NeurodataWithoutBorders · oruebel · Aug 26, 2024 · Aug 8, 2024 · Aug 8, 2024 · Aug 9, 2024
diff --git a/.codespell_ignore b/.codespell_ignore
@@ -0,0 +1,5 @@
+endcode
+code
+param
+brief
+retval
diff --git a/.codespellrc b/.codespellrc
@@ -2,5 +2,6 @@
 builtin = clear,rare,en-GB_to_en-US,names,informal,code
 check-filenames =
 check-hidden =
-skip = */.git,*/build,*/prefix,*/resources,*/.vscode
+skip = */.git,*/build,*/prefix,*/resources,*/.vscode,*/libs
 quiet-level = 2
+ignore-words=./.codespell_ignore
diff --git a/LICENSE b/LICENSE
@@ -18,9 +18,17 @@ 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.
+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

diff --git a/README.md b/README.md
@@ -8,187 +8,37 @@
 [![Docs](https://img.shields.io/badge/AqNWB-Docs-8A2BE2?style=flat)](https://neurodatawithoutborders.github.io/aqnwb/)
 [![Code Stats](https://img.shields.io/badge/AqNWB-Code%20Statistics-8A2BE2?style=flat)](https://nwb-overview.readthedocs.io/en/latest/nwb-project-analytics/docs/source/code_stat_pages/AqNWB_stats.html)
 
+**AqNWB is currently under active development and should not yet be used in practice.**
 
 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.
+Please see the [AqNWB Documentation](https://neurodatawithoutborders.github.io/aqnwb/) for 
+installation instructions and to learn more about AqNWB.
 
 Below is a high-level overview of the project structure and capabilities we are targeting: 
 
 ![Project Overview](resources/images/aqnwb_objective_500px.png)
 
 
-# Requirements
-* A C++17-compliant compiler
-* CMake `>= 3.15`
-* HDF5 `>= 1.10`
-* Boost
-* Additional requirements for building the documentation (optional)
-    * Doxygen
-    * Graphviz
-* Additional requirements for developers (mode `dev`)
-    * cppcheck
-    * clang-format
+<a id="requirements"></a>
+## Requirements
 
-# Building and installing
+- **Minimum Requirements:**
+  - A C++17-compliant compiler
+  - [CMake >= 3.15](https://cmake.org)
+  - [HDF5 >= 1.10](https://github.com/HDFGroup/hdf5)
+  - [Boost](https://www.boost.org/)
+- **Documentation:** Additional requirements for building the documentation (optional)
+  - [Doxygen](https://www.doxygen.nl/)
+  - [Graphviz](https://graphviz.org/)
+- **For Developers:** Additional requirements for developers (mode `dev`)
+  - cppcheck
+  - clang-format (optional, required for ``target=format-check``, ``target=format-fix``)
+  - codespell  (optional, required for ``target=spell-check``, ``target=spell-fix``)
 
