Merge pull request #10 from sanjayankur31/enh/update-v2.1

Update for NeuroML v2.1

.github/workflows/master.yml

@@ -33,7 +33,7 @@ jobs:
       working-directory: ${{github.workspace}}/NeuroML_API_build
       shell: bash
       run: |
-        cmake $GITHUB_WORKSPACE
+        cmake $GITHUB_WORKSPACE -DREGENERATE_BINDINGS=ON
 
     - name: Build
       working-directory: ${{github.workspace}}/NeuroML_API_build

.github/workflows/pr.yml

@@ -26,7 +26,7 @@ jobs:
       working-directory: ${{github.workspace}}/NeuroML_API_build
       shell: bash
       run: |
-        cmake $GITHUB_WORKSPACE
+        cmake $GITHUB_WORKSPACE -DREGENERATE_BINDINGS=ON
 
     - name: Build
       working-directory: ${{github.workspace}}/NeuroML_API_build

.travis.yml

@@ -2,23 +2,22 @@ language: cpp
 
 sudo: required
 
-dist: trusty
+dist: focal
 
 compiler:
     - gcc
-    
+
 install:
     - sudo apt-get update -qq
-    - sudo apt-get install -y -qq cmake libxerces-c-dev
-    
-script: 
+    - sudo apt-get install wget libxerces-c-dev xsdcxx cmake -qq
+
+script:
     - ls -alt
     - mkdir NeuroML_API_build
     - cd NeuroML_API_build
-    - cmake ..
+    - cmake -DREGENERATE_BINDINGS=ON ..
     - make
     - ctest
     - ./create_net network.nml
     - ./example network.nml
     - ls -alt
-

CMakeLists.txt

@@ -3,26 +3,30 @@
 #
 # CMake settings for building & installing the NeuroML2 C++ API
 
-cmake_minimum_required(VERSION 3.5)
+cmake_minimum_required(VERSION 3.14)
 cmake_policy(SET CMP0022 NEW) # Link interfaces for export
 cmake_policy(SET CMP0028 NEW) # Strict use of :: in target names
 cmake_policy(SET CMP0042 NEW) # Mac OS @rpath
 cmake_policy(SET CMP0048 NEW) # VERSION option to project()
 
 # Note: the version number uses Semantic Versioning http://semver.org/
-project(NeuroML_API VERSION 0.1.0)
+project(NeuroML_API
+    VERSION 2.1.0
+    DESCRIPTION "C++ API for NeuroML 2"
+    HOMEPAGE_URL "https://github.com/NeuroML/NeuroML_API"
+    )
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake/modules)
 
 # Developer settable options
 ############################
 
 # Which schema to provide the API for
-set(NeuroML_SCHEMA_PATH "${PROJECT_SOURCE_DIR}/src/schema/NeuroML_v2beta4.xsd"
+set(NeuroML_SCHEMA_PATH "${PROJECT_SOURCE_DIR}/src/schema/NeuroML_v2.1.xsd"
     CACHE PATH
     "Path to the schema file to base the API on.")
 
 get_filename_component(NeuroML_SCHEMA_ABSPATH "${NeuroML_SCHEMA_PATH}" REALPATH)
-get_filename_component(NeuroML_SCHEMA_NAME "${NeuroML_SCHEMA_PATH}" NAME_WE)
+get_filename_component(NeuroML_SCHEMA_NAME "${NeuroML_SCHEMA_ABSPATH}" NAME_WLE)
 
 # Default to shared libs
 option(BUILD_SHARED_LIBS "Build NeuroML API as a shared library" ON)
@@ -52,7 +56,7 @@ configure_file(
     "${PROJECT_SOURCE_DIR}/src/neuroml.hxx.in"
     "${PROJECT_BINARY_DIR}/src/neuroml.hxx"
     )
- 
+
 # Add the binary tree to the search path for include files
 # so that we will find generated sources
 include_directories("${PROJECT_BINARY_DIR}/src")
@@ -61,10 +65,15 @@ include_directories("${PROJECT_BINARY_DIR}/src")
 find_package(XercesC REQUIRED)
 list(APPEND NeuroML_INCLUDES "${XercesC_INCLUDE_DIRS}")
 
