Rename from osi to opensyndrome

Author: anapaulagomes

.gitignore

@@ -173,7 +173,7 @@ cython_debug/
 # temporary
 schema.json
 ollama_schema.json
-osi/to_be_updated__schema.py
+opensyndrome/to_be_updated__schema.py
 
 # data
 *.csv

Dockerfile

@@ -8,4 +8,4 @@ COPY . /app
 
 RUN poetry config virtualenvs.create false && poetry install
 
-ENTRYPOINT ["poetry", "run", "osi"]
+ENTRYPOINT ["uv", "run", "osi"]

Makefile

@@ -17,4 +17,4 @@ ollama_schema:
 					   --use-unique-items-as-set \
 					   --use-default \
 					   --input $(SCHEMA_FILE) \
-					   --output osi/to_be_updated__schema.py
+					   --output opensyndrome/to_be_updated__schema.py

README.md

@@ -11,27 +11,27 @@ From PyPi, install the package with `pip install opensyndrome`. Then run it with
 From Docker, you can run the following command to build the image, tagged `osi`:
 
 ```bash
-docker build -t osi .
+docker build -t opensyndrome .
 ```
 
 Run the container interactively, removing it when it exits
 
 ```bash
-docker run --rm osi
+docker run --rm opensyndrome
 ```
 
 To read a `.env` file, mount it:
 
 ```bash
 docker run --rm -it \
   -v "$(pwd)/.env:/app/.env:ro" \
-  osi
+  opensyndrome
 ```
 
 To name the container and keep it around:
 
 ```bash
-docker run --name osi-cli -it osi
+docker run --name opensyndrome-cli -it opensyndrome
 ```
 
 ## Usage

notebooks/osi_filter_prototype.py

@@ -18,7 +18,7 @@ def _():
     import plotly.graph_objects as go
     from dotenv import load_dotenv
 
-    from osi.filtering import (
+    from opensyndrome.filtering import (
         filter_cases_per_definitions,
         load_definition,
         overlap_definitions,

osi/__init__.py opensyndrome/__init__.pyosi/__init__.py renamed to opensyndrome/__init__.py

@@ -5,12 +5,12 @@
 import jsonschema
 import click
 
-from osi.converters import (
+from opensyndrome.converters import (
     generate_machine_readable_format,
     generate_human_readable_format,
 )
-from osi.filtering import get_schema_filepath, get_definition_dir
-from osi.validators import validate_machine_readable_format
+from opensyndrome.filtering import get_schema_filepath, get_definition_dir
+from opensyndrome.validators import validate_machine_readable_format
 
 
 @click.group()

osi/cli.py opensyndrome/cli.pyosi/cli.py renamed to opensyndrome/cli.py

@@ -8,8 +8,8 @@
 from dotenv import load_dotenv
 from ollama import chat
 
-from osi.filtering import get_schema_filepath
-from osi.schema import OpenSyndromeCaseDefinitionSchema
+from opensyndrome.filtering import get_schema_filepath
+from opensyndrome.schema import OpenSyndromeCaseDefinitionSchema
 
 load_dotenv()
 logger = logging.getLogger(__name__)