memote.suite.results
¶
Provide the memote result object and managers for various situations.
- The
MemoteResult
represents the collective result of running the metabolic model test suite on a given model at a certain point in time. - The
ResultManager
and its subclasses knows how to store a MemoteResult in various data backends (file, SQL, NoSQL). - The
ResultHistoryManager
uses the differentResultManager
s to iterate over and collect a model’s test result history.
Submodules¶
Package Contents¶
Classes¶
MemoteResult |
Collect the metabolic model test suite results. |
ResultManager |
Manage storage of results to JSON files. |
RepoResultManager |
Manage storage of results to JSON files. |
SQLResultManager |
Manage storage of results to a database. |
HistoryManager |
Manage access to results in the commit history of a git repository. |
-
class
memote.suite.results.
MemoteResult
(*args, **kwargs)[source]¶ Bases:
dict
Collect the metabolic model test suite results.
-
static
add_environment_information
(meta)¶ Record environment information.
-
static
-
class
memote.suite.results.
ResultManager
(**kwargs)[source]¶ Bases:
object
Manage storage of results to JSON files.
-
store
(self, result, filename, pretty=True)¶ Write a result to the given file.
Parameters: - result : memote.MemoteResult
The dictionary structure of results.
- filename : str or pathlib.Path
Store results directly to the given filename.
- pretty : bool, optional
Whether (default) or not to write JSON in a more legible format.
-
load
(self, filename)¶ Load a result from the given JSON file.
-
-
class
memote.suite.results.
RepoResultManager
(repository, location, **kwargs)[source]¶ Bases:
memote.suite.results.result_manager.ResultManager
Manage storage of results to JSON files.
Results are stored to and loaded from a specific location (directory) and enriched with git commit meta information.
-
record_git_info
(self, commit=None)¶ Record git meta information.
Parameters: - commit : str, optional
Unique hexsha of the desired commit.
Returns: - GitInfo
Git commit meta information.
-
get_filename
(self, git_info)¶ Create a filename from the storage directory and the commit hash.
Parameters: - git_info : GitInfo
A named tuple with git meta information.
Returns: - str
The path to the file where the result of the current commit is stored.
-
static
add_git
(meta, git_info)¶ Enrich the result meta information with commit data.
-
store
(self, result, commit=None, **kwargs)¶ Store a result in a JSON file attaching git meta information.
Parameters: - result : memote.MemoteResult
The dictionary structure of results.
- commit : str, optional
Unique hexsha of the desired commit.
- kwargs
Passed to parent function.
-
load
(self, commit=None)¶ Load a result from the storage directory.
-
-
class
memote.suite.results.
SQLResultManager
(**kwargs)[source]¶ Bases:
memote.suite.results.repo_result_manager.RepoResultManager
Manage storage of results to a database.
-
store
(self, result, commit=None, **kwargs)¶ Store a result in a JSON file attaching git meta information.
Parameters: - result : memote.MemoteResult
The dictionary structure of results.
- commit : str, optional
Unique hexsha of the desired commit.
- kwargs
Passed to parent function.
-
load
(self, commit=None)¶ Load a result from the database.
-
-
class
memote.suite.results.
HistoryManager
(repository, manager, **kwargs)[source]¶ Bases:
object
Manage access to results in the commit history of a git repository.
Attributes: - manager : memote.RepoResultManager
The manager for accessing individual results.
- current : str
The name of the currently active branch.
-
build_branch_structure
(self, model, skip)¶ Inspect and record the repo’s branches and their history.
-
iter_branches
(self)¶ Iterate over branch names and their commit histories.
-
iter_commits
(self)¶ Iterate over all commit hashes in the repository.
-
load_history
(self, model, skip=('gh-pages', ))¶ Load the entire results history into memory.
Could be a bad idea in a far future.
-
get_result
(self, commit, default=None)¶ Return an individual result from the history if it exists.
-
__contains__
(self, commit)¶ Test for the existence of a result for a commit.