Alyssa Travitz
2ecb01dd2d
CLI interface IS redundant
2024-11-12 11:10:21 -08:00
Alyssa Travitz
69f2d0b25b
capitalize YAML
2024-10-18 11:24:17 -07:00
Alyssa Travitz
bbc535f14d
moving Kartograf link)
2024-10-16 08:43:35 -07:00
Alyssa Travitz
24ef319523
clarity edits to cli_yaml docs
2024-10-16 08:23:09 -07:00
Alyssa Travitz
15394414e2
formatting fixes to cli_basics
2024-10-16 07:44:19 -07:00
IAlibay
7db0c4147f
Updated CHANGELOG for 1.1.0
2024-09-25 22:53:08 +01:00
Mike Henry
dee2b70248
build ofe theme without versioningit intergration ( #914 )
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* build ofe theme without versioningit intergration
* fix commit hash
2024-08-02 14:08:01 -07:00
Mike Henry
e05420729c
update urls to match new scheme + add micromamba install steps
2024-06-26 15:22:11 -07:00
Mike Henry
e50102e9a9
add guide on how to set the loglevel to debug
2024-06-19 04:16:19 -07:00
Mike Henry
e687f03d9e
update intersphinx inventory location for openff.units and scipy
2024-06-19 03:25:56 -07:00
Mike Henry
a7a800b8ee
moved lock file to be before single file installer, added warning
2024-06-12 09:16:37 -07:00
Mike Henry
4661131e0b
Update docs/installation.rst
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2024-06-12 09:10:27 -07:00
Mike Henry
092546f202
Updated installation instructions for conda-lock
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Instead of just pointing users to the installation instructions, we now
provide our own directly in the docs. We emphasise that creating a new
env to install conda-lock into will reduce dependency conflict issues.
2024-06-12 08:29:56 -07:00
Mike Henry
d2236c6a37
Added how to install from conda-lock file
2024-06-10 15:15:34 -07:00
Mike Henry
1982d6255a
Updated CHANGELOG for 1.0.1 ( #860 )
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* Updated CHANGELOG for 1.0.1
* fix capital letters
2024-05-31 13:48:37 -07:00
Mike Henry
5be7f737ca
Add GAFF test (and GAFF skips) to CI ( #847 )
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* see if this is enough to test the removal of gaff
* see if now we get the right error message
* rerun ci
* rerun ci
* see what happens if we the solver do its thing
* add omff version to matrix
* Added note about how to use gaff
* depending on the ommff version, we make sure the test does what we expect
* add an osx arm test since we should be able to do that now
* see if we can install missing stubs
* add missing stubs directly
* we return a sampler and not a system for the rfe
* Apply suggestions from code review
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
* added link to give some context
* testing on python 3.12 now
* unpin numpy
* no openeye toolkits for 3.12
---------
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
2024-05-13 13:40:31 -07:00
Mike Henry
e8492ea43c
debug script for people to test openmm ( #733 )
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* debug script for people to test openmm
* Added news entry
* added checking which platforms can do mixed p
* fix typo in debug script
* added how to run script
* point to new showcase
* give full path to assests to avoid copying notebooking into build env
* rerun ci
* fix mypy env
* looks like we still need to pin mypy but can relax python
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2024-05-06 12:57:29 -07:00
Richard Gowers
3b76941b61
Merge pull request #830 from OpenFreeEnergy/issue_803_userguide_result_networks
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docs: first pass at working with networks page
2024-04-19 12:01:03 +01:00
Richard Gowers
581525b9c2
Apply suggestions from code review
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
2024-04-19 11:26:41 +01:00
Richard Gowers
a6efe2fe29
Merge pull request #834 from OpenFreeEnergy/docs_long_tests_clarify
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docs: clarify long tests slightly
2024-04-19 11:26:08 +01:00
Richard Gowers
7c98fe7717
Update docs/index.rst
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
2024-04-19 11:00:08 +01:00
James Eastwood
dd8e0bc893
copy editing
2024-04-18 15:57:50 -04:00
James R. Baggs Eastwood
d324c31b6d
Merge branch 'main' into issue_746_landing_page
2024-04-18 15:51:17 -04:00
richard gowers
f4f24f8538
docs: clarify long tests slightly
2024-04-18 17:36:52 +01:00
James Eastwood
abcbf01fe8
copy editing the landing page
2024-04-18 10:59:04 -04:00
richard gowers
c18a18a8f9
docs: result network, couple of review comments
2024-04-18 15:37:37 +01:00
Richard Gowers
ad85755fcf
Apply suggestions from code review
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Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
2024-04-18 14:54:23 +01:00
richard gowers
b3ecd1f13b
docs: fixup try link on landing page
2024-04-18 11:46:55 +01:00
richard gowers
837a6000e0
docs: refresh docs landing page
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provides short description of the package on landing page
reworked landing page cards to match current contents better
2024-04-18 11:34:51 +01:00
richard gowers
6398f0e452
docs: first pass at working with networks page
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fixes issue #803
2024-04-18 10:59:15 +01:00
Mike Henry
e6b3d61a7c
add notes from review and do 1 sentence = 1 line
2024-04-18 02:41:51 -07:00
Richard Gowers
d316c52139
Update index.rst
2024-04-18 09:44:30 +01:00
Mike Henry
dfa6509f87
Merge branch 'main' into docs/issue_306
2024-04-17 10:28:33 -07:00
Mike Henry
b562b2c57f
added note about the GUFE package
2024-04-17 10:25:47 -07:00
Mike Henry
7b077e5ba7
Added all to support
2024-04-17 09:54:44 -07:00
Mike Henry
52745c8e15
Merge branch 'main' into docs/min_hardware
2024-04-17 09:48:49 -07:00
Richard Gowers
c6d1835634
Update chemical_systems_and_thermodynamic_cycles.rst
2024-04-16 17:02:08 +01:00
richard gowers
b50eb51211
docs: chemical system docs review comments
2024-04-16 14:04:32 +01:00
Richard Gowers
7a538ecf5f
Apply suggestions from code review
...
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
2024-04-16 14:00:40 +01:00
richard gowers
53f8e297c5
docs: fixup reference to chemical systems docs
2024-04-15 12:26:10 +01:00
richard gowers
7c9d6de8a6
docs: add image of RBFE thermo cycle to chemical system docs
2024-04-15 12:26:01 +01:00
richard gowers
8ee14ed0c5
docs: add crossref to chemicalsystems from RBFE protocol docs
2024-04-15 12:25:45 +01:00
Richard Gowers
220d46333b
Merge branch 'main' into issue_759_chemical_system
2024-04-15 11:48:06 +01:00
richard gowers
3ed1c55fd8
docs: fixup comment which wasn't commenting itself out
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seems to require a blank line
2024-04-15 11:27:19 +01:00
richard gowers
8e3308dafc
docs: fix a couple of references
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define-rbfe and define-rsfe got merged into a new page
shouldn't use relative links in docs to avoid breaks
2024-04-15 11:04:09 +01:00
Hannah Baumann
82125765a5
Merge branch 'main' into docs_protocol_cycles
2024-04-15 02:08:52 -07:00
hannahbaumann
191e511ae3
Add table steps and outputs plain MD guide
2024-04-15 11:08:31 +02:00
hannahbaumann
0b9a2e5144
Add outputs for the plain MD protocol
2024-04-15 10:53:28 +02:00
hannahbaumann
d5b7aee3fa
small fixes
2024-04-15 09:59:23 +02:00
hannahbaumann
41c72ce828
Edit todos
2024-04-15 09:43:37 +02:00
