Merge pull request #91 from aiidateam/release_1.0.0

Prepare release 1.0.0

.docker/my_init.d/add-codes.sh

@@ -2,3 +2,6 @@
 set -em
 
 su -c /opt/add-codes.sh aiida
+
+# Make /opt/aiida-cp2k folder editable for the $SYSTEM_USER.
+chown -R aiida:aiida /opt/aiida-cp2k/

.docker/opt/add-codes.sh

@@ -6,7 +6,4 @@ set -x
 # Environment
 export SHELL=/bin/bash
 
-# Install the ddec and cp2k codes
-CP2K_FOLDER=/home/aiida/code/aiida-cp2k
-
-verdi code show cp2k@localhost || verdi code setup --config ${CP2K_FOLDER}/.docker/cp2k-code.yml --non-interactive
+verdi code show cp2k@localhost || verdi code setup --config /opt/aiida-cp2k/.docker/cp2k-code.yml --non-interactive

.readthedocs.yml

@@ -0,0 +1,7 @@
+build:
+  image: latest
+python:
+  version: 3.6
+  pip_install: true
+  extra_requirements:
+  - "docs"

.travis.yml

@@ -4,20 +4,22 @@ services:
   - docker
 
 before_install:
-  - pip install --user coveralls
   - python .ci/check_travis_tag.py
   - docker build -t aiida_cp2k_test .
-  - docker run -d aiida_cp2k_test
+  - export DOCKERID=`docker run -d aiida_cp2k_test`
   - sleep 30 # wait until the container is launched
 
 script:
-  - "export DOCKERID=`docker ps -qf 'ancestor=aiida_cp2k_test'`"
   - "echo \"Docker ID: $DOCKERID\""
-  - "docker exec -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-cp2k/ && pre-commit run --all-files || ( git status --short ; git diff ; exit 1 ) '"
-  - "docker exec -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'"
+  - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )'
+  - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && py.test --cov aiida_cp2k --cov-append .'
+  - docker exec -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/docs && make'
 
 after_success:
-  - "docker exec -e TRAVIS=\"$TRAVIS\" -e TRAVIS_JOB_ID=\"$TRAVIS_JOB_ID\" -e TRAVIS_BRANCH=\"$TRAVIS_BRANCH\" -it --user aiida \"$DOCKERID\" /bin/bash -l -c 'cd code/aiida-cp2k/ && coveralls'"
+  - docker exec -e TRAVIS=$TRAVIS -e TRAVIS_JOB_ID=$TRAVIS_JOB_ID -e TRAVIS_BRANCH=$TRAVIS_BRANCH -it --user aiida $DOCKERID /bin/bash -l -c 'cd /opt/aiida-cp2k/ && coveralls'
+
+after_script:
+  - docker logs $DOCKERID
 
 git:
   depth: 3

Dockerfile

@@ -7,38 +7,27 @@
 
 FROM aiidateam/aiida-docker-stack
 
-# Install cp2k
-RUN apt-get update && apt-get install -y --no-install-recommends  \
-    cp2k
-
-# Set HOME variable:
+# Set HOME and PATH variables.
 ENV HOME="/home/aiida"
+ENV PATH="${HOME}/.local/bin:${PATH}"
 
-# Install aiida-cp2k
-COPY . ${HOME}/code/aiida-cp2k
-RUN chown -R aiida:aiida ${HOME}/code
+# To prevent the container to exit prematurely.
+ENV KILL_ALL_RPOCESSES_TIMEOUT=50
 
-# Install AiiDA
-USER aiida
-ENV PATH="${HOME}/.local/bin:${PATH}"
+WORKDIR /opt/
 
-# Install aiida-cp2k plugin and coveralls
-WORKDIR ${HOME}/code/aiida-cp2k
-RUN pip install --user .[pre-commit,test]
-RUN pip install --user coveralls
+# Install CP2K.
+RUN apt-get update && apt-get install -y --no-install-recommends cp2k
 
-# Populate reentry cache for aiida user https://pypi.python.org/pypi/reentry/
-RUN reentry scan
+# Install aiida-cp2k plugin.
+COPY . aiida-cp2k
+RUN pip install ./aiida-cp2k[pre-commit,test,docs]
 
-# Install the cp2k code
+# Install coverals.
+RUN pip install coveralls
+
+# Install the cp2k code.
 COPY .docker/opt/add-codes.sh /opt/
 COPY .docker/my_init.d/add-codes.sh /etc/my_init.d/40_add-codes.sh
 
-# Change workdir back to $HOME
-WORKDIR ${HOME}
-
-# Important to end as user root!
-USER root
-
-# Use baseimage-docker's init system.
-CMD ["/sbin/my_init"]
+RUN chown -R aiida:aiida ${HOME}

MANIFEST.in

@@ -1,2 +1 @@
 include setup.json
-include aiida_cp2k/workchains/multistage_protocols/*

README.md

@@ -1,102 +1,38 @@
 [![Build Status](https://travis-ci.org/aiidateam/aiida-cp2k.svg?branch=develop)](https://travis-ci.org/aiidateam/aiida-cp2k)
 [![Coverage Status](https://coveralls.io/repos/github/aiidateam/aiida-cp2k/badge.svg?branch=develop)](https://coveralls.io/github/aiidateam/aiida-cp2k?branch=develop)
 [![PyPI version](https://badge.fury.io/py/aiida-cp2k.svg)](https://badge.fury.io/py/aiida-cp2k)
+[![Documentation Status](https://readthedocs.org/projects/aiida-cp2k/badge/?version=latest)](https://aiida-cp2k.readthedocs.io/en/latest/?badge=latest)
 
 # AiiDA CP2K
-**The CP2K plugin for the AiiDA workflow and provenance engine.**
+[AiiDA](http://www.aiida.net/) plugin for [CP2K](https://www.cp2k.org/).
 
