Merge branch 'master' into dependabot/pip/numpy-gte-1.25.0-and-lt-3.0

.github/workflows/testing.yml

@@ -23,15 +23,14 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
-        cache-dependency-path: setup.py
+        cache-dependency-path: pyproject.toml
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install --quiet -r requirements.txt -r requirements-ci.txt
-        pip install -e .
+        pip install -e '.[ci]'
     - name: pytest
       run: |
-        pytest --cov=pymatgen.analysis.diffusion --durations=30 pymatgen
+        python -m pytest --cov=pymatgen.analysis.diffusion --durations=30 pymatgen
     - name: Upload coverage reports to Codecov
       uses: codecov/codecov-action@v3
       env:

CHANGES.rst

@@ -1,6 +1,10 @@
 Change Log
 ==========
 
+v2024.6.25
+----------
+* Fix broken code due to pymatgen and matplotlib deprecated methods.
+
 v2023.8.15
 ----------
 * Complete migration of pymatgen.analysis.pathfinder over to pymatgen-analysis.diffusion.

README.rst

@@ -1,9 +1,9 @@
-.. image:: https://github.com/materialsvirtuallab/pymatgen-diffusion/actions/workflows/testing.yml/badge.svg
+.. image:: https://github.com/materialsvirtuallab/pymatgen-analysis-diffusion/actions/workflows/testing.yml/badge.svg
       :alt: CI Status
       :target: https://github.com/materialsvirtuallab/pymatgen-diffusion/actions/workflows/testing.yml
 
-.. image:: https://coveralls.io/repos/github/materialsvirtuallab/pymatgen-diffusion/badge.svg?branch=master
-      :target: https://coveralls.io/github/materialsvirtuallab/pymatgen-diffusion?branch=master
+.. image:: https://codecov.io/gh/materialsvirtuallab/pymatgen-analysis-diffusion/graph/badge.svg?token=4lH4UZcXye
+      :target: https://codecov.io/gh/materialsvirtuallab/pymatgen-analysis-diffusion
 
 pymatgen-analysis-diffusion
 ===========================

docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html

@@ -97,11 +97,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
 <span class="sd">            provide the index for each point, and ss in the final sum squared</span>
 <span class="sd">            distances.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">centroids</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">sample</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">points</span><span class="p">),</span> <span class="n">k</span><span class="p">))</span>
-            <span class="k">if</span> <span class="n">initial_centroids</span> <span class="ow">is</span> <span class="kc">None</span>
-            <span class="k">else</span> <span class="n">initial_centroids</span>
-        <span class="p">)</span>
+        <span class="n">centroids</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">random</span><span class="o">.</span><span class="n">sample</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">points</span><span class="p">),</span> <span class="n">k</span><span class="p">))</span> <span class="k">if</span> <span class="n">initial_centroids</span> <span class="ow">is</span> <span class="kc">None</span> <span class="k">else</span> <span class="n">initial_centroids</span>
 
         <span class="c1"># Initialize book keeping vars.</span>
         <span class="n">iterations</span> <span class="o">=</span> <span class="mi">0</span>
@@ -243,9 +239,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
             <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
                 <span class="n">c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">n</span><span class="p">)</span>
                 <span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="n">ind</span><span class="p">:</span>
-                    <span class="n">dist</span><span class="p">,</span> <span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">get_distance_and_image</span><span class="p">(</span>
-                        <span class="n">centroids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">points</span><span class="p">[</span><span class="n">j</span><span class="p">]</span>
-                    <span class="p">)</span>
+                    <span class="n">dist</span><span class="p">,</span> <span class="n">image</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">lattice</span><span class="o">.</span><span class="n">get_distance_and_image</span><span class="p">(</span><span class="n">centroids</span><span class="p">[</span><span class="n">i</span><span class="p">],</span> <span class="n">points</span><span class="p">[</span><span class="n">j</span><span class="p">])</span>
                     <span class="n">c</span> <span class="o">+=</span> <span class="n">points</span><span class="p">[</span><span class="n">j</span><span class="p">]</span> <span class="o">+</span> <span class="n">image</span>
                 <span class="n">c</span> <span class="o">/=</span> <span class="nb">len</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span>
                 <span class="n">c</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mod</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
@@ -272,10 +266,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
             <span class="k">return</span> <span class="kc">True</span>
         <span class="k">if</span> <span class="n">old_centroids</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">False</span>
-        <span class="k">return</span> <span class="nb">all</span><span class="p">(</span>
-            <span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">pbc_diff</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">),</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span>
-            <span class="k">for</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">old_centroids</span><span class="p">,</span> <span class="n">centroids</span><span class="p">)</span>
-        <span class="p">)</span></div>
+        <span class="k">return</span> <span class="nb">all</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">allclose</span><span class="p">(</span><span class="n">pbc_diff</span><span class="p">(</span><span class="n">c1</span><span class="p">,</span> <span class="n">c2</span><span class="p">),</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">])</span> <span class="k">for</span> <span class="n">c1</span><span class="p">,</span> <span class="n">c2</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">old_centroids</span><span class="p">,</span> <span class="n">centroids</span><span class="p">))</span></div>
 </div>
 
 

docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html

@@ -279,11 +279,11 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.rdf</h1><div class="highlig
 
             <span class="n">label</span> <span class="o">=</span> <span class="n">symbol_list</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">symbol_list</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span> <span class="k">else</span> <span class="s2">&quot;-&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">symbol_list</span><span class="p">)</span>
 
-        <span class="n">plt</span> <span class="o">=</span> <span class="n">pretty_plot</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="mi">8</span><span class="p">)</span>
-        <span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interval</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdf</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">4.0</span><span class="p">,</span> <span class="n">zorder</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+        <span class="n">ax</span> <span class="o">=</span> <span class="n">pretty_plot</span><span class="p">(</span><span class="mi">12</span><span class="p">,</span> <span class="mi">8</span><span class="p">)</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">interval</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">rdf</span><span class="p">,</span> <span class="n">label</span><span class="o">=</span><span class="n">label</span><span class="p">,</span> <span class="n">linewidth</span><span class="o">=</span><span class="mf">4.0</span><span class="p">,</span> <span class="n">zorder</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
 
         <span class="k">if</span> <span class="n">loc_peak</span><span class="p">:</span>
-            <span class="n">plt</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span>
+            <span class="n">ax</span><span class="o">.</span><span class="n">scatter</span><span class="p">(</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">peak_r</span><span class="p">,</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">peak_rdf</span><span class="p">,</span>
                 <span class="n">marker</span><span class="o">=</span><span class="s2">&quot;P&quot;</span><span class="p">,</span>
@@ -295,14 +295,13 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.rdf</h1><div class="highlig
                 <span class="n">label</span><span class="o">=</span><span class="s2">&quot;Peaks&quot;</span><span class="p">,</span>
             <span class="p">)</span>
 
-        <span class="n">plt</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;$r$ ($</span><span class="se">\\</span><span class="s2">rm</span><span class="se">\\</span><span class="s2">AA$)&quot;</span><span class="p">)</span>
-        <span class="n">plt</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;$g(r)$&quot;</span><span class="p">)</span>
-        <span class="n">plt</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper right&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="mi">36</span><span class="p">)</span>
-        <span class="n">plt</span><span class="o">.</span><span class="n">xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xlim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-        <span class="n">plt</span><span class="o">.</span><span class="n">ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ylim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
-        <span class="n">plt</span><span class="o">.</span><span class="n">tight_layout</span><span class="p">()</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">set_xlabel</span><span class="p">(</span><span class="s2">&quot;$r$ ($</span><span class="se">\\</span><span class="s2">rm</span><span class="se">\\</span><span class="s2">AA$)&quot;</span><span class="p">)</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">set_ylabel</span><span class="p">(</span><span class="s2">&quot;$g(r)$&quot;</span><span class="p">)</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">legend</span><span class="p">(</span><span class="n">loc</span><span class="o">=</span><span class="s2">&quot;upper right&quot;</span><span class="p">,</span> <span class="n">fontsize</span><span class="o">=</span><span class="mi">36</span><span class="p">)</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">set_xlim</span><span class="p">(</span><span class="n">xlim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">xlim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
+        <span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ylim</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">ylim</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
 
-        <span class="k">return</span> <span class="n">plt</span></div>
+        <span class="k">return</span> <span class="n">ax</span></div>
 
 
 <div class="viewcode-block" id="RadialDistributionFunction.export_rdf">

docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html

@@ -103,9 +103,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.tests.test_clustering</h1><
         <span class="n">initial</span> <span class="o">=</span> <span class="p">[[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">,</span> <span class="mf">0.5</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.25</span><span class="p">,</span> <span class="mf">0.25</span><span class="p">,</span> <span class="mf">0.25</span><span class="p">],</span> <span class="p">[</span><span class="mf">0.5</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">]]</span>
         <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">initial</span><span class="p">:</span>
             <span class="k">for</span> <span class="n">_i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">100</span><span class="p">):</span>
-                <span class="n">pts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span>
-                    <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.01</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span>
-                <span class="p">)</span>
+                <span class="n">pts</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">c</span><span class="p">)</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randn</span><span class="p">(</span><span class="mi">3</span><span class="p">)</span> <span class="o">*</span> <span class="mf">0.01</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">randint</span><span class="p">(</span><span class="mi">3</span><span class="p">))</span>
         <span class="n">pts</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">pts</span><span class="p">)</span>
         <span class="n">k</span> <span class="o">=</span> <span class="n">KmeansPBC</span><span class="p">(</span><span class="n">lattice</span><span class="p">)</span>
         <span class="n">centroids</span><span class="p">,</span> <span class="n">labels</span><span class="p">,</span> <span class="n">ss</span> <span class="o">=</span> <span class="n">k</span><span class="o">.</span><span class="n">cluster</span><span class="p">(</span><span class="n">pts</span><span class="p">,</span> <span class="mi">4</span><span class="p">)</span>