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latest from coda-oss and NITRO (#623)
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* latest from coda-oss

* Squashed 'externals/coda-oss/' changes from 67d6362bcf..d06dc6534d

d06dc6534d mem::AutoPtr for C++17 (#615)
83443602a6 mem::AutoPtr class to aid C++17 transition (#614)
f10fa2009c Release 2022-11-04 (#613)
a32e697044 remove exception specifications (#609)
084f19126a utilities to find files/directories for unittests (#608)
a3cedada96 Merge branch 'master'
fde6c864fa Merge pull request #607 from mdaus/bugfix/change-order-of-config-header-install
c8a0044010 Install the cmake-configured header after installing the xercesc source tree. Otherwise, the original config will persist in the install
dda2c9acda Merge pull request #606 from mdaus/fix-xerces-config
004a00f09b Bump zlib version for conan builds
207f4dbb9f Fix Xerces config issue and install its config.h
b842417671 Add support for debug optimizations.
0f6cda57dc Use enhanced debug information with gcc/gdb.
5047dce1a9 Work around GCC avx support bug.
001ab18751 Rebuild the waf self-extractor with a fix for the FIPS error.
5a7f64fca2 Revert "Rebuild the waf self-extractor with a fix for the FIPS problem."
9f6f775f8f Rebuild the waf self-extractor with a fix for the FIPS problem.
af7229bd83 utilities to find files from a build (#605)
264ae49dd7 be sure downstream projects build w/C++14 (#604)
7a7b13cbd5 "hello world" for HDF5 (#602)
33cff0ff43 more C++14
963e8ff40c Revert "add HDF5 source code (#603)"
7b5e71a006 add HDF5 source code (#603)
ec7bb2e520 add HDF5 source code (#603)
ec26f703e7 build in NITRO and SIX (#601)
f4361a9730 make it easier to write cli unit-tests (#600)
34b6fdeee1 tweak toString() to reduce specialization (#599)
5907b3ed60 remove C++11 workarounds (#598)
caed59480d Release 2022-08-30_cpp14 (#597)
2630d41e08 get rid of merge conflict
652bce3854 Merge branch 'master'
6f41c09d71 Release 2022-08-30 (#596)
838c323d6a Merge branch 'master'
f916680126 Added handler accessor to MinidomParser for inheriting modules (#594)
72d29e9c27 get unittests working when "nested" in other projects (#595)
f8f18fea5f Actually look at unit test results when using waf (#593)
4189c429e8 Merge branch 'master'
cda679ceee more overloads to take a string length (#592)
b95a32bc4c by default, Uri()s aren't validated (#591)
903ee7ffff Merge branch 'master'
173930a6f2 fix a UTF-8 conversion bug (#590)
a1c0a1eea6 Merge branch 'master'
c5c221a832 CODA code inherits from xml.lite classes :-( (#589)
1bfe5fc402 Merge branch 'master'
a4c6294c30 use EncodedStringView instead of _bstr_t (#588)
6c2df8bb62 "main" is now C++14 (not C++20)
2ce4161080 Squashed commit of the following:
3a0f7fd14d Merge branch 'master'
83c982f0cf remove work-arounds to write non-UTF-8 XML (#586)
142fd7185e Merge branch 'master'
ebf6db1762 <bit> is part of C++20
d3aa8aa5ce std::u8string is in C++20, not C++17
03654933c4 changes to math.linear from coda (#587)
d442e5be0f Merge branch 'master'
5a2f8e52f1 release 2022-08-02 (#585)
e5516aba29 tweak names to match utf8:: conventions (#584)
32f08a9e40 Squashed commit of the following:
ee15ba3172 Merge branch 'master'
3083ec7915 move most platform-specific code to EncodedStringView (#583)
bede753547 fix unit-test with C++20
61a8033f62 consistent use of coda_oss:: and std::
5d3bf9eb83 Merge branch 'master'
36371410c0 EncodedString tweaks for XML processing (#582)
cf2016205c remove any vestiges of Expat and libXML (#580)
33538aa0fc update for newer Intel compiler
ed65e4ccc5 Add two patch candidates to fix FIPS problems in waf.
34c40bd397 Merge branch 'master'
a731ebf8e8 release 2022-06-29 (#579)
a9b9d2a9fa Merge branch 'master'
59387bd87b update "ReleaseNotes.md" for recent changes (#578)
24a3f01afe Merge branch 'master'
e4f940854a remove "boost" and "serialize" (#577)
80b70537e9 update to zlib-1.2.12 (#576)
f92811a53b Merge branch 'master'
202084bacb Remove some compiler warnings (#575)
414c25c551 build with C++20 in VS
1a99a29da3 Merge branch 'master'
c61232224b build most code with Visual Studio (#574)
5cca863d7e Merge branch 'master'
6e4d952bea some unit-tests need argc/argv (#573)
36e051d7b6 Add run1D method to GenerationThreadPool (#572)
6d4776235e Merge branch 'master'
0a08b8e4e9 build "coda-oss-lite" as a VS2022 project (#571)
6677cc38e3 simplify creation of encodes string (#570)
ba62c610c1 Add the 'universal_newlines=True' flag to python Popen calls.
984e4a96ce Fix a bug in waf platform detection.
8f1173f4a6 fix build errors
f21af35b0b Merge branch 'master'
d2aca8d4b5 release 2022-05-03 (#569)
ff55fed596 can't replace all TEST_ASSERT macros with functions (#568)
4db8ada411 restore changes clobbered with merge from "master"
a1f36e1839 Merge branch 'master'
89a636a6af fix copy/assignment in EncodedString (#567)
c3fe91d424 latest tweaks to build with C++17 (#566)
a59a51b571 be sure we use a 64-bit time_t (#565)
1f79fb3ddf Poly2D::atY() bugfix (#564)
ac5307662d Testing to see if windows-2019 works with github actions (#563)
8d0726b37e Fix a bug in waf platform detection.
80fe8e9f8a Merge branch 'master'
c662b5aac3 Update ReleaseNotes.md
ef4a3bbd9a Release 2022-02-22 (aka 2/22/22) (#562)
33b0f3f6eb Merge branch 'master'
8bd0c8cf4a Merge branch 'main' of github.com:mdaus/coda-oss
0a0e6cf145 use char16_t on Linux (#560)
7e41b4b5e4 Merge branch 'feature/use-cpp11-code'
fe65bfddfb fix units for ICC, sys::filesystem (#559)
fc99e4b3e6 recreate from "master"
510317c07a use std::filesystem to "implement" sys::filesystem
895f6c77cd always implement sys::filesystem
0d83ae22fc "units" changes from master
b58173b781 latest from "master" (not quite)
793e3442c8 Squashed commit of the following:
91a729f5a2 re-create from "master"
def979170b update to GSL 4.0.0 (#558)
fe365e5a41 fix XML validation for UTF-8 (#557)
502e5829b8 support conversion to std::wstring (#556)
e69422596a Delete codeql-analysis.yml
45bc6a9640 Create codeql-analysis.yml
87d9a7ef54 remove CodeQL
eab5ecb899 Update build_unittest.yml
8ab12d47e9 Delete codeql-analysis.yml
9e542092b8 try running CodeQL as part of build-linux-cmake
de0c50651e Create codeql-analysis.yml
049608782b tweaks to build in "coda" (#554)
0ba24233b9 replace sys::U8string with coda_oss::u8string (#553)
bcee6551f2 add EncodedString class (#552)
c2eecd3925 simplify implementation of EncodedStringView (#551)
c1320ef00d fix 'typename' for other compilers (#550)
ac3b93931f tweaks to make "main" build easier (#549)
78da741cf5 remove sys/Optional.h (#548)
f31730ac77 put our std work-arounds in one place (#547)
