Merge pull request #9 from NorwegianVeterinaryInstitute/dev_ML

Transferred code into a package managed by uv.

.gitignore

@@ -1,2 +1,3 @@
-__pycache__
-api-key.txt
+__pycache__/
+/src/shinylims/__pycache__
+*.pyc

.python-version

@@ -0,0 +1 @@
+3.11.5

LICENSE

@@ -0,0 +1,7 @@
+Copyright 2024 Magnus Leithaug
+
+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.

README.md

@@ -1,26 +1,21 @@
 ### Shinylims
 
 A Python Shiny app for LIMS reporting.
-
-Environment setup:
+This python package is managed with uv (https://docs.astral.sh/uv). To run it, clone the repository and install the package with:
 
 ```
-python -m venv pyshiny-env
-cd pyshiny-env
-source bin/activate
-pip install -r requirements.txt
+uv sync
 ```
 
-Then clone the repo, and open the app.
-
-Runs locally with:
+Then, run the shiny app with:
 
 ```
-shiny run app.py
+uv run uvicorn shinylims.app:app
 ```
 
 Remember to update the manifest before making commits
 
 ```
-rsconnect write-manifest shiny . --overwrite
-```
+uvx --from rsconnect-python --python .venv/Scripts/python.exe rsconnect write-manifest shiny . --overwrite --entrypoint shinylims.app:app
+```
+

manifest.json

@@ -3,40 +3,55 @@
   "locale": "English_United States.1252",
   "metadata": {
     "appmode": "python-shiny",
-    "entrypoint": "app"
+    "entrypoint": "shinylims.app:app"
   },
   "python": {
-    "version": "3.11.9",
+    "version": "3.11.5",
     "package_manager": {
       "name": "pip",
-      "version": "24.0",
+      "version": "24.2",
       "package_file": "requirements.txt"
     }
   },
   "files": {
     "requirements.txt": {
-      "checksum": "b5406ad9b684385870dad2811a0cbb52"
+      "checksum": "2976d8cc4dabb78a47c02b90dc75d48e"
     },
     ".gitignore": {
-      "checksum": "85d6754af8e577056060708790e4049f"
+      "checksum": "a490f4da04fb5b1ec743568fe3380d40"
+    },
+    ".python-version": {
+      "checksum": "215923581f8fcce0029639f7ab16ccb6"
+    },
+    "LICENSE": {
+      "checksum": "bbcd65b7e389067d3922f20a2f9eaf4e"
     },
     "README.md": {
-      "checksum": "e43540e228defc4ae6e2478fa92a24e8"
+      "checksum": "262635faedb2f6c0096957d5b75c6d2c"
     },
-    "app.py": {
-      "checksum": "dcb0e583c2c9f5cde04e5d682457422c"
+    "pyproject.toml": {
+      "checksum": "158312210f1c3c22ec358b734eaa34a6"
     },
-    "data_utils.py": {
-      "checksum": "91c3c9621a893c9f1163077c8633c8d0"
+    "src/shinylims/__init__.py": {
+      "checksum": "d41d8cd98f00b204e9800998ecf8427e"
+    },
+    "src/shinylims/app.py": {
+      "checksum": "b561f7e2b81fff588d93ac091dc6a16b"
     },
-    "styles.css": {
+    "src/shinylims/assets/styles.css": {
       "checksum": "3a235faad5ed32854aa71009d1e7a333"
     },
-    "ui_pages.py": {
+    "src/shinylims/data_utils.py": {
+      "checksum": "91c3c9621a893c9f1163077c8633c8d0"
+    },
+    "src/shinylims/ui_pages.py": {
       "checksum": "da947ff0de151ce45fc2a3d3f9fe9a81"
     },
-    "ui_server.py": {
+    "src/shinylims/ui_server.py": {
       "checksum": "13c704eff839d4b4d8c0e7e801a4b49c"
+    },
+    "uv.lock": {
+      "checksum": "9b96f9b5b26f9ebe3ea91404ecb4ee15"
     }
   }
 }

pyproject.toml

@@ -0,0 +1,19 @@
+[project]
+name = "shinylims-uv"
+version = "0.1.0"
+authors = [
+  { name="Magnus Leithaug", email="[email protected]" },
+]
+
+description = "A shiny app to display lab metadata from clarity LIMS"
+readme = "README.md"
+requires-python = ">=3.11.5"
+dependencies = [
+    "faicons==0.2.2",
+    "itables==2.0.1",
+    "pandas==2.2.2",
+    "pins==0.8.5",
+    "seaborn==0.13.2",
+    "shiny==0.9.0",
+    "shinyswatch==0.6.1",
+]

requirements.txt

@@ -1,8 +1,73 @@
-shiny==0.9.0
-seaborn==0.13.2
-pandas==2.2.2
+# This file was autogenerated by uv via the following command:
+#    uv export --no-hashes -o requirements.txt
+-e .
+anyio==4.6.2.post1
+appdirs==1.4.4
+asgiref==3.8.1
+asttokens==2.4.1
+certifi==2024.8.30
+charset-normalizer==3.4.0
+click==8.1.7 ; platform_system != 'Emscripten'
+colorama==0.4.6 ; sys_platform == 'win32' or platform_system == 'Windows'
+contourpy==1.3.0
+cycler==0.12.1
+decorator==5.1.1
+executing==2.1.0
+faicons==0.2.2
+fonttools==4.54.1
+fsspec==2024.10.0
+h11==0.14.0 ; platform_system != 'Emscripten'
+htmltools==0.5.3
+humanize==4.11.0
+idna==3.10
+importlib-metadata==8.5.0
+importlib-resources==6.4.5
+ipython==8.18.0
 itables==2.0.1
-rsconnect-python==1.23.0
+jedi==0.19.1
+jinja2==3.1.4
+joblib==1.4.2
+kiwisolver==1.4.7
+linkify-it-py==2.0.3
+markdown-it-py==3.0.0
+markupsafe==3.0.2
+matplotlib==3.9.2
+matplotlib-inline==0.1.7
+mdit-py-plugins==0.4.2
+mdurl==0.1.2
+numpy==2.1.2
+packaging==24.1
+pandas==2.2.2
+parso==0.8.4
+pexpect==4.9.0 ; sys_platform != 'win32'
+pillow==11.0.0
 pins==0.8.5
-faicons==0.2.2
+prompt-toolkit==3.0.36
+ptyprocess==0.7.0 ; sys_platform != 'win32'
+pure-eval==0.2.3
+pygments==2.18.0
+pyparsing==3.2.0
+python-dateutil==2.9.0.post0
+python-multipart==0.0.12
+pytz==2024.2
+pyyaml==6.0.2
+questionary==2.0.1 ; platform_system != 'Emscripten'
+requests==2.32.3
+seaborn==0.13.2
+shiny==0.9.0
 shinyswatch==0.6.1
+six==1.16.0
+sniffio==1.3.1
+stack-data==0.6.3
+starlette==0.41.0
+traitlets==5.14.3
+typing-extensions==4.12.2
+tzdata==2024.2
+uc-micro-py==1.0.3
+urllib3==2.2.3
+uvicorn==0.32.0 ; platform_system != 'Emscripten'
+watchfiles==0.24.0 ; platform_system != 'Emscripten'
+wcwidth==0.2.13
+websockets==13.1
+xxhash==3.5.0
+zipp==3.20.2

app.py → src/shinylims/app.py

@@ -10,10 +10,13 @@
 from shinyswatch import theme
 
 # App modules
-from ui_pages import projects_page, wgs_samples_page, prepared_samples_page, seq_page
-from ui_server import setup_projects_page, setup_wgs_samples_page, setup_prepared_samples_page, setup_seq_run_page
-from data_utils import fetch_pinned_data
+from src.shinylims.ui_pages import projects_page, wgs_samples_page, prepared_samples_page, seq_page
+from src.shinylims.ui_server import setup_projects_page, setup_wgs_samples_page, setup_prepared_samples_page, setup_seq_run_page
+from src.shinylims.data_utils import fetch_pinned_data
 
+# Add assets
+from pathlib import Path
+css_path = Path(__file__).parent / "assets" / "styles.css"
 
 ####################
 # CONSTRUCT THE UI #
@@ -25,7 +28,7 @@
     theme.cerulean(),
 
     # Include the custom CSS file
-    ui.head_content(ui.include_css("styles.css")),
+    ui.head_content(ui.include_css(css_path)),
 
     # Push the navbar items to the right
     ui.nav_spacer(),