Patch obitools for not importing too recent packages

ignore the new virtualenv for version 1.12.13
Switch to version 1.12.13
2019-04-01 14:32:05 +02:00 · 2019-04-01 14:12:10 +02:00 · 2019-04-01 14:06:07 +02:00 · 2019-04-01 14:04:17 +02:00 · 2019-04-01 14:00:17 +02:00 · 2019-04-01 13:59:09 +02:00
234 changed files with 1462 additions and 1497 deletions
@@ -0,0 +1,24 @@
+/OBITools-1.1.19/
+/OBITools-1.1.20/
+/OBITools-1.1.21/
+/OBITools-1.1.22/
+/OBITools-1.2.0/
+/obitools.test/
+/build/
+/dist/
+/OBITools-1.2.2/
+/OBITools-1.2.3/
+/OBITools-1.2.4/
+/OBITools-1.2.5/
+/OBITools-1.2.6/
+/OBITools-1.2.7/
+/OBITools-1.2.8/
+/OBITools-1.2.9/
+/OBITools-1.2.10/
+/.DS_Store
+/OBITools-1.2.11/
+/OBITools-1.2.12/
+/obitools.test.old/
+/coucou
+/toto.fasta
+/OBITools-1.2.13/
@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?eclipse-pydev version="1.0"?><pydev_project>
 <pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
-<path>/obitools/src</path>
+<path>/OBITools-1.1/src</path>
 <path>/${PROJECT_DIR_NAME}/distutils.ext</path>
 </pydev_pathproperty>
 <pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python 2.7</pydev_property>
@@ -0,0 +1,2 @@
+*.pyc
+/.DS_Store
@@ -0,0 +1 @@
+/*.pyc
@@ -0,0 +1 @@
+/*.pyc
@@ -13,26 +13,29 @@ import sys

 try:
    from sphinx.setup_command import BuildDoc as ori_build_sphinx
+    
+    class build_sphinx(ori_build_sphinx):
+        '''
+        Build Sphinx documentation in html, epub and man formats 
+        '''
+
+        description = __doc__
+    
+        def run(self):
+            self.builder='html'
+            self.finalize_options()
+            ori_build_sphinx.run(self)
+            self.builder='epub'
+            self.finalize_options()
+            ori_build_sphinx.run(self)
+            self.builder='man'
+            self.finalize_options()
+            ori_build_sphinx.run(self)
+
 except ImportError:
    if not is_serenity() and install_requirements():
        log.info("Restarting installation with all dependencies ok")
        rerun_with_anothe_python(os.path.realpath(sys.executable))
+        
    
-class build_sphinx(ori_build_sphinx):
-    '''
-    Build Sphinx documentation in html, epub and man formats 
-    '''
-
-    description = __doc__
-
-    def run(self):
-        self.builder='html'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='epub'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
-        self.builder='man'
-        self.finalize_options()
-        ori_build_sphinx.run(self)
    
@@ -201,7 +201,5 @@ def setup(**attrs):
    
    if 'ext_modules' not in attrs:
        attrs['ext_modules'] = EXTENTION
-        
-    print "$$$$$$$$$$$$$$$$$$$$$$$$$$$",COMMANDS
-    
+            
    ori_setup(**attrs)
@@ -0,0 +1 @@
+/*.pyc
@@ -0,0 +1 @@
+/*.pyc
@@ -0,0 +1 @@
+/*.pyc
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
coissac	c198e7d8bf	Patch obitools for not importing too recent packages	2019-04-01 14:32:05 +02:00
coissac	a2db4ce5ae	ignore the new virtualenv for version 1.12.13	2019-04-01 14:12:10 +02:00
coissac	0e5ae4dd68	Switch to version 1.12.13	2019-04-01 14:06:07 +02:00
coissac	0d4bb5bbd6	cleaning 2	2019-04-01 14:04:17 +02:00
coissac	ee53992acc	Merge branch 'master' of git.metabarcoding.org:obitools/obitools # Conflicts: # requirements.txt	2019-04-01 14:00:17 +02:00
coissac	45736d1771	Version switch	2019-04-01 13:59:09 +02:00
coissac	de2673174f	cleaning 1	2019-04-01 13:58:16 +02:00
Celine Mercier	1c318bd34d	Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools.git	2019-03-26 11:36:54 +01:00
Celine Mercier	e99684a47d	Fixed --skip-on-error option for embl and genbank files (did not work because python generators can never resume after raising any exception)	2019-03-26 11:36:11 +01:00
Celine Mercier	f8dcd2f401	Fixed requirements.txt triggering errors with the 2 conditions for ipython	2019-03-15 16:34:23 +01:00
Celine Mercier	a43601cffd	obitaxonomy: fixed a bug when trying to add a new species by name	2018-11-01 18:07:56 +01:00
coissac	71cc64977b	Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools.git	2018-09-19 15:52:38 +02:00
Celine Mercier	0cd2814fa7	Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools.git	2018-09-19 15:39:47 +02:00
Celine Mercier	97268211ff	Sphinx: replaced the deprecated 'sphinx.ext.pngmath' extension with 'sphinx.ext.imgmath' (would stop OBITools installation)	2018-09-19 15:36:51 +02:00
coissac	9962c452d8	Switch to version 1.2.11	2017-04-30 19:13:43 +02:00
coissac	abf8fde9f5	Switch to version 1.2.11	2017-04-30 18:57:28 +02:00
coissac	1311cf3c63	Limit Ipython version to stay compatible with python 2.7	2017-04-27 13:49:14 +02:00
coissac	59e2665de9	close #32	2017-04-20 18:46:03 +02:00
coissac	05cc5b06c7	Switch to version 1.2.10	2017-02-01 12:01:24 +01:00
Celine Mercier	54c68bab99	Fixed a bug when parsing embl files: accession ids end with ';' in recent embl formats. The ';' was kept by the old embl parser, resulting in many possible bugs.	2017-01-23 16:56:38 +01:00
coissac	5dc1f4d325	Switch to version 1.2.9 and ask for Cython >= 2.4.0	2016-08-03 09:21:05 +02:00
coissac	8bede453ae	Patch a memory bug in the progress bar printing leading to a bus error with some C compiler and the new version of Cython (0.2.4)	2016-08-03 09:07:49 +02:00
coissac	8cbac7a75e	Remove an extra log added for debuging at the beginning of the output	2016-08-03 07:59:58 +02:00
coissac	1b31d9091a	swithc to version 1.2.8	2016-07-28 08:06:34 +02:00
coissac	eaf50be2ca	Switch to cython 0.24	2016-07-28 08:05:14 +02:00
coissac	b24f993780	Remove some false error warning	2016-07-28 08:03:23 +02:00
coissac	e0bf25d72c	replace _BYTES call by the new .data.as_uchars to reflect the new API	2016-07-28 07:54:59 +02:00
coissac	a4a854a2a8	Merge branch 'master' of git.metabarcoding.org:obitools/obitools Conflicts: src/obitools/align/_lcs.ext.4.c the symbolic link is correctly restored	2016-07-06 15:23:47 +02:00
coissac	a186bf439c	Small changes on distutils.ext	2016-07-06 15:17:15 +02:00
Aurélie Bonin	a6daa709e9	Merge branch 'windows_version' into 'master' Windows version This branch allows for compiling OBITools on windows in the cygwin environment. It asks for installing the following cygwin packages : - binutils - gcc-core - python 2.7 See merge request !1	2016-07-06 15:02:35 +02:00
abonin	22f98eaa4b	switch to the new version 1.2.7	2016-07-06 14:50:56 +02:00
abonin	38504ab03a	Final switch to the new cython interface on array.array	2016-07-06 14:46:31 +02:00
abonin	1b8a867fbf	switch to the new cython interface to array.array	2016-07-06 14:29:43 +02:00
abonin	9a9bd6c60f	switch to the new cython interface to array.array	2016-07-06 14:23:58 +02:00
abonin	6002fbaa98	Remove the reference to arrayarray.h	2016-07-06 14:12:56 +02:00
Aurélie Bonin	e869e16d9f	Adaptation for running with cygwin on windows platform	2016-07-06 11:55:32 +02:00
Aurélie Bonin	3a5ad68013	A very small fastq test file	2016-07-06 11:52:55 +02:00
coissac	b8dc49ef84	Rename members of the DNA profil strucuture to potentiel avoid a compile bug on windows cygwin	2016-06-28 15:13:30 +02:00
coissac	140f26977a	Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools.git	2016-06-28 15:10:39 +02:00
coissac	d96cf37147	Remove a debug trace in the installer	2016-06-28 15:10:12 +02:00
Celine Mercier	20f1c1d337	Fixed a potential bug with the parsing of taxonomic paths when using obitaxonomy after obiaddtaxids on a general UNITE database	2016-06-16 16:40:27 +02:00
coissac	f32ca9e9fa	Patch the obitool url on metabarcoding.org	2016-05-27 14:37:58 +02:00
coissac	a06e79102d	Switch to version 1.2.6	2016-05-27 12:56:14 +02:00
coissac	0e2c486178	Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools.git	2016-05-27 12:52:04 +02:00
Celine Mercier	950bae882b	Numbering version 1.2.5	2016-05-27 11:20:27 +02:00
Celine Mercier	683f3b5bbc	Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools.git	2016-05-26 16:01:03 +02:00
Celine Mercier	5490144788	Fixed a bug in obitaxonomy sometimes triggering an error when adding a new taxon from a file. Also now checks if taxon already in taxonomy.	2016-05-26 15:58:48 +02:00
coissac	42a3f98495	for cython to version 0.23.5 the latest 0.23 version	2016-04-07 12:19:42 +02:00
coissac	c395d76231	patch a bug in the sequence counting of obiselect	2016-04-06 14:46:08 +02:00
coissac	b2d2346eb7	Set the Cython required version to 0.23 because of a bug in the 0.24 version	2016-04-06 14:44:17 +02:00
coissac	ffb33f61a9	Switch to version 1.2.3	2016-04-04 18:49:10 +02:00
Celine Mercier	adbeac9684	Fixed major bug with -f UNITE_FULL option of obiaddtaxids	2016-04-04 16:36:05 +02:00
Celine Mercier	4aac47e639	Merge branch 'master' of git.metabarcoding.org:obitools/obitools	2016-03-30 16:35:49 +02:00
Celine Mercier	2028c69b3f	Fixed typo in obiaddtaxids documentation	2016-03-17 15:05:18 +01:00
coissac	2649cd268c	Switch to version 1.2.2	2016-01-12 20:57:47 +01:00
coissac	46b446f0c8	Add capacity to filter on merged sequences	2016-01-12 20:53:56 +01:00
Celine Mercier	6208cbee02	Fixes #20 and several other bugs related to that function	2016-01-08 11:40:39 +01:00
coissac	1d4c3f99b2	Patch a bug related to the -E et -M options	2015-10-27 20:16:07 +01:00
coissac	ba30e74dc9	Switch the version number to 1.2.1	2015-10-27 18:59:51 +01:00
coissac	0e8b97ca40	Modify the action of the -M option to fit the documentation	2015-10-27 18:58:32 +01:00
coissac	a95ae5126b	Change the ecotag doc according to the new -M option	2015-10-27 18:56:49 +01:00
coissac	0e2f859839	Patch bug in the -E option of ecotag and add the -M option to limit the action of the -E option	2015-10-27 18:48:03 +01:00
coissac	23717f5833	Add a first version of the obisubset tool and tag the version 1.2.0	2015-10-20 22:02:02 +02:00
coissac	fdeaf5956c	Change the way ecoPCRDB are written by obitools. If the obitools is called with several sequence files as input when the ecoPCRDB is requested as output format, the sequences are splitted in several sdx files	2015-10-02 16:36:25 +02:00
coissac	343d9ec6df	Switch to version 1.1.22	2015-08-03 23:16:37 +02:00
coissac	7a993ec841	Patch a wrong import in the file	2015-08-03 23:14:13 +02:00
celinemercier	6170fac081	fixed a problem with the progress bar in obiselect when there is more than one category	2015-07-20 15:24:30 +02:00