From 996584a3e5cc29670ea9af9029e09899036d02f4 Mon Sep 17 00:00:00 2001
From: Sricharan Reddy Varra <srivarra@stanford.edu>
Date: Mon, 24 Jul 2023 14:48:49 -0700
Subject: [PATCH] Next Release v0.6.4 (#1012)

* 0.6.4

* updated environment.yml

* Update README.md

* updated windows setup docs

* added repo verison in git clone

* file fix
---
 README.md                  |  2 +-
 docs/_rtd/windows_setup.md |  9 +++++++--
 environment.yml            | 12 ------------
 setup.py                   |  2 +-
 start_docker.sh            |  2 +-
 5 files changed, 10 insertions(+), 17 deletions(-)

diff --git a/README.md b/README.md
index 4d861bb37..6d2a0c26e 100644
--- a/README.md
+++ b/README.md
@@ -106,7 +106,7 @@ Open terminal and navigate to where you want the code stored.
 If you would like to use the latest version of `ark` simply clone the project and create the Conda environment.
 
 ```sh
-git clone https://github.com/angelolab/ark-analysis.git
+git clone -b v0.6.4 https://github.com/angelolab/ark-analysis.git
 cd ark-analysis
 conda env create -f environment.yml
 ```
diff --git a/docs/_rtd/windows_setup.md b/docs/_rtd/windows_setup.md
index 99f83df9c..324d03430 100644
--- a/docs/_rtd/windows_setup.md
+++ b/docs/_rtd/windows_setup.md
@@ -33,7 +33,7 @@ After finishing the installer guidelines, go to your Command Prompt and type `gi
 
 Go to [Docker for Windows install](https://docs.docker.com/desktop/windows/install) to download `Docker Desktop`. 
 
-Open the shortcut (which should be added to your Desktop after installation) and open `Docker Desktop`. If the engine starts up successfully, Docker has been configured. Note that the engine may take a while to setup properly.
+Open the shortcut (which should be added to your Desktop after installation) and open `Docker Desktop`. If the engine starts up successfully, Docker has been configured. Note that the engine may take a while to set up properly.
 
 ### Setting up the repo
 
@@ -46,7 +46,12 @@ In your Command Prompt, follow similar steps to clone the `ark-analysis` repo an
 To run the script, you have to use `bash start_docker.sh`. If you run into issues with invalid carriage returns (`\r`), please run the following before trying again:
 
 * Run `wsl sudo apt-get install dos2unix`
-* Run `wsl dos2unix start_docker.sh` and `wsl dos2unix update_notebooks.sh`
+* Run the following commands:
+  > `wsl dos2unix start_docker.sh`
+  
+  > `wsl dos2unix start_jupyter.sh`
+
+  > `wsl dos2unix update_notebooks.sh`
 
 ### Addressing `docker` not found
 
diff --git a/environment.yml b/environment.yml
index 59eaae85f..129bcddb4 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,17 +5,5 @@ dependencies:
   - python=3.11
   - pip
   - hdf5
-  - jupyterlab
-  - ipywidgets
-  - tqdm
-  - numpy
-  - pandas
-  - xarray
-  - scipy
-  - scikit-image
-  - matplotlib
-  - seaborn
   - pip:
-    - alpineer>=0.1.8
-    - pyFlowSOM>=0.1.5
     - .[lab_ext]
diff --git a/setup.py b/setup.py
index ee1405940..cd5dd50a5 100644
--- a/setup.py
+++ b/setup.py
@@ -31,5 +31,5 @@
 ]
 
 setup(
-    ext_modules=cythonize(extensions, compiler_directives={"language_level": "3"}),
+    ext_modules=cythonize(extensions, compiler_directives=_compiler_directives),
 )
diff --git a/start_docker.sh b/start_docker.sh
index 25c15c411..885d0dcf3 100755
--- a/start_docker.sh
+++ b/start_docker.sh
@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # define the version number, this needs to be updated every new Docker release
-VERSION='v0.6.3'
+VERSION='v0.6.4'
 
 # check for template developer flag
 JUPYTER_DIR='scripts'