9b7bb571a9 Add an EncodedStringView class (#545)
c0e1da5201 another batch of tweaks to cleanup compiler warnings, etc. (#546)
0f3bfd9d05 added missing "virtual", support unique_ptr (#544)
ca32f99c03 Add option to specify curl installation location. (#501)
2df9c1a819 allow std::filesystem::path to be used for validation (#543)
2891435760 add SinCos for units::Angle (#542)
e430eddefb Delete log4j as 1) it's old, 2) coda-oss doesn't use it, and 3) remove any questions about security vulnerability (#541)
bb11134fd0 xml.lite tweaks (#540)
955b33e215 Release 2021_12_13 (#539)
d73d74d5c1 xml.lite tweaks (#537)
3a90e25c6f use more C++11 functionality (#538)
9ca2a0e50c remove more compiler warnings (#536)
0ec9da1e91 be sure == and != are in-sync (#535)
9084be32c4 fix size_t compiler warnings (#534)
abd6469ec8 fix ICC errors (#533)
09cb36fff4 update version number before cutting a new release (#532)
c29e4d2988 fix ICC warnings/errors from high-side (#531)
91f8f1c089 simplify our std:: implementations (#530)
7c633c7bb5 Further reduce use of std::auto_ptr (#529)
d85883749c Provide support for creating simple version numbers (#528)
b035825929 Merge pull request #527 from mdaus/fix-crypt-h-clash
ffed3d6339 Disable encryption support in minizip build and remove crypt.h header
ee2b2bf8c0 Merge pull request #525 from mdaus/swig-fix
3c02ff2893 Fix config-python prefix issue
6149053d4e Add new config-python module for SWIG compatibility workarounds
30acf5b9af mt::transform_async(), mem::SharedPtr, math::SinCos() (#526)
21efd6a6c9 Implement better workaround for lack of SWIG support for "final"
60837a62ea Revert unneeded changes
0bc994dea7 Fix SWIG path issue for waf build
070f4e9150 Update SWIG generated files
f8472b0c46 Fix SWIG path issues and warnings
e10707f758 Set minimum SWIG version to 4.0.1
b8cdba5c75 Fix waf SWIG build issue
2bd0ee39e5 Enable SWIG in Github waf build
f2b001146f Try fixing SWIG compile issue again
afafabcc28 Fix SWIG compile issue on Linux due to missing macro
7c8d4a81d5 Add SWIG to the CI flow
4023d721c5 Regenerate SWIG bindings
1d8c70109c Add some compile definitions needed by SWIG for CMake build
e5cc58545f Remove some functions which return unique_ptr from SWIG bindings (incompatible).
965a2913dd Remove "final" specifier from structs bound in SWIG (incompatible)
f1bec56014 Merge branch 'master' of https://github.com/mdaus/coda-oss
c01c4d7de5 do in-line initialization (#524)
fb7230ea1e Update CMakeLists.txt
5dfb056898 tweaks for C++17 (#523)
1a7d3ab522 Merge pull request #515 from mdaus/security-and-conan-updates
d13885df66 make it easier to create a new Element with the right encoding (#522)
3fb09e73ab Merge pull request #359 from mdaus/parseArgUpdate
0d546a8f1b Tweak some ArgumentParser tests for the ignoreUnknownArguments option
14bd1f26d4 Merge remote-tracking branch 'origin/master' into parseArgUpdate
cf398c0d36 tweak code for C++11/C++17 (#521)
2d0322b070 reduce use of std::auto_ptr (#520)
853320e90f reduce use of deprecated C++98 code (#519)
4752ba2221 Replace some warning pragmas with macros
32685554ff Merge remote-tracking branch 'origin/master' into security-and-conan-updates
f0350c0cfd Merge pull request #518 from mdaus/bugfix/python3.9-related
fc01df0d8c fix typos in gcc macros
9d356f36cd fix gcc impl
8124da763f remove unreachable code
d034b3a849 clobber warnings from numpy innards
9941a401e1 macros to disable warnings around system headers
8a725bb8f3 Merge pull request #516 from mdaus/mbraswell-enablecpp17-windows
2e7b8165ae Fixed pragma stuff on gcc
9775bb02d9 Fixed pragma stuff on gcc
680d3cce41 Merge branch 'master' of https://github.com/mdaus/coda-oss
8ffd6ed790 forgot to add "units" to CMakeFiles.txt
06835676e5 Remove Auto_ptr flag and make disable warnings cross_platform compatible
d62efece56 Merge branch 'master' of https://github.com/mdaus/coda-oss into mbraswell-enablecpp17-windows
d04042ee9a Merge pull request #517 from mdaus/develop/compiler-warning-helpers
cf5cd16b33 Fix macro usage on gcc
a88bbcd202 Macros to narrowly target disabling warnings
c0d5cdf004 Formatting Changes
be019b44b2 Formatting Changes
2eb04dc9e7 Fixed compiler warnings and added option to compile cpp17 with waf on windows
5d9f27faeb Refactor coda-oss conan recipe
ce66457149 Disable warning for MSVC2017 and earlier
ecfefbfbec Merge remote-tracking branch 'origin/master' into security-and-conan-updates
8b1479881d Merge pull request #514 from mdaus/develop/fix-unused-symbol-errors
1d9a4ec712 Add conan option to use std::regex instead of pcre
6dd5d44576 add required include
4c0ae77811 add required include
1873ceeb8a parameterize build (somewhat)
c9ef567a7a fix Release compile error
e6b47e94ee fix compiler error
eff205ba2d helper macro to fix unusual targets
342098a32c Fix CMake build for modules without include files
5625706ebf Enable cpp17 option for windows builds
98e12b138e Use consistent line endings for *.in template files
d01fea0b73 Configure coda_add_module to install more file extension types
30823f673b Delete stray file
ac7760ba22 Load dependency targets when loading coda-oss for conan build
14781cab8e Implement conan build for openjpeg and pcre2 dependencies
9d955efa53 Exclude unsupported XML backend wrappers from CMake build to remove warnings
1e8c9b2643 Merge remote-tracking branch 'origin/master' into security-and-conan-updates
772d804951 Implement conan build for libjpeg dependency
98b653dea4 Implement conan build for xerces-c dependency
11323e8e98 Implement conan build for zlib dependency
d0e6bf2c4b Improve conan test_package
a03e1294e1 Fix uninitialized member variable warning in mt::AbstractTiedThreadPool
c7bb47b5f8 Remove member variable duplicated in derived class io::ToggleOutputStream
0838ac2ca2 Use consistent line endings for conan recipes and CMake files.
2768e5f07e Update libjpeg to v9d
d75f55bcac Update zlib to 1.2.11
ca2f84cff3 Fix warning in GSL for MSVC 2015 and earlier
1babd19b55 Fix warning in thread tests for MSVC
2f17632496 Fix warning in except module for Visual Studio 2015 and earlier
a485bf6bb1 Fix BIGENDIAN redefinition warning
59543e42b2 Disable warning in dbi for MSVC 2017 and earlier
b4b212834b Fix warnings in numpyutils for MSVC 2017 and earlier
2b179b6587 Fix integer overflow issue
898151ad75 Hook up simple "units" (#513)
4d6beeecc5 Merge pull request #511 from mdaus/develop/horizontal-improved-numerical-precision
c1878b228e Fix for numerical precision issues surrounding horizontal lines
7d1442c66c Merge pull request #510 from mbraswell/fix-testnumelements-build
58fc85f096 Whitespace change to trigger workflow
