Merge pull request c-hofer#24 from c-hofer/iss_23

Iss 23

README.md

@@ -1,18 +1,16 @@
-# chofer_torchex
+# torchph
 
-In this repository I gather my extensions to [PyTorch](http://pytorch.org). 
-The packaging structure tries to reproduce PyTorch's structure in order 
-to facilitate usage for people familiar with PyTorch. 
+This repository contains [PyTorch](http://pytorch.org) extensions to compute
+persistent homology and to differentiate through the persistent homology computation.
+The packaging structure is similar to PyTorch's structure to facilitate usage for people familiar with PyTorch. 
 
 ## Documentation
 
-[Read the docs!](https://c-hofer.github.io/chofer_torchex/)
+[Read the docs!](https://c-hofer.github.io/torchph/)
 
 The folder *tutorials* contains some minimalistic examples in form of Jupyter notebooks
 to demonstrate how to use the `PyTorch` extensions. 
 
-**Note**: For most up-to-date implementations and documentation, checkout the `pershom_devel` branch.
-
 ## Associated publications
 
 If you use any of these extensions, please cite the following works (depending on which functionality you use, obviously :)

docs/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: cf62a3f08efb3a388e373f6c5034a364
+config: 54af9f4344c5084308a0935f67140759
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/_modules/index.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Overview: module code &mdash; chofer_torchex 0.0.1 documentation</title>
+  <title>Overview: module code &mdash; torchph 0.0.0 documentation</title>
 
 
 
@@ -51,7 +51,7 @@
 
 
 
-            <a href="../index.html" class="icon icon-home"> chofer_torchex
+            <a href="../index.html" class="icon icon-home"> torchph
 
 
 
@@ -110,7 +110,7 @@
       <nav class="wy-nav-top" aria-label="top navigation">
 
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../index.html">chofer_torchex</a>
+          <a href="../index.html">torchph</a>
 
       </nav>
 
@@ -157,8 +157,8 @@
            <div itemprop="articleBody">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="chofer_torchex/nn/slayer.html">chofer_torchex.nn.slayer</a></li>
-<li><a href="chofer_torchex/pershom/pershom_backend.html">chofer_torchex.pershom.pershom_backend</a></li>
+<ul><li><a href="torchph/nn/slayer.html">torchph.nn.slayer</a></li>
+<li><a href="torchph/pershom/pershom_backend.html">torchph.pershom.pershom_backend</a></li>
 </ul>
 
            </div>
@@ -171,7 +171,7 @@ <h1>All modules for which code is available</h1>
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2019, Christoph D. Hofer, Roland Kwitt
+        &copy; Copyright 2020, Christoph D. Hofer, Roland Kwitt
 
     </p>
   </div>

docs/_modules/chofer_torchex/pershom/pershom_backend.html → docs/_modules/torchph/pershom/pershom_backend.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>chofer_torchex.pershom.pershom_backend &mdash; chofer_torchex 0.0.1 documentation</title>
+  <title>torchph.pershom.pershom_backend &mdash; torchph 0.0.0 documentation</title>
 
 
 
@@ -51,7 +51,7 @@
 
 
 
-            <a href="../../../index.html" class="icon icon-home"> chofer_torchex
+            <a href="../../../index.html" class="icon icon-home"> torchph
 
 
 
@@ -110,7 +110,7 @@
       <nav class="wy-nav-top" aria-label="top navigation">
 
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../../../index.html">chofer_torchex</a>
+          <a href="../../../index.html">torchph</a>
 
       </nav>
 
@@ -143,7 +143,7 @@
 
           <li><a href="../../index.html">Module code</a> &raquo;</li>
 
-      <li>chofer_torchex.pershom.pershom_backend</li>
+      <li>torchph.pershom.pershom_backend</li>
 
 
       <li class="wy-breadcrumbs-aside">
@@ -158,7 +158,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highlight"><pre>
+  <h1>Source code for torchph.pershom.pershom_backend</h1><div class="highlight"><pre>
 <span></span><span class="sa">r</span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">This module exposes the C++/CUDA backend functionality for Python.</span>
 
@@ -262,7 +262,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
         <span class="k">return</span> <span class="n">raise_error</span>
 
 
-<div class="viewcode-block" id="find_merge_pairings"><a class="viewcode-back" href="../../../pershom.html#chofer_torchex.pershom.pershom_backend.find_merge_pairings">[docs]</a><span class="k">def</span> <span class="nf">find_merge_pairings</span><span class="p">(</span>
+<div class="viewcode-block" id="find_merge_pairings"><a class="viewcode-back" href="../../../pershom.html#torchph.pershom.pershom_backend.find_merge_pairings">[docs]</a><span class="k">def</span> <span class="nf">find_merge_pairings</span><span class="p">(</span>
         <span class="n">pivots</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">max_pairs</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Tensor</span><span class="p">:</span>
@@ -288,7 +288,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
     <span class="k">return</span> <span class="n">__C</span><span class="o">.</span><span class="n">CalcPersCuda__find_merge_pairings</span><span class="p">(</span><span class="n">pivots</span><span class="p">,</span> <span class="n">max_pairs</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="merge_columns_"><a class="viewcode-back" href="../../../pershom.html#chofer_torchex.pershom.pershom_backend.merge_columns_">[docs]</a><span class="k">def</span> <span class="nf">merge_columns_</span><span class="p">(</span>
+<div class="viewcode-block" id="merge_columns_"><a class="viewcode-back" href="../../../pershom.html#torchph.pershom.pershom_backend.merge_columns_">[docs]</a><span class="k">def</span> <span class="nf">merge_columns_</span><span class="p">(</span>
         <span class="n">compr_desc_sort_ba</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">merge_pairs</span><span class="p">:</span> <span class="n">Tensor</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
@@ -308,7 +308,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
     <span class="n">__C</span><span class="o">.</span><span class="n">CalcPersCuda__merge_columns_</span><span class="p">(</span><span class="n">compr_desc_sort_ba</span><span class="p">,</span> <span class="n">merge_pairs</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="read_barcodes"><a class="viewcode-back" href="../../../pershom.html#chofer_torchex.pershom.pershom_backend.read_barcodes">[docs]</a><span class="k">def</span> <span class="nf">read_barcodes</span><span class="p">(</span>
+<div class="viewcode-block" id="read_barcodes"><a class="viewcode-back" href="../../../pershom.html#torchph.pershom.pershom_backend.read_barcodes">[docs]</a><span class="k">def</span> <span class="nf">read_barcodes</span><span class="p">(</span>
         <span class="n">pivots</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">simplex_dimension</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">max_dim_to_read_of_reduced_ba</span><span class="p">:</span> <span class="nb">int</span>
@@ -340,7 +340,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
         <span class="n">max_dim_to_read_of_reduced_ba</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="calculate_persistence"><a class="viewcode-back" href="../../../pershom.html#chofer_torchex.pershom.pershom_backend.calculate_persistence">[docs]</a><span class="k">def</span> <span class="nf">calculate_persistence</span><span class="p">(</span>
+<div class="viewcode-block" id="calculate_persistence"><a class="viewcode-back" href="../../../pershom.html#torchph.pershom.pershom_backend.calculate_persistence">[docs]</a><span class="k">def</span> <span class="nf">calculate_persistence</span><span class="p">(</span>
         <span class="n">compr_desc_sort_ba</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">ba_row_i_to_bm_col_i</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">simplex_dimension</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
@@ -383,7 +383,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
         <span class="n">max_pairs</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="vr_persistence_l1"><a class="viewcode-back" href="../../../pershom.html#chofer_torchex.pershom.pershom_backend.vr_persistence_l1">[docs]</a><span class="k">def</span> <span class="nf">vr_persistence_l1</span><span class="p">(</span>
+<div class="viewcode-block" id="vr_persistence_l1"><a class="viewcode-back" href="../../../pershom.html#torchph.pershom.pershom_backend.vr_persistence_l1">[docs]</a><span class="k">def</span> <span class="nf">vr_persistence_l1</span><span class="p">(</span>
         <span class="n">point_cloud</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">max_dimension</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
         <span class="n">max_ball_diameter</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.0</span>
@@ -416,7 +416,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
         <span class="n">max_ball_diameter</span><span class="p">)</span></div>
 
