Moving from Niels repo

Author: mlindauer

MANIFEST.in

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+include deep_cave/util/logging.yml
+
+include deep_cave/_version.py
+include versioneer.py
+
+include setup.cfg
+include setup.py
+
+include tox.ini
+
+include MANIFEST.in
+include README.md

Makefile

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+# 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     = docs
+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)

Pipfile

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+[[source]]
+name = "pypi"
+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+pytest = ">=6.2.1"
+more-itertools = ">=8.5.0"
+tqdm = ">=4.56.0"
+pipenv-setup = ">=3.1.1"
+tox = ">=3.21.0"
+coverage = ">=5.3.1"
+pytest-cov = ">=2.10.1"
+sphinx = ">=3.4.3"
+recommonmark = ">=0.7.1"
+versioneer = ">=0.19"
+skl2onnx = ">=1.7.0"
+scikit-optimize = ">=0.8.1"
+
+[packages]
+pandas = ">=1.2.0"
+numpy = ">=1.19.0"
+matplotlib = ">=3.3.3"
+dash = ">=1.18.1"
+PyYAML = ">=5.3.1"
+scipy = ">=1.6"
+dash-dangerously-set-inner-html = ">=0.0.2"
+onnxruntime = ">=1.6.0"
+configspace = ">=0.4.17"
+pdpbox = ">=0.2.1"
+fanova = {editable = true,git = "https://github.com/automl/fanova.git@2442ef36856a98f8755089f915ffe8373d9b5046"}
+pyimp = ">=1.1.2"
+dash-bootstrap-components = ">=0.11.1"
+scikit-learn = ">=0.24"
+
+[requires]
+python_version = "3.8"

