Matthew W. Thompson
a8bc518b15
Add back some tests
2022-09-13 16:40:02 -05:00
Matthew W. Thompson
011ab21176
Fix syntax
2022-09-13 16:32:28 -05:00
Matthew W. Thompson
d5eb9dfa99
Try directly uploading coverage report
2022-09-13 16:31:36 -05:00
Matt Thompson
b5be79ebb2
Merge pull request #197 from openmm/dependabot/github_actions/codecov/codecov-action-3.1.0
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Bump codecov/codecov-action from 2.1.0 to 3.1.0
2022-09-09 20:15:15 -05:00
Matt Thompson
bc278d5127
Merge branch 'main' into dependabot/github_actions/codecov/codecov-action-3.1.0
2022-09-09 18:37:50 -05:00
Matt Thompson
140bc79930
Tweak CI: Switch to Micromamba, pin to supported OpenFF Toolkit versions ( #232 )
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* Switch to micromamba for setting up conda environment
Add boilerplate `.gitignore` file
Do not pull from non-standard labels
Install instead of update
Try to figure out why if: {{ false }} still triggers
Syntax?
Tinker
Bring in (full) mamba
Bash thing everywhere
Bring down old toolkit
Do not present un-loadable ff14SB port as available
More pins
* Drop 3.7, add 3.10
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
2022-09-09 17:29:32 +00:00
Mike Henry
d4e6a07d89
add back in openeye toolkit ( #226 )
2022-08-19 16:51:57 -07:00
Mike Henry
3e84351578
test branch protection
2022-08-12 15:25:04 -07:00
Mike Henry
b82f1f3780
test branch protection
2022-08-12 15:21:41 -07:00
Mike Henry
cf9abe273b
test branch protection
2022-08-12 15:12:00 -07:00
Mike Henry
8901ec45b8
make CI work on 'main' branch
2022-08-12 15:10:23 -07:00
Mike Henry
ad63a3a5ff
Merge branch 'main' into dependabot/github_actions/codecov/codecov-action-3.1.0
2022-08-12 14:50:20 -07:00
John Chodera
684ec00b10
Merge pull request #223 from openmm/feat/add_openff-toolkit-testing-to-matrix
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fix syntax issues
2022-08-05 13:23:44 -07:00
Mike Henry
51d1802bb2
fix Error #15 : Initializing libiomp5.dylib, but found libomp.dylib already initialized.
2022-08-05 10:18:18 -07:00
Mike Henry
4834933ba4
fix syntax issues
2022-08-04 10:05:39 -07:00
Mike Henry
ecfa15e34e
pull espaloma from conda-froge
2022-08-04 10:00:51 -07:00
Mike Henry
09c9a33eb6
test newest version of the toolkit
2022-08-04 09:59:44 -07:00
John Chodera
a59b1445d8
Merge pull request #219 from rosemary-cresset/fix-#215
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Fix #215 : Copy gaff dat file to temp dir
2022-08-04 10:52:01 -04:00
John Chodera
23005bd4fc
Merge branch 'master' into fix-#215
2022-08-04 00:02:27 -04:00
Rosemary Mantell
459b651a1e
Use fixed file name for gaff dat to avoid spaces
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When copying the gaff dat file to the temporary directory to avoid
spaces in the path, also use a fixed file name, 'gaff.dat', in case of
spaces in the file name too.
