Repo cleanup (#1055)

* Replace refs to Appveyor/Travis with Azure

* Move code of conduct and issue and PR templates to .github

* Fix typos, formatting, old references

* Remove dummy job from Azure

* Remove unused example documentation code

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,33 @@
+---
+name: Bug report
+about: Create a report to help us fix a bug
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+## Description
+
+<!--Please provide the following in your bug report:-->
+
+## Steps to Reproduce
+
+<!--Provide a minimal code snippet here to reproduce this error.-->
+
+## Environment
+
+<!--Please describe your environment according to the following bullet points.-->
+
+    Python Executable: Conda or Python
+    Python Version: Python 3.5, 3.6, or 3.7
+    Operating System: Windows, macOS or Linux
+    HDMF Version: Version of PyNWB used
+
+## Checklist
+
+- [ ] Have you ensured the feature or change was not already [reported](https://github.com/NeurodataWithoutBorders/pynwb/issues)?
+- [ ] Have you included a brief and descriptive title?
+- [ ] Have you included a clear description of the problem you are trying to solve?
+- [ ] Have you included a minimal code snippet that reproduces the issue you are encountering?
+- [ ] Have you checked our [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,30 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+Briefly describe the needed feature as well as the reasoning behind it
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm trying to achieve [...]
+
+**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.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.
+
+## Checklist
+
+- [ ] Have you ensured the feature or change was not already [reported](https://github.com/NeurodataWithoutBorders/pynwb/issues)?
+- [ ] Have you included a brief and descriptive title?
+- [ ] Have you included a clear description of the problem you are trying to solve?
+- [ ] Have you included a minimal code snippet that reproduces the issue you are encountering?
+- [ ] Have you checked our [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?

docs/PULL_REQUEST_TEMPLATE.md → .github/PULL_REQUEST_TEMPLATE.md

@@ -11,6 +11,6 @@ Show here how to reproduce the new behavior (can be a bug fix or a new feature)
 
 - [ ] Have you checked our [Contributing](https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst) document?
 - [ ] Have you ensured the PR description clearly describes problem and the solution?
-- [ ] Is your contribution compliant with our coding style ? This can be checked running `flake8` from the source directory.
+- [ ] Is your contribution compliant with our coding style? This can be checked running `flake8` from the source directory.
 - [ ] Have you checked to ensure that there aren't other open [Pull Requests](https://github.com/NeurodataWithoutBorders/pynwb/pulls) for the same change?
-- [ ] Have you included the relevant issue number using `#XXX` notation where `XXX` is the issue number ?
+- [ ] Have you included the relevant issue number using `#XXX` notation where `XXX` is the issue number?

Makefile

@@ -46,7 +46,7 @@ checkpdb:
 	find {src,tests} -name "*.py" -exec grep -Hn -e pdb -e breakpoint {} \;
 
 devtest:
-	$(PYTHON) -W ignore:::pynwb.form.build.map: test.py -fpi
+	$(PYTHON) test.py
 
 testclean:
 	rm *.npy *.nwb *.yaml

README.rst

@@ -5,7 +5,7 @@ PyNWB
 Documentation of PyNWB can be found at https://pynwb.readthedocs.io
 
 Latest Release
---------------
+==============
 
 .. image:: https://badge.fury.io/py/pynwb.svg
      :target: https://badge.fury.io/py/pynwb
@@ -15,7 +15,7 @@ Latest Release
 
 
 Build Status
-------------
+============
 
 .. table::
 
@@ -35,7 +35,7 @@ Build Status
 
 
 Overall Health
---------------
+==============
 
 .. image:: https://codecov.io/gh/NeurodataWithoutBorders/pynwb/branch/dev/graph/badge.svg
     :target: https://codecov.io/gh/NeurodataWithoutBorders/pynwb
@@ -67,12 +67,12 @@ See the PyNWB documentation for details http://pynwb.readthedocs.io/en/latest/ge
 Code of Conduct
 ===============
 
-This project and everyone participating in it is governed by our `code of conduct guidelines <docs/CODE_OF_CONDUCT.rst>`_ . By participating, you are expected to uphold this code.
+This project and everyone participating in it is governed by our `code of conduct guidelines <.github/CODE_OF_CONDUCT.rst>`_. By participating, you are expected to uphold this code.
 
 Contributing
 ============
 
-For details on how to contribute to PyNWB see our `contribution guidelines <docs/CONTRIBUTING.rst>`_ .
+For details on how to contribute to PyNWB see our `contribution guidelines <docs/CONTRIBUTING.rst>`_.
 
 LICENSE
 =======

azure-pipelines.yml

@@ -3,30 +3,8 @@ trigger:
 
 jobs:
 
-- job: 'Dummy'
-  displayName: 'Dummy'
-
-  pool:
-    vmImage: 'ubuntu-16.04'
-
-  steps:
-
-  - task: UsePythonVersion@0
-    inputs:
-      versionSpec: '3.7'
-      architecture: 'x64'
-
-  - script: |
-      python -m pip install --upgrade pip
-    displayName: 'Install build dependencies'
-
-  - script: |
-      python --version
-    displayName: 'Check Python version'
-
 - job: 'Test'
   displayName: "Test PyNWB"
-  dependsOn: Dummy
 
   strategy:
     matrix:

docs/CONTRIBUTING.rst

@@ -6,7 +6,7 @@ How to contribute to NWB:N software and documents
 Code of Conduct
 ---------------
 
-This project and everyone participating in it is governed by our `code of conduct guidelines <https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/docs/CONTRIBUTING.rst>`_. By participating, you are expected to uphold this code. Please report unacceptable behavior.
+This project and everyone participating in it is governed by our `code of conduct guidelines <https://github.com/NeurodataWithoutBorders/pynwb/blob/dev/.github/CONTRIBUTING.rst>`_. By participating, you are expected to uphold this code. Please report unacceptable behavior.
 
 .. _sec-contribution-types:
 
@@ -18,11 +18,11 @@ Did you find a bug? or Do you intend to add a new feature or change an existing
 
 * **Identify the appropriate repository** for the change you are suggesting:
 
-   * Use `nwb_schema <https://github.com/NeurodataWithoutBorders/nwb-schema/>`_ for any changes to the NWB:N format schema, schema language, storage and other NWB:N related documents
+   * Use `nwb-schema <https://github.com/NeurodataWithoutBorders/nwb-schema/>`_ for any changes to the NWB:N format schema, schema language, storage, and other NWB:N related documents
    * Use `PyNWB <https://github.com/NeurodataWithoutBorders/pynwb>`_  for any changes regarding the PyNWB API and the corresponding documentation
    * Use `MatNWB <https://github.com/NeurodataWithoutBorders/matnwb>`_  for any changes regarding the PyNWB API and the corresponding documentation
 
-* **Ensure the feature or change was not already reported** by searching on GitHub under `PyNWB Issues <https://github.com/NeurodataWithoutBorders/pynwb/issues>`_ and  `nwh-schema issues <https://github.com/NeurodataWithoutBorders/nwb-schema/issues>`_ , respectively .
+* **Ensure the feature or change was not already reported** by searching on GitHub under `PyNWB Issues <https://github.com/NeurodataWithoutBorders/pynwb/issues>`_ and `nwb-schema issues <https://github.com/NeurodataWithoutBorders/nwb-schema/issues>`_, respectively .
 
 * If you are unable to find an open issue addressing the problem then open a new issue on the respective repository. Be sure to include:
 
@@ -38,25 +38,22 @@ Did you write a patch that fixes a bug or implements a new feature?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 See the ``Contributing Patches and Changes`` section below for details.
 
-
 Do you have questions about NWB:N?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Join the `NWB:N mailing list <http://visitor.r20.constantcontact.com/manage/optin?v=001nQUq2GTjwCjZxK_V2-6RLElLJO1HMVtoNLJ-wGyDCukZQZxu2AFJmNh6NS0_lGMsWc2w9hZpeNn74HuWdv5RtLX9qX0o0Hy1P0hOgMrkm2NoGAX3VoY25wx8HAtIZwredcCuM0nCUGodpvoaue3SzQ%3D%3D>`_ for updates or ask questions on our `google group <https://groups.google.com/forum/#!forum/neurodatawithoutborders>`_.
-
+Ask questions on our `Slack workspace <https://nwb-users.slack.com>`_ or sign up for our `NWB:N mailing list <http://visitor.r20.constantcontact.com/manage/optin?v=001nQUq2GTjwCjZxK_V2-6RLElLJO1HMVtoNLJ-wGyDCukZQZxu2AFJmNh6NS0_lGMsWc2w9hZpeNn74HuWdv5RtLX9qX0o0Hy1P0hOgMrkm2NoGAX3VoY25wx8HAtIZwredcCuM0nCUGodpvoaue3SzQ%3D%3D>`_ for updates.
 
-Informal discussions between developers, users, and team?
+Informal discussions between developers and users?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The https://nwb-users.slack.com slack is currently used  mainly for internal discussions between developers, users, and teams.
-
+The https://nwb-users.slack.com slack is currently used mainly for informal discussions between developers and users.
 
 .. _sec-contributing:
 
 Contributing Patches and Changes
 --------------------------------
 
-The ``dev`` branches of `PyNWB <https://github.com/NeurodataWithoutBorders/pynwb>`_ and `nwb_schema <https://github.com/NeurodataWithoutBorders/nwb-schema/>`_, are protected; you cannot push to them directly. You must upload your changes by pushing a new branch, then submit your changes to the ``dev`` branch via a `Pull Request <https://help.github.com/articles/creating-a-pull-request>`_. This allows us to conduct automated testing of your contribution, and gives us a space for developers to discuss the contribution and request changes. If you decide to tackle an issue, please make yourself an assignee on the issue to communicate this to the team. Don't worry - this does not commit you to solving this issue. It just lets others know who they should talk to about it. 
+The ``dev`` branches of `PyNWB <https://github.com/NeurodataWithoutBorders/pynwb>`_ and `nwb-schema <https://github.com/NeurodataWithoutBorders/nwb-schema/>`_, are protected; you cannot push to them directly. You must upload your changes by pushing a new branch, then submit your changes to the ``dev`` branch via a `Pull Request <https://help.github.com/articles/creating-a-pull-request>`_. This allows us to conduct automated testing of your contribution, and gives us a space for developers to discuss the contribution and request changes. If you decide to tackle an issue, please make yourself an assignee on the issue to communicate this to the team. Don't worry - this does not commit you to solving this issue. It just lets others know who they should talk to about it.
 
 From your local copy directory, use the following commands.
 
@@ -90,7 +87,6 @@ If you have not already, you will need to clone the repo:
     * If you would like help with your contribution, or would like to communicate contributions that are not ready to merge, submit a PR where the title begins with "[WIP]."
     * **NOTE:** Contributed branches will be removed by the development team after the merge is complete and should, hence, not be used after the pull request is complete.
 
-
 .. _sec-issue-labels:
 
 Issue Labels, Projects, and Milestones
@@ -134,15 +130,13 @@ Git Commit Message Styleguide
 Documentation Styleguide
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
-All documentations is written in reStrcuturedText (RST) using Sphinx.
-
+All documentations is written in reStructuredText (RST) using Sphinx.
 
 Did you fix whitespace, format code, or make a purely cosmetic patch in source code?
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Source code changes that are purely cosmetic in nature and do not add anything substantial to the stability, functionality, or testability will generally not be accepted unless they have been approved beforehand. One of the main reasons is that there are a lot of hidden costs in addition to writing the code itself, and with the limited resources of the project, we need to optimize developer time. E.g,. someone needs to test and review PRs, backporting of bug fixes gets harder, it creates noise and pollutes the git repo and many other cost factors.
 
-
 Format Specification Styleguide
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -151,20 +145,20 @@ Format Specification Styleguide
 Python Code Styleguide
 ^^^^^^^^^^^^^^^^^^^^^^
 
-Python coding style is checked via ``flake8`` for automatic checking of PEP8 style during pull requets.
+Python coding style is checked via ``flake8`` for automatic checking of PEP8 style during pull requests.
 
 Endorsement
 -----------
 
 Please don’t take the fact that working with an organization (e.g., during a hackathon or via GitHub) as an endorsement of your work or your organization. It’s okay to say  e.g., “We worked with XXXXX to advance science” but not e.g., “XXXXX supports our work on NWB”.”
 
-Licence and Copyright
+License and Copyright
 =======================
 
-See the `Readme <https://github.com/NeurodataWithoutBorders/pynwb#contributing>`_ and correspoding `licence <https://raw.githubusercontent.com/NeurodataWithoutBorders/pynwb/dev/license.txt>`_ files for details about the copyright and licence.
+See the `license <https://raw.githubusercontent.com/NeurodataWithoutBorders/pynwb/dev/license.txt>`_ files for details about the copyright and license.
 
 As indicated in the PyNWB license: *“You are under no obligation whatsoever to provide any bug fixes, patches, or upgrades to the features, functionality or performance of the source code ("Enhancements") to anyone; however, if you choose to make your Enhancements available either publicly, or directly to Lawrence Berkeley National Laboratory, without imposing a separate written license agreement for such Enhancements, then you hereby grant the following license: a non-exclusive, royalty-free perpetual license to install, use, modify, prepare derivative works, incorporate into other computer software, distribute, and sublicense such enhancements or derivative works thereof, in binary and source code form.”*
 
-Contributors to the NWB code base are expected to use a permissive, non-copyleft open source license. Typically 3-clause BSD i used, but any compatible license is allowed, the MIT and Apache 2.0 licenses being good alternative choices. The GPL and other copyleft licenses are not allowed due to the consternation it generates across many organizations.
+Contributors to the NWB code base are expected to use a permissive, non-copyleft open source license. Typically 3-clause BSD is used, but any compatible license is allowed, the MIT and Apache 2.0 licenses being good alternative choices. The GPL and other copyleft licenses are not allowed due to the consternation it generates across many organizations.
 
 Also, make sure that you are permitted to contribute code. Some organizations, even academic organizations, have agreements in place that discuss IP ownership in detail (i.e., address IP rights and ownership that you create while under the employ of the organization). These are typically signed documents that you looked at on your first day of work and then promptly forgot. We don’t want contributed code to be yanked later due to IP issues.