Merge branch 'develop' into hbondtests

.github/CONTRIBUTING.md

@@ -2,14 +2,17 @@
 
 Thanks for contributing to MDAnalysis!
 
+All members of the MDAnalysis community adhere to our [Code of Conduct](https://www.mdanalysis.org/pages/conduct/). By contributing code and interacting with us on GitHub, the forums, or by any other means you consent to follow the Code of Conduct.
+
 #### Reporting issues
 
 If you've found a defect with MDAnalysis we'd love to know so we can fix it.  Please follow the Issue template so we can quickly diagnose the problem, in particular the piece of code that causes the problem.
 
-If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by the [discussion board](https://groups.google.com/forum/#!forum/mdnalysis-discussion).
+If your issue isn't a defect with the code and instead you require help using MDAnalysis, drop by the [discussion forum](https://groups.google.com/forum/#!forum/mdnalysis-discussion).
 
 #### Contributing code
 
-If you're contributing code, please check out the [Style guide](https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide).
+If you're contributing code, please check out [How to contribute](https://www.mdanalysis.org/UserGuide/contributing.html) in the User Guide and look at the [Style guide](https://github.com/MDAnalysis/mdanalysis/wiki/Style-Guide).
+
+MDAnalysis devs are most easily reached through the [development list](https://groups.google.com/forum/#!forum/mdnalysis-devel).
 
-MDAnalysis devs are most easily reached through the [development board](https://groups.google.com/forum/#!forum/mdnalysis-devel).

.github/ISSUE_TEMPLATE/bug_report.md

@@ -4,19 +4,19 @@ about: Create a report to help us improve
 
 ---
 
-**Expected behavior**
+## Expected behavior ##
 
-A clear and concise description of what you want to do and what you think should happen. (Code to reproduce the behavior can be added below).
+<!-- A clear and concise description of what you want to do and what you think should happen. (Code to reproduce the behavior can be added below). -->
 
 
-**Actual behavior**
+## Actual behavior ##
 
-What happened instead. Add as much detail as you can. Include (copy and paste) stack traces and any output.
+<!-- What happened instead. Add as much detail as you can. Include (copy and paste) stack traces and any output. -->
 
 
-**Code to reproduce the behavior**
+## Code to reproduce the behavior ##
 
-Show us how to reproduce the failiure. If you can, use trajectory files from the test data.
+<!-- Show us how to reproduce the failure. If you can, use trajectory files from the test data. Use the code snipped below as a starting point. -->
 
 ``` python
 import MDAnalysis as mda
@@ -28,7 +28,7 @@ u = mda.Universe(PSF, DCD)
 
 ```
 
-**Currently version of MDAnalysis**
+## Current version of MDAnalysis ##
 
 - Which version are you using? (run `python -c "import MDAnalysis as mda; print(mda.__version__)"`)
 - Which version of Python (`python -V`)?

.github/ISSUE_TEMPLATE/feature_request.md

@@ -4,14 +4,17 @@ about: Suggest an idea for this project
 
 ---
 
-**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 [...]
+## Is your feature request related to a problem? ##
+<!-- A clear and concise description of what the problem is. For example, 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.
+## Describe the solution you'd like ##
+<!-- A description of what you want to happen. For example, I'd like to be able to do [...] -->
 
-**Additional context**
-Add any other context or screenshots about the feature request here.
+
+## Describe alternatives you've considered ##
+<!-- A description of any alternative solutions or features you've considered or possible solutions that you've seen elsewhere. -->
+
+
+## Additional context ##
+<!-- Add any other context or screenshots about the feature request here. -->

.github/ISSUE_TEMPLATE/questions.md

@@ -9,15 +9,15 @@ If you have a **QUESTION** such as
 - how to use MDAnalysis in general
 - how to accomplish something specific,
 - what output means
-- ... or similar questions related to USING MDAnalysis 
+- ... or similar questions related to *USING* MDAnalysis 
 
 then please *ask this question on the user mailing list*
 
    https://groups.google.com/forum/#!forum/mdnalysis-discussion
 
-The issue tracker is meant for DEFECTS ("BUGS"), new FEATURES, and decisions on the API. In order to keep the volume of work on the issue tracker manageable for our volunteer developers, we will IMMEDIATELY CLOSE ISSUES THAT ARE BETTER ANSWERED ON THE USER MAILINGLIST.
+The issue tracker is meant for DEFECTS ("BUGS"), new FEATURES, and decisions on the API. In order to keep the volume of work on the issue tracker manageable for our volunteer developers, we will **IMMEDIATELY CLOSE ISSUES WITH QUESTIONS** as these questions are better answered on the mailing list.
 
