Version bump

mims-harvard · Sep 22, 2017 · a37335f · a37335f
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Showing 94 changed files with 8 additions and 5 deletions.
diff --git a/docs/source/README.rst → docs/README.rst b/docs/source/README.rst → docs/README.rst
diff --git a/docs/source/code/snippet_bd.py → docs/code/snippet_bd.py b/docs/source/code/snippet_bd.py → docs/code/snippet_bd.py
diff --git a/docs/source/code/snippet_bmf.py → docs/code/snippet_bmf.py b/docs/source/code/snippet_bmf.py → docs/code/snippet_bmf.py
diff --git a/docs/source/code/snippet_icm.py → docs/code/snippet_icm.py b/docs/source/code/snippet_icm.py → docs/code/snippet_icm.py
diff --git a/docs/source/code/snippet_lfnmf.py → docs/code/snippet_lfnmf.py b/docs/source/code/snippet_lfnmf.py → docs/code/snippet_lfnmf.py
diff --git a/docs/source/code/snippet_lsnmf.py → docs/code/snippet_lsnmf.py b/docs/source/code/snippet_lsnmf.py → docs/code/snippet_lsnmf.py
diff --git a/docs/source/code/snippet_nmf_conn.py → docs/code/snippet_nmf_conn.py b/docs/source/code/snippet_nmf_conn.py → docs/code/snippet_nmf_conn.py
diff --git a/docs/source/code/snippet_nmf_div.py → docs/code/snippet_nmf_div.py b/docs/source/code/snippet_nmf_div.py → docs/code/snippet_nmf_div.py
diff --git a/docs/source/code/snippet_nmf_fro.py → docs/code/snippet_nmf_fro.py b/docs/source/code/snippet_nmf_fro.py → docs/code/snippet_nmf_fro.py
diff --git a/docs/source/code/snippet_nsnmf.py → docs/code/snippet_nsnmf.py b/docs/source/code/snippet_nsnmf.py → docs/code/snippet_nsnmf.py
diff --git a/docs/source/code/snippet_pmf.py → docs/code/snippet_pmf.py b/docs/source/code/snippet_pmf.py → docs/code/snippet_pmf.py
diff --git a/docs/source/code/snippet_pmfcc.py → docs/code/snippet_pmfcc.py b/docs/source/code/snippet_pmfcc.py → docs/code/snippet_pmfcc.py
diff --git a/docs/source/code/snippet_psmf.py → docs/code/snippet_psmf.py b/docs/source/code/snippet_psmf.py → docs/code/snippet_psmf.py
diff --git a/docs/source/code/snippet_snmf_l.py → docs/code/snippet_snmf_l.py b/docs/source/code/snippet_snmf_l.py → docs/code/snippet_snmf_l.py
diff --git a/docs/source/code/snippet_snmf_r.py → docs/code/snippet_snmf_r.py b/docs/source/code/snippet_snmf_r.py → docs/code/snippet_snmf_r.py
diff --git a/docs/source/code/snippet_snmnmf.py → docs/code/snippet_snmnmf.py b/docs/source/code/snippet_snmnmf.py → docs/code/snippet_snmnmf.py
diff --git a/docs/source/code/usage.py → docs/code/usage.py b/docs/source/code/usage.py → docs/code/usage.py
diff --git a/docs/source/code/usage1.py → docs/code/usage1.py b/docs/source/code/usage1.py → docs/code/usage1.py
diff --git a/docs/source/code/usage2.py → docs/code/usage2.py b/docs/source/code/usage2.py → docs/code/usage2.py
diff --git a/docs/source/code/usage3.py → docs/code/usage3.py b/docs/source/code/usage3.py → docs/code/usage3.py
diff --git a/docs/source/code/usage4.py → docs/code/usage4.py b/docs/source/code/usage4.py → docs/code/usage4.py
diff --git a/docs/source/code/usage5.py → docs/code/usage5.py b/docs/source/code/usage5.py → docs/code/usage5.py
diff --git a/docs/source/code/usage6.py → docs/code/usage6.py b/docs/source/code/usage6.py → docs/code/usage6.py
diff --git a/docs/source/code/usage7.py → docs/code/usage7.py b/docs/source/code/usage7.py → docs/code/usage7.py
diff --git a/docs/source/conf.py → docs/conf.py b/docs/source/conf.py → docs/conf.py
@@ -43,7 +43,7 @@
 
 # General information about the project.
 project = 'Nimfa'
-copyright = '2016, The Nimfa developers'
+copyright = '2017, Marinka Zitnik'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
@@ -52,7 +52,7 @@
 # The short X.Y version.
 version = '1.3'
 # The full version, including alpha/beta/rc tags.
-release = '1.3.1'
+release = '1.3.4'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -199,7 +199,7 @@
 # (source start file, target name, title, author, documentclass [howto/manual]).
 latex_documents = [
   ('index', 'nimfa-APythonLibraryforNonnegativeMatrixFactorization.tex', 'nimfa - A Python Library for Nonnegative Matrix Factorization',
-   'The Nimfa developers', 'manual'),
+   'Marinka Zitnik', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of

diff --git a/docs/source/content-factorization.rst → docs/content-factorization.rst b/docs/source/content-factorization.rst → docs/content-factorization.rst
diff --git a/docs/source/content-initialization.rst → docs/content-initialization.rst b/docs/source/content-initialization.rst → docs/content-initialization.rst
diff --git a/docs/source/content-quality-performance.rst → docs/content-quality-performance.rst b/docs/source/content-quality-performance.rst → docs/content-quality-performance.rst
diff --git a/docs/source/content-utils.rst → docs/content-utils.rst b/docs/source/content-utils.rst → docs/content-utils.rst
diff --git a/docs/source/images/all_aml_consensus2.png → docs/images/all_aml_consensus2.png b/docs/source/images/all_aml_consensus2.png → docs/images/all_aml_consensus2.png
diff --git a/docs/source/images/all_aml_consensus3.png → docs/images/all_aml_consensus3.png b/docs/source/images/all_aml_consensus3.png → docs/images/all_aml_consensus3.png
diff --git a/docs/source/images/base/google-logo.png → docs/images/base/google-logo.png b/docs/source/images/base/google-logo.png → docs/images/base/google-logo.png
diff --git a/docs/source/images/base/orange-logo.png → docs/images/base/orange-logo.png b/docs/source/images/base/orange-logo.png → docs/images/base/orange-logo.png
diff --git a/...rce/images/cbcl_faces_10_iters_SNMF_L.png → docs/images/cbcl_faces_10_iters_SNMF_L.png b/...rce/images/cbcl_faces_10_iters_SNMF_L.png → docs/images/cbcl_faces_10_iters_SNMF_L.png
diff --git a/...rce/images/cbcl_faces_10_iters_SNMF_R.png → docs/images/cbcl_faces_10_iters_SNMF_R.png b/...rce/images/cbcl_faces_10_iters_SNMF_R.png → docs/images/cbcl_faces_10_iters_SNMF_R.png
diff --git a/...urce/images/cbcl_faces_50_iters_LSNMF.png → docs/images/cbcl_faces_50_iters_LSNMF.png b/...urce/images/cbcl_faces_50_iters_LSNMF.png → docs/images/cbcl_faces_50_iters_LSNMF.png
diff --git a/...source/images/cbcl_faces_50_iters_NMF.png → docs/images/cbcl_faces_50_iters_NMF.png b/...source/images/cbcl_faces_50_iters_NMF.png → docs/images/cbcl_faces_50_iters_NMF.png
diff --git a/docs/source/images/documents_basisW1.png → docs/images/documents_basisW1.png b/docs/source/images/documents_basisW1.png → docs/images/documents_basisW1.png
diff --git a/docs/source/images/documents_basisW13.png → docs/images/documents_basisW13.png b/docs/source/images/documents_basisW13.png → docs/images/documents_basisW13.png
diff --git a/docs/source/images/documents_basisW15.png → docs/images/documents_basisW15.png b/docs/source/images/documents_basisW15.png → docs/images/documents_basisW15.png
