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546 Commits

Author SHA1 Message Date
Alyssa Travitz
395ed35837 update notebook names (#1279) 2025-05-20 13:04:46 -07:00
Alyssa Travitz
148af2694c Update cli docs (#1264) 2025-04-30 13:46:11 -07:00
Alyssa Travitz
2d2fef2a07 Fix docs version (#1262) 
* only use major and minor version in docs

* add issue number in comment

* updating version parsing
 2025-04-29 11:03:32 -07:00
Alyssa Travitz
9296aa7fb0 Release prep 1.4.0 (#1253) 
* Updated CHANGELOG for 1.4.0

* changing a word

* fixing formatting

* adding links (thanks mike)

* adding links

* adding description

* updating changelog
 2025-04-25 07:02:27 -07:00
Alyssa Travitz
36f5fb8387 pin to ofe-sphinx-theme v0.2.0 2025-04-23 19:56:57 -07:00
Alyssa Travitz
0e21b35b00 Clean up tutorial index (#1233) 
* switch to concise bulleted list for clarity

* updating description
 2025-04-23 15:52:46 -07:00
Alyssa Travitz
8cc3c4f291 cli gather should allow lists of filepaths (#1212) 
* allowing multiple paths

* first pass at allowing filepaths and wildcards

* updating docstring

* adding missing /

* add tests and sorting

* add news

* updating docstring

* updating docs

* fixing whitespace diff

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2025-04-07 07:13:08 -07:00
Alyssa Travitz
939a7bdd29 moving under the hood to the user guide (#1221) 
* moving under the hood to the user guide

* adding pip to docs env dependencies
 2025-04-03 12:19:12 -07:00
Alyssa Travitz
fde3b1697f add PR 1210 to changelog (#1218) 2025-03-27 15:46:16 -07:00
Alyssa Travitz
e0885fdcac Updated CHANGELOG for 1.3.1 (#1216) 
* Updated CHANGELOG for 1.3.1

* Update docs/CHANGELOG.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Apply suggestions from code review

edits from mikemhenry

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* formatting

* adding PR #

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2025-03-27 15:30:49 -07:00
Alyssa Travitz
66ac2bdc64 migrate json loading to new gufe syntax (#1177) 
* updates to cli from_json

* replacing dump instances with to_json

* Remove unnecessary imports of JSON_HANDLER

* addressing review

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
Co-authored-by: David L. Dotson <dotsdl@gmail.com>
 2025-03-25 23:32:26 +00:00
Alyssa Travitz
31bb2a777d make gufe lowercase in docs (#1190) 
* make gufe lowercase in docs

* Update docs/reference/index.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

* Update docs/reference/api/index.rst

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2025-03-14 09:55:24 -07:00
IAlibay
9546bdbd07 Add some docs 2025-03-10 10:46:24 +00:00
Alyssa Travitz
a011cd010a make conda-lock a subheader of mamba install 2025-02-28 14:50:22 -08:00
Alyssa Travitz
3da2ae9d9e remove macos x86_64 from single file installer list (#1154) 
* remove macos x86_64 from single file installer list

* adding news entry
 2025-02-26 23:19:02 +00:00
Mike Henry
6a984315ac Update installation.rst 2025-02-24 15:07:57 -07:00
Alyssa Travitz
d146762b2f reordering entries for clarity, plus typo fixes (#1140) 
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2025-02-20 11:36:21 -08:00
Alyssa Travitz
446ef8cb74 reordering tutorials (#1141) 
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2025-02-19 22:30:11 +00:00
Mike Henry
a831ffadbe Fix/pin sphinx le73 (#1147) 
* pulls in <7.3 on RTD -- let's just match that

* sort deps and add a space for pins
 2025-02-19 10:31:52 -08:00
Alyssa Travitz
c32f072ae2 update docs build (#1142) 
* updating git ignore and renaming to environment.yml for consistency

* bump to sphinx<7.3

* back to yaml

* test newset sphinx + install from cf

---------

Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2025-02-19 10:55:17 -07:00
Alyssa Travitz
a6767a1afb Release prep v1.3.0 (#1124) 
* updating release checklist

* Revert "updating release checklist"

This reverts commit 894458d44a.

* Updated CHANGELOG for 1.3.0

* fixing up changelog
 2025-02-12 10:46:27 -08:00
Alyssa Travitz
a1b2bb959f Add supported software versions (#1119) 
* adding supported dependencies

* remove outdated apple silicon warning

* updating openmm versions
 2025-02-12 07:08:11 -08:00
Josh Horton
54a4d2b8da Merge branch 'main' into charge_warning 2025-02-12 10:49:26 +00:00
Alyssa Travitz
f7b11d45b1 remove "easy_" prefix from cli output (#1121) 
* easy_rbfe -> rbfe

* remove addressed TODO

* adding news item

* easy_rhfe -> rhfe prefix
 2025-02-11 14:43:21 -08:00
Alyssa Travitz
cf20731ae4 Update docs/tutorials/index.rst 2025-02-11 08:21:20 -08:00
Alyssa Travitz
102c848168 Update docs/guide/introduction.rst 2025-02-11 08:21:11 -08:00
Josh Horton
0abc72d3ce reorder tutorials and add links to cli tutorial 2025-02-11 13:41:11 +00:00
Josh Horton
503aa71d39 add tutorial description to the index 2025-02-07 09:56:32 +00:00
Josh Horton
356d934bf6 add links to tutorials 2025-02-07 09:51:38 +00:00
Josh Horton
0d8a3e3148 add a note on charge generation during network planning 2025-02-06 10:36:53 +00:00
Alyssa Travitz
4bb24610dd Merge branch 'main' into cli-partial-charges 2025-01-30 07:21:06 -08:00
Josh Horton
ea1589a26b fix docs 2025-01-29 17:26:58 +00:00
Josh Horton
80b632c159 Merge branch 'main' into cli-partial-charges 2025-01-29 17:16:42 +00:00
Josh Horton
a07608de8d Merge branch 'main' into bootstrap_error 2025-01-29 17:15:33 +00:00
Josh Horton
4c9a1f0b6f xfail openeye nagl tests, update CLI ref docs 2025-01-29 16:31:35 +00:00
Josh Horton
8552fff0a3 format list 2025-01-29 11:18:47 +00:00
Josh Horton
4caf47c173 Update docs/guide/execution/quickrun_execution.rst 
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
 2025-01-29 11:11:06 +00:00
Josh Horton
c4d102f363 Update docs/guide/execution/quickrun_execution.rst 
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
 2025-01-29 11:10:36 +00:00
Josh Horton
7e320e4630 Update docs/guide/execution/quickrun_execution.rst 
Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>
 2025-01-29 11:10:29 +00:00
Josh Horton
b0405cf16b add --n-protocol-repeats flag info 2025-01-24 13:49:41 +00:00
Josh Horton
d0920a0008 add info on parallel execution and gathering 2025-01-24 13:39:56 +00:00
Josh Horton
c46e7c1e5a add charges to cofactor sdf, fix docs, expose overwrite charges to plan CLI 2025-01-24 11:39:39 +00:00
Josh Horton
6b775a2c16 add news, update docs and fix typos 2025-01-16 10:17:50 +00:00
Alyssa Travitz
e9aaf1f5c7 revert ligand network section to be addressed later 2024-11-15 07:29:39 -08:00
Alyssa Travitz
3b66c5c985 adding See Also section back to alchemical network 2024-11-15 07:29:39 -08:00
Alyssa Travitz
4273a36607 Apply suggestions from code review 
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com>
 2024-11-14 17:19:25 -08:00
Alyssa Travitz
0c8f1304b9 making warning more visible 2024-11-14 12:53:04 -08:00
Alyssa Travitz
6dcf88467f back to bold 2024-11-12 17:00:21 -08:00
Alyssa Travitz
96cb6f1d66 renaming to Results Gathering 2024-11-12 16:51:38 -08:00
Alyssa Travitz
10e13e71c8 making protocol description clearer 2024-11-12 16:50:36 -08:00