solvoing jupyter conflicts, it seems like the ruff routine is doing w…

…eird things to the jupyter
SainsburyWellcomeCentre · Oct 15, 2024 · cdbbd98 · cdbbd98
2 parents d3540a4 + 24be1d0
commit cdbbd98
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -17,10 +17,10 @@ repos:
           - id: trailing-whitespace
             exclude: 'README.md'
     - repo: https://github.com/astral-sh/ruff-pre-commit
-      rev: v0.5.0
+      rev: v0.6.3
       hooks:
         - id: ruff
     - repo: https://github.com/psf/black
-      rev: 24.4.2
+      rev: 24.8.0
       hooks:
           - id: black
diff --git a/examples/agent_examples/stachenfeld_2018_examples.ipynb b/examples/agent_examples/stachenfeld_2018_examples.ipynb
@@ -37,15 +37,14 @@
    "outputs": [],
    "source": [
     "import sys\n",
-    "import numpy as np\n",
-    "import random\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "from scipy.stats import multivariate_normal\n",
     "from tqdm.notebook import tqdm\n",
-    "from neuralplayground.arenas import Simple2D, MergingRoom, Sargolini2006, Hafting2008, BasicSargolini2006,Wernle2018\n",
-    "from neuralplayground.utils import create_circular_wall\n",
-    "from neuralplayground.agents import  Stachenfeld2018\n"
+    "\n",
+    "from neuralplayground.agents import Stachenfeld2018\n",
+    "from neuralplayground.arenas import Hafting2008, MergingRoom, Sargolini2006, Simple2D, Wernle2018\n",
+    "from neuralplayground.utils import create_circular_wall\n"
    ]
   },
   {
@@ -2311,17 +2310,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sys\n",
     "sys.path.append(\"../\")\n",
-    "import numpy as np\n",
-    "import random\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
-    "from scipy.stats import multivariate_normal\n",
     "from tqdm import tqdm\n",
-    "from neuralplayground.arenas import Simple2D, MergingRoom, Sargolini2006, Hafting2008, BasicSargolini2006,Wernle2018\n",
-    "from neuralplayground.utils import create_circular_wall\n",
-    "from neuralplayground.agents import  Stachenfeld2018"
+    "\n",
+    "from neuralplayground.agents import Stachenfeld2018\n",
+    "from neuralplayground.arenas import Hafting2008, MergingRoom, Sargolini2006, Simple2D"
    ]
   },
   {

diff --git a/examples/agent_examples/weber_2018_example.ipynb b/examples/agent_examples/weber_2018_example.ipynb
@@ -66,16 +66,16 @@
     }
    ],
    "source": [
-    "from IPython.display import display, HTML\n",
+    "from IPython.display import HTML, display\n",
+    "\n",
     "display(HTML(\"<style>.container { width:80% !important; }</style>\"))\n",
-    "import sys\n",
-    "from tqdm.notebook import tqdm\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "from neuralplayground.arenas import Simple2D, MergingRoom, Sargolini2006, Hafting2008, BasicSargolini2006,Wernle2018\n",
-    "from neuralplayground.agents import Weber2018, RandomAgent, LevyFlightAgent\n",
-    "from neuralplayground.experiments import Wernle2018Data\n",
-    "from neuralplayground.arenas import Simple2D,Wernle2018,  MergingRoom"
+    "import numpy as np\n",
+    "from tqdm.notebook import tqdm\n",
+    "\n",
+    "from neuralplayground.agents import Weber2018\n",
+    "from neuralplayground.arenas import MergingRoom, Sargolini2006, Simple2D\n",
+    "from neuralplayground.experiments import Wernle2018Data"
    ]
   },
   {
@@ -1309,6 +1309,7 @@
    ],
    "source": [
     "from neuralplayground.comparison import GridScorer\n",
+    "\n",
     "r_out_im=agent.get_rate_map_matrix()\n",
     "GridScorer_Stachenfeld2018 = GridScorer(agent.resolution_width)\n",
     "GridScorer_Stachenfeld2018.plot_grid_score(r_out_im=r_out_im, plot= True)\n",

diff --git a/examples/agent_examples/whittington_2020_example.ipynb b/examples/agent_examples/whittington_2020_example.ipynb
@@ -24,12 +24,11 @@
     "import importlib\n",
     "import os\n",
     "import pickle\n",
+    "\n",
     "import pandas as pd\n",
-    "import matplotlib.pyplot as plt\n",
     "\n",
-    "import neuralplayground.agents.whittington_2020_extras.whittington_2020_analyse as analyse\n",
-    "from neuralplayground.plotting import PlotSim\n",
-    "from neuralplayground.comparison import GridScorer"
+    "from neuralplayground.comparison import GridScorer\n",
+    "from neuralplayground.plotting import PlotSim"
    ]
   },
   {
@@ -56,6 +55,7 @@
    "source": [
     "simulation_id = \"TEM_custom_plot_sim\"\n",
     "from neuralplayground.saved_models import fetch_model_path\n",
+    "\n",
     "save_path = fetch_model_path(\"whittington_2020_in_discritized_objects\")\n",
     "print('save_path')\n",
     "plotting_loop_params = {\"n_episode\": 5000}"
@@ -475,7 +475,7 @@
     }
    ],
    "source": [
-    "agent.plot_rate_map(rate_map_type='g');\n",
+    "agent.plot_rate_map(rate_map_type='g')\n",
     "agent.plot_rate_map(rate_map_type='p');"
    ]
   },

diff --git a/examples/arena_examples/arena_examples.ipynb b/examples/arena_examples/arena_examples.ipynb
@@ -42,10 +42,11 @@
     }
    ],
    "source": [
-    "from IPython.display import display, HTML\n",
+    "from IPython.display import HTML, display\n",
+    "\n",
     "display(HTML(\"<style>.container { width:80% !important; }</style>\"))\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np"
    ]
   },
   {
@@ -61,7 +62,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.arenas import Simple2D, ConnectedRooms"
+    "from neuralplayground.arenas import ConnectedRooms, Simple2D"
    ]
   },
   {
@@ -97,7 +98,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.agents import RandomAgent, LevyFlightAgent, RatMovementAgent\n",
+    "from neuralplayground.agents import RatMovementAgent\n",
+    "\n",
     "# Random agent generates a brownian motion. Levy flight is still experimental.\n",
     "# agent = LevyFlightAgent(step_size=0.8, scale=2.0, loc=0.0, beta=1.0, alpha=0.5, max_action_size=100)\n",
     "agent = RatMovementAgent(step_size=1.0, room_width=room_width, room_depth=room_depth)"
@@ -444,7 +446,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.arenas import BatchEnvironment, Simple2D, DiscreteObjectEnvironment\n",
+    "from neuralplayground.arenas import BatchEnvironment, Simple2D\n",
     "from neuralplayground.experiments import Sargolini2006Data"
    ]
   },
@@ -538,9 +540,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.arenas import Sargolini2006\n",
-    "from neuralplayground.arenas import Hafting2008\n",
-    "from neuralplayground.arenas import Wernle2018"
+    "from neuralplayground.arenas import Hafting2008, Sargolini2006, Wernle2018"
    ]
   },
   {

diff --git a/examples/colab_example.ipynb b/examples/colab_example.ipynb
@@ -58,7 +58,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import neuralplayground\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "from tqdm import tqdm"
@@ -302,7 +301,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.arenas import Simple2D, ConnectedRooms"
+    "from neuralplayground.arenas import Simple2D"
    ]
   },
   {
@@ -311,7 +310,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.agents import RandomAgent, LevyFlightAgent\n",
+    "from neuralplayground.agents import LevyFlightAgent\n",
+    "\n",
     "# Random agent generates a brownian motion. Levy flight is still experimental.\n",
     "agent = LevyFlightAgent(step_size=0.8, scale=2.0, loc=0.0, beta=1.0, alpha=0.5, max_action_size=100)"
    ]
@@ -541,10 +541,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.saved_models import fetch_model_path\n",
     "import pandas as pd\n",
+    "\n",
     "from neuralplayground.comparison import GridScorer\n",
-    "from neuralplayground.plotting.plot_utils import make_plot_trajectories , make_plot_rate_map, make_agent_comparison"
+    "from neuralplayground.plotting.plot_utils import make_agent_comparison\n",
+    "from neuralplayground.saved_models import fetch_model_path"
    ]
   },
   {

diff --git a/examples/comparisons_examples/comparison_board.ipynb b/examples/comparisons_examples/comparison_board.ipynb
@@ -41,21 +41,22 @@
     }
    ],
    "source": [
-    "from IPython.display import display, HTML\n",
+    "from IPython.display import HTML, display\n",
+    "\n",
     "display(HTML(\"<style>.container { width:80% !important; }</style>\"))\n",
-    "import numpy as np\n",
-    "from tqdm.notebook import tqdm\n",
-    "import pandas as pd\n",
     "import os\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "from tqdm.notebook import tqdm\n",
     "\n",
-    "from neuralplayground.experiments import Wernle2018Data, Hafting2008Data, Sargolini2006Data\n",
+    "from neuralplayground.agents import Stachenfeld2018, Weber2018\n",
+    "from neuralplayground.arenas import MergingRoom, Simple2D\n",
     "from neuralplayground.comparison import GridScorer\n",
-    "from neuralplayground.arenas import Simple2D, ConnectedRooms,Wernle2018, MergingRoom, Sargolini2006\n",
-    "from neuralplayground.agents import Weber2018, Stachenfeld2018\n",
-    "from neuralplayground.experiments import Wernle2018Data, Hafting2008Data\n",
-    "from neuralplayground.saved_models import fetch_model_path\n",
-    "from neuralplayground.plotting.plot_utils import make_plot_trajectories , make_plot_rate_map, make_agent_comparison"
+    "from neuralplayground.experiments import Sargolini2006Data, Wernle2018Data\n",
+    "from neuralplayground.plotting.plot_utils import make_agent_comparison\n",
+    "from neuralplayground.saved_models import fetch_model_path"
    ]
   },
   {
@@ -295,10 +296,7 @@
     }
    ],
    "source": [
-    "from neuralplayground.agents import  Stachenfeld2018, Weber2018\n",
-    "from neuralplayground.arenas import Simple2D, MergingRoom, Sargolini2006, Hafting2008, BasicSargolini2006,Wernle2018\n",
-    "from neuralplayground.backend import default_training_loop, episode_based_training_loop\n",
-    "\n",
+    "from neuralplayground.backend import episode_based_training_loop\n",
     "\n",
     "stachenfeld_in_2d_params = {\n",
     "    \"simulation_id\": \"stachenfeld_2018_in_simple2D\",\n",

diff --git a/examples/comparisons_examples/comparison_examples_score.ipynb b/examples/comparisons_examples/comparison_examples_score.ipynb
@@ -33,14 +33,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import sys\n",
-    "from tqdm.notebook import tqdm\n",
     "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
-    "from neuralplayground.arenas import Wernle2018, MergingRoom, Sargolini2006, Simple2D, BasicSargolini2006,Hafting2008\n",
-    "from neuralplayground.agents import Weber2018, Stachenfeld2018, RandomAgent, LevyFlightAgent\n",
-    "from neuralplayground.experiments import Wernle2018Data, Hafting2008Data, Sargolini2006Data\n",
-    "from neuralplayground.comparison import GridScorer\n"
+    "from tqdm.notebook import tqdm\n",
+    "\n",
+    "from neuralplayground.agents import Stachenfeld2018, Weber2018\n",
+    "from neuralplayground.arenas import Hafting2008, Sargolini2006, Simple2D, Wernle2018\n",
+    "from neuralplayground.comparison import GridScorer\n",
+    "from neuralplayground.experiments import Hafting2008Data, Sargolini2006Data, Wernle2018Data\n"
    ]
   },
   {
@@ -62,7 +61,8 @@
     }
    ],
    "source": [
-    "from IPython.display import display, HTML\n",
+    "from IPython.display import HTML, display\n",
+    "\n",
     "display(HTML(\"<style>.container { width:80% !important; }</style>\"))"
    ]
   },
@@ -1259,10 +1259,9 @@
     "import importlib\n",
     "import os\n",
     "import pickle\n",
+    "\n",
     "import pandas as pd\n",
-    "import torch\n",
-    "import matplotlib.pyplot as plt\n",
-    "import neuralplayground.agents.whittington_2020_extras.whittington_2020_analyse as analyse\n",
+    "\n",
     "from neuralplayground.plotting import PlotSim"
    ]
   },
@@ -1274,6 +1273,7 @@
    "source": [
     "simulation_id = \"TEM_custom_plot_sim\"\n",
     "from neuralplayground.saved_models import fetch_model_path\n",
+    "\n",
     "save_path = fetch_model_path(\"whittington_2020_in_discritized_objects\")\n",
     "plotting_loop_params = {\"n_episode\": 5000}"
    ]
@@ -1636,8 +1636,8 @@
     "del training_dict[\"agent_params\"]\n",
     "agent = training_dict[\"agent_class\"](**training_dict[\"params\"])\n",
     "agent.plot_run(tem, model_input, environments)\n",
-    "agent.plot_rate_map(rate_map_type='g');\n",
-    "agent.plot_rate_map(rate_map_type='p');\n",
+    "agent.plot_rate_map(rate_map_type='g')\n",
+    "agent.plot_rate_map(rate_map_type='p')\n",
     "rate_map_mat = agent.get_rate_map_matrix(agent.g_rates,1,2)\n",
     "GridScorer = GridScorer(rate_map_mat.shape[0])\n",
     "GridScorer.plot_grid_score(r_out_im = rate_map_mat, plot= True)\n",

