Fix broken links detected by make linkcheck-files (#484)

# References and relevant issues
Related to
#474

# Description
Fixes a number of broken links detected by `make linkcheck-files`.

A few comments:
- it looks like this link does not exist anymore:
`further-resources/sample_data.md:17: [redirected permanently]
[digitalpathologyassociation.org/whole-slide-imaging-repository](https://digitalpathologyassociation.org/whole-slide-imaging-repository)
to
[https://digitalpathologyassociation.org?preview_error](https://digitalpathologyassociation.org/?preview_error)`.
I tried googling but only found this: http://www.wsirepository.org/ and
it doesn't load. Any ideas?
- How can we replace the following link?
`developers/architecture/app_model.md:288: [broken]
https://github.com/napari/napari/blob/main/napari/_app_model/_submenus.py:
404 Client Error: Not Found for url:
https://github.com/napari/napari/blob/main/napari/_app_model/_submenus.py`
I couldn't find SubmenuItem in the codebase, maybe I'm missing something
- https://github.com/potating-potato has probably deleted their github
account. I suggest we convert the links to static text if we want to
preserve history.
- These hackmd docs seem to only be readable if you are logged in:
https://hackmd.io/fmKp0If5RkiwWIxYYRdKpg and
https://hackmd.io/@talley/SJB_lObBi#What-is-a-virtual-environment Should
we make it readable by all, or ignore in the linkcheck?
- A few links will need to be fixed in npe2, I'll send a follow-up PR
for that.
- This file does not seem to exist anymore, from a search at the btrack
repo: `tutorials/tracking/cell_tracking.md:229: [broken]
https://github.com/quantumjot/btrack/blob/main/models/cell_config.json:
404 Client Error: Not Found for url:
https://github.com/quantumjot/btrack/blob/main/models/cell_config.json`.
Should we replace with a new link?
- I will add a regex to ignore redirects from docs paths to stuff like
"stable/" or "en/latest"

A few items are left, mostly links to old code. I will try to replace
with permalinks where I can, but not sure if I'll be able to find all of
them. If that's the case I might try to ping the original authors for an
appropriate substitution.

---------

Co-authored-by: Peter Sobolewski <76622105+psobolewskiPhD@users.noreply.github.com>

EULA.md

@@ -7,7 +7,7 @@ https://napari.org.
 
 <!-- Links -->
 
-[napari_installers]: https://napari.org/stable/index.html#installation
+[napari_installers]: https://napari.org/stable/tutorials/fundamentals/installation.html
 
 <!-- List of EULAs starts here -->
 <!--

docs/community/governance.md

@@ -74,7 +74,7 @@ developer community (including the SC members) fails to reach such a consensus
 in a reasonable timeframe, the SC is the entity that resolves the issue.
 
 Members of the SC also have the "owner" role within the [napari GitHub organization](https://github.com/napari)
-and are ultimately responsible for managing the napari GitHub account, the [@napari_imaging](https://twitter.com/napari_imaging)
+and are ultimately responsible for managing the napari GitHub account, the [@napari_imaging](https://x.com/napari_imaging)
 twitter account, the [napari website](https://napari.org), and other similar napari owned resources.
 
 The SC will be no less than three members and no more than five members,

docs/community/mission_and_values.md

@@ -76,4 +76,4 @@ As noted above, we'll be beginning to actively work on the plugin infrastructure
 
 ## Acknowledgements
 
-We share a lot of our mission and values with the `scikit-image` project with whom we share founding members, and acknowledge the influence of their [mission and values statement](https://scikit-image.org/docs/dev/values.html) on this document.
+We share a lot of our mission and values with the `scikit-image` project with whom we share founding members, and acknowledge the influence of their [mission and values statement](https://scikit-image.org/docs/stable/about/values.html) on this document.

docs/community/team.md

@@ -47,7 +47,7 @@ You can read a full history of the project’s founding and early development in
 
 Over time, napari has grown to over 80 direct contributors. Talley Lambert, from Harvard Medical School, began contributing around the time of Juan's blog post, and has been a critical driver of napari's development ever since. We have core developers located in three continents and three biweekly community calls spread across the day to try to accommodate users and contributors in any time zone.
 
-Read more about napari’s [mission and values](https://napari.org/community/mission_and_values.html), how to get started as a [contributor](https://napari.org/developers/contributing.html) or join us in our [zulip chat](https://napari.zulipchat.com/login/) for a more synchronous conversation. You can also follow us on [twitter](https://twitter.com/napari_imaging).
+Read more about napari’s [mission and values](https://napari.org/stable/community/mission_and_values.html), how to get started as a [contributor](https://napari.org/stable/developers/contributing.html) or join us in our [zulip chat](https://napari.zulipchat.com/login/) for a more synchronous conversation. You can also follow us on [twitter](https://x.com/napari_imaging).
 
