Update documentation and CHANGES

Preparation for 3.0 release.

Author: JoostJM

CHANGES.rst

@@ -2,21 +2,51 @@
 Release Notes
 =============
 
-.. note::
-    **Upcoming changes in 3.0 release**
-
-    - Removal of deprecated code (e.g. ``commandlinebatch.py``, ``calculateFeatures()`` function in feature classes);
-      deprecated radiomics features are retained.
-    - End of official python 2.7 support
-
-      - No CI-tests for python 2.7
-      - No pre-build binaries for python 2.7 distributed on PyPi and Anaconda Cloud
-      - Compatibility code using six is retained (allowing local build).
-
 ------------
 Next Release
 ------------
 
+---------------
+PyRadiomics 3.0
+---------------
+
+.. warning::
+  As of this release, Python 2.7 testing is removed. Compatibility code such as it is will be left in place, but
+  future changes will not be checked for backwards compatibility. Moreover, no pre-built binaries for python 2.7
+  will be distributed on PyPi or Conda.
+  Finally, some deprecated code is removed (``commandlinebatch.py`` and ``calculateFeatures()``).
+
+Bug Fixes
+#########
+
+- Fix broken Conda deployment (`51c5849 <https://github.com/Radiomics/pyradiomics/commit/51c5849>`_)
+- Fix error in IBSI mapping (labs/pyradiomics-dcm) (`54d6689 <https://github.com/Radiomics/pyradiomics/commit/54d6689>`_)
+- Fix resampling error when spacing is correct, but sizes are different (`ac7458e <https://github.com/Radiomics/pyradiomics/commit/ac7458e>`_)
+- Fix label channel selection (`54a3782 <https://github.com/Radiomics/pyradiomics/commit/54a3782>`_)
+- Use local scope of settings, preventing race conditions in parallel extraction (`43578f7 <https://github.com/Radiomics/pyradiomics/commit/43578f7>`_)
+- Fix resampling for 2D input (`#545 <https://github.com/Radiomics/pyradiomics/pull/545>`_)
+
+Internal API
+############
+
+- Update C API to use large datatype for index pointers (`#500 <https://github.com/Radiomics/pyradiomics/pull/500>`_,
+  `#501 <https://github.com/Radiomics/pyradiomics/pull/501>`_)
+- Update docker CLI to use python 3.6.9 and fix bugs to allow integration with pyradiomics-dcm lab (`#527 <https://github.com/Radiomics/pyradiomics/pull/527>`_)
+- Add option to force path to UNIX style paths, even on windows (`3c0708a <https://github.com/Radiomics/pyradiomics/commit/3c0708a>`_)
+- Removed deprecated code (`fedaa5e <https://github.com/Radiomics/pyradiomics/commit/fedaa5e>`_)
+
+Testing
+#######
+
+- Remove testing and deployment for python 2.7 (`a5a7e61 <https://github.com/Radiomics/pyradiomics/commit/a5a7e61>`_)
+
+Documentation
+#############
+
+- Refactor documentation (`#536 <https://github.com/Radiomics/pyradiomics/pull/536>`_)
+- Fix various typos/wording
+- Clarify use of force2D, and add example settings file (`#558 <https://github.com/Radiomics/pyradiomics/pull/558>`_)
+
 -----------------
 PyRadiomics 2.2.0
 -----------------

README.md

@@ -1,4 +1,4 @@
-# pyradiomics v2.2.0
+# pyradiomics v3.0
 
 ## Build Status
 
@@ -76,8 +76,8 @@ The documentation can then be viewed in a browser by opening `PACKAGE_ROOT\build
 Furthermore, an instruction video is available [here](http://radiomics.io/pyradiomics.html).
 
 ### Installation
-PyRadiomics is OS independent and compatible with both Python 2.7 and Python 3.4, 3.5 and 3.6. As of version 2.0,
-PyRadiomics releases are also made available on PyPi. To install PyRadiomics, ensure you have python
+PyRadiomics is OS independent and compatible with Python >= 3.5. Pre-built binaries are available on
+PyPi and Conda. To install PyRadiomics, ensure you have python
 installed and run:
 
     `python -m pip install pyradiomics`
@@ -158,7 +158,7 @@ This package is covered by the open source [3-clause BSD License](LICENSE.txt).
 <sup>6</sup>Isomics
 
 ### Contact
-We are happy to help you with any questions. Please contact us on the [Radiomics community section of the 3D Slicer Discourse](https://discourse.slicer.org/c/community/radiomics).
+We are happy to help you with any questions. Please contact us on the [Radiomics community section of the 3D Slicer Discourse](https://discourse.slicer.org/c/community/radiomics/23).
 
 We welcome contributions to PyRadiomics. Please read the [contributing guidelines](CONTRIBUTING.rst) on how to
 contribute to PyRadiomics.

docs/faq.rst

@@ -363,11 +363,11 @@ Miscellaneous
 Which python versions is PyRadiomics compatible with?
 #####################################################
 
-PyRadiomics is compatible with both python 2 and python 3. However, the automated testing only uses python versions 2.7,
-3.5, 3.6 and 3.7 (only 64 bits architecture). Python < 2.6 is not supported. Other python versions may be compatible with
-PyRadiomics, but this is not actively tested and therefore not guaranteed to work. In the future, support for python 2.7
-will also be dropped, to compatibility fixes are retained. This means that future releases of PyRadiomics will only have
-pre-built wheels for Python versions >= 3.5.
+PyRadiomics is compatible with python 3. Python 2 support was dropped in PyRadiomics version 3.0, though compatibility
+code was retained. However, the automated testing only uses python versions 3.5, 3.6 and 3.7 (64 bits architecture).
+Python < 2.6 is not supported. Other python versions may be compatible with PyRadiomics, but this is not actively tested
+and therefore not guaranteed to work. Pre-built wheels are only available for the tested versions of python (3.5, 3.6
+and 3.7)
 
 A new version of PyRadiomics is available! Where can I find out what changed?
 #############################################################################
@@ -390,15 +390,14 @@ I found a bug! Where do I report it?
 
 We strive to keep PyRadiomics as bug free as possible by thoroughly testing new additions before including them in the
 stable version. However, nothing is perfect, and some bugs may therefore exist. Report yours by
-`opening an issue <https://github.com/Radiomics/pyradiomics/issues>`_ on the GitHub or contact us at the
-`pyradiomics email list <https://groups.google.com/forum/#!forum/pyradiomics>`_. If you want to help in fixing it, we'd
-welcome you to open up a `pull request <https://github.com/Radiomics/pyradiomics/pulls>`_ with your suggested fix.
+`opening an issue <https://github.com/Radiomics/pyradiomics/issues>`_ on the GitHub. If you want to help in fixing it,
+we'd welcome you to open up a `pull request <https://github.com/Radiomics/pyradiomics/pulls>`_ with your suggested fix.
 
 My question is not listed here...
 #################################
 
 If you have a question that is not listed here, check the
-`pyradiomics email list <https://groups.google.com/forum/#!forum/pyradiomics>`_ or the
+`pyradiomics forum on 3D Slicer discourse <https://discourse.slicer.org/c/community/radiomics/23>`_ or the
 `issues on GitHub <https://github.com/Radiomics/pyradiomics/issues>`_. Feel free to post a new question or issue and
 we'll try to get back to you ASAP.
 

docs/index.rst

@@ -114,8 +114,8 @@ See also the `requirements file <https://github.com/Radiomics/pyradiomics/blob/m
 Installation
 ------------
 
-PyRadiomics is OS independent and compatible with both Python 2.7 and Python >=3.4. As of version 2.0,
-PyRadiomics releases are also made available on PyPi. To install PyRadiomics, ensure you have python
+PyRadiomics is OS independent and compatible with and Python >=3.5. Pre-built binaries are available on
+PyPi and Conda. To install PyRadiomics, ensure you have python
 installed and run:
 
 *  ``python -m pip install pyradiomics``
@@ -155,7 +155,7 @@ Developers
 
 Contact
 -------
-We are happy to help you with any questions. Please contact us on the `Radiomics community section of the 3D Slicer Discourse <https://discourse.slicer.org/>`_.
+We are happy to help you with any questions. Please contact us on the `Radiomics community section of the 3D Slicer Discourse <https://discourse.slicer.org/c/community/radiomics/23>`_.
 
 We'd welcome your contributions to PyRadiomics. Please read the
 :ref:`contributing guidelines <radiomics-contributing-label>` on how to contribute to PyRadiomics. Information on

docs/installation.rst

@@ -14,19 +14,28 @@ There are three ways you can use pyradiomics:
 1. Install via pip
 ------------------
 
-As of version 2.0.0, PyRadiomics will be available for installation via pip. For the python versions
+Pre-built binaries are available on PyPi for installation via pip. For the python versions
 mentioned below, wheels are automatically generated for each release of PyRadiomics, allowing you to
 install pyradiomics without having to compile anything. For other python versions, a source distribution
 is also available, but this requires compiling the C extensions.
 
-* Ensure that you have ``python`` installed on your machine, version 2.7, 3.4, 3.5 or 3.6 (64-bits).
+* Ensure that you have ``python`` installed on your machine, version 3.5, 3.6 or 3.7 (64-bits).
 
-* Install PyRadiomics:
+* Install PyRadiomics::
 
-    * ``python -m pip install pyradiomics``
+    python -m pip install pyradiomics
+
+--------------------
+2. Install via conda
+--------------------
+
+Besides pre-built binaries for PyPi, PyRadiomics is also available on conda cloud.
+To install PyRadiomics on Conda, run::
+
+    conda install -c radiomics pyradiomics
 
 ----------------------
-2. Install from source
+3. Install from source
 ----------------------
 
 PyRadiomics can also be installed from source code. This allows for the bleeding edge version, but does
@@ -35,21 +44,22 @@ of texture matrices and some shape features.
 
 * Ensure you have the version control system ``git`` installed on your machine.
 
-* Ensure that you have ``python`` installed on your machine, at least version 2.7 or 3.4 (64-bits).
+* Ensure that you have ``python`` installed on your machine, at least version 3.5 (64-bits).
+
+* Clone the repository::
 
-* Clone the repository:
+    git clone git://github.com/Radiomics/pyradiomics
 
-  * ``git clone git://github.com/Radiomics/pyradiomics``
 
+* For unix like systems (MacOSX, linux)::
 
-* For unix like systems (MacOSX, linux):
+      cd pyradiomics
+      python -m pip install -r requirements.txt
+      python setup.py install
 
-  * ``cd pyradiomics``
-  * ``python -m pip install -r requirements.txt``
-  * ``python setup.py install``
+  * To use your build for interactive use and development::
 
-  To use your build for interactive use and development:
-  * ``python setup.py build_ext --inplace``
+      python setup.py build_ext --inplace
 
   * If you don't have sudo/admin rights on your machine, you need to locally install numpy, nose, tqdm, PyWavelets, SimpleITK (specified in requirements.txt).
     In a bash shell::
@@ -59,11 +69,11 @@ of texture matrices and some shape features.
       pip install --user -r requirements.txt
       export PYTHONPATH=$HOME/.local/lib64/python2.7/site-packages
 
-* For Windows:
+* For Windows::
 
-  * ``cd pyradiomics``
-  * ``python -m pip install -r requirements.txt``
-  * ``python setup.py install``
+    cd pyradiomics
+    python -m pip install -r requirements.txt
+    python setup.py install
 
 * If the installation fails, check out the :ref:`radiomics-faq-label`. If your error is not listed there,
   contact us by `creating an issue <https://github.com/Radiomics/pyradiomics/issues/new>`_ on the PyRadiomics
@@ -90,14 +100,14 @@ This approach may be preferred if you are interested in using pyradiomics from t
 First, you will need to install Docker on your system, if it is not installed already. You can follow the instructions below to do this.
 
 Once Docker is installed, you can issue ``docker pull radiomics/pyradiomics:CLI`` command in the shell to download the pyradiomics Docker image.
-After that you can invoke pyradiomics tool as follows:
+After that you can invoke pyradiomics tool as follows::
 
-  ``docker run radiomics/pyradiomics:CLI --help``
+  docker run radiomics/pyradiomics:CLI --help
 
 Docker containers cannot directly access the filesystem of the host. In order to pass files as arguments to pyradiomics and to access files that converters create,
-an extra step is required to specify which directories will be used for file exchange using the -v argument:
+an extra step is required to specify which directories will be used for file exchange using the -v argument::
 
-  ``-v <HOST_DIR>:<CONTAINER_DIR>``
+  -v <HOST_DIR>:<CONTAINER_DIR>
 
 The argument above will make the ``HOST_DIR`` path available within the container at ``CONTAINER_DIR`` location. The files that will be read or written by the
 converter run from the docker container should be referred to via the ``CONTAINER_DIR`` path.
@@ -121,12 +131,11 @@ Note `the system requirements <https://docs.docker.com/docker-for-windows/>`_:
 
 **IMPORTANT**: You will also need to share the drive you will be using to communicate data to and from Docker image in Docker Settings as shown in the screenshot below.
 
-Most likely you will experience the display of an error message similar to the one shown below:
-
+Most likely you will experience the display of an error message similar to the one shown below::
 
-  ``C:\Program Files\Docker\Docker\Resources\bin\docker.exe: Error response from daemon: \``
-  ``C: drive is not shared. Please share it in Docker for Windows Settings.``
-  ``See 'C:\Program Files\Docker\Docker\Resources\bin\docker.exe run --help'.``
+  C:\Program Files\Docker\Docker\Resources\bin\docker.exe: Error response from daemon:
+  C: drive is not shared. Please share it in Docker for Windows Settings.
+  See 'C:\Program Files\Docker\Docker\Resources\bin\docker.exe run --help'.
 
 If you have this error, make sure that the drive, where the ``HOST_DIR`` is located, is shared: