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Dependency management - relaxing requirements #1557

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Dependency management - relaxing requirements #1557

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60e36eb
Update pysam version
david4096 Feb 7, 2017
e9cdf9b
Updates pysam version
david4096 Feb 7, 2017
53f8788
Move lxml requirement
david4096 Feb 7, 2017
84f5993
Remove pipedeps and put sphinx in dev requirements
david4096 Feb 7, 2017
eb82578
Remove humanized uptime
david4096 Feb 7, 2017
34365fa
Remove unneeded comment
david4096 Feb 7, 2017
f3eb084
Merge branch 'master' into reqts
david4096 Feb 14, 2017
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4 changes: 2 additions & 2 deletions constraints.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -25,5 +25,5 @@
# ga4gh-schemas==0.6.0a9post2
#
git+git://github.com/ga4gh/ga4gh-common.git@master#egg=ga4gh_common
git+git://github.com/ga4gh/schemas.git@master#egg=ga4gh_schemas
git+git://github.com/ga4gh/ga4gh-client.git@master#egg=ga4gh_client
git+git://github.com/david4096/schemas.git@reqts#egg=ga4gh_schemas
git+git://github.com/david4096/ga4gh-client.git@reqts#egg=ga4gh_client
2 changes: 2 additions & 0 deletions dev-requirements.txt
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Expand Up @@ -26,8 +26,10 @@ PyVCF==0.6.7
freezegun==0.3.6
guppy==0.1.10
snakefood==1.4
lxml==3.4.4
Sphinx==1.4.6
sphinx_rtd_theme
sphinx-argparse==0.1.15
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Why was sphinx-argparse moved into dev-requirements? Will the builds on RTD still work?

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Do you think that should be in requirements? I consider the doc creation as the development dependencies. We can manage RTD build dependencies in a nicer way using the environment.yml. However, this PR is untested on RTD.

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Er, the client has sphinx-argparse in dev-requirements.txt, so moving it seems fine


# Requirements for OIDC provider
pyaml==15.03.1
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7 changes: 0 additions & 7 deletions ga4gh/server/frontend.py
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Expand Up @@ -15,7 +15,6 @@

import flask
import flask.ext.cors as cors
import humanize
import werkzeug
import oic
import oic.oauth2
Expand Down Expand Up @@ -110,12 +109,6 @@ def getLandingMessageHtml(self):
html = flask.render_template("landing_message.html")
return html

def getNaturalUptime(self):
"""
Returns the uptime in a human-readable format.
"""
return humanize.naturaltime(self.startupTime)

def getProtocolVersion(self):
"""
Returns the GA4GH protocol version we support.
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2 changes: 1 addition & 1 deletion ga4gh/server/templates/index.html
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Expand Up @@ -36,7 +36,7 @@ <h3>Operations available</h3>
</div>
<div>
<h3>Uptime</h3>
Running since {{ info.getNaturalUptime()}} ({{ info.getPreciseUptime()}})
Running since {{ info.getPreciseUptime() }}
</div>
<div>
<h3>Configuration</h3>
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38 changes: 6 additions & 32 deletions requirements.txt
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Expand Up @@ -4,10 +4,6 @@
# These requirements are read directly into setup.py, so specify them
# in the order that they should be in in setup.py

### This section is for dependencies of the libraries ###
# these libraries are the set listed by pipdeptree -f -w
# that are dependencies of libraries listed in the next section

# Adding the constraints.txt allows you to choose a specific
# way to resolve our internal dependencies. During development,
# the constraints file will point at the current master branch
Expand All @@ -16,27 +12,6 @@ ga4gh-common
ga4gh-schemas
ga4gh-client

Werkzeug==0.11.5
MarkupSafe==0.23
itsdangerous==0.24
six==1.10.0
pycrypto==2.6.1
Mako==1.0.4
Beaker==1.8.0
funcsigs==0.4
alabaster==0.7.7
cryptography==1.3.1
idna==2.1
pyasn1==0.1.9
enum34==1.1.2
ipaddress==1.0.16
cffi==1.5.2
pycparser==2.14
Jinja2==2.7.3
future==0.15.2
pyjwkest==1.0.1
PyJWT==1.4.2
peewee==2.8.5

### This section is for the actual libraries ###
# these libraries are imported in code that can be reached via
Expand All @@ -46,16 +21,15 @@ peewee==2.8.5
# prefix due to a setuptools bug.
Flask-Cors==2.0.1
Flask==0.10.1
protobuf==3.1.0.post1
humanize==0.5.1
pysam==0.9.0
requests==2.7.0
protobuf>=3.1.0.post1
pysam>=0.10.0
requests>=2.7.0
oic==0.7.6
pyOpenSSL==0.15.1
lxml==3.4.4
pyjwkest==1.0.1
PyJWT==1.4.2
peewee>=2.8.5

# We need sphinx-argparse to build on readthedocs.
sphinx-argparse==0.1.15

# G2P uses a ttl backend
RDFLib==4.2.1
4 changes: 3 additions & 1 deletion tests/datadriven/test_variants.py
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Expand Up @@ -386,8 +386,10 @@ def convertPyvcfNumber(number):
keyMap[key].type, content[contentKey].type)
self.assertEqual(keyMap[key].number, convertPyvcfNumber(
content[contentKey].num))
# pysam introduces opinionated stripping
self.assertEqual(
keyMap[key].description, content[contentKey].desc)
keyMap[key].description,
content[contentKey].desc.rstrip())
testMetaLength = (
1 + len(self._formats) + len(self._infos) - gtCounter)
self.assertEqual(len(keyMap), testMetaLength)
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