-
-![logo](./aiida-cp2k_logo.png)
-
-# Installation
+## Installation
 
 If you use `pip`, you can install it as: 
 ```
 pip install aiida-cp2k
 ```
 
-
-# Features
-Following the philosophy to _''enable without getting in the way''_, this plugin provides access to all of CP2K's capabilities through a small set of well-tested features:
-
-- A full [CP2K input](https://manual.cp2k.org) has to be provided as a nested Python dictionary ([example](./test/test_dft.py)):
-```
-params = {'FORCE_EVAL': {'METHOD': 'Quickstep', 'DFT': { ... }}}
-calc.use_parameters(ParameterData(dict=params))
-```
-
-- Section parameters are stored as key `_` in the dictionary:
-```
-xc_section = {'XC_FUNCTIONAL': {'_': 'LDA'}}
-```
-
-- Repeated sections are stored as a list:
-```
-kind_section = [{'_': 'H', 'BASIS_SET': 'DZVP-MOLOPT-GTH', 'POTENTIAL': 'GTH-LDA'},
-                {'_': 'O', 'BASIS_SET': 'DZVP-MOLOPT-GTH', 'POTENTIAL': 'GTH-LDA'}]
-```
-
-- Most data files (basis sets, pseudo potentials, VdW, etc.) are auto-discovered from CP2K's [data directory](https://github.com/cp2k/cp2k/tree/master/cp2k/data).
-```
-dft_section = {'BASIS_SET_FILE_NAME': 'BASIS_MOLOPT', ...}
-```
-
-- Additional data files can be added as AiiDA SinglefileData ([example](test/test_mm.py)):
-```
-water_pot = SinglefileData(file="/tmp/water.pot")
-calc.use_file(water_pot, linkname="water_pot")
-```
-
-- The start geometry can be provided as AiiDA StructureData ([example](./test/test_dft.py)):
+To install the plugin in an editable mode, run:
 ```
-atoms = ase.build.molecule('H2O', vacuum=2.0)
-calc.use_structure(StructureData(ase=atoms))
+git clone https://github.com/aiidateam/aiida-cp2k
+cd aiida-cp2k
+pip install -e .  # Also installs aiida, if missing (but not postgres/rabbitmq).
 ```
 
-- Alternatively the start geometry can be contained in the CP2K input ([example](./test/test_no_struct.py)):
-```
-coord_section = {' ': ['H    2.0   2.0   2.737166',
-                       'H    2.0   2.0   2.000000']},
-```
+## Links
+* [Documentation](https://aiida-cp2k.readthedocs.io/en/latest/) for the calculation examples and features of the plugin.
+* [Make an issue](https://github.com/aiidateam/aiida-cp2k/issues/new) for bug reports, questions and suggestions.
+* [AiiDA](http://www.aiida.net/) to learn about AiiDA.
+* [Cp2k](https://www.cp2k.org/) to learn about CP2K.
 
-- For restarting a calculation a parent folder can be attached  ([example](./test/test_restart.py)):
-```
-calc2.use_parent_folder(calc1.out.remote_folder)
-```
 
-- By default only the output and restart file (if present) are retrieved. Additional files are retrieved upon request ([example](test/test_mm.py)):
-```
-settings = {'additional_retrieve_list': ["*.cube"]}
-calc.use_settings(ParameterData(dict=settings))
-```
+## License
+MIT
 
-- The final geometry is extracted from the restart file (if present) and stored in AiiDA ([example](./test/test_geopt.py)):
-```
-print(calc.out.output_structure)
-```
 
-- From the CP2K output only the #warnings and final energy are parsed ([example](./test/test_mm.py)):
-```
-print(calc.res.nwarnings, calc.res.energy, calc.res.energy_units)
-```
-
-- The calculation is considered failed if #warnings can not be found ([example](./test/test_failure.py)).
-
-- The conversion of geometries between AiiDA and CP2K has a precision of at least 1e-10 Ångström ([example](./test/test_precision.py)).
-
-- The Python code complies with the [Flake8](http://flake8.pycqa.org) coding conventions.
-
-
-# Testing
-
-Every commit and pull request is automatically tested by [TravisCI](https://travis-ci.org/cp2k/aiida-cp2k/).
-
-To run the tests locally install [Docker](https://docs.docker.com/engine/installation/) and execute the following commands:
-```
-git clone https://github.com/cp2k/aiida-cp2k
-docker build -t aiida_cp2k_test aiida-cp2k
-docker run -it --init aiida_cp2k_test
-```
+## Contact
+yakutovicha@gmail.com
 
 
 ## Acknowledgements

aiida_cp2k/__init__.py

@@ -7,6 +7,6 @@
 ###############################################################################
 """AiiDA-CP2K plugins, parsers, workflows, etc ..."""
 
-__version__ = "1.0.0b6"
+__version__ = "1.0.0"
 
 # EOF