switch ia_app_basic to uv (sectra-medical#8)

Switch ia_app_basic to uv

bump shapely to avoid windows issue

examples/python/README.md

@@ -8,12 +8,13 @@ This document outlines how we suggest you try the examples to get started using
 
 - We assume you have a copy of the document *"Interface Specification: Pathology Image Analysis Application Interface, Sectra Digital Pathology Module"*. At the time of writing, the most recent version was *"Verion 4.1, August 2024"*.
   - This document describes all the REST endpoints and corresponding json schemas.
-  - Contact Sectra support for a copy, see https://my.sectra.com/en-US/support-contact/
+  - Contact Sectra for a copy, see https://forms.office.com/e/WBEsUrLyJV
 
 - You will need to have access to a Sectra PACS with the Digital Pathology module
   - We suggest you start testing in your testing Sectra PACS instance, if such an installatino is available to you.
     - You will need the appropriate permissions to add and configure IA Applications in that Sectra PACS, or be in contact with someone who has
-  - For third party AI vendors, there is an online Sectra PACS available for a fee. Contact Sectra Support and request "discussing access to a test PACS for digital pathology AI vendors".
+  - For third party AI vendors, there is an online Sectra PACS available for a fee.
+    - Use https://forms.office.com/e/WBEsUrLyJV to contact Sectra for discussions.
 
 - You will need ensure TCP/IP connectivity between the Sectra PACS server and the machine running your IA-APP.
   - Both parties will initiate communications, so both servers need to be accessible to each other under appropiate DNS names.
@@ -31,7 +32,7 @@ cd examples/python/ia_app_basic
 ./flask_run.sh
 ```
 
-See the README linked above for how to configure the Sectra DPAT module to connect. 
+See the README linked above for how to configure the Sectra DPAT module to connect.
 
 Once you have succesfully got this basic app working inside the Sectra Pathology module, we strongly suggest you proceed with adopting the practices in the second example below.
 

examples/python/ia_app_basic/README.md

@@ -13,6 +13,11 @@ For a more realistic implementation where WSI processing is done in longer-runni
 
 - Output: a graphical primitive, or a "patch gallery" (see `webserver.py:DEMO_TYPE` and `webserver.py:app_on_userinput` )
 
+**Screenshot**
+
+![pcad_demo_2024-11-21_15-48-thumbnail](https://github.com/user-attachments/assets/51c2d8d6-a549-411a-bc56-38d866e80d60)
+
+
 ### Development notes
 Uses a simple flask server for responding to IA-API requests and a requests-based client for outgoing communications with the IA-API..
 
@@ -32,25 +37,18 @@ In order to try this out you'll need to
 ### Install and run
 
 #### Prerequisites
+We use astral `uv` for python dependency management. Please install it first. See https://docs.astral.sh/uv/ for more install options.
 
-You currently need libgeos to build shapely. On ubuntu `sudo apt install libgeos-dev`.
-The shapely dependency will eventually be removed.
-
-#### Starting
-
-You can run this example in a virtualenv using poetry, or directly in the current python environment.
-
-Using poetry:
 ```
-poetry install
-poetry run python pcaddemo/__main__.py
+curl -LsSf https://astral.sh/uv/install.sh | sh
 ```
 
-As plain-old python:
+#### Starting
+
+Start the webserver:
 
 ```
-pip install -e .
-python pcaddemo/__main__.py
+./flask_run.sh
 ```
 
 ### Configuring the Sectra DPAT Server
@@ -71,6 +69,11 @@ You need to configure the Sectra Pathology Server (SPS) to call this server. Thi
 
 If succesful, you should now be able to right-click in any Pathology Image and select your new IA-APP (you might need to refresh any running sessions).
 
+**Screenshot of configuration where app is running on the same machine as the server**
+
+![edit_thumbnail](https://github.com/user-attachments/assets/4e10cb17-c7d9-462a-bc2c-810fc916770e)
+
+
 
 ## Tested with
 

examples/python/ia_app_basic/flask_run.bat

@@ -1,4 +1,4 @@
 set FLASK_APP=pcaddemo\webserver
 set FLASK_RUN_PORT=5005
 set FLASK_DEBUG=1
-flask run
+uv run -- flask run

examples/python/ia_app_basic/flask_run.sh

@@ -3,4 +3,4 @@ export FLASK_APP=pcaddemo/webserver
 export FLASK_RUN_PORT=5005
 export FLASK_RUN_HOST=0.0.0.0
 export FLASK_DEBUG=1
-flask run
+uv run -- flask run

examples/python/ia_app_basic/pcaddemo/version.py

@@ -1,6 +1,7 @@
 """
 version info
 """
+
 __version__ = "0.1.0"
 
 # this is the minimum version we require, we do not support

examples/python/ia_app_basic/pcaddemo/webserver.py

@@ -19,6 +19,7 @@
 APP_MANUFACTURER = "Sectra (demo)"
 BIND_PORT = 5005
 
+
 def json_resp(data):
     """serialize data to JSON and add appropriate IA-api headers"""
     resp = jsonify(data)
@@ -89,7 +90,7 @@ def app_on_userinput():
     data = request.get_json()
 
     save_filename = f"./debug/userinput_{data['action']}_tmp.json"
-    with open(save_filename, 'w') as file:
+    with open(save_filename, "w") as file:
         json.dump(data, file)
 
     # data['action'] :: create, modify, delete, cancel
@@ -138,9 +139,7 @@ def app_create_primitiveArea(data):
         "content": {
             "style": {"fillStyle": None, "size": None, "strokeStyle": "#FFA500"},
             "polygons": input_polygons,  # same area as user input,
-            "labels": [
-                {"location": min_y_pt, "label": text}
-            ],
+            "labels": [{"location": min_y_pt, "label": text}],
         },
     }