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Author SHA1 Message Date
Celine Mercier b45b496b0e Major update: new type of columns containing indices referring to lines 
in other columns
 2015-11-29 11:57:07 +01:00
Celine Mercier 2cf10cb6f0 Column type is now passed as a character string when creating the column 
(either 'OBI_INT', 'OBI_FLOAT', 'OBI_BOOL', 'OBI_CHAR', 'OBI_STR' or
'OBI_SEQ')
 2015-11-23 15:48:27 +01:00
Celine Mercier 5a5516303d deleting useless .pyc files 2015-11-23 14:43:34 +01:00
Celine Mercier d6a99bafea Fixed a major bug with the versioning of columns that was introduced in 
f6ec8ba9
 2015-11-23 13:34:51 +01:00
Celine Mercier 08f2657e18 Increased maximum line count of columns to 1^9 2015-11-23 13:23:18 +01:00
Celine Mercier 6aa2f92930 DNA sequences are now encoded on 4 bits when they are in IUPAC 2015-11-20 15:32:09 +01:00
Celine Mercier 87044b41d8 modified the encoding function on 2 bits a little 2015-11-20 11:32:47 +01:00
Celine Mercier 6ab1c83302 New column type for DNA sequences. Only for those coded on 2 bits (only 
'ATGCatgc') for now.
 2015-11-19 18:12:48 +01:00
Celine Mercier e371248567 changed version to 0.0.0 2015-11-19 18:11:21 +01:00
Celine Mercier dbf9463238 The endianness of a DMS is now stored in the OBIDMS structure 2015-11-18 15:35:09 +01:00
Celine Mercier eb12af4da4 Fixed minor error in the documentation of a function. 2015-11-16 15:38:01 +01:00
Celine Mercier e8417b4f6f The endianness of an OBIDMS is now stored in an informations file that 
is read when opening the OBIDMS.
 2015-11-16 14:37:51 +01:00
Celine Mercier 6579566c6e Minor changes in code to improve readability and fix C compilation 
warnings
 2015-11-10 14:37:58 +01:00
Celine Mercier 410e2e02a0 When retrieving the header of a column, the version number of the column 
wanted can now be provided.
 2015-11-10 13:30:10 +01:00
Celine Mercier 8ce4f264aa When enlarging a column, the function doesn't try anymore to keep the 
mapped region at the same pointer (never works), and unmap/remap
instead.
 2015-11-10 13:18:36 +01:00
Celine Mercier d885eb48ff The header size when creating a column is now calculated according to 
the size of the header structure and the page size of the platform.
 2015-11-10 13:09:30 +01:00
Celine Mercier 661fe3606a In OBI_CHAR columns, characters are now given and retrieved as decoded 
(unicode) characters.
 2015-11-10 11:24:08 +01:00
Celine Mercier c4b7e579cf Comments in column headers are now working. 2015-11-10 10:56:45 +01:00
Celine Mercier f6ec8ba963 The header size is now directly read in the file when a column or an 
array is opened.
 2015-11-09 17:50:32 +01:00
Celine Mercier 0e3d6ed2d7 Methods __len__ (number of lines used) and __sizeof__ (total size in 
bytes) implemented for columns.
 2015-11-09 15:56:20 +01:00
Celine Mercier 01bfc14503 The data size in bytes is now stored in the header of a column. 2015-11-09 15:55:00 +01:00
Celine Mercier 65c1b1e8b2 Minor changes to make the creation of files and directories cleaner 2015-11-09 15:22:01 +01:00
Celine Mercier b37bd8f21c File descriptors for dms, column and array directories are now stored in 
structures.
 2015-11-09 15:06:02 +01:00
Celine Mercier 05e3956a0c Minor changes in code to improve readability (freeing some character 
strings earlier)
 2015-11-09 11:22:51 +01:00
Celine Mercier 9b066f4327 Major update: obiarrays with columns containing indices referring to 
character strings.
 2015-11-06 17:55:15 +01:00
Celine Mercier 456551ffeb obi arrays that don't work because of cython bug passing wrong pointers 2015-11-03 14:22:00 +01:00
Celine Mercier ecb9d97adb Reorganized the code to have less functions, and the functions to get 
and format the creation date of a column are now working.
