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Merge pull request #838 from MolSSI/rel_55
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Release v0.55
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bennybp authored May 23, 2024
2 parents 3ead276 + 671556d commit eea42a7
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6 changes: 1 addition & 5 deletions .github/PULL_REQUEST_TEMPLATE.md
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@@ -1,11 +1,7 @@
<!-- Thank you for your contribution! -->

## Description
<!-- Thank you for your contribution! -->
<!-- Provide a brief description of the PR's purpose here. -->

## Changelog description
<!-- Provide a brief single sentence for the changelog. -->

## Status
- [ ] Code base linted
- [ ] Ready to go
2 changes: 1 addition & 1 deletion .github/workflows/build_docs.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
with:
fetch-depth: 0 # needed for tag/version

- uses: actions/setup-python@v4
- uses: actions/setup-python@v5
with:
python-version: '3.11'

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2 changes: 1 addition & 1 deletion .github/workflows/core_tests.yml
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Expand Up @@ -28,7 +28,7 @@ jobs:
run: sudo apt update && sudo apt install postgresql postgresql-contrib

- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

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14 changes: 4 additions & 10 deletions .github/workflows/full_tests.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

Expand All @@ -39,11 +39,9 @@ jobs:
# QCFractal Server
#################################################
- name: Configure conda for the QCFractal server
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: qcarchive-server
environment-file: qcarchive/qcarchivetesting/conda-envs/fulltest_server.yaml
auto-activate-base: false
Expand Down Expand Up @@ -72,11 +70,9 @@ jobs:
# QCFractalCompute worker
#################################################
- name: Configure conda for QCFractalCompute worker
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: qcarchive-worker
environment-file: qcarchive/qcarchivetesting/conda-envs/fulltest_worker.yaml
auto-activate-base: false
Expand Down Expand Up @@ -104,11 +100,9 @@ jobs:
# QCPortal client
#################################################
- name: Configure conda for the QCPortal client
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: qcarchive-qcportal
environment-file: qcarchive/qcarchivetesting/conda-envs/fulltest_qcportal.yaml
auto-activate-base: false
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6 changes: 2 additions & 4 deletions .github/workflows/full_tests_snowflake.yml
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ jobs:

steps:
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}

Expand All @@ -34,11 +34,9 @@ jobs:
fetch-depth: 0

- name: Configure conda for the snowflake
uses: conda-incubator/setup-miniconda@v2
uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
miniforge-variant: Mambaforge
miniforge-version: latest
activate-environment: qcarchive-snowflake
environment-file: qcarchivetesting/conda-envs/fulltest_snowflake.yaml
auto-activate-base: false
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29 changes: 29 additions & 0 deletions docs/source/release_notes.rst
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@@ -1,6 +1,35 @@
Release Notes
=============

0.55 / 2024-05-23
-------------------

Some moderate improvements - mainly, the use of ASPW for SQLite, and the removal of the never-used manager log and
serverinfo log tables. Also adds maintenance jobs for removing old access log and completed internal jobs.

This release also adds the ability to more-strictly handle queue tags (to prevent managers with `*` as a tag from pulling
everything).

In addition, lots of smaller bug fixes and improvements.

Notable PRs:

- (:pr:`819`) Fix native_files fields return from server & ORM
- (:pr:`821`) Enable dumping a database from a snowflake
- (:pr:`822`) Fix missing client on cached dataset records
- (:pr:`825`) Fix database constraint violation when program version contains uppercase characters
- (:pr:`826`) Fix type of results in ServiceSubtaskRecord
- (:pr:`829`) Replace sqlite3 (python stdlib module) with APSW
- (:pr:`830`) Remove server stats & compute manager logs
- (:pr:`831`) Add internal job to delete old access log entries
- (:pr:`832`) Add internal job to delete old, finished internal jobs
- (:pr:`834`) Add property to get errored child records
- (:pr:`835`) Better handling of queue tags (strict queue tags and case insensitivity)
- (:pr:`836`) Replace gunicorn with waitress and fix logging issues
- (:pr:`837`) Commit to database after every returned task is processed (to help prevent deadlocks)
- (:pr:`838`) Better handling of passwords with `init-db`


