Merge 0810416 into f2021cb

.github/ISSUE_TEMPLATE/bug-report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**Environment:**
+- OS system:
+- Version:
+- Branch commit ID: 
+- Inputs:
+
+**To Reproduce**
+Steps/commands to reproduce the behaviour:
+ 1.  
+ 2.
+ 3. 
+
+**Expected Results**
+A clear and concise description of what you expected to happen.
+
+**Actual Results or Error Info**
+If applicable, add screenshots to help explain your problem.
+
+**Additional Context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitignore

@@ -1,9 +1,13 @@
 Byte-compiled / optimized
 *__pycache__*
 
+
+
 # distribution
 deeprank.egg-info
 database*
+dist
+build 
 
 # specific architure files
 deeprank/learn/arch_*
@@ -44,10 +48,15 @@ test/*.pdb
 #docs/_static
 #docs/_templates
 
+
 # vscode setting
 .vscode
 
 .DS_Store
 test/1AK4/atomic_features/test_1AK4_100w.dat
 test/2OUL/atomic_features/test_2OUL_1.dat
 test/atomic_pair_interaction.dat
+
+# Mac OSX files
+.DS_Store
+

.travis.yml

@@ -16,7 +16,7 @@ before_install:
   # Useful for debugging any issues with conda
   - conda info -a
 
- # python
+  # python
   - conda install python=3.7
 
   # install openmpi for mpi4py

README.md

@@ -5,7 +5,7 @@
 [![Build Status](https://secure.travis-ci.org/DeepRank/deeprank.svg?branch=master)](https://travis-ci.org/DeepRank/deeprank)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/9252e59633cf46a7ada0c3c614c175ea)](https://www.codacy.com/app/NicoRenaud/deeprank?utm_source=github.com&utm_medium=referral&utm_content=DeepRank/deeprank&utm_campaign=Badge_Grade)
 [![Coverage Status](https://coveralls.io/repos/github/DeepRank/deeprank/badge.svg?branch=master)](https://coveralls.io/github/DeepRank/deeprank?branch=master)
-[![Documentation Status](https://readthedocs.org/projects/deeprank/badge/?version=latest)](http://deeprank.readthedocs.io/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/deeprank/badge/?version=latest)](http://deeprank.readthedocs.io/?badge=latest) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3735042.svg)](https://doi.org/10.5281/zenodo.3735042)
 
 The documentation of the module can be found on readthedocs :
 <http://deeprank.readthedocs.io/en/latest/>
@@ -16,12 +16,14 @@ The documentation of the module can be found on readthedocs :
 
 Minimal information to install the module
 
+
 -   clone the repository `git clone https://github.com/DeepRank/deeprank.git`
 -   go there             `cd deeprank`
 -   install the module   `pip install -e ./`
 -   go int the test dir `cd test`
 -   run the test suite `pytest`
 
+
 ## 2 . Tutorial
 
 We give here the tutorial like introduction to the DeepRank machinery. More informatoin can be found in the documentation <http://deeprank.readthedocs.io/en/latest/>.  We quickly illsutrate here the two main steps of Deeprank :

deeprank/__version__.py

@@ -1 +1 @@
-__version__ = '0.0.1'
+__version__ = '0.1.0'

deeprank/features/AtomicFeature.py

@@ -61,7 +61,7 @@ def __init__(self, pdbfile, param_charge=None, param_vdw=None,
         >>> atfeat.evaluate_pair_interaction(save_interactions=test_name)
         >>>
         >>> # close the db
-        >>> atfeat.sqldb.close()
+        >>> atfeat.sqldb._close()
         """
 
         super().__init__("Atomic")
@@ -939,7 +939,7 @@ def __compute_feature__(pdb_data, featgrp, featgrp_raw):
     atfeat.export_data_hdf5(featgrp_raw)
 
     # close
-    atfeat.sqldb.close()
+    atfeat.sqldb._close()
 
 
 ########################################################################

deeprank/features/BSA.py

@@ -31,7 +31,7 @@ def __init__(self, pdb_data, chainA='A', chainB='B'):
         >>> bsa = BSA('1AK4.pdb')
         >>> bsa.get_structure()
         >>> bsa.get_contact_residue_sasa()
-        >>> bsa.sql.close()
+        >>> bsa.sql._close()
         """
         self.pdb_data = pdb_data
         self.sql = pdb2sql.interface(pdb_data)
@@ -156,7 +156,7 @@ def __compute_feature__(pdb_data, featgrp, featgrp_raw):
     bsa.export_data_hdf5(featgrp_raw)
 
     # close the file
-    bsa.sql.close()
+    bsa.sql._close()
 
 
 ########################################################################
@@ -177,7 +177,7 @@ def __compute_feature__(pdb_data, featgrp, featgrp_raw):
     bsa = BSA(pdb_file)
     bsa.get_structure()
     bsa.get_contact_residue_sasa()
-    bsa.sql.close()
+    bsa.sql._close()
 
     pprint(bsa.feature_data)
     print()

deeprank/features/FullPSSM.py

@@ -180,7 +180,7 @@ def get_feature_value(self, cutoff=5.5):
         # get interface contact residues
         # ctc_res = {"A":[chain 1 residues], "B": [chain2 residues]}
         ctc_res = sql.get_contact_residues(cutoff=cutoff)
-        sql.close()
+        sql._close()
         ctc_res = ctc_res["A"] + ctc_res["B"]
 
         # handle with small interface or no interface