Merge remote-tracking branch 'origin/main'

AutoResearch · Apr 7, 2023 · 3792d09 · 3792d09
2 parents ed6cc30 + 30b3637
commit 3792d09
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diff --git a/.idea/autora.iml b/.idea/autora.iml
diff --git a/README.md b/README.md
@@ -398,8 +398,7 @@ The release process is automated using GitHub Actions.
 - Before you start, ensure that the tokens are up-to-date. If in doubt, try to create and publish a new release 
   candidate version of the package first. The tokens are stored as "organization secrets" enabled for the autora 
   repository, and are called:
-  - PYPI_TOKEN: a token from pypi.org with upload permissions on the AutoResearch/AutoRA project. Current token 
-    expires on 2023-03-01.
+  - PYPI_TOKEN: a token from pypi.org with upload permissions on the AutoResearch/AutoRA project.
   - ANACONDA_TOKEN: a token from anaconda.org with the following scopes on the AutoResearch organization: `repos conda
     api:read api:write`. Current token expires on 2023-03-01.
 - Update [conda recipe](./conda/autora/meta.yaml): 

diff --git a/example/cycle/cycle_results_plots.ipynb → docs/cycle/cycle_results_plots.ipynb b/example/cycle/cycle_results_plots.ipynb → docs/cycle/cycle_results_plots.ipynb
@@ -6,20 +6,26 @@
     " # Examples of using cycle results plotting functions"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "# Uncomment the following line when running on Google Colab\n",
+    "# !pip install autora"
+   ],
+   "metadata": {
+    "collapsed": false
    }
   },
   {
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {
-    "collapsed": true,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": true
    },
    "outputs": [],
    "source": [
@@ -99,10 +105,7 @@
     "cycle.run(5)"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -115,10 +118,7 @@
     "* Default panel configuration is 4 plots to a row."
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -139,10 +139,7 @@
     "plot_results_panel_2d(cycle);  # Add semicolon to supress creating two figures in jupyter notebook"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -151,10 +148,7 @@
     "### Default parameters can be changed by passing in keywords"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -178,10 +172,7 @@
     "                      );"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -194,10 +185,7 @@
     "   * Below shows ways to specify the parameters of the [scatter](https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.scatter.html) points and theory [line](https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.plot.html)."
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -224,10 +212,7 @@
     "                      );"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -236,10 +221,7 @@
     "Saving the figure to an object (above) will allow you to cycle through the axes to make panel-specific edits."
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -265,10 +247,7 @@
     "fig\n"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -280,10 +259,7 @@
     "2. **Slice**: Constructed with `slice()` or `np.s_[]`"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -334,10 +310,7 @@
     "fig.suptitle('Last Cycle')"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -370,10 +343,7 @@
     "fig.supxlabel('x1', y=0.1)"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -423,10 +393,7 @@
     "fig2.suptitle('Last 2 Cycles')"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -436,10 +403,7 @@
     "The 3D plotter has similar functionality as the 2D plotter but will only work with problem spaces where there are exactly 2 independent variable values. Only one dependent value can be plotted at a time."
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -508,10 +472,7 @@
     "cycle_mlr.run(5)"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -532,10 +493,7 @@
     "fig = plot_results_panel_3d(cycle_mlr);  # Add semicolon to supress creating two figures in jupyter notebook"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -559,10 +517,7 @@
     "                      );"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -589,10 +544,7 @@
     "                            );\n"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -607,10 +559,7 @@
     "</div>\n"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%% md\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -638,10 +587,7 @@
     "                            );"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   },
   {
@@ -669,10 +615,7 @@
     "                            );\n"
    ],
    "metadata": {
-    "collapsed": false,
-    "pycharm": {
-     "name": "#%%\n"
-    }
+    "collapsed": false
    }
   }
  ],
@@ -697,4 +640,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 0
-}
+}