Merge pull request #101 from tleonardi/release_v1.0.0rc3

Release v1.0.0rc3

.gitignore

@@ -108,3 +108,4 @@ site/
 data
 docs/demo/results
 tmp
+dev

.travis.yml

@@ -1,29 +1,37 @@
 dist: xenial
 language: python
+
 stage: test
+
 python:
-  - 3.5
   - 3.6
   - 3.7
+
 branches:
   only:
   - master
   - devel
+
+before_install:
+  - pip install poetry
+
 install:
-  - pip install 'pytest>=4.4.0' --upgrade
-  - pip install .
+  - poetry install -v
+
 script:
   - pytest
+
 notifications:
   slack:
     secure: Hz3J3AluB4lN+YxRxsV93IjL0j5pevTDXflw9YN6VWH99BL7OEJxhsOGtqHLqbUDa4+XPVGgFsAXiHZPO19d4jng5uIRbj7VZNFK7gwn58S3GfyMeGOjdYh0fB/xbgYn2jYM1cWGpanwtXq5aDVEHPL2M803UMyyAM2F/HmysRdr50VFYQJQ4It77H+vajtyZGL7ztuAuY2AD10v5PctGk9JYt/EQWbYwdtCSdUNHublwiLRzvyvT/LT//MzsELuMdKzaVPQn01PMjZNerOsBszgscfBEOCSJtLaCjlQwvONWFCx9xP0kVBfMQo55XQaD9cSyswVnigzTihGaozU+149ZTWpB57Xd0tAsQ05GJIatbB+8FGKmFkFjvkxBSGXkL3AYN0engOpZyR4/KHrmKlSu2oCLbJMqvdnjlm/V41IV8UiMCgRCF/kMvHcHtgnBezV36+0eRMEWW7Vz7GAh7Eeqo3kcSTFG6OHD5kkiVoDW+S64cunHcb6k8sM+N/WxadpFV+jzzK/ovoDOA7G7gxhzgONJ8BYC2azZmRf+JfhosbRTh7PgMEi1srOlmJSZAzbE4IVJYcqOWbIdHO+v+1scYepPvzOuCXlD98UNhOOtAaMKXy9zGz2IYgbcswHOdUFnD2ei53pGz5QLJ0VLh7ZpBYfEEVB7uKbKsGuWB8=
+
 jobs:
   include:
     - stage: deploy
       python: 3.7
       install: 
-        - pip install nbconvert
-        - pip install mkdocs pymdown-extensions mknotebooks mkdocs-material
+        - pip install poetry
+        - poetry install -v
       script:
         - mkdocs build
       deploy: &gh-pages

CHANGELOG.md

@@ -0,0 +1,23 @@
+# Changelog
+
+## [v1.0.0rc3]
+
+### Added
+- Reads simulator now uses variability measured from the data
+- Switched to Poetry
+- Improved error reporting in TxComp
+
+### Fixed
+- Fixed multithreading errors
+- Fixed error in SampCompDB.plot_position() (#85)
+- Fixed errors with 0 pvalues (#87 and #90)
+- Fixed error when passing a Whitelist object to SampComp (#91)
+
+## [v1.0.0rc2]
+
+### Added
+- Continuous testing with Travis CI
+- Automatic deployment of docs to gh-pages
+
+### Fixed
+- Fixed "Not enough p-values" error. Issue #68

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 aleg@ebi.ac.uk. 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

CONTRIBUTING.md

@@ -0,0 +1,81 @@
+# Contributing to nanocompore
+
+First of all, thanks for considering contributing to `nanocompore`! 👍 It's people like you that make it rewarding for us to work on `nanocompore`.
+
+`nanocompore` is an open source project, maintained by publicly funded academic researchers.
+
+[repo]: https://github.com/tleonardi/nanocompore
+[issues]: https://github.com/tleonardi/nanocompore/issues
+[new_issue]: https://github.com/tleonardi/nanocompore/issues/new
+[code_of_conduct]: https://github.com/tleonardi/nanocompore/blob/master/docs/code_of_conduct.md
+
+## Code of conduct
+
+Please note that this project is released with a [Contributor Code of Conduct][code_of_conduct.md]. By participating in this project you agree to abide by its terms.
+
+## How you can contribute
+
+There are several ways you can contribute to this project. If you want to know more about why and how to contribute to open source projects like this one, see this [Open Source Guide](https://opensource.guide/how-to-contribute/).
+
+### Share the love ❤️
+
+Think `nanocompore` is useful? Let others discover it, by telling them in person, via Twitter or a blog post.
+
+Using `nanocompore` for a paper you are writing? Please cite it.
+
+### Ask a question ⁉️
+
+Using `nanocompore` and got stuck? Browse the documentation to see if you can find a solution.
+
+Still stuck? Post your question as an [issue on GitHub][new_issue].
+
+While we cannot offer user support, we'll try to do our best to address it, as questions often lead to better documentation or the discovery of bugs.
+
+
+### Propose an idea 💡
+
+Have an idea for a new `nanocompore` feature? Take a look at the [issue list][issues] to see if it isn't included or suggested yet. If not, suggest your idea as an [issue on GitHub][new_issue]. While we can't promise to implement your idea, it helps to:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible.
+
+See below if you want to contribute code for your idea as well.
+
+### Report a bug 🐛
+
+Using `nanocompore` and discovered a bug? That's annoying! Don't let others have the same experience and report it as an [issue on GitHub][new_issue] so we can fix it. A good bug report makes it easier for us to do so, so please include:
+
+* Your operating system name and version (e.g. Mac OS 10.13.6).
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+### Improve the documentation 📖
+
+Noticed a typo on the website? Think a function could use a better example? Good documentation makes all the difference, so your help to improve it is very welcome!
+
+1. Fork [nanocompore][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/).
+2. Edit the README.md file and submit a pull request. We will review your changes and include the fix in the next release.
+
+### Contribute code 📝
+
+Care to fix bugs or implement new functionality for `nanocompore`? Awesome! 👏 Have a look at the [issue list][issues] and leave a comment on the things you want to work on. See also the development guidelines below.
+
+## Development guidelines
+
+We try to follow the [GitHub flow](https://guides.github.com/introduction/flow/) for development and the [PEP 8](https://www.python.org/dev/peps/pep-0008/) style Guide for Python Code.
+
+1. Fork [nanocompore][repo] and clone it to your computer. To learn more about this process, see [this guide](https://guides.github.com/activities/forking/).
+
+2. If you have forked and cloned the project before and it has been a while since you worked on it, [pull changes from the original repo](https://help.github.com/articles/merging-an-upstream-repository-into-your-fork/) to your clone by using `git pull upstream master`.
+
+3. Make your changes and test the modified code.
+
+4. Commit and push your changes.
+
+5. Submit a [pull request](https://guides.github.com/activities/forking/#making-a-pull-request).
+
+
+
+---
+
+This file was adapted from a template created by [peterdesmet](https://gist.github.com/peterdesmet/e90a1b0dc17af6c12daf6e8b2f044e7c).