Add `requires_openeye` decorators when `oechem` is used #275

mattwthompson · 2023-07-13T14:28:35Z

Description

This PR attempts to fix #271 by checking for an OpenEye license when oechem is used and failing out with a descriptive error message. I haven't put the work into testing it in a live run, but the minimal behavior should follow this script:

from openff.utilities.utilities import requires_oe_module

@requires_oe_module("oechem")
def hello():
    from openeye import oechem
    print("hello")

hello()

Running (with openeye-toolkits installed) and mucking with the license path:

$ python script.py && mv ~/.oe_license.txt /tmp && python script.py
hello
LICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
Traceback (most recent call last):
  File "/Users/mattthompson/software/openff-bespokefit/script.py", line 8, in <module>
    hello()
  File "/Users/mattthompson/mambaforge/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/utilities/utilities.py", line 80, in wrapper
    return function(*args, **kwargs)
  File "/Users/mattthompson/mambaforge/envs/openff-toolkit-test/lib/python3.10/site-packages/openff/utilities/utilities.py", line 123, in wrapper
    raise MissingOptionalDependencyError(
openff.utilities.exceptions.MissingOptionalDependencyError: The required openeye.oechem module could not be imported. This is due to a missing license.

I couldn't find other cases in which an openeye.* API is actually called, just this bit I don't understand and here, where it's tracked for provenance, it could possibly be useful to also check that it's licensed. That's not related to the original issue so I didn't change that.

Todos

Notable points that this PR has either accomplished or will accomplish.

Check for a license when oechem is called
Check other calls

Status

Ready to go

jthorton · 2023-07-13T14:43:28Z

Thanks @mattwthompson, I think we just need to catch this new exception here and here for this to work and ill give it a test run!

mattwthompson · 2023-07-13T14:48:44Z

Ah, I see, I guess that's why the tests were failing

codecov · 2023-07-13T14:54:46Z

Codecov Report

Merging #275 (420383c) into main (6050dba) will decrease coverage by 0.19%.
The diff coverage is 100.00%.

Additional details and impacted files

jthorton · 2023-07-13T15:46:05Z

My test run didn't go to plan I originally saw this coming from the branch in #272 where the worker and server were running different environments and I think this PR will fix that, but in testing, I have to use them in the same environment with the license file path edited and a new error from fragmenter appears related to the same thing.

Testing command

openff-bespoke executor run --smiles             "CC(=O)NC1=CC=C(C=C1)O" \
                            --workflow           "default"               \
                            --output             "acetaminophen.json"    \
                            --output-force-field "acetaminophen.offxml"  \
                            --n-qc-compute-workers 2                     \
                            --qc-compute-n-cores   1                     \
                            --default-qc-spec xtb gfn2xtb none

