SPECIES Summer School

cad-polito-it · Sep 7, 2023 · 3057f67 · 3057f67
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diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -20,7 +20,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
-        run: pip install pytest pytest-md networkx numpy scipy tqdm rich joblib
+        run: pip install pytest pytest-md networkx numpy scipy tqdm rich joblib psutil
       - uses: pavelzw/pytest-action@v2.1.0
         with:
           emoji: false

diff --git a/byron/user_messages/messaging.py b/byron/user_messages/messaging.py
@@ -123,18 +123,22 @@ def syntax_warning_hint(message: str, stacklevel_offset: int = 0) -> bool:
 from rich import highlighter as rich_highlighter
 
 
-# console_formatter = logging.Formatter('%(asctime)s ▷ %(levelname)s ▷ %(name)s::%(message)s', datefmt='%H:%M:%S')
 # console_handler = logging.StreamHandler()
 # console_handler.setFormatter(console_formatter)
-console_handler = rich_logging.RichHandler(
-    log_time_format='%H:%M:%S',  # '%H:%M:%S.%f'
-    omit_repeated_times=False,
-    show_path=False,
-    markup=True,
-    highlighter=rich_highlighter.NullHighlighter(),
-    keywords=['▷'],
-)
-console_formatter = logging.Formatter('▷ %(message)s')
+if notebook_mode:
+    console_handler = logging.StreamHandler()
+    # console_formatter = logging.Formatter('%(asctime)s ▷ %(levelname)s ▷ %(name)s::%(message)s', datefmt='%H:%M:%S')
+    console_formatter = logging.Formatter('%(levelname)s ▷ %(message)s')
+else:
+    console_handler = rich_logging.RichHandler(
+        log_time_format='%H:%M:%S',  # '%H:%M:%S.%f'
+        omit_repeated_times=False,
+        show_path=False,
+        markup=True,
+        highlighter=rich_highlighter.NullHighlighter(),
+        keywords=['▷'],
+    )
+    console_formatter = logging.Formatter('▷ %(message)s')
 console_handler.setFormatter(console_formatter)
 logger.handlers = [console_handler]
 # logger.handlers = []

diff --git a/docs/pypi.md b/docs/pypi.md
@@ -15,11 +15,19 @@ Candidate solutions are dumped as text and then evaluated by calling a user-defi
 
 **⚠️ Byron is currently in [alpha](https://en.wikipedia.org/wiki/Software_release_life_cycle#Alpha) and under active development**
 
+As simple as
+
 ```
 pip install --upgrade byron
 ```
 
-Few optional dependencies can enhance Byron, but are not strictly required:
+Few optional dependencies can enhance Byron, but are not strictly required. You can get them with
+
+```
+pip install --upgrade "byron[full]"
+```
+
+or install optional modules one by one
 
 ```
 pip install --upgrade matplotlib
@@ -29,7 +37,7 @@ pip install --upgrade psutil
 
 ## Documentation
 
-Some HOWTO's and examples are available as Jupyter notebooks in the [examples directory](https://github.com/cad-polito-it/byron/tree/pre-alpha/examples/notebooks).
+None yet, but some HOWTO's and examples [are available](https://github.com/cad-polito-it/byron/tree/alpha/examples) in the repo.
 
 ## Contacts
 

diff --git a/examples/onemax/onemax-go/onemax-go.ipynb b/examples/onemax/onemax-go/onemax-go.ipynb
@@ -0,0 +1,263 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "cf8d4bbc-9fe2-43b8-945d-403e6f91b190",
+   "metadata": {},
+   "source": [
+    "This notebook is part of [**Byron v0.8**](https://pypi.org/project/byron/)  \n",
+    "Copyright 2023 Giovanni Squillero and Alberto Tonda  \n",
+    "SPDX-License-Identifier: [Apache-2.0](https://opensource.org/license/apache-2-0/) "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "3bb17efa-7918-4bfe-a5dd-d4a6bcf08165",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:15.766070Z",
+     "start_time": "2023-09-07T21:23:15.760095Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "from pprint import pprint\n",
+    "import logging"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "43a1401d-bf66-4725-83cf-5907f9407928",
+   "metadata": {},
+   "source": [
+    "# Onemax in Go"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "52ad6183-c167-4768-b57c-e91244e29584",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:16.946969Z",
+     "start_time": "2023-09-07T21:23:15.767477Z"
+    }
+   },
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_23482/1429530752.py:1: ByronPerformanceWarning: \n",
+      "  Paranoia checks are enabled in this notebook: performances can be significantly impaired\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
+      "  import byron\n"
+     ]
+    }
+   ],
+   "source": [
+    "import byron"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "outputs": [],
+   "source": [
+    "import golang\n",
+    "\n",
+    "top_frame = golang.framework()"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:16.994590Z",
+     "start_time": "2023-09-07T21:23:16.944536Z"
+    }
+   },
+   "id": "f1cdfbb3ff40b342"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "outputs": [],
+   "source": [
+    "@byron.fitness_function\n",
+    "def dummy_fitness(text):\n",
+    "    return 1 / len(text)"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:17.014319Z",
+     "start_time": "2023-09-07T21:23:16.991071Z"
+    }
+   },
+   "id": "936c134dc57395a7"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "70a6fb4c-9caf-4675-9e55-eb8a792aea1a",
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:17.020873Z",
+     "start_time": "2023-09-07T21:23:16.991832Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "evaluator = byron.evaluator.PythonEvaluator(dummy_fitness)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO ▷ VanillaEA: 🍦 [b]VanillaEA started[/] ┈ ⌛ 0:00:00.00 [t] / ⏱️  0:00:00.00 [byron]\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢1/random_individual() is 0.0049505Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢2/random_individual() is 0.00184162Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢3/random_individual() is 0.00196078Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢4/random_individual() is 0.00155763Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢6/random_individual() is 0.00171821Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢7/random_individual() is 0.00395257Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢8/random_individual() is 0.00219298Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢10/random_individual() is 0.00409836Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢11/random_individual() is 0.00371747Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢13/random_individual() is 0.00369004Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢14/random_individual() is 0.00221729Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢15/random_individual() is 0.00454545Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢16/random_individual() is 0.00244499Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢17/random_individual() is 0.00255102Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢18/random_individual() is 0.00223214Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢19/random_individual() is 0.00289855Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢22/random_individual() is 0.00309598Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢24/random_individual() is 0.0010661Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢27/random_individual() is 0.00367647Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢29/random_individual() is 0.003861Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢32/random_individual() is 0.0018797Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢33/random_individual() is 0.00137174Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢34/random_individual() is 0.00154799Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢35/random_individual() is 0.00179533Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢36/random_individual() is 0.00414938Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢37/random_individual() is 0.00180505Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢38/random_individual() is 0.0035461Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢39/random_individual() is 0.00107875Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢40/random_individual() is 0.00150376Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢41/random_individual() is 0.00172414Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢44/random_individual() is 0.00423729Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢45/random_individual() is 0.00126103Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢46/random_individual() is 0.00144092Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢47/random_individual() is 0.00258398Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢48/random_individual() is 0.00200803Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢49/random_individual() is 0.00230947Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢50/random_individual() is 0.00161031Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢51/random_individual() is 0.00423729Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢52/random_individual() is 0.00185529Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢54/random_individual() is 0.00178571Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢55/random_individual() is 0.00181818Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢56/random_individual() is 0.00212314Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢57/random_individual() is 0.00214133Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢58/random_individual() is 0.00440529Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢59/random_individual() is 0.00147493Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢60/random_individual() is 0.00299401Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢64/random_individual() is 0.00302115Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢65/random_individual() is 0.00229358Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢66/random_individual() is 0.00136612Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢67/random_individual() is 0.00363636Ƒ\n",
+      "INFO ▷ VanillaEA: 🍀 𝐢1 ⇨ fitness: 0.0049505Ƒ / ⚝ 0\n",
+      "INFO ▷ VanillaEA: End of initialization ┈ ⌛ 0:00:00.61 [t] / 🏃 0:00:00.01\n",
+      "DEBUG ▷ generic_node_crossover: n870/Macro❬Text#1❭ <-> n590/Macro❬Text#1❭\n",
+      "DEBUG ▷ generic_node_crossover: n986/Macro❬Text#1❭ <-> n995/Macro❬Text#1❭\n",
+      "DEBUG ▷ generic_node_crossover: Failed (invalid structure)\n",
+      "DEBUG ▷ generic_node_crossover: n120/Frame❬FrameSequence#1❭ <-> n540/Frame❬FrameSequence#1❭\n",
+      "DEBUG ▷ generic_node_crossover: n1056/Frame❬FrameSequence#1❭ <-> n375/Frame❬FrameSequence#1❭\n",
+      "DEBUG ▷ generic_node_crossover: n106/Macro❬User#2❭ <-> n570/Macro❬User#2❭\n",
+      "DEBUG ▷ generic_node_crossover: Failed (invalid structure)\n",
+      "DEBUG ▷ generic_node_crossover: n220/Macro❰prologue❱ <-> n643/Macro❰prologue❱\n",
+      "DEBUG ▷ is_valid: Failed check on n1543: functools.partial(<function _check_instances_number at 0x12dca2e80>, max_instances=1)\n",
+      "DEBUG ▷ generic_node_crossover: Failed (invalid individual)\n",
+      "DEBUG ▷ generic_node_crossover: n1129/Macro❬Text#1❭ <-> n712/Macro❬Text#1❭\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢68/add_macro_to_bunch(𝐢67) is 0.003367Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢70/remove_macro_from_bunch(𝐢11) is 0.00403226Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢71/node_crossover_choosy(𝐢45, 𝐢33) is 0.00116144Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢72/single_parameter_mutation(𝐢6) is 0.00162866Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢74/single_parameter_mutation(𝐢58) is 0.00440529Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢75/leaf_crossover_unfussy(𝐢7, 𝐢32) is 0.00176678Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢76/leaf_crossover_unfussy(𝐢55, 𝐢24) is 0.00101937Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢78/single_parameter_mutation(𝐢44) is 0.00404858Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢79/add_macro_to_bunch(𝐢11) is 0.00325733Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢80/single_parameter_mutation(𝐢44) is 0.00401606Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢82/add_macro_to_bunch(𝐢60) is 0.00280899Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢84/add_macro_to_bunch(𝐢19) is 0.0025641Ƒ\n",
+      "DEBUG ▷ Individual: Fitness of 𝐢85/node_crossover_unfussy(𝐢59, 𝐢39) is 0.00143885Ƒ\n",
+      "INFO ▷ VanillaEA: End of generation 1 (𝐻: 6.3888) ┈ ⌛ 0:00:00.95 [t] / 🏃 0:00:00.01\n",
+      "INFO ▷ VanillaEA: 🍦 [b]VanillaEA completed[/] ┈ ⌛ 0:00:00.95 [t] / ⏱️  0:00:00.95 [byron]\n",
+      "INFO ▷ VanillaEA: 🏆 𝐢1 ⇨ fitness: 0.0049505Ƒ / ⚝ 0 / random_individual()\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": "<byron.classes.population.Population at 0x10f486a90>"
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "byron.ea.vanilla_ea(\n",
+    "        top_frame, evaluator, max_generation=1, mu=50, lambda_=20, max_fitness=64.0\n",
+    "    )"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:17.959181Z",
+     "start_time": "2023-09-07T21:23:16.997064Z"
+    }
+   },
+   "id": "b5294736a8ac382a"
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "outputs": [],
+   "source": [],
+   "metadata": {
+    "collapsed": false,
+    "ExecuteTime": {
+     "end_time": "2023-09-07T21:23:17.959508Z",
+     "start_time": "2023-09-07T21:23:17.956804Z"
+    }
+   },
+   "id": "101801adf0d0415b"
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.4"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}