cleaning up headers and adding apidocs (pydicom#214)

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

.github/workflows/docs.yaml

@@ -0,0 +1,43 @@
+name: Update Docs
+
+on:
+  push:
+    branches: [master]
+
+jobs:
+  generate-docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          ref: "gh-pages"
+
+      - name: Create conda environment
+        run: conda create --quiet -c conda-forge --name deid
+
+      - name: Install deid
+        run: |
+          export PATH="/usr/share/miniconda/bin:$PATH"
+          root=$PWD
+          source activate deid
+          cd /tmp
+          git clone -b add/api-docs https://github.com/pydicom/deid
+          cd deid
+          pip install -e .
+          cd ./docs
+          pip install -r api_docs/requirements.txt
+          /bin/bash ./apidoc.sh
+          cd ../
+          mv $root/.git ./docs/api_docs/.git
+          rm -rf $root
+          mv ./docs/api_docs $root
+          cd $root
+          ls -a
+          git add .
+          git status
+          git config --global user.name "github-actions"
+          git config --global user.email "[email protected]"
+          git config --global pull.rebase true
+          git commit -a -m "Adding changed documentation files"
+          git status
+          git push origin gh-pages

.gitignore

@@ -4,6 +4,7 @@ deid.egg-info
 build
 pypi.sh
 env
+_build
 
 private
 .vscode

LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2017-2022 Vanessa Sochat
+Copyright (c) 2016-2022 Vanessa Sochat
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

deid/config/__init__.py

@@ -1,41 +1,15 @@
-"""
-
-DeidRecipe
-
-Copyright (c) 2017-2022 Vanessa Sochat
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-The functions below assume a configuration file called deid, although the
-user can specify a custom name.
-
-
-"""
-
-from deid.config.utils import load_deid, get_deid, load_combined_deid
-from deid.config.standards import actions, sections, formats
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2016-2022, Vanessa Sochat"
+__license__ = "MIT"
 
+from deid.config.standards import actions, formats, sections
+from deid.config.utils import get_deid, load_combined_deid, load_deid
 from deid.logger import bot
 
 
 class DeidRecipe:
-    """Create a deid recipe to filter and perform operations on a dicom header.
+    """
+    Create a deid recipe to filter and perform operations on a dicom header.
 
     Usage typically looks like:
 
@@ -51,7 +25,6 @@ class DeidRecipe:
           (later in the list overrides earlier loaded).
     base: if True, load a default base (default_base) before custom
     default_base: the default base to load if "base" is True
-
     """
 
     def __init__(self, deid=None, base=False, default_base="dicom"):
@@ -102,7 +75,8 @@ def get_format(self):
         return self._get_section("format")
 
     def _get_named_section(self, section_name, name=None):
-        """Get a named section from the deid recipe.
+        """
+        Get a named section from the deid recipe.
 
         a helper function to return an entire section, or if a name is
         provided, a named section under it. If the section is not
@@ -146,7 +120,8 @@ def _get_actions(self, action=None, field=None, section="header"):
         return header
 
     def get_actions(self, action=None, field=None):
-        """Get deid actions to perform on a header, or a subset based on a type
+        """
+        Get deid actions to perform on a header, or a subset based on a type
 
         A header action is a list with the following:
         {'action': 'REMOVE', 'field': 'AssignedLocation'},
@@ -194,7 +169,8 @@ def ls_fieldlists(self):
     # Init
 
     def _init_deid(self, deid=None, base=False, default_base="dicom"):
-        """Initialize a recipe.
+        """
+        Initialize a recipe.
 
         initialize the recipe with one or more deids, optionally including
         the default. This function is called at init time. If you need to add

deid/config/standards.py

@@ -1,26 +1,6 @@
-"""
-
-Copyright (c) 2017-2022 Vanessa Sochat
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-"""
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2016-2022, Vanessa Sochat"
+__license__ = "MIT"
 
 # Supported formats
 formats = ["dicom"]

deid/config/utils.py

@@ -1,47 +1,25 @@
-"""
-
-Copyright (c) 2017-2022 Vanessa Sochat
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-The functions below assume a configuration file called deid, although the
-user can specify a custom name.
-
-"""
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2016-2022, Vanessa Sochat"
+__license__ = "MIT"
 
 # pylint: skip-file
 
-from deid.logger import bot
-from deid.utils import read_file, get_installdir
-from deid.data import data_base
+import os
+import re
+import sys
+from collections import OrderedDict
+
 from deid.config.standards import (
-    formats,
     actions,
-    sections,
     filters,
-    groups,
+    formats,
     group_actions,
+    groups,
+    sections,
 )
-from collections import OrderedDict
-import os
-import re
-import sys
+from deid.data import data_base
+from deid.logger import bot
+from deid.utils import get_installdir, read_file
 
 
 def load_combined_deid(deids):

deid/data/__init__.py

@@ -1,41 +1,27 @@
-"""
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2016-2022, Vanessa Sochat"
+__license__ = "MIT"
 
+"""
 Simple loading functions for datasets
 
    from deid.data import get_dataset
-
-Copyright (c) 2017-2022 Vanessa Sochat
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
 """
 
 
-from deid.utils import get_installdir
-from deid.logger import bot
 import os
 
+from deid.logger import bot
+from deid.utils import get_installdir
 
 data_base = os.path.dirname(os.path.abspath(__file__))
 
 
 def get_dataset(dataset=None):
-    """get_dataset will return some data provided by the application,
+    """
+    Get a dataset by name.
+
+    get_dataset will return some data provided by the application,
     based on a user-provided label. In the future, we can add https endpoints
     to retrieve online datasets.
     """

deid/dicom/__init__.py

@@ -1,9 +1,4 @@
-from .header import (
-    get_identifiers,
-    replace_identifiers,
-    remove_private_identifiers,
-)
-
-from .utils import get_files
 from .fields import extract_sequence
-from .pixels import has_burned_pixels, DicomCleaner
+from .header import get_identifiers, remove_private_identifiers, replace_identifiers
+from .pixels import DicomCleaner, has_burned_pixels
+from .utils import get_files

deid/dicom/actions/__init__.py

@@ -1,5 +1,5 @@
 from .jitter import jitter_timestamp, jitter_timestamp_func
-from .uids import basic_uuid, dicom_uuid, suffix_uuid, pydicom_uuid
+from .uids import basic_uuid, dicom_uuid, pydicom_uuid, suffix_uuid
 
 # Function lookup
 # Functions here must take an item, field, and value

deid/dicom/actions/jitter.py

@@ -1,30 +1,9 @@
-"""
-
-Copyright (c) 2017-2022 Vanessa Sochat
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-"""
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2016-2022, Vanessa Sochat"
+__license__ = "MIT"
 
 from deid.logger import bot
-from deid.utils import get_timestamp
-from deid.utils import parse_keyvalue_pairs
+from deid.utils import get_timestamp, parse_keyvalue_pairs
 
 # Timestamps
 
@@ -45,7 +24,8 @@ def jitter_timestamp_func(item, value, field, **kwargs):
 
 
 def jitter_timestamp(field, value):
-    """Jitter a timestamp "field" by number of days specified by "value"
+    """
+    Jitter a timestamp "field" by number of days specified by "value"
 
     The value can be positive or negative. This function is grandfathered
     into deid custom funcs, as it existed before they did. Since a custom

deid/dicom/actions/uids.py

@@ -1,31 +1,13 @@
-"""
+__author__ = "Vanessa Sochat"
+__copyright__ = "Copyright 2016-2022, Vanessa Sochat"
+__license__ = "MIT"
 
-Copyright (c) 2022 Vanessa Sochat
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-"""
+import uuid
 
-from deid.utils import parse_keyvalue_pairs
 from pydicom.uid import generate_uid as pydicom_generate_uid
+
 from deid.logger import bot
-import uuid
+from deid.utils import parse_keyvalue_pairs
 
 
 def basic_uuid(item, value, field, **kwargs):