v0.5.0 (#131)

* update develop version numbers

* Add new citing papers

* move plot_fundus to viz module

* fix nasal/temporal labeling for left eyes

* rename axons to bundles

* Update README.md

* Allow passing alpha constant to grid class (#86)

* Allow passing alpha constant to grid class

* Fixed PEP errors

* fixed more PEP errors

* revert to pep compiling with local flake

* changed travis specifications

* changed travis file & binary operators

* pep8 change

* Changed dask parameters from deprecated version

* Update references

* ENH: Switch to codecov (#91)

Add codecov to Travis yml

* add message in plot_fundus when loc_od_x has wrong sign

* Add citing article

* BF: Import `factorial` from `scipy.special` (#94)

Apparently as of scipy 1.0.0 this function was moved out of `scipy.misc`.

* Create CONTRIBUTING.md

* Update issue templates

* Create CODE_OF_CONDUCT.md

* [ENH] Add class for the AlphaIMS implant (#87)

* Added class for the AlphaIMS implant (in implants.py) and added respective isinstance checks and conditional sit.resize (in stimuli.py).

* fix typo in isalphaims

* Add RTD integration: badge, updated conf.py, requirements.txt

* Add boston-train-combined.mp4

* Add boston-train-combined.gif

* Create PULL_REQUEST_TEMPLATE.md (#126)

* [TST] Continuous integration with GitHub Actions for v0.5 (#129)

* add GitHub action on push; skip tests that require ffmpeg

skip ffmpeg doctests; fix flake8

* mark parfor test as expected fail

* add codecov

* drop Py2.7

* change pytest dir

* fix codecov path

* remove Travis

remove Py3.8 from matrix

add artifact upload

pip install wheel

add TestPyPI upload/verification

add runs-on

build on matrix.os

build on matrix.os

fix syntax error

* fix Matplotlib issue on Mac OS X

fix flake8

try to upgrade setuptools

* try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

try to fix Windows io.h issue

fix Windows env

fix Windows env

fix Windows env

add includes ucrt, um, shared

add LIB, PATH

add LIB, PATH

add LIB, PATH

install matplotlib on Win

debug win workflow

debug win workflow

debug win workflow

debug win workflow

* add Ubuntu 16.04, remove wheel building

* add supported platforms to README; document the workflow file

* fix checkout version

* [TST] Automatic wheelhouse build using Azure Pipelines (#130)

* Set up CI with Azure Pipelines

* Try to switch to Py35

* Install requirements

* Skip Py27

* Skip Python 3.8

* Add CIBW_BEFORE_BUILD

* Add CIBW_BEFORE_BUILD_LINUX

* Update requirements.txt

* Update CIBW_BEFORE_BUILD_LINUX

* Update CIBW_BEFORE_BUILD_LINUX

* Update azure-pipelines.yml

* add new release instructions to doc

* add azure triggers

* Remove pr from azure-pipelines.yml

* Add pr to azure-pipelines.yml

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[BUG]"
+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. Import '...'
+3. Run '...'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**System specifications (please complete the following information):**
+- OS: [e.g. iOS]
+- Python version: [e.g. 3.6]
+- pulse2percept version: [e.g. 0.4]
+
+**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 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.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,28 @@
+## Description
+
+<!-- Choose one of the following prefixes for the title of your PR:
+
+     [ENH] for enhancements
+     [FIX] for bug fixes
+     [TST] for new or updated tests
+     [DOC] for new or updated documentation
+     [STY] for stylistic changes
+     [REF] for refactoring existing code
+
+     If your PR is not yet ready to be merged, also add [WIP] to label it as a "work in progress".
+
+     If this is a bug-fix or enhancement, state the issue # it closes.
+     If this is a new feature, reference what paper it implements.
+-->
+
+## Checklist
+
+<!-- It's fine to submit PRs which are a work in progress!
+     But before they are merged, all PRs should provide: -->
+- [ ] [Docstrings for all functions](https://github.com/numpy/numpy/blob/master/doc/example.py)
+- [ ] Gallery example in `./examples` (new features only)
+- [ ] Unit tests
+- [ ] Clean style in [the spirit of PEP8](https://www.python.org/dev/peps/pep-0008/)
+
+<!-- For detailed information on these and other aspects, see the contribution guidelines:
+     https://pulse2percept.readthedocs.io/en/latest/developers/contributing.html -->

.github/workflows/main.yml

@@ -0,0 +1,70 @@
+name: Run CI checks
+
+on: [push, pull_request]
+
+# By default, jobs run in parallel on a fresh instance of the virtual
+# environment. You can force sequential order by specifying a job's
+# dependencies with the "needs" attribute.
+jobs: 
+
+  # Continuous integration: Run unit tests on all supported platforms whenever
+  # someone pushes a new commit or creates a pull request. 
+  build:
+    name: Building on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      max-parallel: 4
+      # Test on all supported platforms using all supported Python versions:
+      matrix:
+        python-version: [3.5, 3.6, 3.7]
+        os: [ubuntu-latest, ubuntu-16.04, windows-latest, macOS-latest]
+
+    steps:
+    - uses: actions/checkout@v1
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v1
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip wheel setuptools
+        # For Windows:
+        pip install matplotlib
+        # Install p2p requirements:
+        pip install -r requirements.txt
+    - name: Lint with flake8
+      run: |
+        pip install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 pulse2percept --ignore N802,N806,W503 --select W504 --count --show-source --statistics
+    - name: Install package (Windows)
+      # https://github.com/pandas-dev/pandas/issues/981
+      if: matrix.os == 'windows-latest'
+      run: |
+        $env:INCLUDE = 'C:\Program Files (x86)\Windows Kits\10\Include\10.0.16299.0\ucrt'
+        $env:INCLUDE += ';C:\Program Files (x86)\Windows Kits\10\Include\10.0.16299.0\shared'
+        $env:INCLUDE += ';C:\Program Files (x86)\Windows Kits\10\Include\10.0.16299.0\um'
+        $env:LIB = 'C:\Program Files (x86)\Windows Kits\10\Lib\10.0.16299.0\ucrt\x64'
+        $env:LIB += ';C:\Program Files (x86)\Windows Kits\10\Lib\10.0.16299.0\um\x64'
+        $env:PATH += ';C:\Program Files (x86)\Windows Kits\10\bin\10.0.16299.0\x64'
+        pip install -e .
+    - name: Install package (Unix)
+      if: matrix.os != 'windows-latest'
+      run: |
+        pip install -e .
+    - name: Run test suite with pytest
+      run: |
+        pip install pytest mock pytest-cov
+        mkdir test_dir
+        cd test_dir
+        pytest --pyargs pulse2percept --cov-report=xml --cov=pulse2percept --doctest-modules
+    - name: Upload coveragei report to codecov.io
+      uses: codecov/codecov-action@v1
+      # Cannot yet post coverage report as comments on the PR, but see:
+      # https://github.com/codecov/codecov-python/pull/214
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: ./test_dir/coverage.xml
+        flags: unittests
+        name: codecov-umbrella
+        yml: ./codecov.yml

CODE_OF_CONDUCT.md

@@ -0,0 +1,76 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, sex characteristics, gender identity and expression,
+level of experience, education, socio-economic status, nationality, personal
+appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+ advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+ address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+ professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at mbeyeler@uw.edu or arokem@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq