Merge f41e940 into 11c8b9d

.gitignore

@@ -11,3 +11,5 @@ build/
 dist/
 .idea/
 .cache/
+.vscode/
+test-results.xml

.travis-data/install_aiida_github.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+git clone https://github.com/aiidateam/aiida_core
+cd aiida_core
+git checkout $AIIDA_DEVELOP_GIT_HASH 
+pip install -e .[docs,pre-commit,testing]
+cd ..

.travis-data/network

@@ -0,0 +1,4 @@
+#!/bin/bash
+# piping through to singularity
+set -e
+singularity exec ${TRAVIS_BUILD_DIR}/ltalirz-singularity-recipe-zeopp-master-ansible.simg /usr/local/bin/network "$@"

.travis.singularity_key.txt

@@ -0,0 +1,70 @@
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+-----END PGP PUBLIC KEY BLOCK-----

.travis.yml

@@ -1,33 +1,43 @@
 language: python
 python:
-- "2.7"
-
-cache: pip
-
-git:
-  depth: 3
+- "3.6"
 
 services:
-- postgresql
+  - postgresql
+  - rabbitmq
 
 addons:
-  postgresql: "9.5"
+  postgresql: "10"
 
 before_install:
-# Upgrade pip setuptools and wheel
-- pip install -U pip wheel setuptools
+  # Upgrade pip setuptools and wheel
+  - pip install -U wheel setuptools coveralls
+  - pip install pip==18.1
+  # install singularity
+  - wget -O- http://neuro.debian.net/lists/trusty.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
+  - sudo apt-key add .travis.singularity_key.txt
+  - sudo apt-get update
+  - sudo apt-get install -y singularity-container
+  - singularity pull shub://ltalirz/singularity-recipe-zeopp:ansible
 
 install:
 - pip install -e .[testing,pre-commit]
+- if [ "$AIIDA_VERSION" == "develop" ]; then .travis-data/install_aiida_github.sh ; fi  # installs develop branch
 - reentry scan -r aiida
-- pip install coveralls
 # add fake network executable
-- cat "#!/bin/bash\necho 'network'" > network; chmod +x network
+#- cat "#!/bin/bash\necho 'network'" > network; chmod +x network
+#- echo -e '#!/bin/bash\nset -e\nsingularity exec ./ltalirz-singularity-recipe-zeopp-master-ansible.simg /usr/local/bin/network "$@"' > network; chmod +x network
 
 env:
   global:
+  - PLUGIN_DIR: aiida-diff
+  - TEST_AIIDA_BACKEND: django
+  - AIIDA_VERSION: develop
+  - AIIDA_DEVELOP_GIT_HASH: e852d66fc51345fbdb8ebf98580a5646d79bc043
   # add network executable to PATH
-  - PATH=${PATH}:${TRAVIS_BUILD_DIR}
+  #- PATH=${PATH}:${TRAVIS_BUILD_DIR}
+  # use 'network' script from .travis-data
+  - PATH=${PATH}:${TRAVIS_BUILD_DIR}/.travis-data
   matrix:
   - TEST_AIIDA_BACKEND: django
     TEST_TYPE: tests
@@ -45,11 +55,33 @@ env:
     TEST_TYPE: pre-commit
 
 script:
-- if [ "$TEST_TYPE" == "tests" ] ; then coverage run --source=aiida_zeopp --append manage.py; fi  # runs unit tests
-# - if [ "$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_zeopp --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
 
 after_success:
-- coveralls
+  - coveralls
 
+jobs:
+    include:
+        - stage: deploy
+          # Make sure the tag is valid semver
+          if: "branch = master AND tag =~ ^v[0-9]+\\.[0-9]+\\.[0-9]+(a|b|rc)?[0-9]*$"
+          addons: skip
+          python: 3.6
+          before_install: skip
+          install: skip
+          before_script: skip
+          script: skip
+          env: ignore
+          after_deploy:
+            - echo "Deployed $TRAVIS_TAG to PyPI"
+          deploy: &pypi
+              provider: pypi
+              skip_existing: true
+              username: aiida-bot
+              password:
+                  # See https://docs.travis-ci.com/user/encryption-keys/ for instructions
+                  secure: "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"
+              on:
+                  repo: ltalirz/aiida-zeopp
+                  tags: true

