Installation Guide Updates per Chris' Comments

This should make things clearer for the user

docs/cpp_api/FeatureCreation.rst

@@ -13,6 +13,13 @@ Features
     node
     node_utils
 
+Non-Linearly Optimized Features
+-------------------------------
+.. toctree::
+    :maxdepth: 3
+
+    param_node
+
 Feature Space
 -------------
 .. toctree::

docs/cpp_api/node.rst

@@ -110,89 +110,3 @@ AbsNode
 -------
 .. doxygenfile:: absolute_value.hpp
    :project: SISSO++
-
-AddParamNode
-------------
-.. doxygenfile:: parameterized_add.hpp
-   :project: SISSO++
-
-SubParamNode
-------------
-.. doxygenfile:: parameterized_subtract.hpp
-   :project: SISSO++
-
-AbsDiffParamNode
-----------------
-.. doxygenfile:: parameterized_absolute_difference.hpp
-   :project: SISSO++
-
-MultParamNode
--------------
-.. doxygenfile:: parameterized_multiply.hpp
-   :project: SISSO++
-
-DivParamNode
-------------
-.. doxygenfile:: parameterized_divide.hpp
-   :project: SISSO++
-
-InvParamNode
-------------
-.. doxygenfile:: parameterized_inverse.hpp
-   :project: SISSO++
-
-SqParamNode
------------
-.. doxygenfile:: parameterized_square.hpp
-   :project: SISSO++
-
-CbParamNode
------------
-.. doxygenfile:: parameterized_cube.hpp
-   :project: SISSO++
-
-SixPowParamNode
----------------
-.. doxygenfile:: parameterized_sixth_power.hpp
-   :project: SISSO++
-
-SqrtParamNode
--------------
-.. doxygenfile:: parameterized_square_root.hpp
-   :project: SISSO++
-
-CbrtParamNode
--------------
-.. doxygenfile:: parameterized_cube_root.hpp
-   :project: SISSO++
-
-ExpParamNode
-------------
-.. doxygenfile:: parameterized_exponential.hpp
-   :project: SISSO++
-
-NegExpParamNode
----------------
-.. doxygenfile:: parameterized_negative_exponential.hpp
-   :project: SISSO++
-
-LogParamNode
-------------
-.. doxygenfile:: parameterized_log.hpp
-   :project: SISSO++
-
-SinParamNode
-------------
-.. doxygenfile:: parameterized_sin.hpp
-   :project: SISSO++
-
-CosParamNode
-------------
-.. doxygenfile:: parameterized_cos.hpp
-   :project: SISSO++
-
-AbsParamNode
-------------
-.. doxygenfile:: parameterized_absolute_value.hpp
-   :project: SISSO++
-

docs/quick_start/Installation.md

 Installation
 ---
 The package uses a CMake build system, and compatible all versions of the C++ standard library after C++ 14.
+You can access the code [here](https://gitlab.mpcdf.mpg.de/tpurcell/cpp_sisso/-/archive/master/cpp_sisso-master.tar.gz)
 
 ### Prerequisites
-To install the sisso++ the following packages are needed:
+To install `SISSO++` the following packages are needed:
 
 - CMake version 3.10 and up
-- A C++ complier (compatible with C++ 14 and later)
+- A C++ compiler (compatible with C++ 14 and later, e.g. gcc 5.0+ or icpc 17.0+)
 - BLAS/LAPACK
 - MPI
 
-Additionally the following packages will be installed if not currently and needed by SISSO++
+Additionally the following packages needed by SISSO++ will be installed (if they are not installed already/if they cannot be found in $PATH)
 
   - [Boost](https://www.boost) (mpi, serialization, system, filesystem, and python libraries)
   - [GTest](https://github.com/google/googletest)
   - [Coin-Clp](https://github.com/coin-or/Clp)
   - [NLopt](https://github.com/stevengj/nlopt)
+  - [{fmt}](https://fmt.dev/latest/index.html) (Used for the C++ 20 [std::format](https://en.cppreference.com/w/cpp/utility/format/format) library)
 
-To build the optional python bindings the following are also needed:
+To build and use the optional python bindings the following are also needed:
 
-- Python 3.6 or greater
+- [Python 3.6 or greater](https://www.python.org/)
+- [numpy](https://numpy.org/)
+- [pandas](https://pandas.pydata.org/)
+- [scipy](https://www.scipy.org/)
+- [seaborn](https://seaborn.pydata.org/)
+- [sklearn](https://scikit-learn.org/stable/index.html)
+- [toml](https://pypi.org/project/toml/)
 
-### Installation Settings
-
-#### `BUILD_PARAMS`
+The setup of the python environment can be done using anaconda with
 
-If `BUILD_PARAMS` is ON then build the operators with non-linearly optimized scale and shift parameters, and the relevant optimization files
-
-#### `BUILD_PYTHON`
-
-If `BUILD_PYTHON` is ON then build the python bindings
-
-#### `BUILD_TESTS`
-
-If `BULD_TESTS` is ON then build GTest based tests
-
-#### `EXTERNAL_BOOST`
-
-If `EXTERNAL_BOOST` is ON then use the pre-built Boost Libraries currently in your path or in `$ENV{BOOST_ROOT}`
+```bash
+conda create -n sissopp_env python=3.9 numpy pandas scipy seaborn scikit-learn toml
+```
 
