Merge pull request #999 from MolSSI/test_clean

Some testing & other cleanup

Author: bennybp

…esting/qcarchivetesting/pytest_config.py conftest.pyqcarchivetesting/qcarchivetesting/pytest_config.py renamed to conftest.py qcarchivetesting/qcarchivetesting/pytest_config.py renamed to conftest.py

@@ -2,10 +2,6 @@
 Contains testing infrastructure for QCFractal.
 """
 
-# This file is normally named conftest.py, but doing so
-# runs into issues with pytest automatically finding this, but also
-# having it be found through the pyproject.toml entry point
-
 import pytest
 
 
@@ -24,11 +20,6 @@ def pytest_addoption(parser):
 
 
 def pytest_collection_modifyitems(config, items):
-    """
-    Handle test triggers based on the CLI flags
-    Use decorators:
-    @pytest.mark.slow
-    """
     runslow = config.getoption("--runslow")
 
     skip_slow = pytest.mark.skip(reason="need --runslow option to run")

pyproject.toml

@@ -0,0 +1,5 @@
+[tool.black]
+line-length = 120
+
+[tool.pytest.ini_options]
+markers = ["slow"]

qcarchivetesting/conda-envs/fulltest_server.yaml

@@ -22,7 +22,6 @@ dependencies:
   - pandas
   - pyjwt>=2.10.0
   - packaging
-  - typing_extensions
   - python-dateutil
   - pytz
 

qcarchivetesting/conda-envs/fulltest_snowflake.yaml

@@ -22,7 +22,6 @@ dependencies:
   - pandas
   - pyjwt>=2.10.0
   - packaging
-  - typing_extensions
   - python-dateutil
   - pytz
 

qcarchivetesting/conda-envs/fulltest_testing.yaml

@@ -22,7 +22,6 @@ dependencies:
   - pandas
   - pyjwt>=2.10.0
   - packaging
-  - typing_extensions
   - python-dateutil
   - pytz
 

qcarchivetesting/conda-envs/fulltest_worker.yaml

@@ -20,7 +20,6 @@ dependencies:
   - pandas
   - pyjwt>=2.10.0
   - packaging
-  - typing_extensions
   - python-dateutil
   - pytz
 

qcarchivetesting/pyproject.toml

@@ -36,17 +36,12 @@ dependencies = [
 
 [project.entry-points.pytest11]
 qcarchive_fixtures = "qcarchivetesting.testing_fixtures"
-qcarchive_conftest = "qcarchivetesting.pytest_config"
 
 
 [tool.setuptools.package-data]
 qcarchivetesting = ["*_data/**", "config_files/**"]
 
 
-[tool.black]
-line-length = 120
-
-
 [tool.versioningit]
 
 

qcfractal/pyproject.toml

@@ -64,20 +64,12 @@ qcfractal-server = "qcfractal.qcfractal_server_cli:main"
 qcfractal = ["alembic.ini", "alembic/script.py.mako"]
 
 
-[tool.black]
-line-length = 120
-
-
 [tool.versioningit]
 
 
 [tool.versioningit.vcs]
 default-tag = "0.0.99" # useful for CI/shallow clones
 
 
-[tool.pytest.ini_options]
-markers = ["slow"]
-
-
 [tool.coverage.run]
 omit = ["qcfractal/alembic/*"]

qcfractal/qcfractal/qcfractal_server_cli.py

@@ -567,59 +567,6 @@ def server_upgrade_db(config):
         sys.exit(1)
 
 
-def server_upgrade_config(config_path):
-    import secrets
-    from qcfractal.old_config import OldFractalQCFConfig
-    from qcfractal.config import convert_old_configuration
-
-    logger = logging.getLogger(__name__)
-
-    logger.info(f"Reading configuration data from {config_path}")
-    with open(config_path, "r") as yf:
-        file_data = yaml.safe_load(yf)
-
-    # Is this really an old config?
-    if "fractal" not in file_data:
-        logger.info(f"Configuration appears to be up-to-date")
-        return
-
-    old_qcf_config = OldFractalQCFConfig(**file_data)
-    new_qcf_config = convert_old_configuration(old_qcf_config)
-
-    # Move the old file out of the way
-    base_backup_path = config_path + ".backup"
-    backup_path = base_backup_path
-
-    # Find a suitable backup name. If the path exists,
-    # add .1, .2, .3, etc, until it does
-    i = 1
-    while os.path.exists(backup_path):
-        backup_path = base_backup_path + f".{i}"
-        i += 1
-
-    logger.info(f"Moving original configuration to {backup_path}")
-    shutil.move(config_path, backup_path)
-
-    # We strip out some stuff from the configuration, including things that were
-    # set to the default
-    new_qcf_config_dict = new_qcf_config.dict(skip_defaults=True)
-    new_qcf_config_dict["database"].pop("base_folder")
-    new_qcf_config_dict.pop("base_folder")
-
-    # Generate secret keys for the user. They can always change it later
-    new_qcf_config_dict["api"]["secret_key"] = secrets.token_hex(24)
-    new_qcf_config_dict["api"]["jwt_secret_key"] = secrets.token_hex(24)
-
-    logger.info(f"Writing new configuration data to  {config_path}")
-    with open(config_path, "w") as yf:
-        yaml.dump(new_qcf_config_dict, yf)
-
-    logger.info("*" * 80)
-    logger.info("Your configuration file has been upgraded, but will most likely need some fine tuning.")
-    logger.info(f"Please edit {config_path} by hand. See the upgrade documentation for details.")
-    logger.info("*" * 80)
-
-
 def server_user(args: argparse.Namespace, config: FractalConfig):
     user_command = args.user_command
 
@@ -901,8 +848,7 @@ def main():
     if args.command == "upgrade-config":
         if args.config is None:
             raise RuntimeError("Configuration file path (--config) is required for upgrading configuration")
-        server_upgrade_config(args.config)
-        exit(0)
+        raise RuntimeError("Upgrade configuration is not yet supported")
 
     # Check for the config path on the command line. The command line
     # always overrides environment variables

qcfractalcompute/pyproject.toml

@@ -41,10 +41,6 @@ qcfractal-compute-manager = "qcfractalcompute.compute_manager_cli:main"
 qcfractalcompute = ["run_scripts/**"]
 
 
-[tool.black]
-line-length = 120
-
-
 [tool.versioningit]