Try to replace nose with pytest

.travis.yml

@@ -17,33 +17,16 @@ install:
   - env
 
   # pip-based installation.
-  #- pip install numpy
   #- travis_wait pip install -q -r requirements.txt
   #- travis_wait pip install -q -r requirements-optional.txt
 
   # Install conda https://conda.io/docs/travis.html
   - source dev_scripts/conda_installer.sh
-
   - source dev_scripts/conda_develop.sh
+  - conda uninstall -y pymatgen
 
-  #- conda config --add channels conda-forge
-  # See https://github.com/BVLC/caffe/issues/3884 and https://docs.continuum.io/mkl-optimizations/
-  #- conda install nomkl
-  #- conda install pandas
-  #- conda install netcdf4 
-  # See https://github.com/ContinuumIO/anaconda-issues/issues/1360
-  #- conda install hdf4=4.2.12
-  #- pip install pytest scripttest
   - if [[ "${PYTHON_VERSION}" == "2.7" ]]; then conda install mock; fi
-  #- pip install pep8 python-coveralls
-  #- conda install matplotlib seaborn
-  #- pip install matplotlib seaborn
-  #- pip install scikit-image
-  #- conda install ipython jupyter nbformat
-  - pip install ipython jupyter nbformat
   - pip install nose nose-exclude
-  #- conda install -c conda-forge ipywidgets
-  #- pip install ipywidgets
 
   # Install abinit from abinit conda channel.
   #- conda install -c gmatteo abinit=8.6.1
@@ -53,18 +36,6 @@ install:
   # Mayavi (optional requirement)
   #- if [[ "${PYTHON_VERSION}" == "2.7" ]]; then conda install mayavi; fi
   #- if [[ "${PYTHON_VERSION}" == "3.6" ]]; then conda install vtk && pip install mayavi; fi
-  #
-  # phonopy is not a requirement but we test scripts in data/runs that use it
-  #- conda install -c conda-forge phonopy
-
-  #- if [[ "${PYTHON_VERSION}" == "2.7" ]]; then rm -rf /home/travis/miniconda/envs/test-environment/lib/python2.7/site-packages/pymatgen*; fi
-  #- if [[ "${PYTHON_VERSION}" == "3.6" ]]; then rm -rf /home/travis/miniconda/envs/test-environment/lib/python3.6/site-packages/pymatgen*; fi
-
-  - conda uninstall -y pymatgen
-
-  # Get pymatgen from matsci
-  #- conda config --add channels matsci
-  #- conda install pymatgen #=4.7.2
 
   # Use my pymatgen fork
   #- git clone --depth=50 https://github.com/gmatteo/pymatgen.git && cd pymatgen && pip install -q -r requirements.txt && pip install -q -r requirements-optional.txt && python setup.py install && cd ../
@@ -80,9 +51,6 @@ install:
   - cp abipy/data/managers/travis_manager.yml ${HOME}/.abinit/abipy/manager.yml
   - ./dev_scripts/pyclean.py .
 
-  # Install bader (http://theory.cm.utexas.edu/henkelman/code/bader/) from matsci
-  #- conda install -c matsci bader
-
 before_script:
     # This to run tests requiring a graphical user e.g. mayavi
     # https://docs.travis-ci.com/user/gui-and-headless-browsers/#Using-xvfb-to-Run-Tests-That-Require-a-GUI

abipy/electrons/charges.py

@@ -114,9 +114,9 @@ class BaderCharges(Charges):
               "BaderCharges.from_files requires the executable bader to be in the path.")
     def from_files(cls, density_path, pseudopotential_paths, with_core=True, workdir=None, **kwargs):
         """
-        Uses the abinit density files and the bader executable from Henkelmann et al. to calculate
+        Uses the abinit density files and the bader executable_ from Henkelmann et al. to calculate
         the bader charges of the system. If pseudopotentials are given, the atomic charges will be
-        extracted as well.
+        extracted as well. See also :cite:`Henkelmann2006`.
 
         The extraction of the core charges may be a time consuming calculation, depending on the
         size of the system. A tuning of the parameters may be required (see Density.ae_core_density_on_mesh).

dev_scripts/runtests.sh

@@ -3,14 +3,16 @@ set -ev  # exit on first error, print each command
 
 echo "PMG_MAPI_KEY: 8pkvwRLQSCVbW2Fe" > ${HOME}/.pmgrc.yaml
 
+abinit --version
+abinit --build
 abicheck.py --with-flow
 
-nosetests -v --with-coverage --cover-package=abipy --logging-level=INFO
-#nosetests abipy -v --with-coverage --cover-package=abipy --logging-level=INFO
+# Run unit tests with nose.
+#nosetests -v --with-coverage --cover-package=abipy --logging-level=INFO --doctest-tests
 
-#pytest --cov-config .coveragerc --cov=abipy -v  abipy # --doctest-modules 
+pytest --cov-config=.coveragerc --cov=abipy -v --doctest-modules --cache-clear abipy 
 # This is to run the integration tests (append results)
-# pytest --cov-config .coveragerc --cov=abipy --cov-append -v abipy/integration_tests
+# pytest --cov-config=.coveragerc --cov=abipy --cov-append -v abipy/integration_tests
 
 # Generate documentation
 if [[ "${PYTHON_VERSION}" == "3.6" && "${TRAVIS_OS_NAME}" == "linux" ]]; then

docs/conf.py

@@ -55,7 +55,7 @@ extensions = [
     'sphinx.ext.inheritance_diagram',
     'sphinxcontrib.programoutput',
     'sphinx_gallery.gen_gallery',
-    #"sphinxarg.ext",         # CLI doc
+    "sphinxarg.ext",         # CLI doc
     #'nbsphinx',
     'sphinxcontrib.bibtex',
     "releases",

docs/links.rst

@@ -31,6 +31,7 @@
 .. _jupyter: http://jupyter.org/
 .. _Python: http://www.python.org/
 .. _spglib: https://atztogo.github.io/spglib/
+.. _bader: http://theory.cm.utexas.edu/henkelman/code/bader/
 .. _ase: https://wiki.fysik.dtu.dk/ase/
 .. _COD: http://www.crystallography.net/cod/
 .. _CIF: http://www.iucr.org/resources/cif

docs/refs.bib

@@ -233,3 +233,18 @@
  year = {2017},
  month = feb,
 }
+@article{Henkelman2006,
+ author = {Henkelman, Graeme and Arnaldsson, Andri and Jónsson, Hannes},
+ doi = {10.1016/j.commatsci.2005.04.010},
+ number = {3},
+ pages = {354-360},
+ source = {Crossref},
+ url = {http://dx.doi.org/10.1016/j.commatsci.2005.04.010},
+ volume = {36},
+ journal = {Computational Materials Science},
+ publisher = {Elsevier BV},
+ title = {A fast and robust algorithm for Bader decomposition of charge density},
+ issn = {0927-0256},
+ year = {2006},
+ month = jun,
+}

setup.cfg

@@ -1,3 +1,6 @@
+[metadata]
+description-file = README.md
+
 [aliases]
 release = register sdist bdist_wheel upload