README.md

@@ -10,9 +10,7 @@ AiiDA plugin for [Zeo++](http://www.zeoplusplus.org/)
 ## Installation
 
 ```shell
-git clone https://github.com/ltalirz/aiida-zeopp aiida-zeopp
-cd aiida-zeopp
-pip install -e .  # also installs aiida, if missing (but not postgres)
+pip install aiida-zeopp
 reentry scan
 verdi quicksetup  # better to set up a new profile
 verdi calculation plugins  # should now show your calclulation plugins
@@ -29,7 +27,7 @@ verdi calculation plugins  # should now show your calclulation plugins
   ```python
   d = { 'sa': [1.82, 1.82, 1000], 'volpo': [1.82, 1.82, 1000], 'chan': 1.2 }
   NetworkParameters = DataFactory('zeopp.parameters')
-  calc.use_parameters(NetworkParameters(dict=d))
+  inputs['parameters'] = NetworkParameters(dict=d)
   ```
  * `NetworkParameters` validates the command line options using [voluptuous](https://github.com/alecthomas/voluptuous).
    Find out about supported options:
@@ -40,7 +38,7 @@ verdi calculation plugins  # should now show your calclulation plugins
  * Add alternative atomic radii file
   ```python
   SinglefileData = DataFactory('singlefile')
-  calc.use_atomic_radii(SinglefileData(file='/path/to/file'))
+  inputs['atomic_radii'] = SinglefileData(file='/path/to/file')
   ```
 
 ## Examples
@@ -50,8 +48,7 @@ See `examples` folder for complete examples of setting up a calculation or workf
 ```shell
 verdi daemon start         # make sure the daemon is running
 cd examples
-verdi run submit.py        # submit test calculation
-verdi calculation list -a  # check status of calculation
+verdi run submit.py        # runs test calculation
 ```
 
 ## Tests
@@ -61,13 +58,13 @@ verdi calculation list -a  # check status of calculation
 The following will discover and run all unit tests:
 ```shell
 pip install -e .[testing]
-python manage.py
+pytest
 ```
 
 ## Analyzing output
 
 ```shell
-$ verdi calculation show 88
+$ verdi process show 88
 -----------  ------------------------------------------------------------------------------
 type         NetworkCalculation
 pk           88
@@ -92,7 +89,7 @@ retrieved            90  FolderData
 structure_cssr       91  SinglefileData
 output_parameters    92  ParameterData
 
-$ verdi calculation res 88
+$ verdi calcjob res 88
 {
   "ASA_A^2": 3532.09,
   "ASA_m^2/cm^3": 1932.13,
@@ -141,15 +138,15 @@ $ verdi calculation res 88
   "Unitcell_volume": 18280.8
 }
 
-$ verdi calculation outputls 88
+$ verdi calcjob outputls 88
 _scheduler-stderr.txt
 _scheduler-stdout.txt
 out.chan
 out.cssr
 out.sa
 out.volpo
 
-$ verdi calculation outputcat 88 -p out.sa
+$ verdi calcjob outputcat 88 -p out.sa
 @ out.sa Unitcell_volume: 18280.8   Density: 0.879097   ASA_A^2: 3532.09 ASA_m^2/cm^3: 1932.13 ASA_m^2/g: 2197.86 NASA_A^2: 0 NASA_m^2/cm^3: 0 NASA_m^2/g: 0
 Number_of_channels: 1 Channel_surface_area_A^2: 3532.09
 Number_of_pockets: 0 Pocket_surface_area_A^2:

aiida_zeopp/__init__.py

@@ -3,4 +3,10 @@
 
 """
 
-__version__ = "0.2.0"
+from __future__ import absolute_import
+__version__ = "1.0.0a1"
+
+# disable psycopg2 warning
+import warnings
+warnings.filterwarnings("ignore", category=UserWarning, module='psycopg2')
+warnings.filterwarnings("ignore", category=UserWarning, module='pymatgen')