Merge pull request #42 from nlesc-nano/CAT_0.5

CAT 0.5

.gitignore

@@ -102,7 +102,7 @@ venv.bak/
 
 # mypy
 .mypy_cache/
-tests/timeit_test.py
 .DS_Store
 docs_out/
 .vscode/
+.doctrees/

.travis.yml

@@ -1,5 +1,6 @@
 sudo: false
-language: python
+language: 
+    python: 3.7
 
 env:
     global:
@@ -18,16 +19,16 @@ install:
     - conda info -a
 
     # Install virtual enviroment
-    - conda install -c conda-forge python==3.7
-    - conda install -c conda-forge h5py
-    - conda install -c conda-forge rdkit
+    - conda create -n CAT python=3.7
+    - conda install -n CAT -c conda-forge h5py rdkit
+    - source activate CAT
 
     # Install qmflows package
     - pip install .[test]
 
 script:
     # Run the unitary tests excluding the expensive computations
-    - pytest -m "not (slow or long)" --cov=CAT test
+    - pytest -m "not (slow or long)" --cov=CAT tests
     - coverage xml && coverage report -m
 
 branches:

CAT/__init__.py

@@ -1,41 +1,45 @@
-""" A collection of tools designed for the construction,
-and subsequent analysis, of various chemical compounds. """
+"""
+CAT
+===
 
-__author__ = "Bas van Beek"
-__email__ = 'b.f.van.beek@vu.nl'
+A collection of tools designed for the construction of various chemical compounds.
+
+"""
 
 from .__version__ import __version__
 
-from .analysis import (
-    init_asa, CRSJob, CRSResults, job_single_point, job_geometry_opt, job_freq,
-    init_bde, get_thermo, get_entropy, init_solv
+from .jobs import (
+    job_single_point, job_geometry_opt, job_freq
+)
+
+from .thermo_chem import (
+    get_thermo, get_entropy
 )
 
 from .attachment import (
     init_qd_opt, init_ligand_opt, init_qd_construction, init_ligand_anchoring
 )
 
 from .data_handling import (
-    Database,
-    mol_to_file,
-    read_mol, set_mol_prop,
-    sanitize_optional, sanitize_input_mol, sanitize_path
+    read_mol, set_mol_prop
 )
 
 from .base import prep
 
 from .utils import get_template
 
+__version__ = __version__
+__author__ = "Bas van Beek"
+__email__ = 'b.f.van.beek@vu.nl'
+
 __all__ = [
-    'init_asa', 'CRSJob', 'CRSResults', 'job_single_point', 'job_geometry_opt', 'job_freq',
-    'init_bde', 'get_thermo', 'get_entropy', 'init_solv',
+    'job_single_point', 'job_geometry_opt', 'job_freq',
+
+    'get_thermo', 'get_entropy',
 
     'init_qd_opt', 'init_ligand_opt', 'init_qd_construction', 'init_ligand_anchoring',
 
-    'Database',
-    'mol_to_file',
-    'read_mol', 'set_mol_prop',
-    'sanitize_optional', 'sanitize_input_mol', 'sanitize_path',
+    'read_mol', 'set_mol_prop'
 
     'prep',
 

CAT/__version__.py

@@ -1 +1 @@
-__version__ = '0.4.6'
+__version__ = '0.5.0'