Merge branch 'distances' of github.com:MDAnalysis/UserGuide into dist…

…ances

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,52 @@
+---
+name: Bug report
+about: Create a report to help us fix mistakes in the user guide
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected from the user guide. Please include a link to the any sections that you reference.
+
+**Actual behavior**
+What is there, or not there, instead. Add as much detail as you can. Include (copy and paste) error messages, stack traces, and output of any code that is related.
+
+If applicable, show us how to reproduce the failure. If you can, use trajectory files from the test data.
+
+``` python
+import MDAnalysis as mda
+from MDAnalysis.tests.datafiles import PSF, DCD,  GRO, PDB, TPR, XTC, TRR,  PRMncdf, NCDF
+
+u = mda.Universe(PSF, DCD)
+
+....
+
+```
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+- Which version of MDAnalysis? (run `python -c "import MDAnalysis as mda; print(mda.__version__)"`)
+- Which version of Python (`python -V`)?
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**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 [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to see in the user guide. e.g. a new page of information? A short Jupyter notebook example? An extended tutorial?
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/questions.md

@@ -0,0 +1,27 @@
+---
+name: Questions
+about: If you want to ask a question please use the mailing list!
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+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 
+
+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 direction of the user guide. 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 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.
+
+Thank you!
+
+The MDAnalysis Development Team

doc/source/conf.py

@@ -72,9 +72,11 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
+
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store',
                     '.ipynb_checkpoints', '**/.ipynb_checkpoints', 'scripts', '.*.ipynb']
 
+
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
@@ -147,6 +149,7 @@
 intersphinx_mapping = {'https://docs.python.org/': None,
                        'https://docs.scipy.org/doc/numpy/': None,
                        'https://www.mdanalysis.org/docs/': None,
+                       'https://docs.pytest.org/en/latest/': None,
                        }
 
 # nbsphinx