Development

.github/workflows/build-frontend-dev.yml

@@ -0,0 +1,42 @@
+name: build frontend
+
+on:
+  push:
+    branches: ["development"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-node@v3
+      with:
+        node-version: 17.9.1
+    - name: switch to frontend branch
+      run: |
+        echo switching to branch ${GITHUB_REF_NAME}-frontend
+        git checkout ${GITHUB_REF_NAME}-frontend || git checkout -b ${GITHUB_REF_NAME}-frontend
+        git merge ${GITHUB_REF_NAME}-frontend
+    - name: build frontend
+      run: |
+        cd frontend
+        yarn
+        cd ..
+        ./build-frontend.sh
+    - name: config git user
+      run: |
+        curl -s -u ${GITHUB_ACTOR}:${{ secrets.GITHUB_TOKEN }} https://api.github.com/users/${GITHUB_ACTOR} > ${GITHUB_ACTOR}.json
+        git config user.email "$(cat ${GITHUB_ACTOR}.json | jq -r .email)"
+        git config user.name "frontend-bot"
+    - name: commit changes
+      run: |
+        git add -f bad/static/brain*
+        git add -f bad/static/index*
+        git status
+        git commit -m"build frontend"
+    - name: push changes
+      run: |
+        git push -u origin ${GITHUB_REF_NAME}-frontend
+

.github/workflows/build-frontend-main.yml

@@ -0,0 +1,36 @@
+name: build frontend
+
+on:
+  push:
+    branches: ["main"]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        fetch-depth: 0
+    - uses: actions/setup-node@v3
+      with:
+        node-version: 17.9.1
+    - name: build frontend
+      run: |
+        cd frontend
+        yarn
+        cd ..
+        ./build-frontend.sh
+    - name: config git user
+      run: |
+        curl -s -u ${GITHUB_ACTOR}:${{ secrets.GITHUB_TOKEN }} https://api.github.com/users/${GITHUB_ACTOR} > ${GITHUB_ACTOR}.json
+        git config user.email "$(cat ${GITHUB_ACTOR}.json | jq -r .email)"
+        git config user.name "frontend-bot"
+    - name: commit changes
+      run: |
+        git add -f bad/static/brain*
+        git add -f bad/static/index*
+        git status
+        git commit -m"build frontend"
+    - name: push changes
+      run: |
+        git push

.github/workflows/tests.yml

@@ -0,0 +1,48 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: test
+
+on:
+  push:
+    branches: ["main", "development"]
+  pull_request:
+    branches: ["main", "development"]
+
+jobs:
+
+  test-ubuntu:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.8", "3.9", "3.10"]
+        mongodb-version: ["4.2"]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Start MongoDB
+        uses: supercharge/mongodb-github-action@1.10.0
+        with:
+          mongodb-version: ${{ matrix.mongodb-version }}
+
+      - name: Install python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m venv env
+          source env/bin/activate
+          pip install -r requirements.txt
+          pip install https://github.com/JamesRitchie/scikit-rvm/archive/master.zip
+
+      - name: Run tests
+        run: |
+          source env/bin/activate
+          ./run-tests.sh

README.md

@@ -1,7 +1,109 @@
 # BrainAGE Designer
 
+[![test](https://github.com/defgsus/brainage-designer/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/defgsus/brainage-designer/actions/workflows/tests.yml)
+[![test](https://github.com/defgsus/brainage-designer/actions/workflows/build-frontend-main.yml/badge.svg?branch=main)](https://github.com/defgsus/brainage-designer/actions/workflows/build-frontend-main.yml)
+
+**Brain** **A**ge **G**ap **E**stimation framework with browser-based user interface.
+
+![screenshot](docs/img/screenshot-analysis.png)
+
+Some of the features:
+
+- all experiments are controlled from the web-UI
+- supports arbitrary preprocessing pipelines
+- fine control over analysis / model creation
+- all experiments are stored to database for revisiting them later
+
+
 ## Installation
 
+### Requirements
+
+- [Python](https://www.python.org/) 3.8 or later
+- [MongoDB](https://www.mongodb.com/) 3.6 or later 
+- [Matlab Runtime](https://www.mathworks.com/products/compiler/matlab-runtime.html) v93 (optional)
+
+### Download
+
+Using the git command-line tool:
+
+```shell
+cd /my/projects  # or where you want to place it
+git clone https://github.com/defgsus/brainage-designer.git
+cd brainage-designer
+git checkout development-frontend
+```
+
+or you can download [a zip file](https://github.com/defgsus/brainage-designer/archive/refs/heads/development-frontend.zip)
+and extract it.
+
+### Running on localhost
+
+```shell
+# create new python environment
+python -m venv env
+# activate     
+source env/bin/activate
+# install python packages
+pip install -r requirements.txt
+pip install https://github.com/JamesRitchie/scikit-rvm/archive/master.zip
+```
+
+[Install MongoDB](https://www.mongodb.com/docs/manual/installation/)
+
+Start server and worker:
+
+```shell
+./start-server.sh
+```
+
+visit [http://localhost:9009](http://localhost:9009)
+
+#### Configuration
+
+The local setup can be configure by creating a `.env` file
+in the root directory. It can have the following entries:
+
+```shell
+# enable debugging mode (mainly for web-server, more text output)
+BAD_DEBUG=true
+
+# -- directories --
+
+# the root path below which everything can be accessed
+BAD_DATA_PATH=/home/me
+# temporary directory to use
+TEMP_PATH=/tmp/brainage-designer
+
+# -- matlab --
+
+# path to the matlab runtime 
+MATLAB_PATH=/home/me/MATLAB_Runtime/v93
+# path to the matlab-based CAT12 toolbox
+CAT12_PATH=/home/me/CAT12.8.1_r2042_R2017b_MCR_Linux
+
+# -- API server --
+
+# change the address of the API (and frontend) server
+SERVER_HOST=localhost
+SERVER_PORT=9009
+
+# -- mongodb --
+
+# rename the database
+DATABASE_NAME=brainage-designer
+# location of the mongodb server
+DATABASE_HOST=localhost
+DATABASE_PORT=27017
+# to handle authentication with mongodb
+DATABASE_USER=brainage-user
+DATABASE_PASSWORD=brainage-password
+```
+
+
+
+## Installation via 'Docker' 
+
 Install a recent version of [Docker Engine](https://docs.docker.com/engine/install/) 
 or the **Docker Desktop** if you can't help it.
 
@@ -46,13 +148,13 @@ docker run -ti -p 80:9009 brainage-designer
 ```
 
 
-## development
+# Development
 
 ### prepare environments
 
 ```shell
-# for python the typical
-virtualenv -p python3 env
+# for python the typical..
+python -m venv env
 source env/bin/activate
 pip install -r requirements.txt
 

bad/config.py

@@ -26,7 +26,7 @@ def _to_bool(x: str) -> bool:
 DATA_PATH: Path = config("BAD_DATA_PATH", default=Path("~/").expanduser(), cast=Path)
 TEMP_PATH: Path = config(
     "BAD_TEMP_PATH",
-    default=str(Path(tempfile.gettempdir()) / "brainage-pipeline"),
+    default=str(Path(tempfile.gettempdir()) / "brainage-designer"),
     cast=Path,
 )
 

bad/process/processdb.py

@@ -4,10 +4,10 @@
 import signal
 import uuid
 import traceback
-from typing import Mapping, Any, Optional, Union, Sequence
+from typing import Mapping, Any, Optional, Union, Sequence, List
 
 import pymongo
-from pymongo.database import Collection, List
+from pymongo.database import Collection
 
 from bad.db import DatabaseMixin
 from bad import logger

frontend/package.json

@@ -0,0 +1,40 @@
+{
+  "source": "src/index.html",
+  "scripts": {
+    "start": "parcel",
+    "build": "parcel build --no-source-maps --no-cache --detailed-report"
+  },
+  "config": {
+    "root": "./src",
+    "dist": "./dist"
+  },
+  "devDependencies": {
+    "@parcel/transformer-inline-string": "2.8.0",
+    "@parcel/transformer-sass": "2.8.0",
+    "buffer": "^5.5.0",
+    "parcel": "^2.8.0",
+    "process": "^0.11.10"
+  },
+  "dependencies": {
+    "@ant-design/icons": "^4.8.0",
+    "@lagunovsky/redux-react-router": "^4.3.0",
+    "@reduxjs/toolkit": "^1.9.0",
+    "antd": "^5.0.0",
+    "axios": "^1.1.3",
+    "history": "^5.3.0",
+    "moment": "^2.29.4",
+    "plotly.js": "^2.24.3",
+    "react": "^18.2.0",
+    "react-dnd": "^16.0.1",
+    "react-dnd-html5-backend": "^16.0.1",
+    "react-dom": "^18.2.0",
+    "react-markdown": "^8.0.4",
+    "react-plotly.js": "^2.6.0",
+    "react-redux": "^8.0.5",
+    "react-router": "^6.4.3",
+    "react-router-dom": "^6.4.3",
+    "redux": "^4.2.0",
+    "redux-toolkit-saga": "^1.2.0",
+    "three": "^0.147.0"
+  }
+}

requirements.txt

@@ -1,13 +1,14 @@
 # h5py==3.1.0    # requires extra package for mac python docker image
-matplotlib==3.6.3
-nibabel==3.2.2
-nilearn==0.9.2
-Pillow==8.4.0
-pymongo==4.1.1
-python-decouple==3.6
-requests==2.27.1
-scipy==1.5.4
-tornado==6.2
-tqdm==4.64.1
+matplotlib==3.7.3
+nibabel==5.1.0  # 3.2.2
+nilearn==0.10.2
+numpy==1.24.4
+Pillow==10.1.0
+pymongo==4.6.0
+python-decouple==3.8
+requests==2.31.0
+scipy==1.10.1
+tornado==6.3.3
+tqdm==4.66.1
 xlrd==2.0.1
-https://github.com/JamesRitchie/scikit-rvm/archive/master.zip
+# https://github.com/JamesRitchie/scikit-rvm/archive/master.zip

tests/modules/test_cat12.py

@@ -10,8 +10,8 @@
 from tests.base import BadTestCase
 
 
-@unittest.skipIf(not config.CAT12_PATH.exists(), "CAT12 package not at it's place")
-@unittest.skipIf(not config.MATLAB_PATH.exists(), "matlab not at it's place")
+@unittest.skipIf(len(str(config.CAT12_PATH)) <= 1 or not config.CAT12_PATH.exists(), "CAT12 package not at it's place")
+@unittest.skipIf(len(str(config.MATLAB_PATH)) <= 1 or not config.MATLAB_PATH.exists(), "matlab not at it's place")
 class TestCat12Modules(BadTestCase):
 
     def test_cat12_version(self):

tests/modules/test_cat12_preprocess.py

@@ -8,8 +8,8 @@
 from tests.base import BadTestCase
 
 
-@unittest.skipIf(not config.CAT12_PATH.exists(), "CAT12 package not at it's place")
-@unittest.skipIf(not config.MATLAB_PATH.exists(), "matlab not at it's place")
+@unittest.skipIf(len(str(config.CAT12_PATH)) <= 1 or not config.CAT12_PATH.exists(), "CAT12 package not at it's place")
+@unittest.skipIf(len(str(config.MATLAB_PATH)) <= 1 or not config.MATLAB_PATH.exists(), "matlab not at it's place")
 class TestCat12PreprocessModule(BadTestCase):
 
     @BadTestCase.tag_long()