From 931a766bba6361afd44daa2d15ddfae3a49c49a9 Mon Sep 17 00:00:00 2001
From: Tim <tim.terf@gmail.com>
Date: Mon, 11 Jan 2021 00:33:58 -0500
Subject: [PATCH 01/18] interface for R

mostly a copy-paste of the matlab interface
---
 nipype/interfaces/r.py | 129 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 129 insertions(+)
 create mode 100644 nipype/interfaces/r.py

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
new file mode 100644
index 0000000000..37010853d8
--- /dev/null
+++ b/nipype/interfaces/r.py
@@ -0,0 +1,129 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Interfaces to run R scripts."""
+import os
+
+from .. import config
+from .base import (
+    CommandLineInputSpec,
+    InputMultiPath,
+    isdefined,
+    CommandLine,
+    traits,
+    File,
+    Directory,
+)
+
+
+def get_r_command():
+    if "NIPYPE_NO_R" in os.environ:
+        return None
+    try:
+        r_cmd = os.environ["RCMD"]
+    except:
+        r_cmd = "R"
+    return r_cmd
+
+
+no_r = get_r_command() is None
+
+
+class RInputSpec(CommandLineInputSpec):
+    """ Basic expected inputs to R interface """
+
+    script = traits.Str(
+        argstr='-e "%s"', desc="R code to run", mandatory=True, position=-1
+    )
+    # non-commandline options
+    rfile = traits.Bool(True, desc="Run R using R script", usedefault=True)
+    script_file = File(
+        "pyscript.R", usedefault=True, desc="Name of file to write R code to"
+    )
+    
+
+class RCommand(CommandLine):
+    """Interface that runs R code
+
+    >>> import nipype.interfaces.r as r
+    >>> r = r.RCommand(rfile=False)  # don't write script file
+    >>> r.inputs.script = "Sys.getenv('USER')"
+    >>> out = r.run()  # doctest: +SKIP
+    """
+
+    _cmd = "R"
+    _default_r_cmd = None
+    _default_rfile = None
+    input_spec = RInputSpec
+
+    def __init__(self, r_cmd=None, **inputs):
+        """initializes interface to r
+        (default 'R')
+        """
+        super(RCommand, self).__init__(**inputs)
+        if r_cmd and isdefined(r_cmd):
+            self._cmd = r_cmd
+        elif self._default_r_cmd:
+            self._cmd = self._default_r_cmd
+
+        if self._default_rfile and not isdefined(self.inputs.rfile):
+            self.inputs.rfile = self._default_rfile
+
+        # For r commands force all output to be returned since r
+        # does not have a clean way of notifying an error
+        self.terminal_output = "allatonce"
+
+    @classmethod
+    def set_default_r_cmd(cls, r_cmd):
+        """Set the default R command line for R classes.
+
+        This method is used to set values for all R
+        subclasses.  However, setting this will not update the output
+        type for any existing instances.  For these, assign the
+        <instance>.inputs.r_cmd.
+        """
+        cls._default_r_cmd = r_cmd
+
+    @classmethod
+    def set_default_rfile(cls, rfile):
+        """Set the default R script file format for R classes.
+
+        This method is used to set values for all R
+        subclasses.  However, setting this will not update the output
+        type for any existing instances.  For these, assign the
+        <instance>.inputs.rfile.
+        """
+        cls._default_rfile = rfile
+
+    def _run_interface(self, runtime):
+        self.terminal_output = "allatonce"
+        runtime = super(RCommand, self)._run_interface(runtime)
+        if "R code threw an exception" in runtime.stderr:
+            self.raise_exception(runtime)
+        return runtime
+
+    def _format_arg(self, name, trait_spec, value):
+        if name in ["script"]:
+            argstr = trait_spec.argstr
+            return self._gen_r_command(argstr, value)
+        return super(RCommand, self)._format_arg(name, trait_spec, value)
+
+    def _gen_r_command(self, argstr, script_lines):
+        """ Generates commands and, if rfile specified, writes it to disk."""
+        if not self.inputs.rfile:
+            # replace newlines with ;, strip comments
+            script = "; ".join([
+                        line
+                        for line in script_lines.split("\n")
+                        if not line.strip().startswith("#")
+                    ])
+            # escape " and $
+            script = script.replace('"','\\"')
+            script = script.replace('$','\\$')
+        else:
+            script_path = os.path.join(os.getcwd(), self.inputs.script_file)
+            with open(script_path, "wt") as rfile:
+                rfile.write(script_lines)
+            script = "source('%s')" % script_path
+
+        return argstr % script

