Merge pull request #36 from lsmo-epfl/release_1.0.0b2

Prepare release 1.0.0b2

.github/workflows/ci.yml

@@ -0,0 +1,85 @@
+name: ci
+
+on: [push, pull_request]
+
+jobs:
+
+  tests:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      matrix:
+        python-version: [3.7]
+        backend: ['django']
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install system dependencies
+      run: |
+        wget -O - "https://github.com/rabbitmq/signing-keys/releases/download/2.0/rabbitmq-release-signing-key.asc" | sudo apt-key add -
+        echo 'deb https://dl.bintray.com/rabbitmq-erlang/debian bionic erlang' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
+        echo 'deb https://dl.bintray.com/rabbitmq/debian bionic main' | sudo tee -a /etc/apt/sources.list.d/bintray.rabbitmq.list
+        sudo rm -f /etc/apt/sources.list.d/dotnetdev.list /etc/apt/sources.list.d/microsoft-prod.list
+        sudo apt update
+        sudo apt install postgresql-10 rabbitmq-server graphviz
+        sudo systemctl status rabbitmq-server.service
+
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[testing]
+        reentry scan -r aiida
+
+    - name: Run test suite
+      env:
+        AIIDA_TEST_BACKEND: ${{ matrix.backend }}
+        PYTEST_ADDOPTS: "--cov-report xml --cov-append"
+      run: py.test tests
+
+    - name: Upload coverage report
+      if: github.repository == 'lsmo-epfl/aiida-lsmo'
+      uses: codecov/codecov-action@v1
+      with:
+        name: aiida-lsmo
+        file: ./coverage.xml
+        fail_ci_if_error: true
+
+  docs:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[docs]
+        reentry scan -r aiida
+    - name: Build docs
+      run: cd docs && make
+
+  pre-commit:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v1
+      with:
+        python-version: 3.7
+    - name: Install python dependencies
+      run: |
+        pip install --upgrade pip
+        pip install -e .[pre-commit,docs,testing]
+        reentry scan -r aiida
+    - name: Run pre-commit
+      run: |
+        pre-commit install
+        pre-commit run --all-files || ( git status --short ; git diff ; exit 1 )

MANIFEST.in

@@ -0,0 +1,4 @@
+include setup.json
+include aiida_lsmo/calcfunctions/*.yaml
+include aiida_lsmo/workchains/isotherm_data/*
+include aiida_lsmo/workchains/cp2k_multistage_protocols/*.yaml

README.md

@@ -5,4 +5,4 @@
 
 AiiDA workflows designed by the LSMO group at EPFL.
 
-The documentation can be found at https://aiida-lsmo.readthedocs.io/en/latest/
+The documentation can be found at https://aiida-lsmo.readthedocs.io/en/latest/ .

aiida_lsmo/__init__.py

@@ -4,4 +4,4 @@
 AiiDA workflows for the LSMO laboratory at EPFL
 """
 
-__version__ = "1.0.0b1"
+__version__ = "1.0.0b2"

aiida_lsmo/utils/other_utilities.py

@@ -1,5 +1,7 @@
 """Other utilities"""
 
+import collections
+import ase
 from aiida.orm import Dict, CifData, StructureData
 from aiida.engine import calcfunction
 
@@ -14,7 +16,6 @@ def dict_merge(dct, merge_dct):
     :param merge_dct: dct merged into dct
     :return: None
     """
-    import collections
     for k in merge_dct.keys():
         if (k in dct and isinstance(dct[k], dict) and isinstance(merge_dct[k], collections.Mapping)):
             dict_merge(dct[k], merge_dct[k])
@@ -35,14 +36,25 @@ def aiida_dict_merge(to_dict, from_dict):
     return Dict(dict=to_dict)
 
 
+def ase_cells_are_similar(ase_a, ase_b, thr=2):
+    """Return True if the cell of two ASE objects are similar up to "thr" decimals.
+    This avoids to give error if two Cells are different at a nth decimal number, tipically because of some truncation.
+    """
+    comp_similar = []
+    for cell_a, cell_b in zip(ase_a.cell, ase_b.cell):
+        comp_similar.append(round(cell_a, thr) == round(cell_b, thr))
+    return all(comp_similar)
+
+
 @calcfunction
 def aiida_cif_merge(aiida_cif_a, aiida_cif_b):
     """Merge the coordinates of two CifData into a sigle one. Note: the two unit cells must be the same."""
-    import ase
+
     ase_a = aiida_cif_a.get_ase()
     ase_b = aiida_cif_b.get_ase()
-    if not (ase_a.cell == ase_b.cell).all():
-        raise ValueError('Attempting to merge two CifData with different unit cells.')
+    if not ase_cells_are_similar(ase_a, ase_b.cell):
+        raise ValueError('Attempting to merge two CifData (<{}> and <{}>) with different unit cells.'.format(
+            aiida_cif_a.pk, aiida_cif_b.pk))
     ase_ab = ase.Atoms(  #Maybe there is a more direct way...
         symbols=list(ase_a.symbols) + list(ase_b.symbols),
         cell=ase_a.cell,
@@ -57,10 +69,9 @@ def aiida_cif_merge(aiida_cif_a, aiida_cif_b):
 @calcfunction
 def aiida_structure_merge(aiida_structure_a, aiida_structure_b):
     """Merge the coordinates of two StructureData into a sigle one. Note: the two unit cells must be the same."""
-    import ase
     ase_a = aiida_structure_a.get_ase()
     ase_b = aiida_structure_b.get_ase()
-    if not (ase_a.cell == ase_b.cell).all():
+    if not ase_cells_are_similar(ase_a, ase_b.cell):
         raise ValueError('Attempting to merge two StructureData with different unit cells.')
     ase_ab = ase.Atoms(  #Maybe there is a more direct way...
         symbols=list(ase_a.symbols) + list(ase_b.symbols),

aiida_lsmo/workchains/cp2k_binding_energy.py

@@ -66,11 +66,11 @@ def define(cls, spec):
                    valid_type=Str,
                    default=lambda: Str('standard'),
                    required=False,
-                   help='The tag of the protocol to be read from {tag}.yaml unless protocol_yaml input is specified')
+                   help='The tag of the protocol tag.yaml. NOTE: only the settings are read, stage is set to GEO_OPT.')
         spec.input('protocol_yaml',
                    valid_type=SinglefileData,
                    required=False,
-                   help='Specify a custom yaml file with the multistage settings (and ignore protocol_tag)')
+                   help='Specify a custom yaml file. NOTE: only the settings are read, stage is set to GEO_OPT.')
         spec.input('protocol_modify',
                    valid_type=Dict,
                    default=lambda: Dict(dict={}),

aiida_lsmo/workchains/sim_annealing.py

@@ -1,7 +1,8 @@
 """Isotherm workchain"""
 
 import os
-
+import ruamel.yaml as yaml
+import ase
 from aiida.plugins import CalculationFactory, DataFactory, WorkflowFactory
 from aiida.orm import Dict, Str
 from aiida.engine import calcfunction
@@ -35,7 +36,6 @@
 @calcfunction
 def get_molecule_dict(molecule_name):
     """Get a Dict from the isotherm_molecules.yaml"""
-    import ruamel.yaml as yaml
     thisdir = os.path.dirname(os.path.abspath(__file__))
     yamlfile = os.path.join(thisdir, "isotherm_data", "isotherm_molecules.yaml")
     with open(yamlfile, 'r') as stream:
@@ -58,7 +58,6 @@ def get_ff_parameters(molecule_dict, isotparam):
 
 def load_yaml():
     """ Load the ff_data.yaml as a dict."""
-    import ruamel.yaml as yaml
     thisdir = os.path.dirname(os.path.abspath(__file__))
     yamlfullpath = os.path.join(thisdir, '..', 'calcfunctions', 'ff_data.yaml')
     with open(yamlfullpath, 'r') as stream:
@@ -68,8 +67,10 @@ def load_yaml():
 
 @calcfunction
 def get_molecule_from_restart_file(structure_cif, molecule_folderdata, input_dict, molecule_dict):
-    """Get a CifData file having the cell of the structure and the geometry of the loaded molecule."""
-    import ase
+    """Get a CifData file having the cell of the initial (unexpanded) structure and the geometry of the loaded molecule.
+    TODO: this is source of error if there are more than one molecule, and the cell has been expandes,
+    as you can not wrap them in the small cell.
+    """
 
     # Get number of guest molecules
     if "number_of_molecules" in input_dict.get_dict():

aiida_lsmo/workchains/zeopp_multistage_ddec.py

@@ -35,12 +35,10 @@ def define(cls, spec):
         super().define(spec)
 
         spec.input('structure', valid_type=CifData, help='input structure')
-        spec.input('zeopp.parameters',
-                   valid_type=NetworkParameters,
-                   default=lambda: NetworkParameters(dict=ZEOPP_PARAMETERS_DEFAULT),
-                   required=False,
-                   help='parameters for zeo++')
-        spec.expose_inputs(ZeoppCalculation, namespace='zeopp', exclude=['parameters', 'structure'])
+        spec.expose_inputs(ZeoppCalculation, namespace='zeopp', exclude=['structure'])
+        spec.inputs['zeopp']['parameters'].default = lambda: NetworkParameters(dict=ZEOPP_PARAMETERS_DEFAULT)
+        spec.inputs['zeopp']['parameters'].required = False
+
         spec.expose_inputs(Cp2kMultistageDdecWorkChain, exclude=['structure'])
 
         spec.outline(cls.run_zeopp_before, cls.run_multistageddec, cls.run_zeopp_after, cls.return_results)

conftest.py

@@ -2,11 +2,56 @@
 For pytest
 initialise a test database and profile
 """
+import os
 import pytest
+from tests import DATA_DIR
 
