Merge branch 'helmholtz_design' of https://github.com/HelmholtzAI-Con…

…sultants-Munich/data-centric-platform into helmholtz_design

.github/workflows/test.yml

@@ -18,7 +18,7 @@ jobs:
     strategy:
       matrix:
         platform: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: [3.9, "3.10"]
+        python-version: [3.9, "3.10", "3.11"]
     env:
       DISPLAY: ':99.0'
     steps:
@@ -44,17 +44,15 @@ jobs:
         run: |
           python -m pip install --upgrade pip
           python -m pip install setuptools  
-          pip install pytest
-          pip install pytest-qt
           pip install pytest-xvfb
           pip install coverage
-          pip install -e ".[testing]"
+          pip install -e ".[dev]"
           pip install matplotlib
         working-directory: src/client
 
       - name: Install server dependencies (for communication tests)
         run: |
-          pip install -e ".[testing]"
+          pip install -e ".[dev]"
         working-directory: src/server
 
       - name: Test with pytest
@@ -94,10 +92,9 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install --upgrade setuptools  
           pip install numpy
-          pip install pytest
           pip install wheel
           pip install coverage
-          pip install -e ".[testing]"
+          pip install -e ".[dev]"
         working-directory: src/server
 
       - name: Test with pytest
@@ -114,4 +111,43 @@ jobs:
           files: src/server/coverage.xml
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+  deploy:
+      # this will run when you have tagged a commit, starting with "v*"
+      # and requires that you have put your twine API key in your 
+      # github secrets (see readme for details)
+      needs: [test_client, test_server]
+      runs-on: ubuntu-latest
+      if: contains(github.ref, 'tags')
+      steps:
+        - uses: actions/checkout@v3
+        - name: Set up Python
+          uses: actions/setup-python@v3
+          with:
+            python-version: "3.x"
+        - name: Install dependencies
+          run: |
+            python -m pip install --upgrade pip
+            pip install twine 
+            pip install build
+
+        - name: Build and publish dcp_client
+          env:
+            TWINE_USERNAME: __token__
+            TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+          run: |
+            git tag
+            python -m build .
+            twine upload dist/*
+          working-directory: src/client
+
+        - name: Build and publish dcp_server
+          env:
+            TWINE_USERNAME: __token__
+            TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
+          run: |
+            git tag
+            python -m build .
+            twine upload dist/*
+          working-directory: src/server
 

.gitignore

@@ -2,12 +2,14 @@
 data/
 in_progress/
 curated/
+uncurated/
 
 # model dir
 *mytrainedmodel/
 
 #configs
 src/client/dcp_client/config.cfg
+src/server/dcp_server/config.cfg
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -80,7 +82,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-docs/_build/
+# docs/build/
 
 # PyBuilder
 target/
@@ -151,8 +153,6 @@ dmypy.json
 .idea/
 
 .DS_Store
-docs/
-test-napari.pub
 data/
 BentoML/
-models/
+

.readthedocs.yaml

@@ -0,0 +1,30 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+    # You can also specify other tool versions:
+    # nodejs: "19"
+    # rust: "1.64"
+    # golang: "1.19"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  # Install both Python packages before building the docs
+  install:
+    - method: pip
+      path: src/client
+    - method: pip
+      path: src/server
+    - requirements: docs/requirements.txt

README.md

@@ -4,7 +4,7 @@
 ![stability-wip](https://img.shields.io/badge/stability-work_in_progress-lightgrey.svg)
 ![tests](https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform/actions/workflows/test.yml/badge.svg?event=push)
 [![codecov](https://codecov.io/gh/HelmholtzAI-Consultants-Munich/data-centric-platform/branch/main/graph/badge.svg)](https://codecov.io/gh/HelmholtzAI-Consultants-Munich/data-centric-platform)
-
+[![Documentation Status](https://readthedocs.org/projects/data-centric-platform/badge/?version=latest)](https://data-centric-platform.readthedocs.io/en/latest/?badge=latest)
 
 
 ## How to use this?
@@ -16,7 +16,7 @@ To run the client GUI follow the instructions described in [DCP Client Installat
 DCP handles all kinds of **segmentation tasks**! Try it out if you need to do:
 * **Instance** segmentation
 * **Semantic** segmentation
-* **Panoptic** segmentation
+* **Multi-class instance** segmentation
 
 ### Toy data
 This repo includes the ```data/``` directory with some toy data which you can use as the *Uncurated dataset* folder. You can create (empty) folders for the other two directories required in the welcome window and start playing around.
@@ -29,3 +29,4 @@ Our platform encourages the use of data centric practices. With the user friendl
 - Focus on data curation: no interaction with model parameters during training and inference
 
 #### *Get more with less!*
+<img src="https://github.com/HelmholtzAI-Consultants-Munich/data-centric-platform/blob/main/src/client/readme_figs/dcp_pipeline.png"  width="200" height="200">

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,2 @@
+sphinx
+sphinx-rtd-theme

docs/source/conf.py

@@ -0,0 +1,48 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = 'DCP'
+copyright = '2024, Christina Bukas, Mariia Koren, Helena Pelin'
+author = 'Christina Bukas, Mariia Koren, Helena Pelin'
+release = '0.1'
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = []
+
+templates_path = ['_templates']
+exclude_patterns = []
+
+language = 'English'
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = 'alabaster'
+#html_static_path = ['_static']
+
+import os
+import sys
+from pathlib import Path
+import sphinx_rtd_theme
+
+# Add parent dir to known paths
+p = Path(__file__).parents[2]
+sys.path.insert(0, os.path.abspath(p))
+sys.path.insert(0, os.path.join(p, 'src/server/dcp_server'))
+# Add the following extensions
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.napoleon',
+    'sphinx_rtd_theme'
+]
+
+# Use RTD theme
+html_theme = "sphinx_rtd_theme"

docs/source/dcp_client.gui.rst

@@ -0,0 +1,34 @@
+dcp\_client.gui package
+=======================
+
+.. automodule:: dcp_client.gui
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Submodules
+----------
+
+dcp\_client.gui.main\_window module
+-----------------------------------
+
+.. automodule:: dcp_client.gui.main_window
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+dcp\_client.gui.napari\_window module
+-------------------------------------
+
+.. automodule:: dcp_client.gui.napari_window
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+dcp\_client.gui.welcome\_window module
+--------------------------------------
+
+.. automodule:: dcp_client.gui.welcome_window
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/dcp_client.rst

@@ -0,0 +1,52 @@
+dcp\_client package
+===================
+
+The dcp_client package contains modules and subpackages for interacting with a server for model inference and training. It provides functionalities for managing GUI windows, handling image storage, and connecting to the server for model operations.
+
+dcp_client.app
+   Defines the core application class and related functionalities.
+    - ``dcp_client.app.Application``: Represents the main application and provides methods for image management, model interaction, and server connectivity.
+    - ``dcp_client.app.DataSync``: Abstract base class for data synchronization operations.
+    - ``dcp_client.app.ImageStorage``: Abstract base class for image storage operations.
+    - ``dcp_client.app.Model``: Abstract base class for model operations.
+
+dcp_client.gui
+   Contains modules for GUI components.
+    - ``dcp_client.gui.main_window``: Defines the main application window and associated event functions.
+    - ``dcp_client.gui.napari_window``: Manages the Napari window and its functionalities.
+    - ``dcp_client.gui.welcome_window``: Implements the welcome window and its interactions.
+
+dcp_client.utils
+   Contains utility modules for various tasks.
+    - ``dcp_client.utils.bentoml_model``: Handles interactions with BentoML for model inference and training.
+    - ``dcp_client.utils.fsimagestorage``: Provides functions for managing images stored in the filesystem.
+    - ``dcp_client.utils.settings``: Defines initialization functions and settings.
+    - ``dcp_client.utils.sync_src_dst``: Implements data synchronization between source and destination.
+    - ``dcp_client.utils.utils``: Offers various utility functions for common tasks.
+
+
+Submodules
+----------
+
+dcp\_client.app module
+----------------------
+
+.. automodule:: dcp_client.app
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+dcp\_client.gui module
+----------------------
+.. toctree::
+   :maxdepth: 4
+
+   dcp_client.gui
+
+dcp\_client.utils module
+------------------------
+.. toctree::
+   :maxdepth: 4
+
+   dcp_client.utils
+