-# Can we regenerate the schema wrapper?
-find_package(XSD QUIET)
-if (XSD_FOUND)
-    list(APPEND NeuroML_INCLUDES "${XSD_INCLUDE_DIRS}")
+# XSD
+find_package(XSD REQUIRED)
+list(APPEND NeuroML_INCLUDES "${XSD_INCLUDE_DIRS}")
+
+# Regenerate bindings?
+set (REGENERATE_BINDINGS OFF CACHE BOOL "Regenerate the C++ bindings. [default: OFF]")
+
+# Yes: and use newly generated copy
+if (REGENERATE_BINDINGS)
     file(GLOB _XSD_DEPS "src/schema/*.txt")
     xsd_schema(NeuroML_SCHEMA_SRCS "${NeuroML_SCHEMA_PATH}" "${_XSD_DEPS}"
                --options-file "${PROJECT_SOURCE_DIR}/src/schema/XsdOptions.txt")
@@ -74,12 +83,12 @@ if (XSD_FOUND)
                               ${PROJECT_SOURCE_DIR}/src/schema
                       COMMENT "Copying new XSD wrappers to source tree"
                       VERBATIM)
-else (XSD_FOUND)
-    # Use pre-generated sources & CodeSynthesis headers shipped with the project
-    set(XSD_INCLUDE_DIR "${PROJECT_SOURCE_DIR}/libxsd")
-    list(APPEND NeuroML_INCLUDES "${XSD_INCLUDE_DIR}" "${PROJECT_SOURCE_DIR}/src/schema")
+else (REGENERATE_BINDINGS)
+    # No: use pre-generated bindings
+    # Will fail if bindings cannot be found in the src/schema directory
+    list(APPEND NeuroML_INCLUDES "${PROJECT_SOURCE_DIR}/src/schema")
     set(NeuroML_SCHEMA_SRCS "${PROJECT_SOURCE_DIR}/src/schema/${NeuroML_SCHEMA_NAME}.cxx")
-endif (XSD_FOUND)
+endif (REGENERATE_BINDINGS)
 
 # The main API library
 add_library(neuroml ${NeuroML_SCHEMA_SRCS} src/NeuroML_custom.cxx)

Doxyfile.in

@@ -38,20 +38,20 @@ PROJECT_NAME           = "NeuroML C++ API"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         =
+PROJECT_NUMBER         = "@CMAKE_PROJECT_VERSION@"
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
 # quick idea about the purpose of the project. Keep the description short.
 
-PROJECT_BRIEF          =
+PROJECT_BRIEF          = "@CMAKE_PROJECT_DESCRIPTION@"
 
 # With the PROJECT_LOGO tag one can specify a logo or an icon that is included
 # in the documentation. The maximum height of the logo should not exceed 55
 # pixels and the maximum width should not exceed 200 pixels. Doxygen will copy
 # the logo to the output directory.
 
-PROJECT_LOGO           =
+PROJECT_LOGO           = "@CMAKE_SOURCE_DIR@/neuroml_logo.png"
 
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path
 # into which the generated documentation will be written. If a relative path is

README.md

@@ -4,6 +4,8 @@ C++ API for NeuroML 2.
 
 [![Build Status](https://travis-ci.org/NeuroML/NeuroML_API.svg?branch=master)](https://travis-ci.org/NeuroML/NeuroML_API)
 [![GitHub](https://img.shields.io/github/license/NeuroML/NeuroML_API)](https://github.com/NeuroML/NeuroML_API/blob/master/License.txt)
+![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/NeuroML/NeuroML_API?include_prereleases)
+![GitHub tag (latest SemVer)](https://img.shields.io/github/v/tag/NeuroML/NeuroML_API)
 [![GitHub pull requests](https://img.shields.io/github/issues-pr/NeuroML/NeuroML_API)](https://github.com/NeuroML/NeuroML_API/pulls)
 [![GitHub issues](https://img.shields.io/github/issues/NeuroML/NeuroML_API)](https://github.com/NeuroML/NeuroML_API/issues)
 [![GitHub Org's stars](https://img.shields.io/github/stars/NeuroML?style=social)](https://github.com/NeuroML)
@@ -12,7 +14,7 @@ C++ API for NeuroML 2.
 
 ## Using the API
 
-For more info on the generated C++ structure, see the [XSD user manual].
+For more info on the generated C++ structure, see the [XSD user manual](https://www.codesynthesis.com/products/xsd/).
 The sample programs in the test folder will also give you a reasonable
 idea of how things work.
 
@@ -36,47 +38,67 @@ If you installed the NeuroML_API in a non-standard location, you may need
 to set the `CMAKE_PREFIX_PATH` CMake variable to that location in order to
 find the package.
 
-## Building the API yourself
+## Building the API
 
-The NeuroML API is built using CMake, and the process works best with
-'out of source' builds, where you build the API in a folder separate
-from the source tree. Having cloned the repository, we therefore suggest
-you create a separate 'NeuroML_API_build' folder adjacent to the source,
-change into it, and run
+The NeuroML API is built using CMake (versions >= 3.14), and the process works
+best with 'out of source' builds, where you build the API in a folder separate
+from the source tree. Having cloned the repository, we therefore suggest you
+create a separate 'NeuroML_API_build' folder adjacent to the source, change
+into it, and then run the build configuration commands:
 
 ```
+mkdir NeuroML_API_build
+cd NeuroML_API_build
 cmake ../NeuroML_API
 ```
 
-to configure the build. You may then run
+You may then run
 
 * `make` to build,
 * `make doc` to build the HTML documentation using Doxygen (in a `docs`
   subfolder of your build folder; only available if Doxygen installed),
 * `ctest` (or `make test`) to run tests,
 * `sudo make install` to install on your system, or
-* `cpack` to generate an installable package (see [cpack documentation]).
+* `cpack` to generate an installable package (see [cpack documentation](https://cmake.org/cmake/help/latest/manual/cpack.1.html)).
 
 The default CMake options should be appropriate for most cases. The only
-essential external dependency is [Xerces C++] which should be found
-automatically if installed.
+essential external dependencies are [Xerces
+C++](http://xerces.apache.org/xerces-c/) and [CodeSynthesis
+XSD](https://www.codesynthesis.com/products/xsd/).
+
+On Ubuntu based systems, you can install Xerces and xsd from the standard
+repositories using `apt`:
+
+```
+sudo apt-get install xsdcxx libxerces-c-dev
+```
+
+On Fedora and other RPM based distributions, you can install Xerces and xsd
+from the standard repositories using `dnf` or `yum`:
+
+```
+sudo dnf install xsd xerces-c-devel
+```
+
+If you install xsd in a non-standard location, please set the `XSD_ROOT`
+_environment_ variable to the root folder for the software (i.e. the folder
+containing `bin` and `libxsd` folders).
 
 You may wish to change the `CMAKE_INSTALL_PREFIX` to specify where the API
 will be installed. The generated library will be placed in a `lib` subfolder,
 and all necessary headers in an `include/neuroml` subfolder.
 
 If you wish to regenerate the C++ bindings (because you have changed the
-XML Schema or xsdcxx options) you will need CodeSynthesis XSD installed on
-your system and findable by CMake. The build will search standard install
-locations, but you can also set the `XSD_ROOT` _environment_ variable to the
-root folder for the software (i.e. the folder containing `bin` and `libxsd`
-folders). You can also change the schema file to use by setting the variable
+XML Schema or xsdcxx options) you will need to pass `REGENERATE_BINDINGS=ON` to
+the CMake command:
+
+```
+cmake -DREGENERATE_BINDINGS=ON ...
+```
+
+You can also change the path to the schema file to use by setting the variable
 `NeuroML_SCHEMA_PATH` in CMake.
 
 Once the bindings have been regenerated, you can run `make copy_wrappers`
 to copy the new versions back into the source tree, for committing to the
 repository.
-
-[XSD user manual]: http://www.codesynthesis.com/projects/xsd/documentation/cxx/tree/manual/
-[cpack documentation]: https://cmake.org/cmake/help/v3.5/manual/cpack.1.html
-[Xerces C++]: http://xerces.apache.org/xerces-c/

cmake/modules/FindXSD.cmake

@@ -79,7 +79,7 @@ MACRO( XSD_SCHEMA NAME FILE EXTRA_DEPS)
   # destination file path sans any extension and then build paths to the
   # generated files.
   #
-  GET_FILENAME_COMPONENT( xs_FILE "${FILE}" NAME_WE )
+  GET_FILENAME_COMPONENT( xs_FILE "${FILE}" NAME_WLE )
   GET_FILENAME_COMPONENT( xs_FILE_DIR "${FILE}" DIRECTORY )
   file(RELATIVE_PATH xs_FILE_REL "${CMAKE_SOURCE_DIR}" "${FILE}" )
 #  set(xs_OUT_TMP "${CMAKE_BINARY_DIR}/${xs_FILE_REL}")