Added parameters and changed custom REF inputs (#51)

* Resurrected backward REF, added REF join argument

* Fixed #38, moved notes+examples to docs

* Removed log

* Merger 'master' into 'dev' (#44)

* Dev (#39)

* Resurrected backward REF, added REF join argument

* Fixed #38, moved notes+examples to docs

* Removed log

* Updated changelog, bumped version docs conf file

* squash! Dev (#39)

* Removed unused import and useless-else-on-loop

* Updated examples in the paper

* Paper updated. Removed spacing in example bullets

* Paper updated. Added spacing for example bullets

* Add more clear explanation in docs #15

* Remove deque map and swo file

* Update commit vrpy submodule

* Update CHANGELOG for JOSS release

* Patch41 (#45)

* Dev (#39)

* Resurrected backward REF, added REF join argument

* Fixed #38, moved notes+examples to docs

* Removed log

* Updated changelog, bumped version docs conf file

* squash! Dev (#39)

* Removed unused import and useless-else-on-loop

* Updated examples in the paper

* Paper updated. Removed spacing in example bullets

* Paper updated. Added spacing for example bullets

* Add more clear explanation in docs #15

* Remove deque map and swo file

* Add test for issue and fix for some cases of #41

* Uncomment mono directional tests

* Patch43 (#48)

* Dev (#39)

* Resurrected backward REF, added REF join argument

* Fixed #38, moved notes+examples to docs

* Removed log

* Updated changelog, bumped version docs conf file

* squash! Dev (#39)

* Removed unused import and useless-else-on-loop

* Updated examples in the paper

* Paper updated. Removed spacing in example bullets

* Paper updated. Added spacing for example bullets

* Add more clear explanation in docs #15

* Remove deque map and swo file

* Update commit vrpy submodule

* Update CHANGELOG for JOSS release

* Initial redesign (failing unittests)

* Remove duplicate imports

* Refactored by Sourcery (#46)

Co-authored-by: Sourcery AI <bot@sourcery.ai>

* Move bidirectional files to algorithms, some fixes

- Fix some tests: tests_issue20 (broken for parallel), tests_issue38
- Moved random state checks to checking.py

* Fix unit tests! Clean up

* Clean up BiDirectional, add kwargs for custom REFs

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>
Co-authored-by: Sourcery AI <bot@sourcery.ai>

* Update README.md

* Revert function in BiDirectional

- Add time limit and threshold parameters
- Add greedy_elimination unit tests (#9)

* Revert to v0.1.1 based fixes

- Clean up in tests
- Update submodule commit

* Remove unused import

* 'Refactored by Sourcery'

* Update path base break using threshold

* Remove search object

* Update tests and docs

Co-authored-by: sourcery-ai[bot] <58596630+sourcery-ai[bot]@users.noreply.github.com>
Co-authored-by: Sourcery AI <bot@sourcery.ai>
Co-authored-by: Sourcery AI <>

CHANGELOG.md

@@ -7,24 +7,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [unreleased]
 
+### Added
+
+- New paramenters: `time_limit` and `threshold`.
+- Custom REF, backward incompatible change: additional argument for more flexibility. These are the current partial path and the accumulated cost. Note that these are optional and do not have to be used. However, a slight modificiation to the function has to be made, simply add `**kwargs` as well as the existing arguments.
+
 ## [v0.1.1] - 21/05/2020
 
 ### Changed
 - BiDirectional:
   - Reverted backward REF as it is required for some problems.
   - Added REF join parameter that is required when joining forward and backward labels using custom REFs.
-- Moved notes and examples from docstrings to the docs folder. 
+- Moved notes and examples from docstrings to the docs folder.
 - Final JOSS paper changes
 
 ## [v0.1.0] - 14/04/2020
 
-### Added 
+### Added
 
 - BiDirectional:
   - Option to chose method for direction selection.
 - [vrpy](https://github.com/Kuifje02/vrpy) submodule.
 
-### Changed 
+### Changed
 
 - BiDirectional:
   - Label storage, divided into unprocessed, generated and non-dominated labels

README.md

@@ -4,7 +4,6 @@
 [![codecov](https://codecov.io/gh/torressa/cspy/branch/master/graph/badge.svg?token=24tyrWinNT)](https://codecov.io/gh/torressa/cspy)
 [![Codacy Badge](https://api.codacy.com/project/badge/Grade/c28f50e92dae4bcc921f1bd142370608)](https://www.codacy.com/app/torressa/cspy?utm_source=github.com&utm_medium=referral&utm_content=torressa/cspy&utm_campaign=Badge_Grade)
 [![JOSS badge](https://joss.theoj.org/papers/25eda55801a528b982d03a6a61f7730d/status.svg)](https://joss.theoj.org/papers/25eda55801a528b982d03a6a61f7730d)
-![PyPI - Python Version](https://img.shields.io/pypi/pyversions/cspy)
 
 <!-- [![BCH compliance](https://bettercodehub.com/edge/badge/torressa/cspy?branch=master)](https://bettercodehub.com/)
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT) -->
@@ -67,6 +66,10 @@ python3 -m pip install cspy
 
 ### Examples
 
+- [`vrpy`](https://github.com/Kuifje02/vrpy) : External vehicle routing framework which uses `cspy` to solve different variants of the vehicle routing problem using column generation.
+- [`cgar`](examples/cgar) : Complex example use of `cspy` in a column generation example applied to the aircraft recovery problem.
+- [`jpath`](examples/jpath) : Simple example showing the necessary graph adptations and the use of custom resource extension functions.
+
 The generic gist to run the algorithms on a specific graph is to load the
 algorithm of choice, say `alg`, call the `alg.run()` method, and query the
 relevant result attributes,
@@ -75,13 +78,6 @@ relevant result attributes,
 - `alg.total_cost` for the accumulated cost of the path;
 - `alg.consumed_resources` for the accumulated resource usage of the path.
 
-I have included a few examples:
-
-- [`jpath`](examples/jpath) : Simple example showing the necessary graph adptations and the use of custom resource extension functions.
-- [`cgar`](examples/cgar) : Complex example use of `cspy` in a column generation example applied to the aircraft recovery problem.
-- [`vrpy`](https://github.com/Kuifje02/vrpy) : (under development) external vehicle routing framework which uses `cspy` to solve different variants of the vehicle routing problem using column generation.
-
-
 ## Running the tests
 
 To run the tests first, clone the repository into a path in your machine `~/path/newfolder` by running
@@ -124,17 +120,23 @@ After that feel free to send a pull request.
 
 If you have a question or need help, feel free to raise an issue explaining it.
 
-Alternatively, email me at `d.torressanchez@lancs.ac.uk`.
+Alternatively, email me at `david.sanchez@sintef.no`.
 
 ## Citing
 
 If you'd like to cite this package, please use the following bib format:
 
 ```none
-@Misc{cspy,
-  author = {Torres Sanchez, David},
-  title = {{cspy : A Python package with a collection of algorithms for the (Resource) Constrained Shortest Path problem}},
-  year = {2019},
-  url = {\url{https://github.com/torressa/cspy}}
+@article{torressa2020,
+  doi = {10.21105/joss.01655},
+  url = {https://doi.org/10.21105/joss.01655},
+  year = {2020},
+  publisher = {The Open Journal},
+  volume = {5},
+  number = {49},
+  pages = {1655},
+  author = {{Torres Sanchez}, David},
+  title = {cspy: A Python package with a collection of algorithms for the (Resource) Constrained Shortest Path problem},
+  journal = {Journal of Open Source Software}
 }
 ```