Commit graph

660 commits

Author SHA1 Message Date
Sergiu Ivanov
12cc862c94 Start the documentation. 2020-11-29 00:02:06 +01:00
Sergiu Ivanov
ae21ea6464 README: Update the roadmap. 2020-11-28 23:26:03 +01:00
Sergiu Ivanov
34fe8a8316 Merge branch 'network-domains' 2020-11-28 23:21:34 +01:00
Sergiu Ivanov
68afb6231a example: Update Threshold Boolean networks. 2020-11-28 23:20:14 +01:00
Sergiu Ivanov
d7d3717c83 networks: Fix build-tbn-state-graph. 2020-11-28 23:12:49 +01:00
Sergiu Ivanov
6c30120376 networks: Remove 01-related state graph functions.
Remove build-full-01-state-graph and
build-full-01-state-graph-annotated.
2020-11-28 23:10:18 +01:00
Sergiu Ivanov
5419278462 networks,tbn->network: Use make-01-network.
Also add some tests.
2020-11-28 23:05:56 +01:00
Sergiu Ivanov
c0ec7369fd networks: Add make-01-network. 2020-11-28 23:01:57 +01:00
Sergiu Ivanov
ce2d10526a example: Update Random functions and networks. 2020-11-28 22:55:44 +01:00
Sergiu Ivanov
5fc4875adf networks: Make table->network infer the domains. 2020-11-28 22:46:43 +01:00
Sergiu Ivanov
a1085d50b8 example: Update Tabulating functions and networks. 2020-11-26 23:26:53 +01:00
Sergiu Ivanov
83deda31a9 example: Stage a forgotten figure. 2020-11-26 23:20:58 +01:00
Sergiu Ivanov
dae4f6570f example: Update the section on Boolean networks. 2020-11-26 23:20:44 +01:00
Sergiu Ivanov
8f9740d2d7 network: Fix the tests for interaction graphs. 2020-11-26 22:36:19 +01:00
Sergiu Ivanov
cdb2149358 network: Fix table->network. 2020-11-26 22:25:25 +01:00
Sergiu Ivanov
a074258b1a networks: Rename and generalize state graph functions.
build-full-state-graph and build-full-state-graph-annotated now
retrieve the domains from the network and are not limited to Boolean
state graphs.
2020-11-26 22:13:57 +01:00
Sergiu Ivanov
34ceccc446 networks: Fix build-syntactic-interaction-graph. 2020-11-23 23:16:11 +01:00
Sergiu Ivanov
fbd6ded717 networks: Fix list-syntactic-interactions. 2020-11-23 23:09:23 +01:00
Sergiu Ivanov
0a4035d9f7 networks: Fix the tests of make-boolean-network-form. 2020-11-22 23:00:26 +01:00
Sergiu Ivanov
f016fbb0ca networks: Fix the tests for network-form->network. 2020-11-22 22:58:21 +01:00
Sergiu Ivanov
354fad2b1d network: Roll back update to its previous version.
I thought I was clever to rewrite update using for/hash, but in fact
this new version only included the updated variables in the new
state :D
2020-11-22 22:50:29 +01:00
Sergiu Ivanov
3abf548ac2 networks: Bug in update. 2020-11-22 22:44:04 +01:00
Sergiu Ivanov
eb3e851a9d networks: Make network and network-form transparent. 2020-11-22 22:38:45 +01:00
Sergiu Ivanov
ff6fa2c88b network: Fix the test for make-boolean-network. 2020-11-22 22:11:25 +01:00
Sergiu Ivanov
b38adc89cf networks: Don't use tabulate-boolean-network. 2020-11-22 22:08:45 +01:00
Sergiu Ivanov
e4751c6ed2 networks: Don't re-export network-form?. 2020-11-22 22:05:41 +01:00
Sergiu Ivanov
0085eb964b networks: Fix make-boolean-network. 2020-11-22 22:02:56 +01:00
Sergiu Ivanov
5475bc5fbf networks: Fix Random networks. 2020-11-22 21:58:00 +01:00
Sergiu Ivanov
2c68055818 networks: Fix constructing functions and networks. 2020-11-22 21:42:41 +01:00
Sergiu Ivanov
3a2453c92e networks: Fix tabulating functions and networks. 2020-11-22 21:41:06 +01:00
Sergiu Ivanov
fd651ba4cc network,Dynamics: Fixes. 2020-11-22 21:35:19 +01:00
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