[med-svn] r17685 - trunk/packages/qiime/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Mon Aug 11 13:41:14 UTC 2014
Author: tille
Date: 2014-08-11 13:41:14 +0000 (Mon, 11 Aug 2014)
New Revision: 17685
Added:
trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version.patch
trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch
trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch
trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch
trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch
Removed:
trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version
trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files
trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests
trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier
trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions
Modified:
trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch
trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch
trunk/packages/qiime/trunk/debian/patches/series
Log:
Normalise patches, DEP3
Modified: trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/check_config_file_in_new_location.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -3,7 +3,7 @@
--- a/scripts/print_qiime_config.py
+++ b/scripts/print_qiime_config.py
-@@ -210,8 +210,7 @@
+@@ -210,8 +210,7 @@ class QIIMEConfig(TestCase):
"""local qiime_config has no extra params"""
qiime_project_dir = get_qiime_project_dir()
Deleted: trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,11 +0,0 @@
---- a/scripts/print_qiime_config.py
-+++ b/scripts/print_qiime_config.py
-@@ -306,7 +306,7 @@
- max_acceptable_version = (1,3,1)
- try:
- from matplotlib import __version__ as matplotlib_lib_version
-- version = tuple(map(int,matplotlib_lib_version.split('.')))
-+ version = tuple(map(lambda x: int(x.replace("rc","")),matplotlib_lib_version.split('.')))
- pass_test = (version >= min_acceptable_version and
- version <= max_acceptable_version)
- version_string = str(matplotlib_lib_version)
Added: trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/detect_matplotlib_version.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -0,0 +1,15 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Mon, 10 Mar 2014 14:20:08 +0000
+Description: Enable proper detection of mathplotlib
+
+--- a/scripts/print_qiime_config.py
++++ b/scripts/print_qiime_config.py
+@@ -306,7 +306,7 @@ class QIIMEDependencyBase(QIIMEConfig):
+ max_acceptable_version = (1,3,1)
+ try:
+ from matplotlib import __version__ as matplotlib_lib_version
+- version = tuple(map(int,matplotlib_lib_version.split('.')))
++ version = tuple(map(lambda x: int(x.replace("rc","")),matplotlib_lib_version.split('.')))
+ pass_test = (version >= min_acceptable_version and
+ version <= max_acceptable_version)
+ version_string = str(matplotlib_lib_version)
Modified: trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/fix_binary_helper_location.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,6 +1,9 @@
+Last-Update: Mon, 06 Aug 2012 09:22:42 +0200
+Description: Fix path to binary helper for denoiser
+
--- a/qiime/denoiser/utils.py
+++ b/qiime/denoiser/utils.py
-@@ -60,8 +60,9 @@
+@@ -60,8 +60,9 @@ def get_denoiser_data_dir():
def get_flowgram_ali_exe():
"""Return the path to the flowgram alignment prog
"""
Deleted: trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,18 +0,0 @@
-This may be a much simpler fix than patching every single mention
-of support_files, but I'm not sure what else this function is used
-to find?
-
---- a/qiime/util.py
-+++ b/qiime/util.py
-@@ -302,8 +302,9 @@
- # Get the directory containing util.py
- current_dir_path = dirname(current_file_path)
- # Return the directory containing the directory containing util.py
-- return dirname(current_dir_path)
--
-+ # In Debian what we actually want is /usr/lib/[qiime]
-+ return "/usr/lib"
-+
- def get_qiime_scripts_dir():
- """ Returns the QIIME scripts directory
-
Added: trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/fix_path_for_support_files.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -0,0 +1,20 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Mon, 10 Mar 2014 14:20:08 +0000
+Description: This may be a much simpler fix than patching every single mention
+ of support_files, but I'm not sure what else this function is used
+ to find?
+
+--- a/qiime/util.py
++++ b/qiime/util.py
+@@ -302,8 +302,9 @@ def get_qiime_project_dir():
+ # Get the directory containing util.py
+ current_dir_path = dirname(current_file_path)
+ # Return the directory containing the directory containing util.py
+- return dirname(current_dir_path)
+-
++ # In Debian what we actually want is /usr/lib/[qiime]
++ return "/usr/lib"
++
+ def get_qiime_scripts_dir():
+ """ Returns the QIIME scripts directory
+
Deleted: trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,34 +0,0 @@
---- a/qiime/test.py
-+++ b/qiime/test.py
-@@ -14,7 +14,7 @@
- from os import chdir, getcwd
- from shutil import copytree, rmtree
- from glob import glob
--from site import addsitedir
-+import sys
- from tempfile import NamedTemporaryFile
- from cogent.util.misc import remove_files
- from qcli.test import (TimeExceededError,
-@@ -669,7 +669,9 @@
- if verbose:
- print 'Tests to run:\n %s' % ' '.join(tests)
-
-- addsitedir(scripts_dir)
-+ #addsitedir(scripts_dir)
-+ # This is not strong enough. The scripts-dir must be the first thing in the PATH
-+ sys.path = [ scripts_dir ] + sys.path
-
- failed_tests = []
- warnings = []
---- a/tests/all_tests.py
-+++ b/tests/all_tests.py
-@@ -94,6 +94,9 @@
- bad_tests.append(unittest_name)
-
- qiime_test_data_dir = join(get_qiime_project_dir(),'qiime_test_data')
-+ #Allow tests to be run without installing test data to system dir
-+ if exists("../qiime_test_data"):
-+ qiime_test_data_dir = "../qiime_test_data"
- qiime_test_data_dir_exists = exists(qiime_test_data_dir)
- if not opts.suppress_script_usage_tests and qiime_test_data_dir_exists:
- if opts.script_usage_tests != None:
Added: trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/fix_script_usage_tests.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -0,0 +1,38 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Mon, 10 Mar 2014 14:20:08 +0000
+Description: Enhancing unit tests
+
+--- a/qiime/test.py
++++ b/qiime/test.py
+@@ -14,7 +14,7 @@ from os.path import isdir, split, join,
+ from os import chdir, getcwd
+ from shutil import copytree, rmtree
+ from glob import glob
+-from site import addsitedir
++import sys
+ from tempfile import NamedTemporaryFile
+ from cogent.util.misc import remove_files
+ from qcli.test import (TimeExceededError,
+@@ -669,7 +669,9 @@ def run_script_usage_tests(test_data_dir
+ if verbose:
+ print 'Tests to run:\n %s' % ' '.join(tests)
+
+- addsitedir(scripts_dir)
++ #addsitedir(scripts_dir)
++ # This is not strong enough. The scripts-dir must be the first thing in the PATH
++ sys.path = [ scripts_dir ] + sys.path
+
+ failed_tests = []
+ warnings = []
+--- a/tests/all_tests.py
++++ b/tests/all_tests.py
+@@ -94,6 +94,9 @@ def main():
+ bad_tests.append(unittest_name)
+
+ qiime_test_data_dir = join(get_qiime_project_dir(),'qiime_test_data')
++ #Allow tests to be run without installing test data to system dir
++ if exists("../qiime_test_data"):
++ qiime_test_data_dir = "../qiime_test_data"
+ qiime_test_data_dir_exists = exists(qiime_test_data_dir)
+ if not opts.suppress_script_usage_tests and qiime_test_data_dir_exists:
+ if opts.script_usage_tests != None:
Deleted: trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,48 +0,0 @@
-This patch twists QIIME's arm to accept running a newer version
-of the RDP classifier by setting RDP_JAR_VERSION_OK, which is done
-by the QIIME wrapper.
-This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6
---- a/qiime/assign_taxonomy.py
-+++ b/qiime/assign_taxonomy.py
-@@ -65,14 +65,20 @@
- "http://qiime.org/install/install.html#rdp-install"
- )
-
-- rdp_jarname = os.path.basename(rdp_jarpath)
-- version_match = re.search("\d\.\d", rdp_jarname)
-- if version_match is None:
-- raise RuntimeError(
-- "Unable to detect RDP Classifier version in file %s" % rdp_jarname
-- )
-+ #Patch for Bio-Linux/Debian. Allow us to reassure QIIME about the version
-+ #of RDP Classifier using an environment variable.
-+ if os.getenv('RDP_JAR_VERSION_OK') is not None :
-+ version = os.getenv('RDP_JAR_VERSION_OK')
-+ else :
-+ rdp_jarname = os.path.basename(rdp_jarpath)
-+ version_match = re.search("\d\.\d", rdp_jarname)
-+ if version_match is None:
-+ raise RuntimeError(
-+ "Unable to detect RDP Classifier version in file %s" % rdp_jarname
-+ )
-+
-+ version = float(version_match.group())
-
-- version = float(version_match.group())
- if version < 2.1:
- raise RuntimeError(
- "RDP Classifier does not look like version 2.2 or greater."
---- a/scripts/assign_taxonomy.py
-+++ b/scripts/assign_taxonomy.py
-@@ -301,6 +301,11 @@
- params['training_data_properties_fp'] = opts.training_data_properties_fp
- params['max_memory'] = "%sM" % opts.rdp_max_memory
-
-+ #Record actual RDP version. This shouldn't fail as it was called once
-+ #already.
-+ params['real_rdp_version'] = str(validate_rdp_version())
-+
-+
- elif assignment_method == 'rtax':
- params['id_to_taxonomy_fp'] = opts.id_to_taxonomy_fp
- params['reference_sequences_fp'] = opts.reference_seqs_fp
Added: trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/make_qiime_accept_new_rdp_classifier.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -0,0 +1,51 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Tue, 11 Jun 2013 16:49:19 +0100
+Description: This patch twists QIIME's arm to accept running a newer version
+ of the RDP classifier by setting RDP_JAR_VERSION_OK, which is done
+ by the QIIME wrapper.
+ This is a nasty hack and hopefully the patch can be dropped for QIIME 1.6
+
+--- a/qiime/assign_taxonomy.py
++++ b/qiime/assign_taxonomy.py
+@@ -65,14 +65,20 @@ def validate_rdp_version(rdp_jarpath=Non
+ "http://qiime.org/install/install.html#rdp-install"
+ )
+
+- rdp_jarname = os.path.basename(rdp_jarpath)
+- version_match = re.search("\d\.\d", rdp_jarname)
+- if version_match is None:
+- raise RuntimeError(
+- "Unable to detect RDP Classifier version in file %s" % rdp_jarname
+- )
++ #Patch for Bio-Linux/Debian. Allow us to reassure QIIME about the version
++ #of RDP Classifier using an environment variable.
++ if os.getenv('RDP_JAR_VERSION_OK') is not None :
++ version = os.getenv('RDP_JAR_VERSION_OK')
++ else :
++ rdp_jarname = os.path.basename(rdp_jarpath)
++ version_match = re.search("\d\.\d", rdp_jarname)
++ if version_match is None:
++ raise RuntimeError(
++ "Unable to detect RDP Classifier version in file %s" % rdp_jarname
++ )
++
++ version = float(version_match.group())
+
+- version = float(version_match.group())
+ if version < 2.1:
+ raise RuntimeError(
+ "RDP Classifier does not look like version 2.2 or greater."
+--- a/scripts/assign_taxonomy.py
++++ b/scripts/assign_taxonomy.py
+@@ -301,6 +301,11 @@ def main():
+ params['training_data_properties_fp'] = opts.training_data_properties_fp
+ params['max_memory'] = "%sM" % opts.rdp_max_memory
+
++ #Record actual RDP version. This shouldn't fail as it was called once
++ #already.
++ params['real_rdp_version'] = str(validate_rdp_version())
++
++
+ elif assignment_method == 'rtax':
+ params['id_to_taxonomy_fp'] = opts.id_to_taxonomy_fp
+ params['reference_sequences_fp'] = opts.reference_seqs_fp
Modified: trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/prevent_download_on_builds.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,6 +1,10 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Mon, 10 Mar 2014 14:20:08 +0000
+Description: Do not try to download uclust at build time
+
--- a/setup.py
+++ b/setup.py
-@@ -175,13 +175,6 @@
+@@ -175,13 +175,6 @@ if build_stack:
else:
print "GHC not installed, so cannot build the Denoiser binary."
Modified: trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/prevent_google_addsense.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -4,8 +4,8 @@
to save user privacy
---- qiime-1.8.0+dfsg.orig.orig/doc/_templates/layout.html
-+++ qiime-1.8.0+dfsg.orig/doc/_templates/layout.html
+--- a/doc/_templates/layout.html
++++ b/doc/_templates/layout.html
@@ -2,8 +2,6 @@
{% block extrahead %}
@@ -15,7 +15,7 @@
{% endblock %}
{% block relbar1 %}
-@@ -43,12 +41,8 @@
+@@ -43,12 +41,8 @@ pathto("_static/PoweredByPycogent.jpg",
<br /></div>
{{ super() }}
<script type="text/javascript">
Deleted: trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,29 +0,0 @@
---- a/scripts/print_qiime_config.py
-+++ b/scripts/print_qiime_config.py
-@@ -467,7 +467,7 @@
- version_string = stdout.strip().split(' ')[1].strip()
- try:
- version = tuple(map(int,version_string.split('.')))
-- pass_test = version == acceptable_version
-+ pass_test = version >= acceptable_version
- except ValueError:
- pass_test = False
- version_string = stdout
-@@ -556,7 +556,7 @@
- version_string = stdout.strip().split(' ')[1].strip('v.')
- try:
- version = tuple(map(int,version_string.split('.')))
-- pass_test = version == acceptable_version
-+ pass_test = version >= acceptable_version
- except ValueError:
- pass_test = False
- version_string = stdout
-@@ -579,7 +579,7 @@
-
- def test_raxmlHPC_supported_version(self):
- """raxmlHPC is in path and version is supported """
-- acceptable_version = [(7,3,0),(7,3,0)]
-+ acceptable_version = [(7,3,0),(7,3,5)]
- self.assertTrue(app_path('raxmlHPC'),
- "raxmlHPC not found. This may or may not be a problem depending on "+\
- "which components of QIIME you plan to use.")
Added: trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch (rev 0)
+++ trunk/packages/qiime/trunk/debian/patches/relax_mothur_blast_raxml_versions.patch 2014-08-11 13:41:14 UTC (rev 17685)
@@ -0,0 +1,33 @@
+Author: Tim Booth <tbooth at ceh.ac.uk>
+Last-Update: Mon, 10 Mar 2014 14:20:08 +0000
+Description: Enable running more tests successfully by relaxing version number
+
+--- a/scripts/print_qiime_config.py
++++ b/scripts/print_qiime_config.py
+@@ -467,7 +467,7 @@ class QIIMEDependencyFull(QIIMEDependenc
+ version_string = stdout.strip().split(' ')[1].strip()
+ try:
+ version = tuple(map(int,version_string.split('.')))
+- pass_test = version == acceptable_version
++ pass_test = version >= acceptable_version
+ except ValueError:
+ pass_test = False
+ version_string = stdout
+@@ -556,7 +556,7 @@ class QIIMEDependencyFull(QIIMEDependenc
+ version_string = stdout.strip().split(' ')[1].strip('v.')
+ try:
+ version = tuple(map(int,version_string.split('.')))
+- pass_test = version == acceptable_version
++ pass_test = version >= acceptable_version
+ except ValueError:
+ pass_test = False
+ version_string = stdout
+@@ -579,7 +579,7 @@ class QIIMEDependencyFull(QIIMEDependenc
+
+ def test_raxmlHPC_supported_version(self):
+ """raxmlHPC is in path and version is supported """
+- acceptable_version = [(7,3,0),(7,3,0)]
++ acceptable_version = [(7,3,0),(7,3,5)]
+ self.assertTrue(app_path('raxmlHPC'),
+ "raxmlHPC not found. This may or may not be a problem depending on "+\
+ "which components of QIIME you plan to use.")
Modified: trunk/packages/qiime/trunk/debian/patches/series
===================================================================
--- trunk/packages/qiime/trunk/debian/patches/series 2014-08-11 13:10:56 UTC (rev 17684)
+++ trunk/packages/qiime/trunk/debian/patches/series 2014-08-11 13:41:14 UTC (rev 17685)
@@ -1,10 +1,10 @@
check_config_file_in_new_location.patch
fix_binary_helper_location.patch
-make_qiime_accept_new_rdp_classifier
-fix_path_for_support_files
-detect_matplotlib_version
-relax_mothur_blast_raxml_versions
+make_qiime_accept_new_rdp_classifier.patch
+fix_path_for_support_files.patch
+detect_matplotlib_version.patch
+relax_mothur_blast_raxml_versions.patch
prevent_google_addsense.patch
-fix_script_usage_tests
+fix_script_usage_tests.patch
prevent_download_on_builds.patch
exclude_tests_that_need_to_fail.patch
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