Changes to openff-qcsubmit to use next QCFractal (#195)

* Fix imports for qcfractal next, remove unnecessary bits * Additional fixes * More name updates * More renames * KeywordSet is no longer * CI conda envs adjusted to use `next` branches * FractalClient -> PortalClient * Dataset updates * Test updates * Data model fixes in test_results * Test fixes... * More dataset cleanup to match qcportal next * Fix missing import * Changes from working session with @bennybp * Update to new qcportal * Fixes for singlepoint dataset * More work on portal updates * Fix where cmiles is for opt datasets * Lint * Lint * More updates for work with next * update test env with beta QCF packages * lint and kick CI * update envs, drop bad test folder temporarily * update PortalClient to snowflake, get a basic submission test working * isort test_submission.py * factor `await_results` out of `basic_submissions_single_spec` * error if await_results fails and pass optional timeout * uncomment other single_spec tests * call await_results with client instead of fulltest_client * update psi4.yaml to work with psi4 1.8, openff-toolkit-base 0.14.0 most of this is from matt's PR #220 with the additional pins on pint and openff-units and the addition of postgresql * pass check_fn to await_results and print more info on error * pass test_submissions through test_basic_submissions_multiple_spec * move RecordStatusEnum import to top level and isort * pass test_submissions through test_basic_submissions_single_pcm_spec * factor out check_last_spec; pass test_basic_submissions_wavefunction * pass test_index_not_changed * don't inherit TorsiondriveDataset.get_specifications * also update torsiondrive_keywords kwarg * and TorsionDriveDataset.type name * pass test_expanding_compute minus object_map check at the end * get rid of enough snowflakes that all tests terminate * add docstring to check_metadata * pass test_optimization_submissions with a minor (?) todo * constraints as additional_keywords in OptimizationDatasetNewEntry * pass test_optimization_submissions_with_constraints * get test_adding_specifications working, but just by disabling half of it * Exposed `find_existing` kwarg for PortalClient datasets in QCSubmit datasets * run CI on python 3.9 * skip tests/results folder for now * standardize on use of fulltest_client instead of snowflake, fix test_adding_compute for OptimizationDatasets * fixed other cases in test_add_compute * fixing more tests in test_submissions * temporarily remove find_existing for testing purposes * more fixes in test_submissions.py * test/dataset class updates to get most dataset tests passing * bring tests/results back online * re-enable tests/results * update two filter tests * More fixes for filters.py and tests * remaining "easy" fixes for test_filters * Fixing more tests in test_results * lining up dataset type names with QCF next * arbitrarily take the last trajectory step in pcm opt test * fix keyword checks * finish fixing test_datasets, note future actions in PR to-dos * fix mocking for singlepoint and optimization to_records tests * manually set portal address * Fix OptimizationResultCollection.to_basic_record_collection, rewire test to use the smallest real opt dataset with hessians to get out of mocking hell * update test_to_records with specs that have no failures * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * get final molecules instead of initial ones in ORC.to_records * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update CI * partial test fixes * fix test_submissions by re-adding dataset.submit's verbose kwarg and fixing spec info lookup * fix submission checking in tests * fix molecule vs. record counting in test_results * fix propagating qc spec keywords(?) * increase timeout for pcm test * try smaller mol and longer timeout for pcm test, fix keywords in that and regular opt test * actually have test_torsiondrive_submissions test torsiondrive submissions * delete caching.py, imports, and tests * fix torsiondrive constraint keyword propagation and tests * stop using cached clients * small cleanups * add specification descriptions to qcportal, update tests * fix smirnoff99frost method * remove print * update invalid-cmiles test, wire up propagation of some attributes to entries * fix inchi lookup in results.py * try fixing test timeouts and reduce output spam * walk back overzealous identifier assignment * testing fixes * clean up unused code+comments * black and isort * re-add pre-commit config * flake8 cleanups * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * fix import and formatting * increase timeout for test_torsiondrive_constraints and format * remove unused imports * update examples and skip unavailable hessian results --------- Co-authored-by: Benjamin Pritchard <[email protected]> Co-authored-by: Matthew W. Thompson <[email protected]> Co-authored-by: Jeffrey Wagner <[email protected]> Co-authored-by: Brent Westbrook <[email protected]> Co-authored-by: Jeff Wagner <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Josh Horton <[email protected]>
openforcefield · Nov 1, 2023 · a968d44 · a968d44
1 parent 68cf309
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         python-version:
-          - "3.9"
+          - 3.9
         cfg:
           - os: ubuntu-latest
             conda-env: basic
@@ -60,7 +60,7 @@ jobs:
 
