Merge pull request #34 from lbl-cbg/add-licensing-info

Add licensing info and clean up repo

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others’ private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project’s leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

CMakeLists.txt

@@ -1,4 +1,7 @@
-cmake_minimum_required(VERSION 3.14)
+cmake_minimum_required(VERSION 3.15)
+if(POLICY CMP0167)
+  cmake_policy(SET CMP0167 NEW)
+endif()
 
 include(cmake/prelude.cmake)
 
@@ -41,17 +44,6 @@ target_include_directories(
 
 target_compile_features(aq-nwb_lib PUBLIC cxx_std_17)
 
-# ---- Declare executable ----
-
-add_executable(aq-nwb_exe src/main.cpp)
-add_executable(aq-nwb::exe ALIAS aq-nwb_exe)
-
-set_property(TARGET aq-nwb_exe PROPERTY OUTPUT_NAME aq-nwb)
-
-target_compile_features(aq-nwb_exe PRIVATE cxx_std_17)
-
-target_link_libraries(aq-nwb_exe PRIVATE aq-nwb_lib)
-
 # ---- Additional libraries needed ----
 find_package(HDF5 REQUIRED COMPONENTS CXX)
 include_directories(${HDF5_INCLUDE_DIRS})

LICENSE

@@ -1,9 +1,34 @@
-MIT License
+AqNWB Copyright (c) 2024, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy). All rights reserved.
 
-Copyright (c) 2024, <add copyright holders here>
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
 
-Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+(1) Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
 
-The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy nor the names of its contributors
+may be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches,
+or upgrades to the features, functionality or performance of the source
+code ("Enhancements") to anyone; however, if you choose to make your
+Enhancements available either publicly, or directly to Lawrence Berkeley
+National Laboratory, without imposing a separate written license agreement
+for such Enhancements, then you hereby grant the following license: a
+non-exclusive, royalty-free perpetual license to install, use, modify,
+prepare derivative works, incorporate into other computer software,
+distribute, and sublicense such enhancements or derivative works thereof,
+in binary and source code form.

Legal.txt

@@ -0,0 +1,14 @@
+AqNWB Copyright (c) 2024, The Regents of the University of California, 
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy). All rights reserved.
+
+If you have questions about your rights to use or distribute this software,
+please contact Berkeley Lab's Intellectual Property Office at
+[email protected].
+
+NOTICE.  This Software was developed under funding from the U.S. Department
+of Energy and the U.S. Government consequently retains certain rights.  As
+such, the U.S. Government has been granted for itself and others acting on
+its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the
+Software to reproduce, distribute copies to the public, prepare derivative 
+works, and perform publicly and display publicly, and to permit others to do so.

README.md

@@ -1,6 +1,12 @@
-# aq-nwb
+# AqNWB
 
-This is the aq-nwb project.
+AqNWB is a C++ API for acquiring neurophysiological data directly into the NWB (Neurodata Without Borders) format.
+Our goal is to provide a lightweight API to integrate with existing acquisition systems.
+
+Please note, AqNWB is currently under development and should not yet be used in practice.
+
+Below is a high-level overview of the project structure and capabilities we are targeting: 
+<img src="resources/images/aqnwb_objective.png" alt="Project Overview" width="500"/>
 
 # Requirements
 * A C++17-compliant compiler
@@ -66,7 +72,64 @@ cmake --build --preset=dev --target=<name of the target>
 ```
 
 #### Target options
-- `docs` : builds to documentation using Doxygen.
 - `format-check` and `format-fix`: run the clang-format tool on the codebase to check errors and to fix them respectively.
-- `run-exe`: runs the executable target `aq-nwb_exe`.
 - `spell-check` and `spell-fix`: run the codespell tool on the codebase to check errors and to fix them respectively.
+- `docs` : builds to documentation using Doxygen. (Note: run `cmake --preset=dev -DBUILD_DOCS=ON` before building to add docs target)
+
+# Code of Conduct
+
+This project and everyone participating in it is govered by our [code of conduct guidelines](./.github/CODE_OF_CONDUCT.md). By participating, you are expected to uphold this code.
+
+# LICENSE
+
+AqNWB Copyright (c) 2024, The Regents of the University of California,
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy). All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+(1) Redistributions of source code must retain the above copyright notice,
+this list of conditions and the following disclaimer.
+
+(2) Redistributions in binary form must reproduce the above copyright
+notice, this list of conditions and the following disclaimer in the
+documentation and/or other materials provided with the distribution.
+
+(3) Neither the name of the University of California, Lawrence Berkeley
+National Laboratory, U.S. Dept. of Energy nor the names of its contributors
+may be used to endorse or promote products derived from this software
+without specific prior written permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+You are under no obligation whatsoever to provide any bug fixes, patches,
+or upgrades to the features, functionality or performance of the source
+code ("Enhancements") to anyone; however, if you choose to make your
+Enhancements available either publicly, or directly to Lawrence Berkeley
+National Laboratory, without imposing a separate written license agreement
+for such Enhancements, then you hereby grant the following license: a
+non-exclusive, royalty-free perpetual license to install, use, modify,
+prepare derivative works, incorporate into other computer software,
+distribute, and sublicense such enhancements or derivative works thereof,
+in binary and source code form.
+
+# COPYRIGHT
+
+AqNWB Copyright (c) 2024, The Regents of the University of California, 
+through Lawrence Berkeley National Laboratory (subject to receipt of any
+required approvals from the U.S. Dept. of Energy). All rights reserved.
+
+If you have questions about your rights to use or distribute this software,
+please contact Berkeley Lab's Intellectual Property Office at
+[email protected].
+
+NOTICE.  This Software was developed under funding from the U.S. Department
+of Energy and the U.S. Government consequently retains certain rights.  As
+such, the U.S. Government has been granted for itself and others acting on
+its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the
+Software to reproduce, distribute copies to the public, prepare derivative 
+works, and perform publicly and display publicly, and to permit others to do so.

cmake/dev-mode.cmake

@@ -5,13 +5,6 @@ if(BUILD_TESTING)
   add_subdirectory(tests)
 endif()
 
-add_custom_target(
-    run-exe
-    COMMAND aq-nwb_exe
-    VERBATIM
-)
-add_dependencies(run-exe aq-nwb_exe)
-
 option(BUILD_DOCS "Build documentation using Doxygen" OFF)
 if(BUILD_DOCS)
   include(cmake/docs.cmake)

cmake/install-rules.cmake

@@ -1,8 +1,3 @@
-install(
-    TARGETS aq-nwb_exe
-    RUNTIME COMPONENT aq-nwb_Runtime
-)
-
 if(PROJECT_IS_TOP_LEVEL)
   include(CPack)
 endif()

src/Types.hpp

@@ -1,7 +1,7 @@
 #pragma once
 
-#include <vector>
 #include <cstddef>
+#include <vector>
 
 namespace AQNWB
 {