 ## Institutional and funding Partners
 

docs/conf.py

@@ -410,12 +410,23 @@ def get_attributes(item, obj, modulename):
 autosummary_ignore_module_all = False
 
 linkcheck_anchors_ignore = [r'^!', r'L\d+-L\d+', r'r\d+', r'issuecomment-\d+']
-
 linkcheck_ignore = [
-    'https://napari.zulipchat.com/',
-    '../_tags',
-    'https://en.wikipedia.org/wiki/Napari#/media/File:Tabuaeran_Kiribati.jpg',
+    "https://napari.zulipchat.com/",
+    "../_tags",
+    "https://en.wikipedia.org/wiki/Napari#/media/File:Tabuaeran_Kiribati.jpg",
+    "http://localhost:8000",
+    "https://datadryad.org/stash/downloads/file_stream/182482",
+    "https://github.com/napari/docs/issues/new/choose",
+    "https://github.com/napari/napari/issues/new/choose",
+    "https://github.com/napari/napari/issues/new",
+    "https://napari-hub.org",
+    "https://github.com/napari/napari/releases/latest",
+    "https://onlinelibrary.wiley.com/doi/10.1002/col.20327",
 ]
+linkcheck_allowed_redirects = {
+    r"https://youtu\.be/.*": r"https://www\.youtube\.com/.*",
+    r"https://github\.com/napari/napari/releases/download/.*": r"https://objects\.githubusercontent\.com/.*",
+}
 
 
 def rewrite_github_anchor(app, uri: str):

docs/developers/architecture/dir_organization.md

@@ -73,7 +73,7 @@ is named `_qapp_model` inside `_qt/`).
   canvas (the canvas is a vispy object onto which you can draw 'visuals').
 * `benchmarks/` - benchmarking code, mostly for checking the performance of layers.
   It is is executed in CI and is run every Sunday. See
-  [`.github/workflows/benchmarks.yml`](https://github.com/napari/napari/tree/main/.github/workflows/benchmarks.yml)
+  [`.github/workflows/benchmarks.yml`](https://github.com/napari/napari/blob/main/.github/workflows/benchmarks.yml)
   for CI workflow details. The benchmarks can also be run locally.
 * `components/` - code that defines all components of the napari viewer, including the
   layerlist, dimensions and camera.

docs/developers/contributing/dev_install.md

@@ -1,7 +1,7 @@
 (dev-installation)=
 ## Setting up a development installation
 
-In order to make changes to `napari`, you will need to [fork](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#forking-a-repository) the
+In order to make changes to `napari`, you will need to [fork](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project) the
 [repository](https://github.com/napari/napari). If you are not familiar with `git`, we recommend reading up on [this guide](https://docs.github.com/en/get-started/using-git/about-git#basic-git-commands).
 
 1. Clone the forked repository to your local machine and change directories:
@@ -22,7 +22,7 @@ In order to make changes to `napari`, you will need to [fork](https://docs.githu
     ::::{tab-set}
 
     :::{tab-item} Using `conda`
-    After [installing `conda`](https://www.anaconda.com/products/distribution), create an environment called `napari-env` with Python {{ python_version }} and activate it.
+    After [installing `conda`](https://www.anaconda.com/download), create an environment called `napari-env` with Python {{ python_version }} and activate it.
 
     {{ conda_create_env }}
     :::
@@ -74,7 +74,7 @@ In order to make changes to `napari`, you will need to [fork](https://docs.githu
 
 5. We use [`pre-commit`](https://pre-commit.com) to format code with
    [`black`](https://github.com/psf/black) and lint with
-   [`ruff`](https://github.com/charliermarsh/ruff) automatically prior to each commit.
+   [`ruff`](https://github.com/astral-sh/ruff) automatically prior to each commit.
    To minimize test errors when submitting pull requests, please install `pre-commit`
    in your environment as follows:
 
@@ -88,7 +88,7 @@ In order to make changes to `napari`, you will need to [fork](https://docs.githu
    see [`black`'s documentation](https://black.readthedocs.io/en/stable/).
 
    Code will also be linted to enforce the stylistic and logistical rules specified
-   in our [`flake8` configuration](https://github.com/napari/napari/blob/main/setup.cfg), which currently ignores
+   in our [`flake8` configuration](https://github.com/napari/napari/blob/main/pyproject.toml), which currently ignores
    [E203](https://lintlyci.github.io/Flake8Rules/rules/E203.html),
    [E501](https://lintlyci.github.io/Flake8Rules/rules/E501.html),
    [W503](https://lintlyci.github.io/Flake8Rules/rules/W503.html) and

docs/developers/contributing/documentation/docs_deployment.md

@@ -55,7 +55,7 @@ through several CI workflows detailed below.
       turn happens on every commit to the `main` branches of either
       `napari/napari` or `napari/docs`).
     - For every commit to the `gh-pages` branch of this repo, the
-      [`unversioned_pages.yml` action](https://github.com/napari/napari.github.io/blob/main/.github/workflows/unversioned_pages.yml)
+      [`unversioned_pages.yml` action](https://github.com/napari/napari.github.io/blob/gh-pages/.github/workflows/unversioned_pages.yml)
       is triggered and copies the latest contents of the index page and the dev
       folder over the "stable" version of the documentation. This ensures that
       both the landing page of the website and the developer documentation,

docs/developers/contributing/documentation/index.md

@@ -40,7 +40,7 @@ by either [uploading file(s) from your computer](https://docs.github.com/en/repo
 [creating and editing a new file](https://docs.github.com/en/repositories/working-with-files/managing-files/creating-new-files)
 or [editing an existing file](https://docs.github.com/en/repositories/working-with-files/managing-files/editing-files)
 on the [napari/docs](https://github.com/napari/docs) GitHub repository.
-It's best if you first [fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) the [napari/docs](https://github.com/napari/docs) repository to your own GitHub account, create a [feature branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository#creating-a-branch), upload/create/edit files through the GitHub web interface, and then [open a pull request from your fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork) back to [napari-docs](https://github.com/napari/docs).
+It's best if you first [fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/fork-a-repo) the [napari/docs](https://github.com/napari/docs) repository to your own GitHub account, create a [feature branch](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository#creating-a-branch), upload/create/edit files through the GitHub web interface, and then [open a pull request from your fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request-from-a-fork) back to [napari-docs](https://github.com/napari/docs).
 
 You will also be able to [preview the documentation](doc_view_ci) as it would appear on [napari.org](https://napari.org/dev) by
 using the `Check the rendered docs here!` action at the bottom of your PR which will go to a preview site on [CircleCI](https://circleci.com/).
@@ -487,7 +487,7 @@ If you are using an IDE, it is likely that it will not use Git Bash by default.
 Alternatively, you can install WSL, which will allow you to run a Linux environment directly on Windows (without any virtual machines, etc.). You need to have Windows 10 version 2004 and higher or Windows 11. Then you can run scripts and command line utilities, as well as python and napari from for example Ubuntu on your Windows machine.
 
 1. Install the [Windows Subsystem for Linux](https://learn.microsoft.com/en-us/windows/wsl/install) and [choose a linux distribution](https://learn.microsoft.com/en-us/windows/wsl/install#change-the-default-linux-distribution-installed).
-We will use Ubuntu for this guide since it is the default WSL distribution, easy to install, and works well with [WSLg](https://github.com/microsoft/wslg). The default method to perform this installation is to run `wsl --install -d Ubuntu` from command prompt as an administrator but you can refer to the [guide](https://docs.microsoft.com/en-us/windows/wsl/install-win10) for other installation methods.
+We will use Ubuntu for this guide since it is the default WSL distribution, easy to install, and works well with [WSLg](https://github.com/microsoft/wslg). The default method to perform this installation is to run `wsl --install -d Ubuntu` from command prompt as an administrator but you can refer to the [guide](https://learn.microsoft.com/en-us/windows/wsl/install) for other installation methods.
 2. Restart your computer. On restart, you will be prompted to create a user account for WSL. This account is separate from your Windows account, but you can use the same username and password if you wish.
 3. [Open up the Ubuntu distribution](https://learn.microsoft.com/en-us/windows/wsl/install#ways-to-run-multiple-linux-distributions-with-wsl) via the `Ubuntu` command and run `sudo apt update && sudo apt upgrade` to update the distribution.
 4. Install a napari development environment in Ubuntu following the [contributor guide](dev-installation) and activate the virtual environment that napari was installed into.

docs/developers/contributing/index.md

@@ -17,7 +17,7 @@ The first step to make changes to napari is to
 set up a [napari development installation](dev-installation).
 
 You can then use git to save your changes and open a
-[pull-request](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) (PR) via the following steps:
+[pull-request](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project) (PR) via the following steps:
 
 1. Make and save your changes:
 
@@ -46,7 +46,7 @@ To set it, use `git config --global user.email your-address@example.com`.
 2. Share your changes:
 
 To push the local changes in your new feature branch to your
-[forked](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#forking-a-repository) repository:
+[forked](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project#forking-a-repository) repository:
 
 ```sh
 git push -u origin your-branch-name
@@ -63,7 +63,7 @@ git remote -vv
 ```
 
 You can then make a
-[PR](https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request) to `napari`'s `main` branch.
+[PR](https://docs.github.com/en/get-started/exploring-projects-on-github/contributing-to-a-project#making-a-pull-request) to `napari`'s `main` branch.
 
 ## napari contribution guides
 

docs/developers/contributing/testing.md

@@ -323,7 +323,7 @@ you patch or replace parts of the code being tested with "fake" behavior or
 return values, so that you can test how a given function would perform *if* it
 were to receive some value from the upstream code.  For a few examples of using
 mocks when testing napari, search the codebase for
-[`unittest.mock`](https://github.com/napari/napari/search?q=%22unittest.mock%22&type=Code)
+[`unittest.mock`](https://github.com/search?q=repo%3Anapari%2Fnapari+%22unittest.mock%22&type=Code)
 
 ## Known issues
 

docs/developers/coredev/core_dev_guide.md

@@ -180,7 +180,7 @@ As a core member, you should be familiar with the following napari guides:
 ### Social resources
 
 - [#napari on image.sc](https://forum.image.sc/tag/napari).
-- [#napari](https://twitter.com/search?q=%23napari&f=live) and [@napari_imaging](https://twitter.com/napari_imaging) on twitter.
+- [#napari](https://x.com/search?q=%23napari&f=live) and [@napari_imaging](https://x.com/napari_imaging) on twitter.
 - [napari zulip](https://napari.zulipchat.com/) community chat channel.
 
 You are not required to monitor the social resources.

docs/developers/coredev/maintenance.md

@@ -11,7 +11,7 @@ will not trigger another action's runs. The possible workaround for this is to c
 But this requires additional actions by core devs.
 
 To get automatically running workflows, we need to create a personal access token (PAT) and add it to the repository secrets.
-For security reasons, it is recommended to create a [fine-grained token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token#creating-a-fine-grained-personal-access-token). It allows us to provide only the required permissions.
+For security reasons, it is recommended to create a [fine-grained token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens). It allows us to provide only the required permissions.
 
 The token should have a one-year expiration date. After that, it needs to be refreshed.
 

docs/developers/coredev/packaging.md

@@ -255,7 +255,7 @@ Generating a `conda`-based installer requires several components in place:
 [4]: https://github.com/pypa/gh-action-pypi-publish
 [6]: https://github.com/conda/constructor
 [7]: https://conda.github.io/constructor/construct-yaml/
-[8]: https://conda-forge.org/docs/maintainer/updating_pkgs.html#rerendering-feedstocks
+[8]: https://conda-forge.org/docs/maintainer/updating_pkgs/#rerendering-feedstocks
 [16]: https://github.com/conda-forge/napari-feedstock/pulls?q=is%3Apr+sort%3Aupdated-desc+is%3Aclosed
 [17]: https://anaconda.org/napari
 [19]: https://nsis.sourceforge.io/Main_Page

docs/developers/coredev/release.md

@@ -55,7 +55,7 @@ Additional `release` dependencies (`python -m pip install -e .[release]`, from t
 The `napari/napari` repository must have a PyPI API token as a GitHub secret.
 This likely has been done already, but if it has not, follow
 [this guide](https://pypi.org/help/#apitoken) to gain a token and
-[this guide](https://docs.github.com/en/actions/security-guides/encrypted-secrets)
+[this guide](https://docs.github.com/en/actions/security-for-github-actions/security-guides/using-secrets-in-github-actions)
 to add it as a secret.
 
 ## Determining the version

docs/developers/index.md

@@ -37,6 +37,6 @@ There are a number of ways to contact the napari community:
 - [zulip](https://napari.zulipchat.com/): the zulip napari community chat channel.
 - [GitHub issue](https://github.com/napari/napari/issues): feel free to open an
   issue in our GitHub repository. Issues and pull-requests are written in [Markdown](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/about-writing-and-formatting-on-github). You can find a comprehensive guide [here](https://docs.github.com/en/get-started/writing-on-github/getting-started-with-writing-and-formatting-on-github/basic-writing-and-formatting-syntax)
-- [Image.sc forum](https://forum.image.sc/tags/napari): napari is a community partner
+- [Image.sc forum](https://forum.image.sc/tag/napari): napari is a community partner
   on the Image.sc forum. All usage support requests should be posted on the forum with
   the tag "napari".