oncoexplorer -> oncopacket

monarch-initiative · Jan 21, 2025 · 25b60e4 · 25b60e4
1 parent 9b8c899
commit 25b60e4
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diff --git a/docs/installation.md b/docs/installation.md
@@ -15,8 +15,8 @@ Feel free to skip this if you already have a virtual environment which you want
 
 
 ```shell
-python3 -m venv oncoexporter-venv
-source oncoexporter-venv/bin/activate
+python3 -m venv oncopacket-venv
+source oncopacket-venv/bin/activate
 ```
 
 
@@ -32,7 +32,7 @@ Next, Oncoexporter can be installed into an existing virtual environment by runn
 
 ```shell
  # Ensure you are in the repo folder
-cd oncoexporter
+cd oncopacket
 python3 -m pip install --editable .
 ```
 

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: oncoexporter
+site_name: oncopacket
 
 theme:
   name: "material"

diff --git a/scripts/run_TCGA_LUAD.py b/scripts/run_TCGA_LUAD.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_bone.py b/scripts/run_bone.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_brain.py b/scripts/run_brain.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_breast.py b/scripts/run_breast.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_cervix.py b/scripts/run_cervix.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_colon.py b/scripts/run_colon.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_heart.py b/scripts/run_heart.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_kidney.py b/scripts/run_kidney.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_liver.py b/scripts/run_liver.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_lung.py b/scripts/run_lung.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_pancreas.py b/scripts/run_pancreas.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_skin.py b/scripts/run_skin.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/scripts/run_thyroid.py b/scripts/run_thyroid.py
@@ -1,7 +1,7 @@
 import os
 from google.protobuf.json_format import MessageToJson
 
-from oncoexporter.cda import CdaTableImporter, configure_cda_table_importer
+from oncopacket.cda import CdaTableImporter, configure_cda_table_importer
 
 '''
 https://cda.readthedocs.io/en/latest/documentation/cdapython/code_update/#returning-a-matrix-of-results

diff --git a/src/oncoexporter/__init__.py b/src/oncoexporter/__init__.py
diff --git a/src/oncoexporter/cda/__init__.py b/src/oncoexporter/cda/__init__.py
diff --git a/src/oncoexporter/cda/_configure.py b/src/oncoexporter/cda/_configure.py
diff --git a/src/oncoexporter/cda/_gdc.orig.py b/src/oncoexporter/cda/_gdc.orig.py