From 9753d93de5c4f1743a51280219b7ae980c5608a6 Mon Sep 17 00:00:00 2001
From: rhoadesScholar <rhoadesj@hhmi.org>
Date: Sun, 11 Feb 2024 13:48:42 -0500
Subject: [PATCH 1/2] Update DaCapo installation instructions

---
 .gitattributes                                |  1 +
 .../finetune_liver_peroxisome.ipynb           | 31 ++++++++++++++++++-
 setup.py                                      |  2 ++
 3 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 .gitattributes

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 000000000..9bc9e6c39
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+*.ipynb
\ No newline at end of file
diff --git a/examples/distance_task/finetune_liver_peroxisome.ipynb b/examples/distance_task/finetune_liver_peroxisome.ipynb
index a75ddda42..45fdd50cd 100644
--- a/examples/distance_task/finetune_liver_peroxisome.ipynb
+++ b/examples/distance_task/finetune_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": {},
@@ -500,7 +529,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "version": "3.10.13"
   },
   "orig_nbformat": 4
  },
diff --git a/setup.py b/setup.py
index 3e6f51064..ed7503f1c 100644
--- a/setup.py
+++ b/setup.py
@@ -41,5 +41,7 @@
         "cattrs",
         "numpy-indexed",
         "click",
+        "ipykernel",
+        "jupyter",
     ],
 )

From b4d535cb168dd208510707bf7e0a2a130f0e6afa Mon Sep 17 00:00:00 2001
From: rhoadesScholar <rhoadesj@hhmi.org>
Date: Sun, 11 Feb 2024 14:08:26 -0500
Subject: [PATCH 2/2] Add environment setup instructions

---
 .../finetune_liver_peroxisome.md              | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/examples/distance_task/finetune_liver_peroxisome.md b/examples/distance_task/finetune_liver_peroxisome.md
index 3c2f14e68..95d2bd5c1 100644
--- a/examples/distance_task/finetune_liver_peroxisome.md
+++ b/examples/distance_task/finetune_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: