Commit Graph

51 Commits

Author SHA1 Message Date
Dennis Heimbigner
e89187d2c2 remove actions debug 2021-09-28 14:09:38 -06:00
Dennis Heimbigner
6b69b9c52c Significantly Improve Amazon S3 Cloud Storage Support
## S3 Related Fixes

* Add comprehensive support for specifying AWS profiles to provide access credentials.
* Parse the files "~/.aws/config" and "~/.aws/credentials to provide credentials for the HDF5 ROS3 driver and to locate default region.
* Add a function to obtain the currently active S3 credentials. The search rules are defined in docs/nczarr.md.
* Provide documentation for the new features.
* Modify the struct NCauth (in include/ncauth.h) to replace specific S3 credentials with a profile name.
* Add a unit test to test the operation of profile and credentials management.
* Add support for URLS of the form "s3://<bucket>/<key>"; this requires obtaining a default region.
* Allows the specification of profile and/or region in a URL of the form "#mode=nczarr,...&aws.region=...&aws.profile=..."

## Misc. Fixes

* Move the ezxml code to libdispatch so that it can be used both by DAP4 and nczarr.
* Modify nclist to provide a deep clone operation.
* Modify ncuri to provide a deep clone operation.
* Modify the .rc file format to allow the specification of a path to be tested when looking for an entry in the .rc file.
* Ensure that the NC_rcload function is called.
* Modify nchttp to support setting request headers.
2021-09-27 18:36:33 -06:00
Dennis Heimbigner
11fe00ea05 Add filter support to NCZarr
Filter support has three goals:

1. Use the existing HDF5 filter implementations,
2. Allow filter metadata to be stored in the NumCodecs metadata format used by Zarr,
3. Allow filters to be used even when HDF5 is disabled

Detailed usage directions are define in docs/filters.md.

For now, the existing filter API is left in place. So filters
are defined using ''nc_def_var_filter'' using the HDF5 style
where the id and parameters are unsigned integers.

This is a big change since filters affect many parts of the code.

In the following, the terms "compressor" and "filter" and "codec" are generally
used synonomously.

### Filter-Related Changes:
* In order to support dynamic loading of shared filter libraries, a new library was added in the libncpoco directory; it helps to isolate dynamic loading across multiple platforms.
* Provide a json parsing library for use by plugins; this is created by merging libdispatch/ncjson.c with include/ncjson.h.
* Add a new _Codecs attribute to allow clients to see what codecs are being used; let ncdump -s print it out.
* Provide special headers to help support compilation of HDF5 filters when HDF5 is not enabled: netcdf_filter_hdf5_build.h and netcdf_filter_build.h.
* Add a number of new test to test the new nczarr filters.
* Let ncgen parse _Codecs attribute, although it is ignored.

### Plugin directory changes:
* Add support for the Blosc compressor; this is essential because it is the most common compressor used in Zarr datasets. This also necessitated adding a CMake FindBlosc.cmake file
* Add NCZarr support for the big-four filters provided by HDF5: shuffle, fletcher32, deflate (zlib), and szip
* Add a Codec defaulter (see docs/filters.md) for the big four filters.
* Make plugins work with windows by properly adding __declspec declaration.

### Misc. Non-Filter Changes
* Replace most uses of USE_NETCDF4 (deprecated) with USE_HDF5.
* Improve support for caching
* More fixes for path conversion code
* Fix misc. memory leaks
* Add new utility -- ncdump/ncpathcvt -- that does more or less the same thing as cygpath.
* Add a number of new test to test the non-filter fixes.
* Update the parsers
* Convert most instances of '#ifdef _MSC_VER' to '#ifdef _WIN32'
2021-09-02 17:04:26 -06:00
Ward Fisher
18086dae10 Correct a typo in the github actions yaml file. 2021-08-25 14:32:01 -06:00
Ward Fisher
7ee0281c74 Test dependency on one-offs updated. 2021-08-25 14:31:09 -06:00
Ward Fisher
48d943864d Syntax debugging. 2021-08-25 14:28:59 -06:00
Ward Fisher
d6f06bf3d6 A bit more twiddling of the github actions workflow. 2021-08-25 14:25:41 -06:00
Ward Fisher
8fc52da9d7 Thanks to newer ctest functionality, if ctest tests fail, re-run just the failed ones with more verbose output. 2021-08-25 12:43:04 -06:00
Ward Fisher
40c3fc2169 Reverse GA workflow. Run the one-off tests first and then run the full test matrix. This should shorten the test/failure cycle. 2021-08-25 11:16:47 -06:00
Ward Fisher
912fd7574c Modify GA workflow a bit. 2021-08-24 15:22:20 -06:00
Ward Fisher
5bcf91f880 Correct spacing issue in GA yaml file. 2021-08-24 15:07:10 -06:00
Ward Fisher
37d6cc9191 Propagate github actions tests into cmake-based stanza. 2021-08-24 14:40:13 -06:00
Ward Fisher
1376067870 Added a one-off stanza for autoconf-based tests on Github Actions. 2021-08-24 14:26:28 -06:00
Edward Hartnett
e8d3198a77 added commas 2021-08-20 05:46:22 -06:00
Edward Hartnett
5c23e72e28 added 1.12.1 to hdf5 versions built by GitHub actions 2021-08-20 05:44:43 -06:00
Dennis Heimbigner
669fd34357 remove push 2021-07-18 13:37:51 -06:00
Ward Fisher
e21ef7bcb0
Merge branch 'master' into dap4fixes2.dmh 2021-06-01 14:11:39 -06:00
Ward Fisher
5b49ee9f3b Temporarily remove distcheck from Github Actions 2021-05-26 13:55:59 -06:00
Ward Fisher
6eaf39f3c3 Revert previous change. 2021-05-26 13:54:40 -06:00
Ward Fisher
a5d7277092 Testing a different theory 2021-05-26 13:44:56 -06:00
Ward Fisher
5f95b7ca9f Temporarily add an ssh-interface when make distcheck fails. 2021-05-26 13:15:12 -06:00
Ward Fisher
ceb9b29e17 Speculating on fix, perhaps a race issue on make distcheck when passed the command to use concurrent processes. 2021-05-26 11:16:22 -06:00
Ward Fisher
e2eb7bb52e Added DISTCHECK_CONFIGURE_FLAGS to Github Actions distcheck stanza. 2021-05-26 10:44:07 -06:00
Ward Fisher
d003f98367 Updated github actions to add make distcheck 2021-05-25 10:55:14 -06:00
Dennis Heimbigner
8ceafa62d4 Improve operation of the DAP4 code and fix bugs
re: e-support EOT-483791

