update README

* document usage in README * remove unused CLI
lsmo-epfl · Apr 7, 2019 · b51711d · b51711d
1 parent f106b5f
commit b51711d
Show file tree

Hide file tree

Showing 6 changed files with 83 additions and 79 deletions.
diff --git a/README.md b/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
-
diff --git a/aiida_qeq/data/data_cli.py b/aiida_qeq/data/data_cli.py
diff --git a/aiida_qeq/data/eqeq.py b/aiida_qeq/data/eqeq.py
@@ -41,7 +41,8 @@ class EQeqParameters(Dict):
     Command line options for eqeq.
     """
 
-    schema = Schema(options)
+    _schema = Schema(options)
+    schema = _schema.schema  # alias for easier printing
 
     # pylint: disable=redefined-builtin
     def __init__(self, dict=None, **kwargs):
@@ -63,7 +64,7 @@ def __init__(self, dict=None, **kwargs):
 
     def validate(self, parameters_dict):
         """Validate command line options."""
-        return EQeqParameters.schema(parameters_dict)
+        return EQeqParameters._schema(parameters_dict)
 
     def cmdline_params(self,
                        structure_file_name,

diff --git a/aiida_qeq/data/qeq.py b/aiida_qeq/data/qeq.py
@@ -57,7 +57,8 @@ class QeqParameters(Dict):
     Command line options for qeq.
     """
 
-    schema = Schema(options)
+    _schema = Schema(options)
+    schema = _schema.schema  # alias for easier printing
 
     # pylint: disable=redefined-builtin
     def __init__(self, dict=None, **kwargs):
@@ -81,7 +82,7 @@ def __init__(self, dict=None, **kwargs):
 
     def validate(self, parameters_dict):
         """Validate command line options."""
-        return QeqParameters.schema(parameters_dict)
+        return QeqParameters._schema(parameters_dict)
 
     def cmdline_params(self,
                        structure_file_name,

diff --git a/examples/submit_eqeq.py b/examples/submit_eqeq.py
@@ -12,7 +12,7 @@
 import aiida_qeq.data.eqeq as data
 from aiida_qeq.data import DATA_DIR
 from aiida.plugins import DataFactory, CalculationFactory
-from aiida.engine import run_get_node
+from aiida.engine import run
 
 # Prepare input parameters
 parameters = DataFactory('qeq.eqeq')({'method': 'ewald'})
@@ -46,5 +46,5 @@
     },
 }
 
-_result, node = run_get_node(CalculationFactory('qeq.eqeq'), **inputs)
-print(node)
+result = run(CalculationFactory('qeq.eqeq'), **inputs)
+print(result)
diff --git a/examples/submit_qeq.py b/examples/submit_qeq.py
@@ -12,7 +12,7 @@
 import aiida_qeq.data.qeq as data
 from aiida_qeq.data import DATA_DIR
 from aiida.plugins import DataFactory, CalculationFactory
-from aiida.engine import run_get_node
+from aiida.engine import run
 
 # Prepare input parameters
 CifData = DataFactory('cif')
@@ -25,7 +25,7 @@
     file=os.path.join(tests.TEST_DIR, 'HKUST1.cif'), parse_policy='lazy')
 
 inputs = {
-    # make sure the "eqeq" binary is in your PATH
+    # make sure the "qeq" binary is in your PATH
     'code': tests.get_code(entry_point='qeq.qeq'),
     # 'configure': data.QeqParameters()
     'structure': cif,
@@ -43,5 +43,5 @@
     },
 }
 
-_result, node = run_get_node(CalculationFactory('qeq.qeq'), **inputs)
-print(node)
+result = run(CalculationFactory('qeq.qeq'), **inputs)
+print(result)