Merge pull request #7 from ltalirz/release_v1.0.0a1

Release v1.0.0a1

.gitignore

@@ -9,3 +9,5 @@
 .coverage
 dist/
 build/
+.vscode
+.pytest_cache/

.travis-data/install_aiida_github.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+# don't want aiida-core to mess with folders in the repo
+git clone https://github.com/aiidateam/aiida_core ../aiida_core
+cd ../aiida_core
+git checkout $AIIDA_DEVELOP_GIT_HASH
+pip install -e .[docs,pre-commit,testing]
+cd ${TRAVIS_BUILD_DIR}

.travis.yml

@@ -1,31 +1,23 @@
 language: python
 python:
+- "3.6"
 - "2.7"
 
-cache: pip
-
 services:
-- postgresql
+  - postgresql
+  - rabbitmq
 
 addons:
-  postgresql: "9.5"
-
-before_install:
-# Upgrade pip setuptools and wheel
-- pip install -U pip wheel setuptools
-
-install:
-- pip install -e .[testing,docs,pre-commit]
-- reentry scan -r aiida
-- pip install coveralls
-# add fake eqeq & egulp executables
-- cat "#!/bin/bash\necho 'eqeq'" > eqeq; chmod +x eqeq
-- cat "#!/bin/bash\necho 'egulp'" > egulp; chmod +x egulp
+  postgresql: "10"
 
 env:
   global:
-  # add eqeq executable to PATH
-  - PATH=${PATH}:${TRAVIS_BUILD_DIR}
+  - AIIDA_VERSION: develop
+  - AIIDA_DEVELOP_GIT_HASH: 409a90d7c8ac8f26792c0f0fbc1f8567f2feb89a
+  # add network executable to PATH
+  #- PATH=${PATH}:${TRAVIS_BUILD_DIR}
+  # add fake executables to path
+  - PATH: "${PATH}:${TRAVIS_BUILD_DIR}/.travis-data"
   matrix:
   - TEST_AIIDA_BACKEND: django
     TEST_TYPE: tests
@@ -36,17 +28,63 @@ env:
     READTHEDOCS: 'True'
   - TEST_AIIDA_BACKEND: django
     TEST_TYPE: pre-commit
-    
+
   # Remove this to enforce the AiiDA coding style
   allow_failures: 
   - TEST_AIIDA_BACKEND: django
     TEST_TYPE: pre-commit
 
+before_install:
+  # Upgrade pip setuptools and wheel
+  - pip install -U wheel setuptools coveralls
+  - pip install pip==18.1
+  # add fake eqeq & egulp executables
+  - cat "#!/bin/bash\necho 'eqeq'" > eqeq; chmod +x eqeq
+  - cat "#!/bin/bash\necho 'egulp'" > egulp; chmod +x egulp
+
+install:
+  - if [ "$AIIDA_VERSION" == "develop" ]; then .travis-data/install_aiida_github.sh ; fi  # installs develop branch
+  - pip install -e .[testing,pre-commit]
+  - reentry scan -r aiida
+
 script:
-- if [ "$TEST_TYPE" == "tests" ] ; then coverage run --append manage.py; fi  # runs unit tests
-- if [ "$TEST_TYPE" == "docs" ] ; then cd docs; make; fi  # creates documentation
-# runs precommit checks but doesn't fail if they don't pass
-- if [ "$TEST_TYPE" == "pre-commit" ] ; then pre-commit install; pre-commit run --all-files || ( git status --short; git diff ; exit 1 ); fi
+  - if [ "$TEST_TYPE" == "tests" ] ; then py.test --cov aiida_qeq --cov-append . ; fi  # runs unit tests
+  - if [ "$TEST_TYPE" == "pre-commit" ] ; then pre-commit install; pre-commit run --all-files || ( git status --short; git diff ; exit 1 ); fi
+  - if [ "$TEST_TYPE" == "docs" ] ; then cd docs; make; fi  # creates documentation
 
 after_success:
-- coveralls
+  - coveralls
+
+jobs:
+  include:
+    - stage: deploy
+      # Make sure the tag is valid semver
+      if: "tag =~ ^v[0-9]+\\.[0-9]+\\.[0-9]+(a|b|rc)?[0-9]*$"
+      services: ignore
+      addons: skip
+      python: 3.6
+      before_install: skip
+      install: skip
+      before_script: skip
+      script: skip
+      env: ignore
+      before_deploy:
+        - echo "About to deploy $TRAVIS_TAG to PyPI"
+      after_deploy:
+        - echo "Deployed $TRAVIS_TAG to PyPI"
+      deploy: &pypi
+        provider: pypi
+        skip_existing: true
+        username: aiida-bot
+        password:
+          # Instructions:
+          # - create deploy bot account on PyPI
+          # - add bot account to your PyPI project
+          # - Install travis cli tool, see https://docs.travis-ci.com/user/encryption-keys/
+          # - cd to your git repository; travis login --org
+          # - travis encrypt <pw of bot account>
+          secure: "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"
+        on:
+          repo: ltalirz/aiida-qeq
+          branch: master
+          tags: true

README.md

@@ -1,6 +1,6 @@
-[![Build Status](https://travis-ci.org/ltalirz/aiida-qeq.svg?branch=master)](https://travis-ci.org/ltalirz/aiida-qeq) 
-[![Coverage Status](https://coveralls.io/repos/github/ltalirz/aiida-qeq/badge.svg?branch=master)](https://coveralls.io/github/ltalirz/aiida-qeq?branch=master) 
-[![Docs status](https://readthedocs.org/projects/aiida-qeq/badge)](http://aiida-qeq.readthedocs.io/) 
+[![Build Status](https://travis-ci.org/ltalirz/aiida-qeq.svg?branch=master)](https://travis-ci.org/ltalirz/aiida-qeq)
+[![Coverage Status](https://coveralls.io/repos/github/ltalirz/aiida-qeq/badge.svg?branch=master)](https://coveralls.io/github/ltalirz/aiida-qeq?branch=master)
+[![Docs status](https://readthedocs.org/projects/aiida-qeq/badge)](http://aiida-qeq.readthedocs.io/)
 [![PyPI version](https://badge.fury.io/py/aiida-qeq.svg)](https://badge.fury.io/py/aiida-qeq)
 
 # aiida-qeq
@@ -9,14 +9,69 @@ AiiDA plugin for computing electronic charges on atoms using equilibration-type
 
 Templated using the [AiiDA plugin cutter](https://github.com/aiidateam/aiida-plugin-cutter).
 
+## Features
+
+### QeQ charges
+ * Add input structure in CIF format
+  ```python
+  CifData = DataFactory('cif')
+  inputs['structure'] = CifData(file='/path/to/file')
+  ```
+
+ * Add parameters for electronegativity and Idempotential data of the elements.
+  ```python
+  SinglefileData = DataFactory('singlefile')
+  inputs['parameters'] = SinglefileData(file='/path/to/file')
+  ```
+
+ * (optional) Specify `configure.input` options using a python dictionary and `QeqParameters`
+  ```python
+  QeqParameters = DataFactory('qeq.qeq')
+  inputs['configure'] = QeqParameters(dict={'save_grid': [True, 'grid.cube']})
+  ```
+
+ * `QeqParameters` validates the command line options using [voluptuous](https://github.com/alecthomas/voluptuous).
+  ```python
+  QeqParameters = DataFactory('qeq.qeq')
+  print(QeqParameters.schema)  # shows supported options
+  ```
+
+### EQeQ charges
+ * Add input structure in CIF format
+  ```python
+  CifData = DataFactory('cif')
+  inputs['structure'] = CifData(file='/path/to/file')
+  ```
+
+ * Add parameters for ionization data of the elements.
+  ```python
+  SinglefileData = DataFactory('singlefile')
+  inputs['ionization_data'] = SinglefileData(file='/path/to/file')
+  ```
+
+ * Add parameters for common oxidation states of the elements.
+  ```python
+  SinglefileData = DataFactory('singlefile')
+  inputs['charge_data'] = SinglefileData(file='/path/to/file')
+  ```
+
+ * Specify command line options using a python dictionary and `EQeqParameters`
+  ```python
+  EQeqParameters = DataFactory('qeq.eqeq')
+  inputs['parameters'] = EQeqParameters(dict={'method': 'ewald'})
+  ```
+
+ * `EQeqParameters` validates the command line options using [voluptuous](https://github.com/alecthomas/voluptuous).
+  ```python
+  QeqParameters = DataFactory('qeq.eqeq')
+  print(EQeqParameters.schema)  # show supported options
+  ```
+
 ## Installation
 
 ```shell
-git clone https://github.com/ltalirz/aiida-qeq .
-cd aiida-qeq
-pip install -e .  # also installs aiida, if missing (but not postgres)
-#pip install -e .[pre-commit,testing] # install extras for more features
-verdi quicksetup  # better to set up a new profile
+pip install aiida-qeq
+verdi quicksetup  # set up a new profile
 verdi calculation plugins  # should now show your calclulation plugins
 ```
 
@@ -30,15 +85,17 @@ verdi daemon start         # make sure the daemon is running
 cd examples
 verdi run submit_qeq.py    # submit qeq test calculation
 verdi run submit_eqeq.py   # submit eqeq test calculation
-verdi calculation list -a  # check status of calculation
+verdi process list -a  # check status of calculation
 ```
 
-## Tests
+## Development
 
-The following will discover and run all unit test:
 ```shell
-pip install -e .[testing]
-python manage.py
+git clone https://github.com/ltalirz/aiida-qeq .
+cd aiida-qeq
+pip install -e .[pre-commit,testing]
+pre-commit install  # enable pre-commit hooks
+pytest              # run unit tests
 ```
 
 ## License
@@ -49,4 +106,3 @@ MIT
 ## Contact
 
 leopold.talirz@gmail.com
-

aiida_qeq/__init__.py

@@ -4,4 +4,4 @@
 AiiDA plugin for computing electronic charges on atoms using equilibration-type models (QEq, EQEq, ...).
 """
 
-__version__ = "0.1.0"
+__version__ = "1.0.0a1"