fixed escaping, updated docs

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.

src/.gitignore

@@ -1 +1,3 @@
 julia*
+config.ini
+last_config.ini

src/Circuitscape.pyt.xml

@@ -1,2 +1,2 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<metadata xml:lang="en"><Esri><CreaDate>20231024</CreaDate><CreaTime>13520600</CreaTime><ArcGISFormat>1.0</ArcGISFormat><SyncOnce>TRUE</SyncOnce><ModDate>20231024</ModDate><ModTime>135206</ModTime></Esri><toolbox name="Circuitscape" alias="Circuitscape"><arcToolboxHelpPath>c:\program files\arcgis\pro\Resources\Help\gp</arcToolboxHelpPath><toolsets/></toolbox><dataIdInfo><idCitation><resTitle>Circuitscape</resTitle></idCitation></dataIdInfo><distInfo><distributor><distorFormat><formatName>ArcToolbox Toolbox</formatName></distorFormat></distributor></distInfo></metadata>
+<metadata xml:lang="en"><Esri><CreaDate>20231024</CreaDate><CreaTime>13520600</CreaTime><ArcGISFormat>1.0</ArcGISFormat><SyncOnce>TRUE</SyncOnce><ModDate>20240124</ModDate><ModTime>133140</ModTime></Esri><toolbox name="Circuitscape" alias="Circuitscape"><arcToolboxHelpPath>c:\program files\arcgis\pro\Resources\Help\gp</arcToolboxHelpPath><toolsets/></toolbox><dataIdInfo><idCitation><resTitle>Circuitscape</resTitle></idCitation></dataIdInfo><distInfo><distributor><distorFormat><formatName>ArcToolbox Toolbox</formatName></distorFormat></distributor></distInfo></metadata>

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.

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}\\"))"'