Update galaxy-data to 24.1.1, add galaxy-schema recipe #49232

corneliusroemer · 2024-07-14T14:45:10Z

Attempt to update galaxy-data to 24.1.1.

galaxy-data now requires another package, galaxy-schema, so this PR also adds that.

I cannot figure out how to get the import tests to pass: galaxy-schema requires pydantic[email] but just installing the extra dependency email-validation does not seem to work. I wonder whether adding the extra [email] to pydantic has some side-effects beyond installing email-validation.

Any help greatly appreciated. I don't use galaxy at all - I just wanted to help update a package that has not received autobumps.

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corneliusroemer · 2024-07-14T15:50:13Z

Blocked by #49230 as we need the other galaxy tools to be available first due to strict minimum pinning of galaxy dependencies

recipes/galaxy-schema/meta.yaml

bernt-matthias · 2024-07-17T08:30:56Z

Hi @corneliusroemer . Thanks for your initiative.

Regarding the email-validator question. In Galaxy's pinnings we list both: email-validator and pydantic[email]. So I guess we need the same here.

corneliusroemer · 2024-07-17T08:52:02Z

@bernt-matthias the problem is that pydantic[email] is not available via conda-forge. See:

Add extra dependencies to recipe conda-forge/pydantic-feedstock#55
How can one effectively install pydantic[email]? Just adding email-validator as an extra dependency doesn't work conda-forge/pydantic-feedstock#128

Unless I'm missing something (which is very possible as I have no clue what pydantic[email] does), it might be necessary to create an additional recipe output for the pydantic-feedstock pydantic-email as conda cannot use pypi dependencies directly.

There was a discussion in conda-forge/pydantic-feedstock#55 that stalled.

bernt-matthias · 2024-07-17T09:00:43Z

The weird thing is that

ImportError: email-validator is not installed, run `pip install pydantic[email]`

seems to be correct, i.e. email-validator is not installed during the test... at least I could not spot it in the list of installed packages.

recipes/galaxy-schema/meta.yaml

corneliusroemer · 2024-07-17T09:18:54Z

@bernt-matthias you're totally right - it doesn't install as a test dependency 😮 No clue why not. When I manually ask for conda-validator or conda_validator it shows up, no problem.

recipes/galaxy-data/meta.yaml

recipes/galaxy-schema/meta.yaml

recipes/galaxy-data/meta.yaml

Co-authored-by: Nicola Soranzo <[email protected]>

nsoranzo · 2024-07-17T16:18:27Z

Progress! Need to update the isa-rwval to 0.10.10 though.

corneliusroemer · 2024-07-17T18:03:06Z

Yay it works!

bernt-matthias

Cool. Thanks a lot @corneliusroemer

bernt-matthias · 2024-07-17T21:23:08Z

Anything else from your side @nsoranzo?

nsoranzo · 2024-07-18T15:22:22Z

recipes/galaxy-data/meta.yaml

@@ -1,49 +1,65 @@
-{% set version = "22.1.1" %}
-{% set sha256 = "27d1fc4ccc0d05adbb49fced1b0bcf59497a702c8bf51e39b058449dc0644cfe" %}
+{% set version = "24.1.1" %}


Suggested change

{% set version = "24.1.1" %}

{% set name = "galaxy-data" %}

{% set version = "24.1.1" %}

nsoranzo · 2024-07-18T15:22:50Z

recipes/galaxy-data/meta.yaml

-{% set version = "22.1.1" %}
-{% set sha256 = "27d1fc4ccc0d05adbb49fced1b0bcf59497a702c8bf51e39b058449dc0644cfe" %}
+{% set version = "24.1.1" %}
+{% set sha256 = "be4d1ba81589cc5e6d4fb38829c1770483cff6c380b7647aa80b7bc90737f573" %}
 {% set galaxy_version = version.split(".")[:2]|join(".") %}

 package:
  name: galaxy-data


Suggested change

name: galaxy-data

name: {{ name }}

nsoranzo · 2024-07-18T15:23:27Z

recipes/galaxy-data/meta.yaml

 {% set galaxy_version = version.split(".")[:2]|join(".") %}

 package:
  name: galaxy-data
  version: {{ version }}

 source:
-  url: https://pypi.io/packages/source/g/galaxy-data/galaxy-data-{{ version }}.tar.gz
+  url: https://pypi.io/packages/source/g/galaxy-data/galaxy_data-{{ version }}.tar.gz


Suggested change

url: https://pypi.io/packages/source/g/galaxy-data/galaxy_data-{{ version }}.tar.gz

url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/galaxy_data-{{ version }}.tar.gz

nsoranzo · 2024-07-18T15:26:40Z

recipes/galaxy-schema/meta.yaml

+    # Disabling all .bco imports as I can't figure out how to install pydantic[email]
+    # Simply installing email-validator as separate dep does not work
+    #- galaxy.schema.bco
+    #- galaxy.schema.bco.description_domain
+    #- galaxy.schema.bco.error_domain
+    #- galaxy.schema.bco.execution_domain
+    #- galaxy.schema.bco.io_domain
+    #- galaxy.schema.bco.parametric_domain
+    #- galaxy.schema.bco.provenance_domain
+    #- galaxy.schema.bco.usability_domain
+    #- galaxy.schema.bco.util


