Version 0.2.0

.env.example

@@ -0,0 +1,24 @@
+# Tiled setup
+TILED_KEY=<your-key>
+DEFAULT_TILED_URI=https://tiled-demo.blueskyproject.io/api/v1/metadata/rsoxs/raw/
+DEFAULT_TILED_QUERY="/primary/data/Small Angle CCD Detector_image"
+
+# Directory setup
+DATA_DIR=/path/to/read/data
+
+# Services URLs
+# If running in docker
+# SPLASH_URL=http://splash:80/api/v0
+# MLEX_COMPUTE_URL=http://job-service:8080/api/v0
+# MLEX_CONTENT_URL=http://content-api:8000/api/v0
+# MONGO_DB_USERNAME=<your-username>
+# MONGO_DB_PASSWORD=<your-password>
+# If running locally
+SPLASH_URL=http://localhost:8087/api/v0
+MLEX_COMPUTE_URL=http://localhost:8080/api/v0
+MLEX_CONTENT_URL=http://localhost:8001/api/v0
+HOST_NICKNAME=local
+
+# Static Tiled setup [Optional]
+STATIC_TILED_URI=
+STATIC_TILED_API_KEY=

.flake8

@@ -0,0 +1,7 @@
+[flake8]
+# 127 is width of the Github code viewer,
+# black default is 88 so this will only warn about comments >127
+max-line-length = 127
+# Ignore errors due to incompatibility with black
+#https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html
+extend-ignore = E203,E701

.github/workflows/publish_docker.yml

@@ -0,0 +1,49 @@
+name: Docker
+
+on:
+  push:
+    branches: [ "main" ]
+    tags: [ 'v*.*.*' ]
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+      # Build and push Docker image with Buildx (don't push on PR)
+      # https://github.com/docker/build-push-action
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          file: Dockerfile
+          push: true
+          platforms: linux/amd64,linux/arm64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/test-lint.yml

@@ -0,0 +1,31 @@
+name: test-and-lint
+
+on: pull_request
+
+jobs:
+  test-and-lint:
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+      - name: Set up Python 3.11.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: '3.11.8'
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+          if [ -f requirements-dev.txt ]; then pip install -r requirements-dev.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Run isort
+        uses: isort/isort-action@master
+      - name: Test formatting with black
+        run: |
+          black . --check

.gitignore

@@ -1,6 +1,171 @@
-/data/*
-*pycache*
-.DS_Store
-.keras
-.Makefile.swp
-._*
+# Docker override
+docker-compose.override.y*ml
+database/*
+
+# Byte-compiled / optimized / DLL files
+**pycache**
+**cache**
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# MacOS
+**.DS_Store**
+
+# Project
+data/*
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+default_language_version:
+    python: python3
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-ast
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: debug-statements
+  - repo: https://github.com/gitguardian/ggshield
+    rev: v1.25.0
+    hooks:
+      - id: ggshield
+        language_version: python3
+        stages: [commit]
+  # Using this mirror lets us use mypyc-compiled black, which is about 2x faster
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 24.2.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]

Dockerfile

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+FROM python:3.11
+MAINTAINER THE MLEXCHANGE TEAM
+
+RUN ls
+COPY pyproject.toml pyproject.toml
+COPY README.md README.md
+
+RUN pip install --upgrade pip &&\
+    pip install .
+
+WORKDIR /app/work
+ENV HOME /app/work
+COPY src src
+COPY frontend.py frontend.py
+COPY gunicorn_config.py gunicorn_config.py
+
+CMD ["bash"]
+CMD gunicorn -c gunicorn_config.py --reload frontend:server

README.md

@@ -3,19 +3,25 @@
 This app provides a training/testing platform for image classification with supervised deep-learning approaches.
 
 ## Running as a standalone application
-First, let's install docker:
 
-* https://docs.docker.com/engine/install/
+1. Start the compute and content services in the [MLExchange platform](https://github.com/mlexchange/mlex). Before moving to the next step, please make sure that the computing API and the content registry are up and running. For more information, please refer to their respective
+README files.
 
-Next, let's setup its dependencies:
-* [mlex_computing_api](https://github.com/mlexchange/mlex_computing_api)
-* [mlex_content_registry](https://github.com/mlexchange/mlex_content_registry)
+2. Start [splash-ml](https://github.com/als-computing/splash-ml)
 
-Before moving to the next step, please make sure that the computing API and the content 
-registry are up and running. For more information, please refer to their respective 
-README files.
-* Next, cd into mlex_mlcoach
-* type `docker-compose up --build` into your terminal
+2. Create a new Python environment and install dependencies:
+```
+conda create -n new_env python==3.11
+conda activate new_env
+pip install .
+```
+
+3. Create a `.env` file using `.env.example` as reference. Update this file accordingly.
+
+4. Start example app:
+```
+python frontend.py
+```
 
 Finally, you can access MLCoach at:
 * Dash app: http://localhost:8062/
@@ -26,10 +32,12 @@ to use this application.
 # Model Description
 **TF-NeuralNetworks:** Assortment of neural networks implemented in [TensorFlow](https://www.tensorflow.org).
 
-Further information can be found in [concepts](/docs/concepts.md).
+Further information can be found in [mlex_image_classification](https://github.com/mlexchange/mlex_image_classification).
+
+To make existing algorithms available in MLCoach, make sure to upload the `model description` to the content registry.
 
 # Copyright
-MLExchange Copyright (c) 2021, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+MLExchange Copyright (c) 2024, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
 
 If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at [email protected].