Merge pull request #46 from geoschem/feature/sphinx-docs

Startings of RTD user guide

.gitmodules

@@ -31,3 +31,6 @@
 [submodule "src/pFUnit"]
 	path = src/pFUnit
 	url = https://github.com/geoschem/pFUnit.git
+[submodule "docs/geos-chem-shared-docs"]
+	path = docs/source/geos-chem-shared-docs
+	url = https://github.com/geoschem/geos-chem-shared-docs.git

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

@@ -0,0 +1,67 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+master_doc = 'index'
+
+# -- Project information -----------------------------------------------------
+
+project = 'GCHP'
+copyright = '2020, GEOS-Chem Support Team'
+author = 'GEOS-Chem Support Team'
+
+# The full version, including alpha/beta/rc tags
+release = '13.0.0-alpha.10'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    "sphinx_rtd_theme",   
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+
+# Display GEOS-Chem logo
+html_favicon = 'geos-chem-shared-docs/_static/favicon.png'
+html_logo = "geos-chem-shared-docs/_static/geos-chem-logo.svg"
+html_theme_options = {
+    'logo_only': True,
+    'display_version': False,
+    'style_nav_header_background': '#FCFCFC',
+}

docs/source/getting-started/quick-start.rst

@@ -0,0 +1,6 @@
+
+
+Quick start
+===========
+
+todo

docs/source/index.rst

@@ -0,0 +1,34 @@
+GEOS-Chem High Performance
+==========================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Getting Started
+
+   getting-started/quick-start.rst
+
+.. toctree::
+   :maxdepth: 2
+   :caption: User Guide
+
+   user-guide/requirements.rst
+   user-guide/downloading.rst
+   user-guide/compiling.rst
+   user-guide/rundir-init.rst
+   user-guide/rundir-config.rst
+   user-guide/running.rst
+
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Step-by-step Guides
+
+   step-by-step/plotting-output.rst
+   step-by-step/stretched-grid.rst
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Help & Reference
+
+   geos-chem-shared-docs/editing_these_docs.rst 

docs/source/step-by-step/plotting-output.rst

@@ -0,0 +1,6 @@
+
+
+Plotting GCHP output
+====================
+
+todo

docs/source/step-by-step/stretched-grid.rst

@@ -0,0 +1,6 @@
+
+
+Stretched-grid simulations
+==========================
+
+todo

docs/source/user-guide/compiling.rst

@@ -0,0 +1,77 @@
+
+Compiling GCHP
+==============
+
+
+Building with CMake is different than with GNU Make (the way to build GEOS-Chem versions prior to
+13.0). With CMake, there are two steps: (1) a cmake command, and (2) a make command. The cmake
+command is used to set major options, and is often run just once per build directory. Running this
+command with :literal:`-DCMAKE_BUILD_TYPE=Debug` will result in a GCHP build with bounds checking and other
+debug options. Additional compile options, such as :literal:`LUO_WETDEP`, can be appended with :literal:`-D`, e.g.
+:literal:`-DLUO_WETDEP=y`.
+
+Create your build directory
+---------------------------
+
+The build directory will contain all files related to building GCHP with a specific environment and
+set of compiler flags. All source code directories outside of the build directory remain unchanged
+during compilation, unlike in earlier versions of GCHP in which :literal:`*.o` files (for example) were
+scattered throughout the source code tree. You can put your build directory in the root directory of
+Code.GCHP or you can put it anywhere else.
+
+For your very first built we recommend that you build from the source code for simplicity.
+
+.. code-block:: console
+
+   $ cd Code.GCHP
+   $ mkdir build
+
+As you get more advanced, you may wish to create your build directory in your run directory or in a
+directory specific to GCHP version.
+
+Configure CMake
+---------------
+
+The first argument passed to the cmake command must be the relative path to the root GCHP directory.
+For the case of the build directory within source code directory, the root GCHP directory is one
+level up.
+
+.. code-block:: console
+
+   $ cd build
+   $ cmake ..
+
+If you store your build directory in your run directory instead then the relative path would be
+:file:`../CodeDir`, making use of the symbolic link to the source code that is automatically generated when
+creating a run directory.
+
+If the last few lines of output from :program:`cmake` look similar to the following snippet then your build was
+configured successfully.
+
+.. code-block:: none
+
+   ...
+   -- Configuring done
+   -- Generating done
+   -- Build files have been written to: /data10/bindle/Code.GCHP/build
+
+Compile
+-------
+
+The full build does not occur until you run the :program:`make` command.
+
+.. code-block:: console
+
+   $ make -j
+
+
+Recompiling
+-----------
+
+Once the above steps have been performed only the :program:`make` step should be necessary each time you need
+to rebuild the code. The exceptions to this are if you change your environment or your compile
+options. In all cases it should never be necessary to run :command:`make clean`. The :program:`make` command already
+checks all components of the build for changes. If you want to rebuild from scratch because you
+changed environments, simply delete all files from the :file:`build/` directory and recompile. You can also
+create a new build directory (with a different name) and compile from there to preserve your
+previous build.

docs/source/user-guide/downloading.rst

@@ -0,0 +1,23 @@
+
+
+Downloading GCHP
+================
+
+When cloning GCHP you will get the :literal:`main` branch by default.
+
+.. code-block:: console
+
+   $ git clone https://github.com/geoschem/gchpctm.git Code.GCHP
+   $ cd Code.GCHP
+   $ git submodule update --init --recursive
+
+If you would like a different version of GCHP you can checkout the branch or tag from the top-level
+directory. Beware that you must always then update the submodules again to checkout the compatible
+submodule versions. If you have any unsaved changes in a submdodule, such as local GEOS-Chem
+development, make sure you commit those to a branch prior to updating versions.
+
+.. code-block:: console
+
+   $ cd Code.GCHP
+   $ git checkout tags/13.0.0-alpha.6
+   $ git submodule update --init --recursive

docs/source/user-guide/requirements.rst

@@ -0,0 +1,80 @@
+Requirements
+============
+
+Software requirements
+---------------------
+
+The following are GCHP's required dependencies:
+
+* Git
+* Fortran compiler (gfortran 8.3 or greater, ifort 18 or greater)
+* CMake (version 3.13 or greater)
+* NetCDF-C, NetCDF-CXX, NetCDF-Fortran
+* MPI (C, C++, and Fortran)
+* ESMF (version 8.0.0 or greater)
+
+You must load your environment file prior to building and running GCHP.
+
+.. code-block:: console
+
+   $ source /home/envs/gchpctm_ifort18.0.5_openmpi4.0.1.env
+
+If you don't already have ESMF 8.0.0+, you will need to download and build it. You only need to
+build ESMF once per compiler and MPI configuration (this includes for ALL users on a cluster!). It
+is therefore worth downloading and building somewhere stable and permanent, as almost no users of
+GCHP would be expected to need to modify or rebuild ESMF except when adding a new compiler or MPI.
+Instructions for downloading and building ESMF are available at the GCHP wiki.
+
+It is good practice to store your environment setup in a text file for reuse. Below are a couple
+examples that load libraries and export the necessary environment variables for building and running
+GCHP. Note that library version information is included in the filename for easy reference. Be sure
+to use the same libraries that were used to create the ESMF build install directory stored in
+environment variable :envvar:`ESMF_ROOT`.
+
+**Environment file example 1**
+
+.. code-block:: bash
+
+   # file: gchpctm_ifort18.0.5_openmpi4.0.1.env
+
+   # Start fresh
+   module --force purge
+
+   # Load modules (some include loading other libraries such as netcdf-C and hdf5)
+   module load intel/18.0.5
+   module load openmpi/4.0.1
+   module load netcdf-fortran/4.5.2
+   module load cmake/3.16.1
+
+   # Set environment variables
+   export CC=gcc
+   export CXX=g++
+   export FC=ifort
+
+   # Set location of ESMF
+   export ESMF_ROOT=/n/lab_shared/libraries/ESMF/ESMF_8_0_1/INSTALL_ifort18_openmpi4
+
+**Environment file example 2**
+
+.. code-block:: bash
+
+   # file: gchpctm_gcc7.4_openmpi.rc
+
+   # Start fresh
+   module --force purge
+
+   # Load modules
+   module load gcc-7.4.0
+   spack load cmake
+   spack load openmpi%gcc@7.4.0
+   spack load hdf5%gcc@7.4.0
+   spack load netcdf%gcc@7.4.0
+   spack load netcdf-fortran%gcc@7.4.0
+
+   # Set environment variables
+   export CC=gcc
+   export CXX=g++
+   export FC=gfortran
+
+   # Set location of ESMF
+   export ESMF_ROOT=/n/home/ESMFv8/DEFAULTINSTALLDIR

docs/source/user-guide/rundir-config.rst

@@ -0,0 +1,6 @@
+
+
+Configuring a run directory
+===========================
+
+todo