Add the :execute method to activate! and withenv

src/env.jl

@@ -4,40 +4,83 @@ This file defines functions for interacting with the environment, such as `withe
 """
 
 """
-    activate!(env)
+    activate!(env; method=:simple)
 
-"Activate" the Conda environment by modifying the given dict of environment variables.
+"Activate" the Conda environment by modifying the given dict of environment variables. When `method` is `:simple`, the environment variables corresponding to meaning any activation hooks provided by conda packages will not be run.
+
+An experimental `method` of `:execute` is available. In this case, the Conda environment will be activated in a bash subshell, meaning all the activation hooks will be run. All environment variables updated or created in this subshell are then changed in the current process. This method requires `bash` to be available, and has only been tested on Linux.
 """
-function activate!(e)
+function activate!(e; method=:simple)
     backend() in (:Null, :Current) && return e
-    old_path = get(e, "PATH", "")
-    d = envdir()
-    path_sep = Sys.iswindows() ? ';' : ':'
-    new_path = join(bindirs(), path_sep)
-    if backend() == :MicroMamba
-        e["MAMBA_ROOT_PREFIX"] = MicroMamba.root_dir()
-        new_path = "$(new_path)$(path_sep)$(dirname(MicroMamba.executable()))"
-    end
-    if old_path != ""
-        new_path = "$(new_path)$(path_sep)$(old_path)"
+    if method == :simple
+        old_path = get(e, "PATH", "")
+        d = envdir()
+        path_sep = Sys.iswindows() ? ';' : ':'
+        new_path = join(bindirs(), path_sep)
+        if backend() == :MicroMamba
+            e["MAMBA_ROOT_PREFIX"] = MicroMamba.root_dir()
+            new_path = "$(new_path)$(path_sep)$(dirname(MicroMamba.executable()))"
+        end
+        if old_path != ""
+            new_path = "$(new_path)$(path_sep)$(old_path)"
+        end
+        e["PATH"] = new_path
+        e["CONDA_PREFIX"] = d
+        e["CONDA_DEFAULT_ENV"] = d
+        e["CONDA_SHLVL"] = "1"
+        e["CONDA_PROMPT_MODIFIER"] = "($d) "
+        e
+    elseif method == :execute
+        d = envdir()
+        hook = join(conda_cmd(`shell hook -s bash -r $d`).exec, " ")
+        activate = join(conda_cmd(`shell activate -s bash -p $d`).exec, " ")
+        steps = [
+            "env",
+            "echo __65ab376884d7456ca97187d18a182250__",
+            "eval \"\$($hook)\"",
+            "eval \"\$($activate)\"",
+            "env"
+        ]
+        steps = join(steps, " && ")
+        cmd = `bash --norc --noprofile -c $steps`
+        out = read(cmd, String)
+        before_env = []
+        after_env = []
+        is_before = true
+        for line in split(out, '\n')
+            if line == "__65ab376884d7456ca97187d18a182250__"
+                is_before = false
+            end
+            if occursin("=", line)
+                bits = split(line, '=', limit=2)
+                if is_before
+                    push!(before_env, bits)
+                else
+                    push!(after_env, bits)
+                end
+            end
+        end
+        for (k, v) in after_env
+            if haskey(e, k)
+                if e[k] != v
+                    e[k] = v
+                end
+            else
+                e[k] = v
+            end
+        end
     end
-    e["PATH"] = new_path
-    e["CONDA_PREFIX"] = d
-    e["CONDA_DEFAULT_ENV"] = d
-    e["CONDA_SHLVL"] = "1"
-    e["CONDA_PROMPT_MODIFIER"] = "($d) "
-    e
 end
 
 """
-    withenv(f::Function)
+    withenv(f::Function, method=:simple)
 
-Call `f()` while the Conda environment is active.
+Call `f()` while the Conda environment is active. See `activate!()` for details of the `method` argument.
 """
-function withenv(f::Function)
+function withenv(f::Function; method=:simple)
     old_env = copy(ENV)
     # shell("activate")
-    activate!(ENV)
+    activate!(ENV; method=method)
     frozen = STATE.frozen
     STATE.frozen = true
     try