Add yaml for pytest

cad-polito-it · Aug 23, 2023 · 3a3b19e · 3a3b19e
1 parent 8347a96
commit 3a3b19e
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Showing 15 changed files with 95 additions and 138 deletions.
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -0,0 +1,28 @@
+name: Run Python tests
+
+on: [push]
+
+jobs:
+  build:
+    name: Run tests
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - uses: szenius/set-timezone@v1.2
+        with:
+          timezoneLinux: "Europe/Berlin"
+      - uses: actions/checkout@v3
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Install dependencies
+        run: pip install pytest pytest-md
+      - uses: pavelzw/pytest-action@v2.1.0
+        with:
+          emoji: false
+          verbose: true
+          job-summary: true
diff --git a/README.md b/README.md
@@ -4,7 +4,7 @@
 [![License: Apache 2.0](https://img.shields.io/badge/license-apache--2.0-green.svg)](https://opensource.org/licenses/Apache-2.0) 
 [![Status: Actrive](https://img.shields.io/badge/status-active-brightgreen.svg)](https://github.com/cad-polito-it/byron)
 ![Language: Python](https://img.shields.io/badge/language-python-blue.svg)
-![Version: 0.1.dev2](https://img.shields.io/badge/version-0.8a1.dev12-orange.svg)
+![Version: 0.1.dev2](https://img.shields.io/badge/version-0.8a1.dev13-orange.svg)
 ![Codename: Don Juan](https://img.shields.io/badge/codename-Don_Juan-pink.svg)
 [![Documentation Status](https://readthedocs.org/projects/byron/badge/?version=pre-alpha)](https://byron.readthedocs.io/en/pre-alpha/?badge=pre-alpha)
 

diff --git a/byron/classes/individual.py b/byron/classes/individual.py
@@ -365,7 +365,7 @@ def run_paranoia_checks(self) -> bool:
 
         # ==[check nodes (semantic)]=========================================
         assert all(
-            n < self._genome.graph["node_count"] for n in self._genome
+            n < self._genome.graph['node_count'] for n in self._genome
         ), f"{PARANOIA_VALUE_ERROR}: Invalid 'node_count' attribute ({self._genome.graph['node_count']})"
 
         assert all(
@@ -402,6 +402,12 @@ def run_paranoia_checks(self) -> bool:
 
         return True
 
+    def consolidate_genome(self) -> None:
+        self._genome = nx.convert_node_labels_to_integers(self._genome)
+        fasten_subtree_parameters(NodeReference(self._genome, NODE_ZERO))
+        self._genome.graph['node_count'] = len(self._genome)
+        self.run_paranoia_checks()
+
     def describe(
         self,
         *,

diff --git a/byron/global_symbols.py b/byron/global_symbols.py
@@ -64,7 +64,7 @@
 from collections import defaultdict
 import multiprocessing
 
-__version__ = "0.8a1.dev12"
+__version__ = "0.8a1.dev13"
 __date__ = "23-08-2023"
 __codename__ = "Don Juan"
 __author__ = "Giovanni Squillero and Alberto Tonda"

diff --git a/byron/operators/_graph_crossover.py b/byron/operators/_graph_crossover.py
@@ -71,6 +71,6 @@ def bunch_random_crossover(p1: Individual, p2: Individual, strength=1.0) -> list
         offspring.genome.add_edge(ed[0], first_locus, **ed[1])
     # offspring._Individual__COUNTER == max(offspring.genome.nodes)
 
-    offspring.genome.graph["node_count"] = max(offspring.genome.nodes) + 1
+    offspring.genome.graph['node_count'] = max(offspring.genome.nodes) + 1
 
     return [offspring]
diff --git a/byron/tools/graph.py b/byron/tools/graph.py
@@ -51,8 +51,8 @@
 
 
 def add_node(G: nx.MultiDiGraph) -> int:
-    node_id = G.graph["node_count"]
-    G.graph["node_count"] += 1
+    node_id = G.graph['node_count']
+    G.graph['node_count'] += 1
     G.add_node(node_id)
     return node_id
 

diff --git a/docs/byron.png b/docs/byron.png
diff --git a/examples/tutorials/constraints/01. macro+parameters.ipynb b/examples/tutorials/constraints/01. macro+parameters.ipynb
@@ -35,7 +35,7 @@
      "text": [
       "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_14867/1429530752.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/pre-alpha/docs/paranoia.md for details]\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
       "  import byron\n"
      ]
     }

diff --git a/examples/tutorials/constraints/02. frames.ipynb b/examples/tutorials/constraints/02. frames.ipynb
@@ -27,7 +27,7 @@
      "text": [
       "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_14886/1429530752.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/pre-alpha/docs/paranoia.md for details]\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
       "  import byron\n"
      ]
     }

diff --git a/examples/tutorials/constraints/03. local references.ipynb b/examples/tutorials/constraints/03. local references.ipynb
@@ -27,7 +27,7 @@
      "text": [
       "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_13920/1429530752.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/pre-alpha/docs/paranoia.md for details]\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
       "  import byron\n"
      ]
     }

diff --git a/examples/tutorials/constraints/04. global references.ipynb b/examples/tutorials/constraints/04. global references.ipynb
@@ -27,7 +27,7 @@
      "text": [
       "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_13937/1429530752.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/pre-alpha/docs/paranoia.md for details]\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
       "  import byron\n"
      ]
     }

diff --git a/examples/tutorials/constraints/05. checks.ipynb b/examples/tutorials/constraints/05. checks.ipynb
@@ -27,7 +27,7 @@
      "text": [
       "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_14015/1429530752.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/pre-alpha/docs/paranoia.md for details]\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
       "  import byron\n"
      ]
     }

diff --git a/examples/tutorials/onemax-go.ipynb b/examples/tutorials/onemax-go.ipynb
@@ -40,7 +40,7 @@
      "text": [
       "/var/folders/31/dkl97hks2c14b663vl55pt440000gn/T/ipykernel_11165/826285489.py:1: RuntimeWarning: \n",
       "  Paranoia checks are enabled in this notebook: performances can be significantly impaired\n",
-      "  [see https://github.com/cad-polito-it/byron/blob/pre-alpha/docs/paranoia.md for details]\n",
+      "  [see https://github.com/cad-polito-it/byron/blob/alpha/docs/paranoia.md for details]\n",
       "  import byron\n"
      ]
     }