Error

{"smiles": "[C:1]([C:2](=[O:3])[N:4]([c:5]1[c:6]([H:7])[c:8]([H:9])[c:10]([O:11][H:12])[c:13]([H:14])[c:15]1[H:16])[H:17])([H:18])([H:19])[H:20]", "stages": [{"type": "qc-generation", "status": "waiting", "error": null}, {
"type": "optimization", "status": "waiting", "error": null}, {"type": "fragmentation", "status": "errored", "error": "{\"type\": \"ValueError\", \"message\": \"No registered toolkits can provide the capability \\\"to_opene
ye\\\" for args \\\"(Molecule with name '' and SMILES '[H][O][c]1[c]([H])[c]([H])[c]([N]([H])[C](=[O])[C]([H])([H])[H])[c]([H])[c]1[H]',)\\\" and kwargs \\\"{'aromaticity_model': 'OEAroModel_MDL'}\\\"\\nAvailable toolkits 
are: [ToolkitWrapper around The RDKit version 2023.03.2, ToolkitWrapper around AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]\\n\", \"traceback\": \"Traceback (most recent call last):\\n  Fil
e \\\"/home/b6056633/micromamba/envs/bespokefit/lib/python3.9/site-packages/celery/app/trace.py\\\", line 477, in trace_task\\n    R = retval = fun(*args, **kwargs)\\n  File \\\"/home/b6056633/micromamba/envs/bespokefit/li
b/python3.9/site-packages/celery/app/trace.py\\\", line 760, in __protected_call__\\n    return self.run(*args, **kwargs)\\n  File \\\"/home/b6056633/programs/openff-bespokefit/openff/bespokefit/executor/services/fragmente
r/worker.py\\\", line 36, in fragment\\n    fragmenter.fragment(molecule, target_bond_smarts=target_bond_smarts)\\n  File \\\"/home/b6056633/micromamba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/fragment
.py\\\", line 916, in fragment\\n    result = self._fragment(molecule, target_bond_smarts)\\n  File \\\"/home/b6056633/micromamba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/fragment.py\\\", line 1019, in
 _fragment\\n    fragments = {\\n  File \\\"/home/b6056633/micromamba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/fragment.py\\\", line 1020, in <dictcomp>\\n    bond: self._build_fragment(\\n  File \\\"/
home/b6056633/micromamba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/fragment.py\\\", line 1191, in _build_fragment\\n    fragment, has_new_stereocenter = cls._atom_bond_set_to_mol(\\n  File \\\"/home/b60
56633/micromamba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/fragment.py\\\", line 391, in _atom_bond_set_to_mol\\n    fragment = extract_fragment(parent, atoms, bonds)\\n  File \\\"/home/b6056633/microma
mba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/chemi.py\\\", line 488, in extract_fragment\\n    fragment = _extract_oe_fragment(molecule, atom_indices, bond_indices)\\n  File \\\"/home/b6056633/micromam
ba/envs/bespokefit/lib/python3.9/site-packages/openff/fragmenter/chemi.py\\\", line 397, in _extract_oe_fragment\\n    oe_molecule = molecule.to_openeye()\\n  File \\\"/home/b6056633/micromamba/envs/bespokefit/lib/python3.
9/site-packages/openff/toolkit/topology/molecule.py\\\", line 5048, in to_openeye\\n    return toolkit_registry.call(\\n  File \\\"/home/b6056633/micromamba/envs/bespokefit/lib/python3.9/site-packages/openff/toolkit/utils/
toolkit_registry.py\\\", line 370, in call\\n    raise ValueError(msg)\\nValueError: No registered toolkits can provide the capability \\\"to_openeye\\\" for args \\\"(Molecule with name '' and SMILES '[H][O][c]1[c]([H])[c
]([H])[c]([N]([H])[C](=[O])[C]([H])([H])[H])[c]([H])[c]1[H]',)\\\" and kwargs \\\"{'aromaticity_model': 'OEAroModel_MDL'}\\\"\\nAvailable toolkits are: [ToolkitWrapper around The RDKit version 2023.03.2, ToolkitWrapper aro
und AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version None]\\n\\n\"}"}], "results": null}

I think this indicates we need to use these decorators here as well.

mattwthompson · 2023-07-14T13:52:00Z

I've opened openforcefield/openff-fragmenter#164 to try to fix that; the branch there is openeye-license

mattwthompson · 2023-07-14T16:11:58Z

That branch should be working now, but you'll have to bump openff-utilities =0.1.9

mattwthompson · 2023-08-09T21:07:10Z

Blocked in some capacity by a new QCSubmit

j-wags · 2023-08-23T19:23:25Z

This should now be unblocked by QCSubmit 0.5.0 (re-enables compatibility with legacy QCF)

mattwthompson · 2023-08-23T20:06:12Z

Blocked by leeping/forcebalance#285

j-wags · 2023-10-13T17:38:08Z

I think this is superseded by #286, @mattwthompson or @jthorton could you confirm? If so (and this is resolved) I'd recommend a BespokeFit 0.2.3 release on Monday, which relaxes pins in the bespokefit conda recipe to allow the use of latest ForceBalance and OFFTK.

jthorton · 2023-10-16T11:10:10Z

I think we still want the openeye decorators in this PR as well.

j-wags · 2023-10-16T15:47:32Z

Ahh, apologies. I missed that detail. Please feel free to revert my PR if you'd like to have that all go in at once!

mattwthompson · 2023-11-07T18:36:50Z

I'm still having troubles with this - maybe my patch to Fragmenter didn't do what it needed it to do?

(bespokefit) [openff-bespokefit] openff-bespoke executor launch &
[1] 34821
(bespokefit) [openff-bespokefit] LICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!

──────────────────────────────── OpenFF Bespoke ────────────────────────────────

⠸ launching the bespoke executorLICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
⠼ launching the bespoke executorLICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
LICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
⠴ launching the bespoke executorLICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
⠴ launching the bespoke executorLICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
[✓] bespoke executor launched
(bespokefit) [openff-bespokefit] openff-bespoke executor submit --smiles 'CC(=O)NC1=CC=C(C=C1)O' --workflow debug
LICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!

