diff --git a/README.rst b/README.rst index 679debc..6bb1803 100644 --- a/README.rst +++ b/README.rst @@ -13,7 +13,7 @@ | | |___ ___ |___ |_____ ___ :|___/ ___ |___ ___ ___ |___ \ | | | | / \ | \ | | | / \:| / | | \ / / \ | \/ | | | | |___/ | | | | | |:| | | | \___ |___/ | \_____ - | | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.3\ + | | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.4\ |____________________________________:_______________________/____________:_____/ @@ -197,6 +197,13 @@ Roughly chronologically, they are so far: * Katarina Brlec * Joe Willis +Thanks also to the `JOSS`_ reviewers, Evan Walter Clarke +Spotte-Smith, Enric Tomás Grau-Luque, and Francesco Nattino; and the +editor Mojtaba Barzegari. An unintimidating and productive review +process, which I would recommend if the opportunity arises! + +.. _JOSS: https://joss.theoj.org/ + License ------- diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle index d9f5180..626d44a 100644 Binary files a/docs/.doctrees/environment.pickle and b/docs/.doctrees/environment.pickle differ diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree index 80e2df9..e5ebe5b 100644 Binary files a/docs/.doctrees/index.doctree and b/docs/.doctrees/index.doctree differ diff --git a/docs/.doctrees/tp.cli.doctree b/docs/.doctrees/tp.cli.doctree index 25a6ffb..ee6a49a 100644 Binary files a/docs/.doctrees/tp.cli.doctree and b/docs/.doctrees/tp.cli.doctree differ diff --git a/docs/.doctrees/tutorial-00.doctree b/docs/.doctrees/tutorial-00.doctree index c536f92..9c651d9 100644 Binary files a/docs/.doctrees/tutorial-00.doctree and b/docs/.doctrees/tutorial-00.doctree differ diff --git a/docs/_images/wideband.png b/docs/_images/wideband.png index cdf200c..336ccdc 100644 Binary files a/docs/_images/wideband.png and b/docs/_images/wideband.png differ diff --git a/docs/_modules/tp.html b/docs/_modules/tp.html index 8d1294b..d620f0f 100644 --- a/docs/_modules/tp.html +++ b/docs/_modules/tp.html @@ -83,6 +83,8 @@ <h1>Source code for tp</h1><div class="highlight"><pre> <span class="c1"># default values and metadata</span> <span class="c1">#"""</span> +<span class="n">__version__</span> <span class="o">=</span> <span class="s1">'3.1.4'</span> + <div class="viewcode-block" id="docstring_replace"><a class="viewcode-back" href="../tp.html#tp.docstring_replace">[docs]</a><span class="k">def</span> <span class="nf">docstring_replace</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span> <span class="k">def</span> <span class="nf">d</span><span class="p">(</span><span class="n">f</span><span class="p">):</span> <span class="n">f</span><span class="o">.</span><span class="vm">__doc__</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="vm">__doc__</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span> diff --git a/docs/_modules/tp/cli/options.html b/docs/_modules/tp/cli/options.html index c3673c1..b2ad4f5 100644 --- a/docs/_modules/tp/cli/options.html +++ b/docs/_modules/tp/cli/options.html @@ -78,6 +78,10 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre> <span class="c1">#Functions</span> <span class="c1">#---------</span> <span class="c1">#</span> +<span class="c1"># administrative_options</span> +<span class="c1"># function for help and version display.</span> +<span class="c1"># axes_limit_function</span> +<span class="c1"># function for setting the axis limits.</span> <span class="c1"># direction_function:</span> <span class="c1"># function for picking the --direction (-d).</span> <span class="c1"># doping_type_option:</span> @@ -104,12 +108,100 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre> <span class="c1"># function for picking the --temperature (-t).</span> <span class="c1"># verbose_option:</span> <span class="c1"># function for increasing the verbosity.</span> -<span class="c1"># axes_limit_function</span> -<span class="c1"># function for setting the axis limits.</span> <span class="c1">#"""</span> <span class="kn">import</span> <span class="nn">click</span> +<div class="viewcode-block" id="adminsitrative_options"><a class="viewcode-back" href="../../../tp.cli.html#tp.cli.options.adminsitrative_options">[docs]</a><span class="k">def</span> <span class="nf">adminsitrative_options</span><span class="p">(</span><span class="n">f</span><span class="p">):</span> + <span class="sd">"""Help and version options.</span> + +<span class="sd"> Allows -h for help (click-nonstandard).</span> + +<span class="sd"> Options</span> +<span class="sd"> -------</span> + +<span class="sd"> --help, -h</span> +<span class="sd"> show help and exit</span> +<span class="sd"> --version</span> +<span class="sd"> show version and exit</span> +<span class="sd"> """</span> + + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">help_option</span><span class="p">(</span><span class="s1">'-h'</span><span class="p">,</span> <span class="s1">'--help'</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">version_option</span><span class="p">(</span><span class="n">package_name</span><span class="o">=</span><span class="s1">'tp'</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + + <span class="k">return</span> <span class="n">f</span></div> + +<div class="viewcode-block" id="axes_limit_function"><a class="viewcode-back" href="../../../tp.cli.html#tp.cli.options.axes_limit_function">[docs]</a><span class="k">def</span> <span class="nf">axes_limit_function</span><span class="p">(</span><span class="n">multiple</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> + <span class="sd">"""Function for creating axes limit options.</span> + +<span class="sd"> Arguments</span> +<span class="sd"> ---------</span> + +<span class="sd"> multiple : bool, optional</span> +<span class="sd"> allow multiple limits. Default: False.</span> +<span class="sd"> c : bool, optional</span> +<span class="sd"> include colour limits. Default: False.</span> + +<span class="sd"> Returns</span> +<span class="sd"> -------</span> +<span class="sd"> decorator</span> +<span class="sd"> axes limit options decorator.</span> +<span class="sd"> """</span> + + <span class="k">def</span> <span class="nf">axes_limit_options</span><span class="p">(</span><span class="n">f</span><span class="p">):</span> + <span class="sd">"""Options for axes limits.</span> +<span class="sd"> </span> +<span class="sd"> Options</span> +<span class="sd"> -------</span> + +<span class="sd"> --xmin : float, optional</span> +<span class="sd"> override minimum x.</span> +<span class="sd"> --xmax : float, optional</span> +<span class="sd"> override maximum x.</span> +<span class="sd"> --ymin : float, optional</span> +<span class="sd"> override minimum y.</span> +<span class="sd"> --ymax : float, optional</span> +<span class="sd"> override maximum y.</span> +<span class="sd"> --cmin : float, optional</span> +<span class="sd"> override minimum colour.</span> +<span class="sd"> --cmax : float, optional</span> +<span class="sd"> override maximum colour.</span> + +<span class="sd"> Returns</span> +<span class="sd"> -------</span> + +<span class="sd"> decorator</span> +<span class="sd"> axes limits options decorator.</span> +<span class="sd"> """</span> + + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--xmin'</span><span class="p">,</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Override minimum x.'</span><span class="p">,</span> + <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> + <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--xmax'</span><span class="p">,</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Override maximum x.'</span><span class="p">,</span> + <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> + <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--ymin'</span><span class="p">,</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Override minimum y.'</span><span class="p">,</span> + <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> + <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--ymax'</span><span class="p">,</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Override maximum y.'</span><span class="p">,</span> + <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> + <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="k">if</span> <span class="n">c</span><span class="p">:</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--cmin'</span><span class="p">,</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Override minimum colour value.'</span><span class="p">,</span> + <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> + <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--cmax'</span><span class="p">,</span> + <span class="n">help</span><span class="o">=</span><span class="s1">'Override maximum colour value.'</span><span class="p">,</span> + <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> + <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> + <span class="k">return</span> <span class="n">f</span> + <span class="k">return</span> <span class="n">axes_limit_options</span></div> + <div class="viewcode-block" id="direction_function"><a class="viewcode-back" href="../../../tp.cli.html#tp.cli.options.direction_function">[docs]</a><span class="k">def</span> <span class="nf">direction_function</span><span class="p">(</span><span class="n">multiple</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> <span class="sd">"""Function to create direction options.</span> <span class="sd"> </span> @@ -700,77 +792,6 @@ <h1>Source code for tp.cli.options</h1><div class="highlight"><pre> <span class="n">show_default</span><span class="o">=</span><span class="kc">False</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> <span class="k">return</span> <span class="n">f</span></div> - -<div class="viewcode-block" id="axes_limit_function"><a class="viewcode-back" href="../../../tp.cli.html#tp.cli.options.axes_limit_function">[docs]</a><span class="k">def</span> <span class="nf">axes_limit_function</span><span class="p">(</span><span class="n">multiple</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> - <span class="sd">"""Function for creating axes limit options.</span> - -<span class="sd"> Arguments</span> -<span class="sd"> ---------</span> - -<span class="sd"> multiple : bool, optional</span> -<span class="sd"> allow multiple limits. Default: False.</span> -<span class="sd"> c : bool, optional</span> -<span class="sd"> include colour limits. Default: False.</span> - -<span class="sd"> Returns</span> -<span class="sd"> -------</span> -<span class="sd"> decorator</span> -<span class="sd"> axes limit options decorator.</span> -<span class="sd"> """</span> - - <span class="k">def</span> <span class="nf">axes_limit_options</span><span class="p">(</span><span class="n">f</span><span class="p">):</span> - <span class="sd">"""Options for axes limits.</span> -<span class="sd"> </span> -<span class="sd"> Options</span> -<span class="sd"> -------</span> - -<span class="sd"> --xmin : float, optional</span> -<span class="sd"> override minimum x.</span> -<span class="sd"> --xmax : float, optional</span> -<span class="sd"> override maximum x.</span> -<span class="sd"> --ymin : float, optional</span> -<span class="sd"> override minimum y.</span> -<span class="sd"> --ymax : float, optional</span> -<span class="sd"> override maximum y.</span> -<span class="sd"> --cmin : float, optional</span> -<span class="sd"> override minimum colour.</span> -<span class="sd"> --cmax : float, optional</span> -<span class="sd"> override maximum colour.</span> - -<span class="sd"> Returns</span> -<span class="sd"> -------</span> - -<span class="sd"> decorator</span> -<span class="sd"> axes limits options decorator.</span> -<span class="sd"> """</span> - - <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--xmin'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Override minimum x.'</span><span class="p">,</span> - <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> - <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> - <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--xmax'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Override maximum x.'</span><span class="p">,</span> - <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> - <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> - <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--ymin'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Override minimum y.'</span><span class="p">,</span> - <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> - <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> - <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--ymax'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Override maximum y.'</span><span class="p">,</span> - <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> - <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> - <span class="k">if</span> <span class="n">c</span><span class="p">:</span> - <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--cmin'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Override minimum colour value.'</span><span class="p">,</span> - <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> - <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> - <span class="n">f</span> <span class="o">=</span> <span class="n">click</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s1">'--cmax'</span><span class="p">,</span> - <span class="n">help</span><span class="o">=</span><span class="s1">'Override maximum colour value.'</span><span class="p">,</span> - <span class="n">multiple</span><span class="o">=</span><span class="n">multiple</span><span class="p">,</span> - <span class="nb">type</span><span class="o">=</span><span class="nb">float</span><span class="p">)(</span><span class="n">f</span><span class="p">)</span> - <span class="k">return</span> <span class="n">f</span> - <span class="k">return</span> <span class="n">axes_limit_options</span></div> </pre></div> </div> diff --git a/docs/genindex.html b/docs/genindex.html index 421f6ad..e48356b 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -125,10 +125,10 @@ <h2 id="A">A</h2> </li> <li><a href="tp.plot.html#tp.plot.phonons.add_multi">add_multi() (in module tp.plot.phonons)</a> </li> - </ul></td> - <td style="width: 33%; vertical-align: top;"><ul> <li><a href="tp.plot.html#tp.plot.heatmap.add_pfdiff">add_pfdiff() (in module tp.plot.heatmap)</a> </li> + </ul></td> + <td style="width: 33%; vertical-align: top;"><ul> <li><a href="tp.plot.html#tp.plot.heatmap.add_pfmap">add_pfmap() (in module tp.plot.heatmap)</a> </li> <li><a href="tp.plot.html#tp.plot.phonons.add_projected_dispersion">add_projected_dispersion() (in module tp.plot.phonons)</a> @@ -142,6 +142,8 @@ <h2 id="A">A</h2> <li><a href="tp.plot.html#tp.plot.heatmap.add_ztdiff">add_ztdiff() (in module tp.plot.heatmap)</a> </li> <li><a href="tp.plot.html#tp.plot.heatmap.add_ztmap">add_ztmap() (in module tp.plot.heatmap)</a> +</li> + <li><a href="tp.cli.html#tp.cli.options.adminsitrative_options">adminsitrative_options() (in module tp.cli.options)</a> </li> <li><a href="tp.axes.html#tp.axes.legend.alphabetise">alphabetise() (in module tp.axes.legend)</a> </li> diff --git a/docs/index.html b/docs/index.html index dd7b61b..c8881be 100644 --- a/docs/index.html +++ b/docs/index.html @@ -85,7 +85,7 @@ <span class="o">|</span> <span class="o">|</span> <span class="o">|</span><span class="n">___</span> <span class="n">___</span> <span class="o">|</span><span class="n">___</span> <span class="o">|</span><span class="n">_____</span> <span class="n">___</span> <span class="p">:</span><span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="n">___</span> <span class="o">|</span><span class="n">___</span> <span class="n">___</span> <span class="n">___</span> <span class="o">|</span><span class="n">___</span> \ <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">/</span> \ <span class="o">|</span> \ <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">/</span> \<span class="p">:</span><span class="o">|</span> <span class="o">/</span> <span class="o">|</span> <span class="o">|</span> \ <span class="o">/</span> <span class="o">/</span> \ <span class="o">|</span> \<span class="o">/</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span><span class="p">:</span><span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span> <span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="o">|</span> \<span class="n">_____</span> -<span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span><span class="o">/</span><span class="p">:</span><span class="o">|</span> \<span class="n">___</span><span class="o">|</span><span class="n">_</span> <span class="o">|</span> \ \<span class="n">___</span> <span class="o">|</span> <span class="p">:</span><span class="mf">3.1</span><span class="o">.</span><span class="mi">3</span>\ +<span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> <span class="o">|</span> \<span class="n">___</span><span class="o">/</span><span class="p">:</span><span class="o">|</span> \<span class="n">___</span><span class="o">|</span><span class="n">_</span> <span class="o">|</span> \ \<span class="n">___</span> <span class="o">|</span> <span class="p">:</span><span class="mf">3.1</span><span class="o">.</span><span class="mi">4</span>\ <span class="o">|</span><span class="n">____________________________________</span><span class="p">:</span><span class="n">_______________________</span><span class="o">/</span><span class="n">____________</span><span class="p">:</span><span class="n">_____</span><span class="o">/</span> </pre></div> </div> @@ -247,6 +247,10 @@ <h1>Contributors<a class="headerlink" href="#contributors" title="Permalink to t <li><p>Katarina Brlec</p></li> <li><p>Joe Willis</p></li> </ul> +<p>Thanks also to the <a class="reference external" href="https://joss.theoj.org/">JOSS</a> reviewers, Evan Walter Clarke +Spotte-Smith, Enric Tomás Grau-Luque, and Francesco Nattino; and the +editor Mojtaba Barzegari. An unintimidating and productive review +process, which I would recommend if the opportunity arises!</p> </div> <div class="section" id="license"> <h1>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h1> diff --git a/docs/objects.inv b/docs/objects.inv index 75c8ec8..3faecc6 100644 Binary files a/docs/objects.inv and b/docs/objects.inv differ diff --git a/docs/searchindex.js b/docs/searchindex.js index ef53697..10d3c16 100644 --- a/docs/searchindex.js +++ b/docs/searchindex.js @@ -1 +1 @@ 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Rates","ThermoParser","Cumulative Lattice Thermal Conductivity","Density of States (DoS)","Gallery","Heatmaps","Installation","tp","Phonons","Projected Phonons","tp package","tp.axes package","tp.cli package","tp.data package","tp.plot package","tp.setup package","Tutorial-00: CLI Fundamentals","Tutorial-01: Python Foundations","Tutorial-02: Individual Customisation","Tutorial-03: Compound Axes","Tutorial-04: Layered Plots","Tutorial-05: Helper Functions","Tutorial-06: Package Customisation","Tutorial-0X: Miscellaneous 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\ No newline at end of file diff --git a/docs/tp.cli.html b/docs/tp.cli.html index 83259da..b5cc40c 100644 --- a/docs/tp.cli.html +++ b/docs/tp.cli.html @@ -108,6 +108,23 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this <div class="section" id="module-tp.cli.options"> <span id="tp-cli-options-module"></span><h2>tp.cli.options module<a class="headerlink" href="#module-tp.cli.options" title="Permalink to this headline">¶</a></h2> <p>Provides groups of options to streamline the CLI</p> +<dl class="py function"> +<dt id="tp.cli.options.adminsitrative_options"> +<code class="sig-prename descclassname">tp.cli.options.</code><code class="sig-name descname">adminsitrative_options</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">f</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tp/cli/options.html#adminsitrative_options"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tp.cli.options.adminsitrative_options" title="Permalink to this definition">¶</a></dt> +<dd><p>Help and version options.</p> +<p>Allows -h for help (click-nonstandard).</p> +<blockquote> +<div><dl class="option-list"> +<dt><kbd><span class="option">--help</span>, <span class="option">-h</span></kbd></dt> +<dd><p>show help and exit</p> +</dd> +<dt><kbd><span class="option">--version</span></kbd></dt> +<dd><p>show version and exit</p> +</dd> +</dl> +</div></blockquote> +</dd></dl> + <dl class="py function"> <dt id="tp.cli.options.axes_limit_function"> <code class="sig-prename descclassname">tp.cli.options.</code><code class="sig-name descname">axes_limit_function</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">multiple</span><span class="o">=</span><span class="default_value">False</span></em>, <em class="sig-param"><span class="n">c</span><span class="o">=</span><span class="default_value">False</span></em><span class="sig-paren">)</span><a class="reference internal" href="_modules/tp/cli/options.html#axes_limit_function"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#tp.cli.options.axes_limit_function" title="Permalink to this definition">¶</a></dt> diff --git a/docs/tutorial-00.html b/docs/tutorial-00.html index 58ef80a..84eb876 100644 --- a/docs/tutorial-00.html +++ b/docs/tutorial-00.html @@ -94,7 +94,7 @@ <h1>Tutorial-00: CLI Fundamentals<a class="headerlink" href="#tutorial-00-cli-fu available functions. Then type in all three parts to get a detailed description of how to use the function, e.g. <code class="docutils literal notranslate"><span class="pre">tp</span> <span class="pre">get</span> <span class="pre">zt</span></code>. If further arguments have been given, this can be accessed with -<code class="docutils literal notranslate"><span class="pre">--help</span></code>, but note <code class="docutils literal notranslate"><span class="pre">-h</span></code> is <em>not</em> a substitute for <code class="docutils literal notranslate"><span class="pre">--help</span></code>.</p> +<code class="docutils literal notranslate"><span class="pre">--help</span></code> or <code class="docutils literal notranslate"><span class="pre">-h</span></code>.</p> <p>Typically, you will need one or more data files, which are inputted directly after the command, e.g. <code class="docutils literal notranslate"><span class="pre">tp</span> <span class="pre">plot</span> <span class="pre">avg-rates</span> <span class="pre">mesh.h5</span></code>. The type of file is hinted at at the top of the <code class="docutils literal notranslate"><span class="pre">--help</span></code>, e.g. diff --git a/examples/00-cli-fundamentals/README.rst b/examples/00-cli-fundamentals/README.rst index f6424df..fe0ed46 100644 --- a/examples/00-cli-fundamentals/README.rst +++ b/examples/00-cli-fundamentals/README.rst @@ -10,7 +10,7 @@ type the full thing in, e.g. ``tp get``, to get a similar list of the available functions. Then type in all three parts to get a detailed description of how to use the function, e.g. ``tp get zt``. If further arguments have been given, this can be accessed with -``--help``, but note ``-h`` is *not* a substitute for ``--help``. +``--help`` or ``-h``. Typically, you will need one or more data files, which are inputted directly after the command, e.g. ``tp plot avg-rates mesh.h5``. The diff --git a/setup.py b/setup.py index 5a297d8..9a4e996 100644 --- a/setup.py +++ b/setup.py @@ -3,10 +3,10 @@ __name__ = 'ThermoParser' __author__ = 'Kieran B. Spooner' __copyright__ = 'Copyright Scanlon Materials Theory Group (2024)' -__version__ = '3.1.3' +__version__ = '3.1.4' # Remember to update the main README header too! __maintainer__ = 'Kieran B. Spooner' __email__ = 'k.b.spooner@bham.ac.uk' -__date__ = 'March 21st 2024' +__date__ = 'April 1st 2024' import os import setuptools @@ -63,6 +63,6 @@ def __init__(self, *args, **kwargs): install_requires=['click', 'h5py', 'matplotlib', 'numpy', 'pymatgen', 'pyyaml', 'scipy', 'setuptools', 'wheel'], extras_require={'docs': ['sphinx', 'sphinx_rtd_theme']}, - python_requires='>=3.6', + python_requires='>=3.8', cmdclass={'install': PostInstallMoveFile}, entry_points={'console_scripts': ['tp = tp.cli.cli:tp_cli']}) diff --git a/tp/__init__.py b/tp/__init__.py index ea1758b..7a12336 100644 --- a/tp/__init__.py +++ b/tp/__init__.py @@ -9,6 +9,8 @@ # default values and metadata #""" +__version__ = '3.1.4' + def docstring_replace(**kwargs): def d(f): f.__doc__ = f.__doc__.format(**kwargs) diff --git a/tp/cli/README.rst b/tp/cli/README.rst index 7e7ae79..306f436 100644 --- a/tp/cli/README.rst +++ b/tp/cli/README.rst @@ -8,8 +8,8 @@ practical differences for the user: 1. The modular structure: the overarching command is ``tp``, running this lists the sub commands, likewise with each of those (e.g. ``tp plot``). The full command currently has three parts, e.g. ``tp plot - waterfall``, after which you add the arguments. ``--help`` grants - information at every step. + waterfall``, after which you add the arguments. ``--help`` or ``-h`` + grants information at every step. 2. Multiple arguments must use the ``--thing`` every time, i.e. in ``argparse`` you may type ``-d a b c``, but in ``click`` you must type ``-d a -d b -d c``. The exception is in ``ztdiff``, where kappa diff --git a/tp/cli/cli.py b/tp/cli/cli.py index 08925d2..962a07a 100644 --- a/tp/cli/cli.py +++ b/tp/cli/cli.py @@ -64,18 +64,21 @@ from tp.cli.options import * @click.group() +@adminsitrative_options def tp_cli(): """Command line tools for transport properties.""" return @tp_cli.group() +@adminsitrative_options def gen(): """Tools for generating calculation inputs.""" return @gen.command(no_args_is_help=True) +@adminsitrative_options @kpoints_options def kpar(kpoints, mesh, poscar): """Suggests KPAR values for VASP. @@ -99,6 +102,7 @@ def kpar(kpoints, mesh, poscar): @gen.command(no_args_is_help=True) +@adminsitrative_options @kpoints_options @click.option('-z', '--zero-kpoints', '--zero-ibzkpt', help='IBZKPT file path. Overrides --zero-mesh.', @@ -137,12 +141,14 @@ def kpoints(kpoints, mesh, poscar, zero_kpoints, zero_mesh, output): @tp_cli.group() +@adminsitrative_options def get(): """Tools for accessing data.""" return @get.command('amset', no_args_is_help=True) +@adminsitrative_options @inputs_function('amset_file', nargs=1) @click.option('-q', '--quantity', help='Quantity to read.', @@ -270,6 +276,7 @@ def get_amset(amset_file, quantity, dtype, doping, direction, temperature, spin, return @get.command('occupation') +@adminsitrative_options @inputs_function('amset_mesh_file', nargs=1) @doping_type_option @doping_function() @@ -340,6 +347,7 @@ def get_occupation(amset_mesh_file, dtype, doping, temperature, spin, poscar): @get.command('boltztrap') +@adminsitrative_options @inputs_function('boltztrap_hdf5', nargs=1) @click.option('-q', '--quantity', help='Quantity to read.', @@ -399,6 +407,7 @@ def get_boltztrap(boltztrap_hdf5, quantity, dtype, doping, direction, temperatur @get.command('phono3py', no_args_is_help=True) +@adminsitrative_options @inputs_function('kappa_hdf5', nargs=1) @click.option('-q', '--quantity', help='Quantity to read.', @@ -492,6 +501,7 @@ def get_phono3py(kappa_hdf5, quantity, direction, temperature, band, qpoint, @get.command('zt', no_args_is_help=True) +@adminsitrative_options @inputs_function('transport_file', nargs=1) @click.option('-k', '--kappa', help='Phono3py kappa-mxxx.hdf5.', @@ -559,12 +569,14 @@ def get_zt(transport_file, kappa, dtype, doping, direction, temperature, max): @tp_cli.group() +@adminsitrative_options def run(): """Tools for transport properties postprocessing.""" return @run.command(no_args_is_help=True) +@adminsitrative_options @click.option('--tmin', help='Set minimum temperature in K. Does not speed up ' @@ -651,12 +663,14 @@ def boltztrap(tmin, tmax, tstep, dmin, dmax, ndope, relaxation_time, lpfac, @tp_cli.group() +@adminsitrative_options def save(): """Tools for saving data.""" return @save.command('cumkappa', no_args_is_help=True) +@adminsitrative_options @inputs_function('kappa_hdf5', nargs=1) @click.option('--mfp/--frequency', help='x-axis quantity. [default: frequency]', @@ -690,6 +704,7 @@ def save_cumkappa(kappa_hdf5, mfp, direction, temperature, output, extension): @save.command('kappa', no_args_is_help=True) +@adminsitrative_options @inputs_function('kappa_hdf5', nargs=1) @direction_function(multiple=True) @click.option('-o', '--output', @@ -720,6 +735,7 @@ def save_kappa(kappa_hdf5, direction, output): @save.command('zt', no_args_is_help=True) +@adminsitrative_options @inputs_function('transport_file', nargs=1) @click.option('-k', '--kappa', help='Phono3py kappa-mxxx.hdf5.', @@ -749,12 +765,14 @@ def save_zt(transport_file, kappa, dtype, direction, interpolate, kind, output): @tp_cli.group() +@adminsitrative_options def plot(): """Tools for plotting.""" return @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('mesh_h5') @click.option('--mfp/--rate', help='Plot mfp instead of rate. [default: rate]', @@ -978,6 +996,7 @@ def avg_rates(mesh_h5, mfp, total, x, crt, exclude, doping, direction, @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('kappa_hdf5') @click.option('--mfp/--frequency', help='x-axis quantity. [default: frequency]', @@ -1098,6 +1117,7 @@ def cumkappa(kappa_hdf5, mfp, percent, xmarkers, ymarkers, direction, @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('dos_dat', nargs=1) @dos_function() @fill_options @@ -1160,6 +1180,7 @@ def dos(dos_dat, poscar, atoms, sigma, projected, total, total_label, @plot.command(no_args_is_help=True) +@adminsitrative_options @click.option('-k', '--kfile', help='Thermal data filename(s). Required for a ' '--component of lattice or total.', @@ -1413,6 +1434,7 @@ def kappa(kfile, efile, component, direction, tmin, tmax, dtype, doping, @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('transport_file', nargs=1) @click.option('-z', '--zt', help='Target ZT.', @@ -1489,6 +1511,7 @@ def kappa_target(transport_file, zt, direction, interpolate, kind, colour, @plot.command('phonons', no_args_is_help=True) +@adminsitrative_options @inputs_function('band_yaml') @click.option('--bandmin', help='Minimum band index.', @@ -1600,6 +1623,7 @@ def converge_phonons(band_yaml, bandmin, bandmax, colour, alpha, linestyle, @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('transport_file') @click.option('-k', '--kfile', help='Thermal data filename(s). Required for a --quantity ' @@ -1994,6 +2018,7 @@ def transport(transport_file, kfile, quantity, direction, tmin, tmax, dtype, @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('kappa_hdf5', nargs=1) @click.option('-y', help='y-axis quantity. Options include frequency, kappa, ' @@ -2149,6 +2174,7 @@ def waterfall(kappa_hdf5, y, x, projected, direction, temperature, colour, alpha @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('band_yaml', nargs=1) @inputs_function('kappa_hdf5', nargs=1) @@ -2204,6 +2230,7 @@ def wideband(band_yaml, kappa_hdf5, temperature, poscar, colour, smoothing, styl @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('transport_file', nargs=1) @click.option('--pf/--zt', help='Power factor instead of ZT. [default: zt]', @@ -2280,6 +2307,7 @@ def ztmap(transport_file, pf, kappa, direction, dtype, interpolate, kind, @plot.command(no_args_is_help=True) +@adminsitrative_options @inputs_function('transport_files', nargs=2) @click.option('--pf/--zt', help='Power factor instead of ZT. [default: zt]', diff --git a/tp/cli/options.py b/tp/cli/options.py index 2466210..4b83bb2 100644 --- a/tp/cli/options.py +++ b/tp/cli/options.py @@ -3,6 +3,10 @@ #Functions #--------- # +# administrative_options +# function for help and version display. +# axes_limit_function +# function for setting the axis limits. # direction_function: # function for picking the --direction (-d). # doping_type_option: @@ -29,12 +33,100 @@ # function for picking the --temperature (-t). # verbose_option: # function for increasing the verbosity. -# axes_limit_function -# function for setting the axis limits. #""" import click +def adminsitrative_options(f): + """Help and version options. + + Allows -h for help (click-nonstandard). + + Options + ------- + + --help, -h + show help and exit + --version + show version and exit + """ + + f = click.help_option('-h', '--help')(f) + f = click.version_option(package_name='tp')(f) + + return f + +def axes_limit_function(multiple=False, c=False): + """Function for creating axes limit options. + + Arguments + --------- + + multiple : bool, optional + allow multiple limits. Default: False. + c : bool, optional + include colour limits. Default: False. + + Returns + ------- + decorator + axes limit options decorator. + """ + + def axes_limit_options(f): + """Options for axes limits. + + Options + ------- + + --xmin : float, optional + override minimum x. + --xmax : float, optional + override maximum x. + --ymin : float, optional + override minimum y. + --ymax : float, optional + override maximum y. + --cmin : float, optional + override minimum colour. + --cmax : float, optional + override maximum colour. + + Returns + ------- + + decorator + axes limits options decorator. + """ + + f = click.option('--xmin', + help='Override minimum x.', + multiple=multiple, + type=float)(f) + f = click.option('--xmax', + help='Override maximum x.', + multiple=multiple, + type=float)(f) + f = click.option('--ymin', + help='Override minimum y.', + multiple=multiple, + type=float)(f) + f = click.option('--ymax', + help='Override maximum y.', + multiple=multiple, + type=float)(f) + if c: + f = click.option('--cmin', + help='Override minimum colour value.', + multiple=multiple, + type=float)(f) + f = click.option('--cmax', + help='Override maximum colour value.', + multiple=multiple, + type=float)(f) + return f + return axes_limit_options + def direction_function(multiple=False): """Function to create direction options. @@ -625,74 +717,3 @@ def verbose_option(f): show_default=False)(f) return f - -def axes_limit_function(multiple=False, c=False): - """Function for creating axes limit options. - - Arguments - --------- - - multiple : bool, optional - allow multiple limits. Default: False. - c : bool, optional - include colour limits. Default: False. - - Returns - ------- - decorator - axes limit options decorator. - """ - - def axes_limit_options(f): - """Options for axes limits. - - Options - ------- - - --xmin : float, optional - override minimum x. - --xmax : float, optional - override maximum x. - --ymin : float, optional - override minimum y. - --ymax : float, optional - override maximum y. - --cmin : float, optional - override minimum colour. - --cmax : float, optional - override maximum colour. - - Returns - ------- - - decorator - axes limits options decorator. - """ - - f = click.option('--xmin', - help='Override minimum x.', - multiple=multiple, - type=float)(f) - f = click.option('--xmax', - help='Override maximum x.', - multiple=multiple, - type=float)(f) - f = click.option('--ymin', - help='Override minimum y.', - multiple=multiple, - type=float)(f) - f = click.option('--ymax', - help='Override maximum y.', - multiple=multiple, - type=float)(f) - if c: - f = click.option('--cmin', - help='Override minimum colour value.', - multiple=multiple, - type=float)(f) - f = click.option('--cmax', - help='Override maximum colour value.', - multiple=multiple, - type=float)(f) - return f - return axes_limit_options