Merge pull request #19 from materials-data-facility/forge-dev

0.5.0 release

.coveragerc

@@ -0,0 +1,3 @@
+[run]
+branch=True
+

.gitignore

@@ -13,7 +13,6 @@ Untitled*.ipynb
 */dist/*
 *.egg*
 
-
-prototypes/forge_sandbox.ipynb
-
 travis.tar
+.coverage
+

.travis.yml

@@ -6,18 +6,20 @@ python:
 - '3.5'
 - '3.6'
 install:
-- pip install -r requirements.txt
-- pip install .
+- pip install -e .
+- pip install pytest pytest-cov coveralls
 env:
 - TEST_ENV=travis
 script:
-- travis_wait 30 py.test
+- travis_wait 50 py.test
 before_install:
 - openssl aes-256-cbc -K $encrypted_4b438100ad6f_key -iv $encrypted_4b438100ad6f_iv
   -in travis.tar.enc -out travis.tar -d
 - tar xvf travis.tar
 - mkdir -p ~/mdf/credentials/
 - mv MDF_Forge_tokens.json ~/mdf/credentials/MDF_Forge_tokens.json
+after_success:
+- coveralls
 notifications:
   email:
     recipients:
@@ -36,4 +38,4 @@ deploy:
     tags: true
   distributions: sdist bdist_wheel
   password:
-    secure: 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
+    secure: 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

README.md

@@ -1,5 +1,5 @@
 # Forge
-[![Build Status](https://travis-ci.org/materials-data-facility/forge.svg?branch=master)](https://travis-ci.org/materials-data-facility/forge) [![PyPI](https://img.shields.io/pypi/v/mdf_forge.svg)](https://pypi.python.org/pypi/mdf-forge)
+[![PyPI](https://img.shields.io/pypi/v/mdf_forge.svg)](https://pypi.python.org/pypi/mdf-forge) [![Build Status](https://travis-ci.org/materials-data-facility/forge.svg?branch=master)](https://travis-ci.org/materials-data-facility/forge) [![Coverage Status](https://coveralls.io/repos/github/materials-data-facility/forge/badge.svg?branch=master)](https://coveralls.io/github/materials-data-facility/forge?branch=master)
 
 Forge is the Materials Data Facility Python package to interface and leverage the MDF Data Discovery service. Forge allows users to perform simple queries and facilitiates moving and synthesizing results.
 

docs/tutorials/1 - Introduction.ipynb

@@ -131,6 +131,64 @@
   {
    "cell_type": "markdown",
    "metadata": {},
+   "source": [
+    "If you want to search on a value with special characters, such as a colon or space, you must wrap the value in double quotes. Otherwise, you may get unexpected results."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'mdf': {'citation': [\"A.P. Bento, A. Gaulton, A. Hersey, L.J. Bellis, J. Chambers, M. Davies, F.A. Krüger, Y. Light, L. Mak, S. McGlinchey, M. Nowotka, G. Papadatos, R. Santos and J.P. Overington (2014) 'The ChEMBL bioactivity database: an update.' Nucleic Acids Res., 42 1083-1090. DOI: 10.1093/nar/gkt1031 PMID: 24214965\",\n",
+       "   \"M. Davies, M. Nowotka, G. Papadatos, F. Atkinson, G.J.P. van Westen, N Dedman, R. Ochoa and J.P. Overington  (2014) 'myChEMBL: A Virtual Platform for Distributing Cheminformatics Tools and Open Data' Challenges 5 (334-337) DOI: 10.3390/challe5020334\",\n",
+       "   'S. Jupp, J. Malone, J. Bolleman, M. Brandizi, M. Davies, L. Garcia, A. Gaulton, S. Gehant, C. Laibe, N. Redaschi, S.M Wimalaratne, M. Martin, N. Le Novère, H. Parkinson, E. Birney and A.M Jenkinson (2014) The EBI RDF Platform: Linked Open Data for the Life Sciences Bioinformatics 30 1338-1339 DOI: 10.1093/bioinformatics/btt765 PMID: 24413672'],\n",
+       "  'collection': 'ChEMBL db',\n",
+       "  'data_contact': {'email': '[email protected]',\n",
+       "   'family_name': 'Overington',\n",
+       "   'full_name': 'John P. Overington',\n",
+       "   'given_name': 'John P.',\n",
+       "   'institution': 'European Molecular Biology Laboratory European Bioinformatics Institute'},\n",
+       "  'data_contributor': [{'email': '[email protected]',\n",
+       "    'family_name': 'Pike',\n",
+       "    'full_name': 'Evan Pike',\n",
+       "    'github': 'dep78',\n",
+       "    'given_name': 'Evan',\n",
+       "    'institution': 'The University of Chicago'}],\n",
+       "  'description': 'ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).vThe data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.',\n",
+       "  'ingest_date': '2017-08-09T17:26:54.157428Z',\n",
+       "  'license': 'https://creativecommons.org/licenses/by-sa/3.0/',\n",
+       "  'links': {'data_doi': 'ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/',\n",
+       "   'landing_page': 'https://www.ebi.ac.uk/chembl/downloads'},\n",
+       "  'mdf_id': '598b45debf9d988c07667735',\n",
+       "  'metadata_version': '0.3.2',\n",
+       "  'resource_type': 'dataset',\n",
+       "  'source_name': 'chembl_db',\n",
+       "  'tags': ['SAR'],\n",
+       "  'title': 'ChEMBL Database',\n",
+       "  'year': 2017}}"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "res = mdf.search('mdf.title:\"ChEMBL Database\"', advanced=True)\n",
+    "res[0]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
    "source": []
   }
  ],