Release/1.5.0 (#389)

* Update changelog. * Add Brandon Butler to CITATION.cff. * Add Corwin Kerr and Pengji Zhou to contributors list. * Add Brandon Butler to docs credits, formatting style. * Allow pydocstyle to run in doc subdirectory. * Fix Sphinx warnings. * Update Zenodo info, make Mike's name match in contributors/creators. * Exclude setup.cfg from pre-commit hooks (bumpversion interferes). * Fix keyring>=21.2.0 incompatibility. * Bump up to version 1.5.0.
glotzerlab · Sep 21, 2020 · 28fe4bc · 28fe4bc
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,9 @@ repos:
     rev: ''
     hooks:
     -   id: end-of-file-fixer
+        exclude: 'setup.cfg'
     -   id: trailing-whitespace
+        exclude: 'setup.cfg'
     -   id: debug-statements
 -   repo: local
     hooks:

diff --git a/.zenodo.json b/.zenodo.json
@@ -51,18 +51,27 @@
             "name": "Alyssa Travitz",
             "orcid": "0000-0001-5953-8807"
         },
-        {
-            "affiliation": "University of Michigan",
-            "name": "Brandon Butler",
-            "orcid": "0000-0001-7739-7796"
-        },
         {
             "affiliation": "National Institute of Technology, Hamirpur",
             "name": "Vishav Sharma"
         },
         {
             "affiliation": "Indian Institute of Technology, Gandhinagar",
             "name": "Abhavya Chandra"
+        },
+        {
+            "affiliation": "Indian Institute of Technology Roorkee",
+            "name": "Hardik Ojha"
+        },
+        {
+            "affiliation": "University of Michigan",
+            "name": "Corwin Kerr",
+            "orcid": "0000-0003-0776-2596"
+        },
+        {
+            "affiliation": "University of Michigan",
+            "name": "Pengji Zhou",
+            "orcid": "0000-0002-1409-9633"
         }
     ],
     "creators": [
@@ -86,6 +95,11 @@
             "name": "Mike Henry",
             "orcid": "0000-0002-3870-9993"
         },
+        {
+            "affiliation": "University of Michigan",
+            "name": "Brandon Butler",
+            "orcid": "0000-0001-7739-7796"
+        },
         {
             "affiliation": "University of Michigan",
             "name": "Paul M. Dodd"
@@ -110,5 +124,5 @@
         "id": "http://www.opensource.org/licenses/BSD-3-Clause"
     },
     "title": "signac",
-    "version": "1.4.0"
+    "version": "1.5.0"
 }
diff --git a/CITATION.cff b/CITATION.cff
@@ -2,7 +2,7 @@
 ---
 cff-version: "1.0.3"
 title: signac
-version: 1.4.0
+version: 1.5.0
 abstract: |
     The signac framework helps users manage and scale file-based workflows, facilitating data
     reuse, sharing, and reproducibility. It provides a simple and robust data model to create
@@ -31,6 +31,11 @@ authors:
     given-names: Mike
     affiliation: "Boise State University"
     orcid: "https://orcid.org/0000-0002-3870-9993"
+  -
+    family-names: Butler
+    given-names: Brandon
+    affiliation: "University of Michigan"
+    orcid: "https://orcid.org/0000-0001-7739-7796"
   -
     family-names: Dodd
     given-names: "Paul M."

diff --git a/changelog.txt b/changelog.txt
@@ -7,28 +7,36 @@ The **signac** package follows `semantic versioning <https://semver.org/>`_.
 Version 1
 =========
 
-next
-----
+[1.5.0] -- 2020-09-20
+---------------------
 
 Added
 +++++
 
  - Type annotations are validated during continuous integration (#313).
  - Added ``_repr_html_`` method in ``ProjectSchema`` class (#314, #324).
  - Allow grouping by variables that are not present in all jobs in the project in ``JobsCursor.groupby`` (#321, #323).
+ - Added parameters ``usecols`` and ``flatten`` to allow selection of columns and flattening of nested data when converting signac data into a pandas DataFrame (#327, #330).
  - Added support for `pre-commit hooks <https://pre-commit.com/>`__ (#355, #358).
+ - Expanded CLI documentation (#187, #359, #377).
+
+Changed
++++++++
+
+ - Docstrings are now written in `numpydoc style <https://numpydoc.readthedocs.io/en/latest/format.html>`__.
 
 Fixed
 +++++
 
  - Fix the ``signac config verify`` command (previously broken) (#301, #302).
  - Warnings now appear when raised by the ``signac`` CLI (#317, #308).
+ - Fix dots in synchronization error messages (#375, #376).
 
 Deprecated
 ++++++++++
 
  - Deprecate the ``create_access_modules`` method in ``Project``, to be removed in 2.0 (#303, #308).
- - The ``MainCrawler`` class has replaced the ``MasterCrawler`` class. Both classes are deprecated.
+ - The ``MainCrawler`` class has replaced the ``MasterCrawler`` class. Both classes are deprecated (#342).
 
 Removed
 +++++++

diff --git a/contributors.yaml b/contributors.yaml
@@ -86,11 +86,21 @@ contributors:
     affiliation: "Indian Institute of Technology, Gandhinagar"
   -
     family-names: Henry
-    given-names: "Michael M."
+    given-names: Mike
     affiliation: "Boise State University"
     orcid: "https://orcid.org/0000-0002-3870-9993"
   -
     family-names: Ojha
     given-names: Hardik
     affiliation: "Indian Institute of Technology Roorkee"
+  -
+    family-names: Kerr
+    given-names: Corwin
+    affiliation: "University of Michigan"
+    orcid: "https://orcid.org/0000-0003-0776-2596"
+  -
+    family-names: Zhou
+    given-names: Pengji
+    affiliation: "University of Michigan"
+    orcid: "https://orcid.org/0000-0002-1409-9633"
 ...
diff --git a/doc/api.rst b/doc/api.rst
@@ -13,8 +13,6 @@ The Project
 
 .. currentmodule:: signac
 
-.. autoclass:: Project
-
 .. rubric:: Attributes
 
 .. autosummary::
@@ -70,8 +68,6 @@ The Job class
 
 .. currentmodule:: signac.contrib.job
 
-.. autoclass:: Job
-
 .. rubric:: Attributes
 
 .. autosummary::

diff --git a/doc/conf.py b/doc/conf.py
@@ -1,33 +1,33 @@
-# -*- coding: utf-8 -*-
-#
-# signac documentation build configuration file, created by
-# sphinx-quickstart on Fri Oct 23 17:41:32 2015.
-#
-# This file is execfile()d with the current directory set to its
-# containing dir.
-#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
-#
-# All configuration values have a default; values that are commented out
-# serve to show the default.
+"""signac documentation build configuration file.
+
+This file is executed with the current directory set to its containing dir.
+
+Note that not all possible configuration values are present in this
+autogenerated file.
+
+All configuration values have a default; values that are commented out serve
+to show the default.
+"""
 
 import sys
 import os
-import shlex
 
 import sphinx_rtd_theme
 from unittest.mock import MagicMock
 
+
 class Mock(MagicMock):
+    """Mocks modules and their contained objects."""
+
     @classmethod
     def __getattr__(cls, name):
         if name == '_mock_methods':
             return []
         if name == 'version_tuple':
-            return (3,0)
+            return (3, 0)
         return Mock()
 
+
 MOCK_MODULES = ['pymongo', 'gridfs', 'mpi4py']
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
 
@@ -69,18 +69,18 @@ def __getattr__(cls, name):
 master_doc = 'index'
 
 # General information about the project.
-project = u'signac'
+project = 'signac'
 copyright = 'The Regents of the University of Michigan'
-author = u'Carl S. Adorf, Vyas Ramasubramani, Bradley D. Dice, Michael M. Henry, Paul M. Dodd, Sharon C. Glotzer'
+author = 'Carl S. Adorf, Vyas Ramasubramani, Bradley D. Dice, Michael M. Henry, Brandon Butler, Paul M. Dodd, Sharon C. Glotzer'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.4.0'
+version = '1.5.0'
 # The full version, including alpha/beta/rc tags.
-release = '1.4.0'
+release = '1.5.0'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -234,25 +234,25 @@ def __getattr__(cls, name):
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements: dict = {
-# The paper size ('letterpaper' or 'a4paper').
-#'papersize': 'letterpaper',
+    # The paper size ('letterpaper' or 'a4paper').
+    # 'papersize': 'letterpaper',
 
-# The font size ('10pt', '11pt' or '12pt').
-#'pointsize': '10pt',
+    # The font size ('10pt', '11pt' or '12pt').
+    # 'pointsize': '10pt',
 
