ENH: Explicitly specify write_text encoding format

When writing reports from nipype the write_text
function could default to using 'ascii' coding
for writing the report.  This would fail if any
part of the report tried to generate a unicode
character.

The issue was encountered when the OS environmental
variable "PS1" had a non-ascii character in the
environmental variable.

The result was a failure of the nipype pipeline
from running due to an exception being thrown
while trying to write the debugging information.

Author: hjmjohnson

nipype/interfaces/tests/test_io.py

@@ -709,7 +709,7 @@ def _mock_get_ssh_client(self):
 
 def test_ExportFile(tmp_path):
     testin = tmp_path / "in.txt"
-    testin.write_text("test string")
+    testin.write_text("test string", encoding='utf-8')
     i = nio.ExportFile()
     i.inputs.in_file = str(testin)
     i.inputs.out_file = str(tmp_path / "out.tsv")

nipype/pipeline/engine/tests/test_nodes.py

@@ -352,7 +352,10 @@ def test_NodeExecutionError(tmp_path, monkeypatch):
     exebin = tmp_path / 'bin'
     exebin.mkdir()
     exe = exebin / 'nipype-node-execution-fail'
-    exe.write_text('#!/bin/bash\necho "Running"\necho "This should fail" >&2\nexit 1')
+    exe.write_text(
+        '#!/bin/bash\necho "Running"\necho "This should fail" >&2\nexit 1',
+        encoding='utf-8',
+    )
     exe.chmod(exe.stat().st_mode | stat.S_IEXEC)
     monkeypatch.setenv("PATH", str(exe.parent.absolute()), prepend=os.pathsep)
 

nipype/pipeline/engine/utils.py

@@ -125,7 +125,7 @@ def write_node_report(node, result=None, is_mapnode=False):
 
     if result is None:
         logger.debug('[Node] Writing pre-exec report to "%s"', report_file)
-        report_file.write_text("\n".join(lines))
+        report_file.write_text("\n".join(lines), encoding='utf-8')
         return
 
     logger.debug('[Node] Writing post-exec report to "%s"', report_file)
@@ -138,7 +138,7 @@ def write_node_report(node, result=None, is_mapnode=False):
     outputs = result.outputs
     if outputs is None:
         lines += ["None"]
-        report_file.write_text("\n".join(lines))
+        report_file.write_text("\n".join(lines), encoding='utf-8')
         return
 
     if isinstance(outputs, Bunch):
@@ -163,7 +163,7 @@ def write_node_report(node, result=None, is_mapnode=False):
             subnode_report_files.append("subnode %d : %s" % (i, subnode_file))
 
         lines.append(write_rst_list(subnode_report_files))
-        report_file.write_text("\n".join(lines))
+        report_file.write_text("\n".join(lines), encoding='utf-8')
         return
 
     lines.append(write_rst_header("Runtime info", level=1))
@@ -205,7 +205,7 @@ def write_node_report(node, result=None, is_mapnode=False):
             write_rst_dict(result.runtime.environ),
         ]
 
-    report_file.write_text("\n".join(lines))
+    report_file.write_text("\n".join(lines), encoding='utf-8')
 
 
 def write_report(node, report_type=None, is_mapnode=False):

nipype/utils/subprocess.py

@@ -102,7 +102,7 @@ def run_command(runtime, output=None, timeout=0.01, write_cmdline=False):
         stderr = open(errfile, "wb")
 
     if write_cmdline:
-        (Path(runtime.cwd) / "command.txt").write_text(cmdline)
+        (Path(runtime.cwd) / "command.txt").write_text(cmdline, encoding='utf-8')
 
     proc = Popen(
         cmdline,

tools/update_requirements.py

@@ -15,4 +15,4 @@
 
 # Write requirements
 lines[1:-1] = requirements
-reqs.write_text("\n".join(lines))
+reqs.write_text("\n".join(lines), encoding='utf-8')

tools/update_zenodo.py

@@ -69,4 +69,6 @@ def decommify(name):
 
     zenodo["creators"] = creators
 
-    zenodo_file.write_text("%s\n" % json.dumps(zenodo, indent=2, ensure_ascii=False))
+    zenodo_file.write_text(
+        "%s\n" % json.dumps(zenodo, indent=2, ensure_ascii=False), encoding='utf-8'
+    )