From 60e36eb1cefb63bd95aa82f879a7aba9007a9e00 Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 6 Feb 2017 21:15:33 -0800 Subject: [PATCH 1/6] Update pysam version --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index a419cebfe..b2bd9fdfd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -48,7 +48,7 @@ Flask-Cors==2.0.1 Flask==0.10.1 protobuf==3.1.0.post1 humanize==0.5.1 -pysam==0.9.0 +pysam==0.10.0 requests==2.7.0 oic==0.7.6 pyOpenSSL==0.15.1 From e9cdf9bca50810869c01fe6b506d2fcdfda42623 Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 6 Feb 2017 22:04:39 -0800 Subject: [PATCH 2/6] Updates pysam version --- tests/datadriven/test_variants.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/tests/datadriven/test_variants.py b/tests/datadriven/test_variants.py index 4972ca1a8..b5fd6c32d 100644 --- a/tests/datadriven/test_variants.py +++ b/tests/datadriven/test_variants.py @@ -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) From 53f878820b4a86a0252e1d80116e275517b29a8c Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 6 Feb 2017 22:41:16 -0800 Subject: [PATCH 3/6] Move lxml requirement Relax version restraint on some packages --- dev-requirements.txt | 1 + requirements.txt | 14 +++++++------- 2 files changed, 8 insertions(+), 7 deletions(-) diff --git a/dev-requirements.txt b/dev-requirements.txt index 08bfc7d50..15c616fe8 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -26,6 +26,7 @@ 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 diff --git a/requirements.txt b/requirements.txt index b2bd9fdfd..54f332b0d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -34,9 +34,7 @@ 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 @@ -46,13 +44,15 @@ peewee==2.8.5 # prefix due to a setuptools bug. Flask-Cors==2.0.1 Flask==0.10.1 -protobuf==3.1.0.post1 +protobuf>=3.1.0.post1 humanize==0.5.1 -pysam==0.10.0 -requests==2.7.0 +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 From 84f59936dfda60df7b1eab7373abde4cda642981 Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 6 Feb 2017 22:51:57 -0800 Subject: [PATCH 4/6] Remove pipedeps and put sphinx in dev requirements Add relaxed client to requirements --- constraints.txt | 2 +- dev-requirements.txt | 1 + requirements.txt | 21 --------------------- 3 files changed, 2 insertions(+), 22 deletions(-) diff --git a/constraints.txt b/constraints.txt index d23c6e20b..ef4298211 100644 --- a/constraints.txt +++ b/constraints.txt @@ -26,4 +26,4 @@ # 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/ga4gh-client.git@reqts#egg=ga4gh_client diff --git a/dev-requirements.txt b/dev-requirements.txt index 15c616fe8..6c9605f2d 100644 --- a/dev-requirements.txt +++ b/dev-requirements.txt @@ -29,6 +29,7 @@ snakefood==1.4 lxml==3.4.4 Sphinx==1.4.6 sphinx_rtd_theme +sphinx-argparse==0.1.15 # Requirements for OIDC provider pyaml==15.03.1 diff --git a/requirements.txt b/requirements.txt index 54f332b0d..2eed6fa11 100644 --- a/requirements.txt +++ b/requirements.txt @@ -16,25 +16,6 @@ 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 - ### This section is for the actual libraries ### # these libraries are imported in code that can be reached via @@ -54,8 +35,6 @@ 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 From eb8257828b835a91271a778adff41f488abaa1bf Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 6 Feb 2017 22:59:54 -0800 Subject: [PATCH 5/6] Remove humanized uptime --- ga4gh/server/frontend.py | 7 ------- ga4gh/server/templates/index.html | 2 +- requirements.txt | 1 - 3 files changed, 1 insertion(+), 9 deletions(-) diff --git a/ga4gh/server/frontend.py b/ga4gh/server/frontend.py index 5172aba18..5919e8cdb 100644 --- a/ga4gh/server/frontend.py +++ b/ga4gh/server/frontend.py @@ -15,7 +15,6 @@ import flask import flask.ext.cors as cors -import humanize import werkzeug import oic import oic.oauth2 @@ -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. diff --git a/ga4gh/server/templates/index.html b/ga4gh/server/templates/index.html index 03835eb67..8e4238cdc 100644 --- a/ga4gh/server/templates/index.html +++ b/ga4gh/server/templates/index.html @@ -36,7 +36,7 @@

Operations available

Uptime

- Running since {{ info.getNaturalUptime()}} ({{ info.getPreciseUptime()}}) + Running since {{ info.getPreciseUptime() }}

Configuration

diff --git a/requirements.txt b/requirements.txt index 2eed6fa11..46575e2ca 100644 --- a/requirements.txt +++ b/requirements.txt @@ -26,7 +26,6 @@ ga4gh-client Flask-Cors==2.0.1 Flask==0.10.1 protobuf>=3.1.0.post1 -humanize==0.5.1 pysam>=0.10.0 requests>=2.7.0 oic==0.7.6 From 34365fad3dda416caf123b612e918add0d53486f Mon Sep 17 00:00:00 2001 From: David Steinberg Date: Mon, 6 Feb 2017 23:03:33 -0800 Subject: [PATCH 6/6] Remove unneeded comment Set schemas relaxed reqts --- constraints.txt | 2 +- requirements.txt | 4 ---- 2 files changed, 1 insertion(+), 5 deletions(-) diff --git a/constraints.txt b/constraints.txt index ef4298211..1a8e0f74e 100644 --- a/constraints.txt +++ b/constraints.txt @@ -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/david4096/schemas.git@reqts#egg=ga4gh_schemas git+git://github.com/david4096/ga4gh-client.git@reqts#egg=ga4gh_client diff --git a/requirements.txt b/requirements.txt index 46575e2ca..ffd7dc6d1 100644 --- a/requirements.txt +++ b/requirements.txt @@ -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