Add local notebook test functionality, fix import directories in notebooks (#65)

* Refactor project dependencies and workflows

- Updated pyproject.toml to streamline dependencies
- Simplified GitHub Actions workflows for documentation and testing
- Removed redundant printer_utils module
- Minor import and type hint improvements in tree and test modules

* Update documentation and testing workflows

- Added documentation dependencies to pyproject.toml
- Simplified GitHub Actions workflows for documentation and testing
- Configured documentation build to use project dependencies
- Enabled pytest workflow on main branch pushes

* fix pyproject syntax

* Update notebooks import directory, add command in makefile that can test notebooks locally (with instruction in CONTRIBUTION.md)

Author: gefanyang

.readthedocs.yaml

@@ -98,7 +98,7 @@ If you are using VScode, it is easy to generate such template automatically usin
 
 - Write tests for new features and bug fixes.
 - Make sure all existing tests pass before submitting changes.
-- Run the test suite locally before submitting your PR: `make test`.
+- Run the test suite locally before submitting your PR: `make test` and `make local-notebook-test`
 
 ### Documentation
 

CONTRIBUTION.md

@@ -2,7 +2,7 @@
 import jax
 import jax.numpy as jnp
 
-from examples.SDE import dot, solve, forward
+from SDE import dot, solve, forward
 
 # functions for pullback and likelihood ratios, see https://arxiv.org/abs/2010.03509 section 6.1 for details
 quadratic = lambda x,H: jnp.dot(x,jnp.dot(H,x))

docs/requirements.txt

@@ -12,22 +12,34 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "ImportError",
+     "evalue": "cannot import name 'FastOrderedExecutor' from 'hyperiax.execution' (/Users/vbd402/Documents/Projects/hyperiax/hyperiax/execution/__init__.py)",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
+      "Cell \u001b[0;32mIn[2], line 3\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[38;5;28;01mimport\u001b[39;00m \u001b[38;5;21;01mhyperiax\u001b[39;00m\n\u001b[1;32m      2\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mjax\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mrandom\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m PRNGKey, split\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mhyperiax\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mexecution\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FastOrderedExecutor\n\u001b[1;32m      4\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mhyperiax\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mtree\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mfasttree\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m FastTree, FastBiTree\n\u001b[1;32m      5\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mhyperiax\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mmodels\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m UpLambda, DownLambda\n",
+      "\u001b[0;31mImportError\u001b[0m: cannot import name 'FastOrderedExecutor' from 'hyperiax.execution' (/Users/vbd402/Documents/Projects/hyperiax/hyperiax/execution/__init__.py)"
+     ]
+    }
+   ],
    "source": [
-    "import hyperiax\n",
+    "import time\n",
+    "import jax\n",
     "from jax.random import PRNGKey, split\n",
-    "from hyperiax.execution import FastOrderedExecutor\n",
+    "from jax import numpy as jnp\n",
+    "from tqdm import tqdm\n",
+    "from matplotlib import pyplot as plt\n",
+    "\n",
     "from hyperiax.tree.fasttree import FastTree, FastBiTree\n",
-    "from hyperiax.models import UpLambda, DownLambda\n",
-    "import jax\n",
-    "from hyperiax.execution.collate import dict_collate\n",
     "from hyperiax.tree.builders import symmetric_topology\n",
-    "import time\n",
-    "from matplotlib import pyplot as plt\n",
-    "from tqdm.auto import tqdm\n",
-    "from jax import numpy as jnp\n",
+    "from hyperiax.execution import FastOrderedExecutor\n",
+    "from hyperiax.execution.collate import dict_collate\n",
+    "from hyperiax.models import UpLambda, DownLambda\n",
     "from hyperiax.models import UpLambda, DownLambda, FuseLambda\n",
     "from hyperiax.models.functional import pass_up\n",
     "from hyperiax.plotting import plot_tree_2d_scatter"
@@ -251,7 +263,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "jaxenv",
+   "display_name": "hyperiax_dev",
    "language": "python",
    "name": "python3"
   },
@@ -265,7 +277,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.11.4"
   }
  },
  "nbformat": 4,