Merge pull request #95 from issp-center-dev/python3-autodoc

Update to Python3 & TRIQS3.0.x

.travis.yml

@@ -12,11 +12,12 @@ before_script:
   - docker-compose up --build -d
 
 script:
-  - docker exec dcore_container make test
+  - docker exec dcore_container pytest tests/non-mpi/*/*.py
+  - docker exec dcore_container pytest tests/mpi/*/*.py
 
 after_script:
   - cd ${ROOTDIR}
-  - docker cp dcore_container:/home/testuser/opt/DCore/share/doc/dcore ${ROOTDIR}/dcore_doc
+  - docker cp dcore_container:/home/triqs/src/DCore/html ${ROOTDIR}/dcore_doc
   - docker-compose stop
   - docker-compose rm -f
   - /bin/bash -x ${ROOTDIR}/.travis_scripts/deploy_docs.sh

Dockerfile

@@ -1,16 +1,36 @@
-FROM shinaoka/triqs1.4_dmft_alps
+FROM flatironinstitute/triqs
+
+RUN sudo apt update && sudo apt install vim make --yes
 
 # Copy host directory
-COPY ./ $HOME/src/DCore
+RUN echo $HOME
+COPY ./ /home/triqs/src/DCore
+RUN sudo chown -R triqs /home/triqs/src
+RUN ls -la /home/triqs/src
+
+# Install TRIQS/HubbardI
+WORKDIR /home/triqs/src
+RUN git clone https://github.com/TRIQS/hubbardI.git
+RUN mkdir hubbardI.build
+WORKDIR /home/triqs/src/hubbardI.build
+RUN cmake -DCMAKE_CXX_COMPILER=mpicxx ../hubbardI
+RUN make && sudo make install
+
+# Install pip & some python libraries
+ENV PATH $PATH:/home/triqs/.local/bin
+RUN curl -kL https://bootstrap.pypa.io/get-pip.py | python3
+RUN pip3 install sphinx wild_sphinx_theme matplotlib pytest numpy -U --user
+
+# Install DCore
+WORKDIR /home/triqs/src/DCore
+RUN ls -la
+RUN python3 setup.py install --user
 
-RUN pip install sphinx wild-sphinx-theme
-# Workaround for a bug in docutils 0.15
-RUN pip install -U docutils==0.14
+# Build doc
+RUN python3 -m dcore.option_tables doc/reference
+RUN sphinx-build -b html doc html
+RUN find /home/triqs/src/DCore/html
 
-WORKDIR $HOME/src/DCore
-RUN mkdir $HOME/build/DCore
-WORKDIR $HOME/build/DCore
-ENV CTEST_OUTPUT_ON_FAILURE=1
-RUN cmake -DCMAKE_VERBOSE_MAKEFILE=ON $HOME/src/DCore -DTRIQS_PATH=$HOME/opt/triqs -DCMAKE_INSTALL_PREFIX=$HOME/opt/DCore -DBUILD_DOC=ON \
- && make -j 2 all && make -j 2 install
-RUN find .
+# Run tests
+#RUN pytest tests/non-mpi/*/*.py
+#RUN pytest tests/mpi/*/*.py

cmake/show_triqs_version.py

@@ -1,6 +1,5 @@
-from __future__ import print_function
 try:
-    from pytriqs import version
+    from triqs import version
 except ImportError:
     print('NOT_FOUND', end='')
 else:

