch:bob/bob.db.rimoner3
bob.db.drishtigs1 = git git@gitlab.idiap.ch:bob/bob.db.drishtigs1
bob.db.refuge = git git@gitlab.idiap.ch:bob/bob.db.refuge
bob.db.iostar = git git@gitlab.idiap.ch:bob/bob.db.iostar
[scripts] [scripts]
recipe = bob.buildout:scripts recipe = bob.buildout:scripts
dependent-scripts=true dependent-scripts=true
requirements.txt
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...@@ -6,4 +6,4 @@ torchvision ...@@ -6,4 +6,4 @@ torchvision
pandas pandas
matplotlib matplotlib
tqdm tqdm
tabulate tabulate
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setup.py
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...@@ -2,124 +2,108 @@ ...@@ -2,124 +2,108 @@
# -*- coding: utf-8 -*- # -*- coding: utf-8 -*-
from setuptools import setup, dist from setuptools import setup, dist
dist.Distribution(dict(setup_requires=['bob.extension']))
dist.Distribution(dict(setup_requires=["bob.extension"]))
from bob.extension.utils import load_requirements, find_packages from bob.extension.utils import load_requirements, find_packages
install_requires = load_requirements() install_requires = load_requirements()
setup( setup(
name="bob.ip.binseg",
name='bob.ip.binseg',
version=open("version.txt").read().rstrip(), version=open("version.txt").read().rstrip(),
description='Binary Segmentation Benchmark Package for Bob', description="Binary Segmentation Benchmark Package for Bob",
url="https://gitlab.idiap.ch/bob/bob.ip.binseg",
url='https://gitlab.idiap.ch/bob/bob.ip.binseg', license="GPLv3",
license='GPLv3',
# there may be multiple authors (separate entries by comma) # there may be multiple authors (separate entries by comma)
author='Tim Laibacher', author="Tim Laibacher",
author_email='tim.laibacher@idiap.ch', author_email="tim.laibacher@idiap.ch",
# there may be a maintainer apart from the author - you decide # there may be a maintainer apart from the author - you decide
#maintainer='?' # maintainer='?'
#maintainer_email='email@example.com' # maintainer_email='email@example.com'
# you may add more keywords separating those by commas (a, b, c, ...) # you may add more keywords separating those by commas (a, b, c, ...)
keywords = "bob", keywords="bob",
long_description=open("README.rst").read(),
long_description=open('README.rst').read(),
# leave this here, it is pretty standard # leave this here, it is pretty standard
packages=find_packages(), packages=find_packages(),
include_package_data=True, include_package_data=True,
zip_safe = False, zip_safe=False,
install_requires=install_requires, install_requires=install_requires,
entry_points={
entry_points={ # main entry for bob binseg cli
"bob.cli": ["binseg = bob.ip.binseg.script.binseg:binseg"],
# main entry for bob hed cli # bob hed sub-commands
'bob.cli': [ "bob.ip.binseg.cli": [
'binseg = bob.ip.binseg.script.binseg:binseg', "train = bob.ip.binseg.script.binseg:train",
"test = bob.ip.binseg.script.binseg:test",
"compare = bob.bin.binseg.script.binseg:compare",
"gridtable = bob.ip.binseg.script.binseg:testcheckpoints",
"visualize = bob.ip.binseg.script.binseg:visualize",
], ],
# bob train configurations
#bob hed sub-commands "bob.ip.binseg.config": [
'bob.ip.binseg.cli': [ "DRIU = bob.ip.binseg.configs.models.driu",
'train = bob.ip.binseg.script.binseg:train', "DRIUBN = bob.ip.binseg.configs.models.driubn",
'test = bob.ip.binseg.script.binseg:test', "DRIUSSL = bob.ip.binseg.configs.models.driussl",
'compare = bob.bin.binseg.script.binseg:compare', "DRIUBNSSL = bob.ip.binseg.configs.models.driubnssl",
'gridtable = bob.ip.binseg.script.binseg:testcheckpoints', "DRIUOD = bob.ip.binseg.configs.models.driuod",
'visualize = bob.ip.binseg.script.binseg:visualize', "HED = bob.ip.binseg.configs.models.hed",
"M2UNet = bob.ip.binseg.configs.models.m2unet",
"M2UNetSSL = bob.ip.binseg.configs.models.m2unetssl",
"UNet = bob.ip.binseg.configs.models.unet",
"ResUNet = bob.ip.binseg.configs.models.resunet",
"IMAGEFOLDER = bob.ip.binseg.configs.datasets.imagefolder",
"CHASEDB1 = bob.ip.binseg.configs.datasets.chasedb1",
"CHASEDB1TEST = bob.ip.binseg.configs.datasets.chasedb1test",
"COVD-DRIVE = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544",
"COVD-DRIVE_SSL = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive",
"COVD-STARE = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608",
"COVD-STARE_SSL = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare",
"COVD-IOSTARVESSEL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024",
"COVD-IOSTARVESSEL_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar",
"COVD-HRF = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168",
"COVD-HRF_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf",
"COVD-CHASEDB1 = bob.ip.binseg.configs.datasets.drivestareiostarhrf960",
"COVD-CHASEDB1_SSL = bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase",
"DRIONSDB = bob.ip.binseg.configs.datasets.drionsdb",
"DRIONSDBTEST = bob.ip.binseg.configs.datasets.drionsdbtest",
"DRISHTIGS1OD = bob.ip.binseg.configs.datasets.dristhigs1od",
"DRISHTIGS1ODTEST = bob.ip.binseg.configs.datasets.dristhigs1odtest",
"DRISHTIGS1CUP = bob.ip.binseg.configs.datasets.dristhigs1cup",
"DRISHTIGS1CUPTEST = bob.ip.binseg.configs.datasets.dristhigs1cuptest",
"DRIVE = bob.ip.binseg.configs.datasets.drive",
"DRIVETEST = bob.ip.binseg.configs.datasets.drivetest",
"HRF = bob.ip.binseg.configs.datasets.hrf1168",
"HRFTEST = bob.ip.binseg.configs.datasets.hrftest",
"IOSTAROD = bob.ip.binseg.configs.datasets.iostarod",
"IOSTARODTEST = bob.ip.binseg.configs.datasets.iostarodtest",
"IOSTARVESSEL = bob.ip.binseg.configs.datasets.iostarvessel",
"IOSTARVESSELTEST = bob.ip.binseg.configs.datasets.iostarvesseltest",
"REFUGECUP = bob.ip.binseg.configs.datasets.refugecup",
"REFUGECUPTEST = bob.ip.binseg.configs.datasets.refugecuptest",
"REFUGEOD = bob.ip.binseg.configs.datasets.refugeod",
"REFUGEODTEST = bob.ip.binseg.configs.datasets.refugeodtest",
"RIMONER3CUP = bob.ip.binseg.configs.datasets.rimoner3cup",
"RIMONER3CUPTEST = bob.ip.binseg.configs.datasets.rimoner3cuptest",
"RIMONER3OD = bob.ip.binseg.configs.datasets.rimoner3od",
"RIMONER3ODTEST = bob.ip.binseg.configs.datasets.rimoner3odtest",
"STARE = bob.ip.binseg.configs.datasets.stare",
"STARETEST = bob.ip.binseg.configs.datasets.staretest",
], ],
#bob train configurations
'bob.ip.binseg.config': [
'DRIU = bob.ip.binseg.configs.models.driu',
'DRIUBN = bob.ip.binseg.configs.models.driubn',
'DRIUSSL = bob.ip.binseg.configs.models.driussl',
'DRIUBNSSL = bob.ip.binseg.configs.models.driubnssl',
'DRIUOD = bob.ip.binseg.configs.models.driuod',
'HED = bob.ip.binseg.configs.models.hed',
'M2UNet = bob.ip.binseg.configs.models.m2unet',
'M2UNetSSL = bob.ip.binseg.configs.models.m2unetssl',
'UNet = bob.ip.binseg.configs.models.unet',
'ResUNet = bob.ip.binseg.configs.models.resunet',
'IMAGEFOLDER = bob.ip.binseg.configs.datasets.imagefolder',
'CHASEDB1 = bob.ip.binseg.configs.datasets.chasedb1',
'CHASEDB1TEST = bob.ip.binseg.configs.datasets.chasedb1test',
'COVD-DRIVE = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544',
'COVD-DRIVE_SSL = bob.ip.binseg.configs.datasets.starechasedb1iostarhrf544ssldrive',
'COVD-STARE = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608',
'COVD-STARE_SSL = bob.ip.binseg.configs.datasets.drivechasedb1iostarhrf608sslstare',
'COVD-IOSTARVESSEL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024',
'COVD-IOSTARVESSEL_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1hrf1024ssliostar',
'COVD-HRF = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168',
'COVD-HRF_SSL = bob.ip.binseg.configs.datasets.drivestarechasedb1iostar1168sslhrf',
'COVD-CHASEDB1 = bob.ip.binseg.configs.datasets.drivestareiostarhrf960',
'COVD-CHASEDB1_SSL = bob.ip.binseg.configs.datasets.drivestareiostarhrf960sslchase',
'DRIONSDB = bob.ip.binseg.configs.datasets.drionsdb',
'DRIONSDBTEST = bob.ip.binseg.configs.datasets.drionsdbtest',
'DRISHTIGS1OD = bob.ip.binseg.configs.datasets.dristhigs1od',
'DRISHTIGS1ODTEST = bob.ip.binseg.configs.datasets.dristhigs1odtest',
'DRISHTIGS1CUP = bob.ip.binseg.configs.datasets.dristhigs1cup',
'DRISHTIGS1CUPTEST = bob.ip.binseg.configs.datasets.dristhigs1cuptest',
'DRIVE = bob.ip.binseg.configs.datasets.drive',
'DRIVETEST = bob.ip.binseg.configs.datasets.drivetest',
'HRF = bob.ip.binseg.configs.datasets.hrf1168',
'HRFTEST = bob.ip.binseg.configs.datasets.hrftest',
'IOSTAROD = bob.ip.binseg.configs.datasets.iostarod',
'IOSTARODTEST = bob.ip.binseg.configs.datasets.iostarodtest',
'IOSTARVESSEL = bob.ip.binseg.configs.datasets.iostarvessel',
'IOSTARVESSELTEST = bob.ip.binseg.configs.datasets.iostarvesseltest',
'REFUGECUP = bob.ip.binseg.configs.datasets.refugecup',
'REFUGECUPTEST = bob.ip.binseg.configs.datasets.refugecuptest',
'REFUGEOD = bob.ip.binseg.configs.datasets.refugeod',
'REFUGEODTEST = bob.ip.binseg.configs.datasets.refugeodtest',
'RIMONER3CUP = bob.ip.binseg.configs.datasets.rimoner3cup',
'RIMONER3CUPTEST = bob.ip.binseg.configs.datasets.rimoner3cuptest',
'RIMONER3OD = bob.ip.binseg.configs.datasets.rimoner3od',
'RIMONER3ODTEST = bob.ip.binseg.configs.datasets.rimoner3odtest',
'STARE = bob.ip.binseg.configs.datasets.stare',
'STARETEST = bob.ip.binseg.configs.datasets.staretest',
]
}, },
# check classifiers, add and remove as you see fit # check classifiers, add and remove as you see fit
# full list here: https://pypi.org/classifiers/ # full list here: https://pypi.org/classifiers/
# don't remove the Bob framework unless it's not a bob package # don't remove the Bob framework unless it's not a bob package
classifiers = [ classifiers=[
'Framework :: Bob', "Framework :: Bob",
'Development Status :: 4 - Beta', "Development Status :: 4 - Beta",
'Intended Audience :: Science/Research', "Intended Audience :: Science/Research",
'License :: OSI Approved :: GNU General Public License v3 (GPLv3)', "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
'Natural Language :: English', "Natural Language :: English",
'Programming Language :: Python', "Programming Language :: Python",
'Programming Language :: Python :: 3', "Programming Language :: Python :: 3",
'Topic :: Scientific/Engineering :: Artificial Intelligence', "Topic :: Scientific/Engineering :: Artificial Intelligence",
'Topic :: Software Development :: Libraries :: Python Modules', "Topic :: Software Development :: Libraries :: Python Modules",
], ],
)
)
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