From 7a1306cca79d2e1b2fe3db8aafe0951866fd22b8 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 17 Apr 2024 07:16:41 +0000 Subject: [PATCH] Add changes for 79b75206a3fdce9e041605720dd4664593b676a4 --- .../py_experimenter/config/index.rst.txt | 2 +- .../database_connector_mysql/index.rst.txt | 5 +- .../experimenter/index.rst.txt | 2 +- .../usage/database_credential_file.rst.txt | 2 +- .../experiment_configuration_file.rst.txt | 2 + autoapi/py_experimenter/config/index.html | 2 +- .../database_connector_mysql/index.html | 6 +- .../py_experimenter/experimenter/index.html | 2 +- changelog.html | 137 +++++++++--------- installation.html | 2 +- objects.inv | Bin 7925 -> 7930 bytes searchindex.js | 2 +- usage/database_credential_file.html | 2 +- usage/experiment_configuration_file.html | 2 + 14 files changed, 86 insertions(+), 82 deletions(-) diff --git a/_sources/autoapi/py_experimenter/config/index.rst.txt b/_sources/autoapi/py_experimenter/config/index.rst.txt index 04316de2..19b5b829 100644 --- a/_sources/autoapi/py_experimenter/config/index.rst.txt +++ b/_sources/autoapi/py_experimenter/config/index.rst.txt @@ -61,7 +61,7 @@ Classes -.. py:class:: DatabaseCfg(provider: str, database_name: str, table_name: str, result_timestamps: bool, keyfields: List[Keyfield], resultfields: Dict[str, str], logtables: Dict[str, Dict[str, str]], logger: logging.Logger) +.. py:class:: DatabaseCfg(provider: str, use_ssh_tunnel: bool, database_name: str, table_name: str, result_timestamps: bool, keyfields: List[Keyfield], resultfields: Dict[str, str], logtables: Dict[str, Dict[str, str]], logger: logging.Logger) Bases: :py:obj:`Cfg` diff --git a/_sources/autoapi/py_experimenter/database_connector_mysql/index.rst.txt b/_sources/autoapi/py_experimenter/database_connector_mysql/index.rst.txt index dfb00267..df1da169 100644 --- a/_sources/autoapi/py_experimenter/database_connector_mysql/index.rst.txt +++ b/_sources/autoapi/py_experimenter/database_connector_mysql/index.rst.txt @@ -17,14 +17,11 @@ Classes -.. py:class:: DatabaseConnectorMYSQL(database_configuration: omegaconf.OmegaConf, use_codecarbon: bool, credential_path: str, use_ssh_tunnel: bool, logger: logging.Logger) +.. py:class:: DatabaseConnectorMYSQL(database_configuration: py_experimenter.config.DatabaseCfg, use_codecarbon: bool, credential_path: str, logger: logging.Logger) Bases: :py:obj:`py_experimenter.database_connector.DatabaseConnector` - Helper class that provides a standard way to create an ABC using - inheritance. - .. py:attribute:: _prepared_statement_placeholder :value: '%s' diff --git a/_sources/autoapi/py_experimenter/experimenter/index.rst.txt b/_sources/autoapi/py_experimenter/experimenter/index.rst.txt index bd5858a4..0af1d152 100644 --- a/_sources/autoapi/py_experimenter/experimenter/index.rst.txt +++ b/_sources/autoapi/py_experimenter/experimenter/index.rst.txt @@ -17,7 +17,7 @@ Classes -.. py:class:: PyExperimenter(experiment_configuration_file_path: str = os.path.join('config', 'experiment_configuration.yml'), database_credential_file_path: str = os.path.join('config', 'database_credentials.yml'), use_ssh_tunnel: bool = False, table_name: str = None, database_name: str = None, use_codecarbon: bool = True, name='PyExperimenter', logger_name: str = 'py-experimenter', log_level: Union[int, str] = logging.INFO, log_file: str = './logs/py-experimenter.log') +.. py:class:: PyExperimenter(experiment_configuration_file_path: str = os.path.join('config', 'experiment_configuration.yml'), database_credential_file_path: str = os.path.join('config', 'database_credentials.yml'), use_ssh_tunnel: Optional[bool] = None, table_name: str = None, database_name: str = None, use_codecarbon: bool = True, name='PyExperimenter', logger_name: str = 'py-experimenter', log_level: Union[int, str] = logging.INFO, log_file: str = './logs/py-experimenter.log') Module handling the initialization, execution and collection of experiments and their respective results. diff --git a/_sources/usage/database_credential_file.rst.txt b/_sources/usage/database_credential_file.rst.txt index 88d27ee0..d868cb62 100644 --- a/_sources/usage/database_credential_file.rst.txt +++ b/_sources/usage/database_credential_file.rst.txt @@ -19,7 +19,7 @@ Below is an example of a database credential file, that connects to a server wit server: example.mysqlserver.com However, for security reasons, databases might only be accessible from a specific IP address. In these cases, one can use an ssh jumphost. This means that ``PyExperimenter`` will first connect to the ssh server -that has access to the database and then connect to the database server from there. This is done by adding an additional ``Ssh`` section to the database credential file. +that has access to the database and then connect to the database server from there. This is done by adding an additional ``Ssh`` section to the database credential file, and can be activated either by a ``PyExperimenter`` keyword argument or in the :ref:`experimenter configuration file <_experiment_configuration_file>`. The following example shows how to connect to a database server using an SSH server with the address ``ssh_hostname`` and the port ``optional_ssh_port``. .. code-block:: yaml diff --git a/_sources/usage/experiment_configuration_file.rst.txt b/_sources/usage/experiment_configuration_file.rst.txt index 6c1de09f..ef11dbcb 100644 --- a/_sources/usage/experiment_configuration_file.rst.txt +++ b/_sources/usage/experiment_configuration_file.rst.txt @@ -14,6 +14,7 @@ The experiment configuration file is primarily used to define the database backe Database: provider: sqlite database: py_experimenter + use_ssh_tunnel: False table: name: example_general_usage keyfields: @@ -69,6 +70,7 @@ The ``Database`` section defines the database and its structure. - ``provider``: The provider of the database connection. Currently, ``sqlite`` and ``mysql`` are supported. In the case of ``mysql`` an additional :ref:`database credential file ` has to be created. - ``database``: The name of the database to create or connect to. +- ``use_ssh_tunnel``: Flag to decide if the database is connected via ssh as defined in the :ref:`database credential file `. This is ignored if ``sqlite`` is chosen as provider. Optional Parameter, default is False. - ``table``: Defines the structure and predefined values for the experiment table. - ``name``: The name of the experiment table to create or connect to. diff --git a/autoapi/py_experimenter/config/index.html b/autoapi/py_experimenter/config/index.html index 7ce30824..27f16603 100644 --- a/autoapi/py_experimenter/config/index.html +++ b/autoapi/py_experimenter/config/index.html @@ -184,7 +184,7 @@

Classes
-class py_experimenter.config.DatabaseCfg(provider: str, database_name: str, table_name: str, result_timestamps: bool, keyfields: List[Keyfield], resultfields: Dict[str, str], logtables: Dict[str, Dict[str, str]], logger: logging.Logger)
+class py_experimenter.config.DatabaseCfg(provider: str, use_ssh_tunnel: bool, database_name: str, table_name: str, result_timestamps: bool, keyfields: List[Keyfield], resultfields: Dict[str, str], logtables: Dict[str, Dict[str, str]], logger: logging.Logger)

Bases: Cfg

Class for the configuration of the database connection. In addition to provider, database_name, and table_name, the class also defined the structure of tables in the keyfields, resultfields, and logtables attributes.

diff --git a/autoapi/py_experimenter/database_connector_mysql/index.html b/autoapi/py_experimenter/database_connector_mysql/index.html index da66194c..cd6d2d16 100644 --- a/autoapi/py_experimenter/database_connector_mysql/index.html +++ b/autoapi/py_experimenter/database_connector_mysql/index.html @@ -123,16 +123,14 @@

Classes

DatabaseConnectorMYSQL

-

Helper class that provides a standard way to create an ABC using

+

-class py_experimenter.database_connector_mysql.DatabaseConnectorMYSQL(database_configuration: omegaconf.OmegaConf, use_codecarbon: bool, credential_path: str, use_ssh_tunnel: bool, logger: logging.Logger)
+class py_experimenter.database_connector_mysql.DatabaseConnectorMYSQL(database_configuration: py_experimenter.config.DatabaseCfg, use_codecarbon: bool, credential_path: str, logger: logging.Logger)

Bases: py_experimenter.database_connector.DatabaseConnector

-

Helper class that provides a standard way to create an ABC using -inheritance.

_prepared_statement_placeholder = '%s'
diff --git a/autoapi/py_experimenter/experimenter/index.html b/autoapi/py_experimenter/experimenter/index.html index 9a5dd319..5f1ba0d9 100644 --- a/autoapi/py_experimenter/experimenter/index.html +++ b/autoapi/py_experimenter/experimenter/index.html @@ -129,7 +129,7 @@

Classes
-class py_experimenter.experimenter.PyExperimenter(experiment_configuration_file_path: str = os.path.join('config', 'experiment_configuration.yml'), database_credential_file_path: str = os.path.join('config', 'database_credentials.yml'), use_ssh_tunnel: bool = False, table_name: str = None, database_name: str = None, use_codecarbon: bool = True, name='PyExperimenter', logger_name: str = 'py-experimenter', log_level: int | str = logging.INFO, log_file: str = './logs/py-experimenter.log')
+class py_experimenter.experimenter.PyExperimenter(experiment_configuration_file_path: str = os.path.join('config', 'experiment_configuration.yml'), database_credential_file_path: str = os.path.join('config', 'database_credentials.yml'), use_ssh_tunnel: bool | None = None, table_name: str = None, database_name: str = None, use_codecarbon: bool = True, name='PyExperimenter', logger_name: str = 'py-experimenter', log_level: int | str = logging.INFO, log_file: str = './logs/py-experimenter.log')

Module handling the initialization, execution and collection of experiments and their respective results.

diff --git a/changelog.html b/changelog.html index f3cb5790..933202a5 100644 --- a/changelog.html +++ b/changelog.html @@ -69,59 +69,60 @@
  • Changelog -
    -

    Fix

    +
    +

    Fix

    • Booleans have been added as strings to the database table in SQLite. This has been fixed by adding a converting the values accordingly before writing them to the database.

    • Bugfix, where the same experiment has been pulled multiple times when using n_jobs > 1.

      • @@ -192,8 +197,8 @@

      Fix

      v1.4.0 (20.02.2024)

      -
      -

      Feature

      +
      +

      Feature

      -
      -

      Fix

      +
      +

      Fix

      • Fix a problem when executing fill_table that caused some entries to occur twice.

      • Temporary CodeCarbon files are automatically removed at termination.

        • @@ -211,15 +216,15 @@

        Fix

        v1.3.2 (23.01.2024)

        -
        -

        Feature

        +
        +

        Feature

        • Add random_order parameter to PyExperimenter.execute() to allow for random order of experiments.

        • Add pause functionality to PyExperimenter to allow for pausing the execution of experiments, which can be continued later on.

        -
        -

        Fix

        +
        +

        Fix

        • Hotfix cluster execution where multiple runners could pull the same experiment.

        • Update logger documentation to reflect the changes of the improved logging.

          • @@ -228,8 +233,8 @@

          Fix

          v1.3.1 (24.07.2023)

          -
          -

          Feature

          +
          +

          Feature

          -
          -

          Fix

          +
          +

          Fix

          • Bugfix escaping of values in sql statements.

          @@ -281,8 +286,8 @@

          Fix<

          v1.2.1 (21/04/2023)

          -
          -

          Feature

          +
          +

          Feature

          • Improve performance addding new experiments to database table

          • Create issue template

            • @@ -292,23 +297,23 @@

            Feature

          v1.2.0 (04/04/2023)

          -
          -

          Feature

          +
          +

          Feature

          • Added logtables functionality, allowing to incrementally log information during the execution of an experiment, which is described in detail in the documentation.

          • Documentation of the usage of PyExperimenter has been reworked in large parts.

          -
          -

          Examples

          +
          +

          Examples

          • An additional logtable example has been added.

          • An issue of the example notebook has been fixed causing them to fail due to missing directories.

          • Improved general example to cover extended functionality of PyExperimenter.reset_experiments().

          -
          -

          Fix

          +
          +

          Fix

          • Start date is now set when pulling an experiment.

          • Supported Python version is now >= 3.9.

            • @@ -328,8 +333,8 @@

            Tests

          v1.1.0 (21/11/2022)

          -
          -

          Feature

          +
          +

          Feature

          -
          -

          Examples

          +
          +

          Examples

          • Updated due to latest changes and renamings

          • Referenced documentation within examples

          -
          -

          Fix

          +
          +

          Fix

          • Bugfix of wrong column order when writing to DB

          • Unfavorable pulling experiments has been changed (see above)

          -
          -

          Tests

          +
          +

          Tests

          • Add workflow to automatically check tests
              @@ -412,8 +417,8 @@

              Tests

          v1.0.0 (04/09/2022)

          -
          -

          Feature

          +
          +

          Feature

          -
          -

          Examples

          +
          +

          Examples

          • Added a Jupyter notebook explaining the general usage of the PyExperimenter.

          • Added a Jupyter notebook explaining how to fill the database table with a conditional experiment grid.

          -
          -

          Fix

          +
          +

          Fix

          • Added checked when resetting a table, that only missing rows are added and no duplicated rows are created.

          • Fixed writing of string containing quotation marks to the database table.

          -
          -

          Tests

          +
          +

          Tests

          • Added tests for all key components of PyExperimenter.

          diff --git a/installation.html b/installation.html index 344b3fe9..02b72bda 100644 --- a/installation.html +++ b/installation.html @@ -104,7 +104,7 @@

          Thereby, the following dependencies are automatically installed:

