Merge branch 'v0.6.2'

changelog.txt

@@ -1,3 +1,11 @@
+0.6.2:
+
+	- Add instructions on how to acknowledge signac in publications to
+	  documentation.
+	- Add cite module for the auto-generation of formatted references and
+	  BibTeX entries.
+	- Remove SSL authentication support.
+
 0.6.1:
 
 	- Bug Fixes:

doc/acknowledge.rst

@@ -0,0 +1,19 @@
+.. _acknowledge:
+
+==================
+How to cite signac
+==================
+
+Please acknowledge the use of this software within the body of your publication for example by copying or adapting the following formulation:
+
+*The computational workflow in general and data management in particular for this publication was primarily supported by the signac data management framework [1, 2].*
+
+  [1] Carl S. Adorf, Paul M. Dodd, and Sharon C. Glotzer. *signac - A Simple Data Management Framework*. 2016. arXiv: 1611.03543 [cs.DB].
+
+  [2] Carl S. Adorf and Paul M. Dodd. *csadorf/signac: v0.6.1*. Dec. 2016. DOI:10.5281/zenodo.192108. URL: https://doi.org/10.5821/zenodo.192108.
+
+References for a specific release versions can be found `here <https://zenodo.org/badge/latestdoi/72946496>`_.
+
+.. tip::
+
+    You can auto-generate the first formatted reference and the corresponding BibTeX file via :py:func:`signac.cite.reference` and :py:func:`signac.cite.bibtex`.

doc/conf.py

@@ -80,7 +80,7 @@ def __getattr__(cls, name):
 # The short X.Y version.
 version = '0.6'
 # The full version, including alpha/beta/rc tags.
-release = '0.6.1'
+release = '0.6.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

doc/index.rst

@@ -6,6 +6,15 @@
 Welcome to signac's documentation!
 ==================================
 
+.. image:: https://zenodo.org/badge/72946496.svg
+   :target: https://zenodo.org/badge/latestdoi/72946496
+
+.. image:: http://mybinder.org/badge.svg
+   :target: http://www.mybinder.org:/repo/csadorf/signac-examples
+
+.. image:: https://img.shields.io/pypi/v/signac.svg
+   :target: https://img.shields.io/pypi/v/signac.svg
+
 .. image:: images/minimal.svg
     :align: right
 
@@ -31,6 +40,9 @@ Contents
     :ref:`quickreference`
       Brief overview of the core functions, to serve as reference.
 
+    :ref:`acknowledge`
+      Instructions on how to acknowledge this software in publications.
+
     :ref:`api`
       The complete API reference.
 
@@ -51,6 +63,7 @@ Please use the `repository's issue tracker <https://bitbucket.org/glotzer/signac
    tutorial
    guide
    reference
+   acknowledge
    signac
 
 Indices and tables

doc/signac.rst

@@ -14,6 +14,9 @@ Module contents
     :show-inheritance:
 
 
+.. automodule:: signac.cite
+    :members:
+
 Subpackages
 -----------
 

setup.py

@@ -7,7 +7,7 @@
 
 setup(
     name='signac',
-    version='0.6.1',
+    version='0.6.2',
     packages=find_packages(),
     zip_safe=True,
 

signac/__init__.py

@@ -14,7 +14,8 @@
 from . import contrib
 from . import db
 from . import gui
-from . common import errors
+from . import cite
+from .common import errors
 from .contrib import Project
 from .contrib import get_project
 from .contrib import init_project
@@ -27,9 +28,10 @@
 from .contrib import filesystems as fs
 from .db import get_database
 
-__version__ = '0.6.1'
+__version__ = '0.6.2'
 
