Deploying to github.io from @ 00e680f 🚀

docs/unstable/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 553a643177046a2117ec0602f31df710
+config: 92fd138d3374dc0a2aefb40cf0eb3dc6
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/unstable/ChangeLog.html

@@ -7,11 +7,14 @@
   <title>Changelog &mdash; clair - Automatic Python/C++ bindings  documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/custom.css" type="text/css" />
+      <link rel="stylesheet" href="_static/copybutton.css" type="text/css" />
 
         <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
+        <script src="_static/clipboard.min.js"></script>
+        <script src="_static/copybutton.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="author" title="About these documents" href="about.html" />
     <link rel="index" title="Index" href="genindex.html" />
@@ -41,14 +44,19 @@
               <ul class="current">
 <li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="install_packages.html">Packages</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="install_packages.html#os-x-brew">OS X (brew)</a></li>
+<li class="toctree-l3"><a class="reference internal" href="install_packages.html#os-x-brew">OS X (brew)</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="install_packages.html#uninstalling">Uninstalling</a></li>
+</ul>
+</li>
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="install_src.html">Compiling from source</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="install_src.html#clair">clair</a></li>
-<li class="toctree-l3"><a class="reference internal" href="install_src.html#c2py">c2py</a></li>
+<li class="toctree-l3"><a class="reference internal" href="install_src.html#c2py">c2py</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="install_src.html#cmake-options">CMake options</a></li>
+</ul>
+</li>
 <li class="toctree-l3"><a class="reference internal" href="install_src.html#set-environment-variables">Set environment variables</a></li>
-<li class="toctree-l3"><a class="reference internal" href="install_src.html#custom-cmake-options">Custom CMake options</a></li>
 </ul>
 </li>
 </ul>

docs/unstable/_sources/cmake.rst.txt

@@ -60,10 +60,9 @@ We introduce an option `GENERATE_PYTHON_BINDINGS` so that the code can not be us
 A variant avoiding the installation of c2py
 ...........................................
 
-It is often convenient to avoid the need to install the `c2py` library completely.
-As `c2py` is a very small library, the cost of recompiling it on the fly is negligeable, 
-but it is often a good strategy to ensure it is compiled with the same compilers, standard libraries etc.
-(it is the recommended strategy for e.g. Google Test).
+It is often convenient to avoid the need to install the `c2py` library completely. 
+As `c2py` is a very small library, the cost of recompiling it in each project is negligeable, 
+but it is often a good strategy to ensure it is compiled with the same compilers, standard libraries, etc.
 
 In order to do this, we can simply modify the `CMakeLists.txt` file as 
 

docs/unstable/_sources/gettingstarted.rst.txt

@@ -10,7 +10,6 @@ Let us begin with a simple example in file `my_module.cpp`.
 
 .. literalinclude:: examples/gs1.cpp
    :language: cpp
-   :linenos:
 
 We just compile the C++ file with `clang` using the ``clair`` plugin as 
 
@@ -22,7 +21,10 @@ We just compile the C++ file with `clang` using the ``clair`` plugin as
    # Linux
    clang++ -fplugin=clair_c2py.so     my_module.cpp -std=c++20 -shared -o my_module.so `c2py_flags`
 
+.. note::
 
+   The compiler search for the plugin in DYLD_LIBRARY_PATH (OS X) or LD_LIBRARY_PATH (linux).
+
 That is it. The Python module is ready to use:
 
 .. code-block:: console
@@ -63,31 +65,32 @@ What happened ?
 ................
 
 In order to call C++ from Python, some **binding code** has to be generated.
-It is a piece of C++ code which "adapt" the C++ functions and classes to the C API of Python.
+It is a piece of C++ code which *adapts* the C++ functions and classes to the C API of Python.
 
 The ``clair_c2py``  **compiler plugin** automatizes this task, by modifying the compilation process of LLVM/clang:
-when compiling the C++ code `my_module.cpp`, it:
+when compiling the C++ code `my_module.cpp` with it, the compiler:
 
-#. parses `my_module.cpp` (the first step of compilation, checking syntax, grammar, ...).
-#. generates the C++/Python bindings write them into `my_module.wrap.cxx`.
-#. compiles the whole into a Python module `my_module.so`.
+#. parses `my_module.cpp` as usual (the first step of a compilation: check syntax and grammar, build the Abstract Syntax Tree or AST).
+#. generates the C++/Python bindings (by analyzing the AST) and write them into `my_module.wrap.cxx`.
+#. compiles the whole code (source + bindings) into a Python module `my_module.so`.
 
 Reusing the bindings without clang
 ..................................
 
 While the generation of the bindings requires  LLVM/clang and the clair plugin, 
-they can reused with any `C++20` compiler. For example, with ``gcc``.
+they can reused with any `C++20` compiler. For example, with ``gcc``:
 
 .. code-block:: bash
 
    g++  my_module.wrap.cxx -std=c++20 -shared -o my_module.so `c2py_flags`
 
 
-(the bindings automatically include the original source file `my_module.cpp`).
+(the binding file includes the original source file `my_module.cpp`).
 
