Rename run_sim, save_snapshot, and load_snapshot to run, save and load.

Project.toml

@@ -1,7 +1,7 @@
 name = "MEDYANSimRunner"
 uuid = "b58a3b99-22e3-44d1-b5ea-258f082a6fe8"
 authors = ["nhz2 <[email protected]>"]
-version = "0.4.2"
+version = "0.5.0"
 
 [deps]
 ArgCheck = "dce04be8-c92d-5529-be00-80e4d2c0e197"

README.md

@@ -40,7 +40,7 @@ These functions can also use the default random number generator, this will auto
 At the end of `main.jl` there should be the lines:
 ```julia
 if abspath(PROGRAM_FILE) == @__FILE__
-    MEDYANSimRunner.run_sim(ARGS; jobs, setup, loop, load_snapshot, save_snapshot, done)
+    MEDYANSimRunner.run(ARGS; jobs, setup, loop, load, save, done)
 end
 ```
 
@@ -59,16 +59,16 @@ The `job` string is also used to seed the default RNG right before `setup` is ca
 
 #### `setup(job::String; kwargs...) -> header_dict, state`
 Return the header dictionary to be written as the `header.json` file in output trajectory.
-Also return the state that gets passed on to `loop` and the state that gets passed to `save_snapshot` and `load_snapshot`.
+Also return the state that gets passed on to `loop` and the state that gets passed to `save` and `load`.
 
 `job::String`: The job. This is used for multi job simulations.
 
-#### `save_snapshot(step::Int, state; kwargs...)-> group::SmallZarrGroups.ZGroup`
+#### `save(step::Int, state; kwargs...)-> group::SmallZarrGroups.ZGroup`
 Return the state of the system as a `SmallZarrGroups.ZGroup`
 This function should not mutate `state`
 
-#### `load_snapshot(step::Int, group::SmallZarrGroups.ZGroup, state; kwargs...) -> state`
-Load the state saved by `save_snapshot`
+#### `load(step::Int, group::SmallZarrGroups.ZGroup, state; kwargs...) -> state`
+Load the state saved by `save`
 This function can mutate `state`.
 `state` may be the state returned from `setup` or the `state` returned by `loop`.
 This function should return the same output if `state` is the state returned by `loop` or the 
@@ -82,7 +82,7 @@ Also return the expected value of step when done will first be true, used for di
 This function should not mutate `state`
 
 #### `loop(step::Int, state; kwargs...) -> state`
-Return the state that gets passed to `save_snapshot`
+Return the state that gets passed to `save`
 
 
 ### Main loop pseudo code
@@ -95,13 +95,13 @@ Random.seed!(collect(reinterpret(UInt64, sha256(job))))
 job_header, state =  setup(job)
 save job_header
 step = 0
-SmallZarrGroups.save_zip(snapshot_zip_file, save_snapshot(step, state))
-state = load_snapshot(step, SmallZarrGroups.load_zip(snapshot_zip_file), state)
+SmallZarrGroups.save_zip(snapshot_zip_file, save(step, state))
+state = load(step, SmallZarrGroups.load_zip(snapshot_zip_file), state)
 while true
     state = loop(step, state)
     step = step + 1
-    SmallZarrGroups.save_zip(snapshot_zip_file, save_snapshot(step, state))
-    state = load_snapshot(step, SmallZarrGroups.load_zip(snapshot_zip_file), state)
+    SmallZarrGroups.save_zip(snapshot_zip_file, save(step, state))
+    state = load(step, SmallZarrGroups.load_zip(snapshot_zip_file), state)
     if done(step::Int, state)[1]
         break
     end

src/run-sim.jl

@@ -25,7 +25,7 @@ function get_version_string()
 end
 
 """
-    run_sim(ARGS; setup, loop, load_snapshot, save_snapshot, done)
+    run(ARGS; setup, loop, load, save, done)
 
 This function should be called at the end of a script to run a simulation.
 It takes keyword arguments:
@@ -41,10 +41,10 @@ is called once at the beginning of the simulation.
  - `loop(step::Int, state; kwargs...) -> state`
 is called once per step of the simulation.
 
-- `save_snapshot(step::Int, state; kwargs...) -> group::SmallZarrGroups.ZGroup`
+- `save(step::Int, state; kwargs...) -> group::SmallZarrGroups.ZGroup`
 is called to save a snapshot.
 
- - `load_snapshot(step::Int, group::SmallZarrGroups.ZGroup, state; kwargs...) -> state`
+ - `load(step::Int, group::SmallZarrGroups.ZGroup, state; kwargs...) -> state`
 is called to load a snapshot.
 
  - `done(step::Int, state; kwargs...) -> done::Bool, expected_final_step::Int`
@@ -54,12 +54,12 @@ is called to check if the simulation is done.
 
 $(CLI_HELP)
 """
-function run_sim(cli_args;
+function run(cli_args;
         jobs::Vector{String},
         setup,
         loop,
-        save_snapshot,
-        load_snapshot,
+        save,
+        load,
         done,
         kwargs...
     )
@@ -78,16 +78,16 @@ function run_sim(cli_args;
                 continue_job(options.out_dir, job;
                     setup,
                     loop,
-                    save_snapshot,
-                    load_snapshot,
+                    save,
+                    load,
                     done,
                 )
             else
                 start_job(options.out_dir, job;
                     setup,
                     loop,
-                    save_snapshot,
-                    load_snapshot,
+                    save,
+                    load,
                     done,
                 )
             end
@@ -98,29 +98,31 @@ function run_sim(cli_args;
             continue_job(options.out_dir, job;
                 setup,
                 loop,
-                save_snapshot,
-                load_snapshot,
+                save,
+                load,
                 done,
             )
         else
             start_job(options.out_dir, job;
                 setup,
                 loop,
-                save_snapshot,
-                load_snapshot,
+                save,
+                load,
                 done,
             )
         end
     end
     return
 end
 
+@deprecate run_sim(cli_args;save_snapshot, load_snapshot, kwargs...) run(cli_args; save=save_snapshot, load=load_snapshot, kwargs...) false
+
 
 function start_job(out_dir, job::String;
         setup,
         loop,
-        save_snapshot,
-        load_snapshot,
+        save,
+        load,
         done,
     )
     basic_name_check.(String.(split(job, '/'; keepempty=true)))
@@ -148,15 +150,15 @@ function start_job(out_dir, job::String;
             write_traj_file(traj, "header.json", codeunits(header_str))
             local step::Int = 0
 
-            state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save_snapshot, load_snapshot, prev_sha256)
+            state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save, load, prev_sha256)
             @info "Simulation started."
             while true
                 copy!(Random.default_rng(), rng_state)
                 state = loop(step, state)
                 copy!(rng_state, Random.default_rng())
 
                 step += 1
-                state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save_snapshot, load_snapshot, prev_sha256)
+                state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save, load, prev_sha256)
 
                 copy!(Random.default_rng(), rng_state)
                 isdone::Bool, expected_final_step::Int64 = done(step::Int, state)
@@ -177,8 +179,8 @@ end
 function continue_job(out_dir, job;
         setup,
         loop,
-        save_snapshot,
-        load_snapshot,
+        save,
+        load,
         done,
     )
     basic_name_check.(String.(split(job, '/'; keepempty=true)))
@@ -232,7 +234,7 @@ function continue_job(out_dir, job;
                 prev_sha256 = bytes2hex(sha256(header_str))
                 write_traj_file(traj, "header.json", codeunits(header_str))
                 step = 0
-                state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save_snapshot, load_snapshot, prev_sha256)
+                state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save, load, prev_sha256)
                 @info "Simulation started."
             else
                 @info "Continuing simulation from step $(step)."
@@ -241,7 +243,7 @@ function continue_job(out_dir, job;
                 reread_sub_snapshot_group = snapshot_group["snap"]
                 rng_state = str_2_rng(attrs(snapshot_group)["rng_state"])
                 copy!(Random.default_rng(), rng_state)
-                state = load_snapshot(step, reread_sub_snapshot_group, state)
+                state = load(step, reread_sub_snapshot_group, state)
                 copy!(rng_state, Random.default_rng())
                 prev_sha256 = bytes2hex(sha256(snapshot_data))
                 if step > 0
@@ -262,7 +264,7 @@ function continue_job(out_dir, job;
                 copy!(rng_state, Random.default_rng())
 
                 step += 1
-                state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save_snapshot, load_snapshot, prev_sha256)
+                state, prev_sha256 = save_load_state!(rng_state, step, state, traj, save, load, prev_sha256)
 
                 copy!(Random.default_rng(), rng_state)
                 isdone, expected_final_step = done(step::Int, state)
@@ -286,14 +288,14 @@ function save_load_state!(
         step::Int,
         state,
         traj::String,
-        save_snapshot,
-        load_snapshot,
+        save,
+        load,
         prev_sha256::String,
     )
     snapshot_group = ZGroup()
 
     copy!(Random.default_rng(), rng_state)
-    sub_snapshot_group = save_snapshot(step, state)
+    sub_snapshot_group = save(step, state)
     copy!(rng_state, Random.default_rng())
 
     snapshot_group["snap"] = sub_snapshot_group
@@ -304,7 +306,7 @@ function save_load_state!(
     reread_sub_snapshot_group = unzip_group(snapshot_data)["snap"]
 
     copy!(Random.default_rng(), rng_state)
-    state = load_snapshot(step, reread_sub_snapshot_group, state)
+    state = load(step, reread_sub_snapshot_group, state)
     copy!(rng_state, Random.default_rng())
 
     write_traj_file(traj, SNAP_PREFIX*string(step)*SNAP_POSTFIX, snapshot_data)

test/example/main.jl

@@ -28,14 +28,14 @@ function setup(job::String; kwargs...)
     header, state
 end
 
-function save_snapshot(step::Int, state; kwargs...)::ZGroup
+function save(step::Int, state; kwargs...)::ZGroup
     # @info "saving states" state
     group = ZGroup()
     group["states"] = state
     group
 end
 
-function load_snapshot(step::Int, group, state; kwargs...)
+function load(step::Int, group, state; kwargs...)
     state .= collect(group["states"])
     state
 end
@@ -52,5 +52,5 @@ function loop(step::Int, state; kwargs...)
 end
 
 if abspath(PROGRAM_FILE) == @__FILE__
-    MEDYANSimRunner.run_sim(ARGS; jobs, setup, loop, load_snapshot, save_snapshot, done)
+    MEDYANSimRunner.run(ARGS; jobs, setup, loop, load, save, done)
 end

test/test_ref_out.jl

@@ -27,11 +27,11 @@ warn_only_logger = MinLevelLogger(current_logger(), Logging.Warn);
         args = ["--out=$test_out","--batch=1"]
         continue_sim && push!(args,"--continue")
         with_logger(warn_only_logger) do
-            MEDYANSimRunner.run_sim(args;
+            MEDYANSimRunner.run(args;
                 UserCode.jobs,
                 UserCode.setup,
-                UserCode.save_snapshot,
-                UserCode.load_snapshot,
+                UserCode.save,
+                UserCode.load,
                 UserCode.loop,
                 UserCode.done,
             )
@@ -77,11 +77,11 @@ end
         args = ["--out=$test_out","--batch=1"]
         continue_sim && push!(args,"--continue")
         with_logger(warn_only_logger) do
-            MEDYANSimRunner.run_sim(args;
+            MEDYANSimRunner.run(args;
                 UserCode.jobs,
                 UserCode.setup,
-                UserCode.save_snapshot,
-                UserCode.load_snapshot,
+                UserCode.save,
+                UserCode.load,
                 UserCode.loop,
                 UserCode.done,
             )
@@ -93,4 +93,25 @@ end
         end
     end
 end
+
+@testset "deprecated full run example" begin
+    test_out = joinpath(@__DIR__, "example/output/deprecated-full")
+    rm(test_out; force=true, recursive=true)
+    args = ["--out=$test_out","--batch=1"]
+    with_logger(warn_only_logger) do
+        MEDYANSimRunner.run_sim(args;
+            UserCode.jobs,
+            UserCode.setup,
+            save_snapshot=UserCode.save,
+            load_snapshot=UserCode.load,
+            UserCode.loop,
+            UserCode.done,
+        )
+    end
+    out_diff = sprint(MEDYANSimRunner.print_traj_diff, joinpath(ref_out,"a"), joinpath(test_out,"a"))
+    if !isempty(out_diff)
+        println(out_diff)
+        @test false
+    end
+end
 end