obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity
148 Commits 18 Branches 66 Tags
e8417b4f6fafc2e8ce640e61934afce5ab3e7171
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
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
Celine Mercier 1d39dcc559 updated documentation 2015-05-18 17:57:10 +02:00
Celine Mercier 196140af35 included the doc from both header files in the documentation 2015-05-13 11:16:50 +02:00
Celine Mercier 5990da3215 first header files for OBIColumns. 2015-05-13 11:06:52 +02:00
Celine Mercier 6e1b92db8f Updated the doc with the idea of OBIDMS release files. 2015-05-12 16:41:12 +02:00
Celine Mercier 3662613551 Closes #4. Updated the doc with new naming conventions for OBIDMS column 
files.
 2015-05-12 15:17:28 +02:00
Celine Mercier d922cceb59 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2015-05-12 14:29:39 +02:00
Celine Mercier db8b54aad6 fixed "ULM" mistake : replaced with "UML" 2015-05-12 14:25:52 +02:00
Celine Mercier aece3281a0 adding Doxyfile 2015-05-12 11:27:08 +02:00
Celine Mercier 6dd6567231 documentation for the OBIDMS ULM 2015-05-11 17:45:47 +02:00
Celine Mercier c99677a6b6 adding the doxygen directories 2015-05-11 17:27:03 +02:00
Celine Mercier e1aa835463 fixed conf.py to put relative paths 2015-05-11 17:23:43 +02:00