github.com/westpa/westpa commits | Ecosyste.ms: OpenCollective

Updated overview pdf in master branch

Former-commit-id: c9bfdc1a7add1514120863068dbff481b6676b7e

91466a7f9f373cd77b629e005f3aa25e979baac7 authored over 7 years ago

Merge pull request #55 from ASinanSaglam/master

Installation instructions update

Former-commit-id: 518e475b412d24f94cc0fad2ad5ab71924e2828f

58e1790cc6976dc8d54d5779065a7bbd347d0da3 authored over 7 years ago

Small formatting fix for installation instructions

Former-commit-id: 5de40c915651b0c5f4ab478450067a955ea29cb2

d7384e7f3507260a7a6f7fbef688469e61c4bc74 authored over 7 years ago

Updated readme and documentation landing page installation instructions

Former-commit-id: 7cb1734f18967fa5887cefeab445a38515a13081

ac4fff186b17fdde9e1695fda015b8f3de34ef81 authored over 7 years ago

Some changes to make the reweighting estimator return bin populations.

Former-commit-id: f22ccdc292d8dd1875e526fbdd8ce204ea9641c8

c1f9626c836fa46df53f81726401d7c74a3ece85 authored over 7 years ago

Ticked up to 1.0B. Seems more or less complete.

Former-commit-id: 1227d2c193974564a9444a0be73a17bbfff75ccd

e956a9003a23a58a7f826701da080707b90d5e7e authored over 7 years ago

Extra arguments are now sorted before hashing, ensuring that the order isn't important.

Former-commit-id: 475a290371b26099cc508106677b6c9a69895298

6217c083de05e91092c2638abf3c539eba444bac authored over 7 years ago

More adjustments.

Former-commit-id: 4d96f40b4e65d4fc6c30c9267efe8ea9566b4ff3

f2342cd740b44685fbece4fcbaea061a5be63c96 authored over 7 years ago

Fixes to the rerun logic; the hash for the assignment file is now part of the hash for the reweight/direct files, so that they can automatically determine if the assignment file is different.

Former-commit-id: d225f8ed9bd3e7f49852b30524cf8c1dadbcecef

5030474fe938ae1ac4d56eab259e5c5ed2ba8f7d authored over 7 years ago

Fixed hashing function, I think.

Former-commit-id: 45985ed0ee5707c58924bf76c7a021647802075b

a8ba8053a43d9b1fe4d724c6e91214bbfb7ff01f authored over 7 years ago

Merge pull request #53 from ASinanSaglam/master

Quickstart guide, Chignolin tutorial and a few more changes

Former-commit-id: 6df8f449449fa4e7c...

8db36ba15b9cf050c8bc450d14d293c65d939467 authored almost 8 years ago

Fixed chinolin png files

Former-commit-id: f2351dd19c7fe19ac648a8ca4f38e193ba735cf1

47d48ce50b70641022f77052edf8d4fe2ec7ac95 authored almost 8 years ago

Fixed header markup

Former-commit-id: f15cc4b0108cdf7049627feab5c0dc9829099bb9

a293261c8a41663204cffc09732963629b1e574c authored almost 8 years ago

Removed bits of latex markup

Former-commit-id: 8cbb5a551b0836baf508b4b3d2442fc4422469e7

1294e05fe91d291b4fb6627ac54549643e899fe3 authored almost 8 years ago

Added Chignolin tutorial, quickstart guide and updated the documentation building a bit

Former-commit-id: 13ea95ebc2870f25445ccf48e95a0e96e6885456

fae17defe37dedcea67539c8c271ccbfd2f6dc8e authored almost 8 years ago

Added westtools to autodoc API

Former-commit-id: 962e2001d1805ab9aff06b20f1486a75b0fd5165

a410e7d9dbd0524b150e7f229ccde7aac66e6c13 authored almost 8 years ago

Merge pull request #51 from ASinanSaglam/master

Minor subheader mismatch fix and an auto generated API test

Former-commit-id: 529c58e5f9835c022...

0e0aafa82a46d242a44d9a773564fbce03470cf6 authored almost 8 years ago

Changed what's loaded in API test

Former-commit-id: c90bdbb8c5c76036d2a646fc8d0760b73bf1c64a

898e7154bca04c240f1a78e567f931ac0a59d4f1 authored almost 8 years ago

Trying to add __all__ to modules

Former-commit-id: ef1ab7f27378a9d07ea8e1a0732c245b01723480

6792438101e8f08909f1d995e9535202eafc486d authored almost 8 years ago

Testing autodoc options

Former-commit-id: e945a394c3ad9f2e22ffe560c78ea62170983d61

01c6df518477ec72c4718c3bff9811077c2f86f9 authored almost 8 years ago

Separated modules, fixed some imports

Former-commit-id: 51c90b0284e89fbd7db53f2370fb07f0fb5a27b0

b0b798e60173a6d9c5dcdbd8a7ea5ec67d831a01 authored almost 8 years ago

Added undoc members temporarily

Former-commit-id: a38589e6acd554b7ddee4569389d3488ab737c18

587f076ebd28c27e9464a9d8a20efa9cc1075db2 authored almost 8 years ago

Further API page testing

Former-commit-id: 839e1ff40e8aaacfbc9166ec6811e4c705975a70

cc24f4e3796439c12169a0dc890d6950b6b68dd6 authored almost 8 years ago

Changed some sphinx defaults for autodoc

Former-commit-id: 847fa2f2e3be5de644c73089c97ebfd234e2bd6d

788a3dfe1eb3ce64cbbadf6bce8a092ed26f1d0f authored almost 8 years ago

Added westpa to api test

Former-commit-id: 1b58efc3ad8325aa7834d5555cd41545b31e13fc

857c3fb2cedf0389c45d432d2697624a10f7c378 authored almost 8 years ago

Added westpa.rc to API test

Former-commit-id: 8e4c20475be14db23566928a3fe401a40d834176

3272976170608254f673ad24af3ee6f2194203cb authored almost 8 years ago

Testing autodoc members option

Former-commit-id: fbf7d76f4c58aded2d07fa10c3d6ce999a7d978a

0f10a4504b456344765de605d9a94339a7ade369 authored almost 8 years ago

Further testing of the auto-api generation

Former-commit-id: 7f6712caa28f06f6806e0728d65a77e5eb04ad14

e068264985d0845309243a64c63009ea6358e81c authored almost 8 years ago

Added some binning API to the test file

Former-commit-id: 1f7b903b4f3190ebffee43d186b23b66e5416455

2539fc4f8be22813e0ee2b845b008c3610a7c7a1 authored almost 8 years ago

Testing auto-api generation

Former-commit-id: f1beea359b36ce71c34913d090cce0632f323660

2cbff2d8bb128010844ed8faf43014104359aec8 authored almost 8 years ago

Fixed a subheader mismatch

Former-commit-id: 28beabf58a07728be5607125a51599f8b3bbabbc

4a502ca1c39b5967ba67960fa59f3e77dbe69d7e authored almost 8 years ago

Merge pull request #49 from ASinanSaglam/master

Minor FAQ/tutorial changes, master pull request

Former-commit-id: c896b465da793d56d10fb3ef81324...

28c21adad69ea03e4d07866cd010eee6775ba3d5 authored almost 8 years ago

Minor fix to FAQ question

Former-commit-id: 52e08ee26bc3c5562b1c4ff5c24dee9358b9ae3d

a6d44a1350e5d470e098be7b02e1f1417b50ca4c authored almost 8 years ago

Added a new question to FAQ

Former-commit-id: caeb85065060d76238db7b51a8df7423116eaa49

98e49c704eda38851e8e6e93e9c6236027dd9888 authored almost 8 years ago

Added tags to video tutorials, fixed a tutorial title

Former-commit-id: e9cdf36885286f5c655be4dd7971ed076735d955

1b6fbcb693f7cbf29e4c9f1fc246f53ffb581f77 authored almost 8 years ago

Merge pull request #47 from ASinanSaglam/master

Checklist/FAQ changes, master pull request

Former-commit-id: 3de669178b21034ab751350e966698b649...

