Make package ready for PyPI

* remove unused packages
* add fields to setup.py to make our package easier to find on PyPI
* remove extra_requires.tf and merged it with install_requires.
* remove lpips_tf from dependencies (it is not on PyPI so it made pushing atlalign to PyPI impossible)
* make Tox install lpips_tf before running tests that require it.

README.md

@@ -54,39 +54,43 @@ brain atlases obtained with ISH gene expression and Nissl stains.
 
 
 ### Official documentation
-All details related to installation and logic are described in the official documentation. Once
-deployed a link will be added. Until then one can generate it locally following the instructions
-below.
+All details related to installation and logic are described in the 
+[official documentation](https://atlas-alignment.readthedocs.io/).
 
 
-### Normal installation
-Make sure the `pip` version is at least `19.1`.
+### Installation
 
-```bash
-pip install --upgrade pip
-pip --version  # make sure >= 19.1
+#### Installation Requirements
+
+Some of the functionalities of `atlalign` depend on the [TensorFlow implementation
+of the Learned Perceptual Image Patch Similarity (LPIPS)](https://github.com/alexlee-gk/lpips-tensorflow). Unfortunately, the
+package is not available on PyPI and must be installed manually as follows.
+```shell script
+pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
 ```
 
-Then one can move on to installing the actual `atlalign` package:
+You can now move on to installing the actual `atlalign` package!
 
+#### Installation from PyPI
+The `atlalign` package can be easily installed from PyPI.
+```shell script
+pip install atlalign
 ```
-pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign[tf]
-```
-The extras entry `[tf]` represents TensorFlow and can be dropped if it is already installed.
 
-
-### Development installation + docs
-As described above, make sure to get the most recent `pip`.
+#### Installation from source
+As an alternative to installing from PyPI, if you want to try the latest version
+you can also install from source. 
+```shell script
+pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign
 ```
+
+#### Installation for development
+If you want a dev install, you should install the latest version from source with
+all the extra requirements for running test and generating docs. 
+```shell script
 git clone https://github.com/BlueBrain/atlas_alignment
 cd atlas_alignment
-pip install -e .[dev,docs,tf]
-```
-
-Assuming the user ran the above it should be possible to generate the docs 
-```
-cd docs
-make clean && make html
+pip install -e .[dev,docs]
 ```
 
 ### Examples

atlalign/metrics.py

@@ -37,7 +37,19 @@
 from functools import wraps
 
 import ants
-import lpips_tf
+
+try:
+    import lpips_tf
+except ModuleNotFoundError as err:
+    raise ModuleNotFoundError(
+        """
+        LPIPS-TensorFlow required but not found.
+
+        Please install it by running the following command:
+        $ pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
+        """
+    ) from err
+
 import numpy as np
 import pandas as pd
 import tensorflow as tf

atlalign/ml_utils/losses.py

@@ -21,7 +21,19 @@
 
 import keras
 import keras.backend as K
-import lpips_tf
+
+try:
+    import lpips_tf
+except ModuleNotFoundError as err:
+    raise ModuleNotFoundError(
+        """
+        LPIPS-TensorFlow required but not found.
+
+        Please install it by running the following command:
+        $ pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
+        """
+    ) from err
+
 import numpy as np
 import tensorflow as tf
 

docs/source/installation.rst

@@ -4,31 +4,41 @@ Installation
 ============
 It is highly recommended to install the project into a new virtual environment.
 
-Requirements
-------------
+Python Requirements
+-------------------
 The project is only available for **Python 3.7**. The main reason for this 
 restriction is an external dependency **ANTsPy** that does
 not provide many precompiled wheels on PyPI.
 
-
-Standard installation
+External Dependencies
 ---------------------
-First of all make sure the :code:`pip` version is at least :code:`19.1`
-(`PyPA <https://pip.pypa.io/en/stable/reference/pip_install/#requirement-specifiers>`_).
+Some of the functionalities of :code:`atlalign` depend on the
+`TensorFlow implementation of the Learned Perceptual Image Patch Similarity <https://github.com/alexlee-gk/lpips-tensorflow>`_.
+Unfortunately, the
+package is not available on PyPI and must be installed manually as follows.
 
 .. code-block:: bash
 
-    pip install --upgrade pip
-    pip --version  # make sure >= 19.1
+    pip install git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
+
+You can now move on to installing the actual `atlalign` package!
 
-Then one can move on to installing the actual :code:`atlalign` package:
+Installation from PyPI
+----------------------
+The :code:`atlalign` package can be easily installed from PyPI.
 
 .. code-block:: bash
 
-    pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign[tf]
+    pip install atlalign
 
-The extras entry :code:`[tf]` represents **TensorFlow** and can be dropped if it is already installed.
+Installation from source
+------------------------
+As an alternative to installing from PyPI, if you want to try the latest version
+you can also install from source.
+
+.. code-block:: bash
 
+    pip install git+https://github.com/BlueBrain/atlas_alignment#egg=atlalign
 
 Development installation
 ------------------------
@@ -37,13 +47,12 @@ following way:
 
 - **dev** - pytest + plugins, flake8, pydocstyle, tox
 - **docs** - sphinx
-- **tf** - tensorflow
 
 .. code-block:: bash
 
     git clone https://github.com/BlueBrain/atlas_alignment
     cd atlas_alignment
-    pip install -e .[dev,docs,tf]
+    pip install -e .[dev,docs]
 
 
 Generating documentation

setup.py

@@ -6,31 +6,49 @@
 
 # Preparations
 VERSION = atlalign.__version__
+DESCRIPTION = "Blue Brain multi-modal registration and alignment toolbox"
+
+LONG_DESCRIPTION = """
+Atlas Alignment is a toolbox to perform multimodal image registration. It
+includes both traditional and supervised deep learning models.
+
+This project originated from the Blue Brain Project efforts on aligning mouse
+brain atlases obtained with ISH gene expression and Nissl stains."""
 
 PYTHON_REQUIRES = "~=3.7.0"
 INSTALL_REQUIRES = [
     "antspyx==0.2.4",
     "allensdk>=0.16.3",
     "imgaug<0.3",
     "Keras==2.2.4",
-    "keras_contrib @ git+http://github.com/keras-team/keras-contrib.git@e1574a1#egg=keras_contrib",
-    "lpips_tf @ git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf",
     "matplotlib>=3.0.3",
     "mlflow",
     "nibabel>=2.4.0",
     "numpy>=1.16.3",
-    "statsmodels>=0.9.0",
     "scikit-image>=0.16.0",
     "scikit-learn>=0.20.2",
     "scipy==1.2.1",
+    "tensorflow>=1.15.4,<2",
 ]
 
 setup(
     name="atlalign",
     version=VERSION,
-    description="Image registration with deep learning",
+    description=DESCRIPTION,
+    long_description=LONG_DESCRIPTION,
+    url="https://github.com/BlueBrain/atlas_alignment",
     author="Blue Brain Project, EPFL",
+    license="LGPLv3",
     packages=find_packages(),
+    classifiers=[
+        "Development Status :: 4 - Beta",
+        "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
+        "Operating System :: Unix",
+        "Programming Language :: Python :: 3",
+        "Topic :: Scientific/Engineering :: Artificial Intelligence",
+        "Topic :: Scientific/Engineering :: Image Processing",
+        "Topic :: Software Development :: Libraries :: Python Modules",
+    ],
     python_requires=PYTHON_REQUIRES,
     install_requires=INSTALL_REQUIRES,
     extras_require={
@@ -39,12 +57,10 @@
             "flake8>=3.7.4",
             "pydocstyle>=3.0.0",
             "pytest>=3.10.1",
-            "pytest-benchmark>=3.2.2",
             "pytest-cov",
             "pytest-mock>=1.10.1",
         ],
         "docs": ["sphinx>=1.3", "sphinx-bluebrain-theme"],
-        "tf": ["tensorflow>=1.15.4,<2"],
     },
     entry_points={"console_scripts": ["label-tool = atlalign.label.cli:main"]},
 )

tox.ini

@@ -9,9 +9,10 @@ envlist =
 
 [testenv]
 download = true
+deps =
+    lpips_tf @ git+http://github.com/alexlee-gk/lpips-tensorflow.git#egg=lpips_tf
 extras =
     dev
-    tf
 commands =
     pytest {posargs:tests}
 
@@ -44,7 +45,6 @@ basepython = python3.7
 changedir = docs
 extras =
     dev
-    tf
     docs
 whitelist_externals = make
 commands =