feat: add eager/lazy loaders for expression systems (#81)

* feat: add expression system loaders * refactor: code cleanup * Update code coverage badge * chore: build without dev dependencies * chore: bump version to v1.5.0 * Update docs --------- Co-authored-by: kvdomingo <[email protected]>
kvdomingo · Apr 5, 2023 · e6c2898 · e6c2898
1 parent 2d068d8
commit e6c2898
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diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
@@ -32,7 +32,7 @@ jobs:
  run: |
  python -m pip install --upgrade pip
  pip install "poetry==1.3.2"
- poetry export --without-hashes -f requirements.txt | pip install -r /dev/stdin
+ poetry export --without-hashes --without dev -f requirements.txt | pip install -r /dev/stdin
  pip install build
 
  - name: Build package

diff --git a/coverage.svg b/coverage.svg
diff --git a/docs/.buildinfo b/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: 4b124703c9422a7eaf1a81649d4f55fa
+config: 3cdfd6296fb51cb45ce3f01e9fcf81ef
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/generated/primerdriver.checks.SequenceChecks.doctree b/docs/.doctrees/generated/primerdriver.checks.SequenceChecks.doctree
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
  URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '1.3.2',
+ VERSION: '1.5.0',
  LANGUAGE: 'en',
  COLLAPSE_INDEX: false,
  BUILDER: 'html',

diff --git a/docs/api.html b/docs/api.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="genindex.html" /><link rel="search" title="Search" href="search.html" /><link rel="next" title="primerdriver.checks.PrimerChecks" href="generated/primerdriver.checks.PrimerChecks.html" /><link rel="prev" title="Software Features" href="software.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>API Reference - PrimerDriver 1.3.2 documentation</title>
+ <title>API Reference - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
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@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.checks.PrimerChecks.html b/docs/generated/primerdriver.checks.PrimerChecks.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="primerdriver.checks.SequenceChecks" href="primerdriver.checks.SequenceChecks.html" /><link rel="prev" title="API Reference" href="../api.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.checks.PrimerChecks - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.checks.PrimerChecks - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
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@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.checks.SequenceChecks.html b/docs/generated/primerdriver.checks.SequenceChecks.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="primerdriver.exceptions.PrimerCheckError" href="primerdriver.exceptions.PrimerCheckError.html" /><link rel="prev" title="primerdriver.checks.PrimerChecks" href="primerdriver.checks.PrimerChecks.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.checks.SequenceChecks - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.checks.SequenceChecks - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?digest=30d1aed668e5c3a91c3e3bf6a60b675221979f0e" />
@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">
@@ -231,16 +231,16 @@ <h1>primerdriver.checks.SequenceChecks<a class="headerlink" href="#primerdriver-
 <tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">are_melting_temps_close</span></code>(fwd_Tm, rev_Tm)</p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_gc_clamped</span></code>(terminate_gc)</p></td>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_gc_clamped</span></code>()</p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_valid_gc_content</span></code>(gc_range)</p></td>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_valid_gc_content</span></code>()</p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_valid_length</span></code>(length_range)</p></td>
+<tr class="row-odd"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_valid_length</span></code>()</p></td>
 <td><p></p></td>
 </tr>
-<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_valid_melting_temp</span></code>(Tm, Tm_range)</p></td>
+<tr class="row-even"><td><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">is_valid_melting_temp</span></code>(melting_temp)</p></td>
 <td><p></p></td>
 </tr>
 </tbody>

diff --git a/docs/generated/primerdriver.exceptions.PrimerCheckError.html b/docs/generated/primerdriver.exceptions.PrimerCheckError.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="primerdriver.input_handler.interactive_handler" href="primerdriver.input_handler.interactive_handler.html" /><link rel="prev" title="primerdriver.checks.SequenceChecks" href="primerdriver.checks.SequenceChecks.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.exceptions.PrimerCheckError - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.exceptions.PrimerCheckError - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?digest=30d1aed668e5c3a91c3e3bf6a60b675221979f0e" />
@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.input_handler.interactive_handler.html b/docs/generated/primerdriver.input_handler.interactive_handler.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="primerdriver.input_handler.single_command_handler" href="primerdriver.input_handler.single_command_handler.html" /><link rel="prev" title="primerdriver.exceptions.PrimerCheckError" href="primerdriver.exceptions.PrimerCheckError.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.input_handler.interactive_handler - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.input_handler.interactive_handler - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?digest=30d1aed668e5c3a91c3e3bf6a60b675221979f0e" />
@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.input_handler.single_command_handler.html b/docs/generated/primerdriver.input_handler.single_command_handler.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="primerdriver.output_handler.interactive_saver" href="primerdriver.output_handler.interactive_saver.html" /><link rel="prev" title="primerdriver.input_handler.interactive_handler" href="primerdriver.input_handler.interactive_handler.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.input_handler.single_command_handler - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.input_handler.single_command_handler - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
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@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.output_handler.interactive_saver.html b/docs/generated/primerdriver.output_handler.interactive_saver.html
@@ -6,7 +6,7 @@
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  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.output_handler.interactive_saver - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.output_handler.interactive_saver - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo-extensions.css?digest=30d1aed668e5c3a91c3e3bf6a60b675221979f0e" />
@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.output_handler.single_command_saver.html b/docs/generated/primerdriver.output_handler.single_command_saver.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="next" title="primerdriver.primer_design.PrimerDesign" href="primerdriver.primer_design.PrimerDesign.html" /><link rel="prev" title="primerdriver.output_handler.interactive_saver" href="primerdriver.output_handler.interactive_saver.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.output_handler.single_command_saver - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.output_handler.single_command_saver - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
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@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">

diff --git a/docs/generated/primerdriver.primer_design.PrimerDesign.html b/docs/generated/primerdriver.primer_design.PrimerDesign.html
@@ -6,7 +6,7 @@
 <link rel="index" title="Index" href="../genindex.html" /><link rel="search" title="Search" href="../search.html" /><link rel="prev" title="primerdriver.output_handler.single_command_saver" href="primerdriver.output_handler.single_command_saver.html" />
 
  <!-- Generated with Sphinx 6.1.3 and Furo 2023.03.27 -->
- <title>primerdriver.primer_design.PrimerDesign - PrimerDriver 1.3.2 documentation</title>
+ <title>primerdriver.primer_design.PrimerDesign - PrimerDriver 1.5.0 documentation</title>
  <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
  <link rel="stylesheet" type="text/css" href="../_static/styles/furo.css?digest=fad236701ea90a88636c2a8c73b44ae642ed2a53" />
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@@ -123,7 +123,7 @@
  </label>
  </div>
  <div class="header-center">
- <a href="../index.html"><div class="brand">PrimerDriver 1.3.2 documentation</div></a>
+ <a href="../index.html"><div class="brand">PrimerDriver 1.5.0 documentation</div></a>
  </div>
  <div class="header-right">
  <div class="theme-toggle-container theme-toggle-header">
@@ -146,7 +146,7 @@
  <div class="sidebar-sticky"><a class="sidebar-brand" href="../index.html">
 
 
- <span class="sidebar-brand-text">PrimerDriver 1.3.2 documentation</span>
+ <span class="sidebar-brand-text">PrimerDriver 1.5.0 documentation</span>
 
 </a><form class="sidebar-search-container" method="get" action="../search.html" role="search">
  <input class="sidebar-search" placeholder="Search" name="q" aria-label="Search">