aa2d3c1a399e48a5e9751d8288f70f8da3b794e1 authored almost 8 years ago

Minor checklist change

Former-commit-id: 0235120fe22159542555f7dae125f92243483ebc

b0d4a4ae06ffb496746a3346dd7d0ce4836751f8 authored almost 8 years ago

Made some basic content changes

Former-commit-id: af0f49a89333044e7a4b37d8a87ca1c8854643f2

a510ce16e271391ee3ff0bbe96ccf300d9559fdc authored almost 8 years ago

Trying ways to add to sidebar automatically

Former-commit-id: accf7c356ce985b498090aef0e93b7b429f76ac9

bed18c8595573975ec10e51e9d858810c105ca3e authored almost 8 years ago

Cross-ref test

Former-commit-id: ba4e43afed018cb2505c7712c4a5547d79f95539

bdbbd749d76f13ab227674c511b05775ac03fa51 authored almost 8 years ago

Testing separate readme file

Former-commit-id: 4ff34b488f03d8ee1c9a032e252c783ce719da8e

a452d0f4aabd58f398f75323e0135c5965a1e239 authored almost 8 years ago

Fixed links

Former-commit-id: 7e10e594f000a8ead99b3589c569ffeed2c091ce

7a0b76d98ea58be5f725d8e59d704b8b3a925446 authored almost 8 years ago

Added faq/checklist links instead

Former-commit-id: 6c8b5287e604288dd6c5632ac116a8dab166a354

3dc89756912ba221bb2ed8a2d6829c5ee4aebbca authored almost 8 years ago

Trying other ways to link to FAQ and checklist

Former-commit-id: f090ab4b0053bbdfb8ee29335fe483e0d07b5128

ae948a2d82a3c2af16ef4eda496f35df4cedd0fa authored almost 8 years ago

Added faq, changed position for checklist

Former-commit-id: 386f800888d376092ab70308f840d9dd2885e657

012562a3c20c2dc4d86d9c928ecf4870320f5215 authored almost 8 years ago

Hopefully fixed the hashing logic, printed output.

Former-commit-id: a50c19a5e814bf088501c5053837c978372a8c9b

e030143e9158bedd473b1eed96655fef15456460 authored almost 8 years ago

Overrode more operators for the WIPIDataset.

Former-commit-id: 98f99657ce8fdcec7139d384719b392fab1eb2e9

953d91268c6b3fe304859f55859a4225134e8b43 authored almost 8 years ago

Made names make more sense.

Former-commit-id: a7d43f3b976df8d6a54be9599e330131000eef40

c8930565f6109def4848bf0051fe4d960cb67125 authored almost 8 years ago

Fixed a sloppy edit.

Former-commit-id: 55dfa61bde49bd0202e74f44f98022f35074f9ac

98bebb9720dac96bbbe12b6ba4f6f58f666851c5 authored almost 8 years ago

Overrode math operators for gussied up numpy datasets.

Former-commit-id: 373340ea8884af220cbe087378390c759a0eb21e

1412db48d2def6d9ad9b1247ba05446e5eb2eba5 authored almost 8 years ago

Added debug mode, more fixes for hashing, can ignore hashes now (-ih/--ignore-hash)

Former-commit-id: 6cc429317c0fd42761befe579085cb002b6b91d7

9e0bd5fed82e13390f0007f2c6e07ffcbeac74a2 authored almost 8 years ago

Updated trace function to significantly increase speed.

Former-commit-id: beab6bc4c8ebc9284c398e210054ed21475f12c8

8de767f5f2e31829c6024892b67f5992dd1e4233 authored almost 8 years ago

Plotting somewhat fixed.

