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
225 changed files with 1091 additions and 1386 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