optuna example (#624)

* optuna example

* use subprocess

* improve optuna example

* add jupyter-black

* rerun optuna

* add jupyter

* format notebooks

.pre-commit-config.yaml

@@ -24,6 +24,8 @@ repos:
     rev: 23.3.0
     hooks:
       - id: black
+        additional_dependencies: [".[jupyter]"]
+        types_or: [python, pyi, jupyter]
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:

docs/source/_examples/index.rst

@@ -30,3 +30,4 @@ The notebooks are organized in the following way:
     09_lazy
     OptionalDVC
     jupyter
+    parameter_optimization

examples/dataclasses_for_parameters.ipynb

@@ -122,16 +122,18 @@
     "    stop: int\n",
     "    step: int = 1\n",
     "\n",
+    "\n",
     "class ParameterConverter(znjson.ConverterBase):\n",
     "    instance = Parameter\n",
     "    representation = \"Parameter\"\n",
     "\n",
     "    def encode(self, obj) -> str:\n",
     "        return dataclasses.asdict(obj)\n",
-    "    \n",
+    "\n",
     "    def decode(self, value: str):\n",
     "        return Parameter(**value)\n",
     "\n",
+    "\n",
     "class ComputeRandomNumber(Node):\n",
     "    param: Parameter = zn.params()\n",
     "    number = zn.outs()\n",
@@ -148,9 +150,7 @@
     "        self.param = param\n",
     "\n",
     "    def run(self):\n",
-    "        self.number = random.randrange(\n",
-    "            self.param.start, self.param.stop, self.param.step\n",
-    "        )"
+    "        self.number = random.randrange(self.param.start, self.param.stop, self.param.step)"
    ]
   },
   {
@@ -221,7 +221,7 @@
     "parameter = Parameter(start=100, stop=200)\n",
     "with Project() as proj:\n",
     "    ComputeRandomNumber(param=parameter)\n",
-    "proj.run(repro=True)\n"
+    "proj.run(repro=True)"
    ]
   },
   {

examples/docs/02_Inheritance.ipynb

@@ -65,6 +65,7 @@
    "source": [
     "# Work in a temporary directory\n",
     "from zntrack.utils import cwd_temp_dir\n",
+    "\n",
     "temp_dir = cwd_temp_dir()\n",
     "\n",
     "!git init\n",
@@ -130,13 +131,16 @@
    "source": [
     "class AddNumber(NodeBase):\n",
     "    \"\"\"Shift input by an offset\"\"\"\n",
+    "\n",
     "    offset: float = zntrack.zn.params()\n",
     "\n",
     "    def run(self):\n",
     "        self.output = self.inputs + self.offset\n",
     "\n",
+    "\n",
     "class MultiplyNumber(NodeBase):\n",
     "    \"\"\"Multiply input by a factor\"\"\"\n",
+    "\n",
     "    factor: float = zntrack.zn.params()\n",
     "\n",
     "    def run(self):\n",
@@ -448,6 +452,7 @@
    "source": [
     "class DivideNumber(NodeBase):\n",
     "    \"\"\"Multiply input by a factor\"\"\"\n",
+    "\n",
     "    divider: float = zntrack.zn.params()\n",
     "\n",
     "    def run(self):\n",
@@ -458,6 +463,7 @@
     "    a0: float = zntrack.zn.params()\n",
     "    a1: float = zntrack.zn.params()\n",
     "\n",
+    "\n",
     "class ManipulateNumber(zntrack.Node):\n",
     "    inputs: float = zntrack.zn.params()\n",
     "    output: float = zntrack.zn.outs()\n",
@@ -629,8 +635,8 @@
     }
    ],
    "source": [
-    "value_handler=DivideNumber(divider=3.0, inputs=None)\n",
-    "polynomial=Polynomial(a0=60.0, a1=10.0)\n",
+    "value_handler = DivideNumber(divider=3.0, inputs=None)\n",
+    "polynomial = Polynomial(a0=60.0, a1=10.0)\n",
     "\n",
     "with zntrack.Project() as project:\n",
     "    manipulate_number = ManipulateNumber(\n",

examples/docs/03_dependencies.ipynb

@@ -258,10 +258,7 @@
    "source": [
     "random_number.load()\n",
     "compute_power.load()\n",
-    "print(\n",
-    "    f\"{random_number.number} ^ {compute_power.power} =\"\n",
-    "    f\" {compute_power.number}\"\n",
-    ")"
+    "print(f\"{random_number.number} ^ {compute_power.power} = {compute_power.number}\")"
    ]
   },
   {
@@ -301,6 +298,7 @@
    "source": [
     "# zntrack: break\n",
     "\n",
+    "\n",
     "class WriteToFile(zntrack.Node):\n",
     "    random_number: RandomNumber = zntrack.zn.deps()\n",
     "    file: Path = zntrack.dvc.outs(zntrack.nwd / \"random_number.txt\")\n",

examples/docs/04_metrics_and_plots.ipynb

@@ -215,7 +215,7 @@
     "with zntrack.Project() as project:\n",
     "    node = MetricAndPlot()\n",
     "\n",
-    "project.run() \n",
+    "project.run()\n",
     "!git add .\n",
     "!git commit -m \"First Run\""
    ]
@@ -623,6 +623,7 @@
     "            \"index\"\n",
     "        )\n",
     "\n",
+    "\n",
     "ZnTrackMetric().write_graph(run=True)"
    ]
   },

examples/docs/08_custom_zntrackoptions.ipynb

@@ -147,8 +147,7 @@
     "            ):\n",
     "                atoms.append(row.toatoms())\n",
     "        # return the data so it can be saved in __dict__\n",
-    "        return atoms\n",
-    "        "
+    "        return atoms"
    ]
   },
   {
@@ -295,7 +294,7 @@
    "source": [
     "node.load()\n",
     "print(node.atoms)\n",
-    "# or \n",
+    "# or\n",
     "AtomsClass.from_rev().atoms"
    ]
   },

examples/docs/09_lazy.ipynb

@@ -127,12 +127,11 @@
    "outputs": [],
    "source": [
     "class PrintOption(zntrack.zn.Output):\n",
-    "\n",
     "    def __init__(self):\n",
-    "        super().__init__(dvc_option = \"outs\", use_repr=False)\n",
+    "        super().__init__(dvc_option=\"outs\", use_repr=False)\n",
     "        # zntrack will try dvc --PrintOption outs.json\n",
     "        # we must tell it to use dvc --outs outs.json instead\n",
-    "        \n",
+    "\n",
     "    def _get_value_from_file(self, instance) -> any:\n",
     "        print(f\"Loading data from files for {instance.name}\")\n",
     "        return super()._get_value_from_file(instance)"
@@ -1316,7 +1315,7 @@
     }
    ],
    "source": [
-    "# With lazy=False we get the results we expect. \n",
+    "# With lazy=False we get the results we expect.\n",
     "# (Except for some random scenarios, where two random numbers are the same.)\n",
     "print(f\"{random_number_1.number} != {random_number_2.number} != {random_number_3.number}\")\n",
     "assert random_number_1.number != random_number_2.number\n",