Merge branch 'release-0.1.5'

* release-0.1.5:
  Bump version: 0.1.4 → 0.1.5
  Add config for bumpversion utility, format changelog.
  Update installation instructions.

.bumpversion.cfg

@@ -0,0 +1,10 @@
+[bumpversion]
+current_version = 0.1.5
+
+[bumpversion:file:pymolprobity/__init__.py]
+
+[bumpversion:file:CHANGELOG.md]
+search = ## Unreleased
+replace = ## Unreleased
+	-
+	-## v{new_version}

CHANGELOG.md

@@ -1,51 +1,78 @@
 # Changelog
+All notable changes to this project will be documented in this file.
 
-All notable changes to this project will be documented in this file.  The format is based on [Keep a Changelog][kacl], and this project adheres to [Semantic Versioning][semver].
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-  [kacl]: https://keepachangelog.com/en/1.0.0/
-  [semver]: https://semver.org/spec/v2.0.0.html
+<!-- Possible subheadings:
+### Added
+### Changed
+### Deprecated
+### Fixed
+### Removed
+### Security
+-->
 
 
 ## Unreleased
 
+## v0.1.5
 
-## 0.1.4
+### Added
+- Config file for use with `bumpversion` utility.
 
-*2019-08-12*
+### Changed
+- Format of this changelog file.
 
-- Added: Citation instructions and release DOIs via GitHub/Zenodo.
-- Added: This changelog file.
+### Fixed
+- Improved instructions for incentive build installation and PATH setup.
 
 
-## 0.1.3
 
-*2019-08-02*
+## v0.1.4
 
-- Added: Python3 compatibility by Thomas Holder ([@speleo3][]).
-- Added: Instructions for symlinking to Phenix-installed Reduce and Probe.
-- Changed: Installation instructions to use Github master zip file by default.
-- Fixed: Several bugs related to Tk interface, by Thomas Holder ([@speleo3][]).
-- Removed: `make` targets "updateenv" and "run".
+### Added
+- Citation instructions and release DOIs via GitHub/Zenodo.
+- This changelog file.
 
 
-## 0.1.2
 
-*2017-01-13*
+## v0.1.3
 
-- Fixed: Parsing of Flipkin output for some atoms ("invalid literal for float" error).
+### Added
+- Python3 compatibility by Thomas Holder ([@speleo3][]).
+- Instructions for symlinking to Phenix-installed Reduce and Probe.
 
-## 0.1.1
+### Changed
+- Installation instructions to use Github master zip file by default.
 
-*2017-01-10*
+### Fixed
+- Several bugs related to Tk interface, by Thomas Holder ([@speleo3][]).
 
-- Changed: Redirect some low-level output to logger instead of console.
-- Fixed: Provide a more informative error message when required executables are not found in PATH.
-- Fixed: An error that occurred when trying to load a non-existant object.
+### Removed
+- `make` targets "updateenv" and "run".
 
 
-## 0.1.0
 
-*2016-10-26*
+## v0.1.2
+
+### Fixed
+- Parsing of Flipkin output for some atoms ("invalid literal for float" error).
+
+
+
+## v0.1.1
+
+### Changed
+- Redirect some low-level output to logger instead of console.
+
+### Fixed
+- Provide a more informative error message when required executables are not found in PATH.
+- An error that occurred when trying to load a non-existant object.
+
+
+
+## v0.1.0
 
 - Initial release
 

README.md

@@ -40,6 +40,8 @@ Detailed instructions are available via the [PyMOL Wiki][].
 
   [PyMOL Wiki]: http://www.pymolwiki.org/index.php/Category:Installation
 
+**Only PyMOL v2.0 or later is supported.**
+
 
 #### MolProbity programs
 
@@ -102,7 +104,8 @@ chmod +x flipkin prekin probe reduce
 ```
 
 You may also wish to download the Richardson group's "slightly modified version
-of the connectivity table published by the PDB" from the [Reduce software page][rp].  This file should be placed in `/usr/local`.  If you don't, you'll
+of the connectivity table published by the PDB" from the [Reduce software
+page][rp].  This file should be placed in `/usr/local`.  If you don't, you'll
 probably get the following error when you run Reduce:
 
   [rp]: http://kinemage.biochem.duke.edu/software/reduce.php
@@ -115,9 +118,11 @@ ERROR CTab(/usr/local/reduce_wwPDB_het_dict.txt): could not open
 ### Installation
 
 Installation of PyMOLProbity itself should be straightforward using PyMOL's
-[Plugin Manager][pm].  (Mac users note: Plugins are only available for MacPyMOL
-if you use the X11 hybrid [tweak][], which entails simply renaming or copying
-`MacPyMOL.app` to `PyMOLX11Hybrid.app` in your Applications folder.)
+[Plugin Manager][pm].  (Mac users note: Plugins are only available for 1.x
+versions of MacPyMOL if you use the X11 hybrid [tweak][], which entails simply
+renaming or copying `MacPyMOL.app` to `PyMOLX11Hybrid.app` in your Applications
+folder. For PyMOL version 2.0 and newer, plugins are built-in and you will not
+need to do this.)
 
   [pm]: http://www.pymolwiki.org/index.php/Plugin_Manager
   [tweak]: http://www.pymolwiki.org/index.php/Plugins#Plugins_on_OS_X
@@ -129,12 +134,42 @@ URL into the *URL* box and click *Fetch*.
     https://github.com/jaredsampson/pymolprobity/archive/master.zip
 
 Confirm you wish to proceed with the download and the plugin will be installed
-automatically.  Alternatively, you can [download][] the zipped plugin archive
-file (or a specific [version][], if desired) and select it using the file chooser.
+automatically.  Alternatively, or if the URL method fails, you can [download][]
+the zipped plugin archive file (or a specific [version][], if desired) and
+select it using the file chooser.
 
   [download]: https://github.com/jaredsampson/pymolprobity/archive/master.zip
   [version]: https://github.com/jaredsampson/pymolprobity/releases
 
+*Note:* If you are using PyMOL version earlier than 2.3.3, the URL-based option
+above will fail due to the presence of thpe `tests` directory, so you will need
+to download the `master.zip` file from the link above, unzip it, delete the
+`tests` directory, and re-zip the file.  This can all be done via the following
+`bash` commands:
+
+```
+curl -o pymolprobity-master.zip -O https://github.com/jaredsampson/pymolprobity/archive/master.zip \
+    && unzip pymolprobity-master.zip \
+    && rm -r pymolprobity-master/tests \
+    && rm pymolprobity-master.zip \
+    && zip -r pymolprobity-master.zip pymolprobity-master
+```
+
+One final step is required if you are using an incentive build and launching
+from an app icon rather than from the terminal.  You will need to ensure that
+the path to the Reduce/Probe executables is included in the shell PATH within
+the PyMOL app environment.  This can be done by editing your `pymolrc` file via
+*File* > *Edit pymolrc* and adding the following lines, changing the path to
+point to the actual location of your MolProbity programs if you have not used
+`/usr/local/bin`.
+
+```
+# for PyMOLProbity plugin, path to reduce/probe/flipkin/prekin executables
+import os
+os.environ['PATH'] += os.pathsep + '/usr/local/bin'
+```
+
+
 ### First run
 
 Now you can open PyMOL, load or fetch a structure, and launch PyMOLProbity from

pymolprobity/__init__.py

@@ -38,7 +38,7 @@
 from __future__ import absolute_import
 
 __author__ = 'Jared Sampson'
-__version__ = '0.1.2'
+__version__ = '0.1.5'
 
 
 import logging