Draft: Overhaul PyDesigner Code

.github/workflows/pydesigner_build.yml

@@ -0,0 +1,39 @@
+# name: Docker Build and Push
+
+# on:
+#     push:
+#       tags:
+#         - '**'
+
+# jobs:
+#   docker:
+#     runs-on: ubuntu-latest
+#     steps:
+#         -
+#             name: Checkout
+#             uses: actions/checkout@v3
+#         -
+#             name: Fetch version
+#             uses: SebRollen/[email protected]
+#             id: version
+#             with:
+#               file: 'pyproject.toml'
+#               field: 'tool.poetry.version'
+#         -
+#             name: Set up QEMU
+#             uses: docker/setup-qemu-action@v3
+#         -
+#             name: Set up Docker Buildx
+#             uses: docker/setup-buildx-action@v3
+#         -
+#             name: Login to Docker Hub
+#             uses: docker/login-action@v3
+#             with:
+#                 username: ${{ secrets.DOCKERHUB_USERNAME }}
+#                 password: ${{ secrets.DOCKERHUB_TOKEN }}
+#         -
+#             name: Build and push
+#             uses: docker/build-push-action@v5
+#             with:
+#                 push: true
+#                 tags: dmri/neurodock:latest,dmri/neurodock:${{ steps.version.outputs.value }}

.github/workflows/pydesigner_ci.yml

@@ -0,0 +1,28 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+    - name: Set up Python
+      uses: actions/setup-python@v3
+    - name: Run Pre-Commit
+      uses: pre-commit/[email protected]
+      with:
+        pre-commit_version: latest
+        python_version: 3.8
+        system: true 
+    # - name: Auto-commit changed files
+    #   uses: stefanzweifel/git-auto-commit-action@v5
+    #   with:
+    #     commit_message: "Pre-commit fixes"
+
+

.gitignore

@@ -7,6 +7,10 @@ __pycache__/
 .vscode/
 /docs/build/
 dist/
+.python-version
+.venv/
+docs/html/
+docs/doctrees/
 
 # Files to ignore
 .DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,37 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 'v4.5.0'
+    hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+
+- repo: https://github.com/python-jsonschema/check-jsonschema
+  rev: '0.27.0'
+  hooks:
+    - id: check-readthedocs
+
+- repo: https://github.com/thclark/pre-commit-sphinx
+  rev: '0.0.3'
+  hooks:
+    - id: build-docs
+      args: ['--html-dir', 'docs/html', '--source-dir', 'docs/source']
+      language_version: python3
+
+- repo: https://github.com/psf/black
+  rev: '23.9.1'
+  hooks:
+    - id: black
+
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: 'v0.1.0'
+  hooks:
+    - id: ruff
+      args: [--fix, --exit-non-zero-on-fix]
+
+- repo: https://github.com/python-poetry/poetry
+  rev: '1.6.0'
+  hooks:
+    - id: poetry-check
+    # - id: poetry-lock
+    - id: poetry-export

.readthedocs.yml

@@ -1,26 +1,25 @@
 # .readthedocs.yml
-# Read the Docs configuration file
+# Read the Docs configuration file for Sphinx projects
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
 # Required
 version: 2
 
-# Build documentation in the docs/source directory with Sphinx
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/source/conf.py
 
-# Build documentation with MkDocs
-#mkdocs:
-#  configuration: mkdocs.yml
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats: all
-
-# Optionally set the version of Python and requirements required to build your docs
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-  version: 3.6
-  install:
-     - requirements: docs/requirements.txt
-     - method: pip
-       path: .
-  system_packages: true
+   install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .

CHANGELOG.rst

@@ -184,8 +184,8 @@ Dec 22, 2020
 
 **Changed**
 
-* Replaced ``preprocessing.util.bvec_is_fullsphere()`` and 
-  ``preprocessing.util.vecs_are_fullsphere()`` with 
+* Replaced ``preprocessing.util.bvec_is_fullsphere()`` and
+  ``preprocessing.util.vecs_are_fullsphere()`` with
   ``preprocessing.mrinfoutil.is_fullsphere()``. Even though datasets
   may be half-shelled, it is inaccurate to label them as such because
   distortion relative to b-value is not linear. As such, the
@@ -383,7 +383,7 @@ Apr 8, 2020
   faster EPI distortion correction without degrading DTI/DKI maps.
 * Documentation moved to ReadTheDocs
 * Moved B0 production module from designer.preprocessing.brainmask to
-  a separate function at ``designer.preprocessing.extractmeanbzero()`` 
+  a separate function at ``designer.preprocessing.extractmeanbzero()``
   that gets called by PyDesigner main. This allows a B0.nii to be
   produced regardless of the ``--mask`` flag.
 
@@ -461,4 +461,4 @@ Initial port of MATLAB code to Python. 200,000,000,000 BCE
 .. _v0.3: https://github.com/m-ama/PyDesigner/releases/tag/v0.3
 .. _v0.2 [The Cupid Release]: https://github.com/m-ama/PyDesigner/releases/tag/v0.2
 .. _dev-0.11: https://github.com/m-ama/PyDesigner/releases/tag/dev-0.11
-.. _0.1-dev: https://github.com/m-ama/PyDesigner/releases/tag/0.1-dev
+.. _0.1-dev: https://github.com/m-ama/PyDesigner/releases/tag/0.1-dev

Dockerfile

@@ -14,61 +14,57 @@
 # ==============================================================================
 
 # Load base Ubuntu image
-FROM debian:buster-slim
+FROM python:3.11-bullseye
 
-# Add LABEL Information
-# ARG BUILD_DATE
-# ARG VCS_REF
-
-# Labels.
-LABEL maintainer="Siddhartha Dhiman ([email protected])"
+# Labels
+LABEL maintainer="Siddhartha Dhiman ([email protected])"
 LABEL org.label-schema.schema-version="1.0.0-rc1"
-LABEL org.label-schema.build-date=$BUILD_DATE
 LABEL org.label-schema.name="dmri/pydesigner"
 LABEL org.label-schema.description="A state-of-the-art difusion and kurtosis MRI processing pipeline"
 LABEL org.label-schema.url="https://github.com/m-ama/"
 LABEL org.label-schema.vcs-url="https://github.com/m-ama/NeuroDock.git"
-LABEL org.label-schema.vcs-ref=$VCS_REF
-LABEL org.label-schema.vendor="MAMA"
+LABEL org.label-schema.vendor="MUSC BRIDGE"
 
-ARG DEBIAN_FRONTEND=noninteractive
+# ARG DEBIAN_FRONTEND=noninteractive
 
 # Initial update
-RUN apt-get update && \
+RUN apt update && \
       apt-get install -y \
       apt-utils \
       wget \
       curl \
       nano \
       software-properties-common \
-      python2.7 python-pip \
+      python3 \
       python3-pip \
       jq \
       libblas-dev \
       liblapack-dev \
       libatlas-base-dev \
-      gfortran
-
-# Install MRTRIX3 dependencies
-RUN apt-get install -y --no-install-recommends \
-      clang \
+      gfortran \
       git \
+      g++ \
+      python \
       libeigen3-dev \
       zlib1g-dev \
-      libqt4-opengl-dev \
+      libqt5opengl5-dev \
+      libqt5svg5-dev \
       libgl1-mesa-dev \
       libfftw3-dev \
       libtiff5-dev \
-      libomp-dev
-
-RUN rm /bin/sh && ln -s /bin/bash /bin/sh
+      libpng-dev
 
 # Copy and install PyDesigner
-RUN mkdir -p /tmp/PyDesigner
-ADD . / /tmp/PyDesigner/
-RUN pip3 install /tmp/PyDesigner
-RUN echo "alias python=python3" >> ~/.bashrc && source ~/.bashrc
-RUN echo "alias pip=pip3" >> ~/.bashrc && source ~/.bashrc
+RUN mkdir -p /pydesigner
+COPY /pydesigner /app/pydesigner
+COPY pyproject.toml app/
+RUN ls
+RUN ls -la /app
+WORKDIR /app
+ENV PYTHONPATH=${PYTHONPATH}:${PWD} 
+RUN pip3 install poetry
+RUN poetry config virtualenvs.create false
+RUN poetry install --no-dev
 
 # Install Python dependencies
 RUN pip3 install --upgrade setuptools && \
@@ -104,3 +100,5 @@ ENV PATH=$PATH:/usr/lib/mrtrix3/bin
 # Remove unwanted packages
 RUN apt-get autoremove && apt-get clean
 RUN rm /tmp/fslinstaller.py && rm -r /tmp/PyDesigner
+
+USER bridge

README.rst

@@ -9,11 +9,15 @@ PyDesigner
 .. image:: https://img.shields.io/github/downloads-pre/m-ama/pydesigner/latest/total?style=flat-square
    :target: https://github.com/m-ama/PyDesigner/releases/latest
    :alt: GitHub release (latest SemVer including pre-releases)
-   
+
 .. image:: https://img.shields.io/readthedocs/pydesigner?style=flat-square
    :target: https://pydesigner.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status
 
+.. image:: https://results.pre-commit.ci/badge/github/muscbridge/PyDesigner/master.svg
+   :target: https://results.pre-commit.ci/latest/github/muscbridge/PyDesigner/master
+   :alt: pre-commit.ci status
+
 Welcome to the official PyDesigner project!
 *******************************************
 
@@ -105,13 +109,13 @@ The PyDesigner software packages is based upon the the references
 listed below. Please be sure to cite them if PyDesigner was used
 in any publications.
 
-1. Jensen JH, Helpern JA, Ramani A, Lu H, Kaczynski K. Diffusional kurtosis imaging: the quantification of non-Gaussian water diffusion by means of MRI. Magn Reson Med 2005;53:1432-1440. doi: 10.1002/mrm.20508 
-2. Jensen JH, Helpern JA. MRI Quantification of non-Gaussian water diffusion by kurtosis analysis. NMR Biomed 2010;23:698-710. doi: 10.1002/nbm.1518 
-3. Fieremans E, Jensen JH, Helpern JA. White matter characterization with diffusional kurtosis imaging. Neuroimage 2011;58:177-188. doi: 10.1016/j.neuroimage.2011.06.006 
-4. Tabesh A, Jensen JH, Ardekani BA, Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Magn Reson Med 2011;65:823-836. doi: 10.1002/mrm.22655 
-5. Glenn GR, Helpern JA, Tabesh A, Jensen JH. Quantitative assessment of diffusional kurtosis anisotropy. NMR Biomed 2015;28:448-459. doi: 10.1002/nbm.3271 
-6. Jensen JH, Glenn GR, Helpern JA. Fiber ball imaging. Neuroimage 2016; 124:824-833. doi: 10.1016/j.neuroimage.2015.09.049 
-7. McKinnon ET, Helpern JA, Jensen JH. Modeling white matter microstructure with fiber ball imaging. Neuroimage 2018;176:11-21. doi: 10.1016/j.neuroimage.2018.04.025 
-8. Ades-Aron B, Veraart J, Kochunov P, McGuire S, Sherman P, Kellner E, Novikov DS, Fieremans E. Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline. Neuroimage. 2018;183:532-543. doi: 10.1016/j.neuroimage.2018.07.066 
+1. Jensen JH, Helpern JA, Ramani A, Lu H, Kaczynski K. Diffusional kurtosis imaging: the quantification of non-Gaussian water diffusion by means of MRI. Magn Reson Med 2005;53:1432-1440. doi: 10.1002/mrm.20508
+2. Jensen JH, Helpern JA. MRI Quantification of non-Gaussian water diffusion by kurtosis analysis. NMR Biomed 2010;23:698-710. doi: 10.1002/nbm.1518
+3. Fieremans E, Jensen JH, Helpern JA. White matter characterization with diffusional kurtosis imaging. Neuroimage 2011;58:177-188. doi: 10.1016/j.neuroimage.2011.06.006
+4. Tabesh A, Jensen JH, Ardekani BA, Helpern JA. Estimation of tensors and tensor-derived measures in diffusional kurtosis imaging. Magn Reson Med 2011;65:823-836. doi: 10.1002/mrm.22655
+5. Glenn GR, Helpern JA, Tabesh A, Jensen JH. Quantitative assessment of diffusional kurtosis anisotropy. NMR Biomed 2015;28:448-459. doi: 10.1002/nbm.3271
+6. Jensen JH, Glenn GR, Helpern JA. Fiber ball imaging. Neuroimage 2016; 124:824-833. doi: 10.1016/j.neuroimage.2015.09.049
+7. McKinnon ET, Helpern JA, Jensen JH. Modeling white matter microstructure with fiber ball imaging. Neuroimage 2018;176:11-21. doi: 10.1016/j.neuroimage.2018.04.025
+8. Ades-Aron B, Veraart J, Kochunov P, McGuire S, Sherman P, Kellner E, Novikov DS, Fieremans E. Evaluation of the accuracy and precision of the diffusion parameter EStImation with Gibbs and NoisE removal pipeline. Neuroimage. 2018;183:532-543. doi: 10.1016/j.neuroimage.2018.07.066
 9. Moss H, McKinnon ET, Glenn GR, Helpern JA, Jensen JH. Optimization of data acquisition and analysis for fiber ball imaging. Neuroimage 2019;200;690-703. doi: 10.1016/j.neuroimage.2019.07.005
-10. Moss HG, Jensen JH. Optimized rectification of fiber orientation density function. Magn Reson Med. 2020 Jul 25. doi: 10.1002/mrm.28406. Online ahead of print. 
+10. Moss HG, Jensen JH. Optimized rectification of fiber orientation density function. Magn Reson Med. 2020 Jul 25. doi: 10.1002/mrm.28406. Online ahead of print.