Conda build (#56)

* Added conda build and fixed broken tests

* Remove debug code

* Removed Azure DevOps pipeline

* Disabling nosetests on mac

* PR review

* Removed macos conda build for now

* bump numpy in requirements file

Co-authored-by: Michael Hansen <mihansen@microsoft>

.github/workflows/ismrmrd_python_conda.yml

@@ -0,0 +1,36 @@
+on:
+  pull_request:
+    branches:    
+      - master
+  release:
+    types:
+      - created
+
+jobs:
+  build-conda-packages:
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b
+      - uses: conda-incubator/setup-miniconda@e81abac10ce2c37423b54eae5af93aa3b4d3475c
+        with:
+          activate-environment: ismrmrd-python-build
+          environment-file: conda/environment.yml
+          python-version: 3.9
+          auto-activate-base: false
+      - name: Build conda package
+        shell: bash -l {0}
+        working-directory: conda
+        run: |
+          ./package.sh
+          echo "Packages built: $(find build_pkg -name ismrmrd-python*.tar.bz2)"
+      - name: Push conda package
+        shell: bash -l {0}
+        if: ${{ github.event_name == 'release' }}
+        env:
+          ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
+        working-directory: conda
+        run: |
+          ./publish_package.sh -u ismrmrd -t "$ANACONDA_TOKEN" -p `find build_pkg -name ismrmrd-python*.tar.bz2`

conda/.gitignore

@@ -0,0 +1,3 @@
+build_pkg/
+.pytest_cache/
+__pycache__/

conda/build.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+set -euo pipefail
+
+python setup.py install

conda/environment.yml

@@ -0,0 +1,7 @@
+name: ismrmrd-python-build
+channels:
+  - conda-forge
+dependencies:
+  - conda-build
+  - anaconda-client
+

conda/meta.yaml

@@ -0,0 +1,36 @@
+{% set data = load_setup_py_data() %}
+
+package:
+  name: ismrmrd-python
+  version: {{ data.get('version') }}
+
+source:
+  path: ../
+
+requirements:
+  build:
+    - numpy>=1.22.0
+    - h5py>=2.3
+    - nose>=1.0
+    - xsdata>=22.2
+
+  run:
+    - xsdata>=22.2
+    - numpy>=1.22.0
+    - h5py>=2.3
+
+test:
+  source_files:
+    - tests
+  requires:
+    - nose
+
+about:
+  home: https://github.com/ismrmrd/ismrmrd-python
+  license: MIT
+  summary: 'Python interface for ISMRMRD'
+  description: |
+    Python interface and utilities for the ISMRM Raw Data (ISMRMRD a.k.a. MRD) format.
+  dev_url: https://github.com/ismrmrd/ismrmrd-python
+  doc_url: https://github.com/ismrmrd/ismrmrd-python
+  doc_source_url: https://github.com/ismrmrd/ismrmrd-python/blob/main/README.md

conda/package.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+set -euo pipefail
+
+usage()
+{
+  cat << EOF
+
+Builds the ismrmrd-python conda package.
+
+Usage: $0
+EOF
+}
+
+output_path="$(dirname "$0")/build_pkg"
+
+# Build up channel directives
+channels=(
+  conda-forge
+)
+
+channel_directives=$(printf -- "-c %s " "${channels[@]}")
+
+mkdir -p "$output_path"
+bash -c "conda build --no-anaconda-upload --output-folder $output_path $channel_directives $(dirname "$0")"

conda/publish_package.sh

@@ -0,0 +1,77 @@
+#!/bin/bash
+set -euo pipefail
+
+usage()
+{
+  cat << EOF
+
+Publishes a conda package.
+
+Usage: $0 [options]
+
+Options:
+  -p|--package_path <path>               Path to the package (tar.gz) to push
+  -u|--user <user>                       Anaconda.org channeluser or organization
+  -t|--token <token>                     Token for uploading to anaconda.org
+  -f|--force                             Force push even if package exists
+  -h| --help  Brings up this menu
+EOF
+}
+
+while [[ $# -gt 0 ]]; do
+  key="$1"
+
+  case $key in
+    -p|--package_path)
+      package_path="$2"
+      shift
+      shift
+      ;;
+    -u|--user)
+      user="$2"
+      shift
+      shift
+      ;;
+    -t|--token)
+      token="$2"
+      shift
+      shift
+      ;;
+    --force)
+      force=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit
+      ;;
+    *)
+      echo "ERROR: unknown option \"$key\""
+      usage
+      exit 1
+      ;;
+  esac
+done
+
+if [[ -z "${package_path:-}" ]]; then
+  echo "You cannot push to anaconda without a package"
+  echo "Please supply a package path with the --package_path argument"
+  exit 1
+fi
+if [[ -z "${token:-}" ]]; then
+  echo "You cannot push to anaconda without a token"
+  echo "Please supply a token with the --token argument"
+  exit 1
+fi
+if [[ -z "${user:-}" ]]; then
+  echo "You cannot push to anaconda without a user"
+  echo "Please supply a user with the --user argument"
+  exit 1
+fi
+
+force_directive="--skip-existing"
+if [[ -n ${force:-} ]]; then
+  force_directive="--force"
+fi
+
+anaconda -t "$token" upload -u "$user" $force_directive "$package_path"

conda/run_test.sh

@@ -0,0 +1,7 @@
+#!/bin/bash
+
+set -euo pipefail
+
+cd tests
+nosetests
+

requirements.txt

@@ -1,6 +1,6 @@
 h5py==2.9.0
 nose==1.3.7
-numpy==1.21.0
+numpy==1.22.0
 PyXB==1.2.6
 six==1.12.0
 xsdata==22.2

setup.py

@@ -61,7 +61,7 @@ def to_uri(filename):
     version='1.12.0',
     author='ISMRMRD Developers',
     description='Python implementation of the ISMRMRD',
-    license='Public Domain',
+    license='MIT',
     keywords='ismrmrd',
     url='https://ismrmrd.github.io',
     long_description = long_description,
@@ -70,7 +70,7 @@ def to_uri(filename):
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Science/Research',
-        'License :: Public Domain',
+        'License :: MIT',
         'Operating System :: OS Independent',
         'Topic :: Scientific/Engineering :: Medical Science Apps.'
         ],

tests/test_common.py

@@ -121,7 +121,7 @@ def create_random_image(seed=42):
     header = create_random_image_properties()
 
     image = ismrmrd.Image.from_array(data, **header)
-    image.attribute_string = "This is a random attribute: {}".format(random.randint(0, 1000))
+    image.attribute_string = "<?xml version='1.0' encoding='UTF-8'?>\n<ismrmrdMeta><meta><name>rando</name><value>{}</value></meta></ismrmrdMeta>".format(random.randint(0, 1000))
 
     return image
 

tests/test_image.py

@@ -22,7 +22,8 @@ def test_new_instance():
     eq_(type(img.data), np.ndarray)
     eq_(img.data.dtype, np.complex64)
 
-    attr = "this is a fake attribute string"
+    attr = "<?xml version='1.0' encoding='UTF-8'?>\n<ismrmrdMeta><meta><name>rando</name><value>blah</value></meta></ismrmrdMeta>"
+
     head = ismrmrd.ImageHeader()
     head.attribute_string_len = len(attr)       # must set attribute_string_len
     head.data_type = ismrmrd.DATATYPE_CXFLOAT   # must set data_type