From b3361325022c591a86f09579a24234457a269b47 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Thu, 27 May 2021 23:18:44 -0400
Subject: [PATCH 02/18] return None if R can't be found

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/r.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
index 37010853d8..06ee212644 100644
--- a/nipype/interfaces/r.py
+++ b/nipype/interfaces/r.py
@@ -19,11 +19,9 @@
 def get_r_command():
     if "NIPYPE_NO_R" in os.environ:
         return None
-    try:
-        r_cmd = os.environ["RCMD"]
-    except:
-        r_cmd = "R"
-    return r_cmd
+    r_cmd = os.getenv("RCMD", default="R")
+    
+    return r_cmd if which(r_cmd) else None
 
 
 no_r = get_r_command() is None

From 2638489e2c02dff35fc583306a6c93e0bc5a3b1c Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Thu, 27 May 2021 23:19:20 -0400
Subject: [PATCH 03/18] remove hardcoded variable

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/r.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
index 06ee212644..c9fd51b392 100644
--- a/nipype/interfaces/r.py
+++ b/nipype/interfaces/r.py
@@ -49,7 +49,7 @@ class RCommand(CommandLine):
     >>> out = r.run()  # doctest: +SKIP
     """
 
-    _cmd = "R"
+    _cmd = get_r_command()
     _default_r_cmd = None
     _default_rfile = None
     input_spec = RInputSpec

From f7cb9b2f6d2e9607d5cc2670856d6227ce0d208e Mon Sep 17 00:00:00 2001
From: Terf <tim.terf@gmail.com>
Date: Thu, 27 May 2021 23:20:06 -0400
Subject: [PATCH 04/18] R interface tests

---
 nipype/interfaces/tests/test_r.py | 100 ++++++++++++++++++++++++++++++
 1 file changed, 100 insertions(+)
 create mode 100644 nipype/interfaces/tests/test_r.py

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
new file mode 100644
index 0000000000..a851e4df6b
--- /dev/null
+++ b/nipype/interfaces/tests/test_r.py
@@ -0,0 +1,100 @@
+# -*- coding: utf-8 -*-
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+import os
+
+import pytest
+import nipype.interfaces.r as r
+
+r_cmd = r.get_r_command()
+no_r = r_cmd is None
+if not no_r:
+    r.RCommand.set_default_r_cmd(r_cmd)
+
+
+def clean_workspace_and_get_default_script_file():
+    # Make sure things are clean.
+    default_script_file = r.RInputSpec().script_file
+    if os.path.exists(default_script_file):
+        os.remove(
+            default_script_file
+        )  # raise Exception('Default script file needed for tests; please remove %s!' % default_script_file)
+    return default_script_file
+
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_cmdline():
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    ri = r.RCommand(script="1 + 1", script_file="testscript", rfile=False)
+
+    assert ri.cmdline == r_cmd + (
+        ' -e "1 + 1"'
+    )
+
+    assert ri.inputs.script == "1 + 1"
+    assert ri.inputs.script_file == "testscript"
+    assert not os.path.exists(ri.inputs.script_file), "scriptfile should not exist"
+    assert not os.path.exists(
+        default_script_file
+    ), "default scriptfile should not exist."
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_r_init():
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    assert r.RCommand._cmd == "R"
+    assert r.RCommand.input_spec == r.RInputSpec
+
+    assert r.RCommand().cmd == r_cmd
+    rc = r.RCommand(r_cmd="foo_m")
+    assert rc.cmd == "foo_m"
+
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_run_interface(tmpdir):
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    rc = r.RCommand(r_cmd="foo_m")
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 1."
+    with pytest.raises(ValueError):
+        rc.run()  # script is mandatory
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 2."
+    if os.path.exists(default_script_file):  # cleanup
+        os.remove(default_script_file)
+
+    rc.inputs.script = "a=1;"
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 3."
+    with pytest.raises(IOError):
+        rc.run()  # foo_m is not an executable
+    assert os.path.exists(default_script_file), "scriptfile should exist 3."
+    if os.path.exists(default_script_file):  # cleanup
+        os.remove(default_script_file)
+
+    cwd = tmpdir.chdir()
+
+    # bypasses ubuntu dash issue
+    rc = r.RCommand(script="foo;", rfile=True)
+    assert not os.path.exists(default_script_file), "scriptfile should not exist 4."
+    with pytest.raises(RuntimeError):
+        rc.run()
+    assert os.path.exists(default_script_file), "scriptfile should exist 4."
+    if os.path.exists(default_script_file):  # cleanup
+        os.remove(default_script_file)
+
+    # bypasses ubuntu dash issue
+    res = r.RCommand(script="a=1;", rfile=True).run()
+    assert res.runtime.returncode == 0
+    assert os.path.exists(default_script_file), "scriptfile should exist 5."
+    cwd.chdir()
+
+
+@pytest.mark.skipif(no_r, reason="R is not available")
+def test_set_rcmd():
+    default_script_file = clean_workspace_and_get_default_script_file()
+
+    ri = r.RCommand()
+    ri.set_default_r_cmd("foo")
+    assert not os.path.exists(default_script_file), "scriptfile should not exist."
+    assert ri._default_r_cmd == "foo"
+    ri.set_default_r_cmd(r_cmd)

