Commit Graph

820 Commits

Author SHA1 Message Date
Edward Hartnett
8681b0d241 more documentaiton 2019-12-20 07:10:13 -07:00
Edward Hartnett
2136063d69 better documentation 2019-12-20 07:05:23 -07:00
Edward Hartnett
6952eb779b documentation updates 2019-12-20 05:36:09 -07:00
Ward Fisher
6c75e97764
Merge pull request #1570 from NOAA-GSD/ejh_compact
enable compact storage for netcdf-4 vars
2019-12-19 16:47:05 -07:00
James Sharpe
c5d1e4bdec Call find_package(MPI) to locate MPI paths and link to libdispatch if required 2019-12-18 16:48:40 +00:00
Edward Hartnett
19fef32a9e better documentation for compact storage 2019-12-16 09:52:59 -07:00
Edward Hartnett
e43a5d952c updated docs for NC_COMPACT 2019-12-04 09:16:33 -07:00
Edward Hartnett
64d821b568 removed non-relaxed coord bounds from test code 2019-11-26 06:20:34 -07:00
Edward Hartnett
5ab7bf7796 now always relax! 2019-11-26 05:36:16 -07:00
Edward Hartnett
2682ffd68d improved docs for cache functions, added libhdf5/hdf5cache.c to Doxyfile.in, added benchmark program for cache settings 2019-11-25 16:33:04 -07:00
Ward Fisher
af8f9ad2cf
Merge pull request #1523 from NetCDF-World-Domination-Council/ejh_udf
User-defined formats must come first in NC_infermodel, plus test
2019-11-15 16:40:07 -07:00
Ward Fisher
e4003be502
Merge pull request #1515 from NetCDF-World-Domination-Council/ejh_att_docs
update for attribute documentation
2019-11-15 16:39:46 -07:00
Ward Fisher
2462cda15e
Merge pull request #1525 from NetCDF-World-Domination-Council/ejh_anon_dims
If HDF5 dataset has multiple anonymous dimensions of the same size, assume they are different dimensions
2019-11-14 16:58:24 -07:00
Constantine Khrulev
91d3a89bdd Fix NC_coord_zero indexing in NCDISPATCH_initialize()
Fixes #1518.
2019-11-14 08:26:33 -09:00
edwardhartnett
b9f57b2b5f now UDF mode flags take priority over NC_NETCDF4 2019-11-13 12:13:33 -07:00
edwardhartnett
0bbe91e438 udf must take priority in NC_infermodel 2019-11-13 12:07:33 -07:00
edwardhartnett
c76dae1c5d added anchors for reading_attributes and writing_attributes, and refs to them, also changed order of files in Doxygen.in 2019-11-08 05:19:51 -07:00
edwardhartnett
09fe16c847 cleanup 2019-11-08 04:47:57 -07:00
edwardhartnett
8b2630913a adding doxygen docs for every att function 2019-11-08 04:45:45 -07:00
edwardhartnett
7919e2c052 fixing documentation for attribute put functions 2019-11-07 12:19:18 -07:00
edwardhartnett
42df9b09e5 fixing documentation for attribute put functions 2019-11-07 11:58:41 -07:00
edwardhartnett
3ecef5e7f0 fixing documentation for attribute get functions 2019-11-07 11:47:27 -07:00
edwardhartnett
209da6563c greater distinction between netCDF-4 and classic formats in attribute documentation 2019-11-07 11:32:57 -07:00
edwardhartnett
f46679c8cc cleanup and minor fixes for attribute rename/delete functions 2019-11-07 09:53:43 -07:00
edwardhartnett
ed8ef60855 cleanup and minor fixes for attribute inq functions 2019-11-07 09:46:23 -07:00
edwardhartnett
d961f7b76e cleanup of documentation format in attributes write code 2019-11-07 09:31:04 -07:00
edwardhartnett
837dccd217 changed format to match other docs, fixed file documentation 2019-11-07 07:09:54 -07:00
Ward Fisher
f77b96b066 Fixed a potential null/garbage free. 2019-10-24 16:37:52 -06:00
Ward Fisher
36ccecf053 Addressing a potential null argument to strlen 2019-10-24 14:28:39 -06:00
Greg Sjaardema
5ecad63c6a
Remove incorrect comment
The comment states that prefix must end in '/', but the '/' is added in the function itself, so the prefix should *not* end in '/' and the comment is incorrect.
2019-10-16 08:40:58 -06:00
Ward Fisher
d001ec8590 Removing a problematic const causing issues on OSX. 2019-10-09 17:18:48 -06:00
Dennis Heimbigner
f1506d552e Change (again), and hopefully simplify, the file model inference algorithm.
* For URL paths, the new approach essentially centralizes all information
  in the URL into the "#mode=" fragment key and uses that value
  to determine the dispatcher for (most) URLs.

