domhmm 1.1.0__tar.gz

domhmm-1.1.0/AUTHORS.md

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+# Authors
+
+DomHMM was created by Marius FW Trollmann and Yusuf Eren Tunç in 2024.
+
+
+All contributing authors are listed in this file below.
+The repository history at https://github.com/BioMemPhys-FAU/domhmm
+and the CHANGELOG show individual code contributions.
+
+## Chronological list of authors
+
+<!--
+The rules for this file:
+  * Authors are sorted chronologically, earliest to latest
+  * Please format it each entry as "Preferred name <GitHub username>"
+  * Your preferred name is whatever you wish to go by --
+    it does *not* have to be your legal name!
+  * Please start a new section for each new year
+  * Don't ever delete anything
+-->
+**2024**
+- Yusuf Eren Tunç <@yusuferentunc>
+
+**2023**
+- Marius FW Trollmann <@m-a-r-i-u-s>

domhmm-1.1.0/CHANGELOG.md

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+# Changelog
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+The rules for this file:
+  * entries are sorted newest-first.
+  * summarize sets of changes - don't reproduce every git log comment here.
+  * don't ever delete anything.
+  * keep the format consistent:
+    * do not use tabs but use spaces for formatting
+    * 79 char width
+    * YYYY-MM-DD date format (following ISO 8601)
+  * accompany each entry with github issue/PR number (Issue #xyz)
+-->
+
+## [Unreleased]
+
+### Authors
+<!-- GitHub usernames of contributors to this release -->
+
+### Added
+<!-- New added features -->
+
+### Fixed
+<!-- Bug fixes -->
+
+### Changed
+<!-- Changes in existing functionality -->
+
+### Deprecated
+<!-- Soon-to-be removed features -->
+
+### Removed
+<!-- Removed features -->