From 0dcf413071ae0d868ac60cd9ecb553d3a5c4e668 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:19:41 -0400
Subject: [PATCH 05/18] Update nipype/interfaces/r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/r.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
index c9fd51b392..d9507b2f94 100644
--- a/nipype/interfaces/r.py
+++ b/nipype/interfaces/r.py
@@ -3,6 +3,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Interfaces to run R scripts."""
 import os
+from shutil import which
 
 from .. import config
 from .base import (

From 190b6f43a43cffed8bca9387a0d6d859570041af Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:20:07 -0400
Subject: [PATCH 06/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index a851e4df6b..52878f78d1 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -4,7 +4,7 @@
 import os
 
 import pytest
-import nipype.interfaces.r as r
+from nipype.interfaces import r
 
 r_cmd = r.get_r_command()
 no_r = r_cmd is None

From 02104a75a75784685774c3932371ceaaf4f4a67d Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:20:33 -0400
Subject: [PATCH 07/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index 52878f78d1..a8a36ad3f0 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -6,8 +6,7 @@
 import pytest
 from nipype.interfaces import r
 
-r_cmd = r.get_r_command()
-no_r = r_cmd is None
+no_r = r.no_r
 if not no_r:
     r.RCommand.set_default_r_cmd(r_cmd)
 

From 6fcf05b89e70b602aacdb7eb7128dcbaabbf09d9 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:22:01 -0400
Subject: [PATCH 08/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index a8a36ad3f0..10f42302b7 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -7,8 +7,6 @@
 from nipype.interfaces import r
 
 no_r = r.no_r
-if not no_r:
-    r.RCommand.set_default_r_cmd(r_cmd)
 
 
 def clean_workspace_and_get_default_script_file():

From b74fc859f3680af3364886d4ec8214bd76c9416b Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:37:40 -0400
Subject: [PATCH 09/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index 10f42302b7..0444d98b71 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -91,7 +91,8 @@ def test_set_rcmd():
     default_script_file = clean_workspace_and_get_default_script_file()
 
     ri = r.RCommand()
+    _default_r_cmd = ri._default_r_cmd
     ri.set_default_r_cmd("foo")
     assert not os.path.exists(default_script_file), "scriptfile should not exist."
     assert ri._default_r_cmd == "foo"
-    ri.set_default_r_cmd(r_cmd)
+    ri.set_default_r_cmd(_default_r_cmd)

