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Merged
merged 3 commits into from
Apr 4, 2025
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spatialdata 0.3.0 #18

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spatialdata 0.3.0
jdblischak Mar 12, 2025
20675ca
MNT: Re-rendered with conda-build 25.3.2, conda-smithy 3.47.1, and co…
Apr 3, 2025
27d7988
Update recipe/meta.yaml
giovp Apr 4, 2025
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2 changes: 1 addition & 1 deletion .scripts/run_docker_build.sh
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47 changes: 33 additions & 14 deletions build-locally.py
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23 changes: 11 additions & 12 deletions recipe/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,55 +1,54 @@
{% set name = "spatialdata" %}
{% set version = "0.2.5" %}
{% set python_min = "3.9" %}
{% set version = "0.3.0" %}
{% set python_min = "3.10" %}

package:
name: {{ name|lower }}
version: {{ version }}

source:
url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/spatialdata-{{ version }}.tar.gz
sha256: 4ed8f30347a524548ce54f5957383dd8165ac27ead1c02c68be322854556d17f
sha256: 9215dd5171ac9ac0eed01a265f43092c8bdb760f0b1e994795fa274c5c638611

build:
noarch: python
script: {{ PYTHON }} -m pip install . -vv
script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
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@LucaMarconato LucaMarconato Apr 21, 2025 •
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@jdblischak could you please comment on --no-deps and --no-build-isolation?

I see that they are added here in spatialdata-feedstock and in these downstream repositories:

but not in these downstream repositories:

Also the parameters are not used in these upstream repositories:

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CC @giovp

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By default, pip will install any missing dependencies. However, all dependencies should be specified in the recipe and installed by conda. Using the flag --no-deps is a best practice to ensure all the required dependencies are defined in the recipe. It should be added to any recipe that is missing it

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By default, pip creates a separate build environment, installs the build requirements, and build the package in this separate environment. Thus this completely defeats the purpose of using the conda recipe to specify the build requirements. Any recipe missing --no-build-isolation should have the flag added. It ensures the package is built by the conda packages indicated in the recipe.

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@jdblischak jdblischak Apr 22, 2025 •
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A good habit when creating a new recipe or updating an existing one is to use grayskull, eg:

grayskull pypi --strict-conda-forge spatialdata
grep script spatialdata/meta.yaml
##   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation

which is the officially recommended method to generate conda-forge recipes.

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Thanks! I will add these parameters to the incoming conda releases.

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I tag also the other devs that are listed as maintainers of the repos above @melonora @timtreis @thewtex

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Quick follow-up to add some more nuance. While the official stance is to add --no-deps --no-build-isolation, there is some debate in the community (conda/grayskull#582, conda/grayskull#584). Essentially in most cases the flags are redundant because conda-build/rattler-build set env vars to accomplish this. However, they are required for recipes with multiple outputs and in the past when conda-build has failed to set the env vars.

Personally, I like including the flags even when they are redundant because they make it more transparent to readers of the recipe that these pip behaviors are being enforced.

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Thank you for the extra details!

number: 0

requirements:
host:
- hatch-vcs
- hatchling
- pip
- python {{ python_min }}
- python {{ python_min }},<3.13
run:
- anndata >=0.9.1
- click
- dask-core >=2024.4.1,<2025
- dask-core >=2024.4.1,<=2024.11.2
- dask-image
- datashader
- fsspec <=2023.6
- fsspec
- geopandas >=0.14
- multiscale-spatial-image >=1.0.0,<2.0.0
- multiscale-spatial-image >=2.0.2
- networkx
- numba
- numpy
- ome-zarr >=0.8.4,<0.10.3
- pandas
- pooch
- pyarrow
- python >={{ python_min }}
- python >={{ python_min }},<3.13
- pytorch
- rich
- scikit-image
- scipy
- shapely >=2.0.1
- spatial-image >=1.1.0
- typing-extensions >=4.8.0
- xarray >=2023.12.0,<2024.10.0
- xarray-datatree
- xarray >=2024.10.0
- xarray-schema
- xarray-spatial >=0.3.5
- zarr
- zarr <3

test:
imports:
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