qdiffusivity 0.1.0__tar.gz

qdiffusivity-0.1.0/AUTHORS.md

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+# Authors
+
+qdiffusivity was created by Shern Ren Tee in 2026.
+
+
+All contributing authors are listed in this file below.
+The repository history at https://github.com/srtee/qdiffusivity
+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
+-->
+
+**2026**
+- Shern Ren Tee <@srtee>

qdiffusivity-0.1.0/CHANGELOG.md

@@ -0,0 +1,37 @@
+# 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 -->

qdiffusivity-0.1.0/CODE_OF_CONDUCT.md

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+# Code of conduct
+
+The qdiffusivity *Code of Conduct* sets the rules for the behavior of
+every member in the qdiffusivity 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
+
+qdiffusivity 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 qdiffusivity 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 qdiffusivity is no exception. It is important
+   that we resolve disagreements and differing views constructively. Remember
+   that we’re different. The strength of qdiffusivity 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 'shernren@gmail.com'. 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 qdiffusivity.
+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. 

qdiffusivity-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026, Shern Ren Tee
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

qdiffusivity-0.1.0/MANIFEST.in

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+include LICENSE
+include MANIFEST.in
+include AUTHORS.md CHANGELOG.md CODE_OF_CONDUCT.md README.md
+
+graft qdiffusivity
+global-exclude *.py[cod] __pycache__ *.so

qdiffusivity-0.1.0/PKG-INFO

@@ -0,0 +1,123 @@
+Metadata-Version: 2.4
+Name: qdiffusivity
+Version: 0.1.0
+Summary: Quantile-based estimation of local diffusivities in molecular dynamics simulations of nanoconfined liquids
+Author-email: Shern Ren Tee <shernren@gmail.com>
+Maintainer-email: Shern Ren Tee <shernren@gmail.com>
+License-Expression: MIT
+Keywords: molecular simulations
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: MDAnalysis>=2.0.0
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-xdist>=2.5; extra == "test"
+Requires-Dist: pytest-cov>=3.0; extra == "test"
+Provides-Extra: doc
+Requires-Dist: sphinx; extra == "doc"
+Requires-Dist: sphinx_rtd_theme; extra == "doc"
+Dynamic: license-file
+
+qdiffusivity
+==============================
+[//]: # (Badges)
+
+| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]  [![Documentation Status][badge_docs]][url_docs]|
+| :----------------- | :------- |
+| **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
+| **Community**      | [![License: MIT License][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
+
+[badge_actions]: https://github.com/srtee/qdiffusivity/actions/workflows/gh-ci.yaml/badge.svg
+[badge_codecov]: https://codecov.io/gh/srtee/qdiffusivity/branch/main/graph/badge.svg
+[badge_commits_since]: https://img.shields.io/github/commits-since/srtee/qdiffusivity/latest
+[badge_docs]: https://readthedocs.org/projects/qdiffusivity/badge/?version=latest
+[badge_license]: https://img.shields.io/badge/License-MIT-yellow.svg
+[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
+[badge_release]: https://img.shields.io/github/release-pre/srtee/qdiffusivity.svg
+[url_actions]: https://github.com/srtee/qdiffusivity/actions?query=branch%3Amain+workflow%3Agh-ci
+[url_codecov]: https://codecov.io/gh/srtee/qdiffusivity/branch/main
+[url_docs]: https://qdiffusivity.readthedocs.io/en/latest/?badge=latest
+[url_latest_release]: https://github.com/srtee/qdiffusivity/releases
+[url_license]: https://opensource.org/licenses/MIT
+[url_mda]: https://www.mdanalysis.org
+
+Quantile-based estimation of local diffusivities in molecular dynamics simulations of nanoconfined liquids
+
+qdiffusivity is bound by a [Code of Conduct](https://github.com/srtee/qdiffusivity/blob/main/CODE_OF_CONDUCT.md).
+
+### Installation
+
+To build qdiffusivity from source,
+we highly recommend using virtual environments.
+If possible, we strongly recommend that you use
+[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
+Below we provide instructions both for `conda` and
+for `pip`.
+
+#### With conda
+
+Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+
+Create a virtual environment and activate it:
+
+```
+conda create --name qdiffusivity
+conda activate qdiffusivity
+```
+
+Install the development and documentation dependencies:
+
+```
+conda env update --name qdiffusivity --file devtools/conda-envs/test_env.yaml
+conda env update --name qdiffusivity --file docs/requirements.yaml
+```
+
+Build this package from source:
+
+```
+pip install -e .
+```
+
+If you want to update your dependencies (which can be risky!), run:
+
+```
+conda update --all
+```
+
+And when you are finished, you can exit the virtual environment with:
+
+```
+conda deactivate
+```
+
+#### With pip
+
+To build the package from source, run:
+
+```
+pip install .
+```
+
+If you want to create a development environment, install
+the dependencies required for tests and docs with:
+
+```
+pip install ".[test,doc]"
+```
+
+### Copyright
+
+The qdiffusivity source code is hosted at https://github.com/srtee/qdiffusivity
+and is available under the [MIT License](https://opensource.org/licenses/MIT) (see the file [LICENSE](https://github.com/srtee/qdiffusivity/blob/main/LICENSE)).
+
+Copyright (c) 2026, Shern Ren Tee
+
+
+#### Acknowledgements
+ 
+Project based on the 
+[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
+Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using qdiffusivity in published work.

qdiffusivity-0.1.0/README.md

@@ -0,0 +1,100 @@
+qdiffusivity
+==============================
+[//]: # (Badges)
+
+| **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since]  [![Documentation Status][badge_docs]][url_docs]|
+| :----------------- | :------- |
+| **Status**         | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
+| **Community**      | [![License: MIT License][badge_license]][url_license]  [![Powered by MDAnalysis][badge_mda]][url_mda]|
+
+[badge_actions]: https://github.com/srtee/qdiffusivity/actions/workflows/gh-ci.yaml/badge.svg
+[badge_codecov]: https://codecov.io/gh/srtee/qdiffusivity/branch/main/graph/badge.svg
+[badge_commits_since]: https://img.shields.io/github/commits-since/srtee/qdiffusivity/latest
+[badge_docs]: https://readthedocs.org/projects/qdiffusivity/badge/?version=latest
+[badge_license]: https://img.shields.io/badge/License-MIT-yellow.svg
+[badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
+[badge_release]: https://img.shields.io/github/release-pre/srtee/qdiffusivity.svg
+[url_actions]: https://github.com/srtee/qdiffusivity/actions?query=branch%3Amain+workflow%3Agh-ci
+[url_codecov]: https://codecov.io/gh/srtee/qdiffusivity/branch/main
+[url_docs]: https://qdiffusivity.readthedocs.io/en/latest/?badge=latest
+[url_latest_release]: https://github.com/srtee/qdiffusivity/releases
+[url_license]: https://opensource.org/licenses/MIT
+[url_mda]: https://www.mdanalysis.org
+
+Quantile-based estimation of local diffusivities in molecular dynamics simulations of nanoconfined liquids
+
+qdiffusivity is bound by a [Code of Conduct](https://github.com/srtee/qdiffusivity/blob/main/CODE_OF_CONDUCT.md).
+
+### Installation
+
+To build qdiffusivity from source,
+we highly recommend using virtual environments.
+If possible, we strongly recommend that you use
+[Anaconda](https://docs.conda.io/en/latest/) as your package manager.
+Below we provide instructions both for `conda` and
+for `pip`.
+
+#### With conda
+
+Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
+
+Create a virtual environment and activate it:
+
+```
+conda create --name qdiffusivity
+conda activate qdiffusivity
+```
+
+Install the development and documentation dependencies:
+
+```
+conda env update --name qdiffusivity --file devtools/conda-envs/test_env.yaml
+conda env update --name qdiffusivity --file docs/requirements.yaml
+```
+
+Build this package from source:
+
+```
+pip install -e .
+```
+
+If you want to update your dependencies (which can be risky!), run:
+
+```
+conda update --all
+```
+
+And when you are finished, you can exit the virtual environment with:
+
+```
+conda deactivate
+```
+
+#### With pip
+
+To build the package from source, run:
+
+```
+pip install .
+```
+
+If you want to create a development environment, install
+the dependencies required for tests and docs with:
+
+```
+pip install ".[test,doc]"
+```
+
+### Copyright
+
+The qdiffusivity source code is hosted at https://github.com/srtee/qdiffusivity
+and is available under the [MIT License](https://opensource.org/licenses/MIT) (see the file [LICENSE](https://github.com/srtee/qdiffusivity/blob/main/LICENSE)).
+
+Copyright (c) 2026, Shern Ren Tee
+
+
+#### Acknowledgements
+ 
+Project based on the 
+[MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
+Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using qdiffusivity in published work.

qdiffusivity-0.1.0/pyproject.toml

@@ -0,0 +1,97 @@
+[build-system]
+requires = [
+  "setuptools >=77",
+  "versioningit",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qdiffusivity"
+description = "Quantile-based estimation of local diffusivities in molecular dynamics simulations of nanoconfined liquids"
+license = "MIT"
+license-files = ["LICENSE", "AUTHORS.md"]
+
+authors = [
+    {name = "Shern Ren Tee", email = "shernren@gmail.com"},
+]
+maintainers = [
+    {name = "Shern Ren Tee", email = "shernren@gmail.com"},
+]
+readme = "README.md"
+requires-python = ">=3.9"
+dependencies = [
+    "MDAnalysis>=2.0.0",
+]
+keywords = [
+    "molecular simulations",
+]
+classifiers = [
+    "Programming Language :: Python :: 3",
+]
+dynamic = [
+    "version",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6.0",
+    "pytest-xdist>=2.5",
+    "pytest-cov>=3.0",
+]
+doc = [
+    "sphinx",
+    "sphinx_rtd_theme",
+]
+
+# [project.urls]
+# source = "https://github.com/srtee/qdiffusivity"
+# documentation = "https://qdiffusivity.readthedocs.io"
+
+[tool.setuptools.packages.find]
+include = ["qdiffusivity"]
+
+[tool.pytest.ini_options]
+minversion = "6.0"
+testpaths = [
+    "qdiffusivity/tests",
+]
+
+[tool.black]
+line-length = 80
+
+[tool.versioningit]
+default-version = "1+unknown"
+
+[tool.versioningit.vcs]
+method = "git"
+# the below line expects tags to look like '1.0.2'.
+# if prefixing with a v, e.g. 'v1.0.2', change it to ["v*"]
+match = ["*"]
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.coverage.run]
+omit = [
+    # Omit the tests
+    "*/tests/*",
+]
+
+[tool.coverage.report]
+exclude_also = [
+    "if TYPE_CHECKING:",
+]
+
+[tool.isort]
+multi_line_output = 3
+include_trailing_comma = true
+force_grid_wrap = 0
+use_parentheses = true
+line_length = 80
+
+[tool.yapf]
+COLUMN_LIMIT = 80
+INDENT_WIDTH = 4
+USE_TABS = false

qdiffusivity-0.1.0/qdiffusivity/__init__.py

@@ -0,0 +1,51 @@
+"""
+qdiffusivity
+Quantile-based estimation of local diffusivities in molecular dynamics
+simulations of nanoconfined liquids
+"""
+
+# Add imports here
+from importlib.metadata import version
+
+from .binned import (
+    LocalDiffusivityQBinned,
+    TransverseDensityQBinned,
+    cic_assign,
+    resolve_bins,
+)
+from .density import (
+    TransverseDensityQKDE,
+    epanechnikov_kernel,
+    kde_1d,
+    select_bandwidth,
+    sheather_jones_bw,
+    silverman_bw,
+)
+from .diffusivity import (
+    LocalDiffusivityQKDE,
+    build_cdf,
+    gaussian_kernel,
+    kde_estimate,
+    select_diff_bandwidth,
+)
+
+__version__ = version("qdiffusivity")
+
+__all__ = [
+    "TransverseDensityQBinned",
+    "TransverseDensityQKDE",
+    "LocalDiffusivityQBinned",
+    "LocalDiffusivityQKDE",
+    "build_cdf",
+    "cic_assign",
+    "epanechnikov_kernel",
+    "gaussian_kernel",
+    "kde_1d",
+    "kde_estimate",
+    "resolve_bins",
+    "select_bandwidth",
+    "select_diff_bandwidth",
+    "sheather_jones_bw",
+    "silverman_bw",
+    "__version__",
+]