MAINT make release 1.1 (#317)

* MAINT make release 1.1

* removed logo

* added long_description_content_type

* TST check manifest works

MANIFEST.in

@@ -24,3 +24,4 @@ recursive-exclude pyglmnet *.pyc
 
 recursive-exclude doc *
 recursive-exclude tests *.py
+exclude tests

README.rst

@@ -8,10 +8,6 @@ A python implementation of elastic-net regularized generalized linear models
 
 `[Documentation (stable version)]`_ `[Documentation (development version)]`_
 
-.. raw:: html
-
-    <img src="pyglmnet-logo.png" height="400px">
-
 `Generalized linear
 models <https://en.wikipedia.org/wiki/Generalized_linear_model>`__ are
 well-established tools for regression and classification and are widely

doc/whats_new.rst

@@ -1,15 +1,17 @@
-:orphan:
-
 .. include:: links.inc
 
 .. _whats_new:
 
 .. currentmodule:: pyglmnet
 
-.. _current:
+=============
+Release notes
+=============
+
+.. _1_0_1:
 
-Current
--------
+Version 1.1
+-----------
 
 Changelog
 ~~~~~~~~~
@@ -19,23 +21,23 @@ Changelog
     - Add support for running :class:`sklearn.model_selection.GridSearchCV` on :class:`pyglmnet.GLM` objects by `Mainak Jas`_.
     - Improved testing of gradients for optimization by `Mainak Jas`_ and `Pavan Ramkumar`_.
     - Improved testing of estimated coefficients at convergence by `Mainak Jas`_ and `Pavan Ramkumar`_
-    - Add `n_iter_` attribute to :class:`pyglmnet.GLM` by `Mainak Jas`_, `Olivier Pieters`_, `Peter Foley`_ and `Chris Rogers`_
-    - Add option to fit intercept or not with a `fit_intercept` boolean by `Drew Harris`_, `Mainak Jas`_ and `Pavan Ramkumar`_
+    - Add ``n_iter_`` attribute to :class:`pyglmnet.GLM` by `Mainak Jas`_, `Olivier Pieters`_, `Peter Foley`_ and `Chris Rogers`_
+    - Add option to fit intercept or not with a ``fit_intercept`` boolean by `Drew Harris`_, `Mainak Jas`_ and `Pavan Ramkumar`_
 
 
 BUG
 ~~~
 
-    - Fixed z cache inconsistency in cdfast when alpha and reg_lambda are nonzero by `Peter Foley`_.
-    - Fixed incorrect usage of the random_state parameter by `Giovanni De Toni`_.
+    - Fixed z cache inconsistency in cdfast when ``alpha`` and ``reg_lambda`` are nonzero by `Peter Foley`_.
+    - Fixed incorrect usage of the ``random_state`` parameter by `Giovanni De Toni`_.
     - Fixed incorrect proximal operator for group lasso by `Yu Umegaki`_.
     - Changed stopping criteria for convergence (a threshold on the change in objective value) which
       stopped too early. The new criteria is a threshold on the change in norm of the beta, by `Pavan Ramkumar`_.
-    - Fixed `group` parameter not being passed for Group Lasso by `Beibin Li`_.
+    - Fixed ``group`` parameter not being passed for Group Lasso by `Beibin Li`_.
     - Fix URL paths when running on Windows by `Scott Otterson`_.
     - Made temporary file handling OS independent and usable on a cluster by `Scott Otterson`_.
-    - Replace `StratifiedKFold()` with `KFold()`, as `StratifiedKFold()` doesn't work for continuous values by `Scott Otterson`_.
-    - :func:`pyglmnet.simulate_glm` accepts `beta0` as float and `beta` of shape (n_features,) only, by `Mainak Jas`_
+    - Replace ``StratifiedKFold()`` with ``KFold()``, as ``StratifiedKFold()`` doesn't work for continuous values by `Scott Otterson`_.
+    - :func:`pyglmnet.simulate_glm` accepts ``beta0`` as float and ``beta`` of shape `(n_features,)` only, by `Mainak Jas`_
 
 API
 ~~~
@@ -46,10 +48,26 @@ API
     - Removed support for fitting `'multinomial'` distribution by `Pavan Ramkumar`_. This option will
       be restored in a future release.
 
-
-.. _changes_0_14:
-
-Version 0.1
+Authors
+~~~~~~~
+
+* Beibin Li
+* Chris Rodgers
+* Drew Harris
+* Giovanni De Toni
+* Mainak Jas
+* Mayank Agarawal
+* Olivier Pieters
+* Pavan Ramkumar
+* Peter Foley
+* Ravi Prakash Garg
+* Scott Otterson
+* Tommy Odland
+* Yu Umegaki
+
+.. _changes_1_0:
+
+Version 1.0
 -----------
 
 Changelog
@@ -62,6 +80,19 @@ Changelog
     - Add multinomial link function by `Daniel Acuna`_
     - Add benchmarks by `Vinicius Marques`_
 
+Authors
+~~~~~~~
+
+* Aid Idrizović
+* Daniel Acuna
+* Eva Dyer
+* Hugo Fernandes
+* Mainak Jas
+* Matt Antalek
+* Pavan Ramkumar
+* Titipat Achakulvisut
+* Vinicius Marques
+
 .. _Aid Idrizović: https://github.com/the872
 .. _Daniel Acuna: https://acuna.io/
 .. _Eva Dyer: http://evadyer.github.io/

pyglmnet/__init__.py

@@ -1,4 +1,4 @@
 from .pyglmnet import GLM, GLMCV, _grad_L2loss, _L2loss, simulate_glm, _gradhess_logloss_1d, _loss, ALLOWED_DISTRS
 from .utils import softmax, label_binarizer, set_log_level
 from .datasets import fetch_tikhonov_data
-__version__ = '1.0.1.dev0'
+__version__ = '1.1'

setup.py

@@ -23,6 +23,7 @@ def get_version():
 MAINTAINER = "Pavan Ramkumar"
 MAINTAINER_EMAIL = "[email protected]"
 LICENSE = "MIT"
+URL = 'http://glm-tools.github.io/pyglmnet/'
 DOWNLOAD_URL = "https://github.com/glm-tools/pyglmnet.git"
 VERSION = get_version()  # Get version without importing
 
@@ -33,9 +34,11 @@ def get_version():
         maintainer_email=MAINTAINER_EMAIL,
         description=DESCRIPTION,
         license=LICENSE,
+        url=URL,
         version=VERSION,
         download_url=DOWNLOAD_URL,
         long_description=open("README.rst").read(),
+        long_description_content_type='text/x-rst',
         classifiers=[
             "Intended Audience :: Science/Research",
             "Intended Audience :: Developers",
@@ -56,4 +59,9 @@ def get_version():
         ],
         platforms="any",
         packages=["pyglmnet"],
+        project_urls={
+            'Documentation': 'http://glm-tools.github.io/pyglmnet/',
+            'Bug Reports': 'https://github.com/glm-tools/pyglmnet/issues',
+            'Source': 'https://github.com/glm-tools/pyglmnet',
+        },
     )