python packages wishlist about easybuild-life-sciences HOT 11 CLOSED

2 more:

easygui should be this tag
https://github.com/robertlugg/easygui/archive/0.98.0.tar.gz

and then we also need
pyinstaller

from easybuild-life-sciences.

Python-2.7.11-foss-2016a-fh1 is built.
The following applications were omitted: ['ipython-genutils', 'ipython', 'os-client-config', 'PyInstaller'] These are not true Python packages, they are separate software packages. Only packages that extend Python (import package) can be part of a PythonPackage using easybuild. These package can be built in separate modules that extend the base Python. Module list:

APScheduler-3.1.0
Babel-2.3.4
Cycler-0.10.0
Cython-0.23.4
Flask-0.11
Flask-Bootstrap-3.3.6.0
Flask-Debug-0.4.3
Flask-Migrate-1.8.0
Flask-SQLAlchemy-2.1
Flask-Script-2.0.5
Flask-WTF-0.12
Jinja2-2.8
Mako-1.0.4
Markdown-2.6.6
Nuitka-0.5.20
PrettyTable-0.7.2
PyMySQL-0.7.4
PyYAML-3.11
Pygments-2.1.3
SQLAlchemy-1.0.13
arff-2.1.0
argparse-1.4.0
astroid-1.4.5
backports.shutil-get-terminal-size-1.0.0
bitstring-3.1.3
blist-1.3.6
bokeh-0.11.1
boto3-1.3.1
cliff-2.0.0
cryptography-1.3.2
darkslide-2.3.3
dateutil-2.5.3
deap-1.0.2
debtcollector-1.4.0
decorator-4.0.9
docutils-0.12
drmaa-0.7.6
easygui-0.98.0
ecdsa-0.13
enum34-1.1.2
flask-appconfig-0.11.1
flask-nav-0.5
freezer-2.0.0
funcsigs-1.0.2
functools32-3.2.3-2
futures-3.0.5
github3.py-1.0.0a4
google-1.9.1
h5py-2.6.0
html5lib-1.0b8
iso8601-0.1.11
keystoneauth1-2.7.0
ldap3-1.3.1
lockfile-0.12.2
matplotlib-1.5.1
mincemeat-0.1.4
mock-2.0.0
monotonic-1.1
mpi4py-1.3.1
msgpack-python-0.4.7
netaddr-0.7.18
netifaces-0.10.4
nose-1.3.7
npyscreen-4.10.5
numpy-1.10.1
oauth-1.0.1
openstacksdk-0.8.6
oslo.config-3.10.0
oslo.context-2.4.0
oslo.i18n-3.6.0
oslo.log-3.8.0
oslo.serialization-2.7.0
oslo.utils-3.11.0
pandas-0.18.1
paramiko-2.0.0
paycheck-1.0.2
pbr-1.10.0
pickleshare-0.7.2
pip-8.1.2
positional-1.1.0
psycopg2-2.6.1
pyasn1-0.1.9
pycrypto-2.6.1
pycurl-7.43.0
pymongo-3.2.2
pymssql-2.1.2
pypandoc-1.1.3
pyparsing-2.1.4
python-cinderclient-1.8.0
python-glanceclient-1.1.1
python-keystoneclient-3.1.0
python-novaclient-4.0.0
python-openstackclient-2.5.0
python-pam-1.8.2
python-swiftclient-3.0.0
pytz-2016.4
qrcode-5.3
requests-2.10.0
rpy2-2.8.0
scipy-0.17.1
setuptools-22.0.5
simplegeneric-0.8.1
simplejson-3.8.2
six-1.10.0
stevedore-1.14.0
tzlocal-1.2.2
uritemplate-0.6
urwid-1.3.1
virtualenv-15.0.2
warlock-1.2.0
watchdog-0.8.3
wrapt-1.10.8

from easybuild-life-sciences.

These addtional modules were loaded with Python-2.7.11-foss-2015b-fh1. (diff between easyconfig and pip list)

argh (0.26.2)
beautifulsoup4 (4.4.1)
botocore (1.4.25)
click (6.6)
dominate (2.2.0)
easygui (0.98.0-UNRELEASED)
enum34 (1.1.6)
functools32 (3.2.3.post2)
inflection (0.3.1)
ipaddress (1.0.16)
itsdangerous (0.24)
jmespath (0.9.0)
jsonpatch (1.14)
jsonpointer (1.10)
jsonschema (2.5.1)
MarkupSafe (0.23)
pathtools (0.1.2)
python-editor (1.0)
singledispatch (3.4.0.3)
uritemplate.py (0.3.0)
visitor (0.1.3)
Werkzeug (0.11.10)

from easybuild-life-sciences.

@fizwit

Kenji says matplotlib works in none of these
Python/2.7.11-foss-2016a, Python/3.5.1-foss-2015b-fh, Python/3.5.1-intel-2015b-fh

I tested Python/3.5.1-foss-2015b-fh and could not import pandas

from easybuild-life-sciences.

Here are some more for the next release:

psutil
pyensembl

from easybuild-life-sciences.

Python-2.7.12-foss-2016b-fh2.eb contains:

psutil (4.3.1)
pyensembl (1.0.3)
alnvu(0.1.0)
seqmagick (0.6.1)

from easybuild-life-sciences.

• configargparse

let's also add configargparse as it seems to be required by storage_crawler/report.py
Traceback (most recent call last):
File "storage_crawler/report.py", line 3, in
import configargparse
ImportError: No module named 'configargparse'

from easybuild-life-sciences.

easygui
does not seem to be part of Python/3.5.2-foss-2016b-fh1

from easybuild-life-sciences.

• ipyparallel
• json2html
• slurm-pipeline

from easybuild-life-sciences.

these are the current packages part of anaconda 3

pip freeze
abstract-rendering==0.5.1
alabaster==0.7.6
anaconda-client==1.1.2
argcomplete==1.0.0
astropy==1.0.6
Babel==2.1.1
beautifulsoup4==4.4.1
bitarray==0.8.1
blaze==0.8.3
bokeh==0.10.0
boto==2.38.0
cffi==1.2.1
clyent==1.1.0
colorama==0.3.3
conda==4.2.13
conda-build==1.18.2
configobj==5.0.6
cryptography==0.9.3
cycler==0.9.0
Cython==0.23.4
cytoolz==0.7.4
datashape==0.4.7
debtcollector==1.0.0
decorator==4.0.4
docutils==0.12
fastcache==1.0.2
Flask==0.10.1
futures==3.0.3
greenlet==0.4.9
h5py==2.5.0
idna==2.0
ipykernel==4.1.1
ipyparallel==4.1.0
ipython==4.0.0
ipython-genutils==0.1.0
ipywidgets==4.1.0
iso8601==0.1.11
itsdangerous==0.24
jdcal==1.0
jedi==0.9.0
Jinja2==2.8
jsonschema==2.4.0
jupyter==1.0.0
jupyter-client==4.1.1
jupyter-console==4.0.3
jupyter-core==4.0.6
lxml==3.4.4
MarkupSafe==0.23
matplotlib==1.5.0
mistune==0.7.1
monotonic==0.4
msgpack-python==0.4.6
multipledispatch==0.4.8
nbconvert==4.0.0
nbformat==4.0.1
netaddr==0.7.18
netifaces==0.10.4
networkx==1.10
nltk==3.1
nose==1.3.7
notebook==4.0.6
numexpr==2.4.4
numpy==1.10.1
odo==0.3.4
openpyxl==2.2.6
oslo.config==3.0.0
oslo.i18n==3.0.0
oslo.serialization==2.0.0
oslo.utils==3.0.0
pandas==0.17.1
path.py==0.0.0
patsy==0.4.0
pbr==1.8.1
pep8==1.6.2
pexpect==3.3
pickleshare==0.5
Pillow==3.0.0
ply==3.8
prettytable==0.7.2
psutil==3.3.0
ptyprocess==0.5
py==1.4.30
pyasn1==0.1.9
pycosat==0.6.1
pycparser==2.14
pycrypto==2.6.1
pycurl==7.19.5.1
pyflakes==1.0.0
Pygments==2.0.2
pyOpenSSL==0.15.1
pyparsing==2.0.3
pytest==2.8.1
python-dateutil==2.4.2
python-keystoneclient==1.8.1
python-swiftclient==2.6.0
pytz==2015.7
PyYAML==3.11
pyzmq==14.7.0
qtconsole==4.1.1
redis==2.10.3
requests==2.12.1
rope-py3k==0.9.4.post1
rpy2==2.7.0
ruamel-yaml===-VERSION
scikit-image==0.11.3
scikit-learn==0.17
scipy==0.16.0
simplegeneric==0.8.1
six==1.10.0
snowballstemmer==1.2.0
sockjs-tornado==1.0.1
Sphinx==1.3.1
sphinx-rtd-theme==0.1.7
spyder==2.3.7
SQLAlchemy==1.0.9
statsmodels==0.6.1
stevedore==1.9.0
sympy==0.7.6.1
tables==3.2.2
terminado==0.5
Theano==0.7.0
toolz==0.7.4
tornado==4.3
traitlets==4.0.0
ujson==1.33
unicodecsv==0.14.1
Werkzeug==0.11.2
wrapt==1.10.5
xlrd==0.9.4
XlsxWriter==0.7.7
xlwt==1.0.0
zmq==0.0.0

from easybuild-life-sciences.

Closing this now as it is a lingering mostly fulfilled issue.

Comments:

Dumping a huge list of module requests like this takes a log of time - I suspect several of us have iterated through this list several times. If possible, we should try to limit issues to single package requests, include source info like PyPi url, and cross reference against existing package lists.

Some of the packages (astropy) have difficult dependencies and will likely go unused by our researchers.

Some of the packages (anaconda-client, conda) are not applicable.

Notes:

futures appears to be a Python 2 package - not sure why it is in anaconda3
ipython is now jupyter
from PyPi re: ipython-genutils: "Pretend this doesn’t exist. Nobody should use it."

from easybuild-life-sciences.