Merge pull request #33 from tomaroberts/dunamai-production-fix

Fixes issue with pip install related to dunamai implementation

.github/workflows/build_and_test_cli.yml

@@ -1,13 +1,13 @@
-# Workflow to build nii2dcm and test different command line interface (CLI) options
+# Workflow to build nii2dcm, run unit tests and then execute command line interface (CLI) end-to-end
 
-name: Build nii2dcm
+name: Build & Test nii2dcm
 
 on:
   pull_request:
 
 jobs:
-  build-and-test:
-    name: Build
+  venv-build-and-test:
+    name: venv + E2E
 
     runs-on: ${{ matrix.os }}
 
@@ -57,6 +57,10 @@ jobs:
         nii2dcm -h
         nii2dcm -v
 
+    - name: Run unit tests
+      run: |
+        pytest tests/
+
     - name: Test DicomMRISVR creation
       run: |
         # run nii2dcm
@@ -65,3 +69,52 @@ jobs:
         ls ./output
         # assert DICOM files exist
         [ -f "./output/IM_0001.dcm" ] && echo "Output DICOM file exists" || exit 1
+
+    - name: Build pytest coverage file
+      run: |
+        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=nii2dcm tests/ | tee pytest-coverage.txt ; echo $?
+
+    - name: Pytest coverage comment
+      id: coverageComment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: ./pytest-coverage.txt
+        junitxml-path: ./pytest.xml
+
+    - name: Update Coverage Badge
+      uses: schneegans/dynamic-badges-action@v1.7.0
+      with:
+        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+        gistID: 57ef8057d04f67dbe6e64df410b83079
+        filename: nii2dcm-pytest-coverage-comment.json
+        label: Coverage Report
+        message: ${{ steps.coverageComment.outputs.coverage }}
+        color: ${{ steps.coverageComment.outputs.color }}
+        namedLogo: python
+
+  container-build-and-test:
+    name: Container
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.9' ]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Build container
+        run: |
+          docker build -t nii2dcm --progress=plain --no-cache .
+          docker ps
+
+      - name: Test nii2dcm container
+        run: |
+          docker run nii2dcm -h
+          echo "nii2dcm version:"
+          docker run nii2dcm -v

.github/workflows/publish_pypi.yml

@@ -27,7 +27,7 @@ permissions:
   actions: write
 
 jobs:
-  testpypi-publish:
+  pypi-publish:
 
     name: Publish to PyPI
     runs-on: ubuntu-latest
@@ -70,7 +70,7 @@ jobs:
 
     - name: Create dist/
       run: |
-        python setup.py sdist bdist_wheel
+        python setup.py bdist_wheel
         twine check dist/*
 
     - name: Publish package to PyPI
@@ -86,6 +86,7 @@ jobs:
         time: '150'  # seconds
 
     - name: Install latest PyPI version in fresh venv
+      id: attempt1
       run: |
         NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
         echo $NII2DCM_VERSION
@@ -97,3 +98,58 @@ jobs:
         nii2dcm -h
         echo "nii2dcm version:"
         nii2dcm -v
+      continue-on-error: true
+
+    - name: Wait longer
+      if: steps.attempt1.outcome != 'success'
+      uses: GuillaumeFalourd/wait-sleep-action@v1
+      with:
+        time: '150'  # seconds
+
+    - name: Re-attempt PyPI install
+      if: steps.attempt1.outcome != 'success'
+      run: |
+        NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
+        echo $NII2DCM_VERSION
+        python -m venv nii2dcm-temp
+        source nii2dcm-temp/bin/activate
+        pip install --upgrade pip
+        pip install setuptools wheel
+        pip install nii2dcm==$NII2DCM_VERSION
+        nii2dcm -h
+        echo "nii2dcm version:"
+        nii2dcm -v
+
+  ghcr-publish:
+    needs: pypi-publish
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ghcr.io/tomaroberts/nii2dcm
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/publish_testpypi.yml

@@ -12,10 +12,12 @@
 # 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:
   push:
     branches:
       - main
@@ -67,7 +69,7 @@ jobs:
 
     - name: Create dist/
       run: |
-        python setup.py sdist bdist_wheel
+        python setup.py bdist_wheel
         twine check dist/*
 
     - name: Publish package to TestPyPI
@@ -84,6 +86,28 @@ jobs:
         time: '150'  # seconds
 
     - name: Install latest TestPyPI version in fresh venv
+      id: attempt1
+      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
+      continue-on-error: true
+
+    - name: Wait longer
+      if: steps.attempt1.outcome != 'success'
+      uses: GuillaumeFalourd/wait-sleep-action@v1
+      with:
+        time: '150'  # seconds
+
+    - name: Re-attempt TestPyPI install
+      if: steps.attempt1.outcome != 'success'
       run: |
         NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
         echo $NII2DCM_VERSION

.gitignore

@@ -48,6 +48,8 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+pytest-coverage.txt
+pytest.xml
 
 # Sphinx documentation
 docs/_build/

Dockerfile

@@ -0,0 +1,29 @@
+# Use the official Python image as the base image
+FROM python:3.9-slim
+
+LABEL org.opencontainers.image.source https://github.com/tomaroberts/nii2dcm
+
+# Setup
+COPY . /home/nii2dcm
+WORKDIR /home/nii2dcm
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    bash git \
+    && apt-get clean
+
+# Update base packages
+RUN pip install --upgrade pip && \
+    pip install setuptools wheel
+
+# Install nii2dcm requirements
+RUN pip install -r requirements.txt
+
+# Build package from source
+RUN pip install .
+
+# Test nii2dcm install
+# To see output locally during build process: docker build -t nii2dcm --progress=plain .
+RUN nii2dcm -h
+
+ENTRYPOINT ["nii2dcm"]

README.md

@@ -20,6 +20,10 @@
     ·
     <a href="https://github.com/tomaroberts/nii2dcm/issues">Request Feature</a>
   </p>
+  <p align="center">
+    <img src="https://github.com/tomaroberts/nii2dcm/actions/workflows/build_and_test_cli.yml/badge.svg?branch=unit-tests">
+    <img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/tomaroberts/57ef8057d04f67dbe6e64df410b83079/raw/nii2dcm-pytest-coverage-comment.json"> 
+</p>
 </div>
 
 
@@ -53,6 +57,7 @@ To install and run nii2dcm locally, you have two options:
 
 ### pip
 
+Create a new Python virtual environment, then:
 ```shell
 pip install nii2dcm
 ```
@@ -74,7 +79,6 @@ python -m pip install --upgrade pip
 
 Install dependencies and nii2dcm:
 ```sh
-pip install setuptools wheel
 pip install -r requirements.txt
 pip install .
 ```
@@ -138,6 +142,26 @@ Currently, attributes to transfer are [listed here in the DicomMRI class](https:
 <p align="right">(<a href="#readme-top">back to top</a>)</p>
 
 
+<!-- Docker -->
+## Docker
+nii2dcm is also available as a Docker container. 
+
+Pull the latest container with:
+```shell
+docker pull ghcr.io/tomaroberts/nii2dcm/nii2dcm:latest
+```
+
+Run the containerised nii2dcm:
+```shell
+# display nii2dcm version
+docker run nii2dcm -v
+
+# perform nii2dcm conversion
+docker run nii2dcm nifti-file.nii.gz dicom-output-directory/ -d MR
+```
+
+<p align="right">(<a href="#readme-top">back to top</a>)</p>
+
 <!-- ROADMAP -->
 ## Roadmap
 

nii2dcm/__main__.py

@@ -23,7 +23,11 @@ def cli(args=None):
 
     parser.add_argument("input_file", type=str, help="[.nii/.nii.gz] input NIfTI file")
     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(
+        "-d", "--dicom_type",
+        type=str,
+        help="[string] type of DICOM. Available types: MR, SVR."
+    )
     parser.add_argument("-r", "--ref_dicom", type=str, help="[.dcm] Reference DICOM file for Attribute transfer")
     parser.add_argument("-v", "--version", action="version", version=__version__)
 

nii2dcm/_version.py

@@ -1,2 +1,2 @@
-from dunamai import Version, Style
-__version__ = Version.from_git().serialize(metadata=False, style=Style.SemVer)
+import dunamai as _dunamai
+__version__ = _dunamai.get_version("nii2dcm", third_choice=_dunamai.Version.from_any_vcs).serialize()

nii2dcm/dcm.py

@@ -11,7 +11,6 @@
 import pydicom as pyd
 from pydicom.dataset import FileDataset, FileMetaDataset
 
-from nii2dcm.utils import dcm_dictionary_update
 from nii2dcm.modules.patient import Patient
 from nii2dcm.modules.general_study import GeneralStudy
 from nii2dcm.modules.patient_study import PatientStudy
@@ -67,7 +66,7 @@ def __init__(self, filename=nii2dcm_temp_filename):
 
         """
         Set Dicom Date/Time
-        Important: doing this once sets all Instances/Series/Study creation dates and times to the same values. Whereas, 
+        Important: doing this once sets all Instances/Series/Study creation dates and times to the same values. Whereas,
         doing this within the Modules would every so slightly offset the times
         """
         # TODO shift to utils.py and propagate to Modules, or, create method within this Dicom class

nii2dcm/dcm_writer.py

@@ -6,19 +6,19 @@
 import pydicom as pyd
 
 
-def write_slice(dcm, img_data, instance_index, output_dir):
+def write_slice(dcm, img_data, slice_index, output_dir):
     """
     write a single DICOM slice
 
     dcm – nii2dcm DICOM object
     img_data - [nX, nY, nSlice] image pixel data, such as from NIfTI file
-    instance_index – instance index (important: counts from 0)
+    slice_index – slice index in nibabel img_data array (important: counts from 0, whereas DICOM instances count from 1)
     output_dir – output DICOM file save location
     """
 
-    output_filename = r'IM_%04d.dcm' % (instance_index + 1)  # begin filename from 1, e.g. IM_0001.dcm
+    output_filename = r'IM_%04d.dcm' % (slice_index + 1)  # begin filename from 1, e.g. IM_0001.dcm
 
-    img_slice = img_data[:, :, instance_index]
+    img_slice = img_data[:, :, slice_index]
 
     # Instance UID – unique to current slice
     dcm.ds.SOPInstanceUID = pyd.uid.generate_uid(None)

nii2dcm/modules/mr_image.py

@@ -24,9 +24,9 @@ def __init__(self):
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.8.3.html#sect_C.8.3.1.1.1
         # For now, will omit thereby inheriting parent value
         # self.ds.ImageType = ''
-    
+
         self.ds.SamplesPerPixel = 1
-    
+
         # PhotometricInterpretation
         # TODO: decide MONOCHROME1 or MONOCHROME2 as default
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2

requirements.txt

@@ -1,3 +1,5 @@
+setuptools
+wheel
 numpy==1.23.2
 matplotlib==3.6.2
 nibabel==5.0.0

setup.py

@@ -3,5 +3,5 @@
 
 setup(
     name="nii2dcm",
-    version=Version.from_git().serialize(metadata=False, style=Style.SemVer),
+    version=Version.from_any_vcs().serialize(metadata=False, style=Style.SemVer),
 )