Merge trunk/develop into develop

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,8 @@
+## Summary
+
+Please write summary of major changes
+
+* Feature 1
+* Feature 2
+* Fix 1
+* Fix 2

.github/workflows/abipy-lint.yml

@@ -0,0 +1,41 @@
+name: AbiPy linting
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: [3.6]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+    - name: Lint with pycodestyle
+      run: |
+        pip install pycodestyle
+        pycodestyle abipy
+      #- name: Lint with mypy
+      #  run: |
+      #    pip install mypy
+      #    mypy abipy
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 --count --show-source --statistics abipy
+        # exit-zero treats all errors as warnings.
+        #flake8 --count --exit-zero --max-complexity=20 --statistics abipy
+        #- name: Lint with pylint
+        #  run: |
+        #    pip install pylint
+        #    # stop the build if there are Python syntax errors or undefined names
+        #    pylint --exit-zero abipy

.gitignore

@@ -4,9 +4,9 @@ Profile.prof
 abipy/examples/flows/flow_*
 abipy/examples/flows/develop/flow_*
 _debug
-__abinb_workdir__
-abinb_*.ipynb
-*.pickle
+#__abinb_workdir__
+#abinb_*.ipynb
+$*.pickle
 
 # cython generated code
 abipy/extensions/*.c
@@ -79,3 +79,4 @@ Untitled.ipynb
 .pydevproject
 gallery/
 modules/
+style.log

.travis.yml

@@ -1,42 +1,34 @@
 language: python
-cache: pip
-
-#dist: precise
-sudo: false
+#cache: pip
 
 env:
   global:
-    - ABINIT_VERSION=8.8.2
-    - ABIPY_PYTEST=yes
-    - OPENBLAS_NUM_THREADS=1
-    - OMP_NUM_THREADS=1
+  - ABINIT_VERSION=8.10.1
+  - ABIPY_PYTEST=yes
+  - OPENBLAS_NUM_THREADS=1
+  - OMP_NUM_THREADS=1
 
 matrix:
   include:
-    - os: linux
-      python: 2.7
-      env: 
-        - ABIPY_INSTALLER=conda
-    - os: linux
-      python: 3.6
-      env: 
-        - ABIPY_INSTALLER=conda ABIPY_COVERALLS=yes
     - os: linux
       python: 3.6
-      env: 
-        - ABIPY_INSTALLER=pip ABIPY_SPHINX=yes ABIPY_PYTEST=no
-    #- os: osx
-    #  python: 3.6
-    #  language: generic
-    #  env: 
-    #    - ABIPY_INSTALLER=conda ABIPY_PYTEST=no
+      env:
+        - ABIPY_INSTALLER=pip ABIPY_PYTEST=no
     - os: linux
       python: 3.7
-      # https://github.com/travis-ci/travis-ci/issues/9815
       dist: xenial
+      env:
+        - ABIPY_INSTALLER=pip ABIPY_COVERALLS=yes
+    - os: linux
+      python: 3.7
+      dist: xenial # https://github.com/travis-ci/travis-ci/issues/9815
       sudo: true
-      env: 
-        - ABIPY_INSTALLER=pip
+      env:
+        - ABIPY_INSTALLER=conda ABIPY_SPHINX=yes
+#- os: linux
+#  python: 3.8
+#  env:
+#    - ABIPY_INSTALLER=conda ABIPY_PYTEST=no
 
 install:
   #- set -ev  # exit on first error, print each command
@@ -47,15 +39,12 @@ install:
       if [ "${ABIPY_INSTALLER}" == "pip" ]; then
         # pip-based installation.
         source dev_scripts/conda_get.sh  # Needed for Abinit
-        echo "Installing abinit from abinit channel ..."
-        conda config --add channels conda-forge
-        conda install -y -c abinit abinit=${ABINIT_VERSION}
-        abinit --version
-        abinit --build
-
+        # We are gonna use the github version
         sed -i '/pymatgen/d' requirements.txt
         travis_wait pip install -r requirements.txt
         travis_wait pip install -r requirements-optional.txt
+        conda install -y -c conda-forge graphviz python-graphviz
+        #pip install graphviz
         #travis_wait pip uninstall -y pymatgen
 
       elif [ "${ABIPY_INSTALLER}" == "conda" ]; then
@@ -67,7 +56,7 @@ install:
       fi
 
   - if [[ "${TRAVIS_PYTHON_VERSION}" == "2.7" ]]; then conda install mock; fi
-  #- pip install graphviz
+  - pip install coverage>=4.4 -U --upgrade-strategy=eager
 
   # Mayavi (optional requirement)
   #- if [[ "${TRAVIS_PYTHON_VERSION}" == "2.7" ]]; then conda install mayavi; fi
@@ -82,7 +71,7 @@ install:
   #- git clone --depth=50 https://github.com/materialsproject/pymatgen.git && cd pymatgen && pip install -r requirements.txt && pip install -r requirements-optional.txt && python setup.py install && cd ../
 
   - python setup.py install
-  - mkdir -p ${HOME}/.abinit/abipy 
+  - mkdir -p ${HOME}/.abinit/abipy
   - cp abipy/data/managers/travis_scheduler.yml ${HOME}/.abinit/abipy/scheduler.yml
   - cp abipy/data/managers/travis_manager.yml ${HOME}/.abinit/abipy/manager.yml
   - ./dev_scripts/pyclean.py .
@@ -91,10 +80,7 @@ before_script:
     # This to run tests requiring a graphical user e.g. mayavi
     # https://docs.travis-ci.com/user/gui-and-headless-browsers/#Using-xvfb-to-Run-Tests-That-Require-a-GUI
     - "export DISPLAY=:99.0"
-    - "sh -e /etc/init.d/xvfb start"
-    - sleep 3 # give xvfb some time to start
-    # https://github.com/travis-ci/travis-ci/issues/6307
-    - if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then rvm get head || true; fi 
+    - if [[ "${TRAVIS_OS_NAME}" == "osx" ]]; then rvm get head || true; fi
 
 # command to run tests
 script: ./dev_scripts/runtests.sh
@@ -113,12 +99,3 @@ notifications:
       - [email protected]
     on_success: change
     on_failure: always
-
-# https://docs.travis-ci.com/user/deployment/pages/
-#deploy:
-#  provider: pages
-#  skip_cleanup: true
-#  github_token: $GITHUB_TOKEN # Set in travis-ci.org dashboard
-#  local_dir: ${TRAVIS_BUILD_DIR}/yourfolder
-#  on:
-#    branch: master