2022-08-03 09:36:30 +01:00
John Chodera
6f1de6fac2
Merge pull request #217 from rosemary-cresset/fix-#216
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Fix #216 : Remove % sign from parmchk2 command
2022-08-02 14:55:24 -07:00
John Chodera
d5fe5d0d3b
Merge pull request #218 from rosemary-cresset/fix-#214
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Fix #214 : Leave temp dir before raising exceptions
2022-08-02 14:54:40 -07:00
John Chodera
364c8e3200
Merge pull request #220 from openmm/feat/remove_openeye_check
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remove oe license check
2022-08-02 14:05:08 -07:00
John Chodera
445c356d9a
Merge pull request #191 from mattwthompson/toolkit-update
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Update for upcoming OpenFF Toolkit API breaks
2022-08-02 14:04:17 -07:00
Mike Henry
6a19869112
missed a few bits on openeye removal
2022-08-01 14:54:57 -07:00
Mike Henry
f37599b132
Merge branch 'master' into toolkit-update
2022-08-01 10:39:58 -07:00
Mike Henry
7a4c1d99dc
Merge branch 'master' into dependabot/github_actions/codecov/codecov-action-3.1.0
2022-08-01 10:39:13 -07:00
Mike Henry
2f151233ae
remove oe license check
2022-08-01 10:37:33 -07:00
Rosemary Mantell
5d07fb377d
Fix #215 : Copy gaff dat file to temp dir
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Copy the gaff dat file to the temporary directory before running
parmchk2 to avoid problems with spaces in the path.
2022-07-15 13:22:47 +01:00
Rosemary Mantell
248e7b88e6
Fix #214 : Leave temp dir before raising exceptions
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Change out of temporary directory before raising an exception that
causes the directory to be deleted as the context manager exits. If not
done, a PermissionError is raised repeatedly on Windows and the
message from the original exception is very difficult to read. This
behaviour was observed for the parmchk2 command, but the fix has also
been applied to the antechamber command.
2022-07-15 12:55:20 +01:00
Rosemary Mantell
7eb612494d
Fix #216 : Remove % sign from parmchk2 command
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Unnecessary % sign in the parmchk2 command string sometimes gets filled
with junk characters on Windows and stops the command from running
successfully. This behaviour only occurs on some Windows systems and
does not occur on Linux or Mac.
2022-07-15 12:33:28 +01:00
John Chodera
068f36fc7f
Merge pull request #213 from openmm/fix-#211
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Fix #211 : Use basename instead of full path for cache database table names
2022-07-14 10:19:17 +02:00
Mike Henry
3adb413691
Merge branch 'master' into toolkit-update
2022-07-12 13:53:55 -07:00
John Chodera
1bdba6b112
Fix missing import
2022-07-12 12:48:01 -04:00
John Chodera
319ca47d4d
Add TODO to use hash in future
2022-07-12 09:45:37 -04:00
John Chodera
eb0f0d0970
Fix #211 : Use basename instead of filepath for cache generation
2022-07-12 09:44:34 -04:00
John Chodera
f9b08ea218
Merge pull request #212 from openmm/fix-gaff2
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Fix #210 : gaff atom type name is now correctly passed
2022-07-12 06:41:21 -07:00
John Chodera
051b2427c4
Fix logic in detecting gaff version
2022-07-12 09:05:36 -04:00
John Chodera
c1b07861d3
Fix #210 : gaff atom type name is now correctly passed
2022-07-12 01:38:58 -04:00
John Chodera
815dfd1d52
Merge pull request #208 from openmm/fix-tests
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Fix accidental elimination of torsions after 0.11.0 release
2022-07-11 22:26:07 -07:00
John Chodera
b8cd9a0175
Test against espaloma master to see if bugfix addresses test failure
2022-07-12 00:44:31 -04:00
John Chodera
975773c4e2
Remove voluminous debug output
2022-07-10 18:22:10 -04:00
John Chodera
95afb47eca
Reduce number of molecules for CI tests
2022-07-10 17:48:11 -04:00
John Chodera
583be46deb
Fix critical bug introduced in PR #198 that meant no torsions were converted into templates
2022-07-10 16:49:25 -04:00
John Chodera
29e186f0f2
Fix and generalize tests to produce more useful error message
2022-07-10 16:30:00 -04:00
John Chodera
08afe1681e
Fix bug in refactored code
2022-07-10 12:12:33 -07:00
John Chodera
ddd4503afc
More debug information
2022-07-09 21:33:49 -07:00
John Chodera
8cb79796e4
Refactor to eliminate some duplication and add debug XML output
2022-07-09 21:06:30 -07:00
John Chodera
7095e66355
Change how we measure relative deviation in vectors to avoid underflow.
2022-07-09 19:59:44 -07:00
Mike Henry
7e2c769003
remove leftover bit from debugging
2022-05-16 15:30:03 -07:00
