Add docs - merge first ?

.readthedocs.yaml

@@ -0,0 +1,19 @@
+# Read the Docs configuration file for MkDocs projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+  - requirements: docs/requirements.txt

docs/CODE_OF_CONDUCT.md

@@ -0,0 +1,137 @@
+# 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, caste, color, 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, Noah Fahlgren
+[[email protected]](mailto:[email protected]) and
+Malia Gehan [[email protected]](mailto:[email protected]).
+Alternatively, information about contacting the Danforth Center Human Resources
+department (including anonymous reporting) can be found at
+[https://www.danforthcenter.org/about-us/accountability/][accountability].
+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 2.1, available at
+[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1].
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][Mozilla CoC].
+
+For answers to common questions about this code of conduct, see the FAQ at
+[https://www.contributor-covenant.org/faq][FAQ]. Translations are available at
+[https://www.contributor-covenant.org/translations][translations].
+
+[homepage]: https://www.contributor-covenant.org
+[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html
+[Mozilla CoC]: https://github.com/mozilla/diversity
+[FAQ]: https://www.contributor-covenant.org/faq
+[translations]: https://www.contributor-covenant.org/translations
+[accountability]: https://www.danforthcenter.org/about-us/accountability

docs/documentation.md

@@ -0,0 +1,19 @@
+## Documentation
+
+PlantCV documentation is hosted on [Read the Docs](https://readthedocs.org/). 
+Using Read the Docs allows the documentation to be versioned along with
+the code. Because Read the Docs supports static content build tools like
+[Mkdocs](http://www.mkdocs.org/), documentation can be written in simple
+Markdown format that will be built into HTML automatically whenever a 
+new version of code is pushed to the PlantCV GitHub repository.
+
+### Updating PlantCV documentation
+
+Follow the [contribution guide](CONTRIBUTING.md) to learn how clone a copy of the PlantCV-Annotate
+repository, edit files, and generate a `pull` request to merge your updates back into the 
+main repository. Changes to PlantCV should be done in a branch, and pull against the 
+`main` branch  which corresponds to the `latest` version of the documentation on Read the Docs.
+
+PlantCV-Annotate is an add-on package to compliment functionality of
+[PlantCV](http://plantcv.danforthcenter.org) so please refer to the 
+[updating guide here](https://plantcv.readthedocs.io/en/latest/documentation/).

docs/index.md

@@ -0,0 +1,33 @@
+# Welcome to the documentation for PlantCV-Annotate
+
+## Overview
+
+[PlantCV-annotate](https://github.com/danforthcenter/plantcv-annotate) is composed of modular functions in order to be applicable to a 
+variety of plant types and imaging systems. In the following documentation we will describe use of each function and 
+provide tutorials on how each function is used in the context of an overall image-processing workflow. Development of 
+PlantCV is ongoing---we encourage input from the greater plant phenomics community. Please post questions and comments 
+on the [GitHub issues page](https://github.com/danforthcenter/plantcv-annotate/issues).
+
+## Getting started
+
+The documentation can be navigated using the sidebar table of contents. Documentation for individual PlantCV functions
+are listed under the headings "PlantCV Namespace". For general information on installation,
+updating, and other questions, see:
+
+* [Installing PlantCV](installation.md)
+
+## Contributing 
+
+If you are interested in contributing to PlantCV, please see:
+
+* [Contribution Guide](CONTRIBUTING.md)
+* [Code of Conduct](CODE_OF_CONDUCT.md)
+
+## Versions
+
+The documentation defaults to the `stable` version of PlantCV which is the current release version available from
+PyPI and Bioconda. Documentation for all releases from v1.1 on are also available via the standard Read the Docs 
+popup/pulldown menu (bottom right corner). Select the `latest` version to get the most up-to-date documentation
+associated with the current code in GitHub.
+
+[Return to the PlantCV homepage](http://plantcv.danforthcenter.org)

docs/installation.md

@@ -0,0 +1,57 @@
+## Installation
+
+### Table of contents
+1. [Supported platforms and dependencies](#dependencies)
+2. [Install via a package manager](#install)
+    - [PyPI](#pypi)
+3. [Installing PlantCV for contributors](#contributors)
+
+### Supported platforms and dependencies <a name="dependencies"></a>
+- Linux 64-bit, x86 processors
+- macOS x86 (Intel) and M (ARM) processors
+- Windows 64-bit, x86 processors
+
+PlantCV requires Python and these [Python packages](https://github.com/danforthcenter/plantcv/blob/main/requirements.txt).
+Additionally, we recommend installing [JupyterLab](https://jupyter.org/).
+
+#### PyPI <a name="pypi"></a>
+
+```bash
+pip install plantcv
+
+```
+
+Or with optional (but recommended) dependencies:
+
+```bash
+pip install plantcv jupyterlab ipympl
+
+```
+
+### Installing PlantCV for contributors <a name="contributors"></a>
+Before getting started, please read our [contributor guidelines](CONTRIBUTING.md) and [code of conduct](CODE_OF_CONDUCT.md).
+
+You can build PlantCV from the source code if you are a developer or want the absolute latest version available.
+As noted above, we recommend installing PlantCV in a virtual environment. We will outline how to do this using `conda`.
+You will also need a [GitHub](https://github.com) account. You will need to
+[clone](https://docs.github.com/en/repositories/creating-and-managing-repositories/cloning-a-repository) the PlantCV
+repository from GitHub before getting started.
+
+To set up your environment, follow these steps in your command-line terminal:
+
+```bash
+# Enter the PlantCV directory
+cd plantcv
+
+# Create a conda environment named "plantcv" (or whatever you like) and automatically install the developer dependencies
+conda env create -n plantcv -f environment.yml
+
+# Activate the plantcv environment (you will have to do this each time you start a new session)
+conda activate plantcv
+
+# Install PlantCV in editable mode so that it updates as you work on new features/updates
+pip install -e .
+
+pip install plantcv-annotate
+pip install -e .
+```

docs/requirements.txt

@@ -0,0 +1 @@
+mkdocs>1

mkdocs.yml

@@ -0,0 +1,24 @@
+site_name: PlantCV-annotate
+site_url: https://plantcv-annotate.readthedocs.io/
+site_description: Plant phenotyping annotation using computer vision
+site_author: PlantCV Development Team
+repo_url: https://github.com/danforthcenter/plantcv-annotate
+copyright: Copyright 2024, Donald Danforth Plant Science Center
+theme: readthedocs
+
+nav:
+- Home: index.md
+- Documentation:
+  - 'Installation': installation.md
+  - 'Analysis Approaches': analysis_approach.md
+  - 'Using Jupyter Notebooks': jupyter.md
+  - 'Contributing':
+    - 'Code of Conduct': CODE_OF_CONDUCT.md
+    - 'Adding/Editing Documentation': documentation.md
+  - 'PlantCV Namespace':
+    - 'Annotation Tools':
+        - 'Points': Points.md
+markdown_extensions:
+  - toc:
+      permalink: True
+  - admonition