0.54.1 / 2024-04-12
-------------------

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2 changes: 1 addition & 1 deletion qcarchivetesting/conda-envs/fulltest_qcportal.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ dependencies:
- pydantic
- zstandard
- apsw
- qcelemental
- qcelemental<0.70a0
- tabulate
- tqdm
- pandas
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2 changes: 1 addition & 1 deletion qcarchivetesting/conda-envs/fulltest_server.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ dependencies:
- pydantic
- zstandard
- apsw
- qcelemental
- qcelemental<0.70a0
- tabulate
- tqdm
- pandas
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7 changes: 3 additions & 4 deletions qcarchivetesting/conda-envs/fulltest_snowflake.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
name: qcarchive-snowflake
channels:
- conda-forge
- conda-forge/label/libint_dev
- defaults

dependencies:
Expand All @@ -17,7 +16,7 @@ dependencies:
- pydantic
- zstandard
- apsw
- qcelemental
- qcelemental<0.70a0
- tabulate
- tqdm
- pandas
Expand All @@ -44,8 +43,8 @@ dependencies:
- torsiondrive

# Worker codes below
- qcengine
- psi4>=1.7
- qcengine<0.70a0
- psi4>=1.9.1
- rdkit

# Testing packages
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7 changes: 3 additions & 4 deletions qcarchivetesting/conda-envs/fulltest_worker.yaml
Original file line number Diff line number Diff line change
@@ -1,7 +1,6 @@
name: qcarchive-worker
channels:
- conda-forge
- conda-forge/label/libint_dev
- defaults

dependencies:
Expand All @@ -16,7 +15,7 @@ dependencies:
- pydantic
- zstandard
- apsw
- qcelemental
- qcelemental<0.70a0
- tabulate
- tqdm
- pandas
Expand All @@ -30,8 +29,8 @@ dependencies:
- parsl

# Worker codes below
- qcengine
- psi4>=1.7
- qcengine<0.70a0
- psi4>=1.9.1
- rdkit

# Geometric service
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2 changes: 1 addition & 1 deletion qcarchivetesting/pyproject.toml
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Expand Up @@ -22,7 +22,7 @@ classifiers = [
]
dependencies = [
"qcfractal",
"qcengine",
"qcengine<0.70a0",
"pytest",
]

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Original file line number Diff line number Diff line change
Expand Up @@ -111,7 +111,7 @@ def test_internal_jobs_client_cancel_running(snowflake: QCATestingSnowflake):

job_1 = snowflake_client.get_internal_job(id_1)
assert job_1.status == InternalJobStatusEnum.cancelled
assert job_1.progress < 50
assert job_1.progress < 70
assert job_1.result == "Internal job cancelled"

finally:
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,7 @@ def test_internal_jobs_socket_recover(storage_socket: SQLAlchemySocket, session:
end_event = threading.Event()
th = threading.Thread(target=storage_socket.internal_jobs.run_loop, args=(end_event,))
th.start()
time.sleep(15)
time.sleep(30)

try:
session.expire(job_1)
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6 changes: 6 additions & 0 deletions qcfractal/qcfractal/qcfractal_server_cli.py
Original file line number Diff line number Diff line change
Expand Up @@ -547,6 +547,12 @@ def server_start_api(config):


def server_upgrade_db(config):

# Always set logging level to INFO, otherwise things are a bit quiet
root_logger = logging.getLogger()
if root_logger.level > logging.INFO:
root_logger.setLevel(logging.INFO)

logger = logging.getLogger(__name__)

# Don't use start_database - we don't want to create the socket (which
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4 changes: 2 additions & 2 deletions qcfractalcompute/qcfractalcompute/test_compute_manager.py
Original file line number Diff line number Diff line change
Expand Up @@ -226,13 +226,13 @@ def test_manager_missed_heartbeats_shutdown(snowflake: QCATestingSnowflake):

snowflake.stop_api()

for i in range(60):
for i in range(90):
time.sleep(1)

if not compute_thread.is_alive():
break
else:
raise RuntimeError("Compute thread did not stop in 60 seconds")
raise RuntimeError("Compute thread did not stop in 90 seconds")

compute_thread._compute_thread.join(5)
assert compute_thread.is_alive() is False
2 changes: 1 addition & 1 deletion qcportal/pyproject.toml
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ dependencies = [
"pydantic",
"zstandard",
"apsw",
"qcelemental",
"qcelemental<0.70a0",
"tabulate",
"tqdm",
"pandas",
Expand Down

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