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Commit Graph

139 Commits

Author SHA1 Message Date
J. Fernando Sánchez
3526fa29d7 Fix bug parallel 2018-12-09 14:06:50 +01:00
J. Fernando Sánchez
53604c1e66 Fix quickstart.rst markdown code 2018-12-09 13:10:00 +01:00
J. Fernando Sánchez
01cc8e9128 Merge branch 'refactor-imports'
* remove leftover import in example
* Update quickstart tutorial
* Add gitlab-ci
* Added missing gexf for tests
* Upgrade to python3.7 and pandas 0.3.4 because pandas has dropped support for
  python 3.4 -> There are some API changes in pandas, and I've updated the code
  accordingly.
* Set pytest as the default test runner
* Update dockerignore
* Skip testing long examples (>1000 steps)
2018-12-09 12:55:12 +01:00
J. Fernando Sánchez
a47ffa815b Fix CI. Skip testing long examples 2018-12-08 20:49:34 +01:00
J. Fernando Sánchez
b41927d7bf remove leftover import in example 2018-12-08 20:35:02 +01:00
J. Fernando Sánchez
70d033b3a9 Update dockerignore 2018-12-08 19:13:56 +01:00
J. Fernando Sánchez
3afed06656 Add gitlab-ci 2018-12-08 19:08:47 +01:00
J. Fernando Sánchez
0a7ef27844 Added missing gexf for tests 2018-12-08 18:53:12 +01:00
J. Fernando Sánchez
2e28b36f6e Python3.7, testing and bug fixes
* Upgrade to python3.7 and pandas 0.3.4 because pandas has dropped support for
python 3.4 -> There are some API changes in pandas, and I've update the code
accordingly.
* Set pytest as the default test runner
2018-12-08 18:53:06 +01:00
J. Fernando Sánchez
bd4700567e Update quickstart tutorial 2018-12-08 18:17:25 +01:00
J. Fernando Sánchez
ff1df62eec All tests pass 2018-12-08 18:17:21 +01:00
J. Fernando Sánchez
9165979b49 merge visualization branch
The web server is included as a submodule.
The dependencies for the web (tornado) are not installed by default, but they
can be installed as an extra:

```
pip install soil[web]
```

Once installed, the soil web can be used like this:

```
soil-web

OR

python -m soil.web
```

There are other minor changes:

* History re-connects to the sqlite database if it is used from a different
thread.
* Environment accepts additional parameters (so it can run simulations with
`visualization_params` or any other in the future).
* The simulator class is no longer necessary
* Logging is done in the same thread, and the simulation is run in a separate
one. This had to be done because it was creating some problems with tornado not
being able to find the current thread during logs, which caused hundreds of
repeated lines in the web "console".
* The player is slightly modified in this version. I noticed that when the
  visualization was playing, if you clicked somewhere it would change for a
  second, and then go back to the previous place. The code for the playback
  seemed too complex, especially speed control, so I rewrote some parts. I
  might've introduced new bugs.
2018-12-07 18:28:19 +01:00
J. Fernando Sánchez
078f8ace9e Merge commit '8fec544772c13efb1dc8a0589240551b9bad27cb' as 'soil/web' 2018-12-07 18:27:57 +01:00
J. Fernando Sánchez
8fec544772 Squashed 'soil/web/' content from commit 4dcd0fc
git-subtree-dir: soil/web
git-subtree-split: 4dcd0fcb3d
2018-12-07 20:30:24 +01:00
J. Fernando Sánchez
5420501d36 Fix state and networkx dynamic attributes 2018-05-07 18:59:19 +02:00
J. Fernando Sánchez
5d89827ccf Fix history bug 2018-05-04 11:21:23 +02:00
J. Fernando Sánchez
fc48ed7e09 Added history class
Now the environment does not deal with history directly, it delegates it to a
specific class. The analysis also uses history instances instead of either
using the database directly or creating a proxy environment.

This should make it easier to change the implementation in the future.

In fact, the change was motivated by the large size of the csv files in previous
versions. This new implementation only stores results in deltas, and it fills
any necessary values when needed.
2018-05-04 10:01:49 +02:00
J. Fernando Sánchez
73c90887e8 Fix pip installation 2018-05-04 09:59:31 +02:00
J. Fernando Sánchez
497c8a55db Add workaround for geometric models
Closes soil/soil#4
2018-02-16 18:04:43 +01:00
J. Fernando Sánchez
7d1c800490 Parallelism and granular exporting options
* Graphs are not saved by default (not backwards compatible)
* Modified newsspread examples
* More granular options to save results (exporting to CSV and GEXF are now
optional)
* Updated tutorial to include exporting options
* Removed references from environment to simulation
* Added parallelism to simulations (can be turned off with a flag or argument).
2017-11-01 14:44:46 +01:00
J. Fernando Sánchez
a4b32afa2f Fix py3.4 and pypi bugs 2017-10-19 18:28:17 +02:00
J. Fernando Sánchez
a7c51742f6 Improved docs
Fixed several bugs
Added convenience methods in soil.analysis
2017-10-19 18:06:33 +02:00
J. Fernando Sánchez
78364d89d5 Fix gephi representation. Add sqlite 2017-10-17 19:48:56 +02:00
J. Fernando Sánchez
af76f54a28 Added rabbits 2017-10-16 19:23:52 +02:00
J. Fernando Sánchez
dbc182c6d0 Compatibility with py3.4 2017-10-09 14:44:21 +02:00
J. Fernando Sánchez
eafecc9e5e Make py3 compatibility explicit 2017-10-09 11:38:16 +02:00
J. Fernando Sánchez
e8988015e2 Add more options to the command line 2017-10-05 16:21:58 +02:00
J. Fernando Sánchez
ccc8e43416 Removed timeout from the simulation examples 2017-10-05 16:07:10 +02:00
J. Fernando Sánchez
347d295b09 Updated to match NetworkX's 2.0 API 2017-10-05 15:54:18 +02:00
J. Fernando Sánchez
bbc5386cf5 Removed logo from header 2017-07-03 18:41:47 +02:00
J. Fernando Sánchez
f8538fe057 Tidying up the repository 2017-07-03 18:40:00 +02:00
J. Fernando Sánchez
e1be3a730e WIP soil
* Pandas integration
* Improved environment
* Logging and data dumps
* Tests
* Added Finite State Machine models
* Rewritten ipython notebook and documentation
2017-07-03 18:17:52 +02:00
Tasio Mendez
764177c634 Added dynamic graph.
Added dynamic graph to ControlModelM2.
2017-05-19 13:55:04 +02:00
Tasio Mendez
cd9b7e096a Updated tutorial
Close #3
2017-05-17 11:09:44 +02:00
Tasio Mendez
5a2fcb5564 Merge fixed 2017-05-16 14:12:20 +02:00
Tasio Mendez
546ad0343b Merge branch 'models' of https://lab.cluster.gsi.dit.upm.es/soil/soil into models 2017-05-16 14:05:13 +02:00
Tasio Mendez
a643735ddb All settings as JSON and documentation updated 2017-05-16 14:02:50 +02:00
Alberto Pascual
59ec790820 gexf now working, end value added 2017-05-04 14:11:22 +02:00
Tasio Mendez
23fc9671c3 Updated readthedocs 2017-04-27 13:15:56 +02:00
Tasio Mendez
f1bb636ca8 Merge branch 'models' of https://lab.cluster.gsi.dit.upm.es/soil/soil into models 2017-04-27 11:35:44 +02:00
Alberto Pascual
f8d8345d5a requirements added for faster install, settings separated in JSON file, now is possible to run different agent simulations at a time 2017-04-26 11:17:50 +02:00
Tasio Mendez
c011943cef Started readthedocs 2017-04-25 13:27:16 +02:00
Tasio Mendez
aaf5f709f1 Settings models 2017-04-24 12:55:00 +02:00
Tasio Mendez
391ce5e9e0 Changed models 2017-04-21 14:19:26 +02:00
Tasio Mendez
2fc7a91ef3 Settings modules 2017-04-21 14:04:30 +02:00
Tasio Mendez
f29f5fa5bf Settings modules 2017-04-21 13:55:42 +02:00
Tasio Mendez
dd4ce15a3d Separate models in modules 2017-04-20 13:36:17 +02:00
cif2cif
d157a5e0b5 added JSON format 2017-01-28 17:14:58 +01:00
cif2cif
d179c166ed changed typo 2017-01-28 11:50:33 +01:00
cif2cif
00e074faf3 added copyright 2017-01-28 11:46:46 +01:00