Former-commit-id: a4d0a7c4bb363a73b9dcb846da38e7a82c6e2d1e

7f2b993908af48094ce82e2e1864bc0aaab3fb1b authored almost 8 years ago

From last night.

Former-commit-id: 27abec1b19239120ce2c2158b18d3e04a802d0fb

61d5564074a861fbf72760827162ee358d8859ba authored almost 8 years ago

Can plot output from trace (not very pretty) in terminal. Needs more work.

Former-commit-id: 976623155ccc9563fe5cc02dc3d30ebc91112d87

8bdb50127a212523a3d8ece529012d79a7eaff0e authored almost 8 years ago

Moved a LOT of other functionality into westtools/wipi.py

Former-commit-id: c0ca432065d680b72703563626e42d69d78b1330

eeb2b5da314a2c7eb00c47e344b10bb3ea2545fe authored almost 8 years ago

Finished moving scheme functionality to own class; WIPI class now just has a few convenient properties for pulling the correct scheme information.

Former-commit-id: e31d4ffb859a4d5f60838c19b30895d714a6b555

b5f97131a0227f7e5452386354435e5fac2b3b19 authored almost 8 years ago

Moved some functionality, added in some headers.

Former-commit-id: abcc2b924f6ed35f03f2a0ebad32c203b37dc282

0b6ef828903278bcf7ad6c47c07f1bf048e99443 authored almost 8 years ago

Slight cleanup; hiding more dictionaries.

Former-commit-id: c313678453099d5169c4e7bab0cbce20ab5f3641

b799731b853b67564369a944387872dffca41be9 authored almost 8 years ago

Fixed plotting issues and hid more dictionaries.

Former-commit-id: 5f79fb18a564d60503a282f5fa15e21029425814

d5d972f26fe73758ff775e89cddec0e771996bf1 authored almost 8 years ago

Future now behaves like current/past; fixed more pointer issues.

Former-commit-id: a6186f3586fb74db1bc33bd9bea4663f29905c6d

3546f90040d9563509180d51c32455b210073654 authored almost 8 years ago

Fixed pointers with custom datasets, and partial plotting support.

Former-commit-id: d4e9a784fb11e8899f6a4d55401f756e974d93d8

cd81187b5ba90d86c875c159fc3f1b6a80cef439 authored almost 8 years ago

From last night.

Former-commit-id: d7984b2ba1a4c7c0d285b2937bee6a25ddec19c8

3003c3031a5c5a9a20c43310eb675c8350c59a85 authored almost 8 years ago

More fun with attributes

Former-commit-id: 3342082620ee1709ae7722f6eab3ead953c92e07

7f1dac06d6b29f832bfe20965f9841fbafd5f88f authored almost 8 years ago

fixed dir issue; things now accessible as attributes and dictionary keys for direct/reweight in current/past properties.

Former-commit-id: 1cf4e8b40443ca1d7d0094d7da9c509ec9f25a32

b0467dbe9fe183738e62947b009e2d3aede184e1 authored almost 8 years ago

Building in more consistent accessing routines.

Former-commit-id: 587c621ab513371358f158ae35311714f09a7b62

0fbb64fee9ebf061d1cc5ff7c23d89590406101d authored almost 8 years ago

Fixed hashing, modifications to how kinetics are called (to update to new scheme).

Former-commit-id: 6de513da81b234497653f30b4ef8ac7165b3cc00

5b3fb10d8f860a1c6fa74065b594091c7c7bfa24 authored almost 8 years ago

Added in hashing check for files to see if the state/bin/command line definitions have been changed to trigger an automatic reanalysis.

Former-commit-id: 730edb538ca44075ce7f4b5d6713cc50437658ec

cead7cb048c4d3976845ab93be85c5c98c9d6314 authored almost 8 years ago

Sorting functionality for subsampling...

Former-commit-id: 68623c3049ac55f1a8f6e2a1d42f45dd7f592f22

13fa83171fcc388a4f6ee005f012376dcaf3aec5 authored almost 8 years ago

Merge branch 'wipython' of https://github.com/westpa/westpa into wipython

Former-commit-id: cc1ed40890504abb37bcf95bf2b17907a090c05b

95f9da8479208a9d2fb628b27ace045acae1ce38 authored almost 8 years ago

Merge pull request #45 from westpa/master

Rebase w_ipa off master.

Former-commit-id: 111ebfe856207102339feb2c3e32601451f0f55e

29bfdfdc01ac4e3e91234243ccd9a63b5af59f5a authored almost 8 years ago

Updated assignmention section in w_ipa to support 'extra' flags (for subsampling).

Former-commit-id: 609152b57be59c60c3c34f0e64a5295041e19ee7

6335998e94eb0e080e66bd6b71ee9933e0d778a4 authored almost 8 years ago

Merge pull request #35 from westpa/west_tools_KineticsRewrite

West tools kinetics rewrite merged.

Former-commit-id: b07237e8e10f83c6d9b35b2d2aa81ca6bb4ee8fc

f01e0410545d3295438911057cede8d59dbb5c1f authored almost 8 years ago

Updated/added copyright date/information to modified files.

Former-commit-id: eb28e07e56cf145b946441ffa75b5dfc50ffa616

e0a43268b373ae2176fdab1da4053ea965df500b authored almost 8 years ago

Added link to overview from documentation

Former-commit-id: 7ffa2eddf52cce4daa702f1ff0fb7c0dc7488d2b

0abdff1927f7a8cb26996700a2d2ffe20f47ea94 authored almost 8 years ago

Merge pull request #42 from ASinanSaglam/master

New overview page

Former-commit-id: b6d3b6a46c3702d220c9e3535b8f7b31829193c9

8d2c6bde56b751bf69e8c68d9c36cdc97e05ac84 authored almost 8 years ago

Re-cythoned _assign.pyx

Former-commit-id: 50cc2f38a47d532c4226fd824231a91471ee0fd6

c984c7f7671deab4728c5d1495789dea8b184c94 authored almost 8 years ago

Merge branch 'west_tools_KineticsRewrite' into wipython

Former-commit-id: d32954953ef154251ac5b4c0dc8406166d58e103

f5dd03b8e2bc71f0cd8d2244f9c85d625617d2b4 authored almost 8 years ago

Fixed merge.

Former-commit-id: 8a62f650226ea4bffba3648afba22d47b95de398

3fa984550833a17bdb126eabfe2fdc3b2b6f80dc authored almost 8 years ago

Updated help text on w_direct.

Former-commit-id: 958db35b254ab3e4f47e6e8f5a36fdcf46916368

27539dedde17cd44d753b06a91484fe9fa2772ed authored almost 8 years ago

Made correlation/bootstrap optional on w_fluxanl.

Former-commit-id: 50ed8d64a3df0e56f0ca7717c75699dce2e4bcfe

71690124c306ccf36456cdb0a48aa31a6d0353da authored almost 8 years ago

Removed errant print statement.

Former-commit-id: f8521e57c5fc4270e1eebe5b8285ffcff6ca847a

c8dea15b64b1633a07d1af7878567e5879dce816 authored almost 8 years ago

Updated ploterr to plot color/ensemble probabilities, and to support both w_direct and w_reweight.

Former-commit-id: 9f8110bce60fd08d8fc49fd4904f255304907106

b3ced5f6933253d8a49df1ffc58bc1b437f20a57 authored almost 8 years ago

Finished removing old rate estimator from Cython and replaced it with current; changed references in w_direct and westpa/__init__ accordingly.

Former-commit-id: 70842ea63b0266a68f64575829e0ff0b6be05caf

1016f29be710dc683caa053a8dca8c4015e4daec authored almost 8 years ago

Added in stubs to w_postanalysis_{reweight/matrix} to ease transition from old toolkit model to new one.

Former-commit-id: 3b572a05caf19ce523707db5f733d13738f7127b

6860f2d82446f87ebdad8a94536f8a4d9e85c4b0 authored almost 8 years ago

Changed the order of subcommands.

Former-commit-id: 131f7387664bf5e065c68706bb0add6cd524b76c

9f6a4dc45343cc706e6cca16dd7028960c2f1bae authored almost 8 years ago

Changed subcommand values and seriously altered docstring text for w_reweight.

Former-commit-id: f6b4d2b0d46699446f14a997f594b884085152e2

f4ed1b1604555ac8ce9c782aae706d7f30c6768c authored almost 8 years ago

Removed indentation from pi.

Former-commit-id: 720f1836ff4f8f2b83f7ff548aefe7bf733ff759

73c63728d975374175e8fc0e284c250f5af00f40 authored almost 8 years ago

More updates on docstrings and help.

Former-commit-id: 956cda6a6eaf41edb90b40f08c681e962e2d1c5a

64926b24956d52cdaf960a117ea4a7f9c29bc867 authored almost 8 years ago

Moved lib/west_tools/westpa/kintool.py to lib/west_tools/westtools/kinetics_tool.py

Former-commit-id: a79d0aa07abf7b9465679cd6ea476a4fff6b82df

82713ffa1d925175eb90e50b48c8cc9f860064d4 authored almost 8 years ago

Fixed more imports and headers.

Former-commit-id: 8ba467471f4e5b56d8b3c38a937c746d46c087f1

f8c7fa8ac869d01dcf8602e8d560979f6c931ca8 authored almost 8 years ago

Fixed a lot of docstrings in w_direct, and fixed the progress indicator (finally).

Former-commit-id: ab587d3cea2d56d812aa29eda23a97cc2783a56d

847ff9056372212f18ec2e4b100c9fa812b4fa72 authored almost 8 years ago

Renamed WESTKinAvg to WESTKineticsBase, cleaned up imports for old w_kinetics.

Former-commit-id: 69984a3eccd44342bfc7a4fae74e922228fd06fa

e5e36433968b7be9d9de8909fd832f49fcd616f6 authored almost 8 years ago

Moved arguments to their respective classes; matrix and kinetics no longer have bootstrapping option flags.

Former-commit-id: 2f372fb6c46a128670658df76d4fdb5d7f350de0

87c9e2d5a5a954be5cbf4c1c931378a423341ebe authored almost 8 years ago

Fixed argument parsing in reweight code.

Former-commit-id: 44d11c3a4311dfc83ae01e68ec83d62429a74cd7

ad7f5f6080603ffab163262eac662a529a84660a authored almost 8 years ago

Bootstrap for evolution datasets is now optional, but on by default.

Former-commit-id: e21bff9578bea8805cf3caefad1efcaa37047fb9

83c60ad5f89444bc66377c7917761fc22f8335e8 authored almost 8 years ago

Ran notebook to add output.

Former-commit-id: 424a800db2d96d9ce700b26dcc7461300b8862fa

cb8d20157df0322092c403bea7177609feb28ab9 authored almost 8 years ago

Documented west.cfg for ODLD, and added example of jupyter notebook usage with w_jupyter.

Former-commit-id: 794402b4804d85cd85f1a78673af7ea05a225008

daf6844caf632d409c05cc974fa28c7ced6623ee authored almost 8 years ago

Merge pull request #37 from westpa/amber_nacl_fix

Fixed Amber Example

Former-commit-id: a5f42a6112d057470b658fa861c312e0186b5001

8103272edef11b37705a1b73a3e680a14f32020d authored almost 8 years ago

Merge pull request #40 from ajd98/master

Amber Na+/Cl- tutorial now specifies WE parameters via YAML rather than system.py

Former-commit...

44ec765648052588c57a1bd9bf6722abfb78b0a6 authored almost 8 years ago