Easy_update has been updated for Python usage. Easy_update updates the
exts_list for Python EasyBuild configs. The program is in the scripts directory
of our easybuild repository:
https://github.com/FredHutch/easybuild-life-sciences
- Updated to use Pypi.org
- Updates checksums
- Easy_update has improved meta data debugging for Python modules.
- search feature to locate single modules and output is in format for
exts_list
- R update features are broken for now, but Python was a necessity.
Search for current version of iPython:
easy_update.py --search iPython --pyver 3.7 --meta
('iPython', '6.4.0', {
'source_urls': ['PYPI_SOURCE'],
'checksums':
['eca537aa61592aca2fef4adea12af8e42f5c335004dfa80c78caf80e8b525e5c'],
}),
'filename': 'ipython-6.4.0.tar.gz'
'packagetype': 'sdist'
'url':
'https://files.pythonhosted.org/packages/ee/01/2a85cd07f5a43fa2e86d60001c213647252662d44a0c2e3d69471a058f1b/ipython-6.4.0.tar.gz'
'python_version': 'source'
'requires_dist': '[u'numpy; python_version >= "3.4" and extra == \'test\'',
u"ipykernel; extra == 'test'", u"nbformat; extra == 'test'", u"pygments; extra
== 'test'", u"testpath; extra == 'test'", u"requests; extra == 'test'", u"nose
(>=0.10.1); extra== 'test'", u"qtconsole; extra == 'qtconsole'", u"ipyparallel;
extra == 'parallel'", u"ipywidgets; extra == 'notebook'", u"notebook; extra ==
'notebook'", u"nbformat; extra == 'nbformat'", u"nbconvert; extra ==
'nbconvert'", u"ipykernel; extra == 'kernel'", u"Sphinx (>=1.3); extra ==
'doc'", u"pygments; extra == 'all'", u"nbconvert; extra == 'all'",
u"ipywidgets; extra == 'all'", u"qtconsole; extra == 'all'", u"testpath; extra
== 'all'", u"Sphinx (>=1.3); extra == 'all'", u"requests; extra == 'all'",
u"ipyparallel; extra == 'all'", u"nose (>=0.10.1); extra == 'all'", u"notebook;
extra == 'all'", u"ipykernel; extra == 'all'", u"nbformat; extra == 'all'",
u'win-unicode-console (>=0.5); sys_platform == "win32" and python_version <
"3.6"', u'colorama; sys_platform == "win32"', u'appnope; sys_platform ==
"darwin"', u'pexpect; sys_platform != "win32"', u'pathlib2; python_version ==
"3.3"', u'typing; python_version <= "3.4"', u'backcall', u'pygments',
u'prompt-toolkit (<2.0.0,>=1.0.15)', u'traitlets (>=4.2)', u'simplegeneric
(>0.8)', u'pickleshare', u'decorator', u'jedi (>=0.10)', u'setuptools
(>=18.5)']'
'requires_python': '>=3.3'
Example run with the current Python 3.7.0 Easyconfig:
./easy_update.py --verbose Python-3.7.0-foss-2018b.eb
versionsuffix not defined
setuptools : 39.2.0 -> 40.0.0 (update) [42, 1]
pip : 10.0.1 (keep) [42, 2]
nose : 1.3.7 (keep) [42, 3]
numpy : 1.14.5 (keep) [42, 4]
scipy : 1.1.0 (keep) [42, 5]
blist : 1.3.6 (keep) [42, 6]
mpi4py : 3.0.0 (keep) [42, 7]
paycheck : 1.0.2 (keep) [42, 8]
pbr : 4.0.4 -> 4.1.0 (update) [42, 9]
Cython : 0.28.3 -> 0.28.4 (update) [42, 10]
six : 1.11.0 (keep) [42, 11]
python-dateutil : 2.7.3 (keep) [42, 12]
deap : 1.2.2 (keep) [42, 13]
decorator : 4.3.0 (keep) [42, 14]
liac-arff : 2.2.2 (keep) [42, 15]
pycrypto : 2.6.1 (keep) [42, 16]
ecdsa : 0.13 (keep) [42, 17]
pycparser : 2.18 (keep) [42, 18]
cffi : 1.11.5 (keep) [42, 19]
asn1crypto : 0.24.0 (keep) [42, 20]
idna : 2.7 (keep) [42, 21]
cryptography : 2.2.2 (keep) [42, 22]
pyasn1 : 0.4.3 (keep) [42, 23]
PyNaCl : 1.2.1 (keep) [42, 24]
bcrypt : 3.1.4 (keep) [42, 25]
paramiko : 2.4.1 (keep) [42, 26]
pyparsing : 2.2.0 (keep) [42, 27]
netifaces : 0.10.7 (keep) [42, 28]
netaddr : 0.7.19 (keep) [42, 29]
mock : 2.0.0 (keep) [42, 30]
pytz : 2018.4 -> 2018.5 (update) [42, 31]
pandas : 0.23.3 (keep) [42, 32]
bitstring : 3.1.5 (keep) [42, 33]
virtualenv : 16.0.0 (keep) [42, 34]
docopt : 0.6.2 (keep) [42, 35]
joblib : 0.11 -> 0.12.0 (update) [42, 36]
chardet : 3.0.4 (keep) [42, 37]
certifi : 2018.4.16 (keep) [42, 38]
urllib3 : 1.23 (keep) [42, 39]
requests : 2.19.1 (keep) [42, 40]
xlrd : 1.1.0 (keep) [42, 41]
py_expression_eval : 0.3.4 (keep) [42, 42]
Updated Packages: 5
New Packages: 0
Dropped Packages: 0
John Dey
HPC Operations
SciComp Computing
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