-We really appreciate you as a user getting in touch with us --- no matter what you want to discuss. But we need your help keeping the amount of work manageable so please use the mailing list for questions and the issue tracker for code-related issues.
+We really appreciate you getting in touch with us --- no matter what you want to discuss. But we need your help keeping the amount of work manageable so please use the mailing list for questions and the issue tracker for code-related issues.
 
 Thank you!
 

README.rst

@@ -8,7 +8,7 @@
 
 MDAnalysis_ is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. 
 
-It works with a a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many other — see the lists of  supported `trajectory formats`_ and `topology formats`_.
+It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported `trajectory formats`_ and `topology formats`_.
 MDAnalysis also includes widely used analysis algorithms in the `MDAnalysis.analysis`_ module.
 
 .. _numfocus-fiscal-sponsor-attribution:
@@ -81,9 +81,9 @@ MDAnalysis issue tracker.)
 Guide for Developers
 ====================
 
-To setup a development environment and run the testsuite you can use this
+To set up a development environment and run the test suite you can use this
 guide_. If you are a new developer who would like to start contributing to
-MDAnalysis as a start you can increase our code coverage, the guides explain how
+MDAnalysis, you can help increase our code coverage, the guides explain how
 to find uncovered code.
 
 

package/AUTHORS

@@ -128,7 +128,14 @@ Chronological list of authors
 2020
   - Charlie Cook
   - Yuanyu Chang
+  - Ivan Hristov
   - Michael Quevillon
+  - Hao Tian
+  - Hugo MacDermott-Opeskin
+  - Anshul Angaria
+  - Shubham Sharma
+
+
 
 External code
 -------------

package/CHANGELOG

@@ -15,11 +15,16 @@ The rules for this file:
 ------------------------------------------------------------------------------
 mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira,
          PicoCentauri, davidercruz, jbarnoud, RMeli, IAlibay, mtiberti, CCook96,
-         Yuan-Yu, xiki-tempula
+         Yuan-Yu, xiki-tempula, HTian1997, Iv-Hristov, hmacdope, AnshulAngaria,
+         ss62171
 
   * 0.21.0
 
 Fixes
+  * Fixed mda.Merge for Universes without coordinates (Issue #2470)(PR #2580)
+  * PCA(align=True) now correctly aligns the trajectory and computes the
+    correct means and covariance matrix (Issue #2561)
+  * Correct args order of base.AnalysisFromFunction (Issue #2503)  
   * encore.dres() returns dimensionality reduction details instead of a
     reference to itself (Issue #2471)
   * Handle exception when PDBWriter is trying to remove an invalid StringIO
@@ -54,11 +59,16 @@ Fixes
     argument. The directives parsed into bonds, angles, impropers, and dihedrals now
     match TPRParser. (PR #2408)
   * Added parmed to setup.py
+  * Fixed example docs for polymer persistence length (#2582)
   * Fixed HydrogenBondAnalysis to return atom indices rather than atom ids (PR #2572).
     Fixed the check for bond information in the _get_dh_pairs method (Issue #2396)
     and added a test case for this.
 
 Enhancements
+  * New analysis.hole2 module for HOLE interfacing. Contains a function (hole) 
+    for running HOLE on singular PDB files and class (HoleAnalysis) for 
+    trajectories (PR #2523)
+  * Changed selection wildcards to support multiple wildcards (#2436)
   * Added coordinate reader and writer for NAMD binary coordinate format (PR #2485)
   * Improved ClusterCollection and Cluster string representations (Issue #2464)
   * XYZ parser store elements attribute (#2420) and XYZ write uses the elements
@@ -135,6 +145,7 @@ Changes
     function calls. (Issue #782)
 
 Deprecations
+  * analysis.hole is deprecated in 1.0 (remove in 2.0)
   * analysis.hbonds.HydrogenBondAnalysis is deprecated in 1.0 (remove in 2.0)
 
 

package/MDAnalysis/analysis/base.py

@@ -33,6 +33,7 @@
 from six.moves import range, zip
 import inspect
 import logging
+import itertools
 
 import numpy as np
 from MDAnalysis import coordinates
@@ -231,18 +232,15 @@ def __init__(self, function, trajectory=None, *args, **kwargs):
         """
         if (trajectory is not None) and (not isinstance(
                 trajectory, coordinates.base.ProtoReader)):
-            args = args + (trajectory,)
+            args = (trajectory,) + args
             trajectory = None
 
         if trajectory is None:
-            for arg in args:
+            # all possible places to find trajectory
+            for arg in itertools.chain(args, six.itervalues(kwargs)):
                 if isinstance(arg, AtomGroup):
                     trajectory = arg.universe.trajectory
-            # when we still didn't find anything
-            if trajectory is None:
-                for arg in six.itervalues(kwargs):
-                    if isinstance(arg, AtomGroup):
-                        trajectory = arg.universe.trajectory
+                    break
 
         if trajectory is None:
             raise ValueError("Couldn't find a trajectory")