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


##
[9.6.0](v9.5.1...v9.6.0)
(2025-06-16)


### Features

* Prefer papermill to nbconvert
([#2857](#2857))
([4263b03](4263b03))


### Bug Fixes

* DeprecationWarning when using snakemake.utils.validate
([#3420](#3420))
([cf72427](cf72427))
* display group jobs on dryrun
([#3435](#3435))
([3bebef4](3bebef4))
* expandvars for special profile keys
([#3597](#3597))
([4020188](4020188))
* fix bug causing --precommand to not being executed before each remote
job ([#3625](#3625))
([e59d125](e59d125))
* improved toggle switch behavior in reports
([#3623](#3623))
([0c4bd23](0c4bd23))
* pass envvars defined via the envvars directive to remote jobs
([#3626](#3626))
([d4890b4](d4890b4))
* remove wms arg, update logging cli docs
([#3622](#3622))
([3a9a5ac](3a9a5ac))
* typo in CondaEnvDirSpec.__eq__ (issue
[#3192](#3192))
([#3613](#3613))
([f4c107f](f4c107f))
* Unclear handling of params overriding with inheritance
([#3624](#3624))
([077ac4a](077ac4a))


### Documentation

* Added snakemake command to execute the rule plot_with_python
([#3608](#3608))
([bd99c11](bd99c11))
* Updated Reporting Section of The Tutorial(Interaction, Visualization,
and Reporting with Snakemake)
([#3606](#3606))
([91e90ba](91e90ba))
* Updated Requirement Section of The Tutorial With Warning of Not
Installing The Tools Manually
([#3607](#3607))
([3bd114b](3bd114b))
* Updated Wrapper Version in Tutorial and Used Simple Rule For
Consistency & Ease
([#3605](#3605))
([b3bcc21](b3bcc21))

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

This commit fixes a regression introduced in Snakemake 9.6.0 where
relative `$ref` references in local config schemas were not correctly
resolved during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute file:// $id in schemas to enforce proper
   local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
   it now receives a file:// URI).

In addition, to prevent future regressions, this commit adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This commit intentionally does *not* restore one specific aspect
of the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this commit always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) where successfully
   run at commit `960f6a89eaa31da6014e810dfcf08f635ac03a6e` (last
   ancestor of current `main` that still uses the old `RefResolver`
   implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
   `cf724272eefcd9b30fb625d2e16380727bef9c3e` (direct child of the
   above, introducing the changes from PR snakemake#3420), the three (nested)
   `$ref`s test fail, verifying this commit/PR caused the regression and
   the tests added in this commit catch that regression.
3. The same tests still fail at commit
   `f1517e83a6a4a193a1148543fc06177eeb11ecb5` (current `main`),
   demonstrating that the regression has not been fixed yet.
4. All tests pass after applying the changes from this commit,
   validating it fixes the regression.

---
fixes snakemake#3648

This commit fixes a regression introduced in Snakemake 9.6.0 where
relative `$ref` references in local config schemas were not correctly
resolved during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute file:// $id in schemas to enforce proper
   local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
   it now receives a file:// URI).

In addition, to prevent future regressions, this commit adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This commit intentionally does *not* restore one specific aspect
of the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this commit always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) where successfully
   run at commit `960f6a89eaa31da6014e810dfcf08f635ac03a6e` (last
   ancestor of current `main` that still uses the old `RefResolver`
   implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
   `cf724272eefcd9b30fb625d2e16380727bef9c3e` (direct child of the
   above, introducing the changes from PR snakemake#3420), the three (nested)
   `$ref`s test fail, verifying this commit/PR caused the regression and
   the tests added in this commit catch that regression.
3. The same tests still fail at commit
   `f1517e83a6a4a193a1148543fc06177eeb11ecb5` (current `main`),
   demonstrating that the regression has not been fixed yet.
4. All tests pass after applying the changes from this commit,
   validating it fixes the regression.

---
fixes snakemake#3648

This commit fixes a regression introduced in Snakemake 9.6.0 where
relative `$ref` references in local config schemas were not correctly
resolved during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute file:// $id in schemas to enforce proper
   local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
   it now receives a file:// URI).

In addition, to prevent future regressions, this commit adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This commit intentionally does *not* restore one specific aspect
of the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this commit always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) where successfully
   run at commit `960f6a89eaa31da6014e810dfcf08f635ac03a6e` (last
   ancestor of current `main` that still uses the old `RefResolver`
   implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
   `cf724272eefcd9b30fb625d2e16380727bef9c3e` (direct child of the
   above, introducing the changes from PR snakemake#3420), the three (nested)
   `$ref`s test fail, verifying this commit/PR caused the regression and
   the tests added in this commit catch that regression.
3. The same tests still fail at commit
   `a9c9d275f1f6a2069b78f79db01f718e2ea16734` (current `main`),
   demonstrating that the regression has not been fixed yet.
4. All tests pass after applying the changes from this commit,
   validating it fixes the regression.

---
fixes snakemake#3648

This commit fixes a regression introduced in Snakemake 9.6.0 where
relative `$ref` references in local config schemas were not correctly
resolved during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute file:// $id in schemas to enforce proper
   local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
   it now receives a file:// URI).

In addition, to prevent future regressions, this commit adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This commit intentionally does *not* restore one specific aspect
of the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this commit always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) were successfully
   run at commit `960f6a89eaa31da6014e810dfcf08f635ac03a6e` (last
   ancestor of current `main` that still uses the old `RefResolver`
   implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
   `cf724272eefcd9b30fb625d2e16380727bef9c3e` (direct child of the
   above, introducing the changes from PR snakemake#3420), the three (nested)
   `$ref`s test fail, verifying this commit/PR caused the regression and
   the tests added in this commit catch that regression.
3. The same tests still fail at commit
   `a9c9d275f1f6a2069b78f79db01f718e2ea16734` (current `main`),
   demonstrating that the regression has not been fixed yet.
4. All tests pass after applying the changes from this commit,
   validating it fixes the regression.

---
fixes snakemake#3648

This commit fixes a regression introduced in Snakemake 9.6.0 where
relative `$ref` references in local config schemas were not correctly
resolved during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute file:// $id in schemas to enforce proper
   local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
   it now receives a file:// URI).

In addition, to prevent future regressions, this commit adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This commit intentionally does *not* restore one specific aspect
of the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this commit always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) were successfully
   run at commit `960f6a89eaa31da6014e810dfcf08f635ac03a6e` (last
   ancestor of current `main` that still uses the old `RefResolver`
   implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
   `cf724272eefcd9b30fb625d2e16380727bef9c3e` (direct child of the
   above, introducing the changes from PR snakemake#3420), the three (nested)
   `$ref`s test fail, verifying this commit/PR caused the regression and
   the tests added in this commit catch that regression.
3. The same tests still fail at commit
   `a9c9d275f1f6a2069b78f79db01f718e2ea16734` (current `main`),
   demonstrating that the regression has not been fixed yet.
4. All tests pass after applying the changes from this commit,
   validating it fixes the regression.

---
fixes snakemake#3648

This commit fixes a regression introduced in Snakemake 9.6.0 where
relative `$ref` references in local config schemas were not correctly
resolved during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute file:// $id in schemas to enforce proper
   local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
   it now receives a file:// URI).

In addition, to prevent future regressions, this commit adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This commit intentionally does *not* restore one specific aspect
of the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this commit always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) were successfully
   run at commit `960f6a89eaa31da6014e810dfcf08f635ac03a6e` (last
   ancestor of current `main` that still uses the old `RefResolver`
   implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
   `cf724272eefcd9b30fb625d2e16380727bef9c3e` (direct child of the
   above, introducing the changes from PR snakemake#3420), the three (nested)
   `$ref`s test fail, verifying this commit/PR caused the regression and
   the tests added in this commit catch that regression.
3. The same tests still fail at commit
   `2eb9079dae29f271aeacff75e59f6c2f6a0d352d` (current `main`),
   demonstrating that the regression has not been fixed yet.
4. All tests pass after applying the changes from this commit,
   validating it fixes the regression.

---
fixes snakemake#3648

This PR fixes a regression introduced in Snakemake 9.6.0 where relative
`$ref` references in local config schemas were not correctly resolved
during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
#3420.

The two required changes were:

1. Injection of an absolute `file://` `$id` in schemas to enforce proper
local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
it now receives a `file://` URI).

In addition, to prevent future regressions, this PR adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This PR intentionally does *not* restore one specific aspect of
the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this PR always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) were successfully run
at commit
[`960f6a89eaa31da6014e810dfcf08f635ac03a6e`](960f6a8)
(last ancestor of current `main` that still uses the old `RefResolver`
implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
[`cf724272eefcd9b30fb625d2e16380727bef9c3e`](cf72427)
(direct child of the above, introducing the changes from PR #3420), the
three (nested) `$ref`s test fail, verifying this commit/PR caused the
regression and the tests added in this commit catch that regression.
3. The same tests still fail at commit
[`2eb9079dae29f271aeacff75e59f6c2f6a0d352d`](2eb9079)
(current `main`), demonstrating that the regression has not been fixed
yet.
4. All tests pass after applying the changes from this PR, validating it
fixes the regression.

### 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).

#### Notes:

This is my first contribution to the project. Thus, I am not familiar
with the codebase.
It is also my first time dealing with `jsonschema` and the both, its
(deprecated) `RefResolver` API (to analyse the old implementation and
design tests accordingly), and its current `resolving` API (to fix the
regression).
Please let me know if you have any adjustments you want/need me to do.

Also, I started from a standalone POC script to make sure I understand
the API, defined tests and then worked on the actual fix off that.
Initially, I overestimated the power of pre-9.6.0's implementation of
the `validate` function and designed a test that tested defaults
propagation across (nested) `$ref`s. Thus, my intermediate solution was
much more complex (and powerful) than this simple (minimal) fix.
I do have a local branch with that work in case anybody is interested in
implementing more powerful defaults value handling during config
validation. Please reach out if there is interest.

---
fixes #3648

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

* **Bug Fixes**
* Schema resolution now enforces local resolution of relative $ref
references, improving validation and default assignment across nested
refs, fragments, allOf/anyOf/defs; may change behavior for schemas that
previously relied on remote resolution.

* **Tests**
* Added comprehensive tests and fixtures covering relative/fragment
references, nested schemas, allOf/anyOf/defs, default handling, and
error scenarios.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

…e#3420)

This PR closes snakemake#2468, by replacing RefResolver functionality with the
referencing library.

### 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

- **Refactor**
- Modernized the data validation process by adopting the latest features
of the JSON Schema Draft 2020-12 specification for improved reliability
and consistency.
- Added schema versioning information to existing schema definitions for
enhanced validation and interoperability.
- **Style**
- Enhanced the formatting of warning messages for clearer and more
readable notifications.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

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


##
[9.6.0](snakemake/snakemake@v9.5.1...v9.6.0)
(2025-06-16)


### Features

* Prefer papermill to nbconvert
([snakemake#2857](snakemake#2857))
([4263b03](snakemake@4263b03))


### Bug Fixes

* DeprecationWarning when using snakemake.utils.validate
([snakemake#3420](snakemake#3420))
([cf72427](snakemake@cf72427))
* display group jobs on dryrun
([snakemake#3435](snakemake#3435))
([3bebef4](snakemake@3bebef4))
* expandvars for special profile keys
([snakemake#3597](snakemake#3597))
([4020188](snakemake@4020188))
* fix bug causing --precommand to not being executed before each remote
job ([snakemake#3625](snakemake#3625))
([e59d125](snakemake@e59d125))
* improved toggle switch behavior in reports
([snakemake#3623](snakemake#3623))
([0c4bd23](snakemake@0c4bd23))
* pass envvars defined via the envvars directive to remote jobs
([snakemake#3626](snakemake#3626))
([d4890b4](snakemake@d4890b4))
* remove wms arg, update logging cli docs
([snakemake#3622](snakemake#3622))
([3a9a5ac](snakemake@3a9a5ac))
* typo in CondaEnvDirSpec.__eq__ (issue
[snakemake#3192](snakemake#3192))
([snakemake#3613](snakemake#3613))
([f4c107f](snakemake@f4c107f))
* Unclear handling of params overriding with inheritance
([snakemake#3624](snakemake#3624))
([077ac4a](snakemake@077ac4a))


### Documentation

* Added snakemake command to execute the rule plot_with_python
([snakemake#3608](snakemake#3608))
([bd99c11](snakemake@bd99c11))
* Updated Reporting Section of The Tutorial(Interaction, Visualization,
and Reporting with Snakemake)
([snakemake#3606](snakemake#3606))
([91e90ba](snakemake@91e90ba))
* Updated Requirement Section of The Tutorial With Warning of Not
Installing The Tools Manually
([snakemake#3607](snakemake#3607))
([3bd114b](snakemake@3bd114b))
* Updated Wrapper Version in Tutorial and Used Simple Rule For
Consistency & Ease
([snakemake#3605](snakemake#3605))
([b3bcc21](snakemake@b3bcc21))

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

This PR fixes a regression introduced in Snakemake 9.6.0 where relative
`$ref` references in local config schemas were not correctly resolved
during validation.

This regression was introduced when refactoring the config validation
from the (deprecated) `RefResolver` to the (current) `resolving` API in
snakemake#3420.

The two required changes were:

1. Injection of an absolute `file://` `$id` in schemas to enforce proper
local reference resolution.
2. A follow-up update to retrieve_uri to correctly load subschemas (as
it now receives a `file://` URI).

In addition, to prevent future regressions, this PR adds tests for
(nested) `$ref`s, `$ref` with remote `$id` (see below), fragment
references, `allOf`/`anyOf` defaults, and `$def`s.

This commit restores pre-9.6.0 behavior and prevents ValidationError
when nested schemas are referenced.

Caveat: This PR intentionally does *not* restore one specific aspect of
the old (`RefResolver` based) implementation:
If a schema file contains an explicit `$id` pointing to a remote copy of
the schema, the old implementation would fetch any references (in- or
external) from that remote URI.
Instead, the implementation introduced by this PR always resolves
references based on the local schema file.
This behaviour is demonstrated (and validated) with the remote `$id`
test mentioned above.

The following checks have been performed to ensure the correctness of
this patch:

1. All tests (but the remote `$id` one, see above) were successfully run
at commit
[`960f6a89eaa31da6014e810dfcf08f635ac03a6e`](snakemake@960f6a8)
(last ancestor of current `main` that still uses the old `RefResolver`
implementation), proving that they cover pre-9.6.0 behaviour.
2. Re-running the same tests at commit
[`cf724272eefcd9b30fb625d2e16380727bef9c3e`](snakemake@cf72427)
(direct child of the above, introducing the changes from PR snakemake#3420), the
three (nested) `$ref`s test fail, verifying this commit/PR caused the
regression and the tests added in this commit catch that regression.
3. The same tests still fail at commit
[`2eb9079dae29f271aeacff75e59f6c2f6a0d352d`](snakemake@2eb9079)
(current `main`), demonstrating that the regression has not been fixed
yet.
4. All tests pass after applying the changes from this PR, validating it
fixes the regression.

### 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).

#### Notes:

This is my first contribution to the project. Thus, I am not familiar
with the codebase.
It is also my first time dealing with `jsonschema` and the both, its
(deprecated) `RefResolver` API (to analyse the old implementation and
design tests accordingly), and its current `resolving` API (to fix the
regression).
Please let me know if you have any adjustments you want/need me to do.

Also, I started from a standalone POC script to make sure I understand
the API, defined tests and then worked on the actual fix off that.
Initially, I overestimated the power of pre-9.6.0's implementation of
the `validate` function and designed a test that tested defaults
propagation across (nested) `$ref`s. Thus, my intermediate solution was
much more complex (and powerful) than this simple (minimal) fix.
I do have a local branch with that work in case anybody is interested in
implementing more powerful defaults value handling during config
validation. Please reach out if there is interest.

---
fixes snakemake#3648

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

* **Bug Fixes**
* Schema resolution now enforces local resolution of relative $ref
references, improving validation and default assignment across nested
refs, fragments, allOf/anyOf/defs; may change behavior for schemas that
previously relied on remote resolution.

* **Tests**
* Added comprehensive tests and fixtures covering relative/fragment
references, nested schemas, allOf/anyOf/defs, default handling, and
error scenarios.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

The `referencing` dependency was introduced in this pull request:
snakemake/snakemake#3420

It was released in version `9.6.0`:
snakemake/snakemake#3611

A `referencing` dependency was added in snakemake version 9.6.0:
snakemake/snakemake#3420

This was not added to the bioconda recipe of `snakemake-minimal` until version 9.19.0:
#64534

So this PR patches the repodata accordingly.

* fix: snakemake depends on referencing since 9.6.0

The `referencing` dependency was introduced in this pull request:
snakemake/snakemake#3420

It was released in version `9.6.0`:
snakemake/snakemake#3611

* fix: bump build number for snakemake recipe update

….0 (#64539)

* fix: add `referencing` dependency for snakemake-minimal >=9.6.0,<9.19.0

A `referencing` dependency was added in snakemake version 9.6.0:
snakemake/snakemake#3420

This was not added to the bioconda recipe of `snakemake-minimal` until version 9.19.0:
#64534

So this PR patches the repodata accordingly.

* fix: also patch build 0 of version 9.19.0

* fix: do proper semantic version comparisons for newly added patch

* fix: consistently use `parse_version()` for any semantic version comparison of version strings

I manually tested that this does not change the patches that are created. I think we just got lucky in the past, in that none of the version numbers went above 9, so that lexicographical sort/comparison just always worked out. But we should enforce the usage, so that copy-pasted comparisons ensure this works for any version number ranges.

* fix: snakemake depends on referencing since 9.6.0

The `referencing` dependency was introduced in this pull request:
snakemake/snakemake#3420

It was released in version `9.6.0`:
snakemake/snakemake#3611

* fix: bump build number for snakemake recipe update

….0 (bioconda#64539)

* fix: add `referencing` dependency for snakemake-minimal >=9.6.0,<9.19.0

A `referencing` dependency was added in snakemake version 9.6.0:
snakemake/snakemake#3420

This was not added to the bioconda recipe of `snakemake-minimal` until version 9.19.0:
bioconda#64534

So this PR patches the repodata accordingly.

* fix: also patch build 0 of version 9.19.0

* fix: do proper semantic version comparisons for newly added patch

* fix: consistently use `parse_version()` for any semantic version comparison of version strings

I manually tested that this does not change the patches that are created. I think we just got lucky in the past, in that none of the version numbers went above 9, so that lexicographical sort/comparison just always worked out. But we should enforce the usage, so that copy-pasted comparisons ensure this works for any version number ranges.