diff --git a/examples/comparisons_examples/comparison_from_manager.ipynb b/examples/comparisons_examples/comparison_from_manager.ipynb
@@ -41,18 +41,17 @@
     }
    ],
    "source": [
-    "from IPython.display import display, HTML\n",
+    "from IPython.display import HTML, display\n",
+    "\n",
     "display(HTML(\"<style>.container { width:80% !important; }</style>\"))\n",
-    "import numpy as np\n",
-    "from tqdm.notebook import tqdm\n",
     "import pandas as pd\n",
-    "from neuralplayground.experiments import Wernle2018Data, Hafting2008Data, Sargolini2006Data\n",
+    "\n",
+    "from neuralplayground.agents import Stachenfeld2018\n",
+    "from neuralplayground.arenas import Simple2D\n",
     "from neuralplayground.comparison import GridScorer\n",
-    "from neuralplayground.arenas import Simple2D, ConnectedRooms,Wernle2018, MergingRoom, Sargolini2006\n",
-    "from neuralplayground.agents import Weber2018, Stachenfeld2018\n",
-    "from neuralplayground.experiments import Wernle2018Data, Hafting2008Data\n",
-    "from neuralplayground.saved_models import fetch_model_path\n",
-    "from neuralplayground.plotting.plot_utils import make_plot_trajectories, make_plot_rate_map, make_agent_comparison"
+    "from neuralplayground.experiments import Sargolini2006Data\n",
+    "from neuralplayground.plotting.plot_utils import make_agent_comparison\n",
+    "from neuralplayground.saved_models import fetch_model_path"
    ]
   },
   {
@@ -770,10 +769,7 @@
     }
    ],
    "source": [
-    "from neuralplayground.agents import  Stachenfeld2018\n",
-    "from neuralplayground.arenas import Simple2D, MergingRoom, Sargolini2006, Hafting2008, BasicSargolini2006,Wernle2018\n",
-    "from neuralplayground.backend import default_training_loop, episode_based_training_loop\n",
-    "\n",
+    "from neuralplayground.backend import episode_based_training_loop\n",
     "\n",
     "stachenfeld_in_2d_params = {\n",
     "    \"simulation_id\": \"stachenfeld_2018_in_simple2D\",\n",

diff --git a/examples/comparisons_examples/simulation_manager.ipynb b/examples/comparisons_examples/simulation_manager.ipynb
@@ -32,8 +32,7 @@
     "\n",
     "from neuralplayground.agents import Stachenfeld2018\n",
     "from neuralplayground.arenas import Simple2D\n",
-    "from neuralplayground.backend import episode_based_training_loop\n",
-    "from neuralplayground.backend import SingleSim"
+    "from neuralplayground.backend import SingleSim, episode_based_training_loop"
    ]
   },
   {
@@ -449,8 +448,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from neuralplayground.backend.default_simulation import stachenfeld_in_2d\n",
-    "from neuralplayground.backend import SimulationManager"
+    "from neuralplayground.backend import SimulationManager\n",
+    "from neuralplayground.backend.default_simulation import stachenfeld_in_2d"
    ]
   },
   {