add Dom's psiapi ipynb to docs, adjust tutorials, update for psiapi i…

…n general.

CMakeLists.txt

@@ -50,10 +50,12 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
 
 #  <<<  Detecting BLAS/LAPACK  >>>
 #
-#    - ENV(MATH_ROOT) "Root directory in which BLAS/LAPACK libraries should be detected (e.g., ${MATH_ROOT}/lib64/libblas.so)"
-#    - BLAS_TYPE "BLAS distribution to target (default: search order MKL>OPENBLAS>ESSL>ATLAS>ACML>SYSTEM_NATIVE on Linux; MKL>Accelerate>... on Mac)"
-#    - LAPACK_TYPE "LAPACK distribution to target (default: search order MKL>OPENBLAS>ESSL>ATLAS>ACML>SYSTEM_NATIVE on Linux; MKL>Accelerate>... on Mac)"
-#    - LAPACK_LIBRARIES "Location of BLAS/LAPACK libraries as a semicolon-separated list of full paths, bypassing math detection"
+#    - ENV(MATH_ROOT) "Root directory where BLAS/LAPACK libraries should be detected (e.g., ${MATH_ROOT}/lib/libblas.so)"
+#    - BLAS_TYPE "Target BLAS distribution for math detection
+#                 (default: search order MKL>OPENBLAS>ESSL>ATLAS>ACML>SYSTEM_NATIVE on Linux; MKL>Accelerate>... on Mac)"
+#    - LAPACK_TYPE "Target LAPACK distribution for math detection
+#                 (default: search order MKL>OPENBLAS>ESSL>ATLAS>ACML>SYSTEM_NATIVE on Linux; MKL>Accelerate>... on Mac)"
+#    - LAPACK_LIBRARIES "Location of BLAS/LAPACK libraries as ";"-separated list of full paths, bypassing math detection"
 #    - LAPACK_INCLUDE_DIRS "Location of BLAS/LAPACK headers (only needed for MKL), bypassing math detection"
 
 #  <<<  Install  >>>
@@ -63,7 +65,8 @@ list(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake)
 #    - CMAKE_INSTALL_LIBDIR "Location within CMAKE_INSTALL_PREFIX to which libraries are installed (default: lib)"
 #    - CMAKE_INSTALL_DATADIR "Location within CMAKE_INSTALL_PREFIX to which resources are installed (default: share)"
 #    - CMAKE_INSTALL_INCLUDEDIR "Location within CMAKE_INSTALL_PREFIX to which headers are installed (default: include)"
-#    - PYMOD_INSTALL_LIBDIR "Location within CMAKE_INSTALL_LIBDIR to which python modules are installed (default: /) must start with /"
+#    - PYMOD_INSTALL_LIBDIR "Location within CMAKE_INSTALL_LIBDIR to which python modules are installed (default: /)
+#                            Must start with /"
 
 ############################  Options: Build What?  ############################
 option(ENABLE_AMBIT "Enables the Ambit tensor library" OFF)

doc/sphinxman/CMakeLists.txt

@@ -27,7 +27,7 @@ if(PERL_FOUND AND SPHINX_FOUND)
         @ONLY)
 