       - name: Install Package
         run: |
-          python -m pip install .
+          python setup.py develop --no-deps
 
       - name: Conda Environment Information
         run: |

diff --git a/.github/workflows/Lint.yaml b/.github/workflows/Lint.yaml
@@ -0,0 +1,37 @@
+name: lint
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+
+      - uses: actions/checkout@v2
+      - uses: actions/[email protected]
+        with:
+          python-version: '3.8'
+      - name: Install the package
+        run: |
+          python setup.py develop --no-deps
+
+      - name: Install isort / black
+        run: |
+          pip install isort black
+
+      - name: Run isort
+        run: |
+          isort --recursive --check-only openff
+
+      - name: Run black
+        run: |
+          black openff --check
diff --git a/.gitignore b/.gitignore
@@ -103,7 +103,4 @@ ENV/
 .mypy_cache/
 
 # PyCharm
-.idea
-
-# macOS
-.DS_Store
+.idea
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -20,4 +20,4 @@ repos:
   rev: 6.1.0
   hooks:
   - id: flake8
-    files: ^openff
+    files: ^openff
diff --git a/devtools/conda-envs/basic.yaml b/devtools/conda-envs/basic.yaml
@@ -19,23 +19,28 @@ dependencies:
 
   - qcengine >=0.25
   - qcelemental >=0.25.1
-  - qcfractal>=0.15.7
+  - qcfractal>0.49
+  - qcarchivetesting>0.49
+  - qcportal>=0.49
+
+  - postgresql
 
   - openeye-toolkits
 
   ### Core dependencies.
 
   # openmmforcefields brings in the full toolkit; if that is ever re-packaged
   # this should be changed to openff-toolkit-base
+
   - openff-toolkit >= 0.14.0
   - openff-units >=0.2.1
   - pydantic =1
   - pyyaml
-  - qcportal>=0.15.7, <0.50.0a0
   - torsiondrive
   - basis_set_exchange
   - typing-extensions
   - h5py>=3.6.0
+  - psycopg2        # for qcfractal to pip-install without issue
 
   # Optional
   - openmmforcefields

diff --git a/devtools/conda-envs/psi4.yaml b/devtools/conda-envs/psi4.yaml
@@ -2,8 +2,8 @@ name: qcsubmit-test-psi4
 
 channels:
   - conda-forge
-  - conda-forge/label/libint_dev  # needed for psi4/libint2
   - openeye
+  - conda-forge/label/libint_dev # for psi4 1.8
 
 dependencies:
 
@@ -19,8 +19,9 @@ dependencies:
 
   - qcengine >=0.25
   - qcelemental >=0.25.1
-  - qcfractal >=0.15.7
-  - qcfractal-core >=0.15.7
+  - qcfractal>0.49
+  - qcarchivetesting>0.49
+  - qcportal>=0.49
 
   - openeye-toolkits
 
@@ -33,7 +34,6 @@ dependencies:
   - rdkit
   - pydantic =1
   - pyyaml
-  - qcportal>=0.15.7, <0.50.0a0
   - torsiondrive
   - basis_set_exchange
   - typing-extensions
@@ -43,3 +43,7 @@ dependencies:
   - openmmforcefields >=0.9.0
   - openff-fragmenter-base >=0.2.0
   - openmm
+
+  - pint=0.21
+  - openff-units=0.2.1
+  - postgresql
diff --git a/docs/conf.py b/docs/conf.py
@@ -52,7 +52,7 @@
 
 master_doc = "index"
 
-language = "en"
+language = 'en'
 
 exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
@@ -105,10 +105,6 @@
         "http://docs.qcarchive.molssi.org/projects/qcelemental/en/latest/",
         None,
     ),
-    "openff.docs": (
-        "https://docs.openforcefield.org/en/latest/",
-        None,
-    ),
 }
 
 # Set up mathjax.

diff --git a/docs/installation.md b/docs/installation.md
@@ -8,8 +8,6 @@ The recommended way to install QCSubmit is via the `conda` package manger:
 conda install -c conda-forge openff-qcsubmit
 ```
 
-If you do not have Conda installed, see the [OpenFF installation guide](openff.docs:install)
-
 ### Optional dependencies
 
 If you have access to the OpenEye toolkits (namely `oechem`, `oequacpac`, `oeomega` and `oedepict`), we recommend installing these also as these can speed up various operations performed by this framework significantly: