Merge pull request #2 from alexisthual/refactoring

Major refactoring of folder structure

Author: alexisthual

.flake8

@@ -0,0 +1,45 @@
+name: Run brain-cockpit api tests
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  unittest:
+    name: Test API
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python_version: "3.7"
+          - os: ubuntu-latest
+            python_version: "3.8"
+          - os: ubuntu-latest
+            python_version: "3.9"
+          - os: ubuntu-latest
+            python_version: "3.10"
+          - os: ubuntu-latest
+            python_version: "3.11"
+          - os: macos-latest
+            python_version: "3.7"
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python_version }}
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e .[test]
+      - name: Lint with pflake8
+        run: |
+          pflake8 api
+      - name: Test with pytest
+        run: |
+          pytest

.github/workflows/api_unit_tests.yml

@@ -0,0 +1,42 @@
+name: Build brain-cockpit front end
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - "*"
+
+jobs:
+  build:
+    name: Build front-end
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            node_version: "14"
+          - os: ubuntu-latest
+            node_version: "16"
+          - os: ubuntu-latest
+            node_version: "18"
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v3
+        with:
+          node-version: ${{ matrix.node_version }}
+
+      - name: Run install
+        uses: borales/actions-yarn@v4
+        with:
+          cmd: install
+          dir: web
+
+      - name: Build production bundle
+        uses: borales/actions-yarn@v4
+        with:
+          cmd: build
+          dir: web

.github/workflows/deploy_site.yml renamed to .github/workflows/build_deploy_docs.yml

@@ -0,0 +1,30 @@
+name: Mirror to Ebrains
+
+# Configure the events that are going to trigger tha automated update of the mirror
+on:
+  push:
+    branches: [main]
+
+# Configure what will be updated
+jobs:
+  # set the job name
+  mirror_to_ebrains:
+    runs-on: ubuntu-latest
+    steps:
+      # this task will push the main branch of the source_repo (github) to the
+      # destination_repo (ebrains gitlab)
+      - name: sync-main
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "alexisthual/brain-cockpit"
+          source_branch: "main"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/alexisthual/brain-cockpit"
+          destination_branch: "main"
+      # this task will push all tags from the source_repo to the destination_repo
+      - name: sync-tags
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "alexisthual/brain-cockpit"
+          source_branch: "refs/tags/*"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/alexisthual/brain-cockpit"
+          destination_branch: "refs/tags/*"

.github/workflows/build_front.yml

@@ -1,31 +1,31 @@
-node_modules
-.eslintcache
-yarn-error.log
-api/public/meshes/*
-public/assets/*
-public/meshes/*
-.env.local
-.env.development
-.env.development.local
-.env.production
-.env.production.local
-.env.test.local
-__pycache__
-.sync-config.cson
-build
-.vscode
+**/node_modules
+**/.eslintcache
+**/yarn-error.log
+**/api/public/meshes/*
+**/public/assets/*
+**/public/meshes/*
+**/.env.local
+**/.env.development
+**/.env.development.local
+**/.env.production
+**/.env.production.local
+**/.env.test.local
+**/__pycache__
+**/.sync-config.cson
+**/build
+**/.vscode
 
 .ipynb_checkpoints
 
 # yarn without zero-installs
 # see https://yarnpkg.com/getting-started/qa#which-files-should-be-gitignored
-.pnp.*
-.yarn/*
-!.yarn/patches
-!.yarn/plugins
-!.yarn/releases
-!.yarn/sdks
-!.yarn/versions
+**/.pnp.*
+**/.yarn/*
+!**/.yarn/patches
+!**/.yarn/plugins
+!**/.yarn/releases
+!**/.yarn/sdks
+!**/.yarn/versions
 
 # Documentation
 doc/_build
@@ -34,4 +34,10 @@ doc/gen_modules
 doc/generated
 doc/modules/generated
 
-*.egg-info
+*.egg-info
+
+# Don't export meshes computed by brain-cockpit
+*.gltf
+*.bin
+
+.pytest_cache

.github/workflows/ebrains_mirror.yml

@@ -1,14 +1,13 @@
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.2.0
+    rev: v3.0.0-alpha.6
     hooks:
       - id: prettier
   - repo: https://github.com/ambv/black
-    rev: stable
+    rev: 23.1.0
     hooks:
       - id: black
-        language_version: python3.7
   - repo: https://github.com/pycqa/flake8
-    rev: 3.7.9
+    rev: 6.0.0
     hooks:
       - id: flake8

.gitignore

@@ -0,0 +1,2 @@
+trailingComma: "es5"
+singleQuote: false

.pre-commit-config.yaml

@@ -6,7 +6,15 @@
 
 `brain-cockpit` is a web-app comprising a Typescript front-end and a Python back-end. It is meant to help explore:
 
-* large surface fMRI datasets projected
-* alignments computed between brains, such as those computed with [fugw](https://alexisthual.github.io/fugw/index.html)
+- large surface fMRI datasets projected on surface meshes
+- alignments computed between brains, such as those computed with [fugw](https://alexisthual.github.io/fugw/index.html)
 
-![Screenshot](https://mybox.inria.fr/thumbnail/192bdcc47f8c4decbac7/1024/Screenshot%20from%202020-12-07%2012-23-45.png)
+You can try our [online demo](https://brain-cockpit.athual.fr/)!
+
+![Screenshot](https://mybox.inria.fr/seafhttp/files/71b1d396-c856-45a7-81c4-a432e9347b7f/main_screenshot.png)
+
+## Acknowledgement
+
+This work has received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation
+under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3).
+It has also been supported by the the KARAIB AI chair (ANR-20-CHIA-0025-01) and the NeuroMind Inria associate team.