diff --git a/docs/source/images/documents_basisW4.png → docs/images/documents_basisW4.png b/docs/source/images/documents_basisW4.png → docs/images/documents_basisW4.png
diff --git a/docs/source/images/documents_basisW5.png → docs/images/documents_basisW5.png b/docs/source/images/documents_basisW5.png → docs/images/documents_basisW5.png
diff --git a/...rce/images/medulloblastoma_consensus2.png → docs/images/medulloblastoma_consensus2.png b/...rce/images/medulloblastoma_consensus2.png → docs/images/medulloblastoma_consensus2.png
diff --git a/...rce/images/medulloblastoma_consensus3.png → docs/images/medulloblastoma_consensus3.png b/...rce/images/medulloblastoma_consensus3.png → docs/images/medulloblastoma_consensus3.png
diff --git a/...mages/orl_faces_200_iters_small_LSNMF.png → ...mages/orl_faces_200_iters_small_LSNMF.png b/...mages/orl_faces_200_iters_small_LSNMF.png → ...mages/orl_faces_200_iters_small_LSNMF.png
diff --git a/.../images/orl_faces_200_iters_small_NMF.png → .../images/orl_faces_200_iters_small_NMF.png b/.../images/orl_faces_200_iters_small_NMF.png → .../images/orl_faces_200_iters_small_NMF.png
diff --git a/...mages/orl_faces_500_iters_large_LSNMF.png → ...mages/orl_faces_500_iters_large_LSNMF.png b/...mages/orl_faces_500_iters_large_LSNMF.png → ...mages/orl_faces_500_iters_large_LSNMF.png
diff --git a/...s/orl_faces_5_iters_small_PSMF_prior5.png → ...s/orl_faces_5_iters_small_PSMF_prior5.png b/...s/orl_faces_5_iters_small_PSMF_prior5.png → ...s/orl_faces_5_iters_small_PSMF_prior5.png
diff --git a/docs/source/index.rst → docs/index.rst b/docs/source/index.rst → docs/index.rst
diff --git a/docs/source/nimfa.datasets.rst → docs/nimfa.datasets.rst b/docs/source/nimfa.datasets.rst → docs/nimfa.datasets.rst
diff --git a/docs/source/nimfa.examples.all_aml.rst → docs/nimfa.examples.all_aml.rst b/docs/source/nimfa.examples.all_aml.rst → docs/nimfa.examples.all_aml.rst
diff --git a/docs/source/nimfa.examples.cbcl_images.rst → docs/nimfa.examples.cbcl_images.rst b/docs/source/nimfa.examples.cbcl_images.rst → docs/nimfa.examples.cbcl_images.rst
diff --git a/docs/source/nimfa.examples.documents.rst → docs/nimfa.examples.documents.rst b/docs/source/nimfa.examples.documents.rst → docs/nimfa.examples.documents.rst
diff --git a/...e/nimfa.examples.gene_func_prediction.rst → docs/nimfa.examples.gene_func_prediction.rst b/...e/nimfa.examples.gene_func_prediction.rst → docs/nimfa.examples.gene_func_prediction.rst
diff --git a/...source/nimfa.examples.medulloblastoma.rst → docs/nimfa.examples.medulloblastoma.rst b/...source/nimfa.examples.medulloblastoma.rst → docs/nimfa.examples.medulloblastoma.rst
diff --git a/docs/source/nimfa.examples.orl_images.rst → docs/nimfa.examples.orl_images.rst b/docs/source/nimfa.examples.orl_images.rst → docs/nimfa.examples.orl_images.rst
diff --git a/...source/nimfa.examples.recommendations.rst → docs/nimfa.examples.recommendations.rst b/...source/nimfa.examples.recommendations.rst → docs/nimfa.examples.recommendations.rst
diff --git a/docs/source/nimfa.examples.rst → docs/nimfa.examples.rst b/docs/source/nimfa.examples.rst → docs/nimfa.examples.rst
