added DicomImage to ImageIn union

.github/workflows/ci-cd.yml

@@ -36,7 +36,7 @@ jobs:
       SCCACHE_CACHE_SIZE: "2G"
 
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
         with:
           submodules: true
       - name: Set Git User
@@ -45,6 +45,12 @@ jobs:
         run: |
           git config --global user.email "[email protected]"
           git config --global user.name "Dummy User"
+      - name: Unset header
+        # checkout@v2 adds a header that makes branch protection report errors
+        # because the Github action bot is not a collaborator on the repo
+        run: git config --local --unset http.https://github.com/.extraheader
+      - name: Fetch tags
+        run: git fetch --prune --unshallow
       - name: install dependencies
         run: |
            sudo apt-get update
@@ -146,14 +152,14 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Download version file
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: VersionFile
         path: mrtrix3_version.txt
     - name: Extract Mrtrix version
       run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
     - name: Download auto-gen pydra
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: AutoGen
         path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
@@ -202,22 +208,22 @@ jobs:
     - name: Fetch tags
       run: git fetch --prune --unshallow
     - name: Download version file
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: VersionFile
         path: mrtrix3_version.txt
     - name: Extract Mrtrix version
       run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
     - name: Download auto-gen pydra
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: AutoGen
         path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}
     - name: Strip auto package from gitignore so it is included in package
       run: |
         sed -i '/\/pydra\/tasks\/mrtrix3\/${{ env.SUBPKG_NAME }}/d' .gitignore
     - name: Download MRtrix3 install
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: MRtrix3
         path: ${{ env.MRTRIX_INSTALL}}
@@ -242,7 +248,7 @@ jobs:
         -e '.[test]'
     - name: Test with pytest
       run: pytest -sv pydra/tasks/mrtrix3 --cov pydra.tasks.mrtrix3 --cov-report xml
-    - uses: codecov/codecov-action@v1
+    - uses: codecov/codecov-action@v2
       if: ${{ always() }}
 
   deploy-fileformats:
@@ -253,6 +259,10 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
@@ -285,6 +295,10 @@ jobs:
       with:
         submodules: recursive
         fetch-depth: 0
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
@@ -320,15 +334,19 @@ jobs:
       run: |
         git config --local user.email "[email protected]"
         git config --local user.name "GitHub Action"
+    - name: Unset header
+      # checkout@v2 adds a header that makes branch protection report errors
+      # because the Github action bot is not a collaborator on the repo
+      run: git config --local --unset http.https://github.com/.extraheader
     - name: Download version file
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: VersionFile
         path: mrtrix3_version.txt
     - name: Extract Mrtrix version
       run: echo "MRTRIX_VERSION=$(cat mrtrix3_version.txt)" >> $GITHUB_ENV
     - name: Download auto-gen pydra
-      uses: actions/download-artifact@v2
+      uses: actions/download-artifact@v4
       with:
         name: AutoGen
         path: pydra/tasks/mrtrix3/${{ env.SUBPKG_NAME }}

pyproject.toml

@@ -79,3 +79,12 @@ per-file-ignores = ["__init__.py:F401"]
 max-line-length = 88
 select = "C,E,F,W,B,B950"
 extend-ignore = ['E203', 'E501', 'E129', 'W503']
+
+
+[tool.mypy]
+python_version = "3.8"
+ignore_missing_imports = true
+strict = true
+namespace_packages = true
+explicit_package_bases = true
+exclude = ["tests", "scripts", "docs", "build", "dist"]

related-packages/fileformats/fileformats/medimage_mrtrix3/in_out.py

@@ -1,7 +1,7 @@
 import sys
 import typing as ty
-from fileformats.application import Dicom
 from fileformats.medimage import (
+    DicomImage,
     DicomDir,
     NiftiGzX,
     NiftiGz,
@@ -40,7 +40,7 @@
     ImageFormatB,
     ImageFormatGzB,
     ImageHeaderB,
-    Dicom,
+    DicomImage,
     DicomDir,
     NiftiGzX,
     NiftiGz,