Merge branch 'mnt/project-mgmt' into 'master'

Migrate to `pyproject.toml`, add `Dockerfile` to generate runtime image

See merge request !6

.docker/bip-dev/README.md

+This docker image is used for running unit tests on the BIP code base. It can
+be built via Gitlab CI / CD by running the `build-dev-docker-image` job.
+
+At the moment the image is published to
+https://hub.docker.com/u/pauldmccarthy/bip-dev/.
\ No newline at end of file

.docker/create_dev_env.sh → .docker/bip-dev/create_dev_env.sh

@@ -9,30 +9,27 @@ channels=(-c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/development/
 conda create -y ${channels[@]}   \
       -p ./${envdir}             \
       "python=${PYTHON_VERSION}" \
-      c-compiler                 \
-      cxx-compiler               \
-      pytest                     \
       coverage                   \
-      pytest-cov                 \
+      dmri-amico                 \
+      file-tree                  \
+      file-tree-fsl              \
       fsl-gradunwarp             \
       fsl-avwutils               \
+      fsl-cluster                \
       fsl-pyfix                  \
-      file-tree file-tree-fsl    \
+      fsl-pipe                   \
       fsl_sub                    \
       fsl_sub_plugin_slurm       \
       fsl_sub_plugin_sge         \
-      jinja2
+      jinja2                     \
+      pytest                     \
+      pytest-cov
+
 
 echo "channels:"                                                        > ${envdir}/.condarc
 echo "  https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/development/" >> ${envdir}/.condarc
 echo "  https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/"      >> ${envdir}/.condarc
 echo "  conda-forge"                                                   >> ${envdir}/.condarc
 
-
-source activate ${envdir}
-pip install dmri-amico
-pip install git+https://git.fmrib.ox.ac.uk/ndcn0236/pipe-tree.git
-
-conda remove -p ${envdir} c-compiler cxx-compiler
 conda clean -y -all
 pip cache purge

.docker/bip-image/Dockerfile

+FROM nvidia/cuda:11.0.3-base-centos7 as base
+
+ENV NVARCH                     x86_64
+ENV NVIDIA_DRIVER_CAPABILITIES compute,utility
+ENV NVIDIA_REQUIRE_CUDA        cuda>=11.0 brand=tesla,driver>=418,driver<419
+ENV NVIDIA_VISIBLE_DEVICES     all
+ENV NV_CUDA_CUDART_VERSION     11.0.221-1
+
+COPY /build_image.sh /build_image.sh
+RUN /bin/bash /build_image.sh && rm /build_image.sh

.docker/bip-image/README.md

+BIP Docker image
+----------------
+
+
+The `Dockerfile` can be used to create a Docker image which contains BIP and
+all of its dependencies. The image contains a full BIP runtime environment,
+including FSL, FreeSurfer and Connectome Workbench. Be warned that the image
+is quite large, on the order of 15GB.
+
+
+1. Clone the BIP repository and change into the image directory:
+   ```
+   git clone https://git.fmrib.ox.ac.uk/fsl/bip.git
+   cd bip/.docker/bip-image
+   ```
+
+2. Build the image:
+
+   ```
+   docker build . -t bip &> build_log.txt
+   ```
+
+3. If the image was built on a different machine than the one it is to be run
+   on, save it to a `.tar.gz` archive:
+   ```
+   docker save bip | gzip -c > bip.tar.gz
+   ```
+
+   Then download the archive to the target machine, and load it:
+
+   ```
+   docker load < bip.tar.gz
+   ```
+
+4. Start a container from the image. Replace `<freesurfer-license>` with the
+   full path to your FreeSurfer license file.
+
+   ```
+   docker run -it                                              \
+     -v <freesurfer-license>:/usr/local/freesurfer/license.txt \
+     bip /bin/bash
+   ```

.docker/bip-image/build_image.sh

+#!/usr/bin/env bash
+
+set -e
+
+SHELL_PROFILE=/root/.bashrc
+
+export TAR_OPTIONS="--no-same-owner"
+export WGET_OPTIONS="--no-check-certificate -q"
+
+# OS / build dependencies
+yum install -y epel-release
+yum install -y \
+    curl \
+    freetype \
+    git \
+    mesa-libGL \
+    nano \
+    openssh-clients \
+    parallel \
+    python3 \
+    tcsh \
+    unzip \
+    wget
+
+# FSL
+FSL_URL=https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
+wget ${WGET_OPTIONS} ${FSL_URL} -O fslinstaller.py
+python fslinstaller.py -V 6.0.7.6 -d /usr/local/fsl
+echo -e '\nexport FSLDIR=/usr/local/fsl/\n'       >> ${SHELL_PROFILE}
+echo -e '\nsource ${FSLDIR}/etc/fslconf/fsl.sh\n' >> ${SHELL_PROFILE}
+rm fslinstaller.py
+
+# BIP
+/usr/local/fsl/bin/mamba install -y -n base --override-channels    \
+  -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/development/ \
+  -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/      \
+  -c conda-forge                                                   \
+   fsl-bip
+
+# ROBEX
+ROBEX_URL=https://www.nitrc.org/frs/download.php/5994/ROBEXv12.linux64.tar.gz//\?i_agree\=1\&download_now\=1
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${ROBEX_URL} -O ROBEX.tar.gz
+tar xf ROBEX.tar.gz && rm ROBEX.tar.gz
+echo -e '\nexport PATH=/usr/local/ROBEX:${PATH}\n' >> ${SHELL_PROFILE}
+popd
+
+# Brainsuite
+BRAINSUITE_URL=http://brainsuite.org/data/BIDS/bse15c.biobank.tgz
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${BRAINSUITE_URL} -O brainsuite.tgz
+tar -xf brainsuite.tgz && rm brainsuite.tgz
+chmod -R ugo+rx BrainSuite15c
+echo -e '\nexport PATH=/usr/local/BrainSuite15c/bin:${PATH}\n' >> ${SHELL_PROFILE}
+popd
+
+# Workbench
+WORKBENCH_URL=https://humanconnectome.org/storage/app/media/workbench/workbench-rh_linux64-v1.5.0.zip
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${WORKBENCH_URL} -O workbench.zip
+unzip workbench.zip && rm workbench.zip
+echo -e '\nexport PATH=/usr/local/workbench/bin_rh_linux64:${PATH}\n' >> ${SHELL_PROFILE}
+popd
+
+# Freesurfer
+FREESURFER_URL=https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz
+pushd /usr/local/
+wget ${WGET_OPTIONS} ${FREESURFER_URL} -O freesurfer.tgz
+tar xf freesurfer.tgz && rm freesurfer.tgz
+echo -e '\nexport FREESURFER_HOME=/usr/local/freesurfer\n' >> ${SHELL_PROFILE}
+echo -e '\nsource ${FREESURFER_HOME}/SetUpFreeSurfer.sh\n' >> ${SHELL_PROFILE}
+popd
+
+# Clean up
+/usr/local/fsl/bin/mamba clean --all --yes --force-pkgs-dirs
+rm -rf /tmp/*
+rm -rf ${HOME}/.cache/
+yum clean all
+rm -rf /var/cache/yum/*

.gitlab-ci.yml

+include:
+ - project: fsl/conda/fsl-ci-rules
+   file:    .gitlab-ci.yml
+
 stages:
  - docker
  - test
-
+ - fsl-ci-pre
+ - fsl-ci-build
+ - fsl-ci-test
+ - fsl-ci-deploy
 
 # Build docker image used for unit tests
 build-dev-docker-image:
@@ -19,8 +26,8 @@ build-dev-docker-image:
     - echo $DOCKER_AUTH_CONFIG > $HOME/.docker/config.json
     - TAG="$(date +%Y%m%d).${CI_COMMIT_SHORT_SHA}"
     - IMAGE="pauldmccarthy/bip-dev"
-    - DOCKERFILE=.docker/Dockerfile
-    - docker build -t "${IMAGE}:${TAG}" -t "${IMAGE}:latest" -f ${DOCKERFILE} ./.docker
+    - DOCKERFILE=.docker/bip-dev/Dockerfile
+    - docker build -t "${IMAGE}:${TAG}" -t "${IMAGE}:latest" -f ${DOCKERFILE} ./.docker/bip-dev
     - docker push "${IMAGE}:${TAG}"
     - docker push "${IMAGE}:latest"
 

README.md

@@ -3,10 +3,24 @@ BRAIN IMAGING PIPELINE
 Fidel Alfaro Almagro, WIN-FMRIB
 June, 2022
 -------------------------------------------
+
 Automated tool
 
 Installation
 ------------
+
+BIP is published as a conda package, and can be installed with a command such as:
+
+```
+mamba install                                                 \
+  -c https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/public/ \
+  -c conda-forge                                              \
+  fsl-bip
+```
+
 If you want to install everythong that is needed from scratch, run:
-```cd /path-to-lib/install_dir/
-python setup.py install```
+
+```
+cd /path-to-lib/install_dir/
+pip install -e .
+```

pyproject.toml

+[build-system]
+requires      = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name            = "bip"
+dynamic         = ["version"]
+description     = "Brain Imaging Pipeline"
+readme          = {file = "README.md", content-type="text/markdown"}
+license         = {text = "Apache License Version 2.0"}
+requires-python = ">=3.8"
+authors         = [{name = "Fidel Alfaro Almagro", email = "fidel.alfaroalmagro@ndcn.ox.ac.uk"}]
+
+[project.scripts]
+bip = "bip.main:main"
+
+[tool.setuptools.dynamic]
+version = {file = "bip/VERSION"}
+
+[tool.pytest.ini_options]
+testpaths = ["bip/tests"]
+addopts   = "-v --cov=bip"
+
+[tool.coverage.run]
+source = ["bip"]
+omit   = ["bip/tests/*"]

requirements.txt

-fslpy
-pyfix
-dmri-amico
-oxasl
-oxasl-deblur
-pickle-mixin
-pickleshare
-niicat
-ipython
-jinja2
-seaborn
-jsonschema
-python-utils
-scikit-image
-scikit-learn
-numpy
-nibabel

setup.cfg

-[tool:pytest]
-testpaths = bip/tests
-addopts   = -v --cov=bip
-
-[coverage:run]
-source = bip
-omit   = bip/tests/*
\ No newline at end of file

setup.py

-import os.path as op
-from setuptools import setup,find_packages
-
-with open('requirements.txt', 'rt') as f:
-    install_requires = [l.strip() for l in f.readlines()]
-
-basedir = op.dirname(__file__)
-version = open(op.join(basedir, 'bip', 'VERSION')).read().strip()
-
-setup(name='bip',
-	version=version,
-	description='Brain Imaging Pipeline',
-	author='Fidel Alfaro Almagro',
-	install_requires=install_requires,
-	packages=find_packages(),
-	include_package_data=True)