* The new approach has the following steps:

  1. canonicalize the path if it is a URL.
  2. use the mode= fragment key to determine the dispatcher
  3. if dispatcher still not determined, then use the mode flags
     argument to nc_open/nc_create to determine the dispatcher.
  4. if the path points to something readable, attempt to read the
     magic number at the front, and use that to determine the dispatcher.
     this case may override all previous cases.

* Misc changes.

  1. Update documentation
  2. Moved some unit tests from libdispatch to unit_test directory.
  3. Fixed use of wrong #ifdef macro in test_filter_reg.c
     [I think this may fix an previously reported esupport query].
2019-09-29 12:59:28 -06:00
Ward Fisher
e7cc899264 Merge branch 'ejh_try2' of https://github.com/NetCDF-World-Domination-Council/netcdf-c into gh1487.wif 2019-09-20 14:04:56 -06:00
Greg Sjaardema
56c0d5cf8a Spelling fixes 2019-09-18 08:03:01 -06:00
edwardhartnett
2cd228bcd4 porting changes from other PR 2019-09-16 11:28:18 -06:00
edwardhartnett
e4ef7b1a65 more unit tests, this time for nc4internal.c 2019-08-21 04:46:00 -06:00
Ed Hartnett
bce3fa6169
Merge branch 'master' into ejh_next 2019-08-16 03:42:32 -06:00
edwardhartnett
94f1a89a40 final removal 2019-08-15 07:05:10 -06:00
edwardhartnett
c7c2892de5 clean up 2019-08-15 06:53:57 -06:00
edwardhartnett
2077729abc removed base_pe functions from dispatch table 2019-08-15 06:51:06 -06:00
edwardhartnett
60f436e7ee starting to remove obsolete _CRAYMPP macros 2019-08-14 06:13:45 -06:00
edwardhartnett
dce6f32a76 documentation 2019-08-13 14:57:43 -06:00
edwardhartnett
f007523826 fixed missing dependency in unit_test Makefile.am 2019-08-13 11:06:06 -06:00
edwardhartnett
978707c319 only run slow nclist test if --enable-large-file-tests is used 2019-08-13 10:55:44 -06:00
edwardhartnett
88077fe26e more comments 2019-08-13 06:31:06 -06:00
edwardhartnett
821b749186 removed unnecessary checking in find_in_NCList() 2019-08-13 06:03:48 -06:00
edwardhartnett
d76114aab3 more testing, sorting out some memory issues in test 2019-08-13 05:45:03 -06:00
edwardhartnett
8b8ece4f4b more testing of nclistmgr.c 2019-08-09 13:49:52 -06:00
edwardhartnett
f20db2e024 more documentation 2019-08-09 11:13:55 -06:00
edwardhartnett
d558873c93 documented functions in nclistmgr.c 2019-08-09 09:15:59 -06:00
edwardhartnett
916802bf4c starting to add doxygen docs for nclistmgr.c 2019-08-09 08:48:28 -06:00
edwardhartnett
fb32957b2b whitespace cleanup 2019-08-09 08:45:39 -06:00
edwardhartnett
3a9207d55c more changes for user-defined formats 2019-08-03 18:33:43 -06:00
edwardhartnett
83c6cd58a7 more changes in support of user-defined formats 2019-08-03 17:19:13 -06:00
edwardhartnett
170c5b0901 removed NC from open in dispatch table 2019-08-01 14:30:20 -06:00
Dennis Heimbigner
4c92fc3405 Remove netcdf-4 conditional on the dispatch table.
Partially address: https://github.com/Unidata/netcdf-c/issues/1056

Currently, some of the entries in the dispatch table
are conditional'd on USE_NETCDF4.

As a step in upgrading the dispatch table for use
with user-defined tables, we remove that conditional.
This means that all dispatch tables must implement the
netcdf-4 specific functions even if only to make them
return NC_ENOTNC4. To simplify this, a set of default
functions are defined in libdispatch/dnotnc4.c to provide this
behavior. The file libdispatch/dnotnc3.c is also relevant to
this.

