Merge pull request #29 from ZviBaratz/tests

Tests

.github/workflows/tests.yml

@@ -32,8 +32,7 @@ jobs:
         sudo apt install -y libmagic1
     - name: Install libmagic (macOS)
       if: matrix.os == 'macos-latest'
-      run: |
-        brew install libmagic
+      run: brew install libmagic
     - name: Install dependencies
       run: |
         python -m site
@@ -42,7 +41,7 @@ jobs:
       run: python -m tox
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v1
-      if: "contains(env.USING_COVERAGE, matrix.python-version) && matrix.os == 'ubuntu-latest'"
+      if: "contains(env.USING_COVERAGE, matrix.python-version)"
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true

README.md

@@ -1,7 +1,7 @@
 [![PyPI version](https://img.shields.io/pypi/v/dicom_parser.svg)](https://pypi.python.org/pypi/pylabber/)
 [![PyPI status](https://img.shields.io/pypi/status/dicom_parser.svg)](https://pypi.python.org/pypi/pylabber/)
 [![GitHub Actions](https://github.com/ZviBaratz/dicom_parser/actions/workflows/tests.yml/badge.svg)](https://github.com/ZviBaratz/dicom_parser/actions/workflows/tests.yml)
-[![codecov.io](https://codecov.io/gh/ZviBaratz/dicom_parser/coverage.svg?branch=master)](https://codecov.io/github/ZviBaratzabbingProject/dicom_parser?branch=master)
+[![codecov.io](https://codecov.io/gh/ZviBaratz/dicom_parser/coverage.svg?branch=master)](https://codecov.io/github/ZviBaratz/dicom_parser?branch=master)
 [![Language grade: Python](https://img.shields.io/lgtm/grade/python/g/ZviBaratz/dicom_parser.svg?logo=lgtm&logoWidth=18)](https://lgtm.com/projects/g/ZviBaratz/dicom_parser/context:python)
 [![Documentation Status](https://readthedocs.org/projects/dicom-parser/badge/?version=latest)](http://dicom-parser.readthedocs.io/?badge=latest)
 

docs/release_notes.rst

@@ -1,10 +1,14 @@
 Release Notes
 =============
 
-1.0.2
+1.1.0
 -----
-  * Added *pyproject.toml* and *setup.cfg* files and created *src/* directory
-  * to conform with newer Python packaging standards.
+  * Updated project structure and packaging to conform with PEP517_ and
+    PEP518_.
+  * Migrated CI to `GitHub Actions`_.
+  * Fixed *dcm* generation by mime-type bug (`#30
+    <https://github.com/ZviBaratz/dicom_parser/issues/30>`_) for nested directories.
+  * Improved tests and increased coverage.
 
 1.0.1
 -----
@@ -120,12 +124,25 @@ First release!
     :class:`~dicom_parser.utils.siemens.csa.header.CsaHeader` class.
 
 
-.. _CSA Headers: https://nipy.org/nibabel/dicom/siemens_csa.html
-.. _dcm2niix: https://github.com/rordenlab/dcm2niix
-.. _django_dicom: https://github.com/TheLabbingProject/django_dicom
-.. _isort: https://pycqa.github.io/isort/
-.. _NIfTI: https://nifti.nimh.nih.gov/
-.. _pydicom: https://github.com/pydicom/pydicom
-.. _Siemens mosaic: https://nipy.org/nibabel/dicom/dicom_mosaic.html
+.. _CSA Headers:
+   https://nipy.org/nibabel/dicom/siemens_csa.html
+.. _dcm2niix:
+   https://github.com/rordenlab/dcm2niix
+.. _django_dicom:
+   https://github.com/TheLabbingProject/django_dicom
+.. _GitHub Actions:
+   https://github.com/ZviBaratz/dicom_parser/actions/workflows/tests.yml
+.. _isort:
+   https://pycqa.github.io/isort/
+.. _NIfTI:
+   https://nifti.nimh.nih.gov/
+.. _PEP517:
+   https://www.python.org/dev/peps/pep-0517/
+.. _PEP518:
+   https://www.python.org/dev/peps/pep-0518/
+.. _pydicom:
+   https://github.com/pydicom/pydicom
+.. _Siemens mosaic:
+   https://nipy.org/nibabel/dicom/dicom_mosaic.html
 .. _value-representation (VR):
    http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_6.2.html

pyproject.toml

@@ -17,10 +17,13 @@ exclude = '''
 line-length = 79
 
 [tool.coverage.run]
-source = ["src/"]
+source = ["dicom_parser"]
 branch = true
-omit = ["*tests*", ".tox/**", "venv/**", "setup.py"]
-command_line = "-m pytest tests/"
+omit = ["*tests*", "venv/**", "setup.py"]
+command_line = "-m pytest tests"
+
+[tool.coverage.paths]
+source = ["src"]
 
