Merge pull request #201 from wellcometrust/release-2021.2.0

Release 2021.2.0

CHANGELOG.md

@@ -1,4 +1,16 @@
-# 2021.01.1
+# 2021.2.0
+
+Major changes
+---
+- Upgrade spacy to v3.0
+- Add native HuggingFace support (#191), re-writting `BertClassifier` using transformers
+- Disables HDBscan from the possible clustering techniques due to a conflict with the new numpy version (#197)
+
+Bug fixes
+---
+- Resolves issues #195 and #198 with thew pip reference resolver, introduced in pip>20.3
+
+# 2021.1.1
 
 Major changes
 ---

README.md

@@ -76,24 +76,22 @@ Verify that `_build/html/index.html` has generated correctly and submit a PR.
 
 ### 2.3 Release a new version (and upload to aws s3/pypi/github)
 
+First create a [github token](https://help.github.com/en/github/authenticating-to-github/creating-a
+-personal-access-token-for-the-command-line), if you haven't one, with artifact write access and
+ export
+ it to the env variables:
+```bash
+export GITHUB_TOKEN=...
+```
+
 The checklist for a new release is:
 
-- [ ] Changed `wellcomeml/__version__.py`
+- [ ] Change `wellcomeml/__version__.py`
 - [ ] Add changelog
 - [ ] `make dist`
-- [ ] Verify new package was generated correctly on the [pip registry](https://pypi.org/project
-/wellcomeml)
-/] and GitHub releases 
-
-Create a [github token](https://help.github.com/en/github/authenticating-to-github/creating-a-personal-access-token-for-the-command-line) with artifact write access and export it to the env variables:
-```bash
-export GITHUB_TOKEN=...
-```
-After making changes, in order to build a new release, run:
+- [ ] Verify new package was generated correctly on the [pip registry](https://pypi.org/project/wellcomeml)
+ and GitHub releases 
 
-```
-make dist
-```
 
 ### 2.4 (Optional) Installing from other locations
 

docs/_build/html/examples.html

@@ -192,7 +192,7 @@ <h2>Bert and Scibert Vectorisers<a class="headerlink" href="#bert-and-scibert-ve
 <div class="section" id="bert-and-scibert-classifiers">
 <h2>Bert and Scibert Classifiers<a class="headerlink" href="#bert-and-scibert-classifiers" title="Permalink to this headline">¶</a></h2>
 <p>The same way as the bert vectorisers, one can use a wrapper to train a text classifier using bert or scibert as base,
-using a <code class="xref py py-class docutils literal notranslate"><span class="pre">BertClassifier</span></code></p>
+using a <a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.bert_classifier" title="wellcomeml.ml.bert_classifier"><code class="xref py py-class docutils literal notranslate"><span class="pre">BertClassifier</span></code></a></p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
 <span class="kn">from</span> <span class="nn">wellcomeml.ml</span> <span class="kn">import</span> <span class="n">BertClassifier</span>
@@ -259,7 +259,7 @@ <h2>Train a Spacy NER model<a class="headerlink" href="#train-a-spacy-ner-model"
 </div>
 <div class="section" id="entity-linking">
 <h2>Entity Linking<a class="headerlink" href="#entity-linking" title="Permalink to this headline">¶</a></h2>
-<p>Link sentences to the most similar document in a corpus using <code class="xref py py-class docutils literal notranslate"><span class="pre">SimilarityEntityLinker</span></code>.</p>
+<p>Link sentences to the most similar document in a corpus using <a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.similarity_entity_linking" title="wellcomeml.ml.similarity_entity_linking"><code class="xref py py-class docutils literal notranslate"><span class="pre">SimilarityEntityLinker</span></code></a>.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">wellcomeml.ml</span> <span class="kn">import</span> <span class="n">SimilarityEntityLinker</span>
 
 <span class="n">entities_kb</span> <span class="o">=</span> <span class="p">{</span>

docs/_build/html/py-modindex.html

@@ -242,6 +242,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="wellcomeml.ml.html#module-wellcomeml.ml.attention"><code class="xref">wellcomeml.ml.attention</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="wellcomeml.ml.html#module-wellcomeml.ml.bert_classifier"><code class="xref">wellcomeml.ml.bert_classifier</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -297,6 +302,11 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="wellcomeml.ml.html#module-wellcomeml.ml.sent2vec_vectorizer"><code class="xref">wellcomeml.ml.sent2vec_vectorizer</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="wellcomeml.ml.html#module-wellcomeml.ml.similarity_entity_linking"><code class="xref">wellcomeml.ml.similarity_entity_linking</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;

docs/_build/html/wellcomeml.html

@@ -205,7 +205,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l1"><a class="reference internal" href="wellcomeml.ml.html">wellcomeml.ml package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#submodules">Submodules</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.attention">wellcomeml.ml.attention module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#wellcomeml-ml-bert-classifier-module">wellcomeml.ml.bert_classifier module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.bert_classifier">wellcomeml.ml.bert_classifier module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.bert_semantic_equivalence">wellcomeml.ml.bert_semantic_equivalence module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.bert_vectorizer">wellcomeml.ml.bert_vectorizer module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.bilstm">wellcomeml.ml.bilstm module</a></li>
@@ -217,7 +217,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.keras_utils">wellcomeml.ml.keras_utils module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.keras_vectorizer">wellcomeml.ml.keras_vectorizer module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.sent2vec_vectorizer">wellcomeml.ml.sent2vec_vectorizer module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#wellcomeml-ml-similarity-entity-linking-module">wellcomeml.ml.similarity_entity_linking module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.similarity_entity_linking">wellcomeml.ml.similarity_entity_linking module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.spacy_classifier">wellcomeml.ml.spacy_classifier module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.spacy_entity_linking">wellcomeml.ml.spacy_entity_linking module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="wellcomeml.ml.html#module-wellcomeml.ml.spacy_knowledge_base">wellcomeml.ml.spacy_knowledge_base module</a></li>