Merge branch 'master' into improve-testing

Author: felixdivo

.github/FUNDING.yml

@@ -0,0 +1,3 @@
+# These are supported funding model platforms
+
+github: rtavenar

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,24 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+A short code sample to reproduce the code
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Environment (please complete the following information):**
+ - OS: [e.g. iOS]
+ - tslearn version [e.g. 0.2.2]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,14 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: new feature
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.

.readthedocs.yml

@@ -0,0 +1,28 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: tslearn/docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: tslearn/docs/requirements_rtd.txt
+    - method: setuptools
+      path: .
+
+build:
+  image: latest

.travis.yml

@@ -25,13 +25,17 @@ install:
 - conda config --set always_yes yes --set changeps1 no
 - conda update -q conda
 - conda info -a
-- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION Cython numpy>=1.14 scipy tensorflow keras
-  scikit-learn numba joblib>=0.12
+- conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION Cython numpy>=1.14 scipy tensorflow==1.* keras
+  scikit-learn numba joblib>=0.12 pandas
 - source activate test-environment
 - pip install pytest
+- if [[ "$TRAVIS_PYTHON_VERSION" == 3.* ]];
+  then pip install cesium;
+  else export DO_NOT_TEST_CESIUM_CAST=1;
+  fi
 - if [[ "$NUMBA_DISABLE_JIT" == 1 ]]; then pip install coverage==4.3 "pytest-cov<2.6"; fi
 - pip install argparse
-- pip install codeclimate-test-reporter
+- pip install codeclimate-test-reporter codecov
 - rm -f tslearn/*.c
 - python setup.py build_ext --inplace
 
@@ -40,10 +44,14 @@ script:
 - python -c "import keras.backend";
   sed -i -e 's/"backend":[[:space:]]*"[^"]*/"backend":\ "'$KERAS_BACKEND'/g' ~/.keras/keras.json;
   echo -e "Running tests with the following config:\n$(cat ~/.keras/keras.json)";
-- if [[ "$NUMBA_DISABLE_JIT" == 1 ]]; then
-  python -m pytest -v tslearn tslearn/tests/ --doctest-modules --ignore tslearn/docs --ignore tslearn/deprecated.py --ignore tslearn/tests/test_estimators.py $KERAS_IGNORE --cov=tslearn;
-  if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then codeclimate-test-reporter; fi
-  else travis_wait 40 python -m pytest -v tslearn tslearn/tests/ --doctest-modules --ignore tslearn/docs --ignore tslearn/deprecated.py $KERAS_IGNORE; fi
+- if [ "$NUMBA_DISABLE_JIT" == 1 ];
+  then python -m pytest -v tslearn tslearn/tests/ --doctest-modules --ignore tslearn/docs --ignore tslearn/deprecated.py $KERAS_IGNORE --cov=tslearn;
+  else python -m pytest -v tslearn tslearn/tests/ --doctest-modules --ignore tslearn/docs --ignore tslearn/deprecated.py $KERAS_IGNORE;
+  fi
+
+after_success:
+- if [ "$NUMBA_DISABLE_JIT" == 1 ]; then codeclimate-test-reporter; fi
+- if [ "$NUMBA_DISABLE_JIT" == 1 ]; then codecov; fi
 
 notifications:
   email: false

CHANGELOG.md

@@ -1,24 +1,109 @@
 # Changelog
 All notable changes to this project will be documented in this file.
 
-The format is based on 
+The format is based on
 [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
-and this project adheres to 
+and this project adheres to
 [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 Changelogs for this project are recorded in this file since v0.2.0.
 
+## [v0.3.1]
+
+### Fixed
+
+* Fixed a bug in `TimeSeriesSVC` and `TimeSeriesSVR` that caused user-input 
+`gamma` to be ignored (always treated as if it were `"auto"`) for `gak` kernel
+
+## [v0.3.0]
+
+### Changed
+
+* `dtw_barycenter_averaging` is made faster by using vectorized computations
+* `dtw_barycenter_averaging` can be restarted several times to reach better
+local optima using a parameter `n_init` set to 1 by default
+* Functions `load_timeseries_txt` and `save_timeseries_txt` from the utils
+module have changed their names to `load_time_series_txt` and 
+`save_time_series_txt`. Old names can still be used but considered deprecated
+and removed from the public API documentation for the sake of harmonization
+* Default value for the maximum number of iterations to train `ShapeletModel` 
+and `SerializableShapeletModel` is now set to 10,000 (used to be 100)
+* `TimeSeriesScalerMeanVariance` and `TimeSeriesScalerMinMax` now ignore any
+NaNs when calling their respective `transform` methods in order to better
+mirror scikit-learn's handling of missing data in preprocessing.
+* `KNeighborsTimeSeries` now accepts variable-length time series as inputs
+when used with metrics that can deal with it (eg. DTW)
+
+### Added
+
+* `KNeighborsTimeSeriesRegressor` is a new regressor based on 
+k-nearest-neighbors that accepts the same metrics as 
+`KNeighborsTimeSeriesClassifier`
+* A `set_weights` method is added to the `ShapeletModel` and  
+`SerializableShapeletModel` estimators
+* `subsequence_path` and `subsequence_cost_matrix` are now part of the public 
+API and properly documented as such with an example use case in which more than
+one path could be of interest (cf. `plot_sdtw.py`)
+* `verbose` levels can be set for all functions / classes that use `joblib`
+for parallel computations and `joblib` levels are used;
+* conversion functions are provided in the `utils` module to interact with
+other Python time series packages (`pyts`, `sktime`, `cesium`, `seglearn`, 
+`tsfresh`, `stumpy`, `pyflux`)
+* `dtw_barycenter_averaging_subgradient` is now available to compute DTW
+barycenter based on subgradient descent
+* `dtw_limited_warping_length` is provided as a way to compute DTW under upper
+bound constraint on warping path length
+* `BaseModelPackage` is a base class for serializing models to hdf5, json and 
+pickle. h5py is added to requirements for hdf5 support.
+* `BaseModelPackage` is used to add serialization functionality to the 
+following models: `GlobalAlignmentKernelKMeans`, `TimeSeriesKMeans`,
+`KShape`, `KNeighborsTimeSeries`, `KNeighborsTimeSeriesClassifier`,
+`PiecewiseAggregateApproximation`, `SymbolicAggregateApproximation`,
+and `OneD_SymbolicAggregateApproximation`
+
+### Changed
+ 
+* When constrained DTW is used, if the name of the constraint is not given but 
+its parameter is set, that is now considered sufficient to identify the 
+constraint.
+
+## [v0.2.4]
+
+### Fixed
+
+* The `tests` subdirectory is now made a python package and hence included in 
+wheels
+
+## [v0.2.2]
+
+### Fixed
+
+* The way version number is retrieved in `setup.py` was not working properly 
+on Python 3.4 (and made the install script fail), switched back to the previous
+version
+
+## [v0.2.1]
+
+### Added
+
+* A `RuntimeWarning` is raised when an `'itakura'` constraint is set
+that is unfeasible given the provided shapes.
+
+### Fixed
+
+* `'itakura'` and `'sakoe_chiba'` were swapped in `metrics.compute_mask`
+
 ## [v0.2.0]
 
 ### Added
 
-* `tslearn` estimators are now automatically tested to match `sklearn` 
-requirements "as much as possible" (cf. `tslearn` needs in 
+* `tslearn` estimators are now automatically tested to match `sklearn`
+requirements "as much as possible" (cf. `tslearn` needs in
 terms of data format, _etc._)
 * `cdist_dtw` and `cdist_gak` now have a `n_jobs` parameter to parallelize
 distance computations using `joblib.Parallel`
-* `n_jobs` is also available as a prameter in 
-`silhouette_score`, `TimeSeriesKMeans`, `KNeighborsTimeSeries`, 
+* `n_jobs` is also available as a prameter in
+`silhouette_score`, `TimeSeriesKMeans`, `KNeighborsTimeSeries`,
 `KNeighborsTimeSeriesClassifier`, `TimeSeriesSVC`,
 `TimeSeriesSVR` and `GlobalAlignmentKernelKMeans`
 
@@ -29,12 +114,12 @@ distance computations using `joblib.Parallel`
 cross-validation tools, even (for those concerned) with variable-length data
 * doctests have been reduced to those necessary for documentation purposes, the
 other tests being moved to `tests/*.py`
-* The list of authors for the `tslearn` bibliographic reference has been 
+* The list of authors for the `tslearn` bibliographic reference has been
 updated to include Johann Faouzi and Gilles Van de Wiele
 * In `TimeSeriesScalerMinMax`, `min` and `max` parameters are now deprecated
 in favor of `value_range`. Will be removed in v0.4
-* In `TimeSeriesKMeans` and `silhouette_score`, `'gamma_sdtw'` is now 
-deprecated as a key for `metric_params` in favor of `gamma`. Will be removed 
+* In `TimeSeriesKMeans` and `silhouette_score`, `'gamma_sdtw'` is now
+deprecated as a key for `metric_params` in favor of `gamma`. Will be removed
 in v0.4
 
 ### Removed

CODE_OF_CONDUCT.md

@@ -0,0 +1,74 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/