-## Build
+## Installation
 
-Here are the steps for building in release mode with a multi-configuration generator:
-
-```sh
-cmake -S . -B build
-cmake --build build --config Release
-```
-
-Note, if you are using custom installations of HDF5 or BOOST that are not being detected 
-automatically by cmake, you can specify `HDF5_ROOT` and `BOOST_ROOT` environment variables to 
-point to install directories of HDF5 and BOOST respectively. 
-
-
-## Install
-
-Here is the command for installing the release mode artifacts with a
-multi-configuration generator:
-
-```sh
-cmake --install build --config Release
-```
-
-## Developing
-
-Build system targets that are only useful for developers of this project are
-hidden if the `aq-nwb_DEVELOPER_MODE` option is disabled. Enabling this
-option makes tests and other developer targets and options available. You can enable
-the option when configuring the build by adding ``-Daq-nwb_DEVELOPER_MODE=ON``, e.g.,:
-
-```sh
-cmake -S . -B build -Daq-nwb_DEVELOPER_MODE=ON
-```
-### Presets
-
-As a developer, you can create your own dev preset by making a `CMakeUserPresets.json` file at the root of
-the project:
-
-```json
-{
-  "version": 2,
-  "cmakeMinimumRequired": {
-    "major": 3,
-    "minor": 15,
-    "patch": 0
-  },
-  "configurePresets": [
-    {
-      "name": "dev",
-      "binaryDir": "${sourceDir}/build/dev",
-      "inherits": ["dev-mode", "ci-<os>"],
-      "cacheVariables": {
-        "CMAKE_BUILD_TYPE": "Debug"
-      }
-    }
-  ],
-  "buildPresets": [
-    {
-      "name": "dev",
-      "configurePreset": "dev",
-      "configuration": "Debug"
-    }
-  ],
-  "testPresets": [
-    {
-      "name": "dev",
-      "configurePreset": "dev",
-      "configuration": "Debug",
-      "output": {
-        "outputOnFailure": true
-      }
-    }
-  ]
-}
-```
-Replace `<os>` in the `CmakeUserPresets.json` file with the name of
-the operating system you have (`win64`, `linux` or `darwin`).
-
-### Configure, build and test
-
-You can configure, build and test the project respectively with the following commands from the project root on
-any operating system with any build system:
-
-```sh
-cmake --preset=dev
-cmake --build --preset=dev
-ctest --preset=dev
-```
-
-### Developer mode targets
-
-Additional targets can be invoked when in development mode using the commands below
-
-```sh
-cmake --build --preset=dev --target=<name of the target>
-```
-
-#### Target options
-- `format-check` and `format-fix`: run the clang-format tool on the codebase to check errors and to fix them respectively.
-- `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](https://github.com/NeurodataWithoutBorders/aqnwb/blob/main/.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.
+See the [AqNWB Documentation](https://neurodatawithoutborders.github.io/aqnwb/) for installation and integration instructions. 
+* [User Installation](https://neurodatawithoutborders.github.io/aqnwb/install_page.html)
+* [Developer Installation](https://neurodatawithoutborders.github.io/aqnwb/dev_install_page.html)
diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in
@@ -8,11 +8,15 @@ PROJECT_NUMBER = "@PROJECT_VERSION@"
 
 # Add sources
 INPUT = "@PROJECT_SOURCE_DIR@/README.md" "@PROJECT_SOURCE_DIR@/src" "@PROJECT_SOURCE_DIR@/docs/pages"
+EXAMPLE_PATH = "@PROJECT_SOURCE_DIR@/tests"  "@PROJECT_SOURCE_DIR@/.github/CODE_OF_CONDUCT.md"  "@PROJECT_SOURCE_DIR@/Legal.txt" "@PROJECT_SOURCE_DIR@/LICENSE"
 IMAGE_PATH = "@PROJECT_SOURCE_DIR@/resources/images"
 EXTRACT_ALL = YES
 RECURSIVE = YES
 OUTPUT_DIRECTORY = "@DOXYGEN_OUTPUT_DIRECTORY@"
 
+# Enable Markdown support
+MARKDOWN_SUPPORT = YES
+
 # Use the README as a main page
 USE_MDFILE_AS_MAINPAGE = "@PROJECT_SOURCE_DIR@/README.md"
 

diff --git a/docs/pages/1_userdocs.dox b/docs/pages/1_userdocs.dox
@@ -0,0 +1,9 @@
+/**
+ * @page userdocs For Users
+ *
+ * This documentation is intended for users of AqNWB, e.g., developers seeking to integrate NWB
+ * with a particular data acquisition software via AqNWB.
+ *
+ * - @subpage install_page
+ * - @subpage hdf5io
+ */
diff --git a/docs/pages/2_devdocs.dox b/docs/pages/2_devdocs.dox
@@ -0,0 +1,13 @@
+/**
+ * @page devdocs For Developers
+ *
+ * This documentation is intended for developers of AqNWB.
+ *
+ * - @subpage dev_install_page
+ * - @subpage testing
+ * - @subpage dev_docs_page
+ * - @subpage code_of_conduct_page
+ * - @subpage license_page
+ * - @subpage copyright_page
+ *
+ */
diff --git a/docs/pages/about.dox b/docs/pages/about.dox
diff --git a/docs/pages/devdocs/code_of_conduct.dox b/docs/pages/devdocs/code_of_conduct.dox
@@ -0,0 +1,7 @@
+/**
+ * @page code_of_conduct_page Code of Conduct
+ *
+ * This project and everyone participating in it is governed by our code of conduct guidelines. By participating, you are expected to uphold this code.
+ * \include CODE_OF_CONDUCT.md
+ */
+
diff --git a/docs/pages/devdocs/copyright.dox b/docs/pages/devdocs/copyright.dox
@@ -0,0 +1,6 @@
+/**
+ * @page copyright_page Copyright
+ *
+ * \include Legal.txt
+ */
+