diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index 4e42786..47021fc 100644
--- 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
index 1893703..3d82d96 100644
--- 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
index 93c9947..eb76c45 100644
--- 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
index e3174bf..7e75bf8 100644
--- 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;
}
\ No newline at end of file
diff --git a/docs/_static/github-banner.svg b/docs/_static/github-banner.svg
new file mode 100644
index 0000000..c47d9dc
--- /dev/null
+++ b/docs/_static/github-banner.svg
@@ -0,0 +1,5 @@
+
+
diff --git a/docs/column_mappings.html b/docs/column_mappings.html
index 623d185..c191199 100644
--- a/docs/column_mappings.html
+++ b/docs/column_mappings.html
@@ -7,7 +7,8 @@
Column Mappings — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -430,7 +430,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Comparison Features — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -1329,7 +1329,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Comparisons — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -225,7 +225,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Configuration — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -986,7 +986,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Feature Selection Transforms — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -248,7 +248,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Index — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -106,7 +106,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
diff --git a/docs/index.html b/docs/index.html
index fa2a68c..4d8f405 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -7,7 +7,8 @@
Welcome to hlink’s documentation! — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -211,7 +211,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Installation — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -136,7 +136,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Introduction — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -148,7 +148,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Link Tasks — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -301,7 +301,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Models — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -212,7 +212,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Pipeline generated features — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -158,7 +158,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Running hlink — hlink 3.7.0 documentation
Navigation
+
+
+
+
+
+
+Navigation
-
- Quick search
-
-
-
-
-
@@ -345,7 +345,7 @@ Quick search
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
|
Search — hlink 3.7.0 documentation
Related Topics
|
Powered by Sphinx 8.1.3
- & Alabaster 0.7.16
+ & Alabaster 1.0.0
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 149159e..01a8b75 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"1:1 substitution by data table": [[12, "substitution-by-data-table"]], "Advanced Config File": [[3, "advanced-config-file"]], "Advanced Usage": [[0, "advanced-usage"]], "Advanced Workflow Examples": [[13, null]], "Aggregate Features": [[1, "aggregate-features"]], "Basic Config File": [[3, "basic-config-file"]], "Basic Usage": [[0, "basic-usage"]], "Blocking": [[3, "blocking"]], "Column Mappings": [[0, null], [3, "column-mappings"]], "Comparison Features": [[1, null], [3, "comparison-features"]], "Comparison Types": [[1, "comparison-types"], [2, "comparison-types"]], "Comparisons": [[2, null], [3, "comparisons"]], "Configuration": [[3, null]], "Configuration API": [[5, "configuration-api"], [5, null]], "Data sources": [[3, "data-sources"]], "Defining Multiple Comparisons": [[2, "defining-multiple-comparisons"]], "Example interactive mode workflow": [[11, "example-interactive-mode-workflow"]], "Example model exploration and FP/FN export workflow": [[13, "example-model-exploration-and-fp-fn-export-workflow"]], "Example training data export with generated ML features": [[13, "example-training-data-export-with-generated-ml-features"]], "Export training data after generating features to reuse in different linking years": [[13, "export-training-data-after-generating-features-to-reuse-in-different-linking-years"]], "Feature Selection Transforms": [[4, null]], "Feature Selections": [[3, "feature-selections"]], "Feature add-ons": [[1, "feature-add-ons"]], "Filter": [[3, "filter"]], "Household Aggregate Features": [[1, "household-aggregate-features"]], "Household Comparisons": [[3, "household-comparisons"]], "Household Matching": [[8, "household-matching"]], "Household training and models": [[3, "household-training-and-models"]], "Installation": [[6, null]], "Installing from PyPI": [[6, "installing-from-pypi"]], "Installing from source": [[6, "installing-from-source"]], "Interactive Mode": [[11, "interactive-mode"]], "Introduction": [[7, null]], "Link Tasks": [[8, null]], "ML model exploration and export of lists of potential false positives/negatives in training data": [[13, "ml-model-exploration-and-export-of-lists-of-potential-false-positives-negatives-in-training-data"]], "Matching": [[8, "matching"]], "Model Exploration and Household Model Exploration": [[8, "model-exploration-and-household-model-exploration"]], "Models": [[9, null]], "Multiple Comparisons": [[3, "multiple-comparisons"]], "Overview": [[2, "overview"], [7, "overview"], [8, "overview"], [8, "id1"], [8, "id4"], [8, "id7"], [8, "id10"], [8, "id13"]], "Pipeline generated features": [[10, null]], "Pipeline-generated Features": [[3, "pipeline-generated-features"]], "Potential Matches Universe": [[3, "potential-matches-universe"]], "Preprocessing": [[8, "preprocessing"]], "Related Configuration Sections": [[8, "related-configuration-sections"], [8, "id3"], [8, "id6"], [8, "id9"], [8, "id12"], [8, "id15"]], "Reporting": [[8, "reporting"]], "Requirements": [[6, "requirements"]], "Running Linking Tasks and Steps": [[11, "running-linking-tasks-and-steps"]], "Running hlink": [[11, null]], "Single Comparison": [[3, "single-comparison"]], "Starting the program": [[11, "starting-the-program"]], "Substitution Columns": [[3, "substitution-columns"]], "Substitution by regex word replace": [[12, "substitution-by-regex-word-replace"]], "Substitutions": [[12, null]], "Task steps": [[8, "task-steps"], [8, "id2"], [8, "id5"], [8, "id8"], [8, "id11"], [8, "id14"]], "Top level configs": [[3, "top-level-configs"]], "Training and Household Training": [[8, "training-and-household-training"]], "Training and models": [[3, "training-and-models"]], "Transformer types": [[10, "transformer-types"]], "Transforms": [[0, "transforms"]], "Using hlink as a Library": [[11, "using-hlink-as-a-library"]], "Welcome to hlink\u2019s documentation!": [[5, null]], "abs_diff": [[1, "abs-diff"]], "add_to_a": [[0, "add-to-a"]], "alias": [[1, "alias"]], "all_equals": [[1, 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Substitutions — hlink 3.7.0 documentation
Substitutions