Merge pull request #182 from hyanwong/doc-URL-corrections

Replace most refs to msprime to refer to tskit

Author: jeromekelleher

docs/file_formats.rst

@@ -42,12 +42,12 @@ Tree sequences
 
 The goal of ``tsinfer`` is to infer correlated genealogies from variation
 data, and it uses the very efficient `succinct tree sequence
-<http://msprime.readthedocs.io/en/stable/interchange.html>`_ data structure
-to encode this output. Please see the `msprime documentation
-<http://msprime.readthedocs.io/en/stable>`_ for details on how to
+<https://tskit.readthedocs.io/en/latest/data-model.html>`_ data structure
+to encode this output. Please see the `tskit documentation
+<https://tskit.readthedocs.io/>`_ for details on how to
 process and manipulate such tree sequences.
 
 The intermediate ``.ancestors.trees`` file produced by the
 :ref:`sec_inference_match_ancestors` step is also a
 tree sequence and can be loaded and analysed using the
-`msprime API <http://msprime.readthedocs.io/en/stable/api.html>`_.
+`tskit API <https://tskit.readthedocs.io/en/latest/python-api.html>`_.

docs/inference.rst

@@ -36,13 +36,12 @@ Data model
 **********
 
 The data model for ``tsinfer`` is tightly integrated with
-``msprime``'s `data model <https://msprime.readthedocs.io/en/stable/interchange.html>`_
+``tskit``'s `data model <https://tskit.readthedocs.io/en/latest/data-model.html>`_
 and uses the same concepts throughout. The intermediate file formats and APIs
 described here provide a bridge between this model and existing data sources. For
 convenience, we provide a brief description of concepts needed for importing
-data into ``tsinfer`` here. Please see the `msprime documentation
-<https://msprime.readthedocs.io/en/stable/index.html>`_ for more detailed
-information.
+data into ``tsinfer`` here. Please see the `tskit documentation
+<https://tskit.readthedocs.io/>`_ for more detailed information.
 
 .. _sec_inference_data_model_individual:
 
@@ -167,8 +166,9 @@ number of recombination events.
 The copying path for each ancestor then describes its ancestry at every
 point in the sequence: from a genealogical perspective, we know its
 parent node. This information is encoded precisely as an `edge
-<http://msprime.readthedocs.io/en/stable/interchange.html#edge-table>`_ in a
-`tree sequence <http://msprime.readthedocs.io/en/stable/interchange.html#data-model>`_.
+<https://tskit.readthedocs.io/en/latest/data-model.html#edge-table>`_ in a
+`tree sequence
+<https://tskit.readthedocs.io/en/latest/data-model.html>`_.
 Thus, we refer to the output of this step as the "ancestors tree sequence",
 which is conventionally stored in a file ending with ``.ancestors.trees``.
 
@@ -200,7 +200,7 @@ The final phase of a ``tsinfer`` inference consists of a number steps:
 
 3. Reduce the resulting tree sequence to a canonical form by
    `simplifying it
-   <http://msprime.readthedocs.io/en/stable/api.html#msprime.TreeSequence.simplify>`_.
+   <https://tskit.readthedocs.io/en/latest/python-api.html#tskit.TreeSequence.simplify>`_.
 
 .. todo::
     1. Describe path compression here and above in the ancestors

docs/installation.rst

@@ -14,10 +14,6 @@ e.g.::
 
 will install ``tsinfer`` to the Python installation corresponding to your
 ``python3`` executable. All requirements should be installed automatically.
-However, there are situations (usually where the GSL libraries are not in the default
-locations) where ``msprime`` installation can fail. Please the
-`msprime installation documentation <https://msprime.readthedocs.io/en/stable/installation.html>`_
-for details on the various to address this problem.
 
 To run the command line interface to ``tsinfer`` you can then use::
 
@@ -36,3 +32,19 @@ first using `venv <https://docs.python.org/3/library/venv.html>`_::
     $ source tsinfer-venv/bin/activate
     (tsinfer-venv) $ pip install tsinfer
     (tsinfer-venv) $ tsinfer --help
+
+.. _sec_installation_installation_problems:
+
+****************
+Potential issues
+****************
+
+One of the dependencies of ``tsinfer``,
+`numcodecs <https://numcodecs.readthedocs.io/>`_, is compiled to
+use AVX2 instructions (where available) when installed using pip. This can lead to
+issues when ``numcodecs`` is compiled on a machine that supports AVX2
+and subsequently run on older machines that do not. To resolve this, ``numcodecs`` has a
+``DISABLE_NUMCODECS_AVX2`` variable which can be turned on before calling
+``pip install``, see
+`these instructions <https://numcodecs.readthedocs.io/en/stable/#installation>`_
+for details.

docs/introduction.rst

@@ -17,6 +17,6 @@ make two very important gains:
    storing and processing the data that we have.
 
 The output of ``tsinfer`` is an :class:`msprime.TreeSequence` and so the
-full `msprime API <https://msprime.readthedocs.io/>`_ can be used to
-analyse real data, in precisely the same way that it is currently used
-to analyse simulation data.
+full `tskit API <https://tskit.readthedocs.io>`_ can be used to
+analyse real data, in precisely the same way that it is commonly used
+to analyse simulation data, for example, from `msprime <https://msprime.readthedocs.io/>`_.