ab74026b9f Fix wscript to successfully build test_num_elements
323283cd78 Merge pull request #509 from mbraswell/develop-mbraswell-cpp17
16a5502896 Added option to enable cpp17
b0625cf5a2 tweak debug stuff (#508)
8455494878 fix RowCol casting (#507)
01fbb5f008 Get std::u8string working right with C++20 (#506)
df9413efae more "noexcept" for fewer code-analysis diagnostics (#505)
e6219f97f9 reduce compiler warnings/code-analysis diagnostics (#504)
4c9ea0ef18 tweaks for VS2019 16.10 (#503)
0d8ea070a5 reduce compiler warnings (#502)
625b8b59d4 reduce compiler warnings (#500)
3795758da0 get rid of more compiler warnings/code-analysis diagnostics (#499)
427f91be85 reduce compiler-warnings and code-analysis diagnostics (#498)
c82dd9e370 cleanup compiler and code-analysis diagnistics (#496)
b5105b54ae reduce compiler warnings (#495)
e0099cc269 Develop/compiler optimizations (#494)
0eeb3f9638 tweaks to python wrappers made in "nitro" (#492)
5f91f70604 fix printf() format string (#491)
55b855a865 Delete codeql-analysis.yml
603c192d3b Update codeql-analysis.yml
f306979e87 Update codeql-analysis.yml
4a1f78f8ef Create codeql-analysis.yml
3c80a65680 add back coda_oss::filesystem::path (#490)
eaea659ed3 tweak how std:: features are exposed (#489)
0492f0d95f simplify code exposing std:: routines (#488)
e5f3d77701 remove code-analysis diagnostics (#485)
5be599e5af make HOME and USERPROFILE the same (#484)
62b22ae019 cleanup more compiler warnings (#483)
c32ec7dcc1 add unit-tests for env-var editing (#482)
311aea4623 allow an environment-variable to be "edited" during expansion (#481)
bbcab13103 static_assert is C++11, don't use it when checking for C++11 (#480)
068562f589 fix glitches in expandEnviromentVariables() (#479)
30ed1d95e2 produce a new Path::expandEnviromentVariables() function (#478)
074a873b28 remove compiler warnings (#477)
e29f65479f latest C++17 tweaks (#476)
c4e681b0ae tweak code when wchar_t is a built-in type (#474)
8449ac29a4 wchar_t might not be a built-in type on old systems (#473)
a62bdb3e64 add operator= to sys::Optional (#472)
8e310a776d use compiler-provided macros to determine features (#470)
88405c8edb "constexpr" can be hard to get right with older compilers; don't even try (#471)
b195ab3efc need at least VS2017 to use the real GSL (#469)
2978f9114f tweaks to build with older compilers (#468)
7235b898d3 The (old) version of SWIG we're using doesn't like certain C++11 features. (#464)
cccde7f126 only look in the Win1252->UTF-8 map as a last resort (#467)
3db09742c1 get rid of more compiler warnings (#465)
5e0d2e8451 get rid of "char8_t" compiler warning (#463)
d710bc6882 make getValue() easier to use (#462)
f5a9284768 make getElement*() be consistent for both 0 and >1 (#461)
88be6dba35 consistently add C++14/17/20 library features (#459)
59c3a7e2ef use coda_oss:: as a drop-in replacement for std:: (#458)
35de4524c4 use sys::Filesystem::path rather than std::string (#457)
cace666005 make sys::Filesystem::path better conform to std::filesystem::path (#456)
f395edc891 remove ambiguous overloads w/C++17 (#455)
eac4371f19 use newly added sys::Optional<> to manage "encoding" (#454)
243ef5e500 don't derive from std::iterator (#453)
a48b011411 Arguments should be "const&" to prevent C4866 (#452)
878bff901f provide std::span (#451)
81727c4854 remove newly added a new pure virtual as that's a breaking change (#450)
93cf0f03ef main -> master (#449)
5af37a7363 be sure code compiles with C++17 (#448)
82b5aecfb5 build with C++17 (#407)
6ffb888d79 reduce compiler warnings (#439)
9137dda7dc GSL (Guideline Support Library) from https://github.com/Microsoft/GSL (#423)
bc5552cd20 update to xerces-c-3.2.3 (#409)
6fe09e1dbb update to openjpeg-2.3.1 (#417)
6405c0ce59 reduce differences in #407 (#438)
2987bbf8d6 tweak how std::filesystem is enabled (#437)
8fd3c2f202 tweak how std::endian is enabled (#436)
138372c886 more straight-forward reduction of std::auto_ptr (#435)
f13c7cec89 straight-forward reduction of std::auto_ptr (#434)
d243b08e1b add mem::auto_ptr for transition to C++17 (#432)
54ed52158e allow clients to specify custom toType and toString (#431)
7f90aab25e remove trailing underscore from macro (#429)
999e490686 with C++11, several sys typedefs are the same on both Windows & *nix (#427)
6f075b1be5 add sys::Byte (#426)
92221bd0d9 allow except::Throwable to derive from std::exception (#421)
a8f52d0ad4 reduce compiler warnings (#424)
63ea20af69 #including <bit> w/C++17 generates warnings (#408)
10ef060313 reduce compiler warnings (#405)
cf233fdcfd forgot Conf.cpp changes for sys::Endian (#403)
cc53b18537 fix several compiler warnings/code-analysis diagnostics (#404)
1db3751a3c implmeent sys::Endian from C++20 (#402)
f042cd6bb9 support std::filesystem if desired (#400)
4895a9f2dc WIN32 is old, but existing code might still use it; _WIN32 is better (#398)
e2a62f8ec2 make it easier to use xml.lite (#396)
1059b7da1c allow for explicit use of a UTF-8 string (#395)
27de8b8a44 Optionally record how std::string is encoded when manipulating XML (#378)
e0018cea75 implement some <filesystem>-like routines until we can use C++17 (#388)
cafb2365b7 Merge pull request #363 from mdaus/feature/fix-compiler-warnings
6a78bec201 use the existing sys::ubyte rather than making our own pre-C++17 std::byte
14c9fc4ca4 fix a couple of G++ compiler warnings via static_cast<>
e596a60070 std::numeric_limits<T>::epsilon() can be "constexpr"
78b0f6bb26 another try at removing the compiler warning from tiff::split()
8e1de21e17 fixed typo; added a few nots about why we're not using strncpy()
fed3ba8cdb retore previous tiff::split() code as the change got rid of the compiler warning but wasn't portable
98a589616d get rid of g++ strncpy() warning
798f847117 don't use memset(0) with C++ objects
7f697d078c casting result of system() to void doesn't get rid of compiler warning
d55a849c51 remove new g++ compiler warnings in WSL
d0aaa29884 Merge pull request #361 from mdaus/feature/fix-compiler-warnings
cc62e866b0 fix compiler warnings
d45c1f9a09 Updates based on peer review comments which include changing ostream to pointer, adding a couple of more tests, and updating all auto_ptr to unique_ptr in unit test.
fb12ba1266 Update ArgumentParser to use a stream as an argument if the ignore unknown argument flag is set to true.
536d2b0cad Added ability to ignore unknown arguments in the ArgumentParser.
27288f49bb Merge pull request #358 from mdaus/conan-options
fd5e1eecb7 Expose additional CMake options in conan recipe
c972161793 Remove unneeded CMake function

git-subtree-dir: externals/coda-oss
git-subtree-split: d06dc6534d713ecce71db9986d8db3bb5f7a213f

* trying to get git subtree working

* Squashed 'externals/nitro/' content from commit 29125a3472

git-subtree-dir: externals/nitro
git-subtree-split: 29125a3472688d0c60803c0d6ed922ac5248f69a

* git subtree for nitro

* pull from main, not master

* Squashed 'externals/coda-oss/' changes from d06dc6534d..8241dfe7e6

8241dfe7e6 remove last vestiges of std::auto_ptr (#616)

git-subtree-dir: externals/coda-oss
git-subtree-split: 8241dfe7e68d566d9b7ca1ccf572279f41cf6848

* latest from nitro

* add externals/nitro to fix merge conflicts

* remove externals/nitro/externals

* Squashed 'externals/nitro/' changes from 29125a3472..52fe000594

52fe000594 latest from coda-oss (#514)
1d29e4d865 remove std::auto_ptr (#513)

git-subtree-dir: externals/nitro
git-subtree-split: 52fe00059422c54625e26162ae3423ab2f19a8bb

* finish deleting externals/nitro/externals

* Squashed 'externals/coda-oss/' changes from 8241dfe7e6..ab45464820

ab45464820 remove C++17 workarounds (#618)
3d5daf702e unittests for creating XML from scratch (#617)

git-subtree-dir: externals/coda-oss
git-subtree-split: ab454648207b2923020bea7614a49def65f1108f

* add externals/nitro/externals for sync_externals

* remove externals/nitro/externals

* Squashed 'externals/nitro/' changes from 52fe000594..ffcce1e304

ffcce1e304 latest from coda-oss (#515)

git-subtree-dir: externals/nitro
git-subtree-split: ffcce1e3048179e93b0a4da5af3085a66dd3ecb4

* latest from coda-oss and nitro

* Squashed 'externals/coda-oss/' changes from ab4546482..566597043

566597043 Conan versioning, hdf5, and pcre2 fixes (#622)
61aa5e430 Squashed commit of the following:
6557ee34c Yet another attempt at finding test files for unittests (#621)
501add035 -march=native for fastest optimization level (#620)
f1dd0a5b4 overloads to make creating XML documents easier (#619)

git-subtree-dir: externals/coda-oss
git-subtree-split: 56659704390d9cd8a19931676454f498b245e027

* latest from coda-oss

* NITRO-2.11.2

* Squashed 'externals/coda-oss/' changes from 566597043..418130d4d

418130d4d trying to fix build error on github
59d2f678e Release 2022-12-14 (#628)
1e8244291 new --with-optz=fastest-possible option (#627)
6ae81142d new --optz=faster option for WAF builds (#626)
11206c179 sym-links don't work on Windows filesystems
edd3e8fb9 overloads to make simplify routine XML processing (#625)
dfece6106 use sym-links rather than copying files (#624)
22f1f0776 build hdf5.lite with WAF (#623)

git-subtree-dir: externals/coda-oss
git-subtree-split: 418130d4d1c02074963117ba112fd69cf477699d

* Squashed 'externals/nitro/' changes from 7306ac86a..46c6702f8

46c6702f8 NITRO-2.11.2 (#521)
cd053bd7f coda-oss 2022-12-14 (#520)
28b65f4dc get unittests working in other projects (#518)
9182384db latest from coda-oss (#517)
ab88a99f5 Merge branch 'master'
b39ccc4c0 Fix conan build issues (#516)
abbf7e318 remove .git directory right away
5be12fc35 merge develop/sync_externals
103dd73ee latest from coda-oss (#508)
f71128d6f Adding tarfile member sanitization to extractall() (#505)

git-subtree-dir: externals/nitro
git-subtree-split: 46c6702f869f30fe2dbb1fb85692f3e714d545f6

* NITRO-2.11.2

* latest from coda-oss

* Squashed 'externals/coda-oss/' changes from c53304a90..1384b8a5e

1384b8a5e Merge pull request #629 from mdaus/zlib-update
ebbd57247 ZIP APIs use std::string in this branch
9cc19fe82 ZIP unittests
b8d25d364 Update zlib to 1.2.13

git-subtree-dir: externals/coda-oss
git-subtree-split: 1384b8a5e260c4a7418904508b1ab671950d8e45

* Squashed 'externals/nitro/' changes from 76047c7d3..bd741e4f1

bd741e4f1 latest from coda-oss (#522)

git-subtree-dir: externals/nitro
git-subtree-split: bd741e4f1e850b290b04343e915ac8fba6637157

* latest from coda-oss

* copy_externals

* Squashed 'externals/coda-oss/' changes from 1384b8a5e..1582c6ac9

1582c6ac9 further progress on implementing hdf5::lite (#631)
0622af1fe rename "11" exception classes to "Ex" (#630)

git-subtree-dir: externals/coda-oss
git-subtree-split: 1582c6ac9e9f26ee4dbaa7018e6c98ab92ca88ec

* Squashed 'externals/nitro/' changes from bd741e4f1..a153ad562

a153ad562 latest from coda-oss (#523)

git-subtree-dir: externals/nitro
git-subtree-split: a153ad562458b05be7b79fe56596c2d4b8eb9567

* copy_externals

* copy_externals

* copy_externals

* Squashed 'externals/coda-oss/' changes from 1582c6ac9..986307c9c

986307c9c Merge branch 'master'
e1b0fa349 commit (but not build) HDF5 source code (#634)
3fd5ddae5 Merge branch 'main' into develop/remove-cpp11-workarounds
37d7ec76e restore C++14 workarounds for older compilers (#632)
244dfdb3d Merge branch 'develop/main' into develop/remove-cpp11-workarounds
714ca4ed7 restore C++14 workarounds for older compilers
640f2247c Delete hdf5-hdf5-1_13_2.tar.gz
eb365cbfb Merge branch 'master' into develop/remove-cpp11-workarounds
57b938eeb don't need __INTEL_COMPILER work-around with C++14
65779f3b1 build C code with -std=gnu99
94dc9280f C++14 work-arounds for an old version of the Intel compiler
3744d05e2 slam-in "main"
82b2fd63b restore some C++14 work-arounds for old compilers that only have partial C++14 support
94f6950a2 Merge branch 'main' into develop/remove-cpp11-workarounds
1ac97fe48 add HDF5 source code (not built) (#612)
8ab982820 Squashed commit of the following:
31781a14a remove C++17 work-arounds
c15f6930c Revert "<filesystem> is in C++17"
0fe38c16f restore recent buld.py changes
0c75411ee <filesystem> is in C++17
bbbcd562a remove C++11 work-arounds
c1e15e9d9 Merge branch 'main' into main-cpp17
bea818fb0 must use C++17 in this branch
91653a096 another place where C++17 is set
7d555f2be back to C++17
b1969d996 merge main
0792c77bf Merge branch 'main' into develop/remove-cpp11-workarounds
e49f273c1 Merge branch 'main' into develop/remove-cpp11-workarounds
240b61044 allow sys::Mutex references, instead of pointers, to be passed to sys::ConditionVar
9500d6f4b Merge branch 'main' into develop/remove-cpp11-workarounds
f1529942f std::make_unique instead of new
be9b6a71c Squashed commit of the following:
62a2ec4e1 Revert "remove our GSL work-around for C++11"
1db082c21 Revert "try the current "main" of GSL"
44b70edde try the current "main" of GSL
4edbf6bad Revert ""There is no warning 4814""
bcd7458be "There is no warning 4814"
c185bf3f1 starting working on MutexCpp11
313bdd1d9 AtomicCounter* files have been removed
c1c448051 remove our GSL work-around for C++11
37ae1193e remove our mem::SharedPtr, it's now always std::shared_ptr
71f3c1299 remove no-longer-used NSPR code
8e77cb210 removed no-longer-used Irix and Solaris files
fabef6966 use std::atomic for all AtomicCounter implementations
ace5b6d5a TEST_FAIL -> TEST_FAIL_MSG
30076c1d1 turns out there was already a TEST_FAIL macro
d73ee16fb need "::" to find global test
ba01c48df remove C++11 workarounds for C++14 features
cbd4a31ae Squashed commit of the following:
b21c203b8 Squashed commit of the following:
5b542c60f Squashed commit of the following:
cb0cf94ff ByteStream.cpp is now warning-free
f5daa37fc cast to DWORD; "const" correctness
bfaf644ff #pragma-away compiler warnings from standard headers
72d202dbe Merge branch 'master' into develop/reduce-compiler-warnings
b076580cd trying to fix GCC compiler warning
1687dc7fc Merge branch 'master' into develop/reduce-compiler-warnings
2c5db86db Merge branch 'master' into develop/reduce-compiler-warnings
6f76c2e3e Update CMakeLists.txt
c3ca4a538 do in-line initialization
8e6733618 remove G++ compiler warning
a0eff51cf Merge branch 'master' into develop/reduce-compiler-warnings
af19d88a6 Merge branch 'master' into develop/reduce-compiler-warnings
ba31cbaa9 use "void*" to avoid reinterpret_cast<>
08da1f8a1 Merge branch 'master' into develop/reduce-compiler-warnings
d1d453a2e Merge branch 'master' into develop/reduce-compiler-warnings
f5074a996 CODA_OSS_NDEBUG is extra gunk and not used; omit for now.
22de48858 don't even bother compiling our own versions of localtime_s() and gmtime_s() if we're not going to use them (compiler warning about "unused static funtion.")
0c92eba58 tweak NDEBUG/CODA_OSS_NDEBUG; update comments
544604775 Don't need to expose our own versions of localtime_s() and gmtime_s()
a050796c1 Merge branch 'develop/reduce-compiler-warnings' of github.com:mdaus/coda-oss into develop/reduce-compiler-warnings
fed604617 older compilers want std::string() as argument to std::logic_error()
cf2c502a6 do more debug & release builds on GitHub
d4aa99256 build some debug targets on Gitlab
368245258 tweak CODA_OSS_DEBUG again for G++
24ba64f71 tweak how CODA_OSS_DEBUG is set
9680e8f0e add check for _GLIBCXX_DEBUG
943218f83 Merge branch 'master' into develop/reduce-compiler-warnings
01c68e705 %#@*@%)*%@ fix RowCol::cast() again! :-(
b8472b457 oops ... gsl::narrow<> should be gsl::narrow_cast<> so that int/double conversion doesn't throw
109255ca8 "final" breaks SWIG; wrap RowCol use of gsl::narrow
e51e4c2ad no need to create local just to return
e546f2510 Merge branch 'master' into develop/reduce-compiler-warnings
d1391f989 use template for to_std_string() overloading
566942680 fix std::char8_t when building with C++20
cf604b1ab fix C++17 build errors
48a0fbedb get rid of coda_oss namespace; use CODA_OSS_cpp17 instead
9706a4336 remove code-analysis diagnostics
50592e4f8 G++ complains about an unneeded call to std::move()
9c7643c3f Merge branch 'master' into develop/reduce-compiler-warnings
ecfe1f8a7 more "noexcept"
b7ac50fb9 Merge branch 'master' into develop/reduce-compiler-warnings
eaecf46ed tweak CODA_OSS_cplusplus from "main"
5773b1ec1 trying to get C++17 WAF build working on Windows
a048a00a1 unique names for waf & CMake
7a5a0d5b2 do a better job of setting CODA_OSS_DEBUG
4355aae92 Merge branch 'master' into develop/reduce-compiler-warnings
1fd8cede2 cleanup for VS 2019 16.10
4dffa1394 explicitly =delete copy/assignment
df8f8920a Merge branch 'master' into develop/reduce-compiler-warnings
42b4e99b6 remove code-analysis diagnostics
70ce322c9 reduce compiler warnings/code-analysis diagnostics when building six
20eac2f49 Merge branch 'master' into develop/reduce-compiler-warnings
ff3ded56d get rid of more compiler warnings/code-analysis diagnostics
669dd51ff Merge branch 'master' into develop/reduce-compiler-warnings
623b65ab9 Merge branch 'master' into develop/reduce-compiler-warnings
11c75df53 fix release build errors
66f048b92 turn on more compiler warnings where possible
eb615e315 consolidate calls to mem::make::unique
a6f5eb690 reduce use of explicit new
84d5e1b01 use mem::make::unique instead of explicit new
019d726ea = default for default constructors
86ab5d8f3 use std::unique_ptr and "const noexcept"
b071972d7 another batch of =default for default constructors
98276da94 more =default for default .ctor()s
ceb7bc596 do default constructors with =default
7bed51750 more code-analysis cleanup
f9c04b117 "noexcept" code-analysis warnings
6586ae390 need gsl::make_span from gsl/span_ext
722089774 remove gsl/mem dependency cycle
d741a0761 use gsl::narrow<> instead of static_cast
99eb4b36e get rid of signed/unsigned mismatch compiler warning
814450522 remove more code-analysis diagnostics
c8441b309 Merge branch 'master' into develop/reduce-compiler-warnings
e6d70a9ff last of "const" from code-analysis
b8445814a mark a few more things as "const" per code-analysis
d18544ec7 don't need to create temporary std::strings
ee7faa979 still more code-analysis cleanup
5cd6f864d cleanup more code-analysis diagnostics
492fb0a86 one more compiler warning about implicitly deleted copy/assignment
b8f782c88 remove compiler warnings about implicitly deleted copy/assignment/move
14d1d1cb8 #pragma-away warnings from GSL
86c40ea6c assert() to prevent some code-analysis diagnostics
7204517a9 make copy/assignment explicit
3ce824079 reduce code-analysis diagnostics
01e367a56 Merge branch 'master' into develop/reduce-compiler-warnings
03f3ddde9 proper printf format
877d7dc93 Merge branch 'master' into develop/reduce-compiler-warnings
5a4a3d575 code-analysis doesn't like C-style casts
a3fdae416 code-analysis doesn't like NULL
6309baedc Merge branch 'master' into develop/reduce-compiler-warnings
d1194a2fe Merge branch 'master' into develop/reduce-compiler-warnings
535b4757d Merge branch 'develop/reduce-compiler-warnings' of github.com:mdaus/coda-oss into develop/reduce-compiler-warnings
a60b95d60 "constexpr" can be hard to get right with older C++11 compilers; don't even try
c07b5303e Merge branch 'master' into develop/reduce-compiler-warnings
04306bbee need at least VS2017 to use the real GSL
796ad820b Merge branch 'master' into develop/reduce-compiler-warnings
16c240cd6 Merge branch 'master' into develop/reduce-compiler-warnings
e07e89f0c turn on "warnings as errors" for CMAKE builds
5c019f891 complex "constexpr" functions not available with our version of g++
4ab074a58 fix a few more compiler warnings ... nearing the end! :-)
dea7ea41b And still more compiler warnings ... almost done 🤞🏻
fbe3bbb20 remove assorted compiler warnings
e60b7fd3c Merge branch 'master' into develop/reduce-compiler-warnings
e9df212c6 Arguments should be "const&" to prevent C4866
94e75cbed Merge branch 'master' into develop/reduce-compiler-warnings
d3130414a Merge branch 'master' into develop/reduce-compiler-warnings
9a5e71f31 Merge branch 'master' into develop/reduce-compiler-warnings
bd27c0232 Merge branch 'master' into develop/reduce-compiler-warnings
c053362d2 remove still more compiler warnings
9f133b85a remove some more compiler warnings
0883c729c Merge branch 'master' into develop/reduce-compiler-warnings
f4b766880 avoid comparision between signed/unsigned to prevent compiler warning
1e6564a6e eliminate more compiler warnings
85a7b8ad0 remove a few compiler warnings
09c82049f Merge branch 'master' into develop/reduce-compiler-warnings
31f1662fa Merge branch 'master' into develop/reduce-compiler-warnings
a313562a3 Merge branch 'feature/fix-compiler-warnings' into develop/reduce-compiler-warnings
8547cdd24 eliminiate GCC warnings from Filesystem.h
b5044b2a2 fix several compiler warnings/code-analysis diagnostics
9d2f90b8c GetEnvironmentVariable() and getenv() aren't quite the same
6faa3666f remove more compiler warnings

