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add meta #51349

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6b7031a
add build.sh, meta.yaml and conda_build_config.yaml
bagari Oct 12, 2024
79b47b0
Update build.sh
bagari Oct 12, 2024
ec43e5c
Update conda_build_config.yaml
bagari Oct 12, 2024
a3efe60
Update meta.yaml
bagari Oct 12, 2024
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28 changes: 28 additions & 0 deletions recipes/meta/build.sh
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#!/bin/bash

unset LD LINK ARCH
export CMAKE_INSTALL_RPATH='$ORIGIN/../lib'
export CMAKE_BUILD_WITH_INSTALL_RPATH=ON

mkdir -p "$PREFIX/bin"
mkdir -p "$PREFIX/lib"
mkdir -p "$PREFIX/share"
mkdir -p $SRC_DIR/build
cd $SRC_DIR/build || exit 1

cmake -S $SRC_DIR -B $SRC_DIR/build \
-DCMAKE_BUILD_TYPE=Release \
-DCMAKE_INSTALL_PREFIX=$PREFIX \
-DCMAKE_CXX_STANDARD=17 \
-DCMAKE_MODULE_PATH=$PREFIX/share/cmake \
-DCMAKE_PREFIX_PATH=$PREFIX \
-DCMAKE_INSTALL_RPATH=$CMAKE_INSTALL_RPATH \
-DCMAKE_BUILD_WITH_INSTALL_RPATH=$CMAKE_BUILD_WITH_INSTALL_RPATH

cmake --build . --config Release || exit 1
cmake --install . || exit 1
rm -rf $SRC_DIR/build

# Install MeTA package
cd ${SRC_DIR} || exit 1
${PYTHON} -m pip install . --no-deps -vv || exit 1
9 changes: 9 additions & 0 deletions recipes/meta/conda_build_config.yaml
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build_variant:
- "osmesa" # [linux]
- "qt" # [osx]

python:
- 3.8
- 3.9
- 3.10
- 3.11
92 changes: 92 additions & 0 deletions recipes/meta/meta.yaml
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{% set name = "meta" %}
{% set version = "1.0.0" %}
{% set sha256 = "96673754c8f8c926bd179a824513de36d0b361eb93b1f7781cbac27ecf520d6e" %}

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

source:
url: https://github.com/bagari/meta/archive/refs/tags/v{{ version }}.tar.gz
sha256: {{ sha256 }}
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build:
number: 0
skip: true # [win] # Windows support will be added in next release.

requirements:
build:
- {{ compiler('cxx') }}
- {{ stdlib("c") }}
- cmake
- make # [not win]
- python {{ python }}
- pip
- git
- setuptools
- boost =1.82
- itk ==5.3.0
- libitk ==5.3.0
- libitk-devel ==5.3.0
- hdf5 >=1.14.2,<1.14.3.0a0
- vtk-base >=9.2.6,<9.3.0 build=*{{ build_variant }}*
- libexpat <2.6
- libexpat >=2.5.0,<3.0a0
- vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*

host:
- qhull
- boost =1.82
- itk ==5.3.0
- libitk ==5.3.0
- libitk-devel ==5.3.0
- hdf5 >=1.14.2,<1.14.3.0a0
- vtk-base >=9.2.6,<9.3.0 build=*{{ build_variant }}*
- python {{ python }}
- libexpat <2.6
- libexpat >=2.5.0,<3.0a0
- vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*

run:
- qhull
- boost =1.82
- itk ==5.3.0
- libitk ==5.3.0
- libitk-devel ==5.3.0
- hdf5 >=1.14.2,<1.14.3.0a0
- vtk-base >=9.2.6,<9.3.0 build=*{{ build_variant }}*
- python {{ python }}
- numpy
- setuptools
- nibabel
- pandas
- pyvista
- scipy
- tqdm
- tslearn
- dipy
- libexpat <2.6
- libexpat >=2.5.0,<3.0a0
- vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*
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🛠️ Refactor suggestion

Consider optimizing dependency management

The requirements section is comprehensive, but there might be room for optimization:

  1. Some dependencies (e.g., boost, itk, hdf5, vtk-base) are repeated across build, host, and run sections with the same version constraints. Consider using conda-forge's run_exports feature to reduce redundancy.

  2. The libexpat dependency has two entries with overlapping version ranges. These could potentially be combined into a single entry.

  3. Ensure that all listed dependencies are necessary for each stage (build, host, run). For example, does the package really need git at build time?

Review each dependency and its presence in different sections. If you need assistance in optimizing this section, please let me know.


test:
imports:
- meta
commands:
- meta --help
- cmrep_vskel --version
- vtklevelset --version
Comment on lines +72 to +78
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🛠️ Refactor suggestion

Enhance test robustness

The test section includes both import and command-line tests, which is good. However, consider the following improvements based on past review suggestions:

  1. For command-line tests, instead of just running with --help or --version, check for specific expected output:
  commands:
    - meta --help 2>&1 | grep -q "Usage:" || exit 1
    - cmrep_vskel --version 2>&1 | grep -q "version" || exit 1
    - vtklevelset --version 2>&1 | grep -q "version" || exit 1

  1. Add more comprehensive import tests to ensure all main modules are importable.

  2. Consider adding functional tests that exercise core features of the package.

Would you like assistance in implementing these test improvements?


about:
home: https://github.com/bagari/meta
license: BSD-3-Clause
license_file: LICENSE.txt
summary: 'Medial Tractography Analysis (MeTA)'
description: |
MeTA is a workflow implemented to minimize microstructural heterogeneity in diffusion MRI (dMRI) metrics by extracting and parcellating the core volume along the bundle length in the voxel-space directly while effectively preserving bundle shape and efficiently capturing the regional variation within and along white matter (WM) bundles.
dev_url: https://github.com/bagari/meta
doc_url: https://github.com/bagari/meta/wiki

extra:
recipe-maintainers:
- bagari
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