From b1a909e874026d70c1f21918e8e3b0a870d193b3 Mon Sep 17 00:00:00 2001
From: Iyad Ba Gari <39617810+bagari@users.noreply.github.com>
Date: Sun, 3 Nov 2024 09:27:26 -0800
Subject: [PATCH] Update meta-neuro version 1.0.0 (#51826)

* update meta.yaml file for meta package version 1.0.0

https://bioconda.github.io/recipes/meta/README.html#package-meta

* Update meta.yaml

* Fix boost version compatibility with ITK

* update ITK version to 5.3.0 to prevent install libitk and version 5.4rc02

* update ITK run section at meta.yaml

* Update meta.yaml

* Add libgl-devel

* Update meta.yaml

* update build_variant

* Include test data into meta folder

Moving test data into the meta folder to solve the input data error does not exist during the container test.

* adding test data

* change and saved test data into $PREFIX/share/meta/example

* add python support 3.8-3.11

Python 3.12 will be supported after ITK updates its release.

* update meta.yaml with skipping python 3.12

* debug "No space left on device" issue

* Drop support python 3.8 to solve storage issue, hopefully

* Update build to rebuild and check storage issue.

* Update meta.yaml

* Build only for python 3.10

* incrementing the build number

* Update meta.yaml

* Update meta.yaml

* Update build.sh

* Update build.sh

* Update meta.yaml

* Delete conda_build_config.yaml

* Update meta.yaml

* support apple arm

* trying support vtk with egl variant

* Update meta.yaml

* keep only support VTK with osmesa for linux

* Update meta.yaml

* last attempt to build all python variants, hope no space error

* force to skip python 3.12

* Update conda_build_config.yaml

* Update package name from meta to meta-neuro

* update folder name as well

* update name to meta-neuro
---
 recipes/{meta => meta-neuro}/build.sh      | 17 ++++--
 recipes/meta-neuro/conda_build_config.yaml | 18 +++++++
 recipes/{meta => meta-neuro}/meta.yaml     | 60 ++++++++++------------
 3 files changed, 57 insertions(+), 38 deletions(-)
 rename recipes/{meta => meta-neuro}/build.sh (71%)
 mode change 100755 => 100644
 create mode 100644 recipes/meta-neuro/conda_build_config.yaml
 rename recipes/{meta => meta-neuro}/meta.yaml (54%)
 mode change 100755 => 100644

diff --git a/recipes/meta/build.sh b/recipes/meta-neuro/build.sh
old mode 100755
new mode 100644
similarity index 71%
rename from recipes/meta/build.sh
rename to recipes/meta-neuro/build.sh
index b7767bfc0161f..b30b786bedb79
--- a/recipes/meta/build.sh
+++ b/recipes/meta-neuro/build.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -ex
 
 unset LD LINK ARCH
 export CMAKE_INSTALL_RPATH='$ORIGIN/../lib'
@@ -8,8 +9,12 @@ mkdir -p "$PREFIX/bin"
 mkdir -p "$PREFIX/lib"
 mkdir -p "$PREFIX/share"
 mkdir -p $SRC_DIR/build
-cd $SRC_DIR/build || exit 1
 
+## copy small test data:
+mkdir -p $PREFIX/share/meta-neuro/example
+cp $SRC_DIR/resources/test.nii.gz $PREFIX/share/meta-neuro/example/
+
+cd $SRC_DIR/build
 cmake -S $SRC_DIR -B $SRC_DIR/build  \
     -DCMAKE_BUILD_TYPE=Release \
     -DCMAKE_INSTALL_PREFIX=$PREFIX \
@@ -19,10 +24,12 @@ cmake -S $SRC_DIR -B $SRC_DIR/build  \
     -DCMAKE_INSTALL_RPATH=$CMAKE_INSTALL_RPATH \
     -DCMAKE_BUILD_WITH_INSTALL_RPATH=$CMAKE_BUILD_WITH_INSTALL_RPATH
 
-cmake --build . --config Release --parallel ${CPU_COUNT} --verbose || exit 1
-cmake --install . || exit 1
+cmake --build . --config Release --parallel ${CPU_COUNT} --verbose
+cmake --install .
+
+# Clean up build directory
 rm -rf $SRC_DIR/build
 
 # Install MeTA package
-cd ${SRC_DIR} || exit 1
-${PYTHON} -m pip install . --no-deps -vv || exit 1
+cd ${SRC_DIR}
+${PYTHON} -m pip install . --no-deps -vv
diff --git a/recipes/meta-neuro/conda_build_config.yaml b/recipes/meta-neuro/conda_build_config.yaml
new file mode 100644
index 0000000000000..09a4e9197bc16
--- /dev/null
+++ b/recipes/meta-neuro/conda_build_config.yaml
@@ -0,0 +1,18 @@
+build_variant:
+  - "osmesa"  # [linux]
+  - "qt"      # [osx]
+
+python:
+  - 3.11.*  *_cpython
+  - 3.10.*  *_cpython
+  - 3.9.*  *_cpython
+
+python_impl:
+  - cpython
+  - cpython
+  - cpython
+
+numpy:
+  - 1.23.*
+  - 1.22.*
+  - 1.22.*
diff --git a/recipes/meta/meta.yaml b/recipes/meta-neuro/meta.yaml
old mode 100755
new mode 100644
similarity index 54%
rename from recipes/meta/meta.yaml
rename to recipes/meta-neuro/meta.yaml
index 331b63318f57e..dfcd922cb0f7c
--- a/recipes/meta/meta.yaml
+++ b/recipes/meta-neuro/meta.yaml
@@ -1,7 +1,6 @@
-{% set name = "meta" %}
+{% set name = "meta-neuro" %}
 {% set version = "1.0.0" %}
-{% set sha256 = "a35dd5bc3ccffaaf83aa488233467ae85dc5374aea3068c34a6dc85ea29e27a9" %}
-{% set build_variant = "osmesa" if linux else "qt" %}
+{% set sha256 = "c67bcad0899fc3f9c890ee26e9c1c2ab1a892430ce00a9ac090e36697efc9434" %}
 
 package:
   name: {{ name|lower }}
@@ -13,9 +12,9 @@ source:
 
 build:
   number: 0
-  skip: true # [not py39]
+  skip: true  # [win ]
   run_exports:
-    - {{ pin_subpackage('meta', max_pin="x") }}
+    - {{ pin_subpackage('meta-neuro', max_pin="x.x.x") }}
 
 requirements:
   build:
@@ -24,45 +23,38 @@ requirements:
     - make  # [not win]
 
   host:
-    - python >=3.9,<3.10
-    - pip
-    - boost =1.82
-    - itk =5.3.0
-    - libitk =5.3.0
-    - libitk-devel =5.3.0
+    - vtk >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - 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 >=2.5.0,<2.6.0
-    - vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libboost-python-devel >=1.82.0,<1.83.0
+    - python
+    - pip
+    - setuptools
 
   run:
-    - qhull
-    - boost =1.82
-    - itk =5.3.0
-    - libitk =5.3.0
-    - libitk-devel =5.3.0
+    - vtk >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - libitk-devel ==5.3.0
     - hdf5 >=1.14.2,<1.14.3.0a0
-    - vtk-base >=9.2.6,<9.3.0 build=*{{ build_variant }}*
-    - numpy >=1.21
-    - nibabel
-    - pandas
-    - pyvista
-    - scipy
+    - libboost-python-devel >=1.82.0,<1.83.0
+    - qhull
+    - python
+    - pip
+    - setuptools
+    - numpy
     - tqdm
-    - tslearn
     - dipy
-    - libexpat >=2.5.0,<2.6.0
-    - vtk-io-ffmpeg >=9.2.6,<9.3.0 build=*{{ build_variant }}*
+    - scipy
+    - pandas
+    - nibabel
+    - tslearn
+    - pyvista
 
 test:
-  source_files:
-    - resources/CST_R.nii.gz
   imports:
     - meta
   commands:
-    - meta --help 2>&1 || exit 1
-    - vtklevelset resources/CST_R.nii.gz CST_R.vtk 0.1 && test -f CST_R.vtk
-    - cmrep_vskel -c 3 -p 1.5 -g CST_R.vtk CST_R_skeleton.vtk && test -f CST_R_skeleton.vtk
+    - vtklevelset $PREFIX/share/meta-neuro/example/test.nii.gz test.vtk 0.1
+    - cmrep_vskel -c 3 -p 1.5 -g test.vtk test_skeleton.vtk
 
 about:
   home: https://github.com/bagari/meta
@@ -76,5 +68,7 @@ about:
 
 extra:
   bulk: true
+  additional-platforms:
+    - osx-arm64
   recipe-maintainers:
     - bagari