-# Additional stuff for the LaTeX preamble.
-#'preamble': '',
+    # Additional stuff for the LaTeX preamble.
+    # 'preamble': '',
 
-# Latex figure (float) alignment
-#'figure_align': 'htbp',
+    # Latex figure (float) alignment
+    # 'figure_align': 'htbp',
 }
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-  (master_doc, 'signac.tex', u'signac Documentation',
-   u'Carl Simon Adorf', 'manual'),
+    (master_doc, 'signac.tex', 'signac Documentation',
+     'Carl Simon Adorf', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -281,7 +281,7 @@ def __getattr__(cls, name):
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'signac', u'signac Documentation',
+    (master_doc, 'signac', 'signac Documentation',
      [author], 1)
 ]
 
@@ -295,9 +295,9 @@ def __getattr__(cls, name):
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-  (master_doc, 'signac', u'signac Documentation',
-   author, 'signac', 'A simple data management framework.',
-   'Miscellaneous'),
+    (master_doc, 'signac', 'signac Documentation',
+     author, 'signac', 'A simple data management framework.',
+     'Miscellaneous'),
 ]
 
 # Documents to append as an appendix to all manuals.

diff --git a/setup.cfg b/setup.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.0
+current_version = 1.5.0
 commit = True
 tag = False
 message = Bump up to version {new_version}.
@@ -15,25 +15,21 @@ max-line-length = 100
 exclude = configobj,passlib,cite.py,conf.py
 
 [pydocstyle]
-# Skip these files:
 match = ^((?!\.sync-zenodo-metadata|setup|benchmark|mpipool|connection|crypt|host|filesystems|indexing).)*\.py$
-# Skip these directories:
-match-dir = ^((?!doc|tests|configobj|db).)*$
-# Skip deprecated methods:
+match-dir = ^((?!tests|configobj|db).)*$
 ignore-decorators = "deprecated"
 ignore = D105, D107, D203, D204, D213
 
-
 [mypy]
 ignore_missing_imports = True
 
 [coverage:run]
 source = signac
-omit =
-    */signac/common/configobj/*.py
+omit = 
+	*/signac/common/configobj/*.py
 
 [tool:pytest]
-filterwarnings =
+filterwarnings = 
 	ignore: .*[The indexing module | get_statepoint] is deprecated.*: DeprecationWarning
 
 [bumpversion:file:setup.py]

diff --git a/setup.py b/setup.py
@@ -28,7 +28,7 @@
 
 setup(
     name='signac',
-    version='1.4.0',
+    version='1.5.0',
     packages=find_packages(),
     zip_safe=True,
     maintainer='signac Developers',

diff --git a/signac/common/crypt.py b/signac/common/crypt.py
@@ -26,7 +26,19 @@ def get_keyring():
 else:
     def get_keyring():
         "Return the system user keyring."
-        return keyring.get_keyring()
+        # In some newer versions of keyring (probably >=21.2.0), no backend is
+        # available, which causes problems for signac's implementation. This
+        # signac feature is already deprecated so this is only enough of a fix
+        # to prevent tests from failing for users with new versions of keyring
+        # installed.
+        try:
+            kr = keyring.get_keyring()
+        except RuntimeError:
+            return None
+        if kr.priority <= 0 or isinstance(kr, keyring.backends.fail.Keyring):
+            return None
+        else:
+            return kr
 
 """
 THIS MODULE IS DEPRECATED!

diff --git a/signac/contrib/project.py b/signac/contrib/project.py
@@ -958,16 +958,17 @@ def groupby(self, key=None, default=None):
             The state point grouping parameter(s) passed as a string,
             iterable of strings, or a callable that will be passed one
             argument, the job (Default value = None).
-        default :
-            A default value to be used when a given state point key is not present (must
-            be sortable).
+        default
+            A default value to be used when a given state point key is not
+            present. The value must be sortable and is only used if not None
+            (Default value = None).
 
         Returns
         -------
         key : str
             Grouped key.
         group : iterable of Jobs
-            Iterable of `Job`s matching this group key.
+            Iterable of `Job` instances matching this group key.
 
         """
         return self.find_jobs().groupby(key, default=default)

diff --git a/signac/version.py b/signac/version.py
@@ -4,7 +4,7 @@
 """Define signac version."""
 
 
-__version__ = "1.4.0"
+__version__ = "1.5.0"
 
 SCHEMA_VERSION = "1"