          [tool.poetry]
 name = "py-experimenter"
-version = "1.4.2a0"
+version = "1.4.2a1"
 description = "The PyExperimenter is a tool for the automatic execution of experiments, e.g. for machine learning (ML), capturing corresponding results in a unified manner in a database."
 authors = [
     "Tanja Tornede <t.tornede@ai.uni-hannover.de>",
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diff --git a/searchindex.js b/searchindex.js
index c8db69bc..b906ee1b 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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"py_experimenter.exceptions.DatabaseConnectionError"]], "databasecreationerror": [[7, "py_experimenter.exceptions.DatabaseCreationError"]], "databaseerror": [[7, "py_experimenter.exceptions.DatabaseError"]], "databasequeryerror": [[7, "py_experimenter.exceptions.DatabaseQueryError"]], "emptyfilldatabasecallerror": [[7, "py_experimenter.exceptions.EmptyFillDatabaseCallError"]], "invalidcolumnerror": [[7, "py_experimenter.exceptions.InvalidColumnError"]], "invalidconfigerror": [[7, "py_experimenter.exceptions.InvalidConfigError"]], "invalidlogfielderror": [[7, "py_experimenter.exceptions.InvalidLogFieldError"]], "invalidlogtableerror": [[7, "py_experimenter.exceptions.InvalidLogtableError"]], "invalidresultfielderror": [[7, "py_experimenter.exceptions.InvalidResultFieldError"]], "invalidvaluesinconfiguration": [[7, "py_experimenter.exceptions.InvalidValuesInConfiguration"]], "missinglogtableerror": [[7, "py_experimenter.exceptions.MissingLogTableError"]], "noconfigfileerror": [[7, "py_experimenter.exceptions.NoConfigFileError"]], "noexperimentsleftexception": [[7, "py_experimenter.exceptions.NoExperimentsLeftException"]], "nopausedexperimentsexception": [[7, "py_experimenter.exceptions.NoPausedExperimentsException"]], "parametercombinationerror": [[7, "py_experimenter.exceptions.ParameterCombinationError"]], "pyexperimentererror": [[7, "py_experimenter.exceptions.PyExperimenterError"]], "sshtunnelerror": [[7, "py_experimenter.exceptions.SshTunnelError"]], "tablehaswrongstructureerror": [[7, "py_experimenter.exceptions.TableHasWrongStructureError"]], "py_experimenter.exceptions": [[7, "module-py_experimenter.exceptions"]], "all (py_experimenter.experiment_status.experimentstatus attribute)": [[8, "py_experimenter.experiment_status.ExperimentStatus.ALL"]], "created (py_experimenter.experiment_status.experimentstatus attribute)": [[8, "py_experimenter.experiment_status.ExperimentStatus.CREATED"]], "done (py_experimenter.experiment_status.experimentstatus 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"reset_experiments() (py_experimenter.experimenter.pyexperimenter method)": [[9, "py_experimenter.experimenter.PyExperimenter.reset_experiments"]], "unpause_experiment() (py_experimenter.experimenter.pyexperimenter method)": [[9, "py_experimenter.experimenter.PyExperimenter.unpause_experiment"]], "py_experimenter": [[10, "module-py_experimenter"]], "resultprocessor (class in py_experimenter.result_processor)": [[11, "py_experimenter.result_processor.ResultProcessor"]], "_add_timestamps_to_results() (py_experimenter.result_processor.resultprocessor static method)": [[11, "py_experimenter.result_processor.ResultProcessor._add_timestamps_to_results"]], "_change_status() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._change_status"]], "_set_machine() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._set_machine"]], "_set_name() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._set_name"]], "_valid_logtable_logs() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._valid_logtable_logs"]], "_valid_result_fields() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._valid_result_fields"]], "_write_emissions() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._write_emissions"]], "_write_error() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor._write_error"]], "process_logs() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor.process_logs"]], "process_results() (py_experimenter.result_processor.resultprocessor method)": [[11, "py_experimenter.result_processor.ResultProcessor.process_results"]], "py_experimenter.result_processor": [[11, "module-py_experimenter.result_processor"]], "combine_fill_table_parameters() (in module py_experimenter.utils)": [[12, "py_experimenter.utils.combine_fill_table_parameters"]], "extract_codecarbon_columns() (in module py_experimenter.utils)": [[12, "py_experimenter.utils.extract_codecarbon_columns"]], "get_timestamp_representation() (in module py_experimenter.utils)": [[12, "py_experimenter.utils.get_timestamp_representation"]], "load_credential_config() (in module py_experimenter.utils)": [[12, "py_experimenter.utils.load_credential_config"]], "py_experimenter.utils": [[12, "module-py_experimenter.utils"]], "write_codecarbon_config() (in module py_experimenter.utils)": [[12, "py_experimenter.utils.write_codecarbon_config"]]}})
\ No newline at end of file
diff --git a/usage/database_credential_file.html b/usage/database_credential_file.html
index f3ad2837..fc4d69af 100644
--- a/usage/database_credential_file.html
+++ b/usage/database_credential_file.html
@@ -118,7 +118,7 @@

          However, for security reasons, databases might only be accessible from a specific IP address. In these cases, one can use an ssh jumphost. This means that PyExperimenter will first connect to the ssh server -that has access to the database and then connect to the database server from there. This is done by adding an additional Ssh section to the database credential file. +that has access to the database and then connect to the database server from there. This is done by adding an additional Ssh section to the database credential file, and can be activated either by a PyExperimenter keyword argument or in the experimenter configuration file. The following example shows how to connect to a database server using an SSH server with the address ssh_hostname and the port optional_ssh_port.

          CREDENTIALS:
   Database:
diff --git a/usage/experiment_configuration_file.html b/usage/experiment_configuration_file.html
index 18a56312..747b5259 100644
--- a/usage/experiment_configuration_file.html
+++ b/usage/experiment_configuration_file.html
@@ -123,6 +123,7 @@
   Database:
     provider: sqlite
     database: py_experimenter
+    use_ssh_tunnel: False
     table:
       name: example_general_usage
       keyfields:
@@ -177,6 +178,7 @@ 
          Database Information
 
        • provider: The provider of the database connection. Currently, sqlite and mysql are supported. In the case of mysql an additional database credential file has to be created.
          • 
 
        • database: The name of the database to create or connect to.
          • 
+
        • use_ssh_tunnel: Flag to decide if the database is connected via ssh as defined in the database credential file. This is ignored if sqlite is chosen as provider. Optional Parameter, default is False.
          • 
 
        • table: Defines the structure and predefined values for the experiment table.