Separate out dependencies in pyproject.

.github/workflows/abc_atlas_access_ci.yaml

@@ -21,6 +21,6 @@ jobs:
       - name: Install
         run: |
           python -m pip install --upgrade pip
-          pip install .
+          pip install ".[test]"
       - name: Test
         run: pytest tests

.github/workflows/deploy_book.yaml

@@ -4,7 +4,7 @@ name: deploy-book
 on:
   push:
     branches:
-    - main 
+    - main
 
 # This job installs dependencies, builds the book, and pushes it to `gh-pages`
 jobs:
@@ -21,7 +21,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -r requirements.txt
+        pip install ".[jupyter-book]"
 
     # Build the book
     - name: Build the book

README.md

@@ -26,3 +26,23 @@ We are not currently supporting this code, but simply releasing it to the
 community AS IS but are not able to provide any guarantees of support. The
 community is welcome to submit issues, but you should not expect an active
 response.
+
+## Installation
+
+To install base package with the cache object in your python environment, use
+pip with the following command:
+
+```console
+pip install git+https://github.com/alleninstitute/abc_atlas_access.git
+```
+
+To install the package with all optional dependencies, specifically those needed
+to re-run the notebooks, you can use the following command:
+
+```console
+pip install "abc_atlas_access[notebooks] @ git+https://github.com/alleninstitute/abc_atlas_access.git"
+```
+
+We assume that you already have Jupyter installed if you are re-running the
+notebooks. Running the [getting_started notebook](https://alleninstitute.github.io/abc_atlas_access/notebooks/getting_started.html)
+will also help you install the package.

pyproject.toml

@@ -4,22 +4,15 @@ build-backend = "hatchling.build"
 
 [project]
 name = "abc_atlas_access"
-version = "0.3.0"
+version = "0.4.0"
 description = "A package for accessing/processing data from the ABC Atlas"
 dependencies = [
   "anndata",
   "boto3",
-  "ghp-import",
-  "matplotlib",
-  "moto",
   "numpy",
   "pandas",
   "pydantic",
-  "pytest",
-  "requests",
-  "scipy",
-  "SimpleITK",
-  "tqdm",
+  "tqdm"
 ]
 requires-python = ">=3.8"
 authors = [
@@ -31,3 +24,18 @@ classifiers = [
   "Development Status :: 4 - Beta",
   "Programming Language :: Python"
 ]
+
+[project.optional-dependencies]
+notebooks = [
+    "matplotlib",
+    "scipy",
+    "SimpleITK"
+]
+jupyter-book = [
+    "ghp-import",
+    "jupyter-book"
+]
+test = [
+    "moto",
+    "pytest"
+]