Merge pull request #57 from beringresearch/tf-extra-requires

Tf extra requires

Author: Szubie

R-package/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ivis
 Title: Artificial neural network-driven visualization of high-dimensional data using triplets. 
-Version: 1.6.0
+Version: 1.7.0
 Authors@R: c(person("Benjamin", "Szubert", email = "[email protected]", role = c("aut", "cre")),
          person("Ignat", "Drozdov", email = "[email protected]", role = c("aut")),
          person("Kevin", "Rue-Albrecht", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872")))
@@ -15,7 +15,7 @@ Imports: reticulate
 License: MIT 
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Suggests: 
     knitr,
     rmarkdown,

R-package/R/install_ivis.R

@@ -19,14 +19,14 @@ install_ivis <- function(){
     cat("Creating a virtual environment (ivis)\n")
     virtual_envs <- env_list()
     if ("ivis" %in% virtual_envs){
-      cat("(ivis) environment already exists. The old environment will be updated.")
+      cat("(ivis) environment already exists. The old environment will be updated. ")
       env_remove("ivis")
     }
 
     envname <- "ivis"
     env_create(envname)
 
-    py_install("ivis", envname="ivis")
+    py_install("ivis[cpu]", envname="ivis")
 }   
 
 

R-package/man/ivis.Rd

@@ -9,18 +9,23 @@ Implementation of the ivis algorithm as described in the paper [Structure-preser
 
 ## Installation
 
-Install the latest ivis release from PyPi:
+Ivis runs on top of TensorFlow, and needs it to be installed to run.
+
+To install the latest ivis release from PyPi running on the CPU TensorFlow package, run:
 
 ```
-pip install ivis
+pip install ivis[cpu]
 ```
 
+If you have CUDA installed and want ivis to use the tensorflow-gpu package, instead run `pip install ivis[gpu]`.
+
+
 Alternatively, you can install the development version from github:
 
 ```
 git clone https://github.com/beringresearch/ivis
 cd ivis
-pip install -r requirements.txt --editable .
+pip install -e '.[cpu]'
 ```
 
 The following **optional dependencies** are needed if using the visualization callbacks while training the Ivis model:

README.md

@@ -1,2 +1,2 @@
-python3 -m pip install --user -e .
+python3 -m pip install --user -e '.[cpu]'
 python3 -m pip install --user pytest

ci_scripts/install.sh

@@ -11,7 +11,9 @@ The latest stable release can be installed from PyPi:
 
 .. code:: bash
 
-  pip install ivis
+  pip install ivis[cpu]
+
+If you have CUDA installed and want ivis to use the tensorflow-gpu package, instead run `pip install ivis[gpu]`.
 
 
 Alternatively, you can use ``pip`` to install the development version directly from github:
@@ -26,7 +28,7 @@ Another option would be to clone the github repository and install from your loc
 
   git clone https://github.com/beringresearch/ivis
   cd ivis
-  pip install -r requirements.txt -e .
+  pip install -e '.[cpu]'
 
 
 Dependencies

docs/python_package.rst

@@ -1 +1 @@
-VERSION = '1.6.0'
+VERSION = '1.7.0'

ivis/version.py

@@ -20,15 +20,16 @@
       license='GNU General Public License v2.0',
       packages=find_packages(),
       install_requires=[
-          'tensorflow',
           'numpy',
-          'scikit-learn',
+          'scikit-learn>0.20.0',
           'annoy>=1.15.2',
           'tqdm'
       ],
       extras_require={
           'tests': ['pytest'],
-          'visualization': ['matplotlib', 'seaborn']
+          'visualization': ['matplotlib', 'seaborn'],
+          'cpu': ['tensorflow>=1.4.0'],
+          'gpu': ['tensorflow-gpu>=1.4.0']
       },
       classifiers=[
           "Programming Language :: Python :: 3",