Modernized some links

docs/api/index.rst

@@ -146,8 +146,7 @@ Read 10x formatted hdf5 files using
 
    read_10x_h5
 
-Read other formats using functions borrowed from `anndata
-<http://anndata.readthedocs.io>`_
+Read other formats using functions borrowed from :mod:`anndata`
 
 .. autosummary::
    :toctree: .

docs/basic_usage.rst

@@ -25,8 +25,7 @@ To facilitate writing memory-efficient pipelines, by default, Scanpy tools opera
 AnnData
 ^^^^^^^
 
-Scanpy is based on `anndata <http://anndata.readthedocs.io>`_, which provides
-the :class:`~anndata.AnnData` class.
+Scanpy is based on :mod:`anndata`, which provides the :class:`~anndata.AnnData` class.
 
 .. raw:: html
 

docs/installation.rst

@@ -7,7 +7,7 @@ Running the following installs most of the requirements::
 
    conda install seaborn scikit-learn statsmodels numba
 
-Pull Scanpy from `PyPI <https://pypi.python.org/pypi/scanpy>`__ (consider using ``pip3`` to access Python 3)::
+Pull Scanpy from `PyPI <https://pypi.org/project/scanpy>`__ (consider using ``pip3`` to access Python 3)::
 
   pip install scanpy
 
@@ -31,7 +31,7 @@ If you're using Docker_, you can use the minimal `fastgenomics/scanpy`_ image fr
 
 .. _Docker: https://en.wikipedia.org/wiki/Docker_(software)
 .. _fastgenomics/scanpy: https://hub.docker.com/r/fastgenomics/scanpy
-  
+
 Trouble shooting
 ~~~~~~~~~~~~~~~~
 
@@ -45,12 +45,12 @@ If you do not have sudo rights (you get a ``Permission denied`` error)::
 - If python-igraph still fails to install, see `here <https://stackoverflow.com/questions/29589696/problems-compiling-c-core-of-igraph-with-python-2-7-9-anaconda-2-2-0-on-mac-osx>`__ or consider installing gcc via ``brew install gcc --without-multilib`` and exporting ``export CC="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"; export CXX="/usr/local/Cellar/gcc/X.x.x/bin/gcc-X"``, where ``X`` and ``x`` refers to the version of ``gcc``; in my case, the path reads ``/usr/local/Cellar/gcc/6.3.0_1/bin/gcc-6``.
 
 **On Windows**, you can follow these steps::
-  
+
     conda install pandas cython
     conda install -c vtraag python-igraph
     conda install -c vtraag louvain
     pip install scanpy
-      
+
 
 Installing Miniconda
 ~~~~~~~~~~~~~~~~~~~~

docs/release_notes.rst

@@ -1,6 +1,6 @@
 .. note::
 
-    Also see the release notes of `anndata <http://anndata.readthedocs.org>`_.
+    Also see the :ref:`release notes <anndata:release_notes>` of :mod:`anndata`.
 
 .. role:: small
 
@@ -141,7 +141,7 @@ Version 0.4.4 :small:`February 26, 2018`
    <https://seaborn.pydata.org/generated/seaborn.clustermap.html>`_ [Waskom16]_
 2. only return `matplotlib.Axis` in plotting functions of ``sc.pl`` when `show=False`, otherwise `None`
 
-... and through `anndata v0.5 <http://anndata.readthedocs.io>`_
+... and through :mod:`anndata` v0.5.
 
 1. inform about duplicates in :class:`~anndata.AnnData.var_names` and resolve them using :func:`~anndata.AnnData.var_names_make_unique`
 2. by default, generate unique observation names in :func:`~anndata.AnnData.concatenate`
@@ -162,7 +162,7 @@ Version 0.4.4 :small:`February 26, 2018`
    <https://github.com/theislab/scanpy_usage/tree/master/171111_SPRING_export>`_,
    `docs <https://scanpy.readthedocs.io/en/latest/api/index.html>`_
 
-... and through `anndata v0.4 <http://anndata.readthedocs.io>`_
+... and through :mod:`anndata` v0.4.
 
 1. towards a common file format for exchanging :class:`~anndata.AnnData` with
    packages such as Seurat and SCDE by reading and writing `.loom
@@ -184,11 +184,10 @@ Version 0.4.4 :small:`February 26, 2018`
 
 **November 16, 2017**: version 0.3
 
-1. :class:`~anndata.AnnData` can be `concatenated <https://anndata.readthedocs.io/en/latest/anndata.AnnData.html>`_
-2. :class:`~anndata.AnnData` is available as a `separate package <https://pypi.python.org/pypi/anndata/>`_
+1. :class:`~anndata.AnnData` can be :meth:`~anndata.AnnData.concatenate` d.
+2. :class:`~anndata.AnnData` is available as a `separate package <https://pypi.org/project/anndata/>`_
 3. results of approximate graph abstraction (AGA) are `simplified <https://github.com/theislab/graph_abstraction>`_
 
-
 **October 25, 2017**: version 0.2.9
 
 Initial release of `approximate graph abstraction (AGA) <https://github.com/theislab/graph_abstraction>`_.

versioneer.py

@@ -271,7 +271,7 @@
 https://creativecommons.org/publicdomain/zero/1.0/ .
 
 [pypi-image]: https://img.shields.io/pypi/v/versioneer.svg
-[pypi-url]: https://pypi.python.org/pypi/versioneer/
+[pypi-url]: https://pypi.org/project/versioneer/
 [travis-image]:
 https://img.shields.io/travis/warner/python-versioneer/master.svg
 [travis-url]: https://travis-ci.org/warner/python-versioneer