 2015-10-15 15:12:45 +02:00
Celine Mercier 0eaa5aa784 Major changes : new cython subclasses to handle columns with multiple 
elements per line in a more efficient way + now elements_names are
passed as a list + new function to recover only the header of a column
 2015-10-14 18:05:34 +02:00
Celine Mercier 21923e213d The unit tests now test for None values 2015-10-12 18:02:40 +02:00
Celine Mercier 6877fc4892 Fixed a critical bug where values were initialized to NA at the wrong 
location when there was multiple elements per line
 2015-10-12 17:54:36 +02:00
Celine Mercier dbed3d9d1d New module for unit testing with PyUnit 2015-10-09 15:42:57 +02:00
Celine Mercier fc8bf16769 Fixed a critical bug in the computation of the new number of lines of a 
column when truncating
 2015-10-09 13:49:48 +02:00
Celine Mercier e114a3c9cb fixed a critical bug where data size was not calculated correctly and 
column directory is now closed when column is closed
 2015-10-09 10:25:40 +02:00
Celine Mercier ebc9f6f512 fixed a bug where Cython was casting doubles in floats 2015-10-08 15:28:30 +02:00
Celine Mercier 2b3f03ec28 Removed deprecated script 2015-10-08 10:46:46 +02:00
Celine Mercier 8fd9c06be2 Fixed missing file for documentation compilation 2015-10-08 10:45:54 +02:00
Celine Mercier b553eef781 Method to close a DMS is uncommented but not complete yet (columns have 
to be closed separately)
 2015-10-08 10:44:13 +02:00
Celine Mercier ee4c513fd4 Fixed a bug where cloning a column would fail if the data was empty 2015-10-08 10:36:02 +02:00
Celine Mercier c013e6ad33 fixed typo in doxygen doc 2015-10-08 10:33:19 +02:00
Celine Mercier c98d567e2f Updated the documentation and restructured a bit because it wasn't 
compiling (note: Breathe not working)
 2015-10-06 11:09:01 +02:00
Celine Mercier 392f110c8d new functions in the OBIDMS_column class to raise NotImplementedError 
exceptions and to get the creation date of a column
 2015-10-02 13:51:26 +02:00
Celine Mercier 6ced3c4896 new functions to get the creation date of a column 2015-10-02 13:47:53 +02:00
Celine Mercier 4b8bf41a71 closes #13, obi_errno is initialized to 0 2015-10-02 13:46:34 +02:00
Celine Mercier c59a244e9d Fixed little typo 2015-09-30 12:07:13 +02:00
Celine Mercier 4b7f2d268b Doxygen documentation corrected and completed. 2015-09-30 12:03:46 +02:00
Celine Mercier 45af8396b8 minor change in variable name for better coherence 2015-09-28 13:52:41 +02:00
Celine Mercier eeebbc77c3 missing __init__ file in previous commit 2015-09-28 13:52:13 +02:00
Celine Mercier 72155c3b73 entirely reworked cython wrapper 2015-09-28 13:51:35 +02:00
Celine Mercier 9aaf2d264a test 2015-09-25 11:29:17 +02:00
Celine Mercier 0951934f77 test 2015-09-25 11:28:23 +02:00
Celine Mercier 68b6ab3224 working on the cython wrapper. This doesn't compile 2015-09-24 11:32:09 +02:00
Celine Mercier b0570ee486 fixed permissions when creating files 2015-09-22 15:52:07 +02:00
Celine Mercier 72105b2aed fixed the computation of the data size when cloning a column 2015-09-22 10:27:17 +02:00
Celine Mercier 9ab8a42340 fixed the mkdir permission mode that forced the user to use sudo to 
write in the created directories
 2015-09-21 15:48:02 +02:00
Celine Mercier 7b606c0477 Column files now always have a size that is a multiple of the page size, 
and the function that enlarges mapped column files tries mapping on next
byte before unmapping/mapping again
 2015-09-21 15:42:29 +02:00
Celine Mercier 7d7dbb1bf9 Handling of single char columns 2015-09-18 15:49:15 +02:00
Celine Mercier 34a3717fb9 The cython function to open a column is now a method of the OBIDMS class 2015-09-17 11:23:50 +02:00
Celine Mercier 2698022aaf New OBIDMS method to list the columns of an OBIDMS 2015-09-15 17:09:31 +02:00
Celine Mercier 90bf15186e Method to get a column's number of lines used 2015-09-14 17:33:40 +02:00
Celine Mercier 5c3bc03bd2 Added the handling of errors with the functions to get a value in a 
column
 2015-09-14 17:04:29 +02:00
Celine Mercier f2231770f1 If an error occurs when cloning a column, the new cloned file is now 
deleted
 2015-09-02 13:06:21 +02:00
Celine Mercier 52e3f2ce4a Columns that are cloned are now closed after cloning 2015-09-02 10:36:00 +02:00
Celine Mercier f0dffaff13 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2015-09-02 10:15:18 +02:00
Celine Mercier f31d8983bb Columns are now enlarged if needed when setting a value 2015-09-01 17:38:08 +02:00
Celine Mercier 3b7536c0df The number of lines used is updated in the header when a value is set, 
and the iteration on the values of a column is done on the number of
lines used (instead of on the total line count).
 2015-08-26 17:25:15 +02:00
Celine Mercier 34ade161de added an obidebug() line 2015-08-26 17:05:37 +02:00
Celine Mercier 48d10ea17c Functions to truncate and/or close a column 2015-08-26 17:01:54 +02:00
Celine Mercier fdc3b96beb Added cython subclasses for columns with _writable or _read for each 
data type. Trying to set a value on a _read subclass raises an
exception.
 2015-08-26 15:34:12 +02:00
Celine Mercier 95dbeb25a0 Added functions to get and set values in columns using the element name 
(for columns with lines made of vectors of elements), for all data types
 2015-08-26 15:05:23 +02:00
Celine Mercier 9d91e907e5 When a column is created, its data is initialized to the NA value of the 
obitype
 2015-08-26 12:00:38 +02:00
Celine Mercier 3f81dc0173 Changed the variable name 'nb_elements' to 'nb_lines' for better clarity 2015-08-26 10:52:19 +02:00
Celine Mercier 8ff3488926 Fix: The number of lines used is set when cloning a column with its data 2015-08-26 10:38:07 +02:00
Celine Mercier 611699252e Files and functions for columns with the data type OBIChar_t, working 
but using char* (needs to be changed)
 2015-08-26 10:31:56 +02:00
Celine Mercier 9ad31fddff Added the possibility to clone a column, with or without its data 2015-08-26 10:29:07 +02:00
Celine Mercier 2162bf4272 obidebug.h for debugging tools 2015-06-26 17:56:15 +02:00
Celine Mercier c454f9612e changed 'column groups' to be called 'column directories' for now. 2015-06-26 17:53:03 +02:00
Celine Mercier 71cd59f775 close file descriptors that don't refer to a directory (as those can not 
be reopened)
 2015-06-24 13:53:12 +02:00
Celine Mercier 719ef61461 changed file names 2015-06-23 18:36:20 +02:00
Celine Mercier 152b34b5f4 Closes #10 : column groups stored in directories 2015-06-23 18:35:34 +02:00
Celine Mercier 61b6c3ce83 Added OBI errnos but work in progress 2015-06-23 17:56:21 +02:00
Celine Mercier 0a78a786c1 fixed replacement *at functions and made get_full_path() function public 2015-06-23 17:55:00 +02:00
Celine Mercier e6e68786f7 private *at functions (openat, mkdirat, opendirat, closedirat) 2015-06-18 17:19:23 +02:00
Celine Mercier 58e7066b9f updated and fixed the documentation 2015-06-17 17:17:54 +02:00
Celine Mercier ed662077b3 fixed bugs and typos in the obidms and obidmscolumn source and header 
files
 2015-06-17 16:51:16 +02:00
Celine Mercier 9f9c20aa4a new OBIDMS_column cython class 2015-06-17 16:49:49 +02:00
Celine Mercier 73ba9fd4c3 updated the OBIDMS class 2015-06-17 16:48:56 +02:00
Celine Mercier 771be89103 updated the documentation (replaced 'release files' with 'version 
files')
 2015-06-17 16:45:04 +02:00
Celine Mercier f740557d96 fixes #9 : replacement function for openat(). 2015-06-17 14:55:05 +02:00
Celine Mercier aff74c72dd updated the documentation 2015-06-10 15:41:14 +02:00
Celine Mercier 5d967f5b7b fixed typos and other minor things 2015-06-10 15:19:02 +02:00
Celine Mercier 9b6de9c411 Attempt at defining some naming conventions. 2015-05-28 17:54:11 +02:00
Celine Mercier 27e246e709 updated the documentation 2015-05-28 17:03:50 +02:00
Celine Mercier ff64d1b2e9 deleting a useless file 2015-05-28 16:35:43 +02:00
Celine Mercier 235a81a534 deleting test data file 2015-05-28 16:35:03 +02:00
Celine Mercier 4759e1cf54 deleting the Breathe sources 2015-05-28 16:34:24 +02:00
Celine Mercier f4a123cd17 updated the documentation with the special values, and the idea of 
column directories and column group directories.
 2015-05-28 16:33:45 +02:00
Celine Mercier 0b031da28c A very basic obicount 2015-05-22 17:54:34 +02:00
Celine Mercier 2073f9f307 OBIDMSColumn file for testing 2015-05-22 17:53:42 +02:00
Celine Mercier f60a98a21d Updated the documentation 2015-05-22 17:52:55 +02:00
Celine Mercier 2395688bd3 adding Doxygen doc generation to the Sphinx Makefile 2015-05-21 11:05:43 +02:00