Merge branch 'release-0.16.0'

Author: Tim

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible 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.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders 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, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+gernat@illinois.edu.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,42 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+---
+
+## Description
+
+_Please provide a clear and concise description of what the bug is._
+
+## To reproduce
+
+_Describe how to reproduce the behavior._
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+## Expected behavior
+
+_Provide a clear and concise description of what you expected to happen._
+
+## Screenshots
+
+_If applicable, add screenshots to help explain your problem._
+
+## Environment
+
+_Please complete the following information._
+ 
+ - Device: [e.g. PC]
+ - Architecture: [e.g. x86_64]
+ - Operating system: [e.g. Linux 4.16.10]
+ - Java Version: [e.g. 1.8.0] 
+ - bTools Version: [e.g. v0.13.0]
+ 
+## Additional context
+
+_Add any other context about the problem here._

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,23 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+---
+
+## Problem
+
+_If your feature request is related to a problem, please provide a clear and concise description of what the problem is._ 
+
+## Solution
+
+_Provide a clear and concise description of what you want to happen._
+
+## Alternatives
+
+_Describe any alternative solutions or features you've considered._
+
+## Additional context
+
+_Add any other context about the feature request here._

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,28 @@
+## Types of changes
+
+_What types of changes does your code introduce? Put an X in the boxes that apply._
+
+- [ ] Bugfix (fixes an issue)
+- [ ] New feature (adds functionality)
+- [ ] Breaking change (causes existing functionality to not work as expected)
+- [ ] Documentation update (modifies documentation only)
+- [ ] Other (if none of the above choices apply)
+
+## Description
+
+_Describe your changes here. What are the current and the new behavior? If your changes fix a bug or resolve a feature request, please link to the corresponding issue._
+
+## Checklist
+
+_Put an X in the boxes that apply. If you're unsure about any of them, please ask._
+
+- [ ] I followed the guidelines in the CONTRIBUTING document
+- [ ] I signed the CLA
+- [ ] My pull request is not a duplicate
+- [ ] Lint and unit tests pass locally with my changes
+- [ ] I added tests that prove my fix is effective or that my feature works
+- [ ] I added necessary documentation (if appropriate)
+
+## Further comments
+
+_Add any other comments about the pull request here._

README.md .github/README.mdREADME.md renamed to .github/README.md

@@ -1,6 +1,6 @@
 # Overview
 
-bTools is a set of programs for identifying and tracking insects in image sequences with the help of a tiny matrix barcode, and for detecting movement as well as mouth-to-mouth exchange of liquid food among honey bees. 
+bTools is a set of programs for identifying and tracking insects in images or videos with the help of a tiny matrix barcode, called bCode. It also contains software for detecting movement and, for honey bees, flight activity and the mouth-to-mouth exchange of liquid (trophallaxis). 
 
 # Getting started
 
@@ -15,7 +15,8 @@ If you want to experiment with the code, please choose a branch and download or
 `Converter.java` - converts raw bCode detection results to a more useful format.  
 `Indexer.java` - indexes raw bCode detection results.  
 `TrophallaxisDetector.java` - detects liquid food exchange among honey bees.  
-`MovementDetector.java` - detects bCode movement.
+`MovementDetector.java` - detects bCode movement.  
+`FlightActivityDetector.java` - detects hive exits and returns.
 
 # Documentation
 

CHANGELOG

@@ -1,3 +1,7 @@
+0.16.0
+
+- Adds flight activity detector.
+
 0.15.1
 
 - Removes header from movement detection files.