Merge pull request #318 from NifTK/release-v0.5.0

Fixed issues in documentation before 0.5.0 release

.gitlab-ci.yml

@@ -31,7 +31,6 @@ testjob:
  only:
  - master
  - dev
- - merging-github-pr-269
  - tags
  script:
  # !!kill coverage in case of hanging processes
@@ -45,9 +44,6 @@ testjob:
  - python -c "import tensorflow as tf; from tensorflow.python.client import device_lib; print device_lib.list_local_devices()"
  - ls -la /dev | grep nvidia
 
- - echo $(python tests/get_gpu_index.py)
- - export CUDA_VISIBLE_DEVICES=$(python tests/get_gpu_index.py)
-
  # removing existing testing data
  - if [ -d models ]; then rm -r models; fi
  - if [ -d testing_data ]; then rm -r testing_data; fi
@@ -80,6 +76,9 @@ testjob:
 
  - pip install -r requirements-gpu.txt
 
+ - echo $(python tests/get_gpu_index.py)
+ - export CUDA_VISIBLE_DEVICES=$(python tests/get_gpu_index.py)
+
  # check whether version command works
  # Git-clone:
  - python net_segment.py --version 2>&1 | grep -E 'NiftyNet.*version.*[0-9]+\.[0-9]+\.[0-9]+'
@@ -167,6 +166,9 @@ testjob:
  - pip install coverage
  - pip install -r requirements-gpu.txt
 
+ - echo $(python tests/get_gpu_index.py)
+ - export CUDA_VISIBLE_DEVICES=$(python tests/get_gpu_index.py)
+
  - python net_download.py testing -r
  - coverage run -a --source . net_segment.py train -c config/highres3dnet_config.ini --batch_size=1 --num_threads=2 --queue_length=40 --max_iter=10
  - coverage run -a --source . net_segment.py inference -c config/highres3dnet_config.ini --batch_size 8 --spatial_window_size 64,64,64 --queue_length 64
@@ -230,7 +232,6 @@ quicktest:
  except:
  - master
  - dev
- - merging-github-pr-269
  - tags
  - 147-revise-contribution-guidelines-to-include-github
  - 150-properly-format-the-bibtex-entry-to-the-ipmi-2017-paper-on-the-main-readme
@@ -289,6 +290,10 @@ quicktest:
  - coverage erase
  # run only fast tests
  - pip install -r requirements-gpu.txt
+
+ - echo $(python tests/get_gpu_index.py)
+ - export CUDA_VISIBLE_DEVICES=$(python tests/get_gpu_index.py)
+
  - python net_download.py testing -r
  - QUICKTEST=True coverage run -a --source . -m unittest discover -s "tests" -p "*_test.py"
  - coverage report --omit='niftynet-dev-test*' -m
@@ -307,7 +312,7 @@ pip-installer:
  only:
  - master
  - dev
- - merging-github-pr-269
+ - release-v0.5.0
  - tags
  script:
  # get the shortened version of last commit's hash
@@ -343,6 +348,10 @@ pip-installer:
  # NiftyNet console entries should fail gracefully if TF not installed
  # i.e. check that the warning displays the TF website
  - cd $niftynet_dir
+
+ - echo $(python tests/get_gpu_index.py)
+ - export CUDA_VISIBLE_DEVICES=$(python tests/get_gpu_index.py)
+
  - set +e
  - python -c "import niftynet" 2>&1 | grep "https://www.tensorflow.org/"
  - set -e
@@ -443,6 +452,10 @@ pip-installer:
  # NiftyNet console entries should fail gracefully if TF not installed
  # i.e. check that the warning displays the TF website
  - cd $niftynet_dir
+
+ - echo $(python tests/get_gpu_index.py)
+ - export CUDA_VISIBLE_DEVICES=$(python tests/get_gpu_index.py)
+
  - set +e
  - python -c "import niftynet" 2>&1 | grep "https://www.tensorflow.org/"
  - set -e

doc/source/index.rst

@@ -122,7 +122,7 @@ Resources
 
 `Model zoo repository`_
 
-Mailing list: [email protected]
+`NiftyNet Google Group / Mailing List`_
 
 `Stack Overflow`_ (for general questions)
 
@@ -131,6 +131,7 @@ Mailing list: [email protected]
 .. _`Source code on GitHub`: https://github.com/NifTK/NiftyNet
 .. _`Model zoo repository`: https://github.com/NifTK/NiftyNetModelZoo/blob/master/README.md
 .. _`Stack Overflow`: https://stackoverflow.com/questions/tagged/niftynet
+.. _`NiftyNet Google Group / Mailing List`: https://groups.google.com/forum/#!forum/niftynet
 
 
 APIs & reference
@@ -188,7 +189,7 @@ If you use NiftyNet in your work, please cite `Gibson and Li, et al. 2017`_:
 
  E. Gibson*, W. Li*, C. Sudre, L. Fidon, D. I. Shakir, G. Wang,
  Z. Eaton-Rosen, R. Gray, T. Doel, Y. Hu, T. Whyntie, P. Nachev, M. Modat,
- D. C. Barratt, S. Ourselin, M. J. Cardoso^ and T. Vercauteren^ 2017.
+ D. C. Barratt, S. Ourselin, M. J. Cardoso† and T. Vercauteren† 2017.
  `NiftyNet: a deep-learning platform for medical imaging.`_
  Computer Methods and Programs in Biomedicine (2017).
 

setup.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 from setuptools import setup, find_packages
+from io import open
 
 import versioneer
 from niftynet.utilities.versioning import get_niftynet_version
@@ -12,7 +13,7 @@
  ' image-guided therapy'
 
 # Get the long description
-with open('pip/long_description.rst') as f:
+with open('README.md', encoding='utf-8') as f:
  long_description = f.read()
 
 setup(
@@ -23,6 +24,7 @@
 
  description=description,
  long_description=long_description,
+ long_description_content_type='text/markdown',
 
  url='http:https://niftynet.io/',
 

tests/get_gpu_index.py

@@ -10,7 +10,7 @@
 p3 = Popen(['sed', 's: MiB::'], stdin=p2.stdout, stdout=PIPE)
 output, error = p3.communicate()
 
-free_memory = [float(x) for x in output.split('\n')[:-1]]
+free_memory = [float(x) for x in output.decode('utf-8').split('\n')[:-1]]
 if free_memory[1] > free_memory[0]:
  print('1')
 else: