Adding CAREamics recipe #28148

jdeschamps · 2024-11-08T12:01:51Z

Adding CAREamics recipe along side sister packages careamics-portfolio and careamics-napari.

careamics: a library for the denoising of scientific microscopy images using deep learning.
careamics-portfolio: a package providing access to several datasets used to illustrate or benchmark denoising algorithms.
careamics-napari: napari plugin for CAREamics.

Notes regarding dependencies

careamics-napari depends on both careamics and careamics-portfolio
careamics depends on PyTorch

Notes regarding build

Because PyTorch is currently not built for Windows in conda-forge, the Windows build is disabled for both careamics and careamics-napari.

Checklist

github-actions · 2024-11-08T12:03:11Z

Hi! This is the staged-recipes linter and your PR looks excellent! 🚀

conda-forge-admin · 2024-11-08T12:03:59Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics/meta.yaml) and found some lint.

Here's what I've got...

For recipes/careamics/meta.yaml:

Jinja2 variable definitions are suggested to take a {%<one space>set<one space><variable name><one space>=<one space><expression><one space>%} form. See lines [2]
requirements: run: python >= 3.9 should not contain a space between relational operator and the version, i.e. python >=3.9

For recipes/careamics/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.
Jinja2 variable references are suggested to take a {{<one space><variable name><one space>}} form. See lines [22].

conda-forge-admin · 2024-11-08T13:08:36Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics/meta.yaml) and found it was in an excellent condition.
I do have some suggestions for making it better though...

For recipes/careamics/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.
Jinja2 variable references are suggested to take a {{<one space><variable name><one space>}} form. See lines [20].

conda-forge-admin · 2024-11-08T18:25:14Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics/meta.yaml, recipes/careamics-napari/meta.yaml, recipes/careamics-portfolio/meta.yaml) and found some lint.

Here's what I've got...

For recipes/careamics/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.
Jinja2 variable references are suggested to take a {{<one space><variable name><one space>}} form. See lines [21].

For recipes/careamics-napari/meta.yaml:

The home item is expected in the about section.

For recipes/careamics-napari/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.
Jinja2 variable references are suggested to take a {{<one space><variable name><one space>}} form. See lines [20].

For recipes/careamics-portfolio/meta.yaml:

The home item is expected in the about section.

For recipes/careamics-portfolio/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.
Jinja2 variable references are suggested to take a {{<one space><variable name><one space>}} form. See lines [20].

conda-forge-admin · 2024-11-08T18:35:36Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics-napari/meta.yaml, recipes/careamics/meta.yaml, recipes/careamics-portfolio/meta.yaml) and found it was in an excellent condition.
I do have some suggestions for making it better though...

For recipes/careamics-napari/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.

For recipes/careamics/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.

For recipes/careamics-portfolio/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.

conda-forge-admin · 2024-11-08T18:39:50Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics/meta.yaml, recipes/careamics-napari/meta.yaml, recipes/careamics-portfolio/meta.yaml) and found some lint.

Here's what I've got...

For recipes/careamics/meta.yaml:

Non noarch packages should have python requirement without any version constraints.

For recipes/careamics-napari/meta.yaml:

Non noarch packages should have python requirement without any version constraints.

For recipes/careamics-portfolio/meta.yaml:

noarch: python recipes should almost always follow the syntax in our documentation. For the host section of the recipe, you should almost always use python {{ python_min }} for the python entry. For the run section of the recipe, you should almost always use python >={{ python_min }} for the python entry. For the test.requires section of the recipe, you should almost always use python {{ python_min }} for the python entry. You may need to override the python_min variable in the conda_build_config.yaml/variants.yaml if the package requires a newer Python version than the currently supported minimum version on conda-forge.

This reverts commit a686f54.

github-actions · 2024-11-08T18:54:58Z

Hi! This is the staged-recipes linter and I found some lint.

It looks like some changes were made outside the recipes/ directory. To ensure everything runs smoothly, please make sure that recipes are only added to the recipes/ directory and no other files are changed.

If these changes are intentional (and you aren't submitting a recipe), please add a maintenance label to the PR.

File-specific lints and/or hints:

.azure-pipelines/azure-pipelines-win.yml:
- lints:
  - Do not edit files outside of the recipes/ directory.
.ci_support/win64.yaml:
- lints:
  - Do not edit files outside of the recipes/ directory.
.scripts/run_win_build.bat:
- lints:
  - Do not edit files outside of the recipes/ directory.

github-actions · 2024-11-08T18:56:07Z

Hi! This is the staged-recipes linter and your PR looks excellent! 🚀

jdeschamps · 2024-11-08T21:47:30Z

I apologize for abusing the CI when trying to debug the linting and the Windows failed build...

@conda-forge/help-python ready for review!

jdeschamps · 2024-11-11T09:08:31Z

Forgot @conda-forge/staged-recipes

github-actions · 2024-11-11T09:08:41Z

To help direct your pull request to the best reviewers, please mention a topic-specifc team if your recipe matches any of the following: conda-forge/help-c-cpp, conda-forge/help-cdts, conda-forge/help-go, conda-forge/help-java, conda-forge/help-julia, conda-forge/help-nodejs, conda-forge/help-perl, conda-forge/help-python, conda-forge/help-python-c, conda-forge/help-r, conda-forge/help-ruby,or conda-forge/help-rust. Thanks!

recipes/careamics-napari/meta.yaml

recipes/careamics/meta.yaml

conda-forge-admin · 2024-11-23T14:39:46Z

Hi! This is the friendly automated conda-forge-linting service.

I wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics-napari/meta.yaml, recipes/careamics/meta.yaml, recipes/careamics-portfolio/meta.yaml) and found some lint.

Here's what I've got...

For recipes/careamics-napari/meta.yaml:

❌ noarch: python recipes are required to have a lower bound on the python version. Typically this means putting python >=3.6 in both host and run but you should check upstream for the package's Python compatibility.

For recipes/careamics-napari/meta.yaml:

ℹ️ noarch: python recipes should usually follow the syntax in our documentation for specifying the Python version.
- For the host section of the recipe, you should usually use python {{ python_min }} for the python entry.
- For the run section of the recipe, you should usually use python >={{ python_min }} for the python entry.
- For the test.requires section of the recipe, you should usually use python {{ python_min }} for the python entry.
- If the package requires a newer Python version than the currently supported minimum version on conda-forge, you can override the python_min variable by adding a Jinja2 set statement at the top of your recipe (or using an equivalent context variable for v1 recipes).
ℹ️ The recipe is not parsable by parser conda-forge-tick (the bot). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.
ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.

For recipes/careamics/meta.yaml:

❌ noarch: python recipes are required to have a lower bound on the python version. Typically this means putting python >=3.6 in both host and run but you should check upstream for the package's Python compatibility.

For recipes/careamics/meta.yaml:

ℹ️ noarch: python recipes should usually follow the syntax in our documentation for specifying the Python version.
- For the host section of the recipe, you should usually use python {{ python_min }} for the python entry.
- For the run section of the recipe, you should usually use python >={{ python_min }} for the python entry.
- For the test.requires section of the recipe, you should usually use python {{ python_min }} for the python entry.
- If the package requires a newer Python version than the currently supported minimum version on conda-forge, you can override the python_min variable by adding a Jinja2 set statement at the top of your recipe (or using an equivalent context variable for v1 recipes).

For recipes/careamics-portfolio/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-forge-tick (the bot). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.
ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/11988004722. Examine the logs at this URL for more detail.}

conda-forge-admin · 2024-11-23T15:59:44Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics-napari/meta.yaml, recipes/careamics-portfolio/meta.yaml, recipes/careamics/meta.yaml) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/careamics-napari/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-forge-tick (the bot). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.
ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.

For recipes/careamics-portfolio/meta.yaml:

ℹ️ The recipe is not parsable by parser conda-forge-tick (the bot). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.
ℹ️ The recipe is not parsable by parser conda-souschef (grayskull). Your recipe may not receive automatic updates and/or may not be compatible with conda-forge's infrastructure. Please check the logs for more information and ensure your recipe can be parsed.

_{This message was generated by GitHub Actions workflow run https://github.com/conda-forge/conda-forge-webservices/actions/runs/11988496963. Examine the logs at this URL for more detail.}

conda-forge-admin · 2024-11-23T16:27:55Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/careamics-napari/meta.yaml, recipes/careamics/meta.yaml, recipes/careamics-portfolio/meta.yaml) and found it was in an excellent condition.

recipes/careamics-napari/meta.yaml

recipes/careamics-portfolio/meta.yaml

recipes/careamics/meta.yaml

Co-authored-by: Uwe L. Korn <[email protected]>

xhochy · 2024-11-24T19:42:20Z

I'm confused why it complains about an undefined python_min. This is working in other PRs 🤔

jdeschamps · 2024-11-24T20:35:39Z

I'm confused why it complains about an undefined python_min. This is working in other PRs 🤔

Beats me. That's why I added it in the first place!

Maybe I'll try to run grayskull again, this time with a better understanding of what the recipe should look like.

jdeschamps · 2024-11-29T11:27:30Z

I'm confused why it complains about an undefined python_min. This is working in other PRs 🤔

Similar problem here: conda-forge/conda-forge.github.io#2351 (comment)

It seems I need to re-render the feedstock.

xhochy · 2024-11-29T12:42:50Z

This is not a feedstock yet. Thus, a rerender is not possible. The build passes on osx, thus everything is fine. Could you submit the recipes individually to staged-recipes? Then I'm happy to merge them.

jdeschamps · 2024-12-01T11:17:32Z

This is not a feedstock yet. Thus, a rerender is not possible. The build passes on osx, thus everything is fine. Could you submit the recipes individually to staged-recipes? Then I'm happy to merge them.

Got it!

Here are the 3 PRs:
#28416
#28417
#28419

Add CAREamics recipe

196f909

github-actions bot added python review-requested labels Nov 8, 2024

jdeschamps added 2 commits November 8, 2024 14:01

Fix python_min in recipe

0908374

Fix jinja syntax and test requirement

044ed74

jdeschamps added 8 commits November 8, 2024 14:17

Fix bioimage.core dependency

f3521b6

Add description

35cf847

Update torch dependency and about field

bfcbf3c

Merge branch 'main' into careamics

810eee3

Merge branch 'main' into careamics

1fa96cc

Relax constraints

1acc506

Add CAREamics portfolio package

72ca850

Add CAREamics napari plugin package

e3ea95d

Fix linting

cf222c1

Skip win build

4889fb6

jdeschamps added 4 commits November 8, 2024 19:43

Fix: Skip win build

e3b86ce

Remove win CI and related files

a686f54

Fix linting

45455ab

Revert "Remove win CI and related files"

07eee32

This reverts commit a686f54.

jdeschamps added 3 commits November 8, 2024 21:20

Skip win build for napari plugin

9694b10

Remove python patch version

0296143

Skip py39 with noarch

7005372

github-actions bot added the staged-recipes label Nov 11, 2024

xhochy requested changes Nov 16, 2024

View reviewed changes

recipes/careamics-napari/meta.yaml Show resolved Hide resolved

recipes/careamics/meta.yaml Show resolved Hide resolved

noarch for all recipes

a123167

jdeschamps added 2 commits November 23, 2024 16:57

Add python_min

950e8ff

Merge branch 'main' into careamics

503f820

Remove duplicate keys

6c71d87

xhochy requested changes Nov 24, 2024

View reviewed changes

recipes/careamics-napari/meta.yaml Outdated Show resolved Hide resolved

recipes/careamics-portfolio/meta.yaml Outdated Show resolved Hide resolved

recipes/careamics/meta.yaml Outdated Show resolved Hide resolved

jdeschamps and others added 5 commits November 24, 2024 14:19

Update recipes/careamics-napari/meta.yaml

e25f4b6

Co-authored-by: Uwe L. Korn <[email protected]>

Update recipes/careamics-portfolio/meta.yaml

832ef9b

Co-authored-by: Uwe L. Korn <[email protected]>

Update recipes/careamics/meta.yaml

d48e2f6

Co-authored-by: Uwe L. Korn <[email protected]>

Merge branch 'main' into careamics

72123dc

Merge branch 'main' into careamics

e009bdc

Merge branch 'main' into careamics

9e61956

Merge branch 'main' into careamics

1c77ad8

This was referenced Dec 1, 2024

Adding CAREamics #28416

Merged

Adding CAREamics-portfolio #28417

Merged

Adding CAREamics-napari #28418

Closed

Add CAREamics-napari #28419

Merged

jdeschamps closed this Dec 1, 2024

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Adding CAREamics recipe #28148

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Adding CAREamics recipe #28148

Adding CAREamics recipe #28148

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Notes regarding dependencies

Notes regarding build

Checklist

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