domhmm-1.1.0/CODE_OF_CONDUCT.md

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+# Code of conduct
+
+The domhmm *Code of Conduct* sets the rules for the behavior of
+every member in the domhmm community so that everyone can
+experience a welcoming, supportive, and productive environment that is
+free from harassment.
+
+<!-- markdown-toc start - Don't edit this section. Run M-x markdown-toc-generate-toc again -->
+**Table of Contents**
+
+- [Code of conduct](#code-of-conduct)
+  - [Code of Conduct and Community Guidelines](#code-of-conduct-and-community-guidelines)
+  - [Scope](#scope)
+  - [Enforcement](#enforcement)
+  - [Acknowledgment](#acknowledgment)
+
+<!-- markdown-toc end -->
+## Code of Conduct and Community Guidelines
+
+domhmm is part of an engaged and respectful community made up of people from all
+over the world. Your involvement helps us to further our mission and to create
+an open platform that serves a broad range of communities, from research and
+education to industry and beyond. This diversity is one of our biggest
+strengths, but it can also lead to communication issues and conflicts.
+Therefore, we have a few ground rules we ask that our community members adhere
+to.
+
+Fundamentally, we are committed to providing a productive,
+harassment-free environment for everyone. Rather than considering this
+code an exhaustive list of things that you can’t do, take it in the
+spirit it is intended - a guide to make it easier to enrich all of us
+and the communities in which we participate.
+
+Importantly: as a member of our community, you are also a steward of these
+values. Not all problems need to be resolved via formal processes, and often a
+quick, friendly but clear word on an online forum or in person can help resolve
+a misunderstanding and de-escalate things.
+
+By embracing the following principles, guidelines and actions to follow or
+avoid, you will help us make domhmm a welcoming and productive community.
+
+1. **Be friendly and patient**.
+
+2. **Be welcoming**. We strive to be a community that welcomes and supports
+   people of all backgrounds and identities. This includes, but is not limited
+   to, members of any race, ethnicity, culture, national origin, color,
+   immigration status, social and economic class, educational level, sex, sexual
+   orientation, gender identity and expression, age, physical appearance, family
+   status, political belief, technological or professional choices, academic
+   discipline, religion, mental ability, and physical ability.
+
+3. **Be considerate**. Your work will be used by other people, and you in turn
+   will depend on the work of others. Any decision you take will affect users
+   and colleagues, and you should take those consequences into account when
+   making decisions. Remember that we're a world-wide community. You may be
+   communicating with someone with a different primary language or cultural
+   background.
+
+4. **Be respectful**. Not all of us will agree all the time, but disagreement is
+   no excuse for poor behavior or poor manners. We might all experience some
+   frustration now and then, but we cannot allow that frustration to turn into a
+   personal attack. It’s important to remember that a community where people
+   feel uncomfortable or threatened is not a productive one.
+
+5. **Be careful in the words that you choose**. Be kind to others. Do not insult
+   or put down other community members. Harassment and other exclusionary
+   behavior are not acceptable. This includes, but is not limited to:
+   * threats or violent language directed against another person
+   * discriminatory jokes and language
+   * posting sexually explicit or violent material
+   * posting (or threatening to post) other people's personally identifying
+     information ("doxing")
+   * personal insults, especially those using racist or sexist terms
+   * unwelcome sexual attention
+   * advocating for, or encouraging, any of the above behavior
+   * repeated harassment of others. In general, if someone asks you to stop,
+     then stop
+
+6. **Moderate your expectations**. Many in our community volunteer their time.
+   They are probably not purposefully ignoring issues, refusing to engage in
+   discussion, avoiding features, etc. but often just unavailable.
+
+7. **When we disagree, try to understand why**. Disagreements, both social and
+   technical, happen all the time and domhmm is no exception. It is important
+   that we resolve disagreements and differing views constructively. Remember
+   that we’re different. The strength of domhmm comes from its varied community
+   that includes people from a wide range of backgrounds. Different people have
+   different perspectives on issues. Being unable to understand why someone
+   holds a viewpoint doesn’t mean they’re wrong. Don’t forget that it is human
+   to err and blaming each other doesn’t get us anywhere. Instead, focus on
+   helping to resolve issues and learning from mistakes.
+
+8. **A simple apology can go a long way**. It can often de-escalate a situation,
+   and telling someone that you are sorry is act of empathy that doesn’t
+   automatically imply an admission of guilt.
+
+
+## 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 'marius.trollmann@fau.de'. The project team will
+review and investigate all complaints, and will respond in a way that it deems
+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.
+
+
+## Acknowledgment
+
+Original text was adapted from
+the
+[*Speak Up!*](http://web.archive.org/web/20141109123859/http://speakup.io/coc.html),
+[*Django*](https://www.djangoproject.com/conduct),
+[*Contributor Covenant*](http://contributor-covenant.org/),
+[*Jupyter*](https://github.com/jupyter/governance/blob/master/conduct/code_of_conduct.md),
+[*MolSSI*](https://github.com/MolSSI/cookiecutter-cms/blob/master/%7B%7Bcookiecutter.repo_name%7D%7D/CODE_OF_CONDUCT.md),
+and [*MDAnalysis*](https://github.com/MDAnalysis/mdanalysis/blob/develop/CODE_OF_CONDUCT.md) projects,
+modified by domhmm.
+We are grateful to those projects for contributing these
+materials under open licensing terms for us to easily reuse.
+
+All content on this page is licensed under a [*Creative Commons
+Attribution*](http://creativecommons.org/licenses/by/3.0/) license. 

domhmm-1.1.0/LICENSE

@@ -0,0 +1,339 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
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+Foundation's software and to any other program whose authors commit to
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+
+  When we speak of free software, we are referring to freedom, not
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+
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+that everyone understands that there is no warranty for this free
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+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
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+Whether that is true depends on what the Program does.
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+You may charge a fee for the physical act of transferring a copy, and
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+  2. You may modify your copy or copies of the Program or any portion
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+distribute such modifications or work under the terms of Section 1
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+These requirements apply to the modified work as a whole.  If
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+                            NO WARRANTY
+
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+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
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+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
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+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
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+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
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+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
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+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

domhmm-1.1.0/MANIFEST.in

@@ -0,0 +1,7 @@
+include LICENSE
+include MANIFEST.in
+include AUTHORS.md CHANGELOG.md CODE_OF_CONDUCT.md README.md
+include versioneer.py
+
+graft domhmm
+global-exclude *.py[cod] __pycache__ *.so