First attempt at ODE integration

.github/workflows/make_docs.yaml

@@ -4,7 +4,7 @@ on:
   push:
     branches:
       - main
-    tags: 
+    tags:
       - '*'
   pull_request:
 
@@ -31,26 +31,23 @@ jobs:
         with:
           version: '1.11'
 
-      - name: Restore Julia cache
+      - name: Restore Julia cache (packages, artifacts, compiled, registries)
         uses: actions/cache@v4
         with:
-          path: ~/.julia
-          key: ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml') }}
+          path: |
+            ~/.julia/packages
+            ~/.julia/artifacts
+            ~/.julia/compiled
+            ~/.julia/registries
+          # include Manifest.toml so cache invalidates when resolved versions change
+          key: ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml','**/Manifest.toml') }}
           restore-keys: |
-           ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml') }}
-      - name: Download BLAS
-        run: sudo apt install -y libopenblas-dev
-      - name: Instantiate Julia environment
-        run: julia --project=. -e 'using Pkg; Pkg.instantiate()'
+           ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml','**/Manifest.toml') }}
+      - name: Install system dependencies
+        run: sudo apt-get update && sudo apt-get install -y libopenblas-dev
 
-      - name: Build package
-        run: julia --project=. -e 'using Pkg; Pkg.build(); Pkg.precompile()'
-
-      - name: Instantiate docs environment
-        run: julia --project=docs -e 'using Pkg; Pkg.instantiate()'
-
-      - name: Add local package to docs environment
-        run: julia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path="."))'
+      - name: Prepare docs environment (develop local package, then instantiate)
+        run: julia --project=docs -e 'using Pkg; Pkg.activate("docs"); Pkg.develop(PackageSpec(path=".")); Pkg.instantiate(update_registry=false)'
 
       - name: Build and deploy documentation
         env:

.github/workflows/test.yaml

@@ -2,6 +2,8 @@ name: Build and Test Julia Package
 
 on:
   pull_request:
+    branches:
+      - main
   push:
     branches:
       - main
@@ -19,19 +21,19 @@ jobs:
         with:
           version: '1.11'
 
-      - name: Restore Julia cache
+      - name: Restore Julia cache (packages, artifacts, compiled, registries)
         uses: actions/cache@v4
         with:
-          path: ~/.julia
-          key: ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml') }}
+          path: |
+            ~/.julia/packages
+            ~/.julia/artifacts
+            ~/.julia/compiled
+            ~/.julia/registries
+          # include Manifest.toml so cache invalidates when resolved versions change
+          key: ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml','**/Manifest.toml') }}
           restore-keys: |
-           ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml') }}
-      - name: Download BLAS
-        run: sudo apt install -y libopenblas-dev
-      - name: Instantiate Julia environment
-        run: julia --project=. -e 'using Pkg; Pkg.instantiate()'
-
-      - name: Build package
-        run: julia --project=. -e 'using Pkg; Pkg.build(); Pkg.precompile()'
-      - name: Run tests
-        run: julia --project=. -e 'using Pkg; Pkg.test("JPEC")'
+           ${{ runner.os }}-julia-${{ hashFiles('**/Project.toml','**/Manifest.toml') }}
+      - name: Install system dependencies
+        run: sudo apt-get update && sudo apt-get install -y libopenblas-dev
+      - name: Run tests (instantiate without registry update + test)
+        run: julia --project=. -e 'using Pkg; Pkg.activate("."); Pkg.instantiate(update_registry=false); include("test/runtests.jl")'

.gitignore

@@ -1,11 +1,15 @@
 *.mod
 *.dylib
-.vscode
+*.dll
+*.so
 *.o
 *.i
-*.so
+*.out
+*.h5
+.vscode
 *.DS_Store
-notebooks/*.in
+.gitattributes
 Manifest.toml
 build.log
-docs/build/
+docs/build/
+anaconda_projects/

Project.toml

@@ -1,17 +1,31 @@
 name = "JPEC"
 uuid = "462872dd-e066-4d2e-b993-6468b5239634"
-authors = ["Matthew Pharr <matthewcpharr@gmail.com>", "Rithik Banerjee <rb3736@columbia.edu>", "Jaebeom Cho <aspire1019@snu.ac.kr>"]
+authors = ["Matthew Pharr <matthewcpharr@gmail.com>", "Rithik Banerjee <rb3736@columbia.edu>", "Jaebeom Cho <aspire1019@snu.ac.kr>", "Jacob Halpern <jmh2363@columbia.edu>"]
 version = "0.1.0"
 license = 'MIT'
 
 [deps]
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
+HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
+DiffEqCallbacks = "4.9.0"
 Documenter = "1.14.1"
+FFTW = "1.9.0"
+HDF5 = "0.17.2"
+LinearAlgebra = "1.11.0"
+OrdinaryDiffEq = "6.102.0"
 Pkg = "1.11.0"
 Plots = "1.40.15"
-Test = "1.11.0"
+Printf = "1.11.0"
+TOML = "1.0.3"
+Test = "1.11.0"

README.md

@@ -1,28 +1,49 @@
-# JPEC
+# Perturbed Equilibrium
 
 This is a work in progress juliafication of the Generalized Perturbed Equilibrium Code suite https://github.com/PrincetonUniversity/GPEC.
 
-## Documentation
+## Documentation Pages
 
 The WIP documentation can be found [here](https://openfusiontoolkit.github.io/JPEC/dev/).
+
+
 ## Developer Notes
 
-### Commit messages
+### GIT Workflow
+
+All developers need to use Vincent Driessen's [GitFlow](http://nvie.com/posts/a-successful-git-branching-model) workflow when editing the GPEC package. PLEASE READ THE ENTIRE POST. It is short, very thorough, and good for both experienced and new git users.
+
+The highlights are,
+  - There are two permanent branches: master and develop
+  - The master branch is only updated for at release ready stages
+  - New features should be developed in short-lived (days) branches coming off of and merging back to the development branch.
+
+Specific instructions are given in the link above as to exactly how to branch and merge these various branches. For example, the --no-ff option should be used when merging in order to keep branch histories. Just follow the examples and you wont go wrong!
+
+#### Using github
+
+Please see [this link](https://docs.google.com/document/d/1XAOTz1IV8ErZAAk-iSuEuddNOLB5XcoVZsAbPKRUUuA/edit?usp=sharing) for a guide on how to discuss your code development using github.
+
+#### Commit messages
 
 To assist with the process of compiling release notes, please confirm to the commit message format:
 ```
 CODE - TAG - Detailed message
 ```
-where CODE is EQUIL, DCON, VAC, etc. and TAGs are short descriptors of the type of commit. Example tags might be WIP (work in progress), MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc. Look through old commits for examples of what tags are commonly used. 
+where CODE is EQUIL, DCON, VAC, etc. and TAGs are short descriptors of the type of commit. Example tags might be WIP (work in progress), MINOR, IMPROVEMENT, BUG FIX, NEW FEATURE, etc. Look through old commits for examples of what tags are commonly used.
 
 Again, this is currently used for the by-hand compilation of release notes. The tags thus need to be human readable but are not strictly inforced to be within some limited set. The objective is to allow a lead developer to skim through commits and pick out only the key new features / bug fixes / improvements to note in the release while not having to read all the work-in-progress or minor changes.
 
-### Code Formatting
+### Julia Tips
+
+#### Revise
 
-To retain consistency in code formatting, we request that all PRs include code formatting cleanup before merging. We will make use of [JuliaFormatter.jl](https://domluna.github.io/JuliaFormatter.jl/stable/), which can be used in both Vim and VSCode. For Vim installation, follow the instructions [here](https://github.com/kdheepak/JuliaFormatter.vim). In VSCode, the [Julia](https://www.julia-vscode.org/docs/dev/userguide/formatter/) extension has built-in capabiltiies for JuliaFormatter.jl. The [folder formatter](https://marketplace.visualstudio.com/items?itemName=MichaKaleta.folderformatter&ssr=false#overview) extension allows formatting of all files within a given folder, which can be useful for larger commits. 
+When developing and recompiling code often, use Revise.jl to speed up the compile times by only recompiling what is impacted by the changed code. Integrate Revise.jl into your default Julia environment for use across projects, do not directly add it to the Project.toml of this particular project. To install Revise.jl in your global environment, open the Julia REPL using the `julia` command, enter the package manager by pressing `]`, and then `add Revise`:
 
-The JuliaFormatter.toml file contains the default settings we will use; this should not be changed unless reformatting the entire repository. 
+Code
 
-### Using github
+    $ julia
+    julia> ]
+    pkg> add Revise
 
-Please see [this link](https://docs.google.com/document/d/1XAOTz1IV8ErZAAk-iSuEuddNOLB5XcoVZsAbPKRUUuA/edit?usp=sharing) for a guide on how to discuss your code development using github. 
+Now, in the top of each Jupyter notebook, you can call `using Revise` at the top of any Jupyter notebook to speed up compile times as you develop and test. Better yet, set up your environement to [use Revise by default](https://timholy.github.io/Revise.jl/stable/config/#Using-Revise-by-default)

build_docs_local.jl

@@ -8,7 +8,7 @@ Pkg.instantiate()
 # Build the package
 Pkg.build()
 
-# Activate and instantiate the docs environment  
+# Activate and instantiate the docs environment
 Pkg.activate("docs")
 Pkg.instantiate()
 

deps/build.jl

@@ -6,82 +6,9 @@
 
 const parent_dir = joinpath(@__DIR__, "..", "src")
 
+include(joinpath(@__DIR__, "build_helpers.jl"))
+
 export build_fortran
 export build_spline_fortran, build_vacuum_fortran
 
-function build_fortran()
-    ENV["FC"] = get(ENV, "FC", "gfortran")
-    # Set OS-dependent flags
-    if Sys.isapple()
-        ENV["LIBS"] = "-framework Accelerate"
-        ENV["LIBSUFFIX"] = ".dylib"
-    elseif Sys.islinux()
-        ENV["LIBS"] = "-lopenblas"
-        ENV["LIBSUFFIX"] = ".so"
-    elseif Sys.iswindows()
-        ENV["LIBS"] = "-lopenblas"
-        ENV["LIBSUFFIX"] = ".dll"
-    else
-        error("Unsupported OS for Fortran build")
-    end
-    ENV["RECURSFLAG"] = "-frecursive"
-    ENV["LEGACYFLAG"] = "-std=legacy"
-    ENV["ZEROFLAG"] = "-finit-local-zero"
-    ENV["FFLAGS"] = "-fPIC"
-    ENV["LDFLAGS"] = "-shared"
-
-    results = [
-        # build_jpec_fortran() add here
-        build_spline_fortran(),
-        build_vacuum_fortran()
-    ]
-
-    if all(results)
-        @info "All Fortran builds succeeded!"
-    else
-        @error "Some Fortran builds failed."
-    end
-
-end
-
-function build_spline_fortran()
-    dir = joinpath(parent_dir, "Splines", "fortran")
-    try
-        run(pipeline(`make -C $dir`))
-        @info "Splines-fortran compiled well"
-        return true
-    catch e
-        @error "Failed to build Splines-fortran: $e"
-        return false
-    end
-end
-
-function build_vacuum_fortran()
-    dir = joinpath(parent_dir, "Vacuum", "fortran")
-    try
-        run(pipeline(`make -C $dir`))
-        @info "Vacuum-fortran compiled well"
-        return true
-    catch e
-        @error "Failed to build Vacuum-fortran: $e"
-        return false
-    end
-
-end
-
-# Example for including more fortran:
-#
-# function build_jpec_fortran()
-#     dir = joinpath(parent_dir, "Gpec", "fortran")
-#     try
-#         run(pipeline(`make -C $dir`, stdout=DevNull, stderr=DevNull))
-#         println("Gpec-fortran compiled well")
-#         return true
-#     catch e
-#         println("Failed to build Gpec-fortran: $e")
-#         return false
-#     end
-# end
-
-
 build_fortran() # Call the build function to execute the builds

deps/build_helpers.jl

@@ -0,0 +1,85 @@
+# How to modify build_helpers.jl:
+# 1) Declare build functions for each Fortran codes as 'build_*_fortran()'
+# 2) Add these functions to the results array in build_fortran()
+# 3) Export the functions you want to be accessible from outside
+
+
+const parent_dir = joinpath(@__DIR__, "..", "src")
+
+export build_spline_fortran, build_vacuum_fortran
+
+function build_fortran()
+    ENV["FC"] = get(ENV, "FC", "gfortran")
+    # Set OS-dependent flags
+    println("Setting up environment for ", Sys.KERNEL)
+    if Sys.isapple()
+        ENV["LIBS"] = "-framework Accelerate"
+        ENV["LIBSUFFIX"] = ".dylib"
+    elseif Sys.islinux()
+        ENV["LIBS"] = "-lopenblas"
+        ENV["LIBSUFFIX"] = ".so"
+    elseif Sys.iswindows()
+        ENV["LIBS"] = "-lopenblas"
+        ENV["LIBSUFFIX"] = ".dll"
+    else
+        error("Unsupported OS for Fortran build")
+    end
+    ENV["RECURSFLAG"] = "-frecursive"
+    ENV["LEGACYFLAG"] = "-std=legacy"
+    ENV["ZEROFLAG"] = "-finit-local-zero"
+    ENV["FFLAGS"] = "-fPIC"
+    ENV["LDFLAGS"] = "-shared"
+
+    results = [
+        # build_jpec_fortran() add here
+        build_spline_fortran(),
+        build_vacuum_fortran(),
+    ]
+
+    if all(results)
+        @info "All Fortran builds succeeded!"
+    else
+        @error "Some Fortran builds failed."
+    end
+
+end
+
+function build_spline_fortran()
+    dir = joinpath(parent_dir, "Splines", "fortran")
+    try
+        run(pipeline(`make -C $dir`))
+        @info "Splines-fortran compiled well"
+        return true
+    catch e
+        @error "Failed to build Splines-fortran: $e"
+        return false
+    end
+end
+
+function build_vacuum_fortran()
+    dir = joinpath(parent_dir, "Vacuum", "fortran")
+    try
+        run(pipeline(`make -C $dir`))
+        @info "Vacuum-fortran compiled well"
+        return true
+    catch e
+        @error "Failed to build Vacuum-fortran: $e"
+        return false
+    end
+
+end
+
+# Example for including more fortran:
+#
+# function build_jpec_fortran()
+#     dir = joinpath(parent_dir, "Gpec", "fortran")
+#     try
+#         run(pipeline(`make -C $dir`, stdout=DevNull, stderr=DevNull))
+#         println("Gpec-fortran compiled well")
+#         return true
+#     catch e
+#         println("Failed to build Gpec-fortran: $e")
+#         return false
+#     end
+# end
+

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+JPEC = "462872dd-e066-4d2e-b993-6468b5239634"
 
 [compat]
 Documenter = "1.0"