Acsf fix (#143)

* Updated ACSF interface and logic. * Fixed linting. * Fixed issue with ACSF G5 calculation, added test. * Moved pymatgen imports. * Re-added black as dependency. * Removed species check from coulomb matrix. * Updated docs. * Updated actions. * Updated docs. * Updated wheel action. * Building wheels. * Building wheels. * Building wheels. * Updated wheel build command. * Migrated to pyproject.toml and ruff. * Updated pymargen dev dependency. * Updated pymargen dev dependency. * Updated docs.
SINGROUP · May 28, 2024 · 893722c · 893722c
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diff --git a/.github/workflows/actions.yml b/.github/workflows/actions.yml
@@ -7,24 +7,25 @@ jobs:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         submodules: recursive
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
-    - name: dependencies
+    - name: install
+      if: always()
       run: |
-        cd ${GITHUB_WORKSPACE}/scripts && ./dependencies.sh
-    - name: lint
+        cd ${GITHUB_WORKSPACE}/scripts && ./install.sh
+    - name: format
       if: always()
       run: |
-        cd ${GITHUB_WORKSPACE}/scripts && ./lint.sh
-    - name: install
+        cd ${GITHUB_WORKSPACE}/scripts && ./format.sh
+    - name: lint
       if: always()
       run: |
-        cd ${GITHUB_WORKSPACE}/scripts && ./install.sh
+        cd ${GITHUB_WORKSPACE}/scripts && ./lint.sh
     - name: test
       if: always()
       run: |

diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -11,25 +11,18 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04]
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest, windows-latest, macos-13, macos-14]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: recursive
 
-      # Used to host cibuildwheel
-      - uses: actions/setup-python@v3
-
-      - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.13.1
-
       - name: Build wheels
-        run: python -m cibuildwheel --output-dir wheelhouse
-        # to supply options, put them in 'env', like:
-        # env:
-        #   CIBW_SOME_OPTION: value
+        uses: pypa/cibuildwheel@v2.18.0
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 ![Build status](https://github.com/SINGROUP/dscribe/actions/workflows/actions.yml/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/SINGROUP/dscribe/badge.svg?branch=master)](https://coveralls.io/github/SINGROUP/dscribe?branch=master)
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 
 DScribe is a Python package for transforming atomic structures into fixed-size
 numerical fingerprints. These fingerprints are often called "descriptors" and

diff --git a/devrequirements.txt b/devrequirements.txt
diff --git a/docs/2.1.x/.buildinfo b/docs/2.1.x/.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: 979ed1add00f32f4bc116afafadc8e3c
+config: d2b1800fed63e4715a5ada69f6a537e2
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/2.1.x/_modules/dscribe/core/lattice.html b/docs/2.1.x/_modules/dscribe/core/lattice.html
@@ -1,22 +1,24 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" >
+<html class="writer-html5" lang="en" data-content_root="../../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>dscribe.core.lattice &mdash; DScribe 2.1.x documentation</title>
-      <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-      <link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
-      <link rel="stylesheet" href="../../../_static/css/style.css" type="text/css" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../../../_static/css/style.css?v=7d1ac55c" />
+
+
   <!--[if lt IE 9]>
     <script src="../../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../../../_static/jquery.js"></script>
-        <script src="../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
-        <script data-url_root="../../../" id="documentation_options" src="../../../_static/documentation_options.js"></script>
-        <script src="../../../_static/doctools.js"></script>
-        <script src="../../../_static/sphinx_highlight.js"></script>
-        <script defer="defer" src="../../../_static/js/versions.js"></script>
+        <script src="../../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../../_static/documentation_options.js?v=c41997dc"></script>
+        <script src="../../../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script defer="defer" src="../../../_static/js/versions.js?v=413e22da"></script>
     <script src="../../../_static/js/theme.js"></script>
     <link rel="author" title="About these documents" href="../../../about.html" />
     <link rel="index" title="Index" href="../../../genindex.html" />
@@ -97,10 +99,13 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd">See the License for the specific language governing permissions and</span>
 <span class="sd">limitations under the License.</span>
 <span class="sd">&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 
 
-<div class="viewcode-block" id="Lattice"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice">[docs]</a><span class="k">class</span> <span class="nc">Lattice</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
+<div class="viewcode-block" id="Lattice">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice">[docs]</a>
+<span class="k">class</span> <span class="nc">Lattice</span><span class="p">(</span><span class="nb">object</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">    A lattice object.  Essentially a matrix with conversion matrices. In</span>
 <span class="sd">    general, it is assumed that length units are in Angstroms and angles are in</span>
@@ -144,7 +149,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
             <span class="bp">self</span><span class="o">.</span><span class="n">_inv_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">linalg</span><span class="o">.</span><span class="n">inv</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_matrix</span><span class="p">)</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_inv_matrix</span>
 
-<div class="viewcode-block" id="Lattice.get_cartesian_coords"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_cartesian_coords">[docs]</a>    <span class="k">def</span> <span class="nf">get_cartesian_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fractional_coords</span><span class="p">):</span>
+<div class="viewcode-block" id="Lattice.get_cartesian_coords">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_cartesian_coords">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_cartesian_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">fractional_coords</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Returns the cartesian coordinates given fractional coordinates.</span>
 
@@ -156,7 +163,10 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">fractional_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_matrix</span><span class="p">)</span></div>
 
-<div class="viewcode-block" id="Lattice.get_fractional_coords"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_fractional_coords">[docs]</a>    <span class="k">def</span> <span class="nf">get_fractional_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cart_coords</span><span class="p">):</span>
+
+<div class="viewcode-block" id="Lattice.get_fractional_coords">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_fractional_coords">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_fractional_coords</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">cart_coords</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Returns the fractional coordinates given cartesian coordinates.</span>
 
@@ -168,6 +178,7 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">cart_coords</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">inv_matrix</span><span class="p">)</span></div>
 
+
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">lengths</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_lengths</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
@@ -206,7 +217,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">Lattice</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">reciprocal_lattice</span><span class="o">.</span><span class="n">matrix</span> <span class="o">/</span> <span class="p">(</span><span class="mi">2</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">pi</span><span class="p">))</span>
 
-<div class="viewcode-block" id="Lattice.get_points_in_sphere"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_points_in_sphere">[docs]</a>    <span class="k">def</span> <span class="nf">get_points_in_sphere</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frac_points</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">zip_results</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
+<div class="viewcode-block" id="Lattice.get_points_in_sphere">
+<a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.lattice.Lattice.get_points_in_sphere">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_points_in_sphere</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">frac_points</span><span class="p">,</span> <span class="n">center</span><span class="p">,</span> <span class="n">r</span><span class="p">,</span> <span class="n">zip_results</span><span class="o">=</span><span class="kc">True</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Find all points within a sphere from the point taking into account</span>
 <span class="sd">        periodic boundary conditions. This includes sites in other periodic</span>
@@ -282,7 +295,9 @@ <h1>Source code for dscribe.core.lattice</h1><div class="highlight"><pre>
                 <span class="n">shifted_coords</span><span class="p">[</span><span class="n">within_r</span><span class="p">],</span>
                 <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">d_2</span><span class="p">[</span><span class="n">within_r</span><span class="p">]),</span>
                 <span class="n">indices</span><span class="p">[</span><span class="n">within_r</span><span class="p">[</span><span class="mi">0</span><span class="p">]],</span>
-            <span class="p">)</span></div></div>
+            <span class="p">)</span></div>
+</div>
+
 </pre></div>
 
            </div>