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Updated packages included with source dist.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,8 @@ | ||
| include *.txt | ||
| include *.rst | ||
| recursive-include dependencies *.txt | ||
| recursive-include mosaic/utest/testdata *.prm | ||
| recursive-include mosaic/utest/testdata *.csv | ||
| recursive-include mosaic/tests/testdata *.prm | ||
| recursive-include mosaic/tests/testdata *.csv | ||
| recursive-include mosaic/tests/testdata *.tsv | ||
| recursive-include mosaic/tests/testdata *.qdf | ||
| recursive-include mosaic/tests/testdata *.bin | ||
| recursive-include mosaic/tests/testdata *.json |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -6,154 +6,162 @@ | |
| from mosaic.tests.mosaicUnitTests import _mosaicUnitTests | ||
|
|
||
| class mosaicBinaries(Command): | ||
| description = "build MOSAIC binaries." | ||
| user_options = [ | ||
| ('inplace', 'i', "build binaries in the current branch"), | ||
| ] | ||
| description = "build MOSAIC binaries." | ||
| user_options = [ | ||
| ('inplace', 'i', "build binaries in the current branch"), | ||
| ] | ||
|
|
||
| def initialize_options(self): | ||
| self.inplace=0 | ||
| def initialize_options(self): | ||
| self.inplace=0 | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| retval=0 | ||
| if not self.inplace: | ||
| retval = os.system("git checkout master") | ||
| def run(self): | ||
| retval=0 | ||
| if not self.inplace: | ||
| retval = os.system("git checkout master") | ||
|
|
||
| if retval==0: | ||
| os.system('sh .scripts/pyinstaller-sh') | ||
| if retval==0: | ||
| os.system('sh .scripts/pyinstaller-sh') | ||
|
|
||
| class mosaicDependencies(Command): | ||
| description = "install MOSAIC dependencies." | ||
| user_options = [ | ||
| ('upgrade', 'u', "force packages to upgrade"), | ||
| ] | ||
| description = "install MOSAIC dependencies." | ||
| user_options = [ | ||
| ('upgrade', 'u', "force packages to upgrade"), | ||
| ] | ||
|
|
||
| def initialize_options(self): | ||
| self.upgrade=0 | ||
| def initialize_options(self): | ||
| self.upgrade=0 | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| # os.system('sh .scripts/build-deps-sh') | ||
| if self.upgrade: | ||
| os.system('pip install -r requirements.txt --upgrade') | ||
| else: | ||
| os.system('pip install -r requirements.txt') | ||
| def run(self): | ||
| # os.system('sh .scripts/build-deps-sh') | ||
| if self.upgrade: | ||
| os.system('pip install -r requirements.txt --upgrade') | ||
| else: | ||
| os.system('pip install -r requirements.txt') | ||
|
|
||
| class mosaicDocumentationDependencies(Command): | ||
| description = "install dependencies for Sphinx documentation." | ||
| user_options = [] | ||
| description = "install dependencies for Sphinx documentation." | ||
| user_options = [] | ||
|
|
||
| def initialize_options(self): | ||
| pass | ||
| def initialize_options(self): | ||
| pass | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| os.system('sh .scripts/build-docs-deps-sh') | ||
| def run(self): | ||
| os.system('sh .scripts/build-docs-deps-sh') | ||
|
|
||
| class mosaicAddons(Command): | ||
| description = "install MOSAIC addons (Mathematica, Igor and Matlab scripts)." | ||