──────────────────────────────── OpenFF Bespoke ────────────────────────────────

1. preparing the bespoke workflow

[✓] 1 molecules found
[✓] fitting schemas generated

2. submitting the workflow

[✓] the following workflows were submitted
┏━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━┳━━━━━━┓
┃ ID ┃ SMILES             ┃ NAME ┃ FILE ┃
┡━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━╇━━━━━━┩
│ 7  │ CC(=O)Nc1ccc(O)cc1 │      │      │
└────┴────────────────────┴──────┴──────┘
(bespokefit) [openff-bespokefit] openff-bespoke executor watch --id 7
LICENSE: Could not open license file specified by OE_LICENSE environment variable "/Users/mattthompson/.oe_license.txt"
LICENSE: Could not open license file "oe_license.txt" in local directory
LICENSE: N.B. OE_DIR environment variable is not set
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!
LICENSE: No product keys!

──────────────────────────────── OpenFF Bespoke ────────────────────────────────

[x] fragmentation failed

 {"type": "ValueError", "message": "No registered toolkits can provide the
 capability \"to_openeye\" for args \"(Molecule with name '' and SMILES
 '[H][O]1([H])([H])([N]([H])[C](=[O])[C]([H])([H])[H])([H])1[H]',)\" and kwargs
 \"{'aromaticity_model': 'OEAroModel_MDL'}\"\nAvailable toolkits are:
 [ToolkitWrapper around The RDKit version 2023.09.1, ToolkitWrapper around
 AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version
 None]\n", "traceback": "Traceback (most recent call last):\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/ce
 lery/app/trace.py\", line 477, in trace_task\n    R = retval = fun(*args,
 **kwargs)\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/ce
 lery/app/trace.py\", line 760, in __protected_call__\n    return
 self.run(*args, **kwargs)\n  File
 \"/Users/mattthompson/software/openff-bespokefit/openff/bespokefit/executor/ser
 vices/fragmenter/worker.py\", line 36, in fragment\n
 fragmenter.fragment(molecule, target_bond_smarts=target_bond_smarts)\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/fragment.py\", line 916, in fragment\n    result =
 self._fragment(molecule, target_bond_smarts)\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/fragment.py\", line 1019, in _fragment\n    fragments = {\n
 File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/fragment.py\", line 1020, in <dictcomp>\n    bond:
 self._build_fragment(\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/fragment.py\", line 1191, in _build_fragment\n    fragment,
 has_new_stereocenter = cls._atom_bond_set_to_mol(\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/fragment.py\", line 391, in _atom_bond_set_to_mol\n    fragment
 = extract_fragment(parent, atoms, bonds)\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/chemi.py\", line 488, in extract_fragment\n    fragment =
 _extract_oe_fragment(molecule, atom_indices, bond_indices)\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/fragmenter/chemi.py\", line 397, in _extract_oe_fragment\n    oe_molecule
 = molecule.to_openeye()\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/toolkit/topology/molecule.py\", line 5048, in to_openeye\n    return
 toolkit_registry.call(\n  File
 \"/Users/mattthompson/mambaforge/envs/bespokefit/lib/python3.9/site-packages/op
 enff/toolkit/utils/toolkit_registry.py\", line 370, in call\n    raise
 ValueError(msg)\nValueError: No registered toolkits can provide the capability
 \"to_openeye\" for args \"(Molecule with name '' and SMILES
 '[H][O]1([H])([H])([N]([H])[C](=[O])[C]([H])([H])[H])([H])1[H]',)\" and kwargs
 \"{'aromaticity_model': 'OEAroModel_MDL'}\"\nAvailable toolkits are:
 [ToolkitWrapper around The RDKit version 2023.09.1, ToolkitWrapper around
 AmberTools version 22.0, ToolkitWrapper around Built-in Toolkit version
 None]\n\n"}
(bespokefit) [openff-bespokefit] conda list openff                     12:34:46  ☁  openeye-decorators ☂ ✭
# packages in environment at /Users/mattthompson/mambaforge/envs/bespokefit:
#
# Name                    Version                   Build  Channel
openff-amber-ff-ports     0.0.3              pyh6c4a22f_0    conda-forge
openff-bespokefit         0.2.2+36.g420383c           dev_0    <develop>
openff-forcefields        2023.08.0          pyh1a96a4e_0    conda-forge
openff-fragmenter-base    0.2.1              pyhd8ed1ab_0    conda-forge
openff-interchange        0.3.10             pyhd8ed1ab_0    conda-forge
openff-interchange-base   0.3.10             pyhd8ed1ab_0    conda-forge
openff-models             0.1.1              pyhca7485f_0    conda-forge
openff-qcsubmit           0.5.0              pyhd8ed1ab_0    conda-forge
openff-toolkit            0.14.4             pyhd8ed1ab_1    conda-forge
openff-toolkit-base       0.14.4             pyhd8ed1ab_1    conda-forge
openff-units              0.2.1              pyh1a96a4e_0    conda-forge
openff-utilities          0.1.11             pyhd8ed1ab_0    conda-forge

mattwthompson · 2024-01-29T17:33:05Z

This has gone stale; if we run into this again it can be revived.

mattwthompson changed the title ~~Add requires_openeye decorators when openeye~~ Add requires_openeye decorators when oechem is used Jul 13, 2023

Add requires_openeye decorators

a6d1cb7

mattwthompson force-pushed the openeye-decorators branch from 4ee8831 to a6d1cb7 Compare July 13, 2023 14:30

Catch exception

afe850e

mattwthompson marked this pull request as ready for review July 13, 2023 14:56

mattwthompson mentioned this pull request Jul 13, 2023

Skip OpenEye functions if license not found, even if installed openforcefield/openff-fragmenter#163

Closed

mattwthompson added 2 commits August 9, 2023 08:21

Merge remote-tracking branch 'upstream/main' into openeye-decorators

0fe28b2

Update test environments

c1058c7

j-wags marked this pull request as draft August 9, 2023 20:13

Update environments

49ec0ac

mattwthompson added 2 commits September 28, 2023 11:15

Merge remote-tracking branch 'upstream/main' into openeye-decorators

2871c0a

Merge remote-tracking branch 'upstream/fb-196' into openeye-decorators

38124b6

mattwthompson added 5 commits October 16, 2023 11:03

Merge remote-tracking branch 'upstream/main' into openeye-decorators

cf5a6e6

Install Interchange

1fe98ec

Merge remote-tracking branch 'upstream/main' into openeye-decorators

a7b610b

Fix merge

5703601

Constrain QCSubmit

420383c

mattwthompson closed this Jan 29, 2024

mattwthompson deleted the openeye-decorators branch September 9, 2024 20:27

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Add `requires_openeye` decorators when `oechem` is used #275

Add `requires_openeye` decorators when `oechem` is used #275

mattwthompson commented Jul 13, 2023

jthorton commented Jul 13, 2023

mattwthompson commented Jul 13, 2023

codecov bot commented Jul 13, 2023 •

edited

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jthorton commented Jul 13, 2023

mattwthompson commented Jul 14, 2023

mattwthompson commented Jul 14, 2023

mattwthompson commented Aug 9, 2023

j-wags commented Aug 23, 2023

mattwthompson commented Aug 23, 2023

j-wags commented Oct 13, 2023

jthorton commented Oct 16, 2023

j-wags commented Oct 16, 2023

mattwthompson commented Nov 7, 2023

mattwthompson commented Jan 29, 2024

Add requires_openeye decorators when oechem is used #275

Add requires_openeye decorators when oechem is used #275

Conversation

mattwthompson commented Jul 13, 2023

Description

Todos

Status

jthorton commented Jul 13, 2023

mattwthompson commented Jul 13, 2023

codecov bot commented Jul 13, 2023 • edited Loading

Codecov Report

jthorton commented Jul 13, 2023

mattwthompson commented Jul 14, 2023

mattwthompson commented Jul 14, 2023

mattwthompson commented Aug 9, 2023

j-wags commented Aug 23, 2023

mattwthompson commented Aug 23, 2023

j-wags commented Oct 13, 2023

jthorton commented Oct 16, 2023

j-wags commented Oct 16, 2023

mattwthompson commented Nov 7, 2023

mattwthompson commented Jan 29, 2024

Add `requires_openeye` decorators when `oechem` is used #275

Add `requires_openeye` decorators when `oechem` is used #275

codecov bot commented Jul 13, 2023 •

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