v0.11.0: new auto_change_directory

Project.toml

@@ -1,7 +1,7 @@
 name = "Pipelines"
 uuid = "ef544631-5c6f-4e9b-994c-12e7a4cd724c"
 authors = ["Jiacheng Chuan <jiacheng_chuan@outlook.com>"]
-version = "0.10.6"
+version = "0.11.0"
 
 [deps]
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"

docs/src/API.md

@@ -61,6 +61,7 @@ isok
 
 ## Redirection
 ```@docs
+Pipelines.auto_change_directory
 redirect_to_files
 restore_stdout
 restore_stderr

docs/src/changelog.md

@@ -1,5 +1,9 @@
 # Change Log
 
+## v0.11.0
+
+- Feat/**Breaking**: new method `auto_change_directory(b::Bool)`. It is necessary because changing directory is not thread-safe in Julia. It was set to `false` in v0.11.0. To make your code compatible with previous version, you can add `Pipelines.auto_change_directory(true)` at the beginning of your code, or use full paths through out your code (recommended).
+
 ## v0.10.6
 
 - Fix: `run(::Program)`: wrap `pwd()` in try-catch block in case the dir no longer exists. It happens because workding dir is not thread safe in Julia. If other program delete the directory, it will fail. 

src/Program.jl

@@ -252,19 +252,39 @@ function Base.run(p::Program, inputs; kwarg...)
     run(p; inputs=inputs, kwarg...)
 end
 
+AUTO_CHANGE_DIRECTORY::Bool = false
+
+"""
+    auto_change_directory(b::Bool)
+
+When running a `Program`, whether automatically change to the directory. 
+
+Default is false since Pipelines v0.11.
+
+Changing directory is not thread-safe in Julia.
+
+Cannot set it in versions <= v0.10.6.
+"""
+function auto_change_directory(b::Bool)
+    global AUTO_CHANGE_DIRECTORY = b
+end
+
 function Base.run(p::Program;
     dir::AbstractString = "", retry::Int = 0,
     stdout = nothing, stderr = nothing, stdlog = stderr, append::Bool = false, _do_parse_program_args::Bool = true, kwarg...
-)
-    if dir != ""
-        dir_backup = try
-            # in case the dir no longer exists. happens because workding dir is not thread safe in Julia. If other program delete the directory, it will fail.
-            pwd()
-        catch
-            ""
+)   
+
+    if AUTO_CHANGE_DIRECTORY
+        if dir != ""
+            dir_backup = try
+                # in case the dir no longer exists. happens because workding dir is not thread safe in Julia. If other program delete the directory, it will fail.
+                pwd()
+            catch
+                ""
+            end
+            dir = abspath(dir)
+            cd(dir) # go to working directory
         end
-        dir = abspath(dir)
-        cd(dir) # go to working directory
     end
 
     if _do_parse_program_args
@@ -288,11 +308,13 @@ function Base.run(p::Program;
         n_try += 1
     end
 
-    if dir != ""
-        try
-            # in case the dir no longer exists. happens because workding dir is not thread safe in Julia. If other program delete the directory, it will fail.
-            cd(dir_backup)
-        catch
+    if AUTO_CHANGE_DIRECTORY
+        if dir != ""
+            try
+                # in case the dir no longer exists. happens because workding dir is not thread safe in Julia. If other program delete the directory, it will fail.
+                cd(dir_backup)
+            catch
+            end
         end
     end
     res
@@ -322,7 +344,7 @@ Return `(success::Bool, outputs::Dict{String})`
 
 - elements in `p.arg_inputs` and `p.arg_outputs`. They will merge to positional arguments `inputs` and `outputs`.
 
-- `dir::AbstractString = ""`: working directory to run the program and store `run_id_file`.
+- `dir::AbstractString = ""`: directory to store `run_id_file`. If set `Pipelines.auto_change_directory(true)`, Program will change to this directory before running. However, changing directory is not thread safe, so it is not recommended.
 
 - `check_dependencies::Bool = true`: check dependencies for `p` (`p.cmd_dependencies`).