move to pytest

* move to pytest for testing * add automatic deploy configuration to travis.yml * update README
lsmo-epfl · Apr 2, 2019 · b50fcb4 · b50fcb4
1 parent 2b148af
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diff --git a/.travis.yml b/.travis.yml
@@ -36,7 +36,7 @@ env:
   - PLUGIN_DIR: aiida-diff
   - TEST_AIIDA_BACKEND: django
   - AIIDA_VERSION: develop
-  - AIIDA_DEVELOP_GIT_HASH: 0ca5d991d039dca2261df3d6ad8da2f03d591caa
+  - AIIDA_DEVELOP_GIT_HASH: e852d66fc51345fbdb8ebf98580a5646d79bc043
   # add network executable to PATH
   #- PATH=${PATH}:${TRAVIS_BUILD_DIR}
   # use 'network' script from .travis-data
@@ -63,3 +63,28 @@ script:
 
 after_success:
   - 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
diff --git a/README.md b/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:

diff --git a/aiida_zeopp/calculations/network.py b/aiida_zeopp/calculations/network.py
@@ -2,6 +2,7 @@
 from aiida.engine import CalcJob
 from aiida.common import (CalcInfo, CodeInfo)
 from aiida.plugins import DataFactory
+from aiida.orm import Data
 import six
 
 NetworkParameters = DataFactory('zeopp.parameters')
@@ -51,6 +52,8 @@ def define(cls, spec):
             'Empty block file. This indicates the calculation of blocked pockets did not finish.'
         )
 
+        spec.outputs.dynamic = True
+        spec.outputs.valid_type = Data
         spec.output(
             'output_parameters',
             valid_type=Dict,

diff --git a/aiida_zeopp/calculations/test_network.py b/aiida_zeopp/calculations/test_network.py
@@ -4,112 +4,88 @@
 from __future__ import absolute_import
 import os
 import io
-
-import aiida_zeopp.tests as zt
-
-
-class TestNetwork(zt.PluginTestCase):
-    def setUp(self):
-        self.code = zt.get_code(entry_point='zeopp.network')
-
-    def test_submit_HKUST1(self):
-        """Test submitting a calculation"""
-        from aiida_zeopp.tests import TEST_DIR
-        from aiida_zeopp.calculations.network import NetworkCalculation
-        from aiida.engine import run_get_node
-
-        # Prepare input parameters
-        from aiida.plugins import DataFactory
-        NetworkParameters = DataFactory('zeopp.parameters')
-        parameters = NetworkParameters(dict={'cssr': True})
-
-        CifData = DataFactory('cif')
-        structure = CifData(
-            file=os.path.join(TEST_DIR, 'HKUST-1.cif'), parse_policy='lazy')
-
-        # set up calculation
-        options = {
-            "resources": {
-                "num_machines": 1,
-                "num_mpiprocs_per_machine": 1,
-            },
-            "max_wallclock_seconds": 3 * 60,
-        }
-
-        inputs = {
-            'code': self.code,
-            'parameters': parameters,
-            'structure': structure,
-            'metadata': {
-                'options': options,
-                'label': "aiida_zeopp format conversion",
-                'description': "Test converting .cif to .cssr format",
-            },
-        }
-
-        _result, node = run_get_node(NetworkCalculation, **inputs)
-
-        cssr = io.open(
-            os.path.join(TEST_DIR, 'HKUST-1.cssr'), 'r',
-            encoding='utf8').read()
-        self.assertEqual(cssr, node.outputs.structure_cssr.get_content())
-
-    def test_submit_MgO(self):
-        """Test submitting a calculation
-
-        This includes a radii file.
-        """
-        from aiida_zeopp.tests import TEST_DIR
-        from aiida_zeopp.calculations.network import NetworkCalculation
-        from aiida.engine import run_get_node
-        from aiida.plugins import DataFactory
-
-        # Prepare input parameters
-        parameters = DataFactory('zeopp.parameters')(
-            dict={
-                'cssr': True,
-                'res': True,
-                'sa': [1.82, 1.82, 5000],
-                'vsa': [1.82, 1.82, 5000],
-                'volpo': [1.82, 1.82, 5000],
-                'chan': 1.2,
-                'ha': False,
-                'strinfo': True,
-                #    'gridG': True,
-            })
-
-        structure = DataFactory('cif')(
-            file=os.path.join(TEST_DIR, 'MgO.cif'), parse_policy='lazy')
-
-        atomic_radii = DataFactory('singlefile')(
-            file=os.path.join(TEST_DIR, 'MgO.rad'))
-
-        # set up calculation
-        options = {
-            "resources": {
-                "num_machines": 1,
-                "num_mpiprocs_per_machine": 1,
-            },
-            "max_wallclock_seconds": 30,
-        }
-
-        inputs = {
-            'code': self.code,
-            'parameters': parameters,
-            'structure': structure,
-            'atomic_radii': atomic_radii,
-            'metadata': {
-                'options': options,
-                'label': "aiida_zeopp format conversion",
-                'description': "Test converting .cif to .cssr format",
-            },
-        }
-
-        _result, node = run_get_node(NetworkCalculation, **inputs)
-
-        self.assertAlmostEqual(
-            node.outputs.output_parameters.get_attribute('Density'),
-            3.18223,
-            places=4)
-        self.assertEqual(
-            node.outputs.output_parameters.get_attribute('ASA_m^2/g'), 0.0)
+import pytest
+
+
+def test_submit_HKUST1(clear_database, network_code, basic_options):  # pylint: disable=unused-argument
+    """Test submitting a calculation"""
+    from aiida_zeopp.tests import TEST_DIR
+    from aiida_zeopp.calculations.network import NetworkCalculation
+    from aiida.engine import run_get_node
+
+    # Prepare input parameters
+    from aiida.plugins import DataFactory
+    NetworkParameters = DataFactory('zeopp.parameters')
+    parameters = NetworkParameters(dict={'cssr': True})
+
+    CifData = DataFactory('cif')
+    structure = CifData(
+        file=os.path.join(TEST_DIR, 'HKUST-1.cif'), parse_policy='lazy')
+
+    inputs = {
+        'code': network_code,
+        'parameters': parameters,
+        'structure': structure,
+        'metadata': {
+            'options': basic_options,
+            'label': "aiida_zeopp format conversion",
+            'description': "Test converting .cif to .cssr format",
+        },
+    }
+
+    _result, node = run_get_node(NetworkCalculation, **inputs)
+
+    cssr = io.open(
+        os.path.join(TEST_DIR, 'HKUST-1.cssr'), 'r', encoding='utf8').read()
+    assert (cssr == node.outputs.structure_cssr.get_content())
+
+
+def test_submit_MgO(clear_database, network_code, basic_options):  # pylint: disable=unused-argument
+    """Test submitting a calculation
+
+    This includes a radii file.
+    """
+    from aiida_zeopp.tests import TEST_DIR
+    from aiida_zeopp.calculations.network import NetworkCalculation
+    from aiida.engine import run_get_node
+    from aiida.plugins import DataFactory
+
+    # Prepare input parameters
+    parameters = DataFactory('zeopp.parameters')(
+        dict={
+            'cssr': True,
+            'res': True,
+            'sa': [1.82, 1.82, 5000],
+            'vsa': [1.82, 1.82, 5000],
+            'volpo': [1.82, 1.82, 5000],
+            'chan': 1.2,
+            'ha': False,
+            'strinfo': True,
+            # 'gridG': True,
+        })
+
+    structure = DataFactory('cif')(
+        file=os.path.join(TEST_DIR, 'MgO.cif'), parse_policy='lazy')
+
+    atomic_radii = DataFactory('singlefile')(
+        file=os.path.join(TEST_DIR, 'MgO.rad'))
+
+    # set up calculation
+    inputs = {
+        'code': network_code,
+        'parameters': parameters,
+        'structure': structure,
+        'atomic_radii': atomic_radii,
+        'metadata': {
+            'options': basic_options,
+            'label': "aiida_zeopp format conversion",
+            'description': "Test converting .cif to .cssr format",
+        },
+    }
+
+    _result, node = run_get_node(NetworkCalculation, **inputs)
+
+    assert pytest.approx(
+        node.outputs.output_parameters.get_attribute('Density'),
+        0.01) == 3.18223
+    assert node.outputs.output_parameters.get_attribute('ASA_m^2/g') == 0.0