Merge pull request #57 from justusschock/old_master

Merge Old Master

Author: justusschock

.travis.yml

@@ -14,28 +14,49 @@ matrix:
 # command to install dependencies
 before_install:
   - pip install -U pip wheel
+  - pip install -r requirements.txt
   - pip install -r requirements_extra_torch.txt
   # install tensorflow only in python 3.6, since lacking support for python 3.7
   # - if [[ "$TRAVIS_PYTHON_VERSION" == "3.6" ]]; then
   #     pip install -r requirements_extra_tf.txt;
   #     pip uninstall -y tensorflow-gpu;
   #     pip install tensorflow==1.12.0;
   #   fi
-  - pip install -r requirements.txt
   - pip install codecov
+  - pip install -r docs/requirements.txt
 
 install:
   - pip install .
+  
 # command to run tests
 script:
   - pytest
   - codecov
+  - if [[ "$TRAVIS_PYTHON_VERSION" == "3.7" ]]; then
+      cd ./docs;
+      make html;
+      make html;
+      make html;
+      touch _build/html/.nojekyll;
+    fi
+    
+before_deploy:
+  - cd $TRAVIS_BUILD_DIR
 
 deploy:
-  provider: pypi
-  user: $PYPI_USERNAME
-  password: $PYPI_PASSWORD
-  on:
-    tags: true
-  distributions: "sdist bdist_wheel"
-  skip_existing: true
+  - provider: pages
+    skip_cleanup: true
+    github_token: $GITHUB_TOKEN  # Set in travis-ci.org dashboard, marked secure
+    keep-history: true
+    on:
+      branch: master
+      condition: "$TRAVIS_PYTHON_VERSION = 3.7"
+    local_dir: docs/_build/html
+  - provider: pypi
+    user: $PYPI_USERNAME
+    password: $PYPI_PASSWORD
+    on:
+      tags: true
+    distributions: "sdist bdist_wheel"
+    skip_existing: true
+

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/justusschock/delira.svg?branch=master)](https://travis-ci.com/justusschock/delira) [![Documentation Status](https://readthedocs.org/projects/delira/badge/?version=master)](https://delira.readthedocs.io/en/master/?badge=master) [![codecov](https://codecov.io/gh/justusschock/delira/branch/master/graph/badge.svg)](https://codecov.io/gh/justusschock/delira)
+[![PyPI version](https://badge.fury.io/py/delira.svg)](https://badge.fury.io/py/delira) [![Build Status](https://travis-ci.com/justusschock/delira.svg?branch=master)](https://travis-ci.com/justusschock/delira) [![Documentation Status](https://readthedocs.org/projects/delira/badge/?version=master)](https://delira.readthedocs.io/en/master/?badge=master) [![codecov](https://codecov.io/gh/justusschock/delira/branch/master/graph/badge.svg)](https://codecov.io/gh/justusschock/delira)
 ![LICENSE](https://img.shields.io/github/license/justusschock/delira.svg)
 
 ![logo](docs/_static/logo/delira.svg "delira - Deep Learning in Radiology")
@@ -9,11 +9,11 @@ Authors: [Justus Schock, Oliver Rippel, Christoph Haarburger](AUTHORS.rst)
 ## Introduction
 Delira was developed as a deep learning framework for medical images such as CT or MRI. Currently, it works on arbitrary data (based on [NumPy](http://www.numpy.org/)). 
 
-Based on [PyTorch](https://pytorch.org), [batchgenerators](https://github.com/MIC-DKFZ/batchgenerators) and [trixi](https://github.com/MIC-DKFZ/trixi) it provides a framework for
+Based on [batchgenerators](https://github.com/MIC-DKFZ/batchgenerators) and [trixi](https://github.com/MIC-DKFZ/trixi) it provides a framework for
 * Dataset loading
 * Dataset sampling
 * Augmentation (multi-threaded) including 3D images with any number of channels
-* A generic trainer class that implements the training process
+* A generic trainer class that implements the training process for all [backends](#choose-backend)
 * Already implemented [models](delira/models) used in medical image processing and exemplaric implementations of most used models in general (like Resnet)
 * Web-based monitoring using [Visdom](https://github.com/facebookresearch/visdom)
 * Model save and load functions
@@ -24,13 +24,14 @@ Delira supports classification and regression problems as well as generative adv
 
 ### Choose Backend
 
-Currently the only available backend is [PyTorch](https://pytorch.org) (or no backend at all) but we are working on support for [TensorFlow](https://tensorflow.org) as well.  If you want to add another backend, please open an issue (it should not be hard at all) and we will guide you during the process of doing so.
+Currently the only available backends are [PyTorch](https://pytorch.org) and [TensorFlow](https://tensorflow.org)(or no backend at all). If you want to add another backend, please open an issue (it should not be hard at all) and we will guide you during the process of doing so.
 
 | Backend                        | Binary Installation         | Source Installation                                                                         | Notes                                                                                                                                                 |
 |--------------------------------|-----------------------------|---------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------|
 | None                           | `pip install delira`        | `pip install git+https://github.com/justusschock/delira.git`                                | Training not possible if backend is not installed separately                                                                                          |
-| [`torch`](https://pytorch.org) | `pip install delira[torch]` | `git clone https://github.com/justusschock/delira.git && cd delira && pip install .[torch]` | `delira` with `torch` backend supports mixed-precision training via [NVIDIA/apex](https://github.com/NVIDIA/apex.git) (must be installed separately). |
-| Full                           | `pip install delira[full]`  | `git clone https://github.com/justusschock/delira.git && cd delira && pip install .[full]`  | All backends are getting installed.                                                                                                                   |
+| [`torch`](https://pytorch.org) | `pip install delira[torch]` | `git clone https://github.com/justusschock/delira.git && cd delira && pip install .[torch]` | `delira` with `torch` backend supports mixed-precision training via [NVIDIA/apex](https://github.com/NVIDIA/apex.git) (must be installed separately). | 
+| [`tf`](https://www.tensorflow.org/) | - | `git clone https://github.com/justusschock/delira.git && cd delira && pip install .[tf]` | the `tf` backend is still very experimental and lacks some [features](https://github.com/justusschock/delira/issues/47) |
+| Full                           | `pip install delira[full]`  | `git clone https://github.com/justusschock/delira.git && cd delira && pip install .[full]`  | All backends will be installed.                                                                                                                   |
 
 ### Docker
 The easiest way to use `delira` is via docker (with the [nvidia-runtime](https://github.com/NVIDIA/nvidia-docker) for GPU-support) and using the [Dockerfile](docker/Dockerfile) or the [prebuild-images](https://cloud.docker.com/u/justusschock/repository/docker/justusschock/delira).

delira/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.2.1'
+__version__ = '0.3.0'
 
 import warnings
 warnings.simplefilter('default', DeprecationWarning)

docs/getting_started.rst

@@ -1,11 +1,8 @@
 Getting started
 ===============
 
-Installation
-------------
-
 Backends
-~~~~~~~~~~~
+--------
 
 Before installing ``delira``, you have to choose a suitable backend.
 ``delira`` handles backends as optional dependencies and tries to escape all uses of a not-installed backend.
@@ -16,6 +13,11 @@ The currently supported backends are:
 
   .. note::
     ``delira`` supports mixed-precision training via `apex <https://github.com/NVIDIA/apex>`_, but ``apex`` must be installed separately
+    
+* `tf <https://tensorflow.org>`_ (very experimental): Suffix ``tf``
+
+  .. note::
+    the ``tf`` backend is still very experimental and may be unstable.
 
 * None: No Suffix
 
@@ -25,15 +27,21 @@ The currently supported backends are:
   Depending on the backend, some functionalities may not be available for you. If you want to ensure, you can use each functionality, please use the ``full`` option, since it installs all backends
 
 .. note:: 
-  Currently the only other planned backend is TensorFlow (which is coming soon). If you want to add a backend like `CNTK <https://www.microsoft.com/en-us/cognitive-toolkit/>`_, `Chainer <https://chainer.org/>`_, `MXNET <https://mxnet.apache.org/>`_ or something similar, please open an issue for that and we will guide you during that process (don't worry, it is not much effort at all).
+  If you want to add a backend like `CNTK <https://www.microsoft.com/en-us/cognitive-toolkit/>`_, `Chainer <https://chainer.org/>`_, `MXNET <https://mxnet.apache.org/>`_ or something similar, please open an issue for that and we will guide you during that process (don't worry, it is not much effort at all).
+
+Installation
+------------
 
 ======== ============================= ============================================================================================= ======================================================================================================================
 Backend  Binary Installation           Source Installation                                                                           Notes
 ======== ============================= ============================================================================================= ======================================================================================================================
 None     ``pip install delira``        ``pip install git+https://github.com/justusschock/delira.git``                                Training not possible if backend is not installed separately
 `torch`_ ``pip install delira[torch]`` ``git clone https://github.com/justusschock/delira.git && cd delira && pip install .[torch]`` ``delira`` with ``torch`` backend supports mixed-precision training via `NVIDIA/apex`_ (must be installed separately).
+`tf`_               --                 ``git clone https://github.com/justusschock/delira.git && cd delira && pip install .[tf]``    The tensorflow backend is still very experimental and lacks some `features`_
 Full     ``pip install delira[full]``  ``git clone https://github.com/justusschock/delira.git && cd delira && pip install .[full]``  All backends are getting installed.
 ======== ============================= ============================================================================================= ======================================================================================================================
 
 .. _torch: https://pytorch.org
 .. _NVIDIA/apex: https://github.com/NVIDIA/apex.git
+.. _tf: https://tensorflow.org
+.. _features: https://github.com/justusschock/delira/issues/47

requirements.txt

@@ -1,5 +1,5 @@
-numpy>=1.15.0,<1.16.0
-scikit-image==0.14.0
+numpy>=1.15.0
+scikit-image>=0.14.0
 scikit-learn>=0.20.0
 jupyter>=1.0.0
 flake8
@@ -14,6 +14,6 @@ tqdm
 visdom>=0.1.8.5
 pyyaml
 trixi-slim
-batchgenerators@git+https://github.com/MIC-DKFZ/batchgenerators.git@91feb74747bfcfb9514d509fb13b854a37847b4d#egg=batchgenerators-0
+batchgenerators>=0.18
 psutil
 nested_lookup