Issue/374/introspection (#381)

* added stages/__init__.py for introspection functions

* added os.path.expandvars to data

* updated stages/__init__.py

* tweek docstrings in src/rail/creation/degradation/observing_condition_degrader.py to avoid issues with sphinx

* fix up gitignore

* updated unit tests for rail.stages

* fix up coverages

* fix up stages

* updated introspection stuff

* added src/rail/core/introspection.py

.gitignore

@@ -11,7 +11,6 @@ __pycache__/
 
 # Distribution / packaging
 .Python
-src/rail/core/_version.py
 build/
 develop-eggs/
 dist/
@@ -28,6 +27,7 @@ wheels/
 .installed.cfg
 *.egg
 MANIFEST
+_version.py
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -131,4 +131,4 @@ venv.bak/
 # data for testing
 /tests/data/
 /examples/estimation/*.hdf5
-/examples/estimation/*.pkl
+/examples/estimation/*.pkl

src/rail/core/__init__.py

@@ -1,4 +1,8 @@
 """Core code for RAIL"""
+import pkgutil
+import setuptools
+import rail
+import os
 
 def find_version():
     """Find the version"""
@@ -15,3 +19,4 @@ def find_version():
 from .stage import RailPipeline, RailStage
 from .utilPhotometry import PhotormetryManipulator, HyperbolicSmoothing, HyperbolicMagnitudes
 from .utilStages import ColumnMapper, RowSelector, LSSTFluxToMagConverter, TableConverter, Dereddener
+from .introspection import RailEnv

src/rail/core/data.py

@@ -44,7 +44,7 @@ def open(self, **kwargs):
         """
         if self.path is None:
             raise ValueError("DataHandle.open() called but path has not been specified")
-        self.fileObj = self._open(self.path, **kwargs)
+        self.fileObj = self._open(os.path.expandvars(self.path), **kwargs)
         return self.fileObj
 
     @classmethod
@@ -59,7 +59,7 @@ def read(self, force=False, **kwargs):
         """Read and return the data from the associated file """
         if self.data is not None and not force:
             return self.data
-        self.set_data(self._read(self.path, **kwargs))
+        self.set_data(self._read(os.path.expandvars(self.path), **kwargs))
         return self.data
 
     def __call__(self, **kwargs):
@@ -78,10 +78,10 @@ def write(self, **kwargs):
             raise ValueError("TableHandle.write() called but path has not been specified")
         if self.data is None:
             raise ValueError(f"TableHandle.write() called for path {self.path} with no data")
-        outdir = os.path.dirname(os.path.abspath(self.path))
+        outdir = os.path.dirname(os.path.abspath(os.path.expandvars(self.path)))
         if not os.path.exists(outdir):  #pragma: no cover
             os.makedirs(outdir, exist_ok=True)
-        return self._write(self.data, self.path, **kwargs)
+        return self._write(self.data, os.path.expandvars(self.path), **kwargs)
 
     @classmethod
     def _write(cls, data, path, **kwargs):
@@ -91,7 +91,7 @@ def initialize_write(self, data_lenght, **kwargs):
         """Initialize file to be written by chunks"""
         if self.path is None:  #pragma: no cover
             raise ValueError("TableHandle.write() called but path has not been specified")
-        self.groups, self.fileObj = self._initialize_write(self.data, self.path, data_lenght, **kwargs)
+        self.groups, self.fileObj = self._initialize_write(self.data, os.path.expandvars(self.path), data_lenght, **kwargs)
 
     @classmethod
     def _initialize_write(cls, data, path, data_lenght, **kwargs):
@@ -159,7 +159,7 @@ def is_written(self):
         """Return true if the associated file has been written """
         if self.path is None:
             return False
-        return os.path.exists(self.path)
+        return os.path.exists(os.path.expandvars(self.path))
 
     def __str__(self):
         s = f"{type(self)} "