     # Static-doc reST files
-    set(STATICDOC abbr_accents.rst adc.rst appendices.rst basissets.rst basissets_byelement.rst bibliography.rst cbs.rst cbs_eqn.rst contributing.rst nbody.rst customizing.rst db.rst detci.rst dfmp2.rst diatomic.rst documentation.rst energy.rst external.rst fchk.rst freq.rst gdma.rst glossary_psivariables.rst index.rst intercalls.rst interfacing.rst introduction.rst methods.rst notes_c.rst notes_py.rst oeprop.rst opt.rst optking.rst plugins.rst programming.rst prop.rst psithonfunc.rst psithoninput.rst quickaddalias.rst basissets_tables.rst quickadddatabase.rst sapt.rst sowreap.rst testsuite.rst tutorial.rst dft_byfunctional.rst scf.rst mrcc.rst psimrcc.rst cc.rst dft.rst fnocc.rst optionshandling.rst basissets_byfamily.rst psipep.rst pep0001.rst dftd3.rst occ.rst molden.rst cubeprop.rst dcft.rst relativistic.rst dkh.rst proc_py.rst psithonmol.rst cfour.rst mrcc_table_energy.rst cfour_table_energy.rst cfour_table_grad.rst libefp.rst conda.rst pcmsolver.rst thermo.rst chemps2.rst fisapt.rst plugin_v2rdm_casscf.rst psi4api.rst addon.rst numpy.rst build_planning.rst build_faq.rst build_obtaining.rst libint.rst erd.rst gcp.rst)
+    set(STATICDOC abbr_accents.rst adc.rst appendices.rst basissets.rst basissets_byelement.rst bibliography.rst cbs.rst cbs_eqn.rst contributing.rst nbody.rst customizing.rst db.rst detci.rst dfmp2.rst diatomic.rst documentation.rst energy.rst external.rst fchk.rst freq.rst gdma.rst glossary_psivariables.rst index.rst intercalls.rst interfacing.rst introduction.rst methods.rst notes_c.rst notes_py.rst oeprop.rst opt.rst optking.rst plugins.rst programming.rst prop.rst psithonfunc.rst psithoninput.rst quickaddalias.rst basissets_tables.rst quickadddatabase.rst sapt.rst sowreap.rst testsuite.rst tutorial.rst dft_byfunctional.rst scf.rst mrcc.rst psimrcc.rst cc.rst dft.rst fnocc.rst optionshandling.rst basissets_byfamily.rst psipep.rst pep0001.rst dftd3.rst occ.rst molden.rst cubeprop.rst dcft.rst relativistic.rst dkh.rst proc_py.rst psithonmol.rst cfour.rst mrcc_table_energy.rst cfour_table_energy.rst cfour_table_grad.rst libefp.rst conda.rst pcmsolver.rst thermo.rst chemps2.rst fisapt.rst plugin_v2rdm_casscf.rst psi4api.rst addon.rst numpy.rst build_planning.rst build_faq.rst build_obtaining.rst libint.rst erd.rst gcp.rst index_tutorials.rst psiapi.ipynb)
     # * compute relative path btwn top_srcdir and objdir/doc/sphinxman
     execute_process(COMMAND ${PYTHON_EXECUTABLE} -c
         "import sys; import os; print('/' + os.path.relpath('${psi4_SOURCE_DIR}', '${CCBD}') + '/../')"
@@ -177,7 +177,7 @@ if(PERL_FOUND AND SPHINX_FOUND)
                 ${CCBD}/source/autodoc_dft_dhybrid.rst
                 #${CCBD}/source/autodoc_dft_scsdhybrid.rst  # commented until populated again to appease Sphinx
                 ${CCBD}/source/autodoc_dft_disp.rst
-        DEPENDS ${psi4_SOURCE_DIR}/psi4/driver/procedures/dft_functional.py
+        DEPENDS ${psi4_SOURCE_DIR}/psi4/driver/procrouting/dft_functional.py
                 ${psi4_SOURCE_DIR}/tests/docs-dft/input.dat
                 ${STAGED_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}/psi4
         COMMENT "Autodoc functionals")

doc/sphinxman/source/conf.py.in

@@ -74,6 +74,8 @@ extensions = [
     'sphinx.ext.graphviz',
     'sphinx.ext.autosummary',
     'sphinx.ext.napoleon',
+    # from Jupyter
+    'nbsphinx',
     # from Cloud
     'cloud_sptheme.ext.index_styling',
     'cloud_sptheme.ext.escaped_samp_literals',
@@ -188,7 +190,7 @@ html_theme_path = [psp.get_theme_dir(), csp.get_theme_dir()]
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = None
+html_title = ''
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
 #html_short_title = None
@@ -295,6 +297,7 @@ latex_documents = [
 # If false, no module index is generated.
 #latex_domain_indices = True
 
+nbsphinx_allow_errors = True
 
 # -- Options for manual page output --------------------------------------------
 

doc/sphinxman/source/index.rst

@@ -39,7 +39,7 @@
 
    introduction
    external
-   tutorial
+   index_tutorials
    psithoninput
    methods
    interfacing

doc/sphinxman/source/index_tutorials.rst

@@ -0,0 +1,37 @@
+.. #
+.. # @BEGIN LICENSE
+.. #
+.. # Psi4: an open-source quantum chemistry software package
+.. #
+.. # Copyright (c) 2007-2017 The Psi4 Developers.
+.. #
+.. # The copyrights for code used from other parties are included in
+.. # the corresponding files.
+.. #
+.. # This program is free software; you can redistribute it and/or modify
+.. # it under the terms of the GNU General Public License as published by
+.. # the Free Software Foundation; either version 2 of the License, or
+.. # (at your option) any later version.
+.. #
+.. # This program is distributed in the hope that it will be useful,
+.. # but WITHOUT ANY WARRANTY; without even the implied warranty of
+.. # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+.. # GNU General Public License for more details.
+.. #
+.. # You should have received a copy of the GNU General Public License along
+.. # with this program; if not, write to the Free Software Foundation, Inc.,
+.. # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+.. #
+.. # @END LICENSE
+.. #
+
+====================
+A |PSIfour| Tutorial
+====================
+
+.. toctree::
+   :maxdepth: 2
+
+   tutorial
+   psiapi.ipynb
+