update: pydicom v3 (#273)

Signed-off-by: vsoch <[email protected]>
Co-authored-by: vsoch <[email protected]>

Author: vsoch

.github/workflows/main.yaml

@@ -11,7 +11,7 @@ jobs:
   formatting:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup black environment
         run: conda create --quiet --name black black
@@ -26,14 +26,13 @@ jobs:
   testing:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Setup conda environment
         run: |
           conda create --quiet --name testing
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate testing
-          pip install matplotlib
           pip install .
 
       - name: Test deid

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 Referenced versions in headers are tagged on Github, in parentheses are for pypi.
 
 ## [vxx](https://github.com/pydicom/deid/tree/master) (master)
+- Update to use pydicom 3 [#267](https://github.com/pydicom/deid/pull/267) (0.4.0)
 - Refactor INCLUDE_REQUIRES and provide max pydicom version [#267](https://github.com/pydicom/deid/pull/267) (0.3.25)
 - Support pydicom.Dataset objects created from BytesIO [#265](https://github.com/pydicom/deid/pull/265) (0.3.24)
 - Exception with missing filters for non-string VR [#256](https://github.com/pydicom/deid/issues/256) (0.3.23)

deid/config/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 from deid.config.standards import actions, formats, sections

deid/config/standards.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 # Supported formats

deid/config/utils.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 # pylint: skip-file

deid/data/__init__.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import os

deid/dicom/actions/jitter.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 from deid.logger import bot

deid/dicom/actions/uids.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import uuid

deid/dicom/fields.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import re

deid/dicom/filter.py

@@ -1,5 +1,5 @@
 __author__ = "Vanessa Sochat"
-__copyright__ = "Copyright 2016-2023, Vanessa Sochat"
+__copyright__ = "Copyright 2016-2025, Vanessa Sochat"
 __license__ = "MIT"
 
 import re
@@ -23,7 +23,7 @@ def apply_filter(dicom, field, filter_name, value):
 
     Parameters
     ==========
-    dicom: the pydicom.dataset Dataset (pydicom.read_file)
+    dicom: the pydicom.dataset Dataset
     field: the name of the field to apply the filter to,
       or the tag number as a string '0xGGGGEEEE'
     filer_name: the name of the filter to apply (e.g., contains)