 ### Installing `SISSO++`
 
@@ -51,6 +47,7 @@ For example, here is `initial_config.cmake` file used to construct `SISSO++` and
 set(CMAKE_CXX_COMPILER g++ CACHE STRING "")
 set(CMAKE_C_COMPILER gcc CACHE STRING "")
 set(CMAKE_CXX_FLAGS "-O3 -march=native" CACHE STRING "")
+set(CMAKE_C_FLAGS "-O3 -march=native" CACHE STRING "")
 
 #################
 # Feature Flags #
@@ -59,24 +56,21 @@ set(BUILD_PYTHON ON CACHE BOOL "")
 set(BUILD_PARAMS ON CACHE BOOL "")
 ```
 
-Here the `-O3` flag is for optimizations, it is recommended to stay as `-O3` or `-O2`, but it can be changed to match compiler requirements.
-
-When building Boost from source (`EXTERNAL_BOOST OFF`) the number of processes used when building Boost may be set using the
-`BOOST_BUILD_N_PROCS` flag in CMake.  For example, to build Boost using 4 processes, the following flag should be included in the
-`initial_config.cmake` file:
+Because we want to build with the python bindings in this example and assuming there is no preexisting python environment, we need to first create/activate it.
+For this example we will use `conda`, but standard python installations or virtual environments are also possible.
 
-```
-#set(BOOST_BUILD_N_PROCS 4 CACHE STRING "")
+```bash
+conda create -n sissopp_env python=3.9 numpy pandas scipy seaborn scikit-learn toml
+conda activate sissopp_env
 ```
 
-This flag will have no effect when linking against external boost, i.e. `EXTERNAL_BOOST ON`.
+Now we can install `SISSO++` using `initial_config.cmake` and the following commands (this assumes gnu compiler and MKL are used, if you are using a different compiler/BLAS library change the flags to the relevant directories)
 
-To install `SISSO++` using `initial_config.cmake` run the following commands (this assumes gnu compiler and MKL are used, if you are using a different compiler/BLAS library change the flags to the relevant directories)
-```
+```bash
 export MKLROOT=/path/to/mkl/
 export BOOST_ROOT=/path/to/boost
 
-cd ~/SISSO++/main directory
+cd ~/cpp_sisso/
 mkdir build/;
 cd build/;
 
@@ -87,6 +81,62 @@ make install
 
 Once all the commands are run `SISSO++` should be in the `~/SISSO++/main directory/bin/` directory.
 
-### Install the Binary Without the Python Bindings
+#### Install the Binary Without the Python Bindings
 To install only the `SISSO++` executable repeat the same commands as above but set `USE_PYTHON` in `initial_config.cmake` to `OFF`.
 
+### Installation Settings for Basic Flags
+
+#### `CMAKE_CXX_COMPILER`
+
+The C++ compiler used to compile the code
+
+#### `CMAKE_C_COMPILER`
+
+The C compiler used to compile external dependencies (GTest and {fmt})
+
+#### `CMAKE_CXX_FLAGS`
+
+Define the flags used by the compiler to build the C++ source files. It is recommended to use `-O2` or `-O3` level of optimizations, but it can be changed to match the compiler.
+
+#### `CMAKE_C_FLAGS`
+
+Define the flags used by the compiler to build the C source files (GTest and {fmt}). It is recommended to use `-O2` or `-O3` level of optimizations, but it can be changed to match the compiler.
+
+### Installation Settings
+
+#### `BUILD_PARAMS`
+
+Default: OFF
+
+If `BUILD_PARAMS` is ON then build the operators with non-linearly optimized scale and shift parameters, and the relevant optimization files. With this flag on `NLopt`, [the parameterized operators](../cpp_api/param_node), and [the non-linear optimization](../cpp_api/nl_opt) classes will be built.
+
+#### `BUILD_PYTHON`
+
+Default: ON
+
+If `BUILD_PYTHON` is ON then build the python bindings
+
+#### `BUILD_TESTS`
+
+Default: OFF
+
+If `BULD_TESTS` is ON then build GTest based tests
+
+#### `EXTERNAL_BOOST`
+
+Default: OFF
+
+If `EXTERNAL_BOOST` is ON then use the pre-built Boost Libraries currently in your path or in `$ENV{BOOST_ROOT}`
+Here the `-O3` flag is for optimizations, it is recommended to stay as `-O3` or `-O2`, but it can be changed to match compiler requirements.
+
+When building Boost from source (`EXTERNAL_BOOST OFF`) the number of processes used when building Boost may be set using the
+`BOOST_BUILD_N_PROCS` flag in CMake.  For example, to build Boost using 4 processes, the following flag should be included in the
+`initial_config.cmake` file:
+
+```
+#set(BOOST_BUILD_N_PROCS 4 CACHE STRING "")
+```
+
+This flag will have no effect when linking against external boost, i.e. `EXTERNAL_BOOST ON`.
+
+We recommend to use `-DEXTERNAL_BOOST=OFF` if you are building the python bindings with an anaconda environment or if you are using non-standard C++ or MPI libraries. If the boost libraries have already been built with the same C++ compiler, MPI library, and Python environment, then `EXTERNAL_BOOST=ON` can be used.