Commit graph

286 commits

Author SHA1 Message Date
Sergiu Ivanov
0018c91fb6 Type list-syntactic-interactions. 2022-05-10 10:41:07 +02:00
Sergiu Ivanov
0336526a84 Type forms->boolean-network. 2022-05-05 11:59:37 +02:00
Sergiu Ivanov
871a923842 Type make-boolean-network-form. 2022-05-05 11:25:10 +02:00
Sergiu Ivanov
7a3cbaa1af Add network-form->network/01. 2022-05-04 01:21:11 +02:00
Sergiu Ivanov
43e29f928b Add network-form->network/boolean. 2022-05-04 01:12:52 +02:00
Sergiu Ivanov
b795be0a39 Type network-form->network as network-form->network/any. 2022-05-03 22:01:13 +02:00
Sergiu Ivanov
181b427cd8 Add update-function-form->update-function/boolean and update-function-form->update-function/01. 2022-05-03 21:41:50 +02:00
Sergiu Ivanov
2c2d8fbbdb update-function-form->update-function → update-function-form->update-function/any 2022-05-03 21:26:36 +02:00
Sergiu Ivanov
320ae55456 Type update-function-form->update-function. 2022-05-03 15:40:23 +02:00
Sergiu Ivanov
b97bbfd972 Type network-form. 2022-05-02 00:27:55 +02:00
Sergiu Ivanov
901720d2f5 Add UpdateFunctionForm. 2022-05-02 00:16:16 +02:00
Sergiu Ivanov
458ba10ab5 Add 01->boolean/state (replacing booleanize-state). 2022-05-01 01:05:35 +02:00
Sergiu Ivanov
aea472acb2 Remove make-state and make-state-booleanize.
make-state is just a longer word for hash, and I never really use
make-state-booleanize.
2022-05-01 00:55:42 +02:00
Sergiu Ivanov
ba30e3dc5e Type update. 2022-05-01 00:33:43 +02:00
Sergiu Ivanov
9a2f1ff527 Type make-01-domains and make-01-network. 2022-04-30 23:21:42 +02:00
Sergiu Ivanov
e867a86d4d Add the type Domain. 2022-04-29 16:10:36 +02:00
Sergiu Ivanov
be729f6ca8 Type make-same-domains, make-boolean-domains, make-boolean-network. 2022-04-29 15:54:15 +02:00
Sergiu Ivanov
883e845d9d Type network and add examples. 2022-04-28 23:47:37 +02:00
Sergiu Ivanov
5efe086d06 Add UpdateFunction and DomainMapping. 2022-04-27 00:15:03 +02:00
Sergiu Ivanov
85566d7479 Start migrating networks to Typed Racket. 2022-04-27 00:10:13 +02:00
Sergiu Ivanov
650801a6d2 Add the untyped submodule to utils. 2022-04-01 00:09:42 +02:00
Sergiu Ivanov
ec50395cb0 networks: Add a copy of lists-transpose.
I will remove this copy when I will have migrated networks to
Typed Racket.
2022-02-13 19:48:21 +01:00
Sergiu Ivanov
75560658a0 networks: eval-with → eval1-with
This makes the type checker happy because it's more precise to use
eval1-with.
2022-01-16 23:15:33 +01:00
Sergiu Ivanov
38660cc0a5 sbn-interaction-graph: Use zero-edges and declare it in the contract. 2021-08-04 17:33:17 +02:00
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
5fc4875adf networks: Make table->network infer the domains. 2020-11-28 22:46:43 +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
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
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
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
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
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
2b60b23bf1 networks: Add group-truth-table-by-nai. 2020-11-08 23:31:11 +01:00
Sergiu Ivanov
59c7108510 networks: Add and illustrate sbn-interaction-graph. 2020-11-08 22:56:46 +01:00
Sergiu Ivanov
bc9a2bd5f8 networks: Add and illustrate pretty-print-tbn-interaction-graph. 2020-11-08 22:30:29 +01:00
Sergiu Ivanov
7af1bb8d79 networks: Add tbn-interaction-graph and explain in example. 2020-11-08 20:29:00 +01:00
Sergiu Ivanov
000c2eeba7 networks: Fix the test for print-org-sbn. 2020-11-05 23:23:48 +01:00
Sergiu Ivanov
79d3ab1ea6 networks: Add print-org-sbn. 2020-11-04 00:06:48 +01:00
Sergiu Ivanov
c4a5327b4b networks: Fix the tests for print-org-tbn. 2020-11-02 23:05:05 +01:00
Sergiu Ivanov
af5a9d07a9 networks: Add print-org-tbn. 2020-11-02 17:58:45 +01:00
Sergiu Ivanov
0edda89642 networks: Add compact-tbn. 2020-11-02 00:08:49 +01:00
Sergiu Ivanov
2a0cfb4dcc network,compact-tbf: Use for/hash instead of hash-filter. 2020-11-01 23:42:51 +01:00
Sergiu Ivanov
f7e44df117 networks: Add compact-tbf. 2020-10-31 00:48:00 +01:00
Sergiu Ivanov
208dc12060 networks: Add normalize-tbn. 2020-10-24 23:51:56 +02:00
Sergiu Ivanov
11ecbf84dc networks: Add normalized-tbn?. 2020-10-24 23:15:13 +02:00
Sergiu Ivanov
e79fef9118 networks: Add build-tbn-state-graph and use it in example. 2020-10-23 00:17:36 +02:00