Merge pull request #128 from rigdenlab/fix_tests

Fix tests

README.rst

@@ -6,7 +6,7 @@ Sequence Independent Molecular Replacement Based on Available Database
    :target: http://simbad.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 
-.. image:: https://img.shields.io/badge/solution%20count-100-blue.svg?style=flat
+.. image:: https://img.shields.io/badge/solution%20count-8-blue.svg?style=flat
    :alt: Solution count
 
 .. image:: https://img.shields.io/badge/DOI-10.1107/S2059798318005752-blue.svg

docs/_static/Simpkin2018.bib

@@ -0,0 +1,12 @@
+@article{Simpkin2018,
+   author = "Simpkin, Adam J. and Simkovic, Felix and Thomas, Jens M. H. and Savko, Martin and Lebedev, Andrey and Uski, Ville and Ballard, Charles and Wojdyr, Marcin and Wu, Rui and Sanishvili, Ruslan and Xu, Yibin and Lisa, Mar{\'\i}a-Natalia and Buschiazzo, Alejandro and Shepard, William and Rigden, Daniel J. and Keegan, Ronan M.",
+   title = "{{\it SIMBAD}: a sequence-independent molecular-replacement pipeline}",
+   journal = "Acta Crystallographica Section D",
+   year = "2018",
+   volume = "74",
+   number = "7",
+   pages = "595--605",
+   month = "Jul",
+   doi = {10.1107/S2059798318005752},
+   url = {https://doi.org/10.1107/S2059798318005752},
+}

docs/_static/Simpkin2020.bib

@@ -0,0 +1,12 @@
+@article{Simpkin2020,
+   author = "Simpkin, Adam J. and Simkovic, Felix and Thomas, Jens M. H. and Savko, Martin and Lebedev, Andrey and Uski, Ville and Ballard, Charles C. and Wojdyr, Marcin and Shepard, William and Rigden, Daniel J. and Keegan, Ronan M.",
+   title = "{Using {\it Phaser} and ensembles to improve the performance of {\it SIMBAD}}",
+   journal = "Acta Crystallographica Section D",
+   year = "2020",
+   volume = "76",
+   number = "1",
+   pages = "1--8",
+   month = "Jan",
+   doi = {10.1107/S2059798319015031},
+   url = {https://doi.org/10.1107/S2059798319015031},
+}

docs/conf.py

@@ -150,6 +150,7 @@
         ('Examples', 'examples'),
         ('Documentation', 'contents'),
         ('Server', 'server'),
+        ('References', 'references'),
     ],
     # Render the next and previous page links in navbar.
     'navbar_sidebarrel':

docs/references.rst

@@ -0,0 +1,40 @@
+.. _references:
+
+Reference List
+--------------
+
+.. list-table:: If you use SIMBAD, please cite:
+   :widths: 1200, 10, 10, 10
+   :class: table-hover
+
+   * - Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard C, Wojdyr M, Wu R, Sanishvili R, Xu Y, Lisa MN, Buschiazzo A, Shepard W, Rigden DJ, & Keegan RM (2018) SIMBAD: a sequence-independent molecular-replacement pipeline. *Acta Cryst. D* **74** (7), 595–605.
+     - .. cssclass:: btn btn-primary btn-sm btn-reference
+
+          `CrossRef <https://doi.org/10.1107/S2059798318005752>`_
+
+     - .. cssclass:: btn btn-default btn-sm btn-reference
+
+          `PubMed <https://www.ncbi.nlm.nih.gov/pubmed/29968670>`_
+
+     - .. cssclass:: btn btn-primary btn-sm btn-reference
+
+          `BibTex <_static/Simpkin2018.bib>`_
+
+
+.. list-table:: If you use SIMBAD with Phaser, please also cite the following:
+   :widths: 1200, 10, 10, 10
+   :class: table-hover
+
+   * - Simpkin AJ, Simkovic F, Thomas JMH, Savko M, Lebedev A, Uski V, Ballard C, Wojdyr M, Shepard W, Rigden DJ, & Keegan RM (2020). Using Phaser and ensembles to improve the performance of SIMBAD. *Acta Cryst. D* **76** (1), 1-8.
+     - .. cssclass:: btn btn-primary btn-sm btn-reference
+
+          `CrossRef <https://doi.org/10.1107/S2059798319015031>`_
+
+     - .. cssclass:: btn btn-default btn-sm btn-reference
+
+          `PubMed <https://www.ncbi.nlm.nih.gov/pubmed/31909738>`_
+
+     - .. cssclass:: btn btn-primary btn-sm btn-reference
+
+          `BibTex <_static/Simpkin2020.bib>`_
+

simbad/util/tests/test_pdb_util.py

@@ -10,7 +10,7 @@
 from simbad.util.pdb_util import PdbStructure
 from simbad.command_line import CCP4RootDirectory
 
-if sys.version.major < 3:
+if sys.version_info.major < 3:
     from urllib2 import urlopen
     from urllib2 import URLError
 else: