Alyssa Travitz
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2ecb01dd2d
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CLI interface IS redundant
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2024-11-12 11:10:21 -08:00 |
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Alyssa Travitz
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69f2d0b25b
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capitalize YAML
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2024-10-18 11:24:17 -07:00 |
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Alyssa Travitz
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bbc535f14d
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moving Kartograf link)
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2024-10-16 08:43:35 -07:00 |
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Alyssa Travitz
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24ef319523
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clarity edits to cli_yaml docs
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2024-10-16 08:23:09 -07:00 |
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Alyssa Travitz
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15394414e2
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formatting fixes to cli_basics
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2024-10-16 07:44:19 -07:00 |
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Mike Henry
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e50102e9a9
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add guide on how to set the loglevel to debug
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2024-06-19 04:16:19 -07:00 |
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Richard Gowers
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3b76941b61
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Merge pull request #830 from OpenFreeEnergy/issue_803_userguide_result_networks
docs: first pass at working with networks page
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2024-04-19 12:01:03 +01:00 |
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Richard Gowers
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581525b9c2
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Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
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2024-04-19 11:26:41 +01:00 |
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richard gowers
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c18a18a8f9
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docs: result network, couple of review comments
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2024-04-18 15:37:37 +01:00 |
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Richard Gowers
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ad85755fcf
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Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
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2024-04-18 14:54:23 +01:00 |
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richard gowers
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6398f0e452
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docs: first pass at working with networks page
fixes issue #803
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2024-04-18 10:59:15 +01:00 |
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Richard Gowers
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c6d1835634
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Update chemical_systems_and_thermodynamic_cycles.rst
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2024-04-16 17:02:08 +01:00 |
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richard gowers
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b50eb51211
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docs: chemical system docs review comments
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2024-04-16 14:04:32 +01:00 |
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Richard Gowers
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7a538ecf5f
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Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>
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2024-04-16 14:00:40 +01:00 |
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richard gowers
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53f8e297c5
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docs: fixup reference to chemical systems docs
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2024-04-15 12:26:10 +01:00 |
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richard gowers
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7c9d6de8a6
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docs: add image of RBFE thermo cycle to chemical system docs
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2024-04-15 12:26:01 +01:00 |
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richard gowers
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8ee14ed0c5
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docs: add crossref to chemicalsystems from RBFE protocol docs
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2024-04-15 12:25:45 +01:00 |
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Richard Gowers
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220d46333b
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Merge branch 'main' into issue_759_chemical_system
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2024-04-15 11:48:06 +01:00 |
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richard gowers
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3ed1c55fd8
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docs: fixup comment which wasn't commenting itself out
seems to require a blank line
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2024-04-15 11:27:19 +01:00 |
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richard gowers
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8e3308dafc
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docs: fix a couple of references
define-rbfe and define-rsfe got merged into a new page
shouldn't use relative links in docs to avoid breaks
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2024-04-15 11:04:09 +01:00 |
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Hannah Baumann
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82125765a5
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Merge branch 'main' into docs_protocol_cycles
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2024-04-15 02:08:52 -07:00 |
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hannahbaumann
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191e511ae3
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Add table steps and outputs plain MD guide
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2024-04-15 11:08:31 +02:00 |
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hannahbaumann
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0b9a2e5144
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Add outputs for the plain MD protocol
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2024-04-15 10:53:28 +02:00 |
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hannahbaumann
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d5b7aee3fa
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small fixes
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2024-04-15 09:59:23 +02:00 |
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hannahbaumann
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41c72ce828
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Edit todos
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2024-04-15 09:43:37 +02:00 |
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richard gowers
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c1d2a2b258
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docs: more tweaks following review
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2024-04-12 14:52:44 +01:00 |
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Richard Gowers
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ab6c254102
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Apply suggestions from code review
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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2024-04-12 14:49:04 +01:00 |
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richard gowers
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7e41f93582
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docs: tweaks following review
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2024-04-12 13:01:19 +01:00 |
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richard gowers
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679ff03d78
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docs: better forward/reverse convergence picture
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2024-04-12 12:36:27 +01:00 |
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richard gowers
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abf433fe70
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docs: check in pictures for RFE analysis section
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2024-04-12 11:05:27 +01:00 |
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richard gowers
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d3be3f41d9
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docs: add example images of analysis
reformat analysis from bullet list to table to have images side by side
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2024-04-12 10:40:12 +01:00 |
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richard gowers
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b01bfe8fa1
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docs: highlight importance of mbar overlap matrix in rbfe docs
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2024-04-12 09:31:08 +01:00 |
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Irfan Alibay
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3e9b847c1c
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Update docs/guide/setup/creating_ligand_networks.rst
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2024-04-11 12:27:58 +01:00 |
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Benjamin Ries
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717778bc70
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Update docs/guide/setup/creating_ligand_networks.rst
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
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2024-04-11 11:34:24 +02:00 |
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Irfan Alibay
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647d8a72cb
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Merge branch 'main' into docs-ligandNetworks-rework
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2024-04-11 07:59:38 +01:00 |
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richard gowers
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e778e4fa21
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docs: fix links to cookbook nblink entities
this adds a reference anchor in the nbsphinx prolog for each nblink included cookbook
include rfe_alchemical_planners in cookbook list
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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a92604dc47
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Actually copy over the right image
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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d2d41469d8
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switch to Hannah's image for the AlchemicalNetwork
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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6d0e1c0286
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Change cookbook and tutorial links to refs
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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9cbaa137e5
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uncommited stuff
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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7d3a39f2a9
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fix create_alchemical_network cookbook link
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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c827a67adc
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fix rbfe_cli_tutorial link
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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2fc8776598
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relative links
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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60b57eaabd
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update index
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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0c5cb0ced0
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remove duplicate files and add reference label
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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e1f571627f
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add reference label
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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1eedfb53fe
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update note
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2024-04-10 17:12:18 +01:00 |
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IAlibay
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d8c705f2eb
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Add alchemical network creation userguide page
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2024-04-10 17:12:18 +01:00 |
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Irfan Alibay
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54347e4cb9
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Merge branch 'main' into docs-ligandNetworks-rework
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2024-04-10 11:17:59 +01:00 |
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richard gowers
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0dd3a73978
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docs: final tweaks to userguide quickrun
clarify can run single sim locally
homogenise quickrun examples
add link to working with results page
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2024-04-10 09:57:15 +01:00 |
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