 .. note::
 
-   On some machines (OS X), check that this c2py has been compiled with gcc too.
+   On some machines (OS X), beware that c2py must be compiled with gcc (in particular the same std C++ library).
+   For any project beyond a simple demo, it is recommended to use CMake setup, Cf :ref:`cmake`.
 
 A typical workflow is therefore:
 

docs/unstable/_sources/install_packages.rst.txt

@@ -14,12 +14,23 @@ Experimental packages of ``c2py`` and ``clair`` are::
 
 They are built from source from the GitHub parcollet/ccq repository.
 
+
 .. note::
 
-   The DYLD_LIBRARY_PATH must be set e.g.::
+   To use the plugin as in the example below, 
+   the DYLD_LIBRARY_PATH must be set e.g.::
 
      export DYLD_LIBRARY_PATH=/opt/homebrew/lib/:$DYLD_LIBRARY_PATH
 
    for clang to find its plugins in brew directory as in the documentation examples.
-
+   Alternatively, you can provide the full path to the plugin.
+   This setup is not necessary to use the CMake targets.
+
+Uninstalling
+............
+
+In order to uninstall all formulas from the `parcollet/ccq` tap, you can use::
+
+        brew uninstall `brew list --full-name -1|grep ccq`
+
 

docs/unstable/_sources/install_src.rst.txt

@@ -15,20 +15,21 @@ Compiling from source
 clair
 -----
 
-#. Download the source code of the latest stable version by cloning the ``c2py`` repository from GitHub::
+#. Download the source code of the latest stable version by cloning the ``clair`` repository from GitHub::
 
      $ git clone https://github.com/flatironinstitute/clair clair.src
 
-#. If you want a particular version, check it out, e.g. (use `git tag` go to see the available version)::
+#. [Optional] If you want a particular version, check it out, e.g. (use `git tag` go to see the available version)::
 
-     $ git checkout 1.1.0
+     $ git checkout v0.1
 
 #. Call cmake, including any additional custom CMake options, see below::
 
-     $ cmake -B clair.build -S clair.src -DCMAKE_INSTALL_PREFIX=path_to_install_dir 
+     $ cmake -B clair.build -S clair.src -DCMAKE_INSTALL_PREFIX=path_to_clair_install_dir 
 
 #. Compile the code, run the tests and install the application (here with 8 cores, change accordingly)::
 
+     $ cd clair.build
      $ make -j 8
      $ ctest -j 8
      $ make -j 8 install
@@ -47,41 +48,41 @@ To install ``c2py``, follow the same procedure as for ``clair``, replacing ``cla
 
      $ git clone https://github.com/flatironinstitute/c2py c2py.src
 
-#. If you want a particular version, check it out, e.g. (use `git tag` go to see the available version)::
+#. [Optional] If you want a particular version, check it out, e.g. (use `git tag` go to see the available version)::
 
-     $ git checkout 1.1.0
+     $ git checkout v0.1
 
 #. Call cmake, including any additional custom CMake options, see below::
 
-     $ cmake -B c2py.build -S c2py.src -DCMAKE_INSTALL_PREFIX=path_to_install_dir 
+     $ cmake -B c2py.build -S c2py.src -DCMAKE_INSTALL_PREFIX=path_to_c2py_install_dir 
 
 #. Compile the code, run the tests and install the application (here with 8 cores, change accordingly)::
 
+     $ cd clair.build
      $ make -j 8
      $ ctest -j 8
      $ make -j 8 install
 
+CMake options
+.............
 
-Set environment variables
--------------------------
-
-To the proper paths into your current shell environment with::
-
-     $ source path_to_install_dir/share/clair/clairvars.sh
-     $ source path_to_install_dir/share/c2py/c2pyvars.sh
-
-
-Custom CMake options
---------------------
-
-The compilation of ``clair`` can be configured using CMake-options::
+The following CMake-options are available for ``clair``::
 
     cmake ...  -DOPTION1=value1 -DOPTION2=value2
 
 +-----------------------------------------------------------------+-----------------------------------------------+
 | Options                                                         | Syntax                                        |
 +=================================================================+===============================================+
-| Specify an installation path                                    | -DCMAKE_INSTALL_PREFIX=path_to_clair          |
-+-----------------------------------------------------------------+-----------------------------------------------+
 | Build the documentation                                         | -DBuild_Documentation=ON                      |
 +-----------------------------------------------------------------+-----------------------------------------------+
+
+
+Set environment variables
+-------------------------
+
+To load the proper paths into your current shell environment with::
+
+     $ source path_to_clair_install_dir/share/clair/clairvars.sh
+     $ source path_to_c2py_install_dir/share/c2py/c2pyvars.sh
+
+