[WIP] Save models to hdf5 and other formats

.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.

CHANGELOG.md

@@ -51,6 +51,13 @@ bound constraint on warping path length
 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

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/

CONTRIBUTING.md

@@ -16,3 +16,121 @@ We are welcoming contributions in the following forms:
 If you would like to contribute by implementing a new feature reported in the Issues, maybe starting with [Issues that are attached the "good first issue" label](https://github.com/rtavenar/tslearn/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22) would be a good idea.
 
 When submitting code, please think about code quality, adding proper docstrings including doctests with high code coverage.
+
+## More details on Pull requests
+
+The preferred workflow for contributing to tslearn is to fork the
+[main repository](https://github.com/rtavenar/tslearn) on
+GitHub, clone, and develop on a branch. Steps:
+
+1. Fork the [project repository](https://github.com/rtavenar/tslearn)
+   by clicking on the 'Fork' button near the top right of the page. This creates
+   a copy of the code under your GitHub user account. For more details on
+   how to fork a repository see [this guide](https://help.github.com/articles/fork-a-repo/).
+
+2. Clone your fork of the tslearn repo from your GitHub account to your local disk:
+
+   ```bash
+   $ git clone git@github.com:YourLogin/tslearn.git
+   $ cd tslearn
+   ```
+
+3. Create a ``feature`` branch to hold your development changes:
+
+   ```bash
+   $ git checkout -b my-feature
+   ```
+
+   Always use a ``feature`` branch. It's good practice to never work on the ``master`` branch!
+
+4. Develop the feature on your feature branch. Add changed files using ``git add`` and then ``git commit`` files:
+
+   ```bash
+   $ git add modified_files
+   $ git commit
+   ```
+
+   to record your changes in Git, then push the changes to your GitHub account with:
+
+   ```bash
+   $ git push -u origin my-feature
+   ```
+
+5. Follow [these instructions](https://help.github.com/articles/creating-a-pull-request-from-a-fork)
+to create a pull request from your fork. This will send an email to the committers.
+
+(If any of the above seems like magic to you, please look up the
+[Git documentation](https://git-scm.com/documentation) on the web, or ask a friend or another contributor for help.)
+
+### Pull Request Checklist
+
+We recommended that your contribution complies with the
+following rules before you submit a pull request:
+
+-  Follow the PEP8 Guidelines.
+
+-  If your pull request addresses an issue, please use the pull request title
+   to describe the issue and mention the issue number in the pull request description. 
+   This will make sure a link back to the original issue is created.
+
+-  All public methods should have informative docstrings with sample
+   usage presented as doctests when appropriate.
+
+-  Please prefix the title of your pull request with `[MRG]` (Ready for
+   Merge), if the contribution is complete and ready for a detailed review.
+   An incomplete contribution -- where you expect to do more work before
+   receiving a full review -- should be prefixed `[WIP]` (to indicate a work
+   in progress) and changed to `[MRG]` when it matures. WIPs may be useful
+   to: indicate you are working on something to avoid duplicated work,
+   request broad review of functionality or API, or seek collaborators.
+   WIPs often benefit from the inclusion of a
+   [task list](https://github.com/blog/1375-task-lists-in-gfm-issues-pulls-comments)
+   in the PR description.
+
+-  When adding additional functionality, provide at least one
+   example script in the ``tslearn/docs/examples/`` folder. Have a look at other
+   examples for reference. Examples should demonstrate why the new
+   functionality is useful in practice and, if possible, compare it
+   to other methods available in tslearn.
+
+-  Documentation and high-coverage tests are necessary for enhancements to be
+   accepted. Bug-fixes or new features should be provided with 
+   [non-regression tests](https://en.wikipedia.org/wiki/Non-regression_testing).
+   These tests verify the correct behavior of the fix or feature. In this
+   manner, further modifications on the code base are granted to be consistent
+   with the desired behavior.
+   For the Bug-fixes case, at the time of the PR, this tests should fail for
+   the code base in master and pass for the PR code.
+
+-  At least one paragraph of narrative documentation with links to
+   references in the literature (with PDF links when possible) and
+   the example.
+
+You can also check for common programming errors with the following
+tools:
+
+
+-  No pyflakes warnings, check with:
+
+  ```bash
+  $ pip install pyflakes
+  $ pyflakes path/to/module.py
+  ```
+
+-  No PEP8 warnings, check with:
+
+  ```bash
+  $ pip install pep8
+  $ pep8 path/to/module.py
+  ```
+
+-  AutoPEP8 can help you fix some of the easy redundant errors:
+
+  ```bash
+  $ pip install autopep8
+  $ autopep8 path/to/pep8.py
+  ```
+
+Bonus points for contributions that include a performance analysis with
+a benchmark script and profiling output (please report on the mailing
+list or on the GitHub issue).

README.md

@@ -43,28 +43,24 @@ Using `pip` should also work fine:
 pip install tslearn
 ```
 
+In this case, you should have `numpy`, `cython` and C++ build tools available
+at build time.
+
 ## Using latest github-hosted version
 
-If you want to get `tslearn`'s latest version, you can refer to the repository hosted at github:
+If you want to get `tslearn`'s latest version, you can refer to the repository 
+hosted at github:
 ```bash
 pip install git+https://github.com/rtavenar/tslearn.git
 ```
 
-## Troubleshooting
-
-It seems on some platforms `Cython` dependency does not install properly.
-If you experiment such an issue, try installing it with the following command:
-
-```bash
-pip install cython
-```
-
-before you start installing `tslearn`.
-If it still does not work, we suggest you switch to `conda` installation.
+In this case, you should have `numpy`, `cython` and C++ build tools available
+at build time.
 
 # Documentation and API reference
 
-The documentation, including a gallery of examples, is hosted at [readthedocs](http://tslearn.readthedocs.io/en/latest/index.html).
+The documentation, including a gallery of examples, is hosted at 
+[readthedocs](http://tslearn.readthedocs.io/en/latest/index.html).
 
 # Already available
 

requirements.txt

@@ -6,3 +6,4 @@ scikit-learn
 joblib>=0.12
 tensorflow<2
 keras
+h5py

requirements_rtd.txt

@@ -8,7 +8,7 @@ ipykernel
 nbsphinx
 sphinx-gallery
 pillow
-tensorflow
+tensorflow<2
 keras
 Pygments
 numba

setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 from codecs import open
 import numpy
 import os
@@ -22,7 +22,7 @@
     long_description=README,
     long_description_content_type='text/markdown',
     include_dirs=[numpy.get_include()],
-    packages=['tslearn'],
+    packages=find_packages(),
     package_data={"tslearn": [".cached_datasets/Trace.npz"]},
     data_files=[("", ["LICENSE"])],
     install_requires=['numpy', 'scipy', 'scikit-learn', 'Cython', 'numba',

tslearn/__init__.py

@@ -1,7 +1,7 @@
 import os
 
 __author__ = 'Romain Tavenard romain.tavenard[at]univ-rennes2.fr'
-__version__ = "0.2.3"
+__version__ = "0.2.5"
 __bibtex__ = r"""@misc{tslearn,
  title={tslearn: A machine learning toolkit dedicated to time-series data},
  author={Tavenard, Romain and Faouzi, Johann and Vandewiele, Gilles},