Hdf5 merge issue 488 v110 (#535)

* close #195. (#196)

* Update HDF5PluginMacros.cmake

* Update HDF5PluginMacros.cmake

* Modify temporary rpath for testing in java example scripts. (#230)

* Fix undefined left shifting of negative numbers (#338)

Undefined Bahavior Sanitizer errored here about left shifting negative numbers.

* Update license url (#332)

* Modify temporary rpath for testing in java example scripts.

* Update URL in source file Copyright headers for web copy of COPYING
file - src and test directories.

* Cleans up a couple of MSVC warnings in testhdf5 (#475)
* Fixes a few testhdf5 warnings raised in Visual Studio

Visual Studio is grumpier about treating pointers like integers than
gcc.

* Committing clang-format changes

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Fix typos and grammar errors. (#476)

* Suppresses the tcheck_version test's abort dialog on Windows (#477)

* Suppresses the tcheck_version test's abort dialog on Windows

Windows raises a modal abort/retry/ignore dialog box when CRT
calls abort(). This change installs a report hook that suppresses
the dialog so that the CMake tests don't time out waiting for a
nonexistent user to click a dialog box.

* Committing clang-format changes

* Removes __cdecl from callback

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Purge the buffer used in type conversion. (#263)

Some of the uniniitialized bits in the buffer may get carried through
all the way to disk, creating a risk for leaks.

We observed an msan error during the floating point output conversion.
Due to the encoding certain bits could remain untouched during the conversion.

In this draft we zero initialize the dbuf used by every convertor.

* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033) (#405)

* Fixed HDFFV-10480 (CVE-2018-11206) and HDFFV-11159 (CVE-2018-14033)
Description
    Checked against buffer size to prevent segfault, in case of data corruption.

    + HDFFV-11159 CVE-2018-14033 Buffer over-read in H5O_layout_decode
    + HDFFV-10480 CVE-2018-11206 Buffer over-read in H5O_fill_new[/old]_decode
Platforms tested:
    Linux/64 (jelly)

* Accidentally left in another occurrence of the previous patch from user
   after a more correct fix was applied, that is the check now accounted
   for the previous advance of the buffer pointer.  Removed it.

* Typo

* Fixed format issues.

* Added test.

* Changed arguments to ADD_H5_TEST

* Fixing arguments to ADD_H5_TEST again.

* Fixing arguments again.

* Took out the CMake changes until Allen can help.

* Added files:

tCVE_2018_11206_fill_old.h5
tCVE_2018_11206_fill_new.h5

* Revert "Took out the CMake changes until Allen can help."

This reverts commit c21324d6e0044994c5cd24b0671e7d1dd41096cc.

* Revert "Fixing arguments again."

This reverts commit 5832a70674339e4b524749adde5a181f8c3a446a.

* Revert "Fixing arguments to ADD_H5_TEST again."

This reverts commit b45de823c22ce83a388d46466ef7c04b66ff05ed.

* Revert "Changed arguments to ADD_H5_TEST"

This reverts commit 16719824f57e52158451ddd261788c0dcaa3ec55.

* Added first argument to ADD_H5_TEST for HDFFV-10480 fix.

* Changed argument 0 to 1

* Revert "Changed argument 0 to 1"

This reverts commit b343d6613ba681b43248dd5820e96389984ebcf7.

* Revert "Added first argument to ADD_H5_TEST for HDFFV-10480 fix."

This reverts commit b8a0f9a9e8ec8e6c6ff38d33195d63edff76a563.

* Added first argument and corrected the second.

* Updated fixes for HDFFV-10480 and HDFFV-11159/HDFFV-11049

* Improved error messages.

* Added description of the current HDF5 branches; added a draft of contribution policy. (#445)

* Added description of the current HDF5 branches.

* Removed capitalization in from Develop, Release, Feature to reflect the real naming schema

* Added a draft of contributions guidance document.

* Fixed typos.

* Fixed section title.

* Fixed typo.

* Fixed typos and formatting.

* Fixed many typos and simplified the text (e.g., removed testing instructions and left pointers to where to find them, etc.)

* Fixed a typo.
 Please enter the commit message for your changes. Lines starting

* Added contributing.md file and rearranged doc entries in alphabetical order.

* ddressed Gerd's review comments; found and fixed more typos.

* Addressed comments from Larry and Scot.

* Fix CMake error message location. (#478)

Print error message if Perl is not found.

* Committing clang-format changes

* Update MANIFEST.

Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: Sean McBride <sean@rogue-research.com>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Yu Feng <rainwoodman@gmail.com>
Co-authored-by: bmribler <39579120+bmribler@users.noreply.github.com>
Co-authored-by: epourmal <epourmal@hdfgroup.org>

1 files changed, 87 insertions, 0 deletions

diff --git a/doc/contributing.md b/doc/contributing.md
new file mode 100644
index 0000000..3f738c8
--- /dev/null
+++ b/doc/contributing.md
@@ -0,0 +1,87 @@
+# How to contribute to HDF5 (Draft)
+
+The HDF Group encourages community members to contribute to the HDF5 project. We accept and are very grateful for any type of contributions 
+from small typos and bug fixes to new features. The HDF Group is committed to work with the code contributors and make contribution process simple and enjoyable.
+
+This document describes guiding principles for the HDF5 code contributors and does not pretend to address any possible 
+contribution. If in doubt, please do not hesitate to ask us for guidance. 
+***Note that no contribution may be accepted unless the donor agrees with the HDF Group software license terms
+found in the COPYING file in the top source directory of every branch.***
+
+
+> We will assume that you are familiar with `git` and `GitHub`.  If not, you may go through the GitHub tutorial found at [https://guides.github.com/activities/hello-world/](https://guides.github.com/activities/hello-world/).  This tutorial should only take around 10 minutes.
+
+## Table of Contents
+
+* [Workflow](#workflow)
+* [Acceptance criteria for pull request](#criteria)
+* [Check List](#checklist)
+
+# Workflow <A NAME="workflow"></A>
+
+The process for contributing code to HDF5 is as follows:
+
+* Open an issue on [HDF5 GitHub](https://github.com/HDFGroup/hdf5/issues).
+
+> This step is ***required*** unless the change is minor (e.g., typo fix). 
+
+* Fork the [HDF5](https://github.com/HDFGroup/hdf5) repository.
+* Make the desired changes to the HDF5 software.
+	* New features should always go to develop branch first and later should be merged to the appropriate maintenance branches.
+	* Bug fixes should go to all appropriate branches (develop and maintenance). 
+* Build and test your changes. Detailed instructions on how to build and test HDF5 can be found in the `INSTALL*` files in the `release_docs` directory.
+* Push your changes to GitHub.
+* Issue a pull request and address any code formatting and testing issues reported.
+
+Once a pull request is correctly formatted and passes **ALL** CI tests, it will be reviewed and evaluated by The HDF Group developers and HDF5 community members who can approve pull requests..
+The HDF Group developers will work with you to assure that the pull request satisfies acceptance criteria described in the next section. 
+
+# Acceptance criteria for pull request <A NAME="criteria"></A>
+
+We appreciate every contribution we receive, but we may not accept them all.  Those that we *do* accept satisfy the following criteria:
+
+* **The pull request has a clear purpose** - What does the pull request address? How does it benefit the HDF5 community? 
+If the pull request does not have a clear purpose and benefits it will not be accepted. 
+
+* **The pull request is documented** - The HDF5 developers must understand not only *what* a change is doing, but *how* it is doing it.
+  Documenting the code makes it easier for us to understand your patch and will help to maintaine the code in the future. 
+
+* **The pull request passes HDF5 regression testing** - Any issue fixed or functionality added should be accompanied by the corresponding 
+tests and pass HDF5 regression testing run by The HDF Group. We do not expect you to perform comprehensive testing across multiple platforms 
+before we accept the pull request. If the pull request does not pass regression testing after the merge, The HDF Group developers will i
+work with you on the fixes. 
+
+* **The pull request does not compromise the principles behind HDF5** - HDF5 has a 100% commitment to backward compatibility.  
+	* Any file ever created with HDF5 must be readable by any future version of HDF5.
+   If the purpose of your patch  is to modify HDF5 data model or file format,
+ **please** discuss this with us first. File format changes and features required by those changes can be introduced only in a new major release. 
+	* HDF5 has a commitment to remaining *machine-independent*; data created on one platform/environment/architecture **must** remain readable by HDF5 on any other. 
+	* For binary compatibility no changes are allowed to public APIs and data structures in the maintenance releases; new APIs can be added.
+
+* **New features are documented** - Any new features should have proper documentation; talk to us if you have any questions.
+
+
+# Checklist <A NAME="checklist"></A>
+
+Please make sure that you check the items applicable to your pull request:
+
+* Code 
+  * [ ] Does the pull request have a corresponding GitHub issue and clear purpose?
+  * [ ] Does the pull request follow HDF5 best practices (naming conventions, code portability, code structure, etc.)? <<TODO: link to the document>>
+  * [ ] If changes were done to autotools build were they added to CMake and vice versa?
+  * [ ] Is the pull request applicable to any other branches? If yes, which ones? Please document it in the GitHub issue.
+  * [ ] Is the new code sufficiently documented for future maintenance?
+  * [ ] Does the new feature require a change to an existing API? See "API Compatibility Macros" document (https://portal.hdfgroup.org/display/HDF5/API+Compatibility+Macros)
+* Documentation
+  * [ ] Was the change described in the release_docs/RELEASE.txt file?
+  * [ ] Was MANIFEST updated if new files had been added to the source?
+  * [ ] Was the new function documented in the corresponding public header file using Doxygen? <<TODO: link to Doxygen instructions>>
+  * [ ] Was new functionality documented for the HDF5 community (the level of documentation depends on the feature; ask us what would be appropriate)
+* Testing
+  * [ ] Does the pull request have tests?
+  * [ ] Does the pull request affect HDF5 library perfromance?
+
+We want as many contributions as we can get, and we are here to help. Feel free to reach out to us if you have any questions
+
+Thank you for your contribution!
+