CHANGELOG.rst

@@ -1,24 +1,46 @@
-* :release:`0.3.0 <2017-12-26>`
-* :feature:`0` Add :ref:`abiview.py` script for a quick visualization of results.
-* :feature:`0` :ref:`abicheck.py` accepts ``-with-flow`` options 
-* :feature:`0` Add AbinitInput.set_spell_check to activate/deactivate spell-checker
-* :feature:`0` Improve coverage
-* :bug:`0 major` Fix bug in in `SigresFile.get_dataframe` if QP states do not start with the same band index.
-* :bug:`0 major` Fix bug in thermodinamical properties (zero-point energy was included twice)
-* :feature:`0` Add ``mpirunner_options`` and ``shell_runner_options`` to |TaskManager|.
-* :feature:`0` Autodetect presence in |DdbFile| of data required for the LO-TO splitting.
-* :feature:`0` Solve problem with visualize in jupyter_ notebooks (files should be produced in workdir)
-* :feature:`0` Change default value of ``shifts`` in :func:`abipy.abio.factories.g0w0_with_ppmodel_inputs`.
-* :feature:`0` Add interface with phononwebsite_: `abiview.py phbands out_PHBST.nc -web`.
-* :feature:`0` Add robots for comparing/analyzing multiple files of the same type (|DdbRobot|, |GsrRobot| ...)
-  Some of the robot capabilities are exposed via the :ref:`abicomp.py` and the :ref:`abirun.py` scripts.
-* :feature:`0` Add several new options to :ref:`abirun.py`, :ref:`abicomp.py` and :ref:`abistruct.py` scripts.
-* :support:`0` Significant improvements to the documentation and the website: add :ref:`plot-gallery` with matplotlib plots
-  and :ref:`flow-gallery` with AbiPy flows are now automatically generated.
-* :feature:`0`: Add Shankland-Koelling-Wood Fourier interpolation scheme.
-  For the theoretical background see :cite:`Euwema1969,Koelling1986,Pickett1988,Madsen2006`.
-* :release:`0.2.0 <2017-03-10>`
-* :feature:`0` This is the first official release in which we have reached a relatively stable API
-  and a well-defined interface with the netcdf files produced by Abinit.
-  We recommend Abinit >= 8.0.8b, version 8.2.2 is required to analyze the electronic fatbands
-  saved in the FATBANDS.nc_ file.
+Release 0.8.0: xxxx-xx-xx
+
+    * Add abicheck.py --create-config option to install predefined yaml configuration files
+    * Add support for NSCF calculations with meta-GGA.
+    * Preliminary support for panel dashboards exposed via `abiopen FILE --panel` and `abistruct panel FILE`.
+      Note that not all Abinit files are supported at present.
+    * Add examples and flows for effective mass calculations
+    * Add examples for quasi-harmonic calculations and post-processing tools
+    * Add support for JSON files (including MSONable format) to abiopen.py
+      Supports `--notebook`, `--panel` options such as `abiopen.py FILE.json --panel`
+    * Improved support for EPH calculations.
+    * Add `primitive` command to `abistruct.py` to get primitive structure from spglib
+
+Release 0.7.0: 2019-10-18
+
+    * Remove support for py2. Now Abipy requires py >= 3.6 (3.8 is not yet supported)
+    * AbiPy now requires pymatgen >= 2019.10.16
+    * Move workflow code from pymatgen to abipy.flowtk
+    * Improved support for EPH calculations.
+
+Release:0.3.0 2017-12-26
+
+    * Add ``abiview.py`` script for a quick visualization of results.
+    * ``abicheck.py`` accepts ``-with-flow`` option
+    * Add AbinitInput.set_spell_check to activate/deactivate spell-checker
+    * Improve coverage
+    * Fix bug in in ``SigresFile.get_dataframe`` if QP states do not start with the same band index.
+    * Fix bug in thermodinamical properties (zero-point energy was included twice)
+    * Add ``mpirunner_options`` and ``shell_runner_options`` to TaskManager.
+    * Autodetect presence in DdbFile of data required for the LO-TO splitting.
+    * Solve problem with visualize in jupyter notebooks (files should be produced in workdir)
+    * Change default value of ``shifts`` in ``abipy.abio.factories.g0w0_with_ppmodel_inputs``.
+    * Add interface with phononwebsite: ``abiview.py phbands out_PHBST.nc -web``.
+    * Add robots for comparing/analyzing multiple files of the same type (``DdbRobot``, ``GsrRobot`` ...)
+      Some of the robot capabilities are exposed via the ``abicomp.py`` and the ``abirun.py`` scripts.
+    * Add several new options to ``abirun.py``, ``abicomp.py`` and ``abistruct.py`` scripts.
+    * Significant improvements to the documentation and the website: add ``plot-gallery`` with matplotlib plots
+      and ``flow-gallery`` with AbiPy flows are now automatically generated.
+    * Add Shankland-Koelling-Wood Fourier interpolation scheme.
+
+Release 0.2.0 <2017-03-10>
+
+    This is the first official release in which we have reached a relatively stable API
+    and a well-defined interface with the netcdf files produced by Abinit.
+    We recommend Abinit >= 8.0.8b, version 8.2.2 is required to analyze the electronic fatbands
+    saved in the FATBANDS.nc file.