 [build-system]
 requires = ["setuptools>=42", "wheel"]

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = dicom_parser
-version = 1.0.2
+version = 1.1.0
 author = Zvi Baratz
 author_email = z.baratz@gmail.com
 description = DICOM files parser meant to facilitate data access.
@@ -48,8 +48,9 @@ all =
     flake8~=3.7
     ipython
     isort~=5.8
+    pickle5~=0.0;python_version<="3.7"
     pytest~=6.2
-    python-magic~=0.4
+    python-magic~=0.4;platform_system!="Windows"
     sphinx~=4.0
     sphinx-rtd-theme~=0.5
     tox~=3.23
@@ -62,14 +63,15 @@ dev =
     ipython
     isort~=5.8
     pytest~=6.2
-    python-magic~=0.4
+    python-magic~=0.4;platform_system!="Windows"
     sphinx~=4.0
     sphinx-rtd-theme~=0.5
     tox~=3.23
 test =
     coverage[toml]~=5.5
+    pickle5~=0.0;python_version<="3.7"
     pytest~=6.2
-    python-magic~=0.4
+    python-magic~=0.4;platform_system!="Windows"
     tox~=3.23
 dist =
     build
@@ -78,7 +80,7 @@ docs =
     sphinx~=4.0
     sphinx-rtd-theme~=0.5
 magic =
-    python-magic~=0.4
+    python-magic~=0.4;platform_system!="Windows"
 
 [options.packages.find]
 where = src

src/dicom_parser/data_element.py

@@ -1,7 +1,6 @@
 """
 Definition of the :class:`DataElement` class.
 """
-
 import re
 from typing import Any
 
@@ -19,11 +18,10 @@ class DataElement:
     :mod:`~dicom_parser.data_elements`.
 
     .. _pydicom: https://github.com/pydicom/pydicom
-
     """
 
     VALUE_REPRESENTATION: ValueRepresentation = None
-    PRIVATE_ELEMENT_DESCRIPTION_PATTERN = r"\[(.*)\]|Private Creator"
+    PRIVATE_ELEMENT_DESCRIPTION_PATTERN: str = r"\[(.*)\]|Private Creator"
 
     def __init__(self, raw: PydicomDataElement):
         """
@@ -34,7 +32,6 @@ def __init__(self, raw: PydicomDataElement):
         raw : PydicomDataElement
             pydicom's data element
         """
-
         self.raw: PydicomDataElement = raw
         self.tag: tuple = parse_tag(self.raw.tag)
         self.keyword: str = self.parse_keyword()
@@ -53,7 +50,6 @@ def __repr__(self) -> str:
         str
             This instance's string representation
         """
-
         return self.__str__()
 
     def __str__(self) -> str:
@@ -65,7 +61,6 @@ def __str__(self) -> str:
         str
             This instance's string representation
         """
-
         return self.to_series().to_string()
 
     def get_private_element_keyword(self) -> str:
@@ -77,7 +72,6 @@ def get_private_element_keyword(self) -> str:
         str
             Private data element keyword
         """
-
         pattern = self.PRIVATE_ELEMENT_DESCRIPTION_PATTERN
         description = self.raw.description()
         private_element_description = re.findall(pattern, description)
@@ -97,7 +91,6 @@ def parse_keyword(self) -> str:
         str
             This instance's keyword
         """
-
         if self.raw.keyword == "":
             return self.get_private_element_keyword()
         return self.raw.keyword
@@ -117,7 +110,6 @@ def parse_value(self, value: Any) -> Any:
         Any
             This instance's parsed value
         """
-
         if isinstance(value, bytes):
             try:
                 return value.decode("utf-8").strip()
@@ -134,7 +126,6 @@ def parse_values(self) -> Any:
         Any
             This instance's parsed value or values
         """
-
         if self.value_multiplicity > 1:
             return tuple(self.parse_value(value) for value in self.raw.value)
         return self.parse_value(self.raw.value)
@@ -148,7 +139,6 @@ def to_dict(self) -> dict:
         dict
             This instance as a dictionary
         """
-
         return {
             "tag": self.tag,
             "keyword": self.keyword,
@@ -166,7 +156,6 @@ def to_series(self) -> pd.Series:
         pd.Series
             This instance as a :class:`Series`
         """
-
         d = self.to_dict()
         return pd.Series(d)
 
@@ -195,7 +184,6 @@ def is_private(self) -> bool:
         bool
             Whether this data element is private or not
         """
-
         # TODO: This should probably be changed to simply check if the tag's
         # group number is odd.
         pattern = self.PRIVATE_ELEMENT_DESCRIPTION_PATTERN
@@ -212,5 +200,4 @@ def is_public(self) -> bool:
         bool
             Whether this data element is public or not
         """
-
         return not self.is_private

src/dicom_parser/data_elements/age_string.py

@@ -2,7 +2,6 @@
 Definition of the :class:`AgeString` class, representing a single "AS" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 
@@ -30,7 +29,6 @@ def parse_value(self, value: str) -> float:
         float
             Age in years
         """
-
         try:
             duration = float(value[:-1])
             units = value[-1]

src/dicom_parser/data_elements/application_entity.py

@@ -2,7 +2,6 @@
 Definition of the :class:`ApplicationEntity` class, representing a single "AE"
 data element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 

src/dicom_parser/data_elements/attribute_tag.py

@@ -2,7 +2,6 @@
 Definition of the :class:`AttributeTag` class, representing a single "AT" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 

src/dicom_parser/data_elements/code_string.py

@@ -2,7 +2,6 @@
 Definition of the :class:`CodeString` class, representing a single "CS" data
 element.
 """
-
 import warnings
 from enum import Enum
 
@@ -44,7 +43,6 @@ def warn_invalid_code_string_value(
         enum : enum.Enum
             An Enum representing the element's valid values
         """
-
         field_name = enum.__name__
         value = exception.args[0]
         warning = f"'{value}' is not a valid {field_name} value!"
@@ -68,7 +66,6 @@ def parse_with_enum(self, value: str, enum: Enum) -> str:
         str
             Parsed "CS" data element value
         """
-
         try:
             return enum[value].value
         except KeyError as exception:
@@ -90,7 +87,6 @@ def parse_value(self, value: str) -> str:
         str
             Parsed "CS" data element value
         """
-
         enum = self.TAG_TO_ENUM.get(self.tag)
         if enum:
             return self.parse_with_enum(value, enum)

src/dicom_parser/data_elements/date.py

@@ -33,7 +33,6 @@ def parse_value(self, value: str) -> datetime.date:
         ValueError
             Failure to parse date from raw value
         """
-
         try:
             return datetime.strptime(value, "%Y%m%d").date()
         except ValueError:

src/dicom_parser/data_elements/date_time.py

@@ -2,7 +2,6 @@
 Definition of the :class:`DateTime` class, representing a single "DT" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 

src/dicom_parser/data_elements/decimal_string.py

@@ -2,7 +2,6 @@
 Definition of the :class:`DecimalString` class, representing a single "DS" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 
@@ -30,7 +29,6 @@ def parse_value(self, value: str) -> float:
         float
             Parsed decimal
         """
-
         try:
             return float(value)
         except (TypeError, ValueError):

src/dicom_parser/data_elements/floating_point_double.py

@@ -2,7 +2,6 @@
 Definition of the :class:`FloatingPointDouble` class, representing a single
 "FD" data element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 

src/dicom_parser/data_elements/floating_point_single.py

@@ -2,7 +2,6 @@
 Definition of the :class:`FloatingPointSingle` class, representing a single
 "FL" data element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 

src/dicom_parser/data_elements/integer_string.py

@@ -2,7 +2,6 @@
 Definition of the :class:`IntegerString` class, representing a single "IS" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 
@@ -30,7 +29,6 @@ def parse_value(self, value: str) -> int:
         int
             Parsed integer
         """
-
         try:
             return int(value)
         except (TypeError, ValueError):

src/dicom_parser/data_elements/long_string.py

@@ -2,7 +2,6 @@
 Definition of the :class:`LongString` class, representing a single "LO" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation
 

src/dicom_parser/data_elements/long_text.py

@@ -2,7 +2,6 @@
 Definition of the :class:`LongText` class, representing a single "LT" data
 element.
 """
-
 from dicom_parser.data_element import DataElement
 from dicom_parser.utils.value_representation import ValueRepresentation