 __all__ = ['__version__', 'contrib', 'db', 'gui', 'errors',
+           'cite',
            'Project', 'get_project', 'init_project',
            'get_database', 'fetch', 'fetch_one',
            'export_one', 'export', 'export_to_mirror',

signac/cite.py

@@ -0,0 +1,65 @@
+# Copyright (c) 2016 The Regents of the University of Michigan
+# All rights reserved.
+# This software is licensed under the BSD 3-Clause License.
+"""Functions to support citing this software."""
+import sys
+
+
+ARXIV_BIBTEX = """@online{signac,
+    author      = {Carl S. Adorf and Paul M. Dodd and Sharon C. Glotzer},
+    title       = {signac - A Simple Data Management Framework},
+    year        = {2016},
+    eprinttype  = {arxiv},
+    eprintclass = {cs.DB},
+    eprint      = {1611.03543}
+}
+"""
+
+
+ARXIV_REFERENCE = "Carl S. Adorf, Paul M. Dodd, and Sharon C. Glotzer. signac - A SimpleData Management Framework. 2016. arXiv:1611.03543 [cs.DB]"
+
+
+def bibtex(file=None):
+    """Generate bibtex entries for signac.
+
+    The bibtex entries will be printed to screen unless a
+    filename or a file-like object are provided, in which
+    case they will be written to the corresponding file.
+
+    .. note::
+
+        A full reference should also include the
+        version of this software. Please refer to the
+        documentation on how to cite a specific version.
+
+    :param file: A str or file-like object.
+        Defaults to sys.stdout.
+    """
+    if file is None:
+        file = sys.stdout
+    elif isinstance(file, str):
+        file = open(file, 'w')
+    file.write(ARXIV_BIBTEX)
+
+
+def reference(file=None):
+    """Generate formatted reference entries for signac.
+
+    The references will be printed to screen unless a
+    filename or a file-like object are provided, in which
+    case they will be written to the corresponding file.
+
+    .. note::
+
+        A full reference should also include the
+        version of this software. Please refer to the
+        documentation on how to cite a specific version.
+
+    :param file: A str or file-like object.
+        Defaults to sys.stdout.
+    """
+    if file is None:
+        file = sys.stdout
+    elif isinstance(file, str):
+        file = open(file, 'w')
+    file.write(ARXIV_REFERENCE + '\n')

signac/common/connection.py

@@ -3,7 +3,6 @@
 # This software is licensed under the BSD 3-Clause License.
 import subprocess
 import logging
-import ssl
 from os.path import expanduser
 
 import pymongo
@@ -17,11 +16,6 @@
 AUTH_SCRAM_SHA_1 = 'SCRAM-SHA-1'
 AUTH_SSL = 'SSL'
 AUTH_SSL_x509 = 'SSL-x509'
-SSL_CERT_REQS = {
-    'none': ssl.CERT_NONE,
-    'optional': ssl.CERT_OPTIONAL,
-    'required': ssl.CERT_REQUIRED
-}
 
 
 def get_subject_from_certificate(fn_certificate):  # pragma no cover
@@ -89,22 +83,6 @@ def _connect_pymongo3(self, host):
                     pymongo.read_preferences.ReadPreference,
                     self._config_get('read_preference', 'PRIMARY')),
                 ** parameters)
-        elif auth_mechanism in (AUTH_SSL, AUTH_SSL_x509):  # pragma  no cover
-            # currently not officially supported
-            client = pymongo.MongoClient(
-                host,
-                ssl=True,
-                ssl_keyfile=expanduser(
-                    self._config_get_required('ssl_keyfile')),
-                ssl_certfile=expanduser(
-                    self._config_get_required('ssl_certfile')),
-                ssl_cert_reqs=SSL_CERT_REQS[
-                    self._config_get('ssl_cert_reqs', 'required')],
-                ssl_ca_certs=expanduser(
-                    self._config_get_required('ssl_ca_certs')),
-                ssl_match_hostname=self._config_get(
-                    'ssl_match_hostname', True),
-                ** parameters)
         else:
             raise_unsupported_auth_mechanism(auth_mechanism)
         self._client = client