Updated main module name to ddcuimap. Revised requirements and pyproject.toml. Other minor changes.

Author: Kevin Armengol

.gitignore

@@ -1,12 +1,12 @@
 # User-specific stuff
-.idea/**/workspace.xml
-.idea/**/tasks.xml
-.idea/**/usage.statistics.xml
+.env
 .idea/**/dictionaries
 .idea/**/shelf
-/notebooks/.ipynb_checkpoints
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/workspace.xml
 /.idea/
-.env
 /dist/
-__pycache__/
 /docs
+/notebooks/.ipynb_checkpoints
+__pycache__/

.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
-        exclude: data_dictionary_cui_mapping/semantic_search/resources/dict_umls_upsert_ids.pkl
+        exclude: ddcuimap/semantic_search/resources/dict_umls_upsert_ids.pkl
     -   id: debug-statements
 
 #-   repo: https://github.com/PyCQA/flake8

README.md

@@ -30,7 +30,7 @@ Below is a sample data dictionary format that can be used as input for this pack
 In order to run and customize these pipelines, you will need to create/edit yaml configuration files located in configs. Run configurations are saved and can be reloaded.
 
 ```bash
-├───data_dictionary_cui_mapping
+├───ddcuimap
 │   ├───configs
 │   │   │   config.yaml
 │   │   │   __init__.py
@@ -54,18 +54,19 @@ In order to run and customize these pipelines, you will need to create/edit yaml
 ## UMLS API and MetaMap Batch Queries
 
 #### Import modules
+
 ```python
 # import batch_query_pipeline modules from metamap OR umls package
-from data_dictionary_cui_mapping.metamap import batch_query_pipeline as mm_bqp
-from data_dictionary_cui_mapping.umls import batch_query_pipeline as umls_bqp
+from ddcuimap.metamap import batch_query_pipeline as mm_bqp
+from ddcuimap.umls import batch_query_pipeline as umls_bqp
 
 # import helper functions for loading, viewing, composing configurations for pipeline run
-from data_dictionary_cui_mapping.utils import helper
+from ddcuimap.utils import helper
 from omegaconf import OmegaConf
 
 # import modules to create data dictionary with curated CUIs and check the file for missing mappings
-from data_dictionary_cui_mapping.curation import create_dictionary_import_file
-from data_dictionary_cui_mapping.curation import check_cuis
+from ddcuimap.curation import create_dictionary_import_file
+from ddcuimap.curation import check_cuis
 ```
 #### Load/edit configuration files
 ```python

data_dictionary_cui_mapping/metamap/__init__.py

@@ -1,4 +1,4 @@
-from data_dictionary_cui_mapping.utils.helper import (
+from ddcuimap.utils.helper import (
     load_config,
     save_config,
     compose_config,