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2 changes: 1 addition & 1 deletion docs/community/governance.md
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Expand Up @@ -42,7 +42,7 @@ among other possibilities. Any community member can become a contributor, and
all are encouraged to do so. By contributing to the project, community members
can directly help to shape its future.

Contributors are encouraged to read the [contributing guide](napari-contributing).
Contributors are encouraged to read the [contributing guide](contributing-code).

### Core developers

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4 changes: 2 additions & 2 deletions docs/community/index.md
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Expand Up @@ -7,7 +7,7 @@ examples, you are welcome to help develop and improve napari.

To ask questions and interact with the team, you can join our
[zulip chat](https://napari.zulipchat.com/login/) or participate in our
[meetings](./meeting_schedule).
[meetings](meeting-schedule).

If you are interested in contributing, check out our
[contributing guide](../developers/index).
[contributing guide](contributing).
2 changes: 2 additions & 0 deletions docs/community/meeting_schedule.md
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(meeting-schedule)=

# Meeting schedule

We hold regular meetings, the timings of which are available on our [public calendar](https://calendar.google.com/calendar/embed?src=c_35r93ec6vtp8smhm7dv5uot0v4%40group.calendar.google.com).
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2 changes: 1 addition & 1 deletion docs/developers/benchmarks.md
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(napari-benchmarks)=
(benchmarks)=
# Benchmarks

While not mandatory for most pull requests, we ask that performance related
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8 changes: 5 additions & 3 deletions docs/developers/contributing.md
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(napari-contributing)=
(contributing-code)=
# Contributing guide

We welcome your contributions! Please see the provided steps below and never hesitate to contact us.

If you are a new user, we recommend checking out the detailed [Github Docs](https://docs.github.com/en).

You can see the general direction for napari development and possible work plans in our current [Roadmap](../roadmaps/index.md).
You can see the general direction for napari development and possible work plans in our current [Roadmap](roadmaps).

(dev-installation)=
## Setting up a development installation
Expand Down Expand Up @@ -55,10 +55,12 @@ In order to make changes to `napari`, you will need to [fork](https://docs.githu
4. Install the package in editable mode, along with all of the developer tools.
```{note}
If you only want to use napari, you can install it on most macOS, Linux and
Windows systems with Python {{ python_version_range }}
by following the directions on the
[instructions page](../tutorials/fundamentals/installation.md#install-as-python-package-recommended).
[instructions page](install-python-package).
```
napari supports different Qt backends, and you can choose which one to install and use.
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8 changes: 4 additions & 4 deletions docs/developers/core_dev_guide.md
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Expand Up @@ -45,7 +45,7 @@ When merging, use GitHub's
to ensure a clean git history.

You should also continue to make your own pull requests as before and in accordance
with the [general contributor guide](napari-contributing). These pull requests still
with the [general contributor guide](contributing-code). These pull requests still
require the approval of another core developer before they can be merged.

## Reviewing
Expand Down Expand Up @@ -80,7 +80,7 @@ consult back with our [mission and values](mission-and-values).
2. **Performance and benchmarks:** As `napari` targets scientific applications that often involve
large multidimensional datasets, high performance is a key value of `napari`. While
every new feature won't scale equally to all sizes of data, keeping in mind performance
and our [benchmarks](napari-benchmarks) during a review may be important, and you may
and our [benchmarks](benchmarks) during a review may be important, and you may
need to ask for benchmarks to be run and reported or new benchmarks to be added.

3. **APIs and stability:** Coding users and plugin developers will make
Expand Down Expand Up @@ -154,11 +154,11 @@ For details on how the documentation and website are built, see
As a core member, you should be familiar with community and developer
resources such as:

- Our [contributor guide](napari-contributing).
- Our [contributor guide](contributing-code).
- Our [code of conduct](napari-coc).
- Our [governance](napari-governance).
- Our [mission and values](mission-and-values).
- Our [benchmarking guide](napari-benchmarks).
- Our [benchmarking guide](benchmarks).
- [PEP8](https://peps.python.org/pep-0008/) for Python style.
- [PEP257](https://peps.python.org/pep-0257/) and the
[NumPy documentation guide](https://numpy.org/devdocs/dev/howto-docs.html#documentation-style)
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2 changes: 1 addition & 1 deletion docs/developers/documentation/docs_deployment.md
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Expand Up @@ -3,7 +3,7 @@
```{note}
This guide is intended for napari core contributors and is not required reading
for regular contributors. If you're looking for information on how to contribute
to the documentation, see [](docs_contributing_guide).
to the documentation, see [](contributing-docs).
```

The napari documentation and website sources are spread over three repositories,
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2 changes: 2 additions & 0 deletions docs/developers/documentation/docs_template.md
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Expand Up @@ -14,6 +14,8 @@ theme:
intro: Template for adding new napari documentation
---

(docs-template)=

# Docs template

This template will guide you to write a well formatted document and prepare it for contribution to napari.org.
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16 changes: 9 additions & 7 deletions docs/developers/documentation/index.md
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(docs_contributing_guide)=
(contributing-docs)=
# Contributing Documentation

This guide will teach you how to submit new documents to napari's usage
Expand Down Expand Up @@ -106,13 +106,13 @@ that could be expanded to include the content you think is lacking.
Go to your local `napari/docs` folder to find examples of documents you might
want to contribute. The paths are listed in parentheses below.

- [**Explanations**](../../guides/index) (in [`napari/docs/guides`](https://github.com/napari/docs/tree/main/docs/guides)):
- [**Explanations**](explanations) (in [`napari/docs/guides`](https://github.com/napari/docs/tree/main/docs/guides)):
in depth content about napari architecture, development choices and some complex features
- [**Tutorials**](../../tutorials/index) (in [`napari/docs/tutorials`](https://github.com/napari/docs/tree/main/docs/tutorials)):
- [**Tutorials**](tutorials) (in [`napari/docs/tutorials`](https://github.com/napari/docs/tree/main/docs/tutorials)):
detailed, reproducible step by step guides, usually combining multiple napari features to complete a potentially complex task
- [**How-tos**](../../howtos/index) (in [`napari/docs/howtos`](https://github.com/napari/docs/tree/main/docs/howtos)):
- [**How-tos**](how-tos) (in [`napari/docs/howtos`](https://github.com/napari/docs/tree/main/docs/howtos)):
simple step by step guides demonstrating the use of common features
- [**Getting started**](../../tutorials/start_index) (in [`napari/docs/tutorials/fundamentals`](https://github.com/napari/docs/tree/main/docs/tutorials/fundamentals)):
- [**Getting started**](getting-started) (in [`napari/docs/tutorials/fundamentals`](https://github.com/napari/docs/tree/main/docs/tutorials/fundamentals)):
these documents are a mix of tutorials and how-tos covering the fundamentals of installing and working with napari for beginners

The [**Examples gallery**](../../gallery) sources are in the [main `napari/napari` repository](https://github.com/napari/napari/tree/main/examples)
Expand All @@ -122,9 +122,11 @@ and show code examples of how to use napari.
:class: tip
If you already have teaching materials e.g. recordings, slide decks or Jupyter notebooks
hosted somewhere, you can add links to these on our [napari workshops](../../further-resources/napari-workshops.md) page.
hosted somewhere, you can add links to these on our [napari workshops](workshops) page.
```

(contributing-docs-step-one)=

## 1. Write your documentation

Our goal is that all tutorials and how-tos are easily downloadable and
Expand All @@ -138,7 +140,7 @@ documents in our repository and on [napari.org](https://napari.org).

If you are amending existing documentation, you can do so in your preferred text
editor. If you wish to add a new tutorial or a how-to, we recommend you use our
[template](./docs_template). Inside the template you'll find handy tips for
[template](docs-template). Inside the template you'll find handy tips for
taking screenshots of the viewer, hiding code cells, using style guides and what
to include in the required prerequisites section.

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(contributing)=

# Contributing

Here you can find resources about the contributing workflow for both code to napari core and documentation of the project, as well as information for onboarding of new core developers.

You can see the general direction for napari development and possible work plans in our current [Roadmap](../roadmaps/index.md).
You can see the general direction for napari development and possible work plans in our current [Roadmap](roadmaps).

## For contributors

- [Contributing guide](./contributing)
- [Contributing documentation](./documentation/index)
- [Translations](./translations)
- [Testing](./testing)
- [Profiling](./profiling)
- [Benchmarks](./benchmarks)
- [Contributing guide](contributing-code)
- [Contributing documentation](contributing-docs)
- [Translations](translations)
- [Testing](napari-testing)
- [Profiling](profiling)
- [Benchmarks](benchmarks)

## For core developers

- [Core Developer guide](./core_dev_guide)
- [Release guide](./release)
- [Maintenance](./maintenance)
- [Core Developer guide](core-dev-guide)
- [Release guide](release)
- [Maintenance](maintenance)

2 changes: 2 additions & 0 deletions docs/developers/maintenance.md
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(maintenance)=

# Maintenance

This document describes maintenance tasks that need to be performed from time to time. Its purpose is to avoid relying on personal memory alone, and it should be updated regularly.
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(profiling)=

# Profiling

In contrast to performance tracing, profiling does not provide information
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(release)=

# Release guide

This guide documents `napari`'s release process.
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5 changes: 3 additions & 2 deletions docs/further-resources/napari-workshops.md
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(napari-workshops)=
(workshops)=
# napari workshops

There have been many workshops and tutorials given about napari.
Expand All @@ -14,7 +14,8 @@ as a starting point.
If you have organized a napari workshop and would like to see it featured here
in this page, you can
[send a Pull Request to the napari/docs repository](../developers/documentation/index.md)
[send a Pull Request](contributing-docs-step-one) to the
[napari/docs repository](https://github.com/napari/docs)
or contact the core developers on [zulip chat](https://napari.zulipchat.com/login/).
```

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Expand Up @@ -396,7 +396,7 @@ Out[12]: 1
context menu might update the items in the menu that are visible and/or enabled:

```python
context_menu.update_from_context(get_context(layer_list))
context_menu.update_from_context(get_context(layer-list))
```

where `update_from_context` is a function that takes in a `Context` and
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4 changes: 2 additions & 2 deletions docs/guides/index.md
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Expand Up @@ -3,8 +3,8 @@

```{note}
These pages describe advanced usage and how napari works internally. If you are
just getting started, check out our [tutorials](../tutorials/index.md) or
[how-to guides](../howtos/index.md) instead.
just getting started, check out our [tutorials](tutorials) or
[how-to guides](how-tos) instead.
```

## Advanced usage
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8 changes: 4 additions & 4 deletions docs/guides/layers.md
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(layers-glance)=
# Layers at a glance

[Layers](napari.layers) are the basic viewable objects that can be added to a
{class}`~napari.layers` are the basic viewable objects that can be added to a
viewer. **napari** supports seven main different layer types: `Image`, `Labels`,
`Points`, `Shapes`, `Surface`, `Tracks` and `Vectors`. Each of the layer types
corresponds to a different data type, visualization, and interactivity. You can
Expand All @@ -22,10 +22,10 @@ viewer.add_image(data, name='astronaut')
```

To learn more about the layers available, see the
[Layers documentation](napari.layers). To learn about how to use the layers currently supported by napari, check out the
[Using layers how-to guides](../../howtos/layers/index). For a gentle
{class}`~napari.layers`. To learn about how to use the layers currently supported by napari, check out the
[Using layers how-to guides](using-layers). For a gentle
introduction, check out the
[Layer list section in the napari viewer tutorial](layer_list).
[Layer list section in the napari viewer tutorial](layer-list).

## Layer visibility

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2 changes: 1 addition & 1 deletion docs/guides/napari_models.md
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Expand Up @@ -27,7 +27,7 @@ The separation of the python models from viewer GUI code allows:
used
* tests to be easily run headlessly
* the python models to be run headlessly (see
[Running napari headlessly](../howtos/headless) for more)
[Running napari headlessly](headless) for more)

## Python models and events

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(docker)=

# Napari in Docker

## Build
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2 changes: 2 additions & 0 deletions docs/howtos/headless.md
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(headless)=

# Running napari headlessly

Running napari headlessly (without opening a napari GUI interface) may be
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18 changes: 9 additions & 9 deletions docs/howtos/index.md
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Expand Up @@ -4,21 +4,21 @@
These guides show you how to complete tasks with napari. They assume you have
already installed **napari**, know how to launch the viewer, and are familiar
with its layout. For help with installation see our
[installation tutorial](../tutorials/fundamentals/installation). For help
[installation tutorial](installation). For help
getting started with the viewer see our
[Getting started guide](../tutorials/fundamentals/getting_started). For
[How to launch napari guide](launch). For
help understanding the organisation of the viewer, including things like the
layers list, the layer properties widgets, the layer control panels, and the
dimension sliders see our [napari viewer](../tutorials/fundamentals/viewer)
dimension sliders see our [napari viewer](viewer-tutorial)
tutorial.

- [Using layers](layers/index): Learn about how to use the layers currently
- [Using layers](using-layers): Learn about how to use the layers currently
supported by napari.
- [Hooking up your own events](./connecting_events): Learn about the event loop
- [Hooking up your own events](connecting-events): Learn about the event loop
and how to use it to interact with napari.
- [napari + ImageJ how-to guide](./napari_imageJ): Learn about how to use napari
- [napari + ImageJ how-to guide](napari-imagej): Learn about how to use napari
and ImageJ simultaneously.
- [napari in Docker](./docker): Learn about using napari in docker.
- [Performance monitoring](./perfmon): Learn about how to monitor napari
- [napari in Docker](docker): Learn about using napari in docker.
- [Performance monitoring](perfmon): Learn about how to monitor napari
performance and diagnose potential problems.
- [napari headless](./headless): Tips on how to run napari headlessly.
- [napari headless](headless): Tips on how to run napari headlessly.
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Expand Up @@ -11,6 +11,8 @@ kernelspec:
name: python3
---

(image-layer)=

# Using the image layer

In this document, you will learn how to use the `napari` image layer, including
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Expand Up @@ -9,4 +9,4 @@ following how-to guides:
```

For a high-level overview of the napari Layers, see
[Layers at a glance](../../guides/layers).
[Layers at a glance](layers-glances).
4 changes: 3 additions & 1 deletion docs/howtos/layers/labels.md
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Expand Up @@ -11,6 +11,8 @@ kernelspec:
name: python3
---

(layers-labels)=

# Using the labels layer

In this document, you will learn about the `napari` `Labels` layer, including
Expand Down Expand Up @@ -103,7 +105,7 @@ and [zarr arrays](https://zarr.readthedocs.io/en/stable/api/core.html). A
Because the labels layer subclasses the image layer it inherits the great
properties of the image layer, like supporting lazy loading and multiscale
images for big data layers. For more information about both these concepts see
the details in the [image layer guide](./image).
the details in the [image layer guide](image-layer).

## Creating a new labels layer

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Expand Up @@ -31,7 +31,7 @@ edge colors of the points. For example, when displaying points of different
classes/types, one could automatically set color the individual points by their
respective class/type. For more details on point properties, see the "setting
point edge and face color with properties" below or the [point annotation
tutorial](../../tutorials/annotation/annotate_points).
tutorial](annotating-points).

## A simple example

Expand Down Expand Up @@ -95,7 +95,7 @@ name of the property and the values are numpy arrays with a value for each point
(i.e., length N for N points in `Points.data`). As we will see below, we can use
the values in a property to set the display properties of the points (e.g., face
color or edge color). To see the points properties in action, please see the
[point annotation tutorial](../../tutorials/annotation/annotate_points).
[point annotation tutorial](annotating-points).

## Creating a new points layer

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4 changes: 2 additions & 2 deletions docs/howtos/layers/surface.md
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Expand Up @@ -110,13 +110,13 @@ the vispy colormap object. You can list all the available colormaps using
It is also possible to create your own colormaps using vispy's
`vispy.color.Colormap` object, see it's full
[documentation here](https://vispy.org/api/vispy.color.colormap.html#vispy.color.colormap.Colormap).
For more detail see the [image layer guide](./image).
For more detail see the [image layer guide](image-layer).

## Adjusting contrast limits

The vertex values of the surface layer get mapped through its colormap according
to values called contrast limits. These are a 2-tuple of values defining how
what values get applied the minimum and maximum of the colormap and follow the
same principles as the `contrast_limits` described in the [image layer
guide](./image). They are also accessible through the same keyword arguments,
guide](image-layer). They are also accessible through the same keyword arguments,
properties, and range slider as in the image layer.
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Expand Up @@ -11,6 +11,8 @@ kernelspec:
name: python3
---

(layers-tracks)=

# Using the tracks layer

In this document, you will learn about the `napari` `Tracks` layer, including
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