requirements: add version numbers and dependencies

Author: mdeff

requirements.txt

@@ -1,22 +1,69 @@
-numpy
-scipy
-pandas
-tables
-scikit-learn
-matplotlib
-seaborn
+# Version numbers have been retrieved from a range of machines and environments.
+# Take them with a grain of salt.
 
-tensorflow-gpu
-#tensorflow
+# Direct dependencies
+#python==3.5  # 3.4 / 3.6
+#pip==1.5.4
+#setuptools==21.0.0
+numpy==1.11.0  # 1.12.1
+scipy==0.17.0  # 0.19.0
+pandas==0.20.0
+scikit-learn==0.18.1
+matplotlib==1.5.1  # 2.0.1
+seaborn==0.7.1
+tqdm==4.11.2
+gensim==2.1.0  # 0.12.4 / 2.0.0  # Only for NLP experiments.
+#graph-tool==2.26  # Cannot be installed with pip.
+tensorflow-gpu==1.1.0  # 0.8.0  # Or tensorflow if not running on GPU.
+#networkx==1.11  # Only considered at some point.
+#networkit==4.2  # Only considered at some point.
 
-jupyter
-ipython
+# Dependencies of the above.
+boto==2.46.1  # 2.40.0
+bz2file==0.98
+cycler==0.10.0  # 0.9.0
+protobuf==3.3.0  # 3.0.0
+pyparsing==2.2.0  # 2.1.4
+python-dateutil==2.6.0  # 2.5.3
+pytz==2016.4  # 2017.2
+requests==2.13.0  # 2.9.1 / 2.10.0
+six==1.10.0
+smart-open==1.5.2  # 1.3.3
+Werkzeug==0.12.1
 
-python-dotenv
-tqdm
+# Jupyter notebook and its dependencies.
+notebook==5.0.0  # 4.2.0
+bleach==2.0.0  # 3.1.1
+decorator==4.0.9  # 4.0.6 / 4.0.11 / 4.4.1
+entrypoints==0.2.2
+html5lib==0.999999999
+ipykernel==4.6.1  # 4.3.1
+ipython==6.0.0  # 4.2.0
+ipython-genutils==0.2.0  # 0.1.0
+jedi==0.10.2
+Jinja2==2.8  # 2.9.6
+jsonschema==2.6.0  # 2.5.1
+jupyter-client==5.0.1  # 4.2.2
+jupyter-core==4.3.0  # 4.1.0
+MarkupSafe==0.23  # 1.0
+mistune==0.7.4
+nbconvert==5.1.1  # 4.2.0
+nbformat==4.3.0  # 4.0.1
+pandocfilters==1.4.1
+pexpect==4.2.1  # 4.0.1
+pickleshare==0.7.4  # 0.7.2
+prompt-toolkit==1.0.10
+ptyprocess==0.5.1
+Pygments==2.2.0  # 2.1.3
+pyzmq==16.0.2  # 15.2.0
+simplegeneric==0.8.1
+terminado==0.6
+testpath==0.3
+tornado==4.3  # 4.2.1 / 4.4.2 / 4.5.1
+traitlets==4.3.2  # 4.2.1
+wcwidth==0.1.7
+webencodings==0.5.1
 
-# Only needed for NLP experiments.
-gensim
-
-# Cannot be installed with pip.
-#graph-tool
+# dotenv and its dependency.
+#python-dotenv==0.6.4
+#click==6.7