Commit graph

579 commits

Author SHA1 Message Date
Sergiu Ivanov
6cfa66694d networks: Remove read-org-network-make-asyn and read-org-network-make-syn.
I think I initially intended these functions for Boolean networks.
I'll see if I add back something similar to these when I will be
fixing example.org.
2020-11-22 21:33:16 +01:00
Sergiu Ivanov
97026a2a42 networks: Say that domain mappings may be empty. 2020-11-22 21:30:50 +01:00
Sergiu Ivanov
27bb25c201 networks: Fix signed interaction graphs. 2020-11-22 21:26:26 +01:00
Sergiu Ivanov
3e35b8e0ab networks, IG: Use forms->boolean-network.
IG = interaction graph
2020-11-22 21:24:05 +01:00
Sergiu Ivanov
ec3c74b5e2 networks: Add forms->boolean-network. 2020-11-22 21:21:31 +01:00
Sergiu Ivanov
a4979d9c9f networks: Add make-boolean-network-form. 2020-11-22 21:18:22 +01:00
Sergiu Ivanov
d5e1819fff networks: Add make-boolean-network. 2020-11-22 21:18:14 +01:00
Sergiu Ivanov
6fd3d41c7e networks: Update the IG-related functions.
IG = interaction graph
2020-11-22 21:06:33 +01:00
Sergiu Ivanov
393f1d2bba networks: Move domain-mapping/c to Basic definitions. 2020-11-22 20:46:53 +01:00
Sergiu Ivanov
cb208a66fc networks: Add one more comment on syntactic IG vs. IG. 2020-11-22 20:42:30 +01:00
Sergiu Ivanov
b8f29d905d networks: Remove make-network-from-forms. 2020-11-22 00:29:36 +01:00
Sergiu Ivanov
236dca704d networks: Update network-form->network. 2020-11-22 00:27:56 +01:00
Sergiu Ivanov
ed03015e81 network: Add domains to network-form. 2020-11-22 00:24:15 +01:00
Sergiu Ivanov
cfe710e6b2 network: Don't use make-network-from-functions in basic definitions. 2020-11-22 00:08:46 +01:00
Sergiu Ivanov
11d75bcc89 networks: Rewrite update. 2020-11-21 23:28:30 +01:00
Sergiu Ivanov
6560dcbe6c networks: Move booleanize-state before its own test case. 2020-11-21 23:15:17 +01:00
Sergiu Ivanov
a654ac5896 network: Remove make-network-from-forms. 2020-11-21 23:13:50 +01:00
Sergiu Ivanov
004e24d83c README: Remove the TODO item about the interaction graphs. 2020-11-21 23:04:14 +01:00
Sergiu Ivanov
a3ac1c7fcd networks: Include domains into the network.
This change is breaking.  The following commits will progressively fix
the whole network module.
2020-11-21 22:53:45 +01:00
Sergiu Ivanov
f1a1123cc4 networks: Make it possible to skip expensive test cases.
At the moment, this is particularly for skipping the tests
constructing the interaction graphs.
2020-11-21 00:53:11 +01:00
Sergiu Ivanov
097c5a7f09 example: Update the presentation of the functions concerning the interaction graphs. 2020-11-19 23:48:50 +01:00
Sergiu Ivanov
fe0fbc3ed0 networks: Add build-signed-interaction-graph/form. 2020-11-19 00:22:01 +01:00
Sergiu Ivanov
0345cd3648 networks: Add build-interaction-graph/form. 2020-11-19 00:14:54 +01:00
Sergiu Ivanov
8e100c2e8b networks: Add build-signed-interaction-graph. 2020-11-18 01:11:37 +01:00
Sergiu Ivanov
0313d81c25 network: Add another self-loop test for get-interaction-sign. 2020-11-18 01:08:40 +01:00
Sergiu Ivanov
c55113f27e network: Bug fix in get-interaction-sign. 2020-11-18 00:46:55 +01:00
Sergiu Ivanov
195d71ed4e networks: Remove interaction? from the tests for get-interaction-sign. 2020-11-18 00:29:45 +01:00
Sergiu Ivanov
a8adc9fb57 README: Add a new TODO item for splitting network into two models. 2020-11-18 00:19:53 +01:00
Sergiu Ivanov
af8428d275 network,build-interaction-graph: Use in-list. 2020-11-18 00:13:00 +01:00
Sergiu Ivanov
d190f76fdf networks: Add build-interaction-graph. 2020-11-18 00:09:15 +01:00
Sergiu Ivanov
ff9654e5c6 network: Add get-interaction-sign. 2020-11-17 23:38:34 +01:00
Sergiu Ivanov
bfc48ff453 networks: Slightly optimize interaction?. 2020-11-15 00:02:44 +01:00
Sergiu Ivanov
8a1f4c682e networks: Add interaction?. 2020-11-14 23:15:39 +01:00
Sergiu Ivanov
d24dadd4cd example: Stage all the figures. 2020-11-12 22:56:53 +01:00
Sergiu Ivanov
ce0925e41e networks: Remove the old functions for building interaction graphs.
These functions mix interaction graphs derived from the expressions
defining the network with deriving the interactions from the dynamics,
which does not always yield the same result.  Also, some functions
only worked for Boolean networks, including get-interaction-sign.
Additionally, these functions are among the first ones I wrote in dds,
so there are a couple of things which can be written in a better way.
2020-11-12 22:54:04 +01:00
Sergiu Ivanov
70de0ec718 README: Add the milestone about the domains. 2020-11-12 17:22:43 +01:00
Sergiu Ivanov
a8f4850139 README: Expand the milestone about interaction graphs. 2020-11-12 17:22:17 +01:00
Sergiu Ivanov
99c74ba659 README: Expand the Scribble milestone to types and include more details. 2020-11-12 17:08:00 +01:00
Sergiu Ivanov
7de4c5ef71 README: Add the Roadmap. 2020-11-12 16:40:24 +01:00
Sergiu Ivanov
60be01d979 networks: Fix and simplify the comment of Inferring interaction graphs. 2020-11-12 01:11:15 +01:00
Sergiu Ivanov
5ece1f6c88 networks: list-interactions → list-syntactic-interactions. 2020-11-12 01:09:18 +01:00
Sergiu Ivanov
681ed0e732 networks: Simplify and fix the comment of update. 2020-11-12 01:08:10 +01:00
Sergiu Ivanov
88caecb98a networks: Properly export dynamics. 2020-11-12 01:07:41 +01:00
Sergiu Ivanov
6d77052ed6 network: Explain why a network does not include the domains. 2020-11-12 01:05:27 +01:00
Sergiu Ivanov
5fd1e5cb5b Revert "BREAKING: Make domains part of the network."
This reverts commit f414ae8966.
2020-11-12 01:03:48 +01:00
Sergiu Ivanov
f414ae8966 BREAKING: Make domains part of the network.
I always keep bringing domains about for my network, which complicates
things a lot.  This commit packages the domains within the network,
which will break a lot of stuff :-) The following commits will fix it all.
2020-11-12 00:58:58 +01:00
Sergiu Ivanov
cde6ee30fa networks: build-interaction-graph → build-syntactic-interaction-graph.
The interaction graph is *not* usually defined in this way.
2020-11-11 15:51:24 +01:00
Sergiu Ivanov
af581f91df example: Illustrate build-reduced-state-graph. 2020-11-11 00:37:12 +01:00
Sergiu Ivanov
3b8ce5eb84 rs: Add pretty-print-reduced-state-graph. 2020-11-11 00:36:49 +01:00
Sergiu Ivanov
ce0d5023bf rs: Add build-reduced-state-graph. 2020-11-10 09:42:50 +01:00