From 0a2367cebc7feb7cba2a92e7df15c62e67065005 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Fri, 8 Mar 2024 09:11:08 -0600 Subject: [PATCH 01/16] documentation structure setup --- .readthedocs.yml | 19 ++++++ docs/CODE_OF_CONDUCT.md | 137 ++++++++++++++++++++++++++++++++++++++++ docs/documentation.md | 19 ++++++ docs/index.md | 33 ++++++++++ docs/installation.md | 31 +++++++++ docs/requirements.txt | 1 + mkdocs.yml | 24 +++++++ 7 files changed, 264 insertions(+) create mode 100644 .readthedocs.yml create mode 100644 docs/CODE_OF_CONDUCT.md create mode 100644 docs/documentation.md create mode 100644 docs/index.md create mode 100644 docs/installation.md create mode 100644 docs/requirements.txt create mode 100644 mkdocs.yml diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..c5587fb --- /dev/null +++ b/.readthedocs.yml @@ -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 diff --git a/docs/CODE_OF_CONDUCT.md b/docs/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..deb3b69 --- /dev/null +++ b/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 +[nfahlgren@danforthcenter.org](mailto:nfahlgren@danforthcenter.org) and +Malia Gehan [mgehan@danforthcenter.org](mailto:mgehan@danforthcenter.org). +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 diff --git a/docs/documentation.md b/docs/documentation.md new file mode 100644 index 0000000..33fb2a0 --- /dev/null +++ b/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-Geopspatial is an add-on package to compliment functionality of +[PlantCV](https://plantcv.org) so please refer to the +[updating guide here](https://plantcv.readthedocs.io/en/latest/documentation/). diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 0000000..b7ee1f8 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,33 @@ +# Welcome to the documentation for PlantCV-Geopspatial + +## Overview + +[PlantCV-Geospatial](https://github.com/danforthcenter/plantcv-geospatial) 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-Geospatial 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-geospatial/issues). + +## Getting started + +The documentation can be navigated using the sidebar table of contents. Documentation for individual PlantCV-Geospatial functions +are listed under the headings "PlantCV Namespace". For general information on installation, +updating, and other questions, see: + +* [Installing PlantCV-Geospatial](installation.md) + +## Contributing + +If you are interested in contributing to PlantCV-Geospatial, please see: + +* [Code of Conduct](CODE_OF_CONDUCT.md) +* [PlantCV Contributing Guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) + +## Versions + +The documentation defaults to the `stable` version of PlantCV-Geospatial which is the current release version available from +PyPI. 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](https://plantcv.org) diff --git a/docs/installation.md b/docs/installation.md new file mode 100644 index 0000000..88b3aa6 --- /dev/null +++ b/docs/installation.md @@ -0,0 +1,31 @@ +## Installation + +### Table of contents +1. [Supported platforms and dependencies](#dependencies) +2. [Install via a package manager](#install) +3. [Installing PlantCV for contributors](#contributors) + +### Supported platforms and dependencies +- Linux 64-bit, x86 processors +- macOS x86 (Intel) and M (ARM) processors +- Windows 64-bit, x86 processors + +First, you must have PlantCV installed, which requires Python and these [Python packages](https://github.com/danforthcenter/plantcv/blob/main/requirements.txt). Follow one of the methods for [PlantCV Installation](https://plantcv.readthedocs.io/en/latest/installation/) and then continue with the instructions below to add PlantCV-Geospatial to your environment. +Additionally, we recommend installing [JupyterLab](https://jupyter.org/). + +### Install via a package manager +[PyPi](https://pypi.org/) installation (after [PlantCV Installation](https://plantcv.readthedocs.io/en/latest/installation/#conda)): + +```bash +# Activate the plantcv environment (you will have to do this each time you start a new session) +conda activate plantcv +# Install plantcv-geospatial in editable mode so that it updates as you work on new features/updates +pip install plantcv-geospatial +pip install -e . +``` + +### Installing PlantCV for contributors +Before getting started, please read our [contributor guidelines](CONTRIBUTING.md) and [code of conduct](CODE_OF_CONDUCT.md). + +You can follow the [PlantCV Installation for Contributor Guide](https://plantcv.readthedocs.io/en/latest/installation/#contributors) and then continue with the instructions above to add PlantCV-Annotate to +your development environment. diff --git a/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 0000000..59fde8e --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1 @@ +mkdocs>1 diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 0000000..9af9e13 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,24 @@ +site_name: PlantCV-Geopspatial +site_url: https://plantcv-geospatial.readthedocs.io/ +site_description: Plant phenotyping for geospatial images using computer vision +site_author: PlantCV Development Team +repo_url: https://github.com/danforthcenter/plantcv-geospatial +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': + - 'Geopspatial Tools': + - +markdown_extensions: + - toc: + permalink: True + - admonition From 077200b6dba3cb094e5b79c14a8a5d8a85c3451b Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Mon, 11 Mar 2024 14:59:29 -0500 Subject: [PATCH 02/16] Update documentation.md remove reference to contributing guide from documentation.md --- docs/documentation.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/documentation.md b/docs/documentation.md index 33fb2a0..499df51 100644 --- a/docs/documentation.md +++ b/docs/documentation.md @@ -9,8 +9,8 @@ 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 +Follow the [installation guide](installation.md#installing-plantcv-for-contributors) to learn how clone a copy of the PlantCV-Annotate +repository. Then see the main PlantCV [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for an overview on how to 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. From f5de50e1cffc1669d901671a334545fc75727b85 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Mon, 11 Mar 2024 15:11:11 -0500 Subject: [PATCH 03/16] Create CONTRIBUTING.md --- docs/CONTRIBUTING.md | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 docs/CONTRIBUTING.md diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md new file mode 100644 index 0000000..5cc48f3 --- /dev/null +++ b/docs/CONTRIBUTING.md @@ -0,0 +1,14 @@ +# Contrbution to PlantCV-Geospatial + +!!! note + PlantCV-Geospatial is an add-on package to PlantCV so please first refer to the main package's [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for the majority of the information on what and how to contribute to either project (including but not limited to reporting bugs, requesting new features, add/revise documentation, and adding tutorials). + +## Overview Of What To Contribute to PlantCV-Geospatial vs. Other Packages + +This document aims to give an overview of what to contribute to PlantCV-Geospatial, and guidelines to +decide which repository is the most appropriate place for new features. Please +[create an issue in GitHub](https://github.com/danforthcenter/plantcv-geospatial/issues) assuming one +does not already exist. + +Functions in the Geospatial toolbox are specific to UAV, satellite, and other types of +georeferenced data. From a37f3cc9730e5776ce1be6d97f6c09b01711ad52 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Mon, 11 Mar 2024 15:11:21 -0500 Subject: [PATCH 04/16] Update mkdocs.yml remove nonexistent files --- mkdocs.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 9af9e13..b41159c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -10,8 +10,6 @@ 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 From 07f90325858ebee5705c2acb526c845df936d863 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Mon, 11 Mar 2024 15:11:45 -0500 Subject: [PATCH 05/16] Create read_geotif.md placeholder to get around "nav" error for having empty list in mkdocs --- docs/read_geotif.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 docs/read_geotif.md diff --git a/docs/read_geotif.md b/docs/read_geotif.md new file mode 100644 index 0000000..2d2f7c0 --- /dev/null +++ b/docs/read_geotif.md @@ -0,0 +1,29 @@ +## Read Geo-tif Data + +Read in data (from tif format, most likely georeferenced image data). + +**plantcv.geospatial.read_geotif**(*filename, mode="rgb"*) + +**returns** [PlantCV Spectral_data](https://plantcv.readthedocs.io/en/latest/Spectral_data/) object instance + +- **Parameters:** + - filename - Filepath to .tif data + - mode - Mode for geotif reading + +- **Context:** + - Used to define a list of coordinates of interest. + +- **Example use:** + - below + + +```python +import plantcv.plantcv as pcv +import plantcv.geospatial as geo + +# Read geotif in +marker = geo.read_geotif(filename="./data/example_img.tif", mode="rgb") + +``` + +**Source Code:** [Here](https://github.com/danforthcenter/plantcv-geospatial/blob/main/plantcv/geospatial/read_geotif.py) From 6718127c4db5d3438f0289ab237865c87eb6313d Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Mon, 11 Mar 2024 15:12:25 -0500 Subject: [PATCH 06/16] Update mkdocs.yml add link to mkdocs --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index b41159c..1bb410c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -15,7 +15,7 @@ nav: - 'Adding/Editing Documentation': documentation.md - 'PlantCV Namespace': - 'Geopspatial Tools': - - + - Read Geo-tif Data: read_geotif.md markdown_extensions: - toc: permalink: True From f798cfcb75f7915c7f603e12e0065ca3d296cbf5 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Mon, 11 Mar 2024 15:17:29 -0500 Subject: [PATCH 07/16] add contributing doc to mkdocs again --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 1bb410c..1cabcb8 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -11,6 +11,7 @@ nav: - Documentation: - 'Installation': installation.md - 'Contributing': + - 'Contributing Guide': CONTRIBUTING.md - 'Code of Conduct': CODE_OF_CONDUCT.md - 'Adding/Editing Documentation': documentation.md - 'PlantCV Namespace': From 353d90369509e3efd14f92bce8fef4e6f40a6344 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Thu, 14 Mar 2024 11:03:45 -0500 Subject: [PATCH 08/16] remove extra whitespace --- docs/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/CONTRIBUTING.md b/docs/CONTRIBUTING.md index 5cc48f3..f08fe8d 100644 --- a/docs/CONTRIBUTING.md +++ b/docs/CONTRIBUTING.md @@ -1,7 +1,7 @@ # Contrbution to PlantCV-Geospatial !!! note - PlantCV-Geospatial is an add-on package to PlantCV so please first refer to the main package's [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for the majority of the information on what and how to contribute to either project (including but not limited to reporting bugs, requesting new features, add/revise documentation, and adding tutorials). + PlantCV-Geospatial is an add-on package to PlantCV so please first refer to the main package's [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for the majority of the information on what and how to contribute to either project (including but not limited to reporting bugs, requesting new features, add/revise documentation, and adding tutorials). ## Overview Of What To Contribute to PlantCV-Geospatial vs. Other Packages From 5e50892d0a19927e96db99ec815ee1c69126659e Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Thu, 14 Mar 2024 11:05:22 -0500 Subject: [PATCH 09/16] refine index.md to make more specific to geospatial --- docs/index.md | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/docs/index.md b/docs/index.md index b7ee1f8..de02334 100644 --- a/docs/index.md +++ b/docs/index.md @@ -3,7 +3,7 @@ ## Overview [PlantCV-Geospatial](https://github.com/danforthcenter/plantcv-geospatial) 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 +variety of plot designs 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-Geospatial 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-geospatial/issues). @@ -23,11 +23,4 @@ If you are interested in contributing to PlantCV-Geospatial, please see: * [Code of Conduct](CODE_OF_CONDUCT.md) * [PlantCV Contributing Guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) -## Versions - -The documentation defaults to the `stable` version of PlantCV-Geospatial which is the current release version available from -PyPI. 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](https://plantcv.org) From 470e3d8db3516bcbf5241292aa915309651f5717 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Thu, 14 Mar 2024 11:07:38 -0500 Subject: [PATCH 10/16] Create changelog.md --- docs/changelog.md | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 docs/changelog.md diff --git a/docs/changelog.md b/docs/changelog.md new file mode 100644 index 0000000..820a7f1 --- /dev/null +++ b/docs/changelog.md @@ -0,0 +1,3 @@ +## Changelog + +All notable changes to this project will be documented below. From 98461726a7f97e3ed650b541990d8c4083ea119d Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Tue, 9 Apr 2024 11:03:27 -0500 Subject: [PATCH 11/16] typo annotate to geospatial --- docs/installation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/installation.md b/docs/installation.md index 88b3aa6..694d785 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -27,5 +27,5 @@ pip install -e . ### Installing PlantCV for contributors Before getting started, please read our [contributor guidelines](CONTRIBUTING.md) and [code of conduct](CODE_OF_CONDUCT.md). -You can follow the [PlantCV Installation for Contributor Guide](https://plantcv.readthedocs.io/en/latest/installation/#contributors) and then continue with the instructions above to add PlantCV-Annotate to +You can follow the [PlantCV Installation for Contributor Guide](https://plantcv.readthedocs.io/en/latest/installation/#contributors) and then continue with the instructions above to add PlantCV-Geospatial to your development environment. From ad85e90ca161ae45c94f16619708cb0d6472b25b Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Tue, 9 Apr 2024 11:04:59 -0500 Subject: [PATCH 12/16] remove copied over "context" section --- docs/read_geotif.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/docs/read_geotif.md b/docs/read_geotif.md index 2d2f7c0..d49898a 100644 --- a/docs/read_geotif.md +++ b/docs/read_geotif.md @@ -10,9 +10,6 @@ Read in data (from tif format, most likely georeferenced image data). - filename - Filepath to .tif data - mode - Mode for geotif reading -- **Context:** - - Used to define a list of coordinates of interest. - - **Example use:** - below From 262895f6e541a11bd0a28bd07bded94b3db0d8a7 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Tue, 9 Apr 2024 11:14:09 -0500 Subject: [PATCH 13/16] refer to internal contributing guide rather than linking out --- docs/documentation.md | 7 +++---- docs/index.md | 2 +- docs/installation.md | 7 ++++--- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/docs/documentation.md b/docs/documentation.md index 499df51..7a1beb7 100644 --- a/docs/documentation.md +++ b/docs/documentation.md @@ -1,6 +1,6 @@ ## Documentation -PlantCV documentation is hosted on [Read the Docs](https://readthedocs.org/). +PlantCV-Geospatial 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 @@ -9,9 +9,8 @@ new version of code is pushed to the PlantCV GitHub repository. ### Updating PlantCV documentation -Follow the [installation guide](installation.md#installing-plantcv-for-contributors) to learn how clone a copy of the PlantCV-Annotate -repository. Then see the main PlantCV [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for an overview on how to 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 +Follow the [installation guide](installation.md#installing-plantcv-geospatial-for-contributors) to learn how clone a copy of the PlantCV-Annotate +repository. Then see the main PlantCV [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for an overview on how to edit files, and generate a `pull` request to merge your updates back into the repository. Changes to PlantCV-Geospatial 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-Geopspatial is an add-on package to compliment functionality of diff --git a/docs/index.md b/docs/index.md index de02334..8ef5d21 100644 --- a/docs/index.md +++ b/docs/index.md @@ -21,6 +21,6 @@ updating, and other questions, see: If you are interested in contributing to PlantCV-Geospatial, please see: * [Code of Conduct](CODE_OF_CONDUCT.md) -* [PlantCV Contributing Guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) +* [PlantCV-Geospatial Contributing Guide](CONTRIBUTING.md) [Return to the PlantCV homepage](https://plantcv.org) diff --git a/docs/installation.md b/docs/installation.md index 694d785..7e95021 100644 --- a/docs/installation.md +++ b/docs/installation.md @@ -3,7 +3,7 @@ ### Table of contents 1. [Supported platforms and dependencies](#dependencies) 2. [Install via a package manager](#install) -3. [Installing PlantCV for contributors](#contributors) +3. [Installing PlantCV-Geospatial for contributors](#contributors) ### Supported platforms and dependencies - Linux 64-bit, x86 processors @@ -20,11 +20,12 @@ Additionally, we recommend installing [JupyterLab](https://jupyter.org/). # Activate the plantcv environment (you will have to do this each time you start a new session) conda activate plantcv # Install plantcv-geospatial in editable mode so that it updates as you work on new features/updates -pip install plantcv-geospatial +git clone https://github.com/danforthcenter/plantcv-geospatial.git +cd plantcv-geospatial pip install -e . ``` -### Installing PlantCV for contributors +### Installing PlantCV-Geospatial for contributors Before getting started, please read our [contributor guidelines](CONTRIBUTING.md) and [code of conduct](CODE_OF_CONDUCT.md). You can follow the [PlantCV Installation for Contributor Guide](https://plantcv.readthedocs.io/en/latest/installation/#contributors) and then continue with the instructions above to add PlantCV-Geospatial to From 025c0839a206dc2962e259895966720a88113813 Mon Sep 17 00:00:00 2001 From: HaleySchuhl Date: Tue, 9 Apr 2024 14:30:44 -0500 Subject: [PATCH 14/16] more specific to geospatial --- docs/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/index.md b/docs/index.md index 8ef5d21..e3bb0be 100644 --- a/docs/index.md +++ b/docs/index.md @@ -11,7 +11,7 @@ on the [GitHub issues page](https://github.com/danforthcenter/plantcv-geospatial ## Getting started The documentation can be navigated using the sidebar table of contents. Documentation for individual PlantCV-Geospatial functions -are listed under the headings "PlantCV Namespace". For general information on installation, +are listed under the headings "PlantCV-Geospatial Namespace". For general information on installation, updating, and other questions, see: * [Installing PlantCV-Geospatial](installation.md) From 651b05be66606968aa984ee0401c4af0e9c1320e Mon Sep 17 00:00:00 2001 From: Noah Fahlgren Date: Thu, 11 Apr 2024 10:40:05 -0500 Subject: [PATCH 15/16] Fix name of add-on package --- docs/documentation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/documentation.md b/docs/documentation.md index 7a1beb7..e7a995c 100644 --- a/docs/documentation.md +++ b/docs/documentation.md @@ -9,7 +9,7 @@ new version of code is pushed to the PlantCV GitHub repository. ### Updating PlantCV documentation -Follow the [installation guide](installation.md#installing-plantcv-geospatial-for-contributors) to learn how clone a copy of the PlantCV-Annotate +Follow the [installation guide](installation.md#installing-plantcv-geospatial-for-contributors) to learn how clone a copy of the PlantCV-Geospatial repository. Then see the main PlantCV [contributing guide](https://plantcv.readthedocs.io/en/latest/CONTRIBUTING/) for an overview on how to edit files, and generate a `pull` request to merge your updates back into the repository. Changes to PlantCV-Geospatial 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. From 908cb5d3bb51e437f031fd4b4032df1f64d3159d Mon Sep 17 00:00:00 2001 From: Noah Fahlgren Date: Thu, 11 Apr 2024 10:44:35 -0500 Subject: [PATCH 16/16] Add page to TOC --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index 1cabcb8..c69c28c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -10,6 +10,7 @@ nav: - Home: index.md - Documentation: - 'Installation': installation.md + - 'Change Log': changelog.md - 'Contributing': - 'Contributing Guide': CONTRIBUTING.md - 'Code of Conduct': CODE_OF_CONDUCT.md