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Build container completely with conda (no pip) #697

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16 of 18 tasks
HippocampusGirl opened this issue Feb 8, 2024 · 0 comments
Open
16 of 18 tasks

Build container completely with conda (no pip) #697

HippocampusGirl opened this issue Feb 8, 2024 · 0 comments
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@HippocampusGirl @lalalavi
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enhancement New feature or request

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HippocampusGirl commented Feb 8, 2024 •
edited by lalalavi

  1. Check conda-forge if we can get the package from there (if we spell it differently or use a different version)
  2. Write recipe

General Python dependencies

  • "atpublic==4.0"
  • "fasteners==0.19"
  • "flufl-lock==8.0.2"
  • "line-profiler==4.1.2"
  • "num2words==0.5.13"
  • "sqlalchemy==1.3.24"
  • "stackprinter==0.2.10"
  • "tzdata==2023.3"

Neuroimaging dependencies

Example of a recipe
https://github.com/conda-forge/traits-feedstock/blob/main/recipe/meta.yaml
@HippocampusGirl HippocampusGirl added the enhancement New feature or request label Feb 8, 2024
@lalalavi lalalavi mentioned this issue Feb 16, 2024
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HippocampusGirl pushed a commit that referenced this issue Feb 16, 2024
@lalalavi
Fix URLs and start migration to conda for build (#702)
73788d2 
This pull request addresses issue [#697](#697 ). All of the python dependencies have been either found in conga-forge in another number for the version, or with another name. The only python package exception is `sqlalchemy` where for some reason pip continues to install it even though there is a recipe available in condaforge. 

The reason we want to migrate entirely to conda management is to simplify the `requirements.sh` file and the build of the `Dockerfile`. The next pull request will address the remaining packages, for which we expect to build a custom recipe for all.

* Fix PNAS_Smith09_rsn10.nii.gz download link

* Conda recipe for niflow, improved dockerfile phrasing, deprecated line_profiler

* Replace buildkit syntax with a copy instruction

* Typo was breaking build for niflow

* Control all pypi based python dependencies through conda

* Tzdata was breaking build because it  corresponds to a different package in conda

* Upgrade pybids to the first version submitted in conda

* Roll back bids as upgrade breaks tests, include nitransforms recipe

* recipe pybids
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