Merge branch 'dev/examples' of https://github.com/janelia-cellmap/dacapo

 into dev/examples

.gitattributes

@@ -0,0 +1 @@
+*.ipynb

examples/distance_task/liver_peroxisome.ipynb

@@ -21,6 +21,35 @@
     "These are then combined in a single **dacapo.experiments.Run** that includes your starting point (whether you want to start training from scratch or continue off of a previously trained model) and stopping criterion (the number of iterations you want to train)."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Environment setup\n",
+    "If you have not already done so, you will need to install DaCapo. You can do this by first creating a new environment and then installing DaCapo using pip.\n",
+    "\n",
+    "```bash\n",
+    "conda create -n dacapo python=3.10\n",
+    "conda activate dacapo\n",
+    "```\n",
+    "\n",
+    "Then, you can install DaCapo using pip, via GitHub:\n",
+    "\n",
+    "```bash\n",
+    "pip install git+https://github.com/janelia-cellmap/dacapo.git\n",
+    "```\n",
+    "\n",
+    "Or you can clone the repository and install it locally:\n",
+    "\n",
+    "```bash\n",
+    "git clone https://github.com/janelia-cellmap/dacapo.git\n",
+    "cd dacapo\n",
+    "pip install -e .\n",
+    "```\n",
+    "\n",
+    "Be sure to select this environment in your Jupyter notebook or JupyterLab."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

examples/distance_task/liver_peroxisome.md

@@ -13,6 +13,29 @@ DaCapo has 4 major configurable components:
 
 These are then combined in a single **dacapo.experiments.Run** that includes your starting point (whether you want to start training from scratch or continue off of a previously trained model) and stopping criterion (the number of iterations you want to train).
 
+## Environment setup
+If you have not already done so, you will need to install DaCapo. We recommend you do this by first creating a new environment and then installing DaCapo using pip.
+
+```bash
+conda create -n dacapo python=3.10
+conda activate dacapo
+```
+
+Then, you can install DaCapo using pip, via GitHub:
+
+```bash
+pip install git+https://github.com/janelia-cellmap/dacapo.git
+```
+
+Or you can clone the repository and install it locally:
+
+```bash
+git clone https://github.com/janelia-cellmap/dacapo.git
+cd dacapo
+pip install -e .
+```
+
+
 ## Config Store
 
 To define where the data goes, create a dacapo.yaml configuration file. Here is a template:

setup.py

@@ -41,5 +41,7 @@
         "cattrs",
         "numpy-indexed",
         "click",
+        "ipykernel",
+        "jupyter",
     ],
 )