The primary fix is to modify the various dispatch tables to
remove the conditional and use the functions in
libdispatch/dnotnc4.c as appropriate. In practice, all of the
existing tables are prepared to handle this, so the only
real change is to remove the conditionals.

Misc. Unrelated fixes
1. Fix some annoying warnings in ncvalidator.

Notes:
1. This has not been tested with either pnetcdf or hdf4 enabled.
   When those are enabled, it is possible that there are still
   some conditionals that need to be fixed.
2019-07-20 13:59:40 -06:00
Dennis Heimbigner
000f22b12a Fix encoding of a DAP2 constraint specified outside the URL.
re: github issue #1425

The 'ncdump -v' command causes a constraint to be sent
to the opendap code (in libdap2). This is a separate path
from specifying the constraint via a URL.

This separate path encoded its constraint using code independent
of and duplicative of that provided by ncuri.c and this duplicate
code did not properly encode the constraint, which might include
square brackets.

Solution chosen here was to get rid of the duplicate code and
ensure that all URL escaping is performed in the ncuribuild function
in the ncuri.c file.

Also removed the use of the NEWESCAPE conditional in ncuri.c
because it is no longer needed.
2019-07-14 15:56:29 -06:00
Ward Fisher
9db0e26b80
Merge pull request #1432 from NetCDF-World-Domination-Council/ejh_dispatch
create header netcdf_dispatch.h
2019-07-09 12:58:28 -06:00
Ward Fisher
281ac5ff15
Merge pull request #1431 from NetCDF-World-Domination-Council/ejh_remove_macro
remove unused macro USE_REFCOUNT
2019-07-09 12:58:17 -06:00
Ward Fisher
8b1c4e3ff8
Merge pull request #1410 from Unidata/ansifix2.dmh
Fix ncconfigure.h to solve a -ansi problem with strdup()
2019-07-09 12:57:31 -06:00
Ed Hartnett
d408006d06 handle UDF formats on NC_create() 2019-07-05 13:39:50 -06:00
Ed Hartnett
620f17d5ef finidhed removing refcount from dfile.c 2019-07-04 15:46:15 -06:00
Ed Hartnett
f6ea863011 finidhed removing refcount from dfile.c 2019-07-04 15:45:49 -06:00
Ed Hartnett
0727ccf5ad starting to take out ref count stuff 2019-07-04 15:45:03 -06:00
Ed Hartnett
edf1f92042 starting to take out ref count stuff 2019-07-04 15:44:01 -06:00
Ed Hartnett
41cef20d1a fixed handling of NULL name in nc_open 2019-06-30 04:56:24 -06:00
Dennis Heimbigner
4de0c555e1 Fix nctime to not include ncconfigure.h
re: https://github.com/Unidata/netcdf-c/pull/1411

Turns out that the real problem here is that nctime.c
is including ncconfigure.h rather than config.h.
2019-05-30 12:47:50 -06:00
Ward Fisher
d6a3944199
Merge pull request #1409 from Unidata/nccopydefault.dmh
Nccopy was overriding default chunking when it should not.
2019-05-29 15:26:09 -06:00
Dennis Heimbigner
06498ff16a various fixes 2019-05-23 16:35:03 -06:00
Ed Hartnett
1d9f28fb70 changing USE_NETCDF4 to USE_HDF5 in dfilter.c 2019-05-22 07:36:22 -06:00
Dennis Heimbigner
331a1f1c63 Centralize calls to curl_global_init and curl_global_cleanup
re: https://github.com/Unidata/netcdf-c/issues/1388

1. Centralize calls to curl_global_init and curl_global_cleanup
   to libdispatch/ddispatch.c
2. Make the above calls if options require curl: currently
   any of DAP2, DAP4, or byterange.
3. Side issue: Fix obscure bug in mmapio.c involving non-persistent mmap.
2019-05-03 13:22:54 -06:00
Ward Fisher
3b34a82e19 Merge branch 'master' into threads_part1.dmh 2019-05-01 14:41:13 -06:00
Ward Fisher
5410967b00 Merge branch 'master' into addfilter.dmh 2019-04-30 14:51:25 -06:00
Ward Fisher
6446ff37c5
Merge pull request #1368 from jschueller/mingw
Fix MinGW build
2019-04-03 17:32:22 -06:00
Dennis Heimbigner
6934aa2e8b Thread safety: step 1: cleanup
re: https://github.com/Unidata/netcdf-c/issues/1373 (partial)

