diff --git a/README.md b/README.md
index 795aba0..781b242 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-# Circuitscape Python Script Tool for ESRI Arc Pro
+# Circuitscape Python Script Tool for ArcGIS Pro
## Installation and Usage
@@ -28,18 +28,12 @@ and run via python using `subprocess.Popen`.
## Bugs and Caveats
The limitations of Arc Pro Python script tools as well as Python <-> Julia interprocess communications necessitate
-certain limitations. Among these
-
-1. There is no way to cancel running jobs.
- Using the 'cancel' option in a running tool is typically ineffective (Arc Pro only cancels a python script between
- lines). To cancel a running process, you will need to exit Arc Pro completely (or kill it in task manager).
-1. Errors do not always show as failed runs in Arc Pro. To be sure, click "View Details".
-1. The tool does not respect any environment settings in Arc Pro.
+certain limitations. See [src/INSTALL.md](src/INSTALL.md) for more information.
Please report other issues at
https://github.com/jessjaco/circuitscape-arc-pro/issues.
## Acknowledgements
-The tool was authored by Jesse Anderson and guided by Kimberly Hall with The Nature Conservancy. Funding for this
+The tool was authored by Jesse Anderson as guided by Kimberly Hall with The Nature Conservancy. Funding for this
project was provided by The Wilburforce Foundation.
diff --git a/src/.gitignore b/src/.gitignore
index 3254439..bf5b1b6 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -1 +1,3 @@
julia*
+config.ini
+last_config.ini
diff --git a/src/Circuitscape.pyt.xml b/src/Circuitscape.pyt.xml
index 1f7cded..3caa50c 100644
--- a/src/Circuitscape.pyt.xml
+++ b/src/Circuitscape.pyt.xml
@@ -1,2 +1,2 @@
-20231024135206001.0TRUE20231024135206c:\program files\arcgis\pro\Resources\Help\gpCircuitscapeArcToolbox Toolbox
+20231024135206001.0TRUE20240124133140c:\program files\arcgis\pro\Resources\Help\gpCircuitscapeArcToolbox Toolbox
diff --git a/src/INSTALL.md b/src/INSTALL.md
index 65e748c..60e058b 100644
--- a/src/INSTALL.md
+++ b/src/INSTALL.md
@@ -8,15 +8,38 @@ Navigate to the unzipped location and select "Circuitscape.pyt".
## Usage
-The Circuitscape Toolbox shadows the full functionality of Circuitscape in Julia.
-Simply parameterize and hit run. A blank black shell window will pop up, which
-you can ignore. To monitor while running , select "View Details" at the bottom
+The toolbox shadows the full functionality of Circuitscape and Omniscape in Julia.
+Simply parameterize and hit run. To monitor while running , select "View Details" at the bottom
of the Arc Pro Toolbox window.
Please note the first model run will take longer than usual, as the tool is
-downloading, installing and testing Circuitscape.
+downloading, installing and testing Circuitscape and Omniscape.
+
+## Circuitscape tips
+The parameterization of the output file is a bit clunky. If it's not clear by the help bubble,
+you need to specify a new file with an ".out" extension. If using the file browser, navigate
+to the folder you wish the place the output, and type a name ending in .out (e.g. "model.out")
+and the bottom, then hit OK.
+
+## Omniscape tips
+The output location for Omniscape (the "Project Name" dialog) is a folder. Otherwise it is best
+to define it similarly to the Circuitscape instructions above. That is, navigate to a location
+and type the name of the (new) folder at the bottom. If you use an existing folder, an
+exclamation point will appear in the tool window, but it will still run.
+
+The JULIA_NUM_THREADS environment variable, which defines the number of parallel threads to use
+is represented by the "Number of Threads" parameter under "Calculation Options". Just noting
+as this (along with making sure "Parallelize" is checked) can speed up calculations immensely.
+(See Omniscape documentation for more info).
+
## Known Issues
- Sometimes when you add the toolbox in Arc Pro, it doesn't appear. For now the best
solution is to exit Arc Pro and try again.
+
+- There is no way to cancel running jobs. Using the 'cancel' option in a running tool is typically
+ ineffective (Arc Pro only cancels a python script between lines). To cancel a running process,
+ you will need to exit Arc Pro completely (or kill it in task manager).
+- Errors do not always show as failed runs in Arc Pro. To be sure, click "View Details".
+- The tool does not respect any environment settings in Arc Pro.
\ No newline at end of file
diff --git a/src/last_config.ini b/src/last_config.ini
deleted file mode 100644
index df92367..0000000
--- a/src/last_config.ini
+++ /dev/null
@@ -1,26 +0,0 @@
-project_name = C:\Users\jesse\AppData\Local\Temp\ArcGISProTemp17320\Untitled\Untitled_index
-resistance_file = C:\Users\jesse\OneDrive\Desktop\res1000x.asc
-radius = 5
-block_size = 1
-resistance_is_conductance = False
-source_from_resistance = True
-r_cutoff = inf
-reclassify_resistance = False
-write_reclassified_resistance = False
-allow_different_projections = False
-buffer = 0.0
-source_threshold = 0.0
-connect_four_neighbors_only = False
-mask_nodata = True
-parallelize = True
-parallel_batch_size = 10.0
-precision = double
-solver = cg+amg
-calc_normalized_current = False
-calc_flow_potential = False
-write_raw_currmap = True
-write_as_tif = True
-conditional = False
-n_conditions = 1.0
-comparison1 = within
-comparison2 = within
diff --git a/src/runner.py b/src/runner.py
index 6364e08..192ff51 100644
--- a/src/runner.py
+++ b/src/runner.py
@@ -10,14 +10,14 @@
def run_circuitscape(config_file: Path, command_args: dict, messages) -> None:
- working_dir = Path(__file__).resolve().parent
+ working_dir = str(Path(__file__).resolve().parent).replace("\\", "/")
config_file_fixed = str(config_file).replace("\\", "/")
command = f'"using Pkg; Pkg.activate(realpath(\\"{working_dir}\\")); Pkg.instantiate(); using Circuitscape; compute(realpath(\\"{config_file_fixed}\\"))"'
return run_julia_command(command, command_args, messages)
def run_omniscape(config_file: Path, command_args: dict, messages) -> None:
- working_dir = Path(__file__).resolve().parent
+ working_dir = str(Path(__file__).resolve().parent).replace("\\", "/")
config_file_fixed = str(config_file).replace("\\", "/")
command = f'"using Pkg; Pkg.activate(realpath(\\"{working_dir}\\")); Pkg.instantiate(); using Omniscape; run_omniscape(realpath(\\"{config_file_fixed}\\"))"'