Merge pull request #72 from drbergman/development

v0.0.12

Author: Daniel Bergman

.github/workflows/CI.yml

@@ -35,12 +35,12 @@ jobs:
         compiler: ["g++"]
         include:
           - os: "macOS-latest"
-            julia-version: '1'
+            julia-version: 'lts'
             shell: "bash"
             compiler: "g++-14"
             arch: "arm64"
           - os: "macOS-latest"
-            julia-version: 'lts'
+            julia-version: '1'
             shell: "bash"
             compiler: "g++-14"
             arch: "arm64"
@@ -83,13 +83,13 @@ jobs:
     - name: Run all tests
       uses: julia-actions/julia-runtest@v1
       env:
-        JULIA_NUM_THREADS: 8
+        PCVCT_NUM_PARALLEL_SIMS: 8
         PHYSICELL_CPP: ${{ matrix.compiler }} # maybe necessary for windows??
         PCVCT_PUBLIC_REPO_AUTH: ${{ secrets.PUBLIC_REPO_AUTH }}
     - uses: julia-actions/julia-processcoverage@v1
     - uses: codecov/codecov-action@v5
       with:
-        file: lcov.info
+        files: lcov.info
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: false
 

.gitignore

@@ -1,5 +1,6 @@
 .DS_Store
 test.jl
+/data
 *.db
 .vscode
 

Project.toml

@@ -1,7 +1,7 @@
 name = "pcvct"
 uuid = "3c374bc7-7384-4f83-8ca0-87b8c727e6ff"
 authors = ["Daniel Bergman <[email protected]> and contributors"]
-version = "0.0.11"
+version = "0.0.12"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -42,7 +42,7 @@ LightXML = "0.9"
 LinearAlgebra = "1.10"
 MAT = "0.10"
 Parameters = "0.12"
-PhysiCellXMLRules = "0.0.1 - 0.0.2"
+PhysiCellXMLRules = "0.0.3"
 Pkg = "1.10.0"
 QuasiMonteCarlo = "0.3"
 RecipesBase = "1.3.4"

docs/src/lib/VCTAnalysis.md

@@ -4,7 +4,7 @@ CollapsedDocStrings = true
 
 # VCTAnalysis
 
-This folder holds functionality for analyzing output from the model.
+Analyze output from a pcvct project.
 
 ```@autodocs
 Modules = [pcvct]

docs/src/lib/VCTClasses.md

@@ -4,7 +4,7 @@ CollapsedDocStrings = true
 
 # VCTClasses
 
-This file contains the class definitions for the hierarchical structure connecting simulations to trials.
+Class definitions for the hierarchical structure connecting simulations to trials.
 
 ```@autodocs
 Modules = [pcvct]

docs/src/lib/VCTCompilation.md

@@ -4,7 +4,7 @@ CollapsedDocStrings = true
 
 # VCTCompilation
 
-This file contains the functions used to compile a PhysiCell project, including using the necessary compiler macros.
+Compile a PhysiCell project in pcvct. Includes the necessary compiler macros and checks PhysiCell version by the commit hash of the PhysiCell repository.
 
 ```@autodocs
 Modules = [pcvct]

docs/src/lib/VCTCreation.md

@@ -0,0 +1,12 @@
+```@meta
+CollapsedDocStrings = true
+```
+
+# VCTCreation
+
+Create a new pcvct project.
+
+```@autodocs
+Modules = [pcvct]
+Pages = ["VCTCreation.jl"]
+```

docs/src/lib/VCTDatabase.md

@@ -0,0 +1,12 @@
+```@meta
+CollapsedDocStrings = true
+```
+
+# VCTDatabase
+
+Create and manage the pcvct database.
+
+```@autodocs
+Modules = [pcvct]
+Pages = ["VCTDatabase.jl"]
+```

docs/src/lib/VCTDeletion.md

@@ -4,7 +4,7 @@ CollapsedDocStrings = true
 
 # VCTDeletion
 
-This file holds functionality for deleting output.
+Safely delete output from a pcvct project.
 
 ```@autodocs
 Modules = [pcvct]

docs/src/lib/VCTExport.md

@@ -0,0 +1,12 @@
+```@meta
+CollapsedDocStrings = true
+```
+
+# VCTExport
+
+This file holds the functions for exporting a simulation to a `user_project` format.
+
+```@autodocs
+Modules = [pcvct]
+Pages = ["VCTExport.jl"]
+```