diff --git a/docs/source/nimfa.examples.synthetic.rst → docs/nimfa.examples.synthetic.rst b/docs/source/nimfa.examples.synthetic.rst → docs/nimfa.examples.synthetic.rst
diff --git a/...source/nimfa.methods.factorization.bd.rst → docs/nimfa.methods.factorization.bd.rst b/...source/nimfa.methods.factorization.bd.rst → docs/nimfa.methods.factorization.bd.rst
diff --git a/...ource/nimfa.methods.factorization.bmf.rst → docs/nimfa.methods.factorization.bmf.rst b/...ource/nimfa.methods.factorization.bmf.rst → docs/nimfa.methods.factorization.bmf.rst
diff --git a/...ource/nimfa.methods.factorization.icm.rst → docs/nimfa.methods.factorization.icm.rst b/...ource/nimfa.methods.factorization.icm.rst → docs/nimfa.methods.factorization.icm.rst
diff --git a/...rce/nimfa.methods.factorization.lfnmf.rst → docs/nimfa.methods.factorization.lfnmf.rst b/...rce/nimfa.methods.factorization.lfnmf.rst → docs/nimfa.methods.factorization.lfnmf.rst
diff --git a/...rce/nimfa.methods.factorization.lsnmf.rst → docs/nimfa.methods.factorization.lsnmf.rst b/...rce/nimfa.methods.factorization.lsnmf.rst → docs/nimfa.methods.factorization.lsnmf.rst
diff --git a/...ource/nimfa.methods.factorization.nmf.rst → docs/nimfa.methods.factorization.nmf.rst b/...ource/nimfa.methods.factorization.nmf.rst → docs/nimfa.methods.factorization.nmf.rst
diff --git a/...rce/nimfa.methods.factorization.nsnmf.rst → docs/nimfa.methods.factorization.nsnmf.rst b/...rce/nimfa.methods.factorization.nsnmf.rst → docs/nimfa.methods.factorization.nsnmf.rst
diff --git a/...ource/nimfa.methods.factorization.pmf.rst → docs/nimfa.methods.factorization.pmf.rst b/...ource/nimfa.methods.factorization.pmf.rst → docs/nimfa.methods.factorization.pmf.rst
diff --git a/...rce/nimfa.methods.factorization.pmfcc.rst → docs/nimfa.methods.factorization.pmfcc.rst b/...rce/nimfa.methods.factorization.pmfcc.rst → docs/nimfa.methods.factorization.pmfcc.rst
diff --git a/...urce/nimfa.methods.factorization.psmf.rst → docs/nimfa.methods.factorization.psmf.rst b/...urce/nimfa.methods.factorization.psmf.rst → docs/nimfa.methods.factorization.psmf.rst
diff --git a/docs/source/nimfa.methods.factorization.rst → docs/nimfa.methods.factorization.rst b/docs/source/nimfa.methods.factorization.rst → docs/nimfa.methods.factorization.rst
diff --git a/...ce/nimfa.methods.factorization.sepnmf.rst → docs/nimfa.methods.factorization.sepnmf.rst b/...ce/nimfa.methods.factorization.sepnmf.rst → docs/nimfa.methods.factorization.sepnmf.rst
diff --git a/...urce/nimfa.methods.factorization.snmf.rst → docs/nimfa.methods.factorization.snmf.rst b/...urce/nimfa.methods.factorization.snmf.rst → docs/nimfa.methods.factorization.snmf.rst
diff --git a/...ce/nimfa.methods.factorization.snmnmf.rst → docs/nimfa.methods.factorization.snmnmf.rst b/...ce/nimfa.methods.factorization.snmnmf.rst → docs/nimfa.methods.factorization.snmnmf.rst
diff --git a/docs/source/nimfa.methods.rst → docs/nimfa.methods.rst b/docs/source/nimfa.methods.rst → docs/nimfa.methods.rst
diff --git a/docs/source/nimfa.methods.seeding.fixed.rst → docs/nimfa.methods.seeding.fixed.rst b/docs/source/nimfa.methods.seeding.fixed.rst → docs/nimfa.methods.seeding.fixed.rst
diff --git a/docs/source/nimfa.methods.seeding.nndsvd.rst → docs/nimfa.methods.seeding.nndsvd.rst b/docs/source/nimfa.methods.seeding.nndsvd.rst → docs/nimfa.methods.seeding.nndsvd.rst
diff --git a/docs/source/nimfa.methods.seeding.random.rst → docs/nimfa.methods.seeding.random.rst b/docs/source/nimfa.methods.seeding.random.rst → docs/nimfa.methods.seeding.random.rst
diff --git a/...source/nimfa.methods.seeding.random_c.rst → docs/nimfa.methods.seeding.random_c.rst b/...source/nimfa.methods.seeding.random_c.rst → docs/nimfa.methods.seeding.random_c.rst
diff --git a/...rce/nimfa.methods.seeding.random_vcol.rst → docs/nimfa.methods.seeding.random_vcol.rst b/...rce/nimfa.methods.seeding.random_vcol.rst → docs/nimfa.methods.seeding.random_vcol.rst
diff --git a/docs/source/nimfa.methods.seeding.rst → docs/nimfa.methods.seeding.rst b/docs/source/nimfa.methods.seeding.rst → docs/nimfa.methods.seeding.rst
diff --git a/docs/source/nimfa.models.mf_fit.rst → docs/nimfa.models.mf_fit.rst b/docs/source/nimfa.models.mf_fit.rst → docs/nimfa.models.mf_fit.rst
diff --git a/docs/source/nimfa.models.mf_track.rst → docs/nimfa.models.mf_track.rst b/docs/source/nimfa.models.mf_track.rst → docs/nimfa.models.mf_track.rst
diff --git a/docs/source/nimfa.models.nmf.rst → docs/nimfa.models.nmf.rst b/docs/source/nimfa.models.nmf.rst → docs/nimfa.models.nmf.rst
diff --git a/docs/source/nimfa.models.nmf_mm.rst → docs/nimfa.models.nmf_mm.rst b/docs/source/nimfa.models.nmf_mm.rst → docs/nimfa.models.nmf_mm.rst
diff --git a/docs/source/nimfa.models.nmf_ns.rst → docs/nimfa.models.nmf_ns.rst b/docs/source/nimfa.models.nmf_ns.rst → docs/nimfa.models.nmf_ns.rst
diff --git a/docs/source/nimfa.models.nmf_std.rst → docs/nimfa.models.nmf_std.rst b/docs/source/nimfa.models.nmf_std.rst → docs/nimfa.models.nmf_std.rst
diff --git a/docs/source/nimfa.models.rst → docs/nimfa.models.rst b/docs/source/nimfa.models.rst → docs/nimfa.models.rst
diff --git a/docs/source/nimfa.models.smf.rst → docs/nimfa.models.smf.rst b/docs/source/nimfa.models.smf.rst → docs/nimfa.models.smf.rst
diff --git a/docs/source/nimfa.utils.linalg.rst → docs/nimfa.utils.linalg.rst b/docs/source/nimfa.utils.linalg.rst → docs/nimfa.utils.linalg.rst
diff --git a/docs/source/nimfa.utils.rst → docs/nimfa.utils.rst b/docs/source/nimfa.utils.rst → docs/nimfa.utils.rst
diff --git a/docs/source/nimfa.utils.utils.rst → docs/nimfa.utils.utils.rst b/docs/source/nimfa.utils.utils.rst → docs/nimfa.utils.utils.rst
diff --git a/nimfa/__init__.py b/nimfa/__init__.py
@@ -12,7 +12,7 @@
 """
 
 __license__ = 'BSD'
-__version__ = '1.3.2'
+__version__ = '1.3.4'
 __maintainer__ = 'Marinka Zitnik'
 __email__ = 'marinka@cs.stanford.edu'
 

diff --git a/setup.cfg b/setup.cfg
@@ -1,2 +1,5 @@
 [bdist_wheel]
 universal=1
+
+[metadata]
+description-file = README.md
diff --git a/setup.py b/setup.py
@@ -15,7 +15,7 @@
 KEYWORDS = ['matrix factorization', 'nonnegative matrix factorization',
             'bioinformatics', 'data mining', 'machine learning']
 LICENSE = 'BSD'
-VERSION = '1.3.2'
+VERSION = '1.3.4'
 ISRELEASED = True
 
 INSTALL_REQUIRES = (