* Add a new set of remote tests based on using the thredds-test server.
* Improve error reporting when server requests fail.
* Fix handing of _NCProperties attribute
2021-05-21 20:46:56 -06:00
Ward Fisher
95719addd2 Added 1.0.1 to test matrix in support of https://github.com/Unidata/netcdf-c/pull/1931#issuecomment-804312933 2021-03-26 14:50:22 -06:00
Dennis Heimbigner
911d0a5deb Enable nczarr testing in github actions.
Changes:
1. add "use_nczarr: [ nczarr_off, nczarr_on ]" to matrix
2. add libzip-dev to the apt installs (might need caching).
3. convert deprecated "--enable-netcdf-4" to "--enable-hdf5" (also for cmake)
2021-01-27 11:30:48 -07:00
Ward Fisher
bb2b864674 Added more updates 2020-12-16 09:34:42 -07:00
Ward Fisher
3e01272cee Added an apt update stanza to the github action script. 2020-12-16 09:19:21 -07:00
Ward Fisher
5fed325180 Cleaned up orphaned github action files, modified GA to run on PR instead of push. 2020-12-07 11:16:04 -07:00
Ward Fisher
4cf290dc0b
Merge pull request #1897 from DennisHeimbigner/oceanunavail.dmh
Disable use of opendap2.oceanbrowser.net
2020-12-04 16:11:47 -07:00
Ward Fisher
7fce4b3482 Clean up, bring over a new action script. This one uses apt and cached builds instead of conda. 2020-12-04 15:38:13 -07:00
Ward Fisher
1814da1f7f Temporarily reducing test matrix. 2020-12-03 12:20:52 -07:00
Ward Fisher
04640abe32 Github Action debugging. 2020-12-03 12:12:07 -07:00
Ward Fisher
9b9ca97712 Explicitly link rt library for github actions. 2020-12-03 12:09:24 -07:00
Ward Fisher
d263a48637 Correct previous 'fix' that wasn't. 2020-12-03 12:03:34 -07:00
Ward Fisher
f48ccb465d Address link issue on github actions platform. 2020-12-03 11:59:25 -07:00
Dennis Heimbigner
c797eb29ad remove worflows and fix ifdef 2020-12-02 16:36:09 -07:00
Dennis Heimbigner
af89295852 ignore 2020-12-01 22:09:13 -07:00
Dennis Heimbigner
5b8842b373
manual.yml 2020-12-01 22:06:16 -07:00
Dennis Heimbigner
62036cbf45
ignore.yml 2020-12-01 22:01:44 -07:00
Dennis Heimbigner
8cf8c31df4
automake-dmh.yml 2020-12-01 21:59:52 -07:00
Dennis Heimbigner
c164650cb6 rename 2020-12-01 21:58:10 -07:00
Dennis Heimbigner
6cdddd7596 update workflows 2020-12-01 21:53:33 -07:00
Dennis Heimbigner
0aa80f91d6 manual workflow 2020-12-01 21:48:39 -07:00
Ward Fisher
1ba45b9e9a Adding github actions to netcdf-c for CI purposes. 2020-11-30 11:21:51 -07:00
Ward Fisher
cca0f8d46e Moved code of conduct and contributing to .github folder. 2019-10-08 10:27:32 -06:00
Ward Fisher
a747922bff Adopted codeowners file from metpy project; this is a technical ownership and is not asserting ownership of code/copyright. Any code that does not have an obvious owner (from the perspective of github) will default to @WardF and @DennisHeimbigner 2018-03-16 14:46:08 -06:00
Ward Fisher
d813448e2b Put CONTRIBUTING.md back in top level of repository. 2016-02-24 10:55:56 -07:00
Ward Fisher
e1cfa5aca1 Added a roughed-in issue template. 2016-02-24 10:55:12 -07:00