Sergiu Ivanov
e2788be237
Add the Scribble files for almost all modules.
...
The generics module will probably disappear or take a different shape
in the near future.
2020-11-29 17:43:20 +01:00
Sergiu Ivanov
8487b64287
Rename manual → dds.
2020-11-29 17:15:24 +01:00
Sergiu Ivanov
596e1b7b5d
Prepare for writing the documentation.
2020-11-29 00:28:46 +01:00
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