* Mark some global constants be const to indicate to make them easier to track.
* Hide direct access to the ncrc_globalstate behind a function call.
* Convert dispatch tables to constants (except the user defined ones)
  This has some consequences in terms of function arguments needing to be marked
  as const also.
* Remove some no longer needed global fields
* Aggregate all the globals in nclog.c
* Uniformly replace nc_sizevector{0,1} with NC_coord_{zero,one}
* Uniformly replace nc_ptrdffvector1 with NC_stride_one
* Remove some obsolete code
2019-03-30 14:06:20 -06:00
Ward Fisher
752a040bb0 Merge branch 'master' into cleanup.wif 2019-03-26 15:33:40 -06:00
Dennis Heimbigner
4026323383 Fix minor --ansi warnings in dinfermodel.c and bzlib.c
re:

Needed to provide centralized definitions of fileno and fdopen;
also need to #include sys/types.h
2019-03-22 15:16:47 -06:00
Ward Fisher
5ee026f843 Cleaned up some errant conflict resolution fenceposting. 2019-03-21 15:56:27 -06:00
Ward Fisher
cb7bec8dbc Merge branch 'master' into cleanup.wif 2019-03-21 14:39:57 -06:00
Dennis Heimbigner
8d0bced60d Allow in-line definition of filters
Priority: Low

re: issue https://github.com/Unidata/netcdf-c/issues/1329

HDF5 has the ability to programmatically define new filters,
as opposed to using HDF5_PLUGIN_PATH env variable.
This PR adds support for that feature.
Not clear how useful this is, though.
See docs/filters.md for details.
2019-03-21 11:33:27 -06:00
Ward Fisher
e2b31ffae4
Merge branch 'master' into byterange.dmh 2019-03-19 12:05:44 -06:00
Ward Fisher
3de2cf3d55
Merge pull request #1346 from wkliao/nc_mpiio
move checking for flag conflict to nc_create_par
2019-03-19 12:04:38 -06:00
Julien Schueller
a3c2031071 Fix MinGW build
Som Win32 includes are also needed on MinGW
2019-03-17 09:18:56 +01:00
Ward Fisher
b066336b5c Merge branch 'master' into cleanup.wif 2019-03-06 12:25:44 -07:00
Ward Fisher
3bed028d52 Correcting div by zero error, minor resource leak. 2019-03-05 14:24:17 -07:00
Wei-keng Liao
142cd5b5ca as NC_MPIIO has deprecated, move checking for flag conflict to nc_create_par 2019-02-26 11:01:35 -06:00
Ed Hartnett
26f4bfdd28 added comment about function ordering 2019-02-25 12:23:54 -07:00
Ed Hartnett
d0a6e9c246 more work on var documentation 2019-02-25 12:20:53 -07:00
Ed Hartnett
ea5e7f9b9a fixing some documentation issues in hdf5var.c 2019-02-25 10:44:05 -07:00
Ed Hartnett
d47006fd3f fixing some documentation issues in hdf5var.c 2019-02-25 10:32:17 -07:00
Ed Hartnett
160186d52e more doc cleanup 2019-02-25 08:35:18 -07:00
Ed Hartnett
c2c2f8e044 cleanup of var docs 2019-02-25 08:25:12 -07:00
Ed Hartnett
c620d8c5c7 more documentation cleanup 2019-02-25 08:15:43 -07:00
Ed Hartnett
2f8f5baf0f more documentation cleanup 2019-02-25 08:14:42 -07:00
Ed Hartnett
3277ef2359 formatting cleanup 2019-02-25 07:58:55 -07:00
Ed Hartnett
0e204ebe0c formatting cleanup 2019-02-25 07:55:29 -07:00
Ed Hartnett
7dc9097d62 cleaned away uncorrect section 2019-02-25 07:48:29 -07:00
Ed Hartnett
2dd178bfa1 documentation cleanup 2019-02-25 07:37:23 -07:00
Ed Hartnett
f83c8a5d3a documentation of dim rename for netcdf-4 vs classic 2019-02-25 07:32:06 -07:00
Ed Hartnett
fba4c19953 documentation cleanup 2019-02-25 07:28:35 -07:00