git-subtree-dir: externals/coda-oss
git-subtree-split: 986307c9c05f6b341e78245d220115fabe5b2fdb

* Squashed 'externals/nitro/' changes from e1a64da1f..08cbb96f9

08cbb96f9 build with older C++14 compilers (#524)

git-subtree-dir: externals/nitro
git-subtree-split: 08cbb96f95ca26da1ee8a42bf408551dc208e37a

* copy_externals

* latest from coda-oss and nitro

* latest from coda-oss and nitro

* Squashed 'externals/coda-oss/' changes from 986307c9c..b44709a95

b44709a95 added ComplexSpansView utility (#635)

git-subtree-dir: externals/coda-oss
git-subtree-split: b44709a950f710ff790aae6f9f8eb9f6ec6b0df8

* Squashed 'externals/nitro/' changes from 08cbb96f9..c71acc492

c71acc492 latest from coda-oss (#526)

git-subtree-dir: externals/nitro
git-subtree-split: c71acc492f4e00dfd0a3d10147deea0f819135bd

* copy_externals

* --depth 1 for git-clone

* latest from coda-oss

* Squashed 'externals/coda-oss/' changes from b44709a95..b04ccca17

b04ccca17 remove more C++11 work-arounds (#641)
e460970a7 increase GCC warnings (#640)
91284249b provide ComplexView iterator support (#639)
453b7ec68 try to get std::make_unique working with old Intel compiler (#638)
5736cfd4d is_trivially_copyable for old Intel compiler (#637)
7c2aea38f use H5 SDK naming conventions (#636)
fc3008b8d use 'modern' C pre-processor

git-subtree-dir: externals/coda-oss
git-subtree-split: b04ccca17493e538130c350208da59be42eb6bc7

* Squashed 'externals/nitro/' changes from c71acc492..4ccdf5b37

4ccdf5b37 latest from coda-oss (#527)

git-subtree-dir: externals/nitro
git-subtree-split: 4ccdf5b3750bc565d45e7b5f3ca161ddb3b6ecb4