doc/about.rst

@@ -0,0 +1,78 @@
+.. index:: DFTTools
+
+.. module:: dcore
+
+DCore
+=====
+
+integrated **D**\ MFT software for **Cor**\ related **e**\ lectrons
+
+What is DCore?
+--------------
+
+`DCore <https://github.com/issp-center-dev/DCore>`_ is aimed at model calculations and ab-initio calculations by the dynamical mean-field theory (DMFT).
+This package consists of programs with text-based and hdf5-based interface.
+These programs enable users to perform DMFT calculations and analyze results without writing computer code.
+
+License
+-------
+
+The DCore package is published under the
+`GNU General Public License, version 3 <http://www.gnu.org/licenses/gpl.html>`_.
+
+The following files are from the TRIQS (Toolbox for Research on Interacting Quantum Systems).
+
+- https://github.com/issp-center-dev/DCore/blob/develop/python/impurity_solvers/triqs_hubbard_I_impl.py
+- https://github.com/issp-center-dev/DCore/tree/develop/python/converters
+
+We would like to express our sincere gratitude to TRIQS's developers.
+
+This package of ver.1.0 was developed under the support of "Project for advancement of software usability in materials science" by The Institute for Solid State Physics, The University of Tokyo. The copyright of DCore ver.1.0 belongs to The University of Tokyo.
+
+Authors & Quotation
+-------------------
+
+**Developers**:
+
+- ver. 2.0
+
+  H. Shinaoka, J. Otsuki, K. Yoshimi, M. Kawamura, N. Takemori, Y. Motoyama
+
+- ver. 1.1 (released on 2019/1/25)
+
+- ver. 1.0 (released on 2018/3/24)
+
+  H. Shinaoka, J. Otsuki, K. Yoshimi, M. Kawamura, T. Kato
+
+**Related papers**:
+This package depends on TRIQS libraries and applications.
+Please cite relevant papers for these original libraries.
+
+* `TRIQS libraries <https://triqs.github.io/triqs/2.1.x/about.html>`_
+* `TRIQS/DFTTools <https://triqs.github.io/dft_tools/2.1.x/about.html>`_
+
+In addition to the above two libraries, you may use impurity solvers listed below.
+
+* `TRIQS/cthyb <https://triqs.github.io/cthyb/2.1.x/about.html>`_
+* `TRIQS/hubbardI <https://triqs.github.io/triqs/1.4/applications/hubbardI/about.html>`_
+* `ALPS/CT-HYB <https://github.com/ALPSCore/CT-HYB/wiki/Citation>`_
+* `ALPS/CT-HYB-SEGMENT <https://github.com/ALPSCore/CT-HYB-SEGMENT>`_
+
+For some of them, they provide a BibTeX entry for each paper in the above cites.
+
+GitHub repository
+-----------------
+
+You can download the source code of **DCore** from https://github.com/issp-center-dev/DCore.
+
+Contents
+-----------------
+:doc:`Contents <contents>`
+
+Disclaimer
+----------
+
+The program is provided as is, i.e. WITHOUT ANY WARRANTY of any kind, as
+stated in the license.  In particular, its authors and contributors will take
+no responsibility for any possible bugs or any improper use of these programs,
+including those resulting in incorrect scientific publications.

doc/conf.py.in → doc/conf.py

@@ -1,9 +1,6 @@
 # -*- coding: utf-8 -*-
-#
-# TRIQS documentation build configuration file
 
 import sys
-#sys.path.insert(0, "@TRIQS_SPHINXEXT_PATH@/numpydoc")
 
 extensions = ['sphinx.ext.autodoc',
               'sphinx.ext.mathjax',
@@ -18,31 +15,23 @@
 source_suffix = '.rst'
 todo_include_todos = True
 
-#spelling_lang='en_US'
-#spelling_word_list_filename='spelling_wordlist.txt'
-
-
 project = u'DCore'
 copyright = u'2017, The University of Tokyo'
-version = '@DCORE_VERSION@'
-
-#mathjax_path = "@TRIQS_MATHJAX_PATH@/MathJax.js?config=default"
-templates_path = ['@CMAKE_SOURCE_DIR@/doc/_templates']
 
 html_theme = 'wild'
 import wild_sphinx_theme
 html_theme_path = [wild_sphinx_theme.get_theme_dir()]
 
-#html_theme_path = ['@TRIQS_THEMES_PATH@']
 html_show_sphinx = False
 html_context = {'header_title': 'DCore',
                 'header_subtitle': 'integrated DMFT software for CORrelated Electrons',
                 'header_links': [['Install', 'install'],
                                  ['Documentation', 'documentation'],
-                                 ['Presentatation', 'presentation'],
+                                 #['Presentatation', 'presentation'],
                                  ['Issues', 'issues'],
                                  ['About DCore', 'about']]}
-html_static_path = ['@CMAKE_SOURCE_DIR@/doc/_static']
+#html_static_path = ['@CMAKE_SOURCE_DIR@/doc/_static']
+html_static_path = ['_static']
 #html_sidebars = {'index': ['sideb.html', 'searchbox.html']}
 html_sidebars = {'**': ['globaltoc.html', 'relations.html', 'searchbox.html']}
 
@@ -63,4 +52,4 @@
 
 # overwrite css of html_theme
 def setup(app):
-    app.add_stylesheet('dcore.css')
+    app.add_css_file('dcore.css')

doc/impuritysolvers/how_to_integrate.rst

@@ -4,12 +4,12 @@ How to integrate your own solver
 You can use your own impurity solver from DCore by wrapping the executable as appropriate.
 The null solver serves as a template of wrapper code.
 
-    :download:`null_solver.py <../../python/dcore/impurity_solvers/null_solver.py>`
+    :download:`null_solver.py <../../src/dcore/impurity_solvers/null_solver.py>`
 
 Follow the instructions below.
 
 ..
-    .. literalinclude:: ../../python/dcore/impurity_solvers/null_solver.py
+    .. literalinclude:: ../../src/dcore/impurity_solvers/null_solver.py
        :language: python
 
 Copy the template
@@ -69,7 +69,7 @@ Edit the template
         self._Delta_iw = delta(self._G0_iw)
         Delta_tau = make_block_gf(GfImTime, self.gf_struct, self.beta, self.n_tau)
         for name, block in self._Delta_iw:
-            Delta_tau[name] << InverseFourier(self._Delta_iw[name])
+            Delta_tau[name] << Fourier(self._Delta_iw[name])
 
         # (1c) Set U_{ijkl} for the solver
         # for i, j, k, l in product(range(self.n_flavors), repeat=4):