Turn into package (#6)

* Add github builds

* Add more to .gitignore

Author: scaramallion

PULL_REQUEST_TEMPLATE.md .github/PULL_REQUEST_TEMPLATE.mdPULL_REQUEST_TEMPLATE.md renamed to .github/PULL_REQUEST_TEMPLATE.md

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+name: build
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  solo:
+    # Matrix builds without pydicom
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install and run pytest
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pytest
+
+  pydicom-dev:
+    # Matrix builds with development pydicom
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest
+        pip install git+https://github.com/pydicom/pydicom
+    - name: Test with pytest
+      run: |
+        pytest
+
+  pydicom-release:
+    # Matrix builds with released pydicom
+    runs-on: ubuntu-latest
+    timeout-minutes: 20
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pytest pydicom
+    - name: Test with pytest
+      run: |
+        pytest

.github/workflows/pytest-builds.yml

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+# .gitignore file
+
+# Backup files
+*~
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Lock files used by the Emacs editor.
+.\#*
+
+# Temporary files used by editors.
+*.swp
+*.orig
+*.bak
+
+# A hidden file created by the Mac OS X Finder.
+.DS_Store
+
+# python byte-code files
+*.pyc
+*.pyo
+
+# Build/dist files
+dist/*
+build/*
+distribute*.tar.gz
+py3source
+.tox/*
+
+# Distribution / packaging
+.Python
+env/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Docs build
+docs/_build/*
+doc/_build/*
+doc/auto_examples/*
+doc/generated/*
+doc/reference/generated/*
+
+# coverage.py files
+.coverage
+
+# PyCharm IDE files
+*.idea*
+
+
+# jupyter notebooks
+*.ipynb
+.ipynb_checkpoints/*
+tests/test_pixel.py
+
+# mypy
+pydicom-data/.mypy_cache/*
+
+# vscode
+.vscode/*
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+.pytest_cache

.gitignore

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+
+from data_store._version import __version__
+from data_store.utils import DataStore

data_store/__init__.py

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+"""Version information for pydicom-data based on PEP396 and 440."""
+
+
+import re
+
+
+__version__ = '1.0.0.dev0'
+
+
+VERSION_PATTERN = r"""
+    v?
+    (?:
+        (?:(?P<epoch>[0-9]+)!)?                           # epoch
+        (?P<release>[0-9]+(?:\.[0-9]+)*)                  # release segment
+        (?P<pre>                                          # pre-release
+            [-_\.]?
+            (?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
+            [-_\.]?
+            (?P<pre_n>[0-9]+)?
+        )?
+        (?P<post>                                         # post release
+            (?:-(?P<post_n1>[0-9]+))
+            |
+            (?:
+                [-_\.]?
+                (?P<post_l>post|rev|r)
+                [-_\.]?
+                (?P<post_n2>[0-9]+)?
+            )
+        )?
+        (?P<dev>                                          # dev release
+            [-_\.]?
+            (?P<dev_l>dev)
+            [-_\.]?
+            (?P<dev_n>[0-9]+)?
+        )?
+    )
+    (?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))?       # local version
+"""
+
+
+def is_canonical(version: str) -> bool:
+    """Return True if `version` is a PEP440 conformant version."""
+    match = re.match(
+        r'^([1-9]\d*!)?(0|[1-9]\d*)'
+        r'(\.(0|[1-9]\d*))'
+        r'*((a|b|rc)(0|[1-9]\d*))'
+        r'?(\.post(0|[1-9]\d*))'
+        r'?(\.dev(0|[1-9]\d*))?$', version)
+
+    return match is not None
+
+
+assert is_canonical(__version__)

data_store/_version.py

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+"""Tests for the interface with pydicom."""
+
+import os
+from pathlib import Path
+
+import pytest
+
+from pydicom.data import get_testdata_file
+
+
+class TestPydicom:
+    """Test the interface with pydicom works correctly."""
+    def setup(self):
+        self.data_path = Path(__file__).resolve().parent.parent.parent / "data"
+
+    def test_pydicom_local(self):
+        """Test that pydicom gets its own test data."""
+        fname = "CT_small.dcm"
+        assert "pydicom/data/test_files" in get_testdata_file(fname)
+
+    def test_pydicom_external(self):
+        """Test that pydicom uses external data sources first."""
+        fname = "693_UNCI.dcm"
+        assert os.fspath(self.data_path / fname) == get_testdata_file(fname)

data_store/tests/test_pydicom.py

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+"""Tests for utils.py"""
+
+import os
+from pathlib import Path
+
+import pytest
+
+from data_store import DataStore
+
+
+class TestDataStore:
+    """Test the interface for the data sources"""
+    def setup(self):
+        self.data_path = Path(__file__).resolve().parent.parent.parent / "data"
+        self.fname = "693_UNCI.dcm"
+
+    def test_data_path(self):
+        """Test the path to the data is correct."""
+        s = DataStore()
+        assert self.data_path == s.data_path
+
+    def test_get_path(self):
+        """Test retrieving a file path."""
+        s = DataStore()
+        result = s.get_path(self.fname)
+        assert isinstance(result, str)
+        assert os.fspath(self.data_path / self.fname) == result
+
+        with pytest.raises(ValueError, match=r"No file found named"):
+            s.get_path("693_UNCI")
+
+    def test_get_path_raises_bad_fname(self):
+        """Test get_path raises if no matching filename."""
+        s = DataStore()
+        msg = r"No file found named 'no matching name.txt'"
+        with pytest.raises(ValueError, match=msg):
+            s.get_path("no matching name.txt")
+
+    def test_get_path_raises_bad_dtype(self):
+        """Test get_path raises if unsupported dtype."""
+        s = DataStore()
+        msg = r"No files available for the data type"
+        with pytest.raises(ValueError, match=msg):
+            s.get_path(self.fname, dtype=1)
+
+    def test_get_paths(self):
+        """Test get_paths."""
+        s = DataStore()
+        files = s.get_paths('693*')
+        assert len(files) == 3
+        assert isinstance(files[0], str)
+
+    def test_get_paths_bad_dtype(self):
+        """Test get_paths returns empty list if unsupported dtype."""
+        s = DataStore()
+        assert [] == s.get_paths("*", dtype=1)

data_store/tests/test_utils.py

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+
+from enum import IntEnum
+import fnmatch
+import os
+from pathlib import Path
+from typing import List
+
+
+class DataTypes(IntEnum):
+    """Constants for data types."""
+    DATASET = 0
+    CHARSET = 1
+    PALETTE = 2
+    DICOMDIR = 3
+
+
+class DataStore:
+    """Interface to pydicom-data data storage.
+
+    Attributes
+    ----------
+    data_path : pathlib.Path
+        The absolute path to the data directory.
+    """
+    def __init__(self) -> None:
+        """Initialise a new Interface."""
+        self.data_path = Path(__file__).resolve().parent.parent / "data"
+
+    def get_path(self, name: str, dtype: int = DataTypes.DATASET) -> str:
+        """Return the absolute path to the first file with filename `name`
+
+        Parameters
+        ----------
+        name : str
+            The filename of the file
+        dtype : int, optional
+            The type of data to search for, default ``0`` (DICOM dataset).
+
+        Returns
+        -------
+        str
+            The absolute path to the first file found with filename `name`.
+
+        Raises
+        ------
+        ValueError
+            If no file found with a matching filename.
+        """
+        if dtype != DataTypes.DATASET:
+            raise ValueError("No files available for the data type")
+
+        matches = [m for m in self.data_path.glob(name)]
+        if matches:
+            return os.fspath(matches[0])
+
+        raise ValueError(f"No file found named '{name}'")
+
+    def get_paths(self, pattern: str, dtype: int = DataTypes.DATASET) -> List[str]:
+        """Return a list of absolute paths for files matching `pattern`.
+
+        Parameters
+        ----------
+        pattern : str
+            A string pattern to filter the files.
+        dtype : int, optional
+            The type of data to search for, default ``0`` (DICOM dataset).
+
+        Returns
+        -------
+        list of str
+            A list of absolute paths to files with filenames matching
+            `pattern`.
+        """
+        if dtype != DataTypes.DATASET:
+            return []
+
+        return [os.fspath(p) for p in self.data_path.glob(pattern)]