* latest from coda-oss

* --depth 1 for git-clone

* latest from coda-oss and nitro

* latest from coda-oss and NITRO

* Squashed 'externals/coda-oss/' changes from b04ccca17..9cfe9a4a8

9cfe9a4a8 Merge branch 'master'
e989b0910 createElement() needs to be virtual (#646)
4bdaf10d9 Change xml lite function to virtual (#645)
d17b57a54 Merge branch 'master'
fa00a5430 move debug -g flags to be turned on only if debugging (#644)
6be8f0a2e move debug -g flags to be turned on only if debugging (#644)
44ab72854 routines for simple writing to HDF5 files (#643)
aabc5818e remove more C++11 work-arounds (#642)

git-subtree-dir: externals/coda-oss
git-subtree-split: 9cfe9a4a8b92e982a5afce3938219dc3dc38bcc2

* Squashed 'externals/nitro/' changes from 4ccdf5b37..24ff32863

24ff32863 -j 6 seems to work for SIX, how about NITRO?
713ee8538 -j 6 seems to work for SIX, how about NITRO?

git-subtree-dir: externals/nitro
git-subtree-split: 24ff328636e3acbf1745e49df45b787403ecb113

* latest from coda-oss and NITRO

* Squashed 'externals/coda-oss/' changes from 9cfe9a4a8..b9ea37bbf

b9ea37bbf xml::lite::Validator can be moved (#648)

git-subtree-dir: externals/coda-oss
git-subtree-split: b9ea37bbf3fce6f09a8e1b4bb2deb6abb57ca075

* Squashed 'externals/nitro/' changes from 24ff32863..463c9e418

463c9e418 latest from coda-oss (#531)

git-subtree-dir: externals/nitro
git-subtree-split: 463c9e4189a86679ff6d9d2d57cdafadcf9281ce

* latest from coda-oss and NITRO
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J. Daniel Smith authored Feb 6, 2023
1 parent dece749 commit a6f2812
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6 changes: 4 additions & 2 deletions externals/coda-oss/.gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,8 +2,8 @@
*~
*.pyc
__pycache__/
# Build artifacts

# Build artifacts
install/
install-*/
target/
Expand All @@ -20,6 +20,7 @@ CMakeFiles/
Makefile
modules/**/Makefile
out/
CMakeSettings.json

# Waf
.waf-*
Expand Down Expand Up @@ -51,4 +52,5 @@ project.sln
**/x64/
*.vcxproj.user

CMakeSettings.json
# Unit-tests
TEST_*_TMP.*
27 changes: 15 additions & 12 deletions externals/coda-oss/build/build.py
Original file line number Diff line number Diff line change
Expand Up @@ -891,12 +891,6 @@ def configureCompilerOptions(self):
# If you want the plugins to not depend on Intel libraries,
# configure with:
# --with-cflags=-static-intel --with-cxxflags=-static-intel --with-linkflags=-static-intel
if cxxCompiler == 'gcc':
config['cxx']['debug'] = '-ggdb3'
config['cxx']['optz_debug'] = '-Og'
elif cxxCompiler == 'icpc':
config['cxx']['debug'] = '-g'
config['cxx']['optz_debug'] = ''
if cxxCompiler == 'g++' or cxxCompiler == 'icpc':
config['cxx']['warn'] = warningFlags.split()
config['cxx']['verbose'] = '-v'
Expand Down Expand Up @@ -931,12 +925,21 @@ def configureCompilerOptions(self):

self.env.append_value('LINKFLAGS', linkFlags.split())

if ccCompiler == 'gcc':
config['cc']['debug'] = '-ggdb3'
config['cc']['optz_debug'] = '-Og'
elif ccCompiler == 'icc':
config['cc']['debug'] = '-g'
config['cc']['optz_debug'] = ''
if Options.options.debugging:
if cxxCompiler == 'g++':
config['cxx']['debug'] = '-ggdb3'
config['cxx']['optz_debug'] = '-Og'
elif cxxCompiler == 'icpc':
config['cxx']['debug'] = '-g'
config['cxx']['optz_debug'] = ''

if ccCompiler == 'gcc':
config['cc']['debug'] = '-ggdb3'
config['cc']['optz_debug'] = '-Og'
elif ccCompiler == 'icc':
config['cc']['debug'] = '-g'
config['cc']['optz_debug'] = ''

if ccCompiler == 'gcc' or ccCompiler == 'icc':
config['cc']['warn'] = warningFlags.split()
config['cc']['verbose'] = '-v'
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
* \file Read.h
* \brief HDF File-reading API
*
* These are simple routines to read HDF5 files; they're loosly modeled after the MATLab API
* These are simple routines to read HDF5 files; they're loosely modeled after the MATLab API
* https://www.mathworks.com/help/matlab/import_export/import-hdf5-files.html
*/

Expand All @@ -39,16 +39,17 @@
#include "sys/filesystem.h"
#include "types/RowCol.h"

#include "SpanRC.h"

namespace hdf5
{
namespace lite
{

CODA_OSS_API types::RowCol<size_t> readFile(const coda_oss::filesystem::path&, const std::string& loc, std::vector<double>&);
CODA_OSS_API types::RowCol<size_t> readFile(const coda_oss::filesystem::path&, const std::string& loc, std::vector<float>&);
CODA_OSS_API SpanRC<double> readFile(const coda_oss::filesystem::path&, const std::string& loc, std::vector<double>&);
CODA_OSS_API SpanRC<float> readFile(const coda_oss::filesystem::path&, const std::string& loc, std::vector<float>&);

}
}

#endif // CODA_OSS_hdf5_lite_Read_h_INCLUDED_

115 changes: 115 additions & 0 deletions externals/coda-oss/modules/c++/hdf5.lite/include/hdf5/lite/SpanRC.h
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@@ -0,0 +1,115 @@
/* =========================================================================
* This file is part of hdf5.lite-c++
* =========================================================================
*
* (C) Copyright 2022, Maxar Technologies, Inc.
*
* hdf5.lite-c++ is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this program; If not,
* see <http://www.gnu.org/licenses/>.
*
*/

#ifndef CODA_OSS_hdf5_lite_SpanRC_h_INCLUDED_
#define CODA_OSS_hdf5_lite_SpanRC_h_INCLUDED_
#pragma once

/*!
* \file SpanRC.h
*
* This is a super-simple version of C++23's mdspan. It's here because 1) don't want widespread use, and
* 2) CODA already has a View2D.
*/

#include <assert.h>

#include "config/Exports.h"
#include "coda_oss/span.h"
#include "types/RowCol.h"

namespace hdf5
{
namespace lite
{

template<typename T>
struct SpanRC final
{
using size_type = types::RowCol<size_t>;
using element_type = T;
using pointer = T*;
using reference = T&;

SpanRC() = default;
SpanRC(pointer p, size_type rc) noexcept : s_(p, rc.area()), rc_(rc)
{
}
SpanRC(pointer p, size_t r, size_t c) noexcept : SpanRC(p, size_type(r, c))
{
}
SpanRC(const SpanRC&) noexcept = default;

constexpr pointer data() const noexcept
{
return s_.data();
}

/*constexpr*/ reference operator[](size_t idx) const noexcept
{
assert(idx < size()); // prevents "constexpr" in C++11
return data()[idx];
}
/*constexpr*/ reference operator()(size_t r, size_t c) const noexcept
{
const auto offset = (r * dims().col) + c;
return (*this)[offset];
}
/*constexpr*/ reference operator[](size_type idx) const noexcept
{
return (*this)(idx.row, idx.col);
}

constexpr size_t size() const noexcept
{
assert(s_.size() == rc_.area());
return s_.size();
}
constexpr size_t area() const noexcept
{
return size();
}

constexpr size_type size_bytes() const noexcept
{
return s_.size_bytes();
}

constexpr bool empty() const noexcept
{
return s_.empty();
}

const auto& dims() const
{
return rc_;
}

private:
types::RowCol<size_t> rc_;
coda_oss::span<T> s_;
};

}
}

#endif // CODA_OSS_hdf5_lite_SpanRC_h_INCLUDED_
80 changes: 80 additions & 0 deletions externals/coda-oss/modules/c++/hdf5.lite/include/hdf5/lite/Write.h
Original file line number Diff line number Diff line change
@@ -0,0 +1,80 @@
/* =========================================================================
* This file is part of hdf5.lite-c++
* =========================================================================
*
* (C) Copyright 2023, Maxar Technologies, Inc.
*
* hdf5.lite-c++ is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with this program; If not,
* see <http://www.gnu.org/licenses/>.
*
*/

#ifndef CODA_OSS_hdf5_lite_Write_h_INCLUDED_
#define CODA_OSS_hdf5_lite_Write_h_INCLUDED_
#pragma once

/*!
* \file Read.h
* \brief HDF File-reading API
*
* These are simple routines to write HDF5 files; they're loosely modeled after the MATLab API
* https://www.mathworks.com/help/matlab/ref/h5create.html
* https://www.mathworks.com/help/matlab/ref/h5write.html
*/

#include <string>
#include <vector>

#include "config/Exports.h"
#include "sys/filesystem.h"
#include "types/RowCol.h"

#include "SpanRC.h"

namespace hdf5
{
namespace lite
{
template<typename TDataSet> // currently implemented for float and double
CODA_OSS_API void createFile(const coda_oss::filesystem::path&, const std::string& ds, const types::RowCol<size_t>&);
CODA_OSS_API void createFile(const coda_oss::filesystem::path&, const std::string& ds, SpanRC<const double>);
inline void createFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<double> data_)
{
SpanRC<const double> data(data_.data(), data_.dims());
createFile(path, ds, data);
}
CODA_OSS_API void createFile(const coda_oss::filesystem::path&, const std::string& ds, SpanRC<const float>);
inline void createFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<float> data_)
{
SpanRC<const float> data(data_.data(), data_.dims());
createFile(path, ds, data);
}

CODA_OSS_API void writeFile(const coda_oss::filesystem::path&, const std::string& loc, SpanRC<const double>);
inline void writeFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<double> data_)
{
SpanRC<const double> data(data_.data(), data_.dims());
writeFile(path, ds, data);
}
CODA_OSS_API void writeFile(const coda_oss::filesystem::path&, const std::string& loc, SpanRC<const float>);
inline void writeFile(const coda_oss::filesystem::path& path, const std::string& ds, SpanRC<float> data_)
{
SpanRC<const float> data(data_.data(), data_.dims());
writeFile(path, ds, data);
}

}
}

#endif // CODA_OSS_hdf5_lite_Write_h_INCLUDED_
17 changes: 9 additions & 8 deletions externals/coda-oss/modules/c++/hdf5.lite/source/Read.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -56,16 +56,17 @@ static void read(const H5::DataSet& dataset, std::vector<float>& result)
dataset.read(result.data(), mem_type);
}
template<typename T>
static types::RowCol<size_t> readDatasetT(const H5::DataSet& dataset, std::vector<T>& result)
static hdf5::lite::SpanRC<T> readDatasetT(const H5::DataSet& dataset, std::vector<T>& result)
{
if (dataset.getTypeClass() != H5T_FLOAT)
{
const except::Context context("getTypeClass() != H5T_FLOAT", __FILE__, __LINE__, "readDatasetT");
throw hdf5::lite::DataSetException(context);
}

const auto retval = hdf5::lite::details::getSimpleExtentSize(dataset);
result.resize(retval.area());
const auto dims = hdf5::lite::details::getSimpleExtentSize(dataset);
result.resize(dims.area());
hdf5::lite::SpanRC<T> retval(result.data(), dims);

// dataset.read() doesn't care about the buffer type ... that's because H5Dread() also
// uses void*. However, the LT API has H5LTread_dataset_double() and H5LTread_dataset_float(),
Expand All @@ -74,16 +75,16 @@ static types::RowCol<size_t> readDatasetT(const H5::DataSet& dataset, std::vecto
return retval;
}

inline types::RowCol<size_t> readDataset_(const H5::DataSet& dataset, std::vector<float>& result)
inline hdf5::lite::SpanRC<float> readDataset_(const H5::DataSet& dataset, std::vector<float>& result)
{
return readDatasetT(dataset, result);
}
inline types::RowCol<size_t> readDataset_(const H5::DataSet& dataset, std::vector<double>& result)
inline hdf5::lite::SpanRC<double> readDataset_(const H5::DataSet& dataset, std::vector<double>& result)
{
return readDatasetT(dataset, result);
}
template<typename T>
static types::RowCol<size_t> readFile_(const coda_oss::filesystem::path& fileName, const std::string& datasetName,
static hdf5::lite::SpanRC<T> readFile_(const coda_oss::filesystem::path& fileName, const std::string& datasetName,
std::vector<T>& result)
{
/*
Expand All @@ -94,12 +95,12 @@ static types::RowCol<size_t> readFile_(const coda_oss::filesystem::path& fileNam
return readDataset_(dataset, result);
}

types::RowCol<size_t> hdf5::lite::readFile(const coda_oss::filesystem::path& fileName, const std::string& loc,
hdf5::lite::SpanRC<double> hdf5::lite::readFile(const coda_oss::filesystem::path& fileName, const std::string& loc,
std::vector<double>& result)
{
return details::try_catch_H5Exceptions(readFile_<double>, __FILE__, __LINE__, fileName, loc, result);
}
types::RowCol<size_t> hdf5::lite::readFile(const coda_oss::filesystem::path& fileName, const std::string& loc,
hdf5::lite::SpanRC<float> hdf5::lite::readFile(const coda_oss::filesystem::path& fileName, const std::string& loc,
std::vector<float>& result)
{
return details::try_catch_H5Exceptions(readFile_<float>, __FILE__, __LINE__, fileName, loc, result);
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