Merge branch '78-get_absolute_path_of_file'

Author: MattClarkson

.github/workflows/ci.yml

@@ -29,7 +29,7 @@ jobs:
           coverage erase
           coverage run -a --source ./sksurgerycore -m pytest -v -s ./tests/
           coverage report -m
-          pylint --rcfile=tests/pylintrc --ignore _version.py sksurgerycore tests
+          pylint --rcfile=tests/pylintrc sksurgerycore tests
 
       - name: Run coveralls
         run: |

sksurgerycore/utilities/file_utilities.py

@@ -7,25 +7,29 @@
 
 def get_absolute_path_of_file(file_name, dir_name=None):
     """
-    Filenames in our .json config could be absolute or relative to the
-    current working dir. This method tries to find the valid, full file path.
+    This method tries to setup an absolute pathname.
+    Tt doesn't actually check if the file exists.
+    If dir_name is provided, it is used as a prefix.
+    If dir_name is None, the function is equivalent
+    to os.path.abspath(file_name).
 
-    :param file_name:
-    :param dir_name: prefix, for example, the dirname of our .json file.
-    :return: absolute path name of file if found, otherwise None.
+    :param file_name: str, the file name to convert to absolute path.
+    :param dir_name: str or None, optional prefix directory.
+    :return: absolute path name
+    :raises ValueError if file_name is empty or None.
     """
-    if not file_name:
-        raise ValueError("Empty file_name.")
-    file = None
-    if os.path.isabs(file_name):
-        if os.path.isfile(file_name):
-            file = file_name
-    elif dir_name is not None:
-        joined = os.path.join(dir_name, file_name)
-        if os.path.isfile(joined):
-            file = joined
-    elif os.getcwd() is not None:
-        joined = os.path.join(os.getcwd(), file_name)
-        if os.path.isfile(joined):
-            file = joined
-    return file
+    if file_name is None:
+        raise ValueError("file_name is None.")
+    if not isinstance(file_name, str):
+        raise TypeError("file_name is not a string.")
+    if file_name.strip() == "":
+        raise ValueError("file_name is empty.")
+    fname = file_name.strip()
+    if dir_name is not None:
+        if not isinstance(dir_name, str):
+            raise TypeError("dir_name is not a string.")
+        if dir_name.strip() == "":
+            raise ValueError("dir_name is empty.")
+        dir_name = dir_name.strip()
+        fname = os.path.join(dir_name, fname)
+    return os.path.abspath(fname)

tests/pylintrc

@@ -9,7 +9,7 @@
 
 # Add files or directories to the blacklist. They should be base names, not
 # paths.
-ignore=CVS
+ignore=CVS, _version.py
 
 # Add files or directories matching the regex patterns to the blacklist. The
 # regex matches against base names, not paths.

tests/utilities/test_file_utilities.py

@@ -7,6 +7,26 @@
 
 import sksurgerycore.utilities.file_utilities as fu
 
+def test_get_absolute_file_exceptions():
+    with pytest.raises(ValueError) as excinfo:
+        fu.get_absolute_path_of_file(None)
+    assert "file_name is None." in str(excinfo.value)
+
+    with pytest.raises(TypeError) as excinfo:
+        fu.get_absolute_path_of_file(123)
+    assert "file_name is not a string." in str(excinfo.value)
+
+    with pytest.raises(ValueError) as excinfo:
+        fu.get_absolute_path_of_file("   ")
+    assert "file_name is empty." in str(excinfo.value)
+
+    with pytest.raises(TypeError) as excinfo:
+        fu.get_absolute_path_of_file("file.txt", dir_name=123)
+    assert "dir_name is not a string." in str(excinfo.value)
+
+    with pytest.raises(ValueError) as excinfo:
+        fu.get_absolute_path_of_file("file.txt", dir_name="   ")
+    assert "dir_name is empty." in str(excinfo.value)
 
 def test_get_absolute_file():
 
@@ -21,3 +41,11 @@ def test_get_absolute_file():
 
     fp3 = fu.get_absolute_path_of_file(this_file, cwd)
     assert fp3 == fp
+
+    # Similar to test for fp, but file doesn't exist.
+    # So, really just checking that we always get an absolute path.
+    fp4 = fu.get_absolute_path_of_file("nonsense.txt")
+    assert fp4 is not None
+    assert os.path.basename(fp4) == "nonsense.txt"
+    assert os.path.isabs(fp4)
+    assert os.path.dirname(fp4) == cwd

tox.ini

@@ -4,7 +4,7 @@ envlist = test,lint
 skipsdist = True
 
 [testenv]
-basepython=python3.10
+basepython=python3.13
 passenv = *
 deps=-rrequirements-dev.txt
 
@@ -16,7 +16,7 @@ commands = coverage erase
            coverage report -m
 
 [testenv:lint]
-commands=pylint --rcfile=tests/pylintrc --ignore _version.py sksurgerycore tests
+commands=pylint --rcfile=tests/pylintrc sksurgerycore tests
 
 [testenv:docs]
 changedir = docs