 
-<div class="viewcode-block" id="vr_persistence"><a class="viewcode-back" href="../../../pershom.html#chofer_torchex.pershom.pershom_backend.vr_persistence">[docs]</a><span class="k">def</span> <span class="nf">vr_persistence</span><span class="p">(</span>
+<div class="viewcode-block" id="vr_persistence"><a class="viewcode-back" href="../../../pershom.html#torchph.pershom.pershom_backend.vr_persistence">[docs]</a><span class="k">def</span> <span class="nf">vr_persistence</span><span class="p">(</span>
         <span class="n">distance_matrix</span><span class="p">:</span> <span class="n">Tensor</span><span class="p">,</span>
         <span class="n">max_dimension</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
         <span class="n">max_ball_diameter</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.0</span>
@@ -463,7 +463,7 @@ <h1>Source code for chofer_torchex.pershom.pershom_backend</h1><div class="highl
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2019, Christoph D. Hofer, Roland Kwitt
+        &copy; Copyright 2020, Christoph D. Hofer, Roland Kwitt
 
     </p>
   </div>

docs/_sources/index.rst.txt

@@ -1,4 +1,4 @@
-.. chofer_torchex documentation master file, created by
+.. torchph documentation master file, created by
    sphinx-quickstart on Mon Feb  4 13:39:08 2019.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
@@ -51,7 +51,7 @@ Get started
 
    install/index
 
-Follow the :doc:`instructions<install/index>` to install ``chofer_torchex``.
+Follow the :doc:`instructions<install/index>` to install ``torchph``.
 
 Functionality
 =============
@@ -74,7 +74,7 @@ samples and (2) doing the same using a pre-computed distance matrix.
     import numpy as np
 
     # import VR persistence computation functionality
-    from chofer_torchex.pershom import vr_persistence_l1, vr_persistence
+    from torchph.pershom import vr_persistence_l1, vr_persistence
 
     # import scipy methods to compute pairwise distance matrices
     from scipy.spatial.distance import pdist

docs/_sources/install/index.rst.txt

@@ -30,20 +30,20 @@ Second, we install PyTorch (v1.4) using
     conda install pytorch torchvision cudatoolkit=10.1 -c pytorch
 
 
-Third, we clone the ``chofer_torchex`` repository from GitHub and make
+Third, we clone the ``torchph`` repository from GitHub and make
 it available within Anaconda.
 
 .. code-block:: bash
 
     cd /tmp/
-    git clone https://github.com/c-hofer/chofer_torchex.git
-    conda develop /tmp/chofer_torchex
+    git clone https://github.com/c-hofer/torchph.git
+    conda develop /tmp/torchph
 
 A quick check if everything works can be done with
 
 .. code-block:: python
 
-    >>> import chofer_torchex
+    >>> import torchph
 
 .. note::
 

docs/_sources/nn.rst.txt

@@ -1,5 +1,5 @@
 ``nn`` 
 ======
 
-.. automodule:: chofer_torchex.nn.slayer
+.. automodule:: torchph.nn.slayer
    :members:

docs/_sources/pershom.rst.txt

@@ -1,5 +1,5 @@
 ``pershom``
 ===========
 
-.. automodule:: chofer_torchex.pershom.pershom_backend
+.. automodule:: torchph.pershom.pershom_backend
    :members: