Merge branch 'dev-stable' of https://github.com/QuantumPackage/qp2 in…

…to dev-stable

.readthedocs.yaml

@@ -0,0 +1,32 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#    - pdf
+#    - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

@@ -2,6 +2,9 @@
 executables for Quantum Package. Please use ifort as long as you can, and
 consider switching to gfortran in the long term.
 
+---
+
+
 # Quantum Package 2.2
 
 <!--- img src="https://raw.githubusercontent.com/QuantumPackage/qp2/master/data/qp2.png" width="250" --->

docs/ref

@@ -20,5 +20,5 @@ Then, to reference for "myref" just type :ref:`myref`
   or use `IRPF90`_ and define
   _IRPF90: http://irpf90.ups-tlse.fr
   somewhere
-* References of published results with QP should be added into docs/source/research.bib in bibtex
+* References of published results with QP should be added into docs/source/references.bib in bibtex
   format

docs/requirements.txt

@@ -1,2 +1,2 @@
-sphinxcontrib-bibtex==0.4.0
-sphinx-rtd-theme==0.4.2
+sphinxcontrib-bibtex
+sphinx-rtd-theme

docs/source/appendix/contributors.rst

@@ -2,13 +2,13 @@
 Contributors
 ============
 
-The |qp| is maintained by 
+The |qp| is maintained by
 
-Anthony Scemama 
+Anthony Scemama
   | `Laboratoire de Chimie et Physique Quantiques <http://www.lcpq.ups-tlse.fr/>`_,
   | CNRS - Université Paul Sabatier
   | Toulouse, France
-  | [email protected] 
+  | [email protected]
 
 
 Emmanuel Giner
@@ -18,27 +18,27 @@ Emmanuel Giner
   | [email protected]
 
 
-Thomas Applencourt
-  | `Argonne Leadership Computing Facility <http://www.alcf.anl.gov/>`_
-  | Argonne, USA
-  | [email protected]
-
-
-
 The following people have contributed to this project (by alphabetical order):
 
+* Abdallah Ammar
+* Thomas Applencourt
 * Roland Assaraf
 * Pierrette Barbaresco
 * Anouar Benali
 * Chandler Bennet
 * Michel Caffarel
+* Vijay Gopal Chilkuri
+* Yann Damour
 * Grégoire David
+* Amanda Dumi
 * Anthony Ferté
-* Madeline Galbraith 
+* Madeline Galbraith
 * Yann Garniron
 * Kevin Gasperich
+* Fabris Kossoski
 * Pierre-François Loos
 * Jean-Paul Malrieu
+* Antoine Marie
 * Barry Moore
 * Julien Paquier
 * Barthélémy Pradines
@@ -49,6 +49,7 @@ The following people have contributed to this project (by alphabetical order):
 * Mikaël Véril
 
 
-If you have contributed and don't appear in this list, please modify this file
+If you have contributed and don't appear in this list, please modify the file
+`$QP_ROOT/docs/source/appendix/contributors.rst`
 and submit a pull request.
 

docs/source/appendix/references.rst

@@ -0,0 +1,8 @@
+References
+==========
+
+.. bibliography:: /references.bib
+   :style: unsrt
+   :all:
+
+

docs/source/auto_generate.py

@@ -29,7 +29,8 @@ def generate_modules(abs_module, entities):
     rst += ["", "EZFIO parameters", "----------------", ""]
     config_file = configparser.ConfigParser()
     with open(EZFIO, 'r') as f:
-        config_file.readfp(f)
+#        config_file.readfp(f)
+        config_file.read_file(f)
         for section in config_file.sections():
             doc = config_file.get(section, "doc")
             doc = "    " + doc.replace("\n", "\n\n    ")+"\n"

docs/source/conf.py

@@ -70,7 +70,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -208,3 +208,5 @@
 
 # -- Extension configuration -------------------------------------------------
 
+bibtex_bibfiles = [ "references.bib" ]
+

docs/source/intro/intro.rst

@@ -11,25 +11,25 @@ The |qp|
 What it is
 ==========
 
-The |qp| is an open-source **programming environment** for quantum chemistry. 
-It has been built from the **developper** point of view in order to help 
-the design of new quantum chemistry methods, 
-especially for `wave function theory <https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods>`_ (|WFT|). 
+The |qp| is an open-source **programming environment** for quantum chemistry.
+It has been built from the **developper** point of view in order to help
+the design of new quantum chemistry methods,
+especially for `wave function theory <https://en.wikipedia.org/wiki/Ab_initio_quantum_chemistry_methods>`_ (|WFT|).
 
-From the **user** point of view, the |qp| proposes a stand-alone path 
-to use optimized selected configuration interaction |sCI| based on the 
-|CIPSI| algorithm that can efficiently reach near-full configuration interaction 
-|FCI| quality for relatively large systems (see for instance :cite:`Caffarel_2016,Caffarel_2016.2,Loos_2018,Scemama_2018,Dash_2018,Garniron_2017.2,Loos_2018,Garniron_2018,Giner2018Oct`). 
-To have a simple example of how to use the |CIPSI| program, go to the `users_guide/quickstart`. 
+From the **user** point of view, the |qp| proposes a stand-alone path
+to use optimized selected configuration interaction |sCI| based on the
+|CIPSI| algorithm that can efficiently reach near-full configuration interaction
+|FCI| quality for relatively large systems.
+To have a simple example of how to use the |CIPSI| program, go to the `users_guide/quickstart`.
 
 
 The main goal is the development of selected configuration interaction |sCI|
 methods and multi-reference perturbation theory |MRPT| in the
-determinant-driven paradigm. It also contains the very basics of Kohn-Sham `density functional theory <https://en.wikipedia.org/wiki/Density_functional_theory>`_ |KS-DFT| and `range-separated hybrids <https://aip.scitation.org/doi/10.1063/1.1383587>`_ |RSH|.  
+determinant-driven paradigm. It also contains the very basics of Kohn-Sham `density functional theory <https://en.wikipedia.org/wiki/Density_functional_theory>`_ |KS-DFT| and `range-separated hybrids <https://aip.scitation.org/doi/10.1063/1.1383587>`_ |RSH|.
 
-The determinant-driven framework allows the programmer to include any arbitrary set of 
-determinants in the variational space, and thus gives a complete freedom in the methodological 
-development. The basic ingredients of |RSH| together with those of the |WFT| framework available in the |qp| library allows one to easily develop range-separated DFT (|RSDFT|) approaches (see for instance the plugins at `<https://gitlab.com/eginer/qp_plugins_eginer>`_). 
+The determinant-driven framework allows the programmer to include any arbitrary set of
+determinants in the variational space, and thus gives a complete freedom in the methodological
+development. The basic ingredients of |RSH| together with those of the |WFT| framework available in the |qp| library allows one to easily develop range-separated DFT (|RSDFT|) approaches (see for instance the plugins at `<https://gitlab.com/eginer/qp_plugins_eginer>`_).
 
 All the programs are developed with the `IRPF90`_ code generator, which considerably simplifies
 the collaborative development, and the development of new features.
@@ -40,20 +40,20 @@ What it is not
 ==============
 
 The |qp| is *not* a general purpose quantum chemistry program.
-First of all, it is a *library* to develop new theories and algorithms in quantum chemistry. 
+First of all, it is a *library* to develop new theories and algorithms in quantum chemistry.
 Therefore, beside the use of the programs of the core modules, the users of the |qp| should develop their own programs.
 
 The |qp| has been designed specifically for |sCI|, so all the
 algorithms which are programmed are not adapted to run SCF or DFT calculations
 on thousands of atoms. Currently, the systems targeted have less than 600
-molecular orbitals. This limit is due to the memory bottleneck induced by the storring of the two-electron integrals (see ``mo_two_e_integrals`` and ``ao_two_e_integrals``). 
+molecular orbitals. This limit is due to the memory bottleneck induced by the storring of the two-electron integrals (see ``mo_two_e_integrals`` and ``ao_two_e_integrals``).
 
 The |qp| is *not* a massive production code. For conventional
 methods such as Hartree-Fock, CISD or MP2, the users are recommended to use the
 existing standard production codes which are designed to make these methods run
 fast. Again, the role of the |qp| is to make life simple for the
 developer. Once a new method is developed and tested, the developer is encouraged
-to consider re-expressing it with an integral-driven formulation, and to 
+to consider re-expressing it with an integral-driven formulation, and to
 implement the new method in open-source production codes, such as `NWChem`_
 or |GAMESS|.