-pytest_plugins = ['aiida.manage.tests.pytest_fixtures']  # pylint: disable=invalid-name
+pytest_plugins = ['aiida.manage.tests.pytest_fixtures', 'aiida_testing.mock_code']  # pylint: disable=invalid-name
 
 
 @pytest.fixture(scope='function', autouse=True)
 def clear_database_auto(clear_database):  # pylint: disable=unused-argument
     """Automatically clear database in between tests."""
+
+
+@pytest.fixture(scope='function')
+def cp2k_code(mock_code_factory):
+    """Create mocked "cp2k" code."""
+    return mock_code_factory(
+        label='cp2k-7.1',
+        data_dir_abspath=DATA_DIR,
+        entry_point='cp2k',
+        # files *not* to copy into the data directory
+        ignore_files=('_aiidasubmit.sh'))
+
+
+@pytest.fixture(scope='function')
+def raspa_code(mock_code_factory):
+    """Create mocked "raspa" code."""
+    return mock_code_factory(
+        label='raspa-e968334',
+        data_dir_abspath=DATA_DIR,
+        entry_point='raspa',
+        # files *not* to copy into the data directory
+        ignore_files=('_aiidasubmit.sh',))
+
+
+@pytest.fixture(scope='function')
+def zeopp_code(mock_code_factory):
+    """Create mocked "zeo++" code."""
+    return mock_code_factory(
+        label='zeopp-0.3',
+        data_dir_abspath=DATA_DIR,
+        entry_point='zeopp.network',
+        # files *not* to copy into the data directory
+        ignore_files=('_aiidasubmit.sh', 'UFF.rad'))
+
+
+@pytest.fixture(scope='function')
+def mg_mof74_cifdata():
+    """CifData for Mg MOF74 CIF."""
+    from aiida.orm import CifData  # pylint: disable=import-outside-toplevel
+    with open(os.path.join(DATA_DIR, 'Mg_MOF_74.cif'), 'rb') as handle:
+        cif = CifData(file=handle)
+
+    return cif

docs/source/index.rst

@@ -5,8 +5,6 @@
 The aiida-lsmo plugin for `AiiDA`_
 =====================================================
 
-``aiida-lsmo`` is available at http://github.com/yakutovicha/aiida-lsmo
-
 
 .. toctree::
    :maxdepth: 1

setup.cfg

@@ -0,0 +1,9 @@
+[coverage:run]
+parallel=true
+
+[tool:pytest] 
+addopts = --durations=0 --cov=aiida_lsmo
+filterwarnings =
+    ignore::DeprecationWarning:frozendict:
+    ignore::DeprecationWarning:sqlalchemy_utils:
+    ignore::DeprecationWarning:reentry:

setup.json

@@ -1,6 +1,6 @@
 {
     "name": "aiida-lsmo",
-    "version": "1.0.0b1",
+    "version": "1.0.0b2",
     "author": "Aliaksandr Yakutovich, Daniele Ongari, Leopold Talirz",
     "author_email": "[email protected]",
     "description": "AiiDA workflows for the LSMO laboratory at EPFL",
@@ -10,8 +10,7 @@
         "Programming Language :: Python :: 3.6",
         "Programming Language :: Python :: 3.7"
     ],
-    "setup_requires": ["reentry"],
-    "reentry_register": true,
+    "include_package_data": true,
     "install_requires": [
         "aiida-core >= 1.0.0",
         "aiida-cp2k >= 1.0.0b6",
@@ -51,7 +50,9 @@
     ],
     "extras_require": {
         "testing": [
-            "pytest==4.4.1"
+            "pgtest~=1.3.1",
+            "aiida-testing @ git+https://github.com/ltalirz/aiida-testing@fix-args#egg=aiida-testing",
+            "pytest-cov~=2.6"
         ],
         "pre-commit": [
                 "pre-commit==1.17.0",

tests/__init__.py

@@ -0,0 +1,5 @@
+"""Tests for aiida-lsmo."""
+import os
+
+THIS_DIR = os.path.dirname(os.path.abspath(__file__))
+DATA_DIR = os.path.join(THIS_DIR, 'data')