run: make shell not load config files

Config files like `~/.zshenv`, `~/.bashenv` etc, are loaded on each
shell invocation, which might overwrite the environment breaking the
commands we are trying to wrap. To fix that, we need to provide
appropriate flags to the shell we are using to avoid loading those
configs.

Fixes #2506

dvc/stage.py

@@ -789,8 +789,34 @@ class Stage(object):
 
     def _run(self):
         self._check_missing_deps()
-        executable = os.getenv("SHELL") if os.name != "nt" else None
-        self._warn_if_fish(executable)
+
+        kwargs = {"cwd": self.wdir, "env": fix_env(None), "close_fds": True}
+
+        if os.name == "nt":
+            kwargs["shell"] = True
+            cmd = self.cmd
+        else:
+            # NOTE: when you specify `shell=True`, `Popen` [1] will default to
+            # `/bin/sh` on *nix and will add ["/bin/sh", "-c"] to your command.
+            # But we actually want to run the same shell that we are running
+            # from right now, which is usually determined by the `SHELL` env
+            # var. So instead, we compose our command on our own, making sure
+            # to include special flags to prevent shell from reading any
+            # configs and modifying env, which may change the behavior or the
+            # command we are running. See [2] for more info.
+            #
+            # [1] https://github.com/python/cpython/blob/3.7/Lib/subprocess.py
+            #                                                            #L1426
+            # [2] https://github.com/iterative/dvc/issues/2506
+            #                                           #issuecomment-535396799
+            kwargs["shell"] = False
+            executable = os.getenv("SHELL") or "/bin/sh"
+
+            self._warn_if_fish(executable)
+
+            opts = {"zsh": ["--no-rcs"], "bash": ["--noprofile", "--norc"]}
+            name = os.path.basename(executable).lower()
+            cmd = [executable] + opts.get(name, []) + ["-c", self.cmd]
 
         main_thread = isinstance(
             threading.current_thread(), threading._MainThread
@@ -799,14 +825,7 @@ class Stage(object):
         p = None
 
         try:
-            p = subprocess.Popen(
-                self.cmd,
-                cwd=self.wdir,
-                shell=True,
-                env=fix_env(os.environ),
-                executable=executable,
-                close_fds=True,
-            )
+            p = subprocess.Popen(cmd, **kwargs)
             if main_thread:
                 old_handler = signal.signal(signal.SIGINT, signal.SIG_IGN)
             p.communicate()