Merge branch 'main' into refactor-nested-cross-validation

ipums · Dec 3, 2024 · 40f344e · 40f344e
2 parents b9c2123 + 37e3a57
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diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
@@ -1,6 +1,13 @@
 name: HLink Docker CI
 
-on: [pull_request, push]
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
 
 env:
   HLINK_TAG: hlink:githubactions
@@ -28,9 +35,6 @@ jobs:
     - name: Check formatting with black
       run: docker run $HLINK_TAG-${{ matrix.python_version}} black --check .
 
-    - name: Lint with flake8
-      run: docker run $HLINK_TAG-${{ matrix.python_version}} flake8 --count .
-
     - name: Test
       run: docker run $HLINK_TAG-${{ matrix.python_version}} pytest
 

diff --git a/doc/developer.md b/doc/developer.md
@@ -19,9 +19,23 @@ To set up a copy of this project for development,
 
 ## Running Tests
 
-To run the project's test suite, run `pytest` in the root project directory. Running all of the tests
-can take a while, depending on your computer's hardware and setup. To run a subset of tests that test some but not
-all of the core features, try `pytest -m quickcheck`. These tests should run much more quickly.
+To run the project's test suite, run `pytest` in the root project directory.
+Running all of the tests can take a while, depending on your computer's
+hardware and setup. If you are working on a particular bug or feature, there
+are several good ways to filter the tests to run just tests that interest you.
+Check out the pytest documentation
+[here](https://docs.pytest.org/en/latest/how-to/usage.html#specifying-which-tests-to-run).
+
+In particular, the `-k` argument is helpful for running only tests with names
+that match the topics you are interested in, like this:
+
+```
+pytest -k "lightgbm or xgboost"
+```
+
+The GitHub Actions workflow runs all of the tests on each push or PR to the
+main branch. It runs the tests on several versions of Python and in several
+different Python environments.
 
 ## Building the Scala Jar
 

diff --git a/docs/_sources/substitutions.md.txt b/docs/_sources/substitutions.md.txt
@@ -9,7 +9,11 @@ You must supply a substitution file and either specify `regex_word_replace=true`
 
 ## 1:1 substitution by data table
 
-Performs a 1:1 replacement on a filtered subset of the data table.  If the input column data equals a value in the first column of the substitution file, it is replaced with the data in the second column of the substitution file.  Used to replace variant name forms with standardized name forms, filtering on sex.
+Performs a 1:1 replacement on a filtered subset of the data table.  If the
+input column data equals a value in the second column of the substitution file,
+it is replaced with the data in the first column of the substitution file.
+Used to replace variant name forms with standardized name forms, filtering on
+a column like sex which may affect common names.
 
 * Attributes:
   * `join_column` -- Type: `string`.  Column to filter input data on.

diff --git a/docs/_static/alabaster.css b/docs/_static/alabaster.css
@@ -1,5 +1,3 @@
-@import url("basic.css");
-
 /* -- page layout ----------------------------------------------------------- */
 
 body {
@@ -160,8 +158,8 @@ div.sphinxsidebar input {
     font-size: 1em;
 }
 
-div.sphinxsidebar #searchbox input[type="text"] {
-    width: 160px;
+div.sphinxsidebar #searchbox {
+    margin: 1em 0;
 }
 
 div.sphinxsidebar .search > div {
@@ -263,10 +261,6 @@ div.admonition p.last {
     margin-bottom: 0;
 }
 
-div.highlight {
-    background-color: #fff;
-}
-
 dt:target, .highlight {
     background: #FAF3E8;
 }
@@ -454,7 +448,7 @@ ul, ol {
 }
 
 pre {
-    background: #EEE;
+    background: unset;
     padding: 7px 30px;
     margin: 15px 0px;
     line-height: 1.3em;
@@ -485,15 +479,15 @@ a.reference {
     border-bottom: 1px dotted #004B6B;
 }
 
+a.reference:hover {
+    border-bottom: 1px solid #6D4100;
+}
+
 /* Don't put an underline on images */
 a.image-reference, a.image-reference:hover {
     border-bottom: none;
 }
 
-a.reference:hover {
-    border-bottom: 1px solid #6D4100;
-}
-
 a.footnote-reference {
     text-decoration: none;
     font-size: 0.7em;
@@ -509,68 +503,7 @@ a:hover tt, a:hover code {
     background: #EEE;
 }
 
-
-@media screen and (max-width: 870px) {
-
-    div.sphinxsidebar {
-    	display: none;
-    }
-
-    div.document {
-       width: 100%;
-
-    }
-
-    div.documentwrapper {
-    	margin-left: 0;
-    	margin-top: 0;
-    	margin-right: 0;
-    	margin-bottom: 0;
-    }
-
-    div.bodywrapper {
-    	margin-top: 0;
-    	margin-right: 0;
-    	margin-bottom: 0;
-    	margin-left: 0;
-    }
-
-    ul {
-    	margin-left: 0;
-    }
-
-	li > ul {
-        /* Matches the 30px from the "ul, ol" selector above */
-		margin-left: 30px;
-	}
-
-    .document {
-    	width: auto;
-    }
-
-    .footer {
-    	width: auto;
-    }
-
-    .bodywrapper {
-    	margin: 0;
-    }
-
-    .footer {
-    	width: auto;
-    }
-
-    .github {
-        display: none;
-    }
-
-
-
-}
-
-
-
-@media screen and (max-width: 875px) {
+@media screen and (max-width: 940px) {
 
     body {
         margin: 0;
@@ -580,12 +513,16 @@ a:hover tt, a:hover code {
     div.documentwrapper {
         float: none;
         background: #fff;
+        margin-left: 0;
+        margin-top: 0;
+        margin-right: 0;
+        margin-bottom: 0;
     }
 
     div.sphinxsidebar {
         display: block;
         float: none;
-        width: 102.5%;
+        width: unset;
         margin: 50px -30px -20px -30px;
         padding: 10px 20px;
         background: #333;
@@ -620,8 +557,14 @@ a:hover tt, a:hover code {
 
     div.body {
         min-height: 0;
+        min-width: auto; /* fixes width on small screens, breaks .hll */
         padding: 0;
     }
+
+    .hll {
+        /* "fixes" the breakage */
+        width: max-content;
+    }
 
     .rtd_doc_footer {
         display: none;
@@ -635,13 +578,18 @@ a:hover tt, a:hover code {
         width: auto;
     }
 
-    .footer {
-        width: auto;
-    }
-
     .github {
         display: none;
     }
+
+    ul {
+        margin-left: 0;
+    }
+
+    li > ul {
+       /* Matches the 30px from the "ul, ol" selector above */
+        margin-left: 30px;
+    }
 }
 
 
@@ -705,4 +653,11 @@ nav#breadcrumbs li+li:before {
     div.related {
         display: none;
     }
+}
+
+img.github  {
+    position: absolute;
+    top: 0;
+    border: 0;
+    right: 0;
 }
diff --git a/docs/_static/github-banner.svg b/docs/_static/github-banner.svg
diff --git a/docs/column_mappings.html b/docs/column_mappings.html
@@ -7,7 +7,8 @@
 
     <title>Column Mappings &#8212; hlink 3.7.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
+    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=686e5160" />
+    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=27fed22d" />
     <script src="_static/documentation_options.js?v=229cbe3b"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
@@ -369,7 +370,16 @@ <h1 class="logo"><a href="index.html">hlink</a></h1>
 
 
 
-<h3>Navigation</h3>
+
+<search id="searchbox" style="display: none" role="search">
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
@@ -403,16 +413,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<search id="searchbox" style="display: none" role="search">
-  <h3 id="searchlabel">Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
-      <input type="submit" value="Go" />
-    </form>
-    </div>
-</search>
-<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -430,7 +430,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
       |
       <a href="_sources/column_mappings.md.txt"

diff --git a/docs/comparison_features.html b/docs/comparison_features.html
@@ -7,7 +7,8 @@
 
     <title>Comparison Features &#8212; hlink 3.7.0 documentation</title>
     <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=d1102ebc" />
-    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=12dfc556" />
+    <link rel="stylesheet" type="text/css" href="_static/basic.css?v=686e5160" />
+    <link rel="stylesheet" type="text/css" href="_static/alabaster.css?v=27fed22d" />
     <script src="_static/documentation_options.js?v=229cbe3b"></script>
     <script src="_static/doctools.js?v=9bcbadda"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
@@ -1267,7 +1268,16 @@ <h1 class="logo"><a href="index.html">hlink</a></h1>
 
 
 
-<h3>Navigation</h3>
+
+<search id="searchbox" style="display: none" role="search">
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false" placeholder="Search"/>
+      <input type="submit" value="Go" />
+    </form>
+    </div>
+</search>
+<script>document.getElementById('searchbox').style.display = "block"</script><h3>Navigation</h3>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="introduction.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
@@ -1302,16 +1312,6 @@ <h3>Related Topics</h3>
   </ul></li>
 </ul>
 </div>
-<search id="searchbox" style="display: none" role="search">
-  <h3 id="searchlabel">Quick search</h3>
-    <div class="searchformwrapper">
-    <form class="search" action="search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
-      <input type="submit" value="Go" />
-    </form>
-    </div>
-</search>
-<script>document.getElementById('searchbox').style.display = "block"</script>
 
 
 
@@ -1329,7 +1329,7 @@ <h3 id="searchlabel">Quick search</h3>
 
       |
       Powered by <a href="https://www.sphinx-doc.org/">Sphinx 8.1.3</a>
-      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 0.7.16</a>
+      &amp; <a href="https://alabaster.readthedocs.io">Alabaster 1.0.0</a>
 
       |
       <a href="_sources/comparison_features.md.txt"