These can be restored now?

nsoranzo · 2024-07-18T15:30:13Z

recipes/galaxy-schema/meta.yaml

+  license: MIT
+  license_family: MIT


Suggested change

license: MIT

license_family: MIT

license: AFL-3.0

* Update galaxy-data to 24.1.1 * Add galaxy-schema recipe * Sync requirements from setup.cfg * f * Update meta.yaml * Update meta.yaml * fix indent * Update meta.yaml * Update meta.yaml * Update recipes/galaxy-schema/meta.yaml * Update meta.yaml * let's try email_validator as well * Update recipes/galaxy-data/meta.yaml Co-authored-by: Nicola Soranzo <[email protected]> * Update recipes/galaxy-schema/meta.yaml Co-authored-by: Nicola Soranzo <[email protected]> * Update isa-rwval * fix dependencies * fix isa-rwval sha * tiny edits --------- Co-authored-by: Nicola Soranzo <[email protected]> Co-authored-by: mencian <[email protected]>

corneliusroemer added 2 commits July 14, 2024 16:44

Update galaxy-data to 24.1.1

d7aaa86

Add galaxy-schema recipe

5981e36

corneliusroemer changed the title ~~Update galaxy-data to 24.1.1~~ Update galaxy-data to 24.1.1, add galaxy-schema recipe Jul 14, 2024

corneliusroemer requested a review from bernt-matthias July 14, 2024 15:08

corneliusroemer added 2 commits July 14, 2024 17:21

Sync requirements from setup.cfg

73481a8

f

467933d

corneliusroemer added 3 commits July 14, 2024 23:12

Update meta.yaml

009987d

Update meta.yaml

c5fc43a

fix indent

f6c3bde

TobyBaril mentioned this pull request Jul 15, 2024

Pull requests failing in testing during docker run #49250

Closed

corneliusroemer added 2 commits July 15, 2024 12:46

Update meta.yaml

ab9df62

Update meta.yaml

35713a8

corneliusroemer commented Jul 15, 2024

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corneliusroemer added 2 commits July 15, 2024 13:57

Update recipes/galaxy-schema/meta.yaml

cddbe6a

Update meta.yaml

11477e5

corneliusroemer changed the title ~~Update galaxy-data to 24.1.1, add galaxy-schema recipe~~ Help wanted: Update galaxy-data to 24.1.1, add galaxy-schema recipe Jul 16, 2024

corneliusroemer added help wanted new version labels Jul 16, 2024

corneliusroemer requested a review from bgruening July 16, 2024 12:58

corneliusroemer commented Jul 17, 2024

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recipes/galaxy-schema/meta.yaml Outdated Show resolved Hide resolved

let's try email_validator as well

8ad0088

nsoranzo reviewed Jul 17, 2024

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nsoranzo reviewed Jul 17, 2024

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corneliusroemer and others added 2 commits July 17, 2024 12:55

Update recipes/galaxy-data/meta.yaml

f91604f

Co-authored-by: Nicola Soranzo <[email protected]>

Update recipes/galaxy-schema/meta.yaml

db601b4

Co-authored-by: Nicola Soranzo <[email protected]>

corneliusroemer added 3 commits July 17, 2024 18:43

Update isa-rwval

48c17ff

fix dependencies

7de4544

fix isa-rwval sha

f17872a

corneliusroemer requested a review from nsoranzo July 17, 2024 18:02

corneliusroemer changed the title ~~Help wanted: Update galaxy-data to 24.1.1, add galaxy-schema recipe~~ Update galaxy-data to 24.1.1, add galaxy-schema recipe Jul 17, 2024

corneliusroemer added please review & merge set to ask for merge and removed help wanted labels Jul 17, 2024

bernt-matthias approved these changes Jul 17, 2024

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tiny edits

9c7e3f7

mencian approved these changes Jul 18, 2024

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nsoranzo reviewed Jul 18, 2024

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corneliusroemer merged commit 0dcb544 into master Jul 18, 2024
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corneliusroemer deleted the galaxy-data branch July 18, 2024 15:31

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Update galaxy-data to 24.1.1, add galaxy-schema recipe #49232

Update galaxy-data to 24.1.1, add galaxy-schema recipe #49232

corneliusroemer commented Jul 14, 2024 •

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nsoranzo Jul 18, 2024

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nsoranzo Jul 18, 2024

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nsoranzo Jul 18, 2024

	{% set version = "24.1.1" %}
	{% set name = "galaxy-data" %}
	{% set version = "24.1.1" %}

	url: https://pypi.io/packages/source/g/galaxy-data/galaxy_data-{{ version }}.tar.gz
	url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/galaxy_data-{{ version }}.tar.gz

Update galaxy-data to 24.1.1, add galaxy-schema recipe #49232

Update galaxy-data to 24.1.1, add galaxy-schema recipe #49232

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corneliusroemer commented Jul 14, 2024 • edited Loading

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corneliusroemer commented Jul 14, 2024 •

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