Modern python packaging + v0.1.8 (#38)

* modern packaging * ruff check * add tests folder to coverage * update doc to v0.1.8 * remove test folder
raphaelvallat · Dec 21, 2024 · 98970eb · 98970eb
1 parent 1e2c48a
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diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
diff --git a/.github/workflows/python_tests.yml b/.github/workflows/python_tests.yml
@@ -12,7 +12,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     runs-on: ${{ matrix.platform }}
 
@@ -30,10 +30,15 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-test.txt
-        pip install .
+        pip install ".[test]"
 
     - name: Test with pytest
       run: |
-        pytest --cov --verbose
+        pytest --cov --cov-report=xml --verbose
+
+    - name: Upload coverage report
+      if: ${{ matrix.platform == 'ubuntu-latest' && matrix.python-version == 3.9 }}
+      uses: codecov/codecov-action@v4
+      with:
+        token: d5ef1de8-d1c4-4d89-b304-4d8fffdf9906
+        file: ./coverage.xml
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -0,0 +1,13 @@
+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: "Linting"
+        uses: astral-sh/ruff-action@v1
+      - name: "Formatting"
+        uses: astral-sh/ruff-action@v1
+        with:
+          args: "format --check"
diff --git a/.gitignore b/.gitignore
@@ -105,3 +105,4 @@ desktop.ini
 docs/build/doctrees/
 docs/generated/
 .DS_Store
+push_pypi.md
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,4 +1,3 @@
 # Add README, LICENSE and requirements :
 include README.rst
 include LICENSE
-include requirements.txt
diff --git a/README.rst b/README.rst
@@ -41,6 +41,15 @@ or conda
   conda config --set channel_priority strict
   conda install antropy
 
+To build and install from source, clone this repository or download the source archive and decompress the files
+
+.. code-block:: shell
+
+  cd antropy
+  pip install ".[test]"     # install the package
+  pip install -e ".[test]"  # or editable install
+  pytest
+
 **Dependencies**
 
 - `numpy <https://numpy.org/>`_

diff --git a/codecov.yml b/codecov.yml
diff --git a/docs/build/html/.buildinfo b/docs/build/html/.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: 3a25f3b4fb97564eec51e3b795229bc5
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 7a843bd555ee874c00dbc710835f6133
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/build/html/_modules/antropy/entropy.html b/docs/build/html/_modules/antropy/entropy.html
@@ -4,16 +4,16 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>antropy.entropy &#8212; antropy 0.1.7 documentation</title>
+    <title>antropy.entropy &#8212; antropy 0.1.8 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/bootstrap-sphinx.css?v=9f61996d" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
     <link rel="stylesheet" type="text/css" href="../../_static/style.css?v=917eae1c" />
-    <script src="../../_static/documentation_options.js?v=ca7ad2ea"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/documentation_options.js?v=22607128"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
-    <script src="../../_static/copybutton.js?v=fe0808e4"></script>
+    <script src="../../_static/copybutton.js?v=fd10adb8"></script>
     <link rel="icon" href="../../_static/antropy.ico"/>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
@@ -39,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html">
           antropy</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.1.7</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.1.8</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -81,11 +81,12 @@
   <h1>Source code for antropy.entropy</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;Entropy functions&quot;&quot;&quot;</span>
 
+<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">factorial</span><span class="p">,</span> <span class="n">log</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">numba</span> <span class="kn">import</span> <span class="n">jit</span><span class="p">,</span> <span class="n">types</span>
-<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">factorial</span><span class="p">,</span> <span class="n">log</span>
-<span class="kn">from</span> <span class="nn">sklearn.neighbors</span> <span class="kn">import</span> <span class="n">KDTree</span>
 <span class="kn">from</span> <span class="nn">scipy.signal</span> <span class="kn">import</span> <span class="n">periodogram</span><span class="p">,</span> <span class="n">welch</span>
+<span class="kn">from</span> <span class="nn">sklearn.neighbors</span> <span class="kn">import</span> <span class="n">KDTree</span>
 
 <span class="kn">from</span> <span class="nn">.utils</span> <span class="kn">import</span> <span class="n">_embed</span><span class="p">,</span> <span class="n">_xlogx</span>
 
@@ -1154,7 +1155,7 @@ <h1>Source code for antropy.entropy</h1><div class="highlight"><pre>
     </p>
     <p>
         &copy; Copyright 2018-2024, Raphael Vallat.<br/>
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 7.4.7.<br/>
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 8.1.3.<br/>
     </p>
   </div>
 </footer>

diff --git a/docs/build/html/_modules/antropy/fractal.html b/docs/build/html/_modules/antropy/fractal.html
@@ -4,16 +4,16 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>antropy.fractal &#8212; antropy 0.1.7 documentation</title>
+    <title>antropy.fractal &#8212; antropy 0.1.8 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../../_static/bootstrap-sphinx.css?v=9f61996d" />
     <link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
     <link rel="stylesheet" type="text/css" href="../../_static/style.css?v=917eae1c" />
-    <script src="../../_static/documentation_options.js?v=ca7ad2ea"></script>
-    <script src="../../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../../_static/documentation_options.js?v=22607128"></script>
+    <script src="../../_static/doctools.js?v=9bcbadda"></script>
     <script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
-    <script src="../../_static/copybutton.js?v=fe0808e4"></script>
+    <script src="../../_static/copybutton.js?v=fd10adb8"></script>
     <link rel="icon" href="../../_static/antropy.ico"/>
     <link rel="index" title="Index" href="../../genindex.html" />
     <link rel="search" title="Search" href="../../search.html" />
@@ -39,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="../../index.html">
           antropy</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.1.7</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.1.8</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -81,9 +81,10 @@
   <h1>Source code for antropy.fractal</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;Fractal functions&quot;&quot;&quot;</span>
 
+<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">floor</span><span class="p">,</span> <span class="n">log</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">numba</span> <span class="kn">import</span> <span class="n">jit</span><span class="p">,</span> <span class="n">types</span>
-<span class="kn">from</span> <span class="nn">math</span> <span class="kn">import</span> <span class="n">log</span><span class="p">,</span> <span class="n">floor</span>
 
 <span class="kn">from</span> <span class="nn">.entropy</span> <span class="kn">import</span> <span class="n">num_zerocross</span>
 <span class="kn">from</span> <span class="nn">.utils</span> <span class="kn">import</span> <span class="n">_linear_regression</span><span class="p">,</span> <span class="n">_log_n</span>
@@ -558,7 +559,7 @@ <h1>Source code for antropy.fractal</h1><div class="highlight"><pre>
     </p>
     <p>
         &copy; Copyright 2018-2024, Raphael Vallat.<br/>
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 7.4.7.<br/>
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 8.1.3.<br/>
     </p>
   </div>
 </footer>

diff --git a/docs/build/html/_modules/index.html b/docs/build/html/_modules/index.html
@@ -4,16 +4,16 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; antropy 0.1.7 documentation</title>
+    <title>Overview: module code &#8212; antropy 0.1.8 documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
     <link rel="stylesheet" type="text/css" href="../_static/bootstrap-sphinx.css?v=9f61996d" />
     <link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
     <link rel="stylesheet" type="text/css" href="../_static/style.css?v=917eae1c" />
-    <script src="../_static/documentation_options.js?v=ca7ad2ea"></script>
-    <script src="../_static/doctools.js?v=9a2dae69"></script>
+    <script src="../_static/documentation_options.js?v=22607128"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
     <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/clipboard.min.js?v=a7894cd8"></script>
-    <script src="../_static/copybutton.js?v=fe0808e4"></script>
+    <script src="../_static/copybutton.js?v=fd10adb8"></script>
     <link rel="icon" href="../_static/antropy.ico"/>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -39,7 +39,7 @@
         </button>
         <a class="navbar-brand" href="../index.html">
           antropy</a>
-        <span class="navbar-text navbar-version pull-left"><b>0.1.7</b></span>
+        <span class="navbar-text navbar-version pull-left"><b>0.1.8</b></span>
       </div>
 
         <div class="collapse navbar-collapse nav-collapse">
@@ -98,7 +98,7 @@ <h1>All modules for which code is available</h1>
     </p>
     <p>
         &copy; Copyright 2018-2024, Raphael Vallat.<br/>
-      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 7.4.7.<br/>
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 8.1.3.<br/>
     </p>
   </div>
 </footer>

diff --git a/docs/build/html/_sources/changelog.rst.txt b/docs/build/html/_sources/changelog.rst.txt
@@ -3,6 +3,11 @@
 What's new
 ##########
 
+v0.1.8 (December 2024)
+----------------------
+
+- Switch to modern python packaging
+- Use ruff instead of black/flake8
 
 v0.1.7 (December 2024)
 ----------------------

diff --git a/docs/build/html/_sources/index.rst.txt b/docs/build/html/_sources/index.rst.txt
@@ -36,6 +36,15 @@ or conda
   conda config --set channel_priority strict
   conda install antropy
 
+To build and install from source, clone this repository or download the source archive and decompress the files
+
+.. code-block:: shell
+
+  cd antropy
+  pip install ".[test]"     # install the package
+  pip install -e ".[test]"  # or editable install
+  pytest
+
 **Dependencies**
 
 - `numpy <https://numpy.org/>`_

diff --git a/docs/build/html/_static/basic.css b/docs/build/html/_static/basic.css
@@ -1,12 +1,5 @@
 /*
- * basic.css
- * ~~~~~~~~~
- *
  * Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 /* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
 /* -- search page ----------------------------------------------------------- */
 
 ul.search {
-    margin: 10px 0 0 20px;
-    padding: 0;
+    margin-top: 10px;
 }
 
 ul.search li {
-    padding: 5px 0 5px 20px;
-    background-image: url(file.png);
-    background-repeat: no-repeat;
-    background-position: 0 7px;
+    padding: 5px 0;
 }
 
 ul.search li a {

diff --git a/docs/build/html/_static/copybutton.js b/docs/build/html/_static/copybutton.js
@@ -20,7 +20,7 @@ const messages = {
   },
   'fr' : {
     'copy': 'Copier',
-    'copy_to_clipboard': 'Copié dans le presse-papier',
+    'copy_to_clipboard': 'Copier dans le presse-papier',
     'copy_success': 'Copié !',
     'copy_failure': 'Échec de la copie',
   },
@@ -224,7 +224,7 @@ var copyTargetText = (trigger) => {
   var target = document.querySelector(trigger.attributes['data-clipboard-target'].value);
 
   // get filtered text
-  let exclude = '.linenos, .gp';
+  let exclude = '.linenos';
 
   let text = filterText(target, exclude);
   return formatCopyText(text, '>>> |\\.\\.\\. |\\$ ', true, true, true, true, '', '')

diff --git a/docs/build/html/_static/doctools.js b/docs/build/html/_static/doctools.js
@@ -1,12 +1,5 @@
 /*
- * doctools.js
- * ~~~~~~~~~~~
- *
  * Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 "use strict";
 

diff --git a/docs/build/html/_static/documentation_options.js b/docs/build/html/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.7',
+    VERSION: '0.1.8',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/build/html/_static/language_data.js b/docs/build/html/_static/language_data.js
@@ -1,13 +1,6 @@
 /*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
  */
 
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];