From f72b5106d17d149b7f0b48f5ff7ecdfe604534b0 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:38:25 -0400
Subject: [PATCH 10/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index 0444d98b71..ae8cb49402 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -20,17 +20,15 @@ def clean_workspace_and_get_default_script_file():
 
 
 @pytest.mark.skipif(no_r, reason="R is not available")
-def test_cmdline():
-    default_script_file = clean_workspace_and_get_default_script_file()
-
-    ri = r.RCommand(script="1 + 1", script_file="testscript", rfile=False)
+def test_cmdline(tmp_path):
+    ri = r.RCommand(script="1 + 1", script_file=str(tmp_path / "testscript"), rfile=False)
 
     assert ri.cmdline == r_cmd + (
         ' -e "1 + 1"'
     )
 
     assert ri.inputs.script == "1 + 1"
-    assert ri.inputs.script_file == "testscript"
+    assert ri.inputs.script_file == str(tmp_path / "testscript")
     assert not os.path.exists(ri.inputs.script_file), "scriptfile should not exist"
     assert not os.path.exists(
         default_script_file

From 3d64c265b8ea580fc2d11cf056585264c9b9f4b0 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:38:59 -0400
Subject: [PATCH 11/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index ae8cb49402..ae5ea21bb2 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -38,7 +38,7 @@ def test_cmdline(tmp_path):
 def test_r_init():
     default_script_file = clean_workspace_and_get_default_script_file()
 
-    assert r.RCommand._cmd == "R"
+    assert r.RCommand._cmd == r.get_r_command()
     assert r.RCommand.input_spec == r.RInputSpec
 
     assert r.RCommand().cmd == r_cmd

From c4cb5396efc7feb99b08763ebc5080b4d3fb8a10 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Mon, 31 May 2021 19:39:22 -0400
Subject: [PATCH 12/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index ae5ea21bb2..9c7c370f28 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -34,6 +34,7 @@ def test_cmdline(tmp_path):
         default_script_file
     ), "default scriptfile should not exist."
 
+
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_r_init():
     default_script_file = clean_workspace_and_get_default_script_file()

From 9cad3cdddc66f8d0d2f8dc6c5c8a22cb3e071c0a Mon Sep 17 00:00:00 2001
From: Terf <tim.terf@gmail.com>
Date: Tue, 1 Jun 2021 10:52:10 -0400
Subject: [PATCH 13/18] @effigies R interface suggestions

---
 nipype/interfaces/r.py            | 25 ++++----------
 nipype/interfaces/tests/test_r.py | 57 ++++++-------------------------
 2 files changed, 17 insertions(+), 65 deletions(-)

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
index d9507b2f94..89b799b0ce 100644
--- a/nipype/interfaces/r.py
+++ b/nipype/interfaces/r.py
@@ -51,8 +51,6 @@ class RCommand(CommandLine):
     """
 
     _cmd = get_r_command()
-    _default_r_cmd = None
-    _default_rfile = None
     input_spec = RInputSpec
 
     def __init__(self, r_cmd=None, **inputs):
@@ -62,37 +60,26 @@ def __init__(self, r_cmd=None, **inputs):
         super(RCommand, self).__init__(**inputs)
         if r_cmd and isdefined(r_cmd):
             self._cmd = r_cmd
-        elif self._default_r_cmd:
-            self._cmd = self._default_r_cmd
-
-        if self._default_rfile and not isdefined(self.inputs.rfile):
-            self.inputs.rfile = self._default_rfile
 
         # For r commands force all output to be returned since r
         # does not have a clean way of notifying an error
         self.terminal_output = "allatonce"
 
-    @classmethod
-    def set_default_r_cmd(cls, r_cmd):
+    def set_default_r_cmd(self, r_cmd):
         """Set the default R command line for R classes.
 
         This method is used to set values for all R
-        subclasses.  However, setting this will not update the output
-        type for any existing instances.  For these, assign the
-        <instance>.inputs.r_cmd.
+        subclasses. 
         """
-        cls._default_r_cmd = r_cmd
+        self._cmd = r_cmd
 
-    @classmethod
-    def set_default_rfile(cls, rfile):
+    def set_default_rfile(self, rfile):
         """Set the default R script file format for R classes.
 
         This method is used to set values for all R
-        subclasses.  However, setting this will not update the output
-        type for any existing instances.  For these, assign the
-        <instance>.inputs.rfile.
+        subclasses.
         """
-        cls._default_rfile = rfile
+        self._rfile = rfile
 
     def _run_interface(self, runtime):
         self.terminal_output = "allatonce"
diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index 9c7c370f28..fdf7528d40 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -8,48 +8,28 @@
 
 no_r = r.no_r
 
-
-def clean_workspace_and_get_default_script_file():
-    # Make sure things are clean.
-    default_script_file = r.RInputSpec().script_file
-    if os.path.exists(default_script_file):
-        os.remove(
-            default_script_file
-        )  # raise Exception('Default script file needed for tests; please remove %s!' % default_script_file)
-    return default_script_file
-
-
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_cmdline(tmp_path):
-    ri = r.RCommand(script="1 + 1", script_file=str(tmp_path / "testscript"), rfile=False)
+    default_script_file = str(tmp_path / "testscript")
+    ri = r.RCommand(script="1 + 1", script_file=default_script_file, rfile=False)
+    r_cmd = r.get_r_command()
 
     assert ri.cmdline == r_cmd + (
         ' -e "1 + 1"'
     )
 
     assert ri.inputs.script == "1 + 1"
-    assert ri.inputs.script_file == str(tmp_path / "testscript")
+    assert ri.inputs.script_file == default_script_file
     assert not os.path.exists(ri.inputs.script_file), "scriptfile should not exist"
     assert not os.path.exists(
         default_script_file
     ), "default scriptfile should not exist."
 
 
-@pytest.mark.skipif(no_r, reason="R is not available")
-def test_r_init():
-    default_script_file = clean_workspace_and_get_default_script_file()
-
-    assert r.RCommand._cmd == r.get_r_command()
-    assert r.RCommand.input_spec == r.RInputSpec
-
-    assert r.RCommand().cmd == r_cmd
-    rc = r.RCommand(r_cmd="foo_m")
-    assert rc.cmd == "foo_m"
-
-
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_run_interface(tmpdir):
-    default_script_file = clean_workspace_and_get_default_script_file()
+    os.chdir(tmpdir)
+    default_script_file = r.RInputSpec().script_file
 
     rc = r.RCommand(r_cmd="foo_m")
     assert not os.path.exists(default_script_file), "scriptfile should not exist 1."
@@ -67,31 +47,16 @@ def test_run_interface(tmpdir):
     if os.path.exists(default_script_file):  # cleanup
         os.remove(default_script_file)
 
-    cwd = tmpdir.chdir()
-
-    # bypasses ubuntu dash issue
-    rc = r.RCommand(script="foo;", rfile=True)
-    assert not os.path.exists(default_script_file), "scriptfile should not exist 4."
-    with pytest.raises(RuntimeError):
-        rc.run()
-    assert os.path.exists(default_script_file), "scriptfile should exist 4."
-    if os.path.exists(default_script_file):  # cleanup
-        os.remove(default_script_file)
-
-    # bypasses ubuntu dash issue
-    res = r.RCommand(script="a=1;", rfile=True).run()
-    assert res.runtime.returncode == 0
-    assert os.path.exists(default_script_file), "scriptfile should exist 5."
-    cwd.chdir()
 
 
 @pytest.mark.skipif(no_r, reason="R is not available")
-def test_set_rcmd():
-    default_script_file = clean_workspace_and_get_default_script_file()
+def test_set_rcmd(tmpdir):
+    os.chdir(tmpdir)
+    default_script_file = r.RInputSpec().script_file
 
     ri = r.RCommand()
-    _default_r_cmd = ri._default_r_cmd
+    _default_r_cmd = ri._cmd
     ri.set_default_r_cmd("foo")
     assert not os.path.exists(default_script_file), "scriptfile should not exist."
-    assert ri._default_r_cmd == "foo"
+    assert ri._cmd == "foo"
     ri.set_default_r_cmd(_default_r_cmd)

From 6aab778ead6f0cd4be34956a1dca7b93ba621531 Mon Sep 17 00:00:00 2001
From: Tim Robert-Fitzgerald <tim.terf@gmail.com>
Date: Tue, 1 Jun 2021 12:17:34 -0400
Subject: [PATCH 14/18] Update nipype/interfaces/tests/test_r.py

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 nipype/interfaces/tests/test_r.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index fdf7528d40..9f7477777e 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -51,7 +51,7 @@ def test_run_interface(tmpdir):
 
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_set_rcmd(tmpdir):
-    os.chdir(tmpdir)
+    cwd = tmpdir.chdir()
     default_script_file = r.RInputSpec().script_file
 
     ri = r.RCommand()
@@ -60,3 +60,4 @@ def test_set_rcmd(tmpdir):
     assert not os.path.exists(default_script_file), "scriptfile should not exist."
     assert ri._cmd == "foo"
     ri.set_default_r_cmd(_default_r_cmd)
+    cwd.chdir()

From 7f3713b9e702dc194fdcfae2151f4189cafd3e89 Mon Sep 17 00:00:00 2001
From: Terf <tim.terf@gmail.com>
Date: Tue, 1 Jun 2021 12:28:14 -0400
Subject: [PATCH 15/18] ran `make specs`

---
 nipype/interfaces/tests/test_auto_RCommand.py | 31 +++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 nipype/interfaces/tests/test_auto_RCommand.py

diff --git a/nipype/interfaces/tests/test_auto_RCommand.py b/nipype/interfaces/tests/test_auto_RCommand.py
new file mode 100644
index 0000000000..adfcf36cf0
--- /dev/null
+++ b/nipype/interfaces/tests/test_auto_RCommand.py
@@ -0,0 +1,31 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from ..r import RCommand
+
+
+def test_RCommand_inputs():
+    input_map = dict(
+        args=dict(
+            argstr="%s",
+        ),
+        environ=dict(
+            nohash=True,
+            usedefault=True,
+        ),
+        rfile=dict(
+            usedefault=True,
+        ),
+        script=dict(
+            argstr='-e "%s"',
+            mandatory=True,
+            position=-1,
+        ),
+        script_file=dict(
+            extensions=None,
+            usedefault=True,
+        ),
+    )
+    inputs = RCommand.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value

From 7f92f638d5813c5267c44e6f8a39f9b45051c0bb Mon Sep 17 00:00:00 2001
From: Terf <tim.terf@gmail.com>
Date: Tue, 1 Jun 2021 12:53:53 -0400
Subject: [PATCH 16/18] un-chdir R test

---
 nipype/interfaces/tests/test_r.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index 9f7477777e..f15eadac55 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -28,7 +28,7 @@ def test_cmdline(tmp_path):
 
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_run_interface(tmpdir):
-    os.chdir(tmpdir)
+    cwd = tmpdir.chdir()
     default_script_file = r.RInputSpec().script_file
 
     rc = r.RCommand(r_cmd="foo_m")
@@ -46,6 +46,7 @@ def test_run_interface(tmpdir):
     assert os.path.exists(default_script_file), "scriptfile should exist 3."
     if os.path.exists(default_script_file):  # cleanup
         os.remove(default_script_file)
+    cwd.chdir()
 
 
 

From 52e1a983826c1fd040620b5546e798ddaf4a81dc Mon Sep 17 00:00:00 2001
From: Terf <tim.terf@gmail.com>
Date: Tue, 1 Jun 2021 14:35:43 -0400
Subject: [PATCH 17/18] ran `black .`

---
 nipype/interfaces/r.py            | 26 ++++++++++++++------------
 nipype/interfaces/tests/test_r.py |  6 ++----
 2 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
index 89b799b0ce..f9719ce777 100644
--- a/nipype/interfaces/r.py
+++ b/nipype/interfaces/r.py
@@ -21,7 +21,7 @@ def get_r_command():
     if "NIPYPE_NO_R" in os.environ:
         return None
     r_cmd = os.getenv("RCMD", default="R")
-    
+
     return r_cmd if which(r_cmd) else None
 
 
@@ -29,7 +29,7 @@ def get_r_command():
 
 
 class RInputSpec(CommandLineInputSpec):
-    """ Basic expected inputs to R interface """
+    """Basic expected inputs to R interface"""
 
     script = traits.Str(
         argstr='-e "%s"', desc="R code to run", mandatory=True, position=-1
@@ -39,7 +39,7 @@ class RInputSpec(CommandLineInputSpec):
     script_file = File(
         "pyscript.R", usedefault=True, desc="Name of file to write R code to"
     )
-    
+
 
 class RCommand(CommandLine):
     """Interface that runs R code
@@ -69,7 +69,7 @@ def set_default_r_cmd(self, r_cmd):
         """Set the default R command line for R classes.
 
         This method is used to set values for all R
-        subclasses. 
+        subclasses.
         """
         self._cmd = r_cmd
 
@@ -95,17 +95,19 @@ def _format_arg(self, name, trait_spec, value):
         return super(RCommand, self)._format_arg(name, trait_spec, value)
 
     def _gen_r_command(self, argstr, script_lines):
-        """ Generates commands and, if rfile specified, writes it to disk."""
+        """Generates commands and, if rfile specified, writes it to disk."""
         if not self.inputs.rfile:
             # replace newlines with ;, strip comments
-            script = "; ".join([
-                        line
-                        for line in script_lines.split("\n")
-                        if not line.strip().startswith("#")
-                    ])
+            script = "; ".join(
+                [
+                    line
+                    for line in script_lines.split("\n")
+                    if not line.strip().startswith("#")
+                ]
+            )
             # escape " and $
-            script = script.replace('"','\\"')
-            script = script.replace('$','\\$')
+            script = script.replace('"', '\\"')
+            script = script.replace("$", "\\$")
         else:
             script_path = os.path.join(os.getcwd(), self.inputs.script_file)
             with open(script_path, "wt") as rfile:
diff --git a/nipype/interfaces/tests/test_r.py b/nipype/interfaces/tests/test_r.py
index f15eadac55..6550a32747 100644
--- a/nipype/interfaces/tests/test_r.py
+++ b/nipype/interfaces/tests/test_r.py
@@ -8,15 +8,14 @@
 
 no_r = r.no_r
 
+
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_cmdline(tmp_path):
     default_script_file = str(tmp_path / "testscript")
     ri = r.RCommand(script="1 + 1", script_file=default_script_file, rfile=False)
     r_cmd = r.get_r_command()
 
-    assert ri.cmdline == r_cmd + (
-        ' -e "1 + 1"'
-    )
+    assert ri.cmdline == r_cmd + (' -e "1 + 1"')
 
     assert ri.inputs.script == "1 + 1"
     assert ri.inputs.script_file == default_script_file
@@ -49,7 +48,6 @@ def test_run_interface(tmpdir):
     cwd.chdir()
 
 
-
 @pytest.mark.skipif(no_r, reason="R is not available")
 def test_set_rcmd(tmpdir):
     cwd = tmpdir.chdir()

From e576c9057bdbb7403fe7672225af784a06f28d2c Mon Sep 17 00:00:00 2001
From: Terf <tim.terf@gmail.com>
Date: Tue, 1 Jun 2021 15:22:09 -0400
Subject: [PATCH 18/18] skip in CI as R isn't installed

---
 nipype/interfaces/r.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nipype/interfaces/r.py b/nipype/interfaces/r.py
index f9719ce777..a586de183c 100644
--- a/nipype/interfaces/r.py
+++ b/nipype/interfaces/r.py
@@ -45,8 +45,8 @@ class RCommand(CommandLine):
     """Interface that runs R code
 
     >>> import nipype.interfaces.r as r
-    >>> r = r.RCommand(rfile=False)  # don't write script file
-    >>> r.inputs.script = "Sys.getenv('USER')"
+    >>> r = r.RCommand(rfile=False) # doctest: +SKIP
+    >>> r.inputs.script = "Sys.getenv('USER')" # doctest: +SKIP
     >>> out = r.run()  # doctest: +SKIP
     """