| user_options = [ | ||
| ('mathematica', 'm', "install Mathematica scripts"), | ||
| ('igor', 'i', "install IGOR SQLite drivers") | ||
| ] | ||
|
|
||
| def initialize_options(self): | ||
| self.mathematica = 0 | ||
| self.igor = 0 | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| if self.mathematica: | ||
| os.system('sh .scripts/install-addons-sh ') | ||
| elif self.igor: | ||
| os.system( 'sh .scripts/install-igor-addons-sh' ) | ||
| else: | ||
| os.system('sh .scripts/install-addons-sh ') | ||
| os.system( 'sh .scripts/install-igor-addons-sh' ) | ||
| description = "install MOSAIC addons (Mathematica, Igor and Matlab scripts)." | ||
| user_options = [ | ||
| ('mathematica', 'm', "install Mathematica scripts"), | ||
| ('igor', 'i', "install IGOR SQLite drivers") | ||
| ] | ||
|
|
||
| def initialize_options(self): | ||
| self.mathematica = 0 | ||
| self.igor = 0 | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| if self.mathematica: | ||
| os.system('sh .scripts/install-addons-sh ') | ||
| elif self.igor: | ||
| os.system( 'sh .scripts/install-igor-addons-sh' ) | ||
| else: | ||
| os.system('sh .scripts/install-addons-sh ') | ||
| os.system( 'sh .scripts/install-igor-addons-sh' ) | ||
|
|
||
| class mosaicDocs(Command): | ||
| description = "build MOSAIC documentation." | ||
| user_options = [ ('all', None, "build HTML and PDF documentation (default)"), | ||
| ('html', None, "build HTML documentation"), | ||
| ('pdf', None, "build PDF documentation"), | ||
| ('rebuild', None, "rebuild HTML and PDF documentation"), | ||
| ] | ||
|
|
||
| def initialize_options(self): | ||
| self.html = 0 | ||
| self.pdf = 0 | ||
| self.all = 0 | ||
| self.rebuild = 0 | ||
| self.upload = 0 | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| # always build docs in the master branch. | ||
| os.system("git checkout master") | ||
| if self.html: | ||
| os.system("make -C _docs html") | ||
| elif self.pdf: | ||
| os.system("make -C _docs latexpdf") | ||
| elif self.rebuild: | ||
| os.system("make -C _docs clean html latexpdf") | ||
| else: | ||
| os.system("make -C _docs html latexpdf") | ||
| description = "build MOSAIC documentation." | ||
| user_options = [ ('all', None, "build HTML and PDF documentation (default)"), | ||
| ('html', None, "build HTML documentation"), | ||
| ('pdf', None, "build PDF documentation"), | ||
| ('rebuild', None, "rebuild HTML and PDF documentation"), | ||
| ] | ||
|
|
||
| def initialize_options(self): | ||
| self.html = 0 | ||
| self.pdf = 0 | ||
| self.all = 0 | ||
| self.rebuild = 0 | ||
| self.upload = 0 | ||
|
|
||
| def finalize_options(self): | ||
| pass | ||
|
|
||
| def run(self): | ||
| # always build docs in the master branch. | ||
| os.system("git checkout master") | ||
| if self.html: | ||
| os.system("make -C _docs html") | ||
| elif self.pdf: | ||
| os.system("make -C _docs latexpdf") | ||
| elif self.rebuild: | ||
| os.system("make -C _docs clean html latexpdf") | ||
| else: | ||
| os.system("make -C _docs html latexpdf") | ||
|
|
||
| setup( | ||
| cmdclass={ | ||
| 'test' : _mosaicUnitTests(Command), | ||
| 'nosetests' : _mosaicUnitTests(Command), | ||
| 'mosaic_tests' : _mosaicUnitTests(Command), | ||
| 'mosaic_docs' : mosaicDocs, | ||
| 'mosaic_bin' : mosaicBinaries, | ||
| 'mosaic_deps' : mosaicDependencies, | ||
| 'mosaic_docs_deps' : mosaicDocumentationDependencies, | ||
| 'mosaic_addons' : mosaicAddons | ||
| }, | ||
| name='mosaic-nist', | ||
| version=mosaic.__version__, | ||
| author='Arvind Balijepalli', | ||
| author_email='[email protected]', | ||
| packages=[ | ||
| 'mosaic', | ||
| 'mosaic.utest', | ||
| 'mosaic.qdf', | ||
| 'mosaic.abf', | ||
| 'mosaic.utilities' | ||
| ], | ||
| scripts=[ | ||
| 'bin/analysis.py', | ||
| 'addons/mathematica/MosaicAnalysis.m', | ||
| 'addons/mathematica/MosaicUtils.m', | ||
| 'addons/mathematica/Util.m', | ||
| 'addons/MATLAB/openandquery.m', | ||
| 'icons/icon_100px.png', | ||
| 'icons/error-128.png', | ||
| 'icons/warning-128.png', | ||
| '.scripts/install-addons-sh', | ||
| '.scripts/pyinstaller-sh', | ||
| 'data/eventMD-PEG28-stepResponseAnalysis.sqlite', | ||
| 'data/eventMD-PEG28-cusumLevelAnalysis.sqlite', | ||
| 'data/.settings', | ||
| 'data/SingleChan-0001.qdf', | ||
| 'data/SingleChan-0001_state.txt', | ||
| 'commit-hash', | ||
| 'requirements.txt' | ||
| ], | ||
| install_requires=open('requirements.txt').read().splitlines(), | ||
| url='https://usnistgov.github.io/mosaic/', | ||
| license='LICENSE.txt', | ||
| description='A Modular Single-Molecule Analysis Interface.', | ||
| long_description=open('README.rst').read(), | ||
| cmdclass={ | ||
| 'test' : _mosaicUnitTests(Command), | ||
| 'nosetests' : _mosaicUnitTests(Command), | ||
| 'mosaic_tests' : _mosaicUnitTests(Command), | ||
| 'mosaic_docs' : mosaicDocs, | ||
| 'mosaic_bin' : mosaicBinaries, | ||
| 'mosaic_deps' : mosaicDependencies, | ||
| 'mosaic_docs_deps' : mosaicDocumentationDependencies, | ||
| 'mosaic_addons' : mosaicAddons | ||
| }, | ||
| name='mosaic-nist', | ||
| version=mosaic.__version__, | ||
| author='Arvind Balijepalli', | ||
| author_email='[email protected]', | ||
| packages=[ | ||
| 'mosaic', | ||
| 'mosaic.filters', | ||
| 'mosaic.mdio', | ||
| 'mosaic.trajio', | ||
| 'mosaic.process', | ||
| 'mosaic.partition', | ||
| 'mosaic.apps', | ||
| 'mosaic.tests', | ||
| 'mosaic.trajio.qdf', | ||
| 'mosaic.trajio.abf', | ||
| 'mosaic.utilities' | ||
| ], | ||
| scripts=[ | ||
| 'bin/analysis.py', | ||
| 'addons/mathematica/MosaicAnalysis.m', | ||
| 'addons/mathematica/MosaicUtils.m', | ||
| 'addons/mathematica/Util.m', | ||
| 'addons/MATLAB/openandquery.m', | ||
| 'icons/icon_100px.png', | ||
| 'icons/error-128.png', | ||
| 'icons/warning-128.png', | ||
| '.scripts/install-addons-sh', | ||
| '.scripts/pyinstaller-sh', | ||
| 'data/eventMD-PEG28-stepResponseAnalysis.sqlite', | ||
| 'data/eventMD-PEG28-cusumLevelAnalysis.sqlite', | ||
| 'data/.settings', | ||
| 'data/SingleChan-0001.qdf', | ||
| 'data/SingleChan-0001_state.txt', | ||
| 'commit-hash', | ||
| 'requirements.txt', | ||
| 'DISCLAIMER.TXT', | ||
| 'LICENSE.TXT' | ||
| ], | ||
| install_requires=open('requirements.txt').read().splitlines(), | ||
| url='https://usnistgov.github.io/mosaic/', | ||
| license='LICENSE.txt', | ||
| description='A Modular Single-Molecule Analysis Interface.', | ||
| long_description=open('README.rst').read(), | ||
| ) | ||