Merge pull request #969 from openml/develop

Prepare 11.0 release

.flake8

@@ -0,0 +1,10 @@
+[flake8]
+max-line-length = 100
+show-source = True
+select = C,E,F,W,B,T
+ignore = E203, E402, W503
+per-file-ignores =
+    *__init__.py:F401
+exclude =
+    venv
+    examples

.pre-commit-config.yaml

@@ -0,0 +1,28 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 19.10b0
+    hooks:
+      - id: black
+        args: [--line-length=100]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.761
+    hooks:
+      - id: mypy
+        name: mypy openml
+        files: openml/*
+      - id: mypy
+        name: mypy tests
+        files: tests/*
+  - repo: https://gitlab.com/pycqa/flake8
+    rev: 3.8.3
+    hooks:
+      - id: flake8
+        name: flake8 openml
+        files: openml/*
+        additional_dependencies:
+          - flake8-print==3.1.4
+      - id: flake8
+        name: flake8 tests
+        files: tests/*
+        additional_dependencies:
+          - flake8-print==3.1.4

.travis.yml

@@ -15,11 +15,17 @@ env:
   - TEST_DIR=/tmp/test_dir/
   - MODULE=openml
   matrix:
-  - DISTRIB="conda" PYTHON_VERSION="3.5" SKLEARN_VERSION="0.21.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.21.2"
-  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.21.2" RUN_FLAKE8="true" SKIP_TESTS="true"
-  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.21.2" COVERAGE="true" DOCPUSH="true"
-  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.20.2"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.23.1" COVERAGE="true" DOCPUSH="true" SKIP_TESTS="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.23.1" RUN_FLAKE8="true" SKIP_TESTS="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.8" SKLEARN_VERSION="0.23.1" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.23.1" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.23.1" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.8" SKLEARN_VERSION="0.22.2" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.22.2" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.22.2" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.7" SKLEARN_VERSION="0.21.2" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.21.2" TEST_DIST="true"
+  - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.20.2"
   # Checks for older scikit-learn versions (which also don't nicely work with
   # Python3.7)
   - DISTRIB="conda" PYTHON_VERSION="3.6" SKLEARN_VERSION="0.19.2"

CONTRIBUTING.md

@@ -1,7 +1,76 @@
-How to contribute
------------------
+This document describes the workflow on how to contribute to the openml-python package.
+If you are interested in connecting a machine learning package with OpenML (i.e.
+write an openml-python extension) or want to find other ways to contribute, see [this page](https://openml.github.io/openml-python/master/contributing.html#contributing).
 
-The preferred workflow for contributing to the OpenML python connector is to
+Scope of the package
+--------------------
+
+The scope of the OpenML Python package is to provide a Python interface to
+the OpenML platform which integrates well with Python's scientific stack, most
+notably [numpy](http://www.numpy.org/), [scipy](https://www.scipy.org/) and
+[pandas](https://pandas.pydata.org/).
+To reduce opportunity costs and demonstrate the usage of the package, it also
+implements an interface to the most popular machine learning package written
+in Python, [scikit-learn](http://scikit-learn.org/stable/index.html).
+Thereby it will automatically be compatible with many machine learning
+libraries written in Python.
+
+We aim to keep the package as light-weight as possible and we will try to
+keep the number of potential installation dependencies as low as possible.
+Therefore, the connection to other machine learning libraries such as
+*pytorch*, *keras* or *tensorflow* should not be done directly inside this
+package, but in a separate package using the OpenML Python connector.
+More information on OpenML Python connectors can be found [here](https://openml.github.io/openml-python/master/contributing.html#contributing).
+
+Reporting bugs
+--------------
+We use GitHub issues to track all bugs and feature requests; feel free to
+open an issue if you have found a bug or wish to see a feature implemented.
+
+It is recommended to check that your issue complies with the
+following rules before submitting:
+
+-  Verify that your issue is not being currently addressed by other
+   [issues](https://github.com/openml/openml-python/issues)
+   or [pull requests](https://github.com/openml/openml-python/pulls).
+
+-  Please ensure all code snippets and error messages are formatted in
+   appropriate code blocks.
+   See [Creating and highlighting code blocks](https://help.github.com/articles/creating-and-highlighting-code-blocks).
+
+-  Please include your operating system type and version number, as well
+   as your Python, openml, scikit-learn, numpy, and scipy versions. This information
+   can be found by running the following code snippet:
+```python
+import platform; print(platform.platform())
+import sys; print("Python", sys.version)
+import numpy; print("NumPy", numpy.__version__)
+import scipy; print("SciPy", scipy.__version__)
+import sklearn; print("Scikit-Learn", sklearn.__version__)
+import openml; print("OpenML", openml.__version__)
+```
+
+Determine what contribution to make
+-----------------------------------
+Great! You've decided you want to help out. Now what?
+All contributions should be linked to issues on the [Github issue tracker](https://github.com/openml/openml-python/issues).
+In particular for new contributors, the *good first issue* label should help you find
+issues which are suitable for beginners.  Resolving these issues allow you to start
+contributing to the project without much prior knowledge. Your assistance in this area 
+will be greatly appreciated by the more experienced developers as it helps free up 
+their time to concentrate on other issues.
+
+If you encountered a particular part of the documentation or code that you want to improve,
+but there is no related open issue yet, open one first.
+This is important since you can first get feedback or pointers from experienced contributors.
+
+To let everyone know you are working on an issue, please leave a comment that states you will work on the issue
+(or, if you have the permission, *assign* yourself to the issue). This avoids double work!
+
+General git workflow
+--------------------
+
+The preferred workflow for contributing to openml-python is to
 fork the [main repository](https://github.com/openml/openml-python) on
 GitHub, clone, check out the branch `develop`, and develop on a new branch
 branch. Steps:
@@ -109,75 +178,79 @@ following rules before you submit a pull request:
  - If any source file is being added to the repository, please add the BSD 3-Clause license to it.
 
 
-You can also check for common programming errors with the following
-tools:
-
--  Code with good unittest **coverage** (at least 80%), check with:
-
+First install openml with its test dependencies by running
   ```bash
-  $ pip install pytest pytest-cov
-  $ pytest --cov=. path/to/tests_for_package
+  $ pip install -e .[test]
   ```
-
--  No style warnings, check with:
-
+from the repository folder.
+Then configure pre-commit through
+ ```bash
+ $ pre-commit install
+ ```
+This will install dependencies to run unit tests, as well as [pre-commit](https://pre-commit.com/).
+To run the unit tests, and check their code coverage, run:
   ```bash
-  $ pip install flake8
-  $ flake8 --ignore E402,W503 --show-source --max-line-length 100
+  $ pytest --cov=. path/to/tests_for_package
   ```
-
--  No mypy (typing) issues, check with:
-
+Make sure your code has good unittest **coverage** (at least 80%).
+
+Pre-commit is used for various style checking and code formatting.
+Before each commit, it will automatically run:
+ - [black](https://black.readthedocs.io/en/stable/) a code formatter.
+   This will automatically format your code.
+   Make sure to take a second look after any formatting takes place,
+   if the resulting code is very bloated, consider a (small) refactor.
+   *note*: If Black reformats your code, the commit will automatically be aborted.
+   Make sure to add the formatted files (back) to your commit after checking them.
+ - [mypy](https://mypy.readthedocs.io/en/stable/) a static type checker.
+   In particular, make sure each function you work on has type hints.
+ - [flake8](https://flake8.pycqa.org/en/latest/index.html) style guide enforcement.
+   Almost all of the black-formatted code should automatically pass this check,
+   but make sure to make adjustments if it does fail.
+    
+If you want to run the pre-commit tests without doing a commit, run:
   ```bash
-  $ pip install mypy
-  $ mypy openml --ignore-missing-imports --follow-imports skip
+  $ pre-commit run --all-files
   ```
+Make sure to do this at least once before your first commit to check your setup works.
 
-Filing bugs
------------
-We use GitHub issues to track all bugs and feature requests; feel free to
-open an issue if you have found a bug or wish to see a feature implemented.
-
-It is recommended to check that your issue complies with the
-following rules before submitting:
-
--  Verify that your issue is not being currently addressed by other
-   [issues](https://github.com/openml/openml-python/issues)
-   or [pull requests](https://github.com/openml/openml-python/pulls).
-
--  Please ensure all code snippets and error messages are formatted in
-   appropriate code blocks.
-   See [Creating and highlighting code blocks](https://help.github.com/articles/creating-and-highlighting-code-blocks).
+Executing a specific unit test can be done by specifying the module, test case, and test.
+To obtain a hierarchical list of all tests, run
 
--  Please include your operating system type and version number, as well
-   as your Python, openml, scikit-learn, numpy, and scipy versions. This information
-   can be found by running the following code snippet:
+  ```bash
+  $  pytest --collect-only
+
+    <Module 'tests/test_datasets/test_dataset.py'>
+      <UnitTestCase 'OpenMLDatasetTest'>
+        <TestCaseFunction 'test_dataset_format_constructor'>
+        <TestCaseFunction 'test_get_data'>
+        <TestCaseFunction 'test_get_data_rowid_and_ignore_and_target'>
+        <TestCaseFunction 'test_get_data_with_ignore_attributes'>
+        <TestCaseFunction 'test_get_data_with_rowid'>
+        <TestCaseFunction 'test_get_data_with_target'>
+      <UnitTestCase 'OpenMLDatasetTestOnTestServer'>
+        <TestCaseFunction 'test_tagging'>
+   ```
 
-  ```python
-  import platform; print(platform.platform())
-  import sys; print("Python", sys.version)
-  import numpy; print("NumPy", numpy.__version__)
-  import scipy; print("SciPy", scipy.__version__)
-  import sklearn; print("Scikit-Learn", sklearn.__version__)
-  import openml; print("OpenML", openml.__version__)
-  ```
+You may then run a specific module, test case, or unit test respectively:
+```bash
+  $ pytest tests/test_datasets/test_dataset.py
+  $ pytest tests/test_datasets/test_dataset.py::OpenMLDatasetTest
+  $ pytest tests/test_datasets/test_dataset.py::OpenMLDatasetTest::test_get_data
+```
 
-New contributor tips
---------------------
+*NOTE*: In the case the examples build fails during the Continuous Integration test online, please 
+fix the first failing example. If the first failing example switched the server from live to test 
+or vice-versa, and the subsequent examples expect the other server, the ensuing examples will fail 
+to be built as well.
 
-A great way to start contributing to openml-python is to pick an item
-from the list of [Good First Issues](https://github.com/openml/openml-python/labels/Good%20first%20issue)
-in the issue tracker. Resolving these issues allow you to start
-contributing to the project without much prior knowledge. Your
-assistance in this area will be greatly appreciated by the more
-experienced developers as it helps free up their time to concentrate on
-other issues.
+Happy testing!
 
 Documentation
 -------------
 
 We are glad to accept any sort of documentation: function docstrings,
-reStructuredText documents (like this one), tutorials, etc.
+reStructuredText documents, tutorials, etc.
 reStructuredText documents live in the source code repository under the
 doc/ directory.
 

Makefile

@@ -9,7 +9,7 @@ all: clean inplace test
 
 clean:
 	$(PYTHON) setup.py clean
-	rm -rf dist
+	rm -rf dist openml.egg-info
 
 in: inplace # just a shortcut
 inplace:

README.md

@@ -1,9 +1,14 @@
-[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+# OpenML-Python
 
 A python interface for [OpenML](http://openml.org), an online platform for open science collaboration in machine learning.
 It can be used to download or upload OpenML data such as datasets and machine learning experiment results.
-You can find the documentation on the [openml-python website](https://openml.github.io/openml-python).
-If you wish to contribute to the package, please see our [contribution guidelines](https://github.com/openml/openml-python/blob/develop/CONTRIBUTING.md).
+
+## General
+
+* [Documentation](https://openml.github.io/openml-python).
+* [Contribution guidelines](https://github.com/openml/openml-python/blob/develop/CONTRIBUTING.md).
+
+[![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 
 Master branch:
 
@@ -16,3 +21,22 @@ Development branch:
 [![Build Status](https://travis-ci.org/openml/openml-python.svg?branch=develop)](https://travis-ci.org/openml/openml-python)
 [![Build status](https://ci.appveyor.com/api/projects/status/blna1eip00kdyr25/branch/develop?svg=true)](https://ci.appveyor.com/project/OpenML/openml-python/branch/develop)
 [![Coverage Status](https://coveralls.io/repos/github/openml/openml-python/badge.svg?branch=develop)](https://coveralls.io/github/openml/openml-python?branch=develop)
+
+## Citing OpenML-Python
+
+If you use OpenML-Python in a scientific publication, we would appreciate a reference to the
+following paper:
+
+[Matthias Feurer, Jan N. van Rijn, Arlind Kadra, Pieter Gijsbers, Neeratyoy Mallik, Sahithya Ravi, Andreas Müller, Joaquin Vanschoren, Frank Hutter<br/>
+**OpenML-Python: an extensible Python API for OpenML**<br/>
+*arXiv:1911.02490 [cs.LG]*](https://arxiv.org/abs/1911.02490)
+
+Bibtex entry:
+```bibtex
+@article{feurer-arxiv19a,
+  author    = {Matthias Feurer and Jan N. van Rijn and Arlind Kadra and Pieter Gijsbers and Neeratyoy Mallik and Sahithya Ravi and Andreas Müller and Joaquin Vanschoren and Frank Hutter},
+  title     = {OpenML-Python: an extensible Python API for OpenML},
+  journal   = {arXiv:1911.02490},
+  year      = {2019},
+}
+```

appveyor.yml

@@ -5,10 +5,10 @@ environment:
 #     CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\appveyor\\scikit-learn-contrib\\run_with_env.cmd"
 
  matrix:
-    - PYTHON: "C:\\Python35-x64"
-      PYTHON_VERSION: "3.5"
+    - PYTHON: "C:\\Python3-x64"
+      PYTHON_VERSION: "3.6"
       PYTHON_ARCH: "64"
-      MINICONDA: "C:\\Miniconda35-x64"
+      MINICONDA: "C:\\Miniconda36-x64"
 
 matrix:
     fast_finish: true
@@ -35,7 +35,9 @@ install:
   # Install the build and runtime dependencies of the project.
   - "cd C:\\projects\\openml-python"
   - "pip install .[examples,test]"
-  - conda install --quiet --yes scikit-learn=0.20.0
+  - "pip install scikit-learn==0.21"
+  # Uninstall coverage, as it leads to an error on appveyor
+  - "pip uninstall -y pytest-cov"
 
 
 # Not a .NET project, we build scikit-learn in the install step instead