Updated changes in the documentation due to the restructuring

README.rst

@@ -92,12 +92,7 @@ The structure of the program is simple: the main routines
 are written in Python utlizing NumPy and SciPy where
 necessary. In addition there are calls to external
 routines through Cython, particularly the optional libraries.
-It should support Python > 2.7 and Python 3.
-
-The main driver for the program is the ``t4me.py`` file
-located in the main directory. This is used to execute
-the program and call necessary subroutines. In its standard
-configuration this should serve most users.
+Only support for Python3 is confirmed.
 
 Contributing and versioning
 ***************************

bpdocs

@@ -5,7 +5,7 @@ branch=$(git branch | sed -n -e 's/^\* \(.*\)/\1/p')
 
 # check that we are on the right branch
 if [ $branch != "updated_documentation" ]; then
- echo "Please make sure you issue this command on the 'updated_documentation' branch."
+ echo "Please make sure you issue this command on an 'updated_documentation' branch."
  exit
 fi
 
@@ -24,16 +24,14 @@ cd ..
 # updated docs
 git add docs/_build/html
 git commit -m "Updated documentation for later gh-pages push"
-git push origin updated_documentation
 
 # switch branches and pull the data we want
 git checkout gh-pages && rm -rf *
 touch .nojekyll
 git checkout updated_documentation docs/_build/html
 
 # now we only need html content for gh-pages
-mv ./docs/_build/html/* ./
-rm -rf ./docs
+mv ./docs/_build/html/* ./ && rm -rf ./docs
 
 # add, commit and push gh-pages
 git add -A
@@ -42,3 +40,10 @@ git push origin gh-pages
 
 # switch back to branch
 git checkout updated_documentation
+
+# Clean stuff
+cd docs
+make clean
+# Some LaTeX folder that needs to be removed
+rm -rf docs/auto
+cd ..

build_skw

@@ -5,4 +5,3 @@ cd skw
 make
 make lib
 cd ..
-

docs/conf.py

@@ -14,7 +14,6 @@
 
 import sys
 import os
-import shlex
 import sphinx_bootstrap_theme
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -61,17 +60,17 @@
 
 # General information about the project.
 project = u'T4ME'
-copyright = u'2016, Espen Flage-Larsen'
+copyright = u'2019, Espen Flage-Larsen'
 author = u'Espen Flage-Larsen'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = '1.1'
 # The full version, including alpha/beta/rc tags.
-release = '1'
+release = '1.1.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/install.rst

@@ -1,56 +1,68 @@
 Installing
 ==========
 
-Please consult the :file:`setup.py` file for details on
-how to configure the location of the include and libraries.
+Basic install
+-------------
+First make sure Spglib is installed
 
-Only Spglib (in principle the only requirement for minimal
-functionality against calculations based on first-principle
-data) is included as a Git submodule. This can be activated by
+::
+
+ pip install spglib
+
+Then install T4ME by executing the command
 
 ::
 
- git submodule init
- git submodule update
+ pip install t4me
+
+This will give the user the posibility to calculate the transport coefficients
+using integration routines in SciPy. For other integration and interpolation routines
+the user needs to follow the following recipe.
+
+Advanced install
+----------------
+For more advanced functionality (interpolation and other integration routines) the
+user should determine which external libraries are needed and install them based
+on their respective documentation.
+
+The :file:`setup.py` file assume in its supplied form that the user installs the libraries
+in the standard folders, e.g. `$HOME/include` and `$HOME/lib` for the include and library
+files, respectively. If other locations are needed, please adapt the :file:`setup.py`
+file.
 
-And Spglib can be build with the included :file:`build_spglib`
+As an example, we want to enable the tetrahedron integration. A Spglib interface needs to be compiled.
+This can be build with the included :file:`build_spglib` file.
 
 ::
 
  ./build_spglib
 
-It is possible to build Spglib elsewhere, but consult
-:file:`build_spglib` and make sure that the
-:file:`tetrahedron_method.h` is also inside the include
-directory. For instance, if access to Git is difficult one
-should make a `spglib` folder in the main T4ME directory
-and place a recent Spglib version there. This would give the
-same data structure as if using the Git submodule.
-The build script :file:`build_spglib` can then be executed.
+If that was successfull, T4ME can then be built by issuing the following command
 
-All other libraries need to be built externally and linked in.
+::
+
+ pip install .
 
-Then execute
+or
 
 ::
 
-  python setup.py build_ext --inplace
+ pip install -e .[dev]
 
-To build the necessary parts of interfaces used in T4ME. You should
-now be able to now execute t4me.py which is
-the main driver routine
+Another example. We want to enable SKW interpolation. The SKW routines can be built (assuming Intel MKL is installed) by issuing
 
 ::
 
-  python t4me.py
+ ./build_skw
 
-This should execute cleanly. However, it might be usefull
-to run T4ME from other locations. In order to for this to
-work, the main directory of T4ME needs to be added to
-your ``PYTHONPATH`` environmental variable. Usually, this can
-be done (in bash) by adding the following to your
-:file:`.bashrc` or :file:`.bash_profile`
+If successfull, T4ME can then be installed by issuing one of the two commands listed above. If other FFT routines are to be used, please modify :file:`skw/Makefile`.
+
+All other libraries need to be built externally and linked in.
+
+Upon successfull completion of the installation, T4ME is executed with the command
 
 ::
 
- export PYTHONPATH=$PYTHONPATH:/home/username/somepath/t4me
+ t4me
+
+An `input` directory is needed which should contain the input files.

docs/preq.rst

@@ -5,14 +5,16 @@ In its basic form T4ME only need the following
 dependency:
 
 - `Spglib <https://atztogo.github.io/spglib/>`_.
- Which is placed as a Git submodule and handles the
- setup of the mapping between the full and reduced k-point
- grid.
+ This can be installed with
+
+::
+
+ pip install spglib
 
 Additional optional dependencies include:
 
-- `mpi4py <https://code.google.com/archive/p/pypar/>`_,
- Used to parallelize (not yet enabled).
+- `Spglib <https://atztogo.github.io/spglib/>`_,
+ A custom interface to Spglib to enable tetrahedron integration.
 - `GNU Scientific Library <https://www.gnu.org/software/gsl/>`_,
  Used to solve the analytical Fermi-Dirac integrals.
 - `Einspline <http:https://einspline.sourceforge.net/>`_,

docs/tests.rst

@@ -1,13 +1,17 @@
 Running tests
 =============
 
-Several tests are included, which can be used to test the installation,
-but more importantly assist in verify development steps.
+Several tests are included, which can be used to test the installation.
 
 Currently only basic functionality is tested and developers
 are encouraged to write tests for any added functionality.
 
-Tests can be run by setting the ``run_tests`` in the general parameter file,
-typically the file :file:`param.yml`.
+Tests are executed by issuing
 
-Most of the tests rely on the GSL library, so please install it.
+::
+
+ pytest
+
+In the base directory.
+
+Most of the tests rely on the GSL library, so please install it. If it is not present the tests relying on this will skip.