From 9b71836faa06e254e8399744e0a852115e303676 Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Wed, 9 Mar 2022 10:20:22 -0800
Subject: [PATCH 1/5] more readme cleanup

---
 README.md     |  7 +++++--
 RELEASE_NOTES | 17 -----------------
 2 files changed, 5 insertions(+), 19 deletions(-)
 delete mode 100644 RELEASE_NOTES

diff --git a/README.md b/README.md
index 2cf28137..2e6a4d93 100644
--- a/README.md
+++ b/README.md
@@ -25,9 +25,11 @@ Table of contents
   - [_Using the source code repository_](#using-the-source-code-repository)
 - [Usage](#usage)
   - [_Simple example to illustrate the use of SpatialPy_](#simple-example-to-illustrate-the-use-of-spatialpy)
+<!--
   - [_Docker environment_](#docker-environment)
   - [_Debugging_](#debugging)
   - [_Profiling_](#profiling)
+-->
 - [Getting help](#getting-help)
 - [Contributing](#contributing)
 - [License](#license)
@@ -72,8 +74,8 @@ SpatialPy provides simple object-oriented abstractions for defining a model of a
 
 The `run()` method can be customized using keyword arguments to select different solvers, random seed, data return type and more.  For more detailed examples on how to use SpatialPy, please see the Jupyter notebooks contained in the [examples](https://github.com/StochSS/SpatialPy/tree/main/examples) subdirectory.
 
-
-### Docker environment
+<!-- 
+### Docker environment (DOES NOT WORK)
 
 You can use Docker to create a repeatable environment for developing and debugging SpatialPy. The supplied Dockerfile starts a jupyter server with SpatialPy dependencies installed.
 
@@ -102,6 +104,7 @@ You can invoke `solver.run_debugger()` anytime after you instantiate a solver in
 ### Profiling
 
 To enable profiling, both `solver.compile()` and `solver.run()` need to be invoked with `profile=True`. If you don't run `solver.compile()` explicitly, invoking `solver.run()` with `profile=True` will run `compile()` correctly for you.
+-->
 
 Getting help
 ------------
diff --git a/RELEASE_NOTES b/RELEASE_NOTES
deleted file mode 100644
index 718c22b1..00000000
--- a/RELEASE_NOTES
+++ /dev/null
@@ -1,17 +0,0 @@
-                                 RELEASE NOTES
-                             	   SpatialPy
-
-These are release notes for SpatialPy.
-----------------------------------------
-Date: 2/25/2021
-Version: 0.5.0+beta
-----------------------------------------
-- Initial beta release
-----------------------------------------
-Date: 3/9/2021
-Version: 0.5.1+beta
-----------------------------------------
-- Added pickling Results
-- Added add_mesh() function
-- timespan() now includes option to set timestep size
-- Added ability to read StochSS domains

From af6d642fc54e137676ebbf7817ab91a6189ef662 Mon Sep 17 00:00:00 2001
From: Brian Drawert <brian@drawert.net>
Date: Wed, 9 Mar 2022 11:17:12 -0800
Subject: [PATCH 2/5] Bumped version 1.0.1

---
 spatialpy/__version__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spatialpy/__version__.py b/spatialpy/__version__.py
index 22fc6782..9ebc0fc0 100644
--- a/spatialpy/__version__.py
+++ b/spatialpy/__version__.py
@@ -23,7 +23,7 @@
 # @website https://github.com/StochSS/SpatialPy
 # =============================================================================
 
-__version__      = '1.0'
+__version__      = '1.0.1'
 __title__        = 'SpatialPy'
 __description__  = 'Python Interface for Spatial Stochastic Biochemical Simulations'
 __url__          = 'https://spatialpy.github.io/SpatialPy/'

From e10dbfdded7bfe866f6dfd5f8dcc26019f01b0dc Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 15 Mar 2022 14:53:51 -0400
Subject: [PATCH 3/5] Updated version to v1.0.2.

---
 spatialpy/__version__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/spatialpy/__version__.py b/spatialpy/__version__.py
index 9ebc0fc0..46a5efd9 100644
--- a/spatialpy/__version__.py
+++ b/spatialpy/__version__.py
@@ -23,7 +23,7 @@
 # @website https://github.com/StochSS/SpatialPy
 # =============================================================================
 
-__version__      = '1.0.1'
+__version__      = '1.0.2'
 __title__        = 'SpatialPy'
 __description__  = 'Python Interface for Spatial Stochastic Biochemical Simulations'
 __url__          = 'https://spatialpy.github.io/SpatialPy/'

From 5f10cb0ef374a6c7bb34debedf095d92d1e4e374 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 15 Mar 2022 14:59:37 -0400
Subject: [PATCH 4/5] Added test_notebook to unit tests for testing.

---
 test/run_unit_tests.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/test/run_unit_tests.py b/test/run_unit_tests.py
index b35fb3f3..a99aca7a 100755
--- a/test/run_unit_tests.py
+++ b/test/run_unit_tests.py
@@ -33,11 +33,13 @@
     import test_species
     import test_parameter
     import test_reaction
+    import test_notebooks
     
     modules = [
         test_species,
         test_parameter,
-        test_reaction
+        test_reaction,
+        test_notebooks
     ]
 
     for module in modules:

From cc0b3c6da2a2f0ca80e5b26375bd65be6dedb012 Mon Sep 17 00:00:00 2001
From: Bryan Rumsey <bmrumsey@gmail.com>
Date: Tue, 15 Mar 2022 15:02:50 -0400
Subject: [PATCH 5/5] Added missing test env deps.

---
 .github/workflows/run-unit-tests.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/run-unit-tests.yml b/.github/workflows/run-unit-tests.yml
index cabdc656..6f6c939d 100644
--- a/.github/workflows/run-unit-tests.yml
+++ b/.github/workflows/run-unit-tests.yml
@@ -23,6 +23,8 @@ jobs:
         python3 -m pip install --upgrade pip
         python3 -m pip install -r requirements.txt
         python3 -m pip install coverage
+        python3 -m pip install nbformat
+        python3 -m pip install nbconvert
         
     - name: Run tests
       run: coverage run test/run_unit_tests.py