Merge pull request #25 from tomaroberts/23-gha-testpypi

Adds GitHub Action to automatically publish every pushed version to TestPyPI, then verifies build

.github/workflows/build_and_test_cli.yml

@@ -56,6 +56,7 @@ jobs:
     - name: Test nii2dcm install
       run: |
         nii2dcm -h
+        nii2dcm -v
 
     - name: Test DicomMRISVR creation
       run: |

.github/workflows/publish_testpypi.yml

@@ -0,0 +1,82 @@
+# Publish to TestPyPI
+#
+# This workflow publishes nii2dcm on TestPyPI prior to production release onto PyPI. The workflow is intended to catch
+# any issues arising during the release procedure to prevent unnecessary versioning issues on PyPI
+#
+# This workflow will upload a Python Package using Twine when a release is created. For more information see:
+# https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+#
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Publish package to TestPyPI
+
+on:
+  pull_request
+
+permissions:
+  contents: read
+
+jobs:
+  testpypi-publish:
+
+    name: Publish release to TestPyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/nii2dcm
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for PyPI trusted publishing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+
+    - name: Build package
+      run: python -m build --sdist --wheel --outdir dist/
+
+    - name: Display nii2dcm version
+      id: nii2dcm-version
+      run: |
+        pip install -e .
+        echo "nii2dcm version:"
+        nii2dcm -v
+
+    - name: Publish package to TestPyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        user: __token__
+        password: ${{ secrets.TESTPYPI_API_TOKEN }}
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true
+
+    - name: Wait to allow TestPyPI to update
+      uses: GuillaumeFalourd/wait-sleep-action@v1
+      with:
+        time: '150'  # seconds
+
+    - name: Install latest TestPyPI version in fresh venv
+      run: |
+        NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
+        echo $NII2DCM_VERSION
+        python -m venv nii2dcm-temp
+        source nii2dcm-temp/bin/activate
+        pip install --upgrade pip
+        pip install setuptools wheel
+        pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ nii2dcm==$NII2DCM_VERSION
+        nii2dcm -h
+        echo "nii2dcm version:"
+        nii2dcm -v

.gitignore

@@ -88,5 +88,8 @@ _im*
 *.nii
 *.nii.gz
 
+# Omit _version.py as required by setuptools_scm
+nii2dcm/_version.py
+
 # Permit Test Data
 !tests/data/DicomMRISVR/t2-svr-atlas-35wk.nii.gz

nii2dcm/__main__.py

@@ -6,6 +6,7 @@
 import argparse
 from pathlib import Path
 from nii2dcm.run import run_nii2dcm
+from nii2dcm._version import __version__
 
 
 def cli(args=None):
@@ -24,7 +25,7 @@ def cli(args=None):
     parser.add_argument("output_dir", type=str, help="[directory] output DICOM path")
     parser.add_argument("-d", "--dicom_type", type=str, help="[string] type of DICOM. e.g. MR, CT, US, XR, etc.")
     parser.add_argument("-r", "--ref_dicom", type=str, help="[.dcm] Reference DICOM file for Attribute transfer")
-    parser.add_argument("-v", "--version", action="version", version="0.1.0")
+    parser.add_argument("-v", "--version", action="version", version=__version__)
 
     args = parser.parse_args()
 

nii2dcm/modules/image_pixel.py

@@ -29,14 +29,14 @@ def __init__(self):
         self.ds.BitsAllocated = 1
         self.ds.BitsStored = ''
         self.ds.HighBit = ''
-    
+
         # PixelRepresentation
         # Enumerated values either: unsigned integer or two's complement
         # Setting = 0, as observed in real DICOM
         self.ds.PixelRepresentation = 0
-    
+
         self.ds.SmallestImagePixelValue = ''
         self.ds.LargestImagePixelValue = ''
-    
+
         # PixelData written in dcm_writer via Pydicom
         self.ds.PixelData = ''

nii2dcm/nii.py

@@ -39,7 +39,7 @@ def fnT1N(A, N):
         sliceIndices = np.repeat(range(1, nZ+1), nF)
         voxelSpacing = dimZ
         zLocLast = (voxelSpacing * nZ) - voxelSpacing
-        sliceLoca = np.repeat( np.linspace(0, zLocLast, num=nZ), nF)
+        sliceLoca = np.repeat(np.linspace(0, zLocLast, num=nZ), nF)
 
         # Windowing & Signal Intensity
         maxI = np.amax(nii_img)

pyproject.toml

@@ -0,0 +1,11 @@
+[build-system]
+requires = ["setuptools>=64.0.0", "wheel", "setuptools_scm[toml]>=6.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "nii2dcm"
+dynamic = ["version"]
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"  # required for PyPI and TestPyPI
+write_to = "nii2dcm/_version.py"

scripts/create_3d_dicom.py

@@ -14,8 +14,8 @@
 
 
 NII2DCM_DIR = r'/Users/tr17/code/nii2dcm'
-INPUT_DIR   = r'/Users/tr17/code/nii2dcm/input/'
-OUTPUT_DIR  = r'/Users/tr17/code/nii2dcm/output'
+INPUT_DIR = r'/Users/tr17/code/nii2dcm/input/'
+OUTPUT_DIR = r'/Users/tr17/code/nii2dcm/output'
 
 if not os.path.isdir(OUTPUT_DIR):
     os.makedirs(OUTPUT_DIR)

setup.cfg

@@ -0,0 +1,24 @@
+[metadata]
+name = nii2dcm
+version = attr: nii2dcm._version.__version__
+description= nii2dcm: NIfTI to DICOM creation with Python
+url = https://github.com/tomaroberts/nii2dcm
+author = Tom Roberts
+author_email = t.roberts@kcl.ac.uk
+long_description = file:README.md
+long_description_content_type = text/markdown
+
+[options]
+packages = find:
+python_requires = <3.11
+install_requires =
+    numpy==1.23.2
+    matplotlib==3.6.2
+    nibabel==5.0.0
+    pydicom==2.3.0
+    twine==4.0.2
+include_package_data=True
+
+[options.entry_points]
+console_scripts =
+    nii2dcm = nii2dcm.__main__:cli