Fix handling of pathlib.Path objects (#143)

CHANGES.rst

@@ -8,6 +8,7 @@
 - Fix ``datetime.utcnow()`` DeprecationWarning [#134]
 - Provide ``asn_n_members=1`` when opening the ``Step`` dataset for
  ``get_crds_parameters`` [#142]
+- Fix bug in handling of ``pathlib.Path`` objects as ``Step`` inputs [#143]
 
 0.5.1 (2023-10-02)
 ==================

src/stpipe/log.py

@@ -5,6 +5,7 @@
 import io
 import logging
 import os
+import pathlib
 import sys
 import threading
 from contextlib import contextmanager
@@ -176,7 +177,7 @@ def load_configuration(config_file):
 
  Parameters
  ----------
- config_file : str or readable file-like object
+ config_file : str, pathlib.Path instance or readable file-like object
  """
 
  def _level_check(value):
@@ -192,6 +193,8 @@ def _level_check(value):
  return value
 
  spec = config_parser.load_spec_file(LogConfig)
+ if isinstance(config_file, pathlib.Path):
+ config_file = str(config_file)
  config = ConfigObj(config_file, raise_errors=True, interpolation=False)
  val = validate.Validator()
  val.functions["level"] = _level_check

src/stpipe/step.py

@@ -18,6 +18,7 @@
  split,
  splitext,
 )
+from pathlib import Path
 from typing import ClassVar
 
 try:
@@ -248,7 +249,7 @@ def from_config_section(
  If not provided, try the following (in order):
  - The ``name`` parameter in the config file fragment
  - The name of returned class
- config_file : str, optional
+ config_file : str or pathlib.Path, optional
  The path to the config file that created this step, if
  any. This is used to resolve relative file name
  parameters in the config file.
@@ -323,7 +324,7 @@ def __init__(
  fully-qualified name for this step, and to determine
  the mode in which to run this step.
 
- config_file : str path, optional
+ config_file : str or pathlib.Path, optional
  The path to the config file that this step was initialized
  with. Use to determine relative path names of other config files.
 
@@ -907,7 +908,7 @@ def set_primary_input(self, obj, exclusive=True):
 
  Parameters
  ----------
- obj : str or instance of AbstractDataModel
+ obj : str, pathlib.Path, or instance of AbstractDataModel
  The object to base the name on. If a datamodel,
  use Datamodel.meta.filename.
 
@@ -920,8 +921,8 @@ def set_primary_input(self, obj, exclusive=True):
  err_message = f"Cannot set master input file name from object {obj}"
  parent_input_filename = self.search_attr("_input_filename")
  if not exclusive or parent_input_filename is None:
- if isinstance(obj, str):
- self._input_filename = obj
+ if isinstance(obj, (str, Path)):
+ self._input_filename = str(obj)
  elif isinstance(obj, AbstractDataModel):
  try:
  self._input_filename = obj.meta.filename
@@ -1298,7 +1299,7 @@ def export_config(self, filename, include_metadata=False):
 
  Parameters
  ----------
- filename : str or pathlib.PurePath
+ filename : str or pathlib.Path
  Path to config file.
 
  include_metadata : bool, optional
@@ -1376,7 +1377,7 @@ def build_config(cls, input, **kwargs): # noqa: A002
  if "config_file" in kwargs:
  config_file = kwargs["config_file"]
  del kwargs["config_file"]
- config_from_file = config_parser.load_config_file(config_file)
+ config_from_file = config_parser.load_config_file(str(config_file))
  config_parser.merge_config(config, config_from_file)
  config_dir = os.path.dirname(config_file)
  else:

tests/test_logger.py

@@ -13,8 +13,8 @@ def _clean_up_logging():
  stpipe_log.load_configuration(io.BytesIO(stpipe_log.DEFAULT_CONFIGURATION))
 
 
-def test_configuration(tmpdir):
- logfilename = tmpdir.join("output.log")
+def test_configuration(tmp_path):
+ logfilename = tmp_path / "output.log"
 
  configuration = f"""
 [.]

tests/test_step.py

@@ -76,9 +76,9 @@ class ListArgStep(Step):
 
 
 @pytest.fixture()
-def config_file_pipe(tmpdir):
+def config_file_pipe(tmp_path):
  """Create a config file"""
- config_file = str(tmpdir / "simple_pipe.asdf")
+ config_file = tmp_path / "simple_pipe.asdf"
 
  tree = {
  "class": "test_step.SimplePipe",
@@ -104,9 +104,9 @@ def config_file_pipe(tmpdir):
 
 
 @pytest.fixture()
-def config_file_step(tmpdir):
+def config_file_step(tmp_path):
  """Create a config file"""
- config_file = str(tmpdir / "simple_step.asdf")
+ config_file = tmp_path / "simple_step.asdf"
 
  tree = {
  "class": "test_step.SimpleStep",
@@ -122,9 +122,9 @@ def config_file_step(tmpdir):
 
 
 @pytest.fixture()
-def config_file_list_arg_step(tmpdir):
+def config_file_list_arg_step(tmp_path):
  """Create a config file"""
- config_file = str(tmpdir / "list_arg_step.asdf")
+ config_file = tmp_path / "list_arg_step.asdf"
 
  tree = {
  "class": "test_step.ListArgStep",
@@ -287,6 +287,10 @@ def test_step_list_args(config_file_list_arg_step):
  "science.fits", config_file=config_file_list_arg_step
  )
  assert returned_config_file == config_file_list_arg_step
+
+ # Command line tests below need the config file path to be a string
+ returned_config_file = str(returned_config_file)
+
  c, *_ = cmdline.just_the_step_from_cmdline(
  [
  "filename.fits",
@@ -376,10 +380,10 @@ def test_step_list_args(config_file_list_arg_step):
  )
 
 
-def test_logcfg_routing(tmpdir):
- cfg = f"""[*]\nlevel = INFO\nhandler = file:{tmpdir}/myrun.log"""
+def test_logcfg_routing(tmp_path):
+ cfg = f"""[*]\nlevel = INFO\nhandler = file:{tmp_path}/myrun.log"""
 
- logcfg_file = str(tmpdir / "stpipe-log.cfg")
+ logcfg_file = tmp_path / "stpipe-log.cfg"
 
  with open(logcfg_file, "w") as f:
  f.write(cfg)
@@ -394,7 +398,7 @@ def test_logcfg_routing(tmpdir):
  logdict[log].removeHandler(handler)
  handler.close()
 
- with open(tmpdir / "myrun.log") as f:
+ with open(tmp_path / "myrun.log") as f:
  fulltext = "\n".join(list(f))
 
  assert "called out a warning" in fulltext