<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
	- Introduced host-specific logging to enhance monitoring capabilities.
- Added a new `HOST` option to the Quietness settings for improved
configuration flexibility.

- **Bug Fixes**
- Improved logging behavior by ensuring host information is prioritized
in logging output.

- **Documentation**
	- Updated documentation to reflect new logging features and settings.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

<!--Add a description of your PR here-->

This fixes #2774.

1. When inferring memory or disk from a string, *_mb now divides the
bytes by 1e6 (SI) instead of 2^20 (binary) and takes the ceiling instead
of rounding.
2. The inference of *_mib now properly multiplies by 1.048576 instead of
0.95367431640625 (this is also equivalent to dividing by the original
value, which used the wrong operation)
3. After inferring resources from string-based resources, Snakemake now
updates `resources` so that the inference of mem_mib and disk_mib will
use the newly inferred value.
4. mem_mib and disk_mib are now inferred regardless of whether resources
are inferred from human readable values.

All space requests are now correct, but we may want to consider using
`humanfriendly.parse_size(value, binary=True)` instead of
`humanfriendly.parse_size(value)` for `mem`, since SI memory units are
rarely used, but this would be an enhancement rather than a pure bugfix.

Many thanks to @hermidalc for their help.

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **New Features**
- Enhanced precision for converting megabytes to mebibytes, improving
accuracy in data handling.
- Updated resource inference to ensure memory and disk values are
rounded up, increasing the minimum allocations.

- **Bug Fixes**
- Streamlined resource inference logic for clarity and maintainability,
reducing potential errors.

- **Tests**
- Added new Snakemake rules for testing resource allocation across
different capacities, ensuring accurate output in multiple units.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Leandro Hermida <[email protected]>

The [Zed editor](https://github.com/zed-industries/zed) now has a
[snakemake extension](https://github.com/lvignoli/zed-snakemake).
There was no dedicated place in the docs to link to it, so I added an
editor integration section to the installation page, it seemed the best
place.

It lacks some prose, I was unsure of what maintainers would like to have
in this section.

### QC

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Documentation**
- Updated the installation guide for Mamba with clearer instructions and
recommendations.
- Added a new section on "Editor integrations," providing links to
plugins for Snakemake to enhance user workflow.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Documentation**
- Corrected a typographical error in the Snakemake rules documentation
for improved clarity on shell command invocation.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

…ut files) (#3050)

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **New Features**
- Enhanced output file handling to ensure that output files are not
older than their corresponding input files, preventing potential
execution issues.

- **Improvements**
- Improved clarity in variable naming for better readability and
understanding of output path handling.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

<!--Add a description of your PR here-->

I initially wanted to fix only the Mambaforge mentions in the Setup
tutorial, but then noticed several warnings when building the docs so I
tried tackling those as well. Here is a list:

- Replace Mambaforge by Miniforge in the Setup tutorial
- Remove deprecated `sphinxawesome_theme.highlighting` extension
- Fix broken links in the docs (internal links and links to API docs)
- Fix headings that the did not show up in HTML (Bash examples)
- Fix warnings about duplicate external links (e.g. links named "here")
by making them anonymous with a double underscore.
- Replace sub-worfklows by modules in Additional Features tutorial about
modularization

Let me know if these are too unrelated for a single PR and you want me
to split it.

Thank you!

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case. (N.A., I think)
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->

## Summary by CodeRabbit

- **Documentation Updates**
- Removed outdated highlighting extension from documentation
configuration.
	- Updated references in cloud execution documentation for clarity.
- Enhanced hyperlink formatting throughout various documentation files
for consistency.
- Clarified terminology related to modularization and workflow
management.
- Revised tutorial content to reflect the transition from "Mambaforge"
to "Miniforge" for Python installation instructions.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

…me possible offline (cont. of #2904) (#3026)

The original PR has been reverted in main because it does not seem to
work will with developer installation mode (assets are not installed in
the right place in that case).

cc @fs82 

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

## Summary by CodeRabbit

- **New Features**
- Introduced structured asset management within the Snakemake framework,
allowing for better handling and deployment of external resources.

- **Improvements**
- Enhanced package metadata handling for improved maintainability and
accessibility of license and source files.
- Enabled the inclusion of additional package data during installation,
ensuring necessary files are available.

- **Bug Fixes**
- Improved reliability by transitioning to local paths for resource
referencing, enhancing accessibility and reducing dependency on external
URLs.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

with flag `print-compilation`, it is not intend to execute the code,
which can be incomplete, and running it will waste time and print errors
to the screen.

Also, I add some asserts to some properties as they are typing as
Optional.

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

- **New Features**
- Introduced a reusable decorator that standardizes resource settings in
the Workflow API.

- **Enhancements**
- Improved type annotations for better clarity and type safety across
multiple classes.
- Added assertions in critical methods to ensure necessary settings are
initialized before use.

- **Refactor**
- Streamlined several function signatures and internal logic for
enhanced readability and maintainability.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

---------

Co-authored-by: Johannes Köster <[email protected]>
Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).


<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit


- **Bug Fixes**
- Improved the method resolution for wildcards, enhancing stability and
preventing potential issues in complex inheritance scenarios.

<!-- end of auto-generated comment: release notes by coderabbit.ai -->

🤖 I have created a release *beep* *boop*
---


##
[8.19.0](v8.18.2...v8.19.0)
(2024-08-29)


### Features

* check consistency of output file mtimes (must be newer than input
files) ([#3050](#3050))
([666cf62](666cf62))
* print host name when executing workflow
([#3048](#3048))
([b0ff787](b0ff787))


### Bug Fixes

* `mem` and `disk` inference fixes
([#3040](#3040))
([7530794](7530794))
* avoid error accessing superclass in ioutils
([#3056](#3056))
([a66a5f5](a66a5f5))
* disable execute after print compilation
([#3041](#3041))
([86ed3cd](86ed3cd))
* download report assets upon package build such that reports become
possible offline (cont. of
[#2904](#2904))
([#3026](#3026))
([e8dad4b](e8dad4b))


### Documentation

* Add 'Editor integrations' section to Installation page
([#3045](#3045))
([9a4006d](9a4006d))
* Fix typo (seesee to see)
([#3037](#3037))
([de201fb](de201fb))
* various documentation fixes
([#3052](#3052))
([b11460c](b11460c))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>