Conda build (#99)

* Added conda build

.github/workflows/siemens_to_ismrmrd_conda.yml

@@ -0,0 +1,36 @@
+on:
+  pull_request:
+    branches:    
+      - master
+  release:
+    types:
+      - created
+
+jobs:
+  build-conda-packages:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@2541b1294d2704b0964813337f33b291d3f8596b
+      - uses: conda-incubator/setup-miniconda@e81abac10ce2c37423b54eae5af93aa3b4d3475c
+        with:
+          activate-environment: siemens-to-ismrmrd-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 siemens_to_ismrmrd*.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 siemens_to_ismrmrd*.tar.bz2`

CMakeLists.txt

@@ -18,7 +18,7 @@ message(STATUS "Looking for packages in : ${CMAKE_PREFIX_PATH}")
 #VERSIONING
 set(SIEMENS_TO_ISMRMRD_VERSION_MAJOR 1)
 set(SIEMENS_TO_ISMRMRD_VERSION_MINOR 2)
-set(SIEMENS_TO_ISMRMRD_VERSION_PATCH 3)
+set(SIEMENS_TO_ISMRMRD_VERSION_PATCH 4)
 set(SIEMENS_TO_ISMRMRD_VERSION_STRING ${SIEMENS_TO_ISMRMRD_VERSION_MAJOR}.${SIEMENS_TO_ISMRMRD_VERSION_MINOR}.${SIEMENS_TO_ISMRMRD_VERSION_PATCH})
 
 # Generate the converter_version.h header file

conda/.gitignore

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

conda/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+set -euo pipefail
+
+mkdir -p build
+cd build
+cmake -G Ninja -DBUILD_DYNAMIC=ON -DCMAKE_PREFIX_PATH=${PREFIX} -DCMAKE_INSTALL_PREFIX=${PREFIX} ../
+ninja
+ninja install

conda/environment.yml

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

conda/meta.yaml

@@ -0,0 +1,39 @@
+{% set major = load_file_regex(load_file='CMakeLists.txt', regex_pattern='(?<=set\(SIEMENS_TO_ISMRMRD_VERSION_MAJOR )([^\)]+)') %}
+{% set minor = load_file_regex(load_file='CMakeLists.txt', regex_pattern='(?<=set\(SIEMENS_TO_ISMRMRD_VERSION_MINOR )([^\)]+)') %}
+{% set patch = load_file_regex(load_file='CMakeLists.txt', regex_pattern='(?<=set\(SIEMENS_TO_ISMRMRD_VERSION_PATCH )([^\)]+)') %}
+
+package:
+  name: siemens_to_ismrmrd
+  version: {{ major.group(1) }}.{{ minor.group(1) }}.{{ patch.group(1) }}
+
+source:
+  path: ../
+
+requirements:
+  build:
+    - boost=1.76.0
+    - clang>=13.0.1        # [osx]
+    - clangxx>=13.0.1      # [osx]
+    - cmake>=3.20.0
+    - gcc_linux-64>=9.0.0  # [linux64] 
+    - gxx_linux-64>=9.0.0  # [linux64]
+    - ismrmrd=1.11.1
+    - libxml2=2.9.12
+    - libxslt=1.1.33 
+    - ninja=1.10.*
+
+  run:
+    - ismrmrd=1.11.1
+    - boost=1.76.0
+    - libxml2=2.9.12
+    - libxslt=1.1.33 
+
+about:
+  home: https://github.com/ismrmrd/siemens_to_ismrmrd
+  license: MIT
+  summary: 'Siemens to ISMRM Raw Data (ISMRMRD) converter'
+  description: |
+    Command line tool for converting Siemens raw data (*.dat) files to ISMRMRD files.
+  dev_url: https://github.com/ismrmrd/siemens_to_ismrmrd
+  doc_url: https://github.com/ismrmrd/siemens_to_ismrmrd
+  doc_source_url: https://github.com/ismrmrd/siemens_to_ismrmrd/blob/master/README.md

conda/package.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+set -euo pipefail
+
+usage()
+{
+  cat << EOF
+
+Builds the siemens_to_ismrmrd conda package.
+
+Usage: $0
+EOF
+}
+
+output_path="$(dirname "$0")/build_pkg"
+
+# Build up channel directives
+channels=(
+  ismrmrd
+  conda-forge
+)
+
+channel_directives=$(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 +1,10 @@
+#!/bin/bash
+
+set -euo pipefail
+
+# We are just printing help text, which will fail if dependencies are missing
+siemens_to_ismrmrd -h
+siemens_to_ismrmrd -v
+
+
+

main.cpp

@@ -515,15 +515,15 @@ int main(int argc, char* argv[]) {
 
         if (vm.count("help")) {
             std::cout << display_options << "\n";
-            return 1;
+            return 0;
         }
 
         if (vm.count("version")) {
             std::cout << "Converter version is: " << SIEMENS_TO_ISMRMRD_VERSION_MAJOR << "."
                 << SIEMENS_TO_ISMRMRD_VERSION_MINOR << "." << SIEMENS_TO_ISMRMRD_VERSION_PATCH << "\n";
             std::cout << "Built against ISMRMRD version: " << ISMRMRD_VERSION_MAJOR << "." << ISMRMRD_VERSION_MINOR
                 << "." << ISMRMRD_VERSION_PATCH << "\n";
-            return 1;
+            return 0;
         }
     }