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Version 0.2 (#17)
## Runs - Groups were replaced by `GroupedRun`. Hence, a group can be used as a normal run (`AbstractRun`). - Groups are only created if the runs are compatible (via function `check_equality`). ## Plugins - Integrated Parallel Coordinates. - Configurations Cube and Parallel Coordinates show the real config values and not the encoded anymore. - Changed plugin interfaces (check_run_compatibility, check_runs_compatibility, load_inputs, load_dependency_inputs). - Enhanced native group selection drastically. - Added icons to the plugins. - Removed ICE for now as too many bugs were found. ## Others - Added typehints. - Added tests for caches, basic layouts and other utils. - Added tools (mypy, flake8 and blake) - Performance increase in `general` as a folder is only transformed to a run if selected. ## Known Bugs - fANOVA does not work if the configspace includes constants. Co-authored-by: PhMueller <[email protected]> Co-authored-by: dwoiwode <[email protected]> Co-authored-by: Dominik Woiwode <[email protected]>
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‎.DS_Store‎

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‎.flake8‎

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[flake8]
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show-source = True
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max-line-length = 100
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extend-exclude =
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venv
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.venv
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build
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extend-ignore =
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# No whitespace before ':' in [x : y]
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E203
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# No lambdas — too strict
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E731

‎.github/workflows/pytest.yml‎

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name: PyTest
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on: [ push ]
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jobs:
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pytest:
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name: PyTest
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Add conda to system path
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run: |
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# $CONDA is an environment variable pointing to the root of the miniconda directory
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echo $CONDA/bin >> $GITHUB_PATH
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- name: Setup Python 3.9
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uses: actions/setup-python@v2
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with:
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python-version: 3.9
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- name: Install dependencies
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run: |
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conda env update --file environment.yml --name base
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pip install .
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pip install .[dev]
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- name: Run pytest
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run: pytest tests

‎.gitignore‎

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*cache*
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!*cache.py
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!*caches.py
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docs/*
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__pycache__
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*.rdb
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examples/logs/SMAC
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examples/logs/BOHB
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smac3-output*
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.DS_Store
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pending
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__init__.pyc
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__init__.pyc
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examples/logs*
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examples/*
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!examples/logs/DeepCAVE
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!examples/record
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examples/record/_*.py
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*.sh
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!run.sh
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.vscode
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*.egg-info
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docs/apidoc
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docs/html
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docs/pages/examples

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/pycqa/isort
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rev: 5.10.1
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hooks:
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- id: isort
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name: isort imports deepcave
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files: deepcave/.*
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args: [--check]
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- id: isort
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name: isort imports test
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files: test/.*
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args: [--check]
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- repo: https://github.com/ambv/black
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rev: 21.12b0
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hooks:
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- id: black
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name: black formatter deepcave
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files: deepcave/.*
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args: [--check]
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- id: black
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name: black formatter test
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files: test/.*
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args: [--check]
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- id: black
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name: black formatter examples
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files: examples/.*
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args: [--check]
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# This is disabled as most modules fail this
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- repo: https://github.com/pycqa/pydocstyle
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rev: 6.1.1
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hooks:
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- id: pydocstyle
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files: DISABLED # deepcave/.*
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always_run: false
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additional_dependencies: ["toml"] # Needed to parse pyproject.toml
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v0.930
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hooks:
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- id: mypy
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name: mypy deepcave
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files: deepcave/.*
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- repo: https://gitlab.com/pycqa/flake8
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rev: 4.0.1
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hooks:
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- id: flake8
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name: flake8 deepcave
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files: deepcave/.*
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- id: flake8
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name: flake8 test
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files: test/.*

‎CHANGELOG.md‎

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# 0.2
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## Runs
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- Groups were replaced by `GroupedRun`. Hence, a group can be used as a normal run (`AbstractRun`).
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- Groups are only created if the runs are compatible (via function `check_equality`).
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## Plugins
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- Integrated Parallel Coordinates.
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- Configurations Cube and Parallel Coordinates show the real config values and not
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the encoded anymore.
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- Changed plugin interfaces (check_run_compatibility, check_runs_compatibility,
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load_inputs, load_dependency_inputs).
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- Enhanced native group selection drastically.
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- Added icons to the plugins.
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- Removed ICE for now as too many bugs were found.
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## Others
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- Added typehints.
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- Added tests for caches, basic layouts and other utils.
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- Added tools (mypy, flake8 and blake)
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- Performance increase in `general` as a folder is only transformed to a run if selected.
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## Known Bugs
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- fANOVA does not work if the configspace includes constants.
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# 0.1.1
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## Plugins
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- ICE/PDP: Added uncertainties
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- fANOVA: Works with no budgets now
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## Others
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- Installable via pip
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# 0.1
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## Features
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- Recorder: Record your runs and save them directly as DeepCAVE files.
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- Matplotlib mode: Alternatively, plugins can output Matplotlib rendered plots.
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## Plugins
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- StaticPlugin: Uses queue to process the result.
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- Individual Conditional Expectation / Partial Dependency Plots: Shows how individual instances behave.
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- fANOVA: Shows Hyperparameter Importance.
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## Converters
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- DeepCAVE
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- SMAC
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- BOHB (Beta)
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- BOHB (Beta)

‎Dockerfile‎

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# syntax=docker/dockerfile:1
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FROM continuumio/miniconda3
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# Install linux dependencies
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RUN apt-get update -y
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RUN apt install -y build-essential
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RUN apt-get install -y swig
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RUN apt-get install -y redis-server
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# Copy files
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COPY . /DeepCAVE
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WORKDIR /DeepCAVE
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RUN conda update conda -y
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# Create new environment
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RUN conda env create -f environment.yml
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# Make RUN commands use the new environment:
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SHELL ["conda", "run", "-n", "DeepCAVE", "/bin/bash", "-c"]
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# Install DeepCAVE
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RUN pip install .

‎MANIFEST.in‎

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include requirements.txt
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include extras_require.json
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include loggin.yml
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include start.sh

‎Makefile‎

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install:
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pip install -r requirements.txt
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# NOTE: Used on linux, limited support outside of Linux
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#
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# A simple makefile to help with small tasks related to development of deepcave
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# These have been configured to only really run short tasks. Longer form tasks
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# are usually completed in github actions.
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.PHONY: help install-dev check format pre-commit clean clean-build build publish test
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help:
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@echo "Makefile deepcave"
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@echo "* install-dev to install all dev requirements and install pre-commit"
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@echo "* check to check the source code for issues"
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@echo "* format to format the code with black and isort"
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@echo "* pre-commit to run the pre-commit check"
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@echo "* clean to clean the dist and doc build files"
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@echo "* build to build a dist"
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@echo "* publish to help publish the current branch to pypi"
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@echo "* tests to run the tests"
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PYTHON ?= python
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CYTHON ?= cython
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PYTEST ?= python -m pytest
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CTAGS ?= ctags
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PIP ?= python -m pip
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MAKE ?= make
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BLACK ?= black
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ISORT ?= isort
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PYDOCSTYLE ?= pydocstyle
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MYPY ?= mypy
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PRECOMMIT ?= pre-commit
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FLAKE8 ?= flake8
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DIR := ${CURDIR}
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DIST := ${CURDIR}/dist
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install-dev:
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$(PIP) install -e ".[dev]"
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pre-commit install
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check-black:
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$(BLACK) deepcave examples tests --check || :
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check-isort:
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$(ISORT) deepcave tests --check || :
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check-pydocstyle:
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$(PYDOCSTYLE) deepcave || :
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check-mypy:
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$(MYPY) deepcave || :
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check-flake8:
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$(FLAKE8) deepcave || :
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$(FLAKE8) tests || :
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# pydocstyle does not have easy ignore rules, instead, we include as they are covered
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check: check-black check-isort check-mypy check-flake8 # check-pydocstyle
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pre-commit:
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$(PRECOMMIT) run --all-files
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format-black:
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$(BLACK) deepcave tests examples
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format-isort:
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$(ISORT) deepcave tests
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format: format-black format-isort
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clean-build:
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$(PYTHON) setup.py clean
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rm -rf ${DIST}
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# Clean up any builds in ./dist as well as doc
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clean:
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rm -rf cache
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clean-build
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rm -rf cache
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# Build a distribution in ./dist
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build:
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$(PYTHON) setup.py bdist
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# Publish to testpypi
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# Will echo the commands to actually publish to be run to publish to actual PyPi
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# This is done to prevent accidental publishing but provide the same conveniences
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publish: clean-build build
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$(PIP) install twine
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$(PYTHON) -m twine upload --repository testpypi ${DIST}/*
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@echo
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@echo "Test with the following line:"
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@echo "pip install --index-url https://test.pypi.org/simple/ auto-sklearn"
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@echo
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@echo "Once you have decided it works, publish to actual pypi with"
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@echo "python -m twine upload dist/*"
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tests:
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$(PYTEST) tests
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‎README.md‎

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## Installation
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First, make sure you have
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[swig](https://www.dev2qa.com/how-to-install-swig-on-macos-linux-and-windows/) and
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[redis-server](https://flaviocopes.com/redis-installation/) installed on your
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computer.
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If you are on an Non-Intel Mac you have to add
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```
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git clone https://github.com/automl/DeepCAVE.git
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cd DeepCAVE
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conda create -n DeepCAVE python=3.9
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make install
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export DISABLE_SPRING=true
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export OBJC_DISABLE_INITIALIZE_FORK_SAFETY=YES
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to your ```~/.bash_profile``` to enable multi-processing.
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Afterwards, follow the instructions:
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export PYTHONPATH=$(pwd)
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git clone https://github.com/automl/DeepCAVE.git
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cd DeepCAVE
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conda env create -f environment.yml
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conda activate DeepCAVE
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pip install .
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```
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from deep_cave import Recorder, Objective
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configspace = CS.ConfigurationSpace(seed=0)
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configspace.add_hyperparameter(alpha)
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with Recorder(configspace, objectives=["accuracy", "mse"]) as r:
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accuracy = Objective("accuracy", lower=0, upper=1, optimize="upper")
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mse = Objective("mse", lower=0)
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with Recorder(configspace, objectives=[accuracy, mse]) as r:
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## Visualizing and Evaluating
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The webserver as well as the queue/workers can be started by running ``` ./run.sh ```.
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The webserver as well as the queue/workers can be started by running
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```
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deepcave --start
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```
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or
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```
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./start.sh
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```
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Visit `http://127.0.0.1:8050/` to get started.
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![interface](interface.png)
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![interface](media/interface.png)
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