Pipfile.lock

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+# DeepCAVE
+
+# Quickstart;
+
+```shell
+# clone with submodules
+git clone --recurse-submodules [email protected]:Nielsmitie/DeepCAVE.git
+# install dependencies
+pipenv install --dev
+# enter pipenv shell
+pipenv shell
+# for non IDE user add deep_cave to PYTHONPATH otherwise set deep_cave as source
+export PYTHONPATH=[path/to/DeepCAVE]
+
+# generate some testing data by running the test scripts
+python tests/api_tests/api_test.py
+# set the environmental variable for the server
+export STUDIES_LOCATION='tests/studies'
+# start the server
+python deep_cave/server/__init__.py
+# visit the displayed website and select the signle experiment and start
+# experimenting
+```
+
+Additional information is displayed below.
+
+### Setup
+
+#### Cloning with submodules
+Clone the project. (LCBench doesn't have a setup.py
+so install it as a git submodule)
+```shell script
+git clone --recurse-submodules [email protected]:Nielsmitie/DeepCAVE.git
+```
+
+#### Install dependencies
+
+To manage dependencies this project uses pipenv.
+The first order requirements are listed human-readable in
+Pipefile. The locked versions and sub-dependencies are in Pipefile.lock.
+
+Install dependencies
+```shell script
+pipenv install --dev
+```
+
+if pyrfr fails for fanova, then you might need to install swig 3 or install
+the correct swig version.
+```shell
+sudo apt-get remove swig
+sudo apt install swig3.0
+sudo ln -s /usr/bin/swig3.0 /usr/bin/swig
+pipenv shell
+pip uninstall pyrfr
+pip install pyrfr --no-cache
+```
+
+### Data preparation for testing
+Download data from [LCBench](https://figshare.com/projects/LCBench/74151),
+unpack and move them to the data dir.
+To run the tests download "six_datasets_lw.zip", unpack it and
+move it into the `test/data` directory.
+
+### Usage
+
+#### Generate Data
+
+To generate data from a hyperband run with the "Fashion-MNIST" dataset
+run tests/api_tests/lcbench_test.py or tests/api_tests/api_test.py or
+tests/api_tests/log_model_test.py.
+
+To generate multi-fidelity random data run api_test.py.
+
+#### Visualization
+
+Run 
+```
+deep_cave.server.__init__.py
+```
+
+with the set environment variables:
+- `STUDIES_LOCATION`: Set to the location of the saved study files. (If you are
+following the tutorial above this should be `../../tests/studies`)
+- `MODELS_LOCATION`: Set to location of the saved model files 
+  (maybe `../../tests/models`) ()
+- `CONVERTER`: If you want a converter instead of the default backend.
+  (not need for this tutorial, but when you want to import data from a 
+  non DeepCAVE source)
+  
+Set the environment variables either via console
+```
+export MODELS_LOCATION="../../tests/studies"
+```
+or via IDE or via pipenv, by including a .env file inside the project.
+
+Another way would be to modify the deep_cave/server/config.py directly.
+
+### Extending
+
+#### Analysis Plugins
+
+To customize the analysis, create a new file with a class that inherits from
+deep_cave.server.plugins.plugin.Plugin. Implement all necessary methods and
+properties.
+
+Include the plugin into the server by setting the environment variable
+`EXTERNAL_PLUGIN_LOCATIONS` with a string value of comma separated absolute paths
+to your plugin dir. Use wildcards to import more than one class per path.
+
+E.g.
+```
+export EXTERNAL_PLUGIN_LOCATIONS='/home/[user]/projects/plugins/*'
+```
+
+The plugin will be loaded on start up and checked.
+The plugin will be available in the UI.
+
+##### Converts
+
+The internal representation of data is abstracted away from the physical
+location and format. A converter can be used to load data in an
+arbitrary format or save it in any format.
+
+To make this customization as easy as possible it is possible to load
+converters from the local filesystem directly into the project, without
+modifying it directly.
+
+In order to use this feature, specify an environment variable called
+`EXTERNAL_CONVERTER_LOCATIONS`  and specify a directory with wildcards
+
+```
+export EXTERNAL_CONVERTER_LOCATIONS='/home/[user]/projects/converters/*'
+```
+
+### Packaging
+
+#### Pipfile
+
+The pipfile contains the requirements with specified versions.
+This is necessary so that when this code is packaged there aren't
+any problems with the client code.
+
+Pipfile.lock contains the specified dependency versions.
+
+#### Setup.py
+
+Contains all information needed for packaging this code.
+
+Add the dependencies to setup.py via:
+```shell script
+pipenv run pipenv-setup sync --pipfile --dev
+```
+Again, only sync the general requirements to avoid conflict
+when installing this package.
+
+
+#### MANIFEST.in
+
+Include the files, like logging.yml that also need to be packaged.
+
+
+### Testing
+
+#### Pytest
+
+All tests are run with pytest.
+```shell script
+pipenv run pytest
+```
+All tests are inside the tests directory. Each file with the suffix
+\_test.py is a test. In each file the functions with the prefix test\_
+are run by the pytest command
+
+#### Tox
+
+For test automation tox is used.
+
+- It creates an environment with a specified python version
+- It packages the project according to setup.py
+- It runs all the tests on the created package
+- It generates the docs
+- It updates the dependencies inside setup.py
+
+#### CI
+
+Tox can then be used inside a CI system to run automated testing.
+
+MISSING: Download the necessary data for testing.
+
+### Documentation
+
+Use [Numpy](https://numpydoc.readthedocs.io/en/latest/format.html)/Pandas
+style doc-strings on code.
+
+In `docs` the .rst files are used to generate documentation for
+this project. The resulting website can be found in `build`.
+
+Regenerate docs/modules
+```shell
+sphinx-apidoc -o docs/deep_cave deep_cave
+```
+Building docs will be automatically done when running tox.
+Otherwise run
+```
+pipenv run python setup.py build_sphinx
+```
+
+View the docs under DeepCAVE/build/index.html (open in Browser).
+Currently everything is documented in Code an no additional
+doc pages were created.
+
+
+# How it should work in the future
+
+## Install
+
+Install from repo, when publicly avaialble
+```shell script
+pip install -e https://github.com/Nielsmitie/DeepCAVE
+```
+Another way to install is documented in the `setup` section.
+
+Alternative, clone repo and install it locally
+```shell script
+git clone https://github.com/Nielsmitie/DeepCAVE
+cd DeepCAVE
+pip install -e .
+```
+
+When a package is uploaded to pypi
+```shell
+pip install deepcave
+```
+
+
+## Usage
+
+### Logging
+Start a project with deep_cave installed.
+
+```python
+import deep_cave
+
+config = {'lr': 1e-8}
+fidelity = 2
+
+with deep_cave.start_trial(config, fidelity) as trial:
+    trial.log_metric(.05)
+```
+
+Set location for the saved file via deep_cave.set_tracking_uri.
+
+### Visualization
+
+To start the server run
+```shell script
+deep_cave server
+# or
+pipenv run python deep_cave/server/__init__.py
+```
+with the correct environment variables set.
+
+
+### Download Chrome Driver (for UI testing) (Deprecated)
+
+Download the [chrome driver](https://chromedriver.storage.googleapis.com/index.html?path=87.0.4280.20/)
+or [firefox driver](https://github.com/mozilla/geckodriver/releases)
+and unpack it into /usr/bin or /usr/local/bin. See the 
+[selenium website](https://www.selenium.dev/selenium/docs/api/py/index.html)
+for further information on the setup

README.md

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+"""
+
+.. code:: python
+    import deep_cave
+
+    config = {'lr': 1e8}
+    fidelity = 2
+
+    with deep_cave.start_trial(config, fidelity) as trial:
+        trial.log_metric(.5)
+
+"""
+
+# mlflow style access to API via __init__.py
+
+from .logger import (
+    start_trial,
+    end_trial,
+    start_study,
+    end_study,
+    log_surrogate
+)
+
+from .store.state import (
+    set_study,
+    get_study,
+    set_tracking_uri,
+    get_tracking_uri,
+    set_registry_uri,
+    get_registry_uri
+)
+
+__all__ = [
+    'start_trial',
+    'end_trial',
+    'start_study',
+    'end_study',
+    'set_study',
+    'get_study',
+    'set_tracking_uri',
+    'get_tracking_uri',
+    'set_registry_uri',
+    'get_registry_uri',
+    'log_surrogate'
+]
+
+from ._version import get_versions
+__version__ = get_versions()['version']
+del get_versions