v0.6.0 release prep

pepkit · Dec 22, 2023 · ede50e3 · ede50e3
1 parent 7dc0711
commit ede50e3
Show file tree

Hide file tree

Showing 5 changed files with 34 additions and 47 deletions.
diff --git a/docs/api_docs.md b/docs/api_docs.md
@@ -265,18 +265,6 @@ def retrieve_one(self, *args, **kwargs)
 
 
 
-```python
-def sample_name(self)
-```
-
-Unique identifier of the record
-#### Returns:
-
-- `str`:  unique identifier of the record
-
-
-
-
 ```python
 def schema(self)
 ```
@@ -586,18 +574,6 @@ def retrieve_one(self, *args, **kwargs)
 
 
 
-```python
-def sample_name(self)
-```
-
-Unique identifier of the record
-#### Returns:
-
-- `str`:  unique identifier of the record
-
-
-
-
 ```python
 def schema(self)
 ```
@@ -693,7 +669,7 @@ Pipestat standardizes reporting of pipeline results and pipeline status manageme
 
 
 ```python
-def __init__(self, project_name: Optional[str]=None, record_identifier: Optional[str]=None, schema_path: Optional[str]=None, results_file_path: Optional[str]=None, database_only: Optional[bool]=True, config_file: Optional[str]=None, config_dict: Optional[dict]=None, flag_file_dir: Optional[str]=None, show_db_logs: bool=False, pipeline_type: Optional[str]=None, pipeline_name: Optional[str]='default_pipeline_name', result_formatter: staticmethod=<function default_formatter at 0x7faeac58bbe0>, multi_pipelines: bool=False, output_dir: Optional[str]=None)
+def __init__(self, project_name: Optional[str]=None, record_identifier: Optional[str]=None, schema_path: Optional[str]=None, results_file_path: Optional[str]=None, database_only: Optional[bool]=True, config_file: Optional[str]=None, config_dict: Optional[dict]=None, flag_file_dir: Optional[str]=None, show_db_logs: bool=False, pipeline_type: Optional[str]=None, pipeline_name: Optional[str]='default_pipeline_name', result_formatter: staticmethod=<function default_formatter at 0x7f47f614fbe0>, multi_pipelines: bool=False, output_dir: Optional[str]=None)
 ```
 
 Initialize the PipestatManager object
@@ -716,6 +692,12 @@ Initialize the PipestatManager object
 
 
 
+```python
+def check_multi_results(self)
+```
+
+
+
 ```python
 def clear_status(self, *args, **kwargs)
 ```
@@ -913,6 +895,18 @@ def report(self, *args, **kwargs)
 
 
 
+```python
+def resolve_results_file_path(self, results_file_path)
+```
+
+Replace {record_identifier} in results_file_path if it exists.
+#### Parameters:
+
+- `results_file_path` (`str`):  YAML file to report into, if file isused as the object back-end
+
+
+
+
 ```python
 def result_schemas(self)
 ```
@@ -926,13 +920,14 @@ Result schema mappings
 
 
 ```python
-def retrieve_many(self, record_identifiers: List[str]) -> Union[Any, Dict[str, Any]]
+def retrieve_many(self, record_identifiers: List[str], result_identifier: Optional[str]=None) -> Union[Any, Dict[str, Any]]
 ```
 
 
 #### Parameters:
 
 - `record_identifiers` (``):  list of record identifiers
+- `result_identifier` (`str`):  single record_identifier
 
 
 #### Returns:
@@ -948,18 +943,6 @@ def retrieve_one(self, *args, **kwargs)
 
 
 
-```python
-def sample_name(self)
-```
-
-Unique identifier of the record
-#### Returns:
-
-- `str`:  unique identifier of the record
-
-
-
-
 ```python
 def schema(self)
 ```
@@ -1041,4 +1024,4 @@ def table(self, *args, **kwargs)
 
 
 
-*Version Information: `pipestat` v0.6.0a3, generated by `lucidoc` v0.4.4*
+*Version Information: `pipestat` v0.6.0a11, generated by `lucidoc` v0.4.4*
diff --git a/docs/changelog.md b/docs/changelog.md
@@ -2,7 +2,7 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
-## [0.6.0] - 2023-12-XX
+## [0.6.0] - 2023-12-22
 ### Added
 - `select_records`, which allows for a single API for selecting attributes (result_identifiers) given filter_conditions and/or columns
 - `retrieve_one`, and `retrieve_many` which allows for selecting one or multiple records given record_identifier

diff --git a/docs/usage.md b/docs/usage.md
@@ -72,7 +72,8 @@ options:
   -i I, --result-identifier I  ID of the result to report; needs to be defined in the
                                schema
   -r R, --record-identifier R  ID of the record to report the result for. If not provided
-                               'RECORD_IDENTIFIER' env var will be used. Currently not set
+                               'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
+                               Currently not set
   -v V, --value V              Value of the result to report
   -o, --overwrite              Whether the result should override existing ones in case of
                                name clashes
@@ -144,7 +145,8 @@ options:
   -i I, --result-identifier I  ID of the result to report; needs to be defined in the
                                schema
   -r R, --record-identifier R  ID of the record to report the result for. If not provided
-                               'RECORD_IDENTIFIER' env var will be used. Currently not set
+                               'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
+                               Currently not set
 ```
 
 ## `pipestat retrieve --help`
@@ -177,7 +179,8 @@ options:
                                pipestat backend.
   -p P, --pipeline-type P      project or sample level pipeline type.
   -r R, --record-identifier R  ID of the record to report the result for. If not provided
-                               'RECORD_IDENTIFIER' env var will be used. Currently not set
+                               'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
+                               Currently not set
 ```
 
 ## `pipestat status --help`
@@ -225,7 +228,8 @@ options:
   --flag-dir FD                Path to the flag directory in case YAML file is the
                                pipestat backend.
   -r R, --record-identifier R  ID of the record to report the result for. If not provided
-                               'RECORD_IDENTIFIER' env var will be used. Currently not set
+                               'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
+                               Currently not set
   -p P, --pipeline-type P      project or sample level pipeline type.
 ```
 
@@ -262,7 +266,8 @@ options:
   --flag-dir FD                Path to the flag directory in case YAML file is the
                                pipestat backend.
   -r R, --record-identifier R  ID of the record to report the result for. If not provided
-                               'RECORD_IDENTIFIER' env var will be used. Currently not set
+                               'PIPESTAT_RECORD_IDENTIFIER' env var will be used.
+                               Currently not set
   -p P, --pipeline-type P      project or sample level pipeline type.
 ```
 
diff --git a/pipestat/_version.py b/pipestat/_version.py
@@ -1 +1 @@
-__version__ = "0.6.0a11"
+__version__ = "0.6.0"
diff --git a/requirements/requirements-test.txt b/requirements/requirements-test.txt
@@ -14,7 +14,6 @@ eido
 psycopg
 pydantic>=1.10.7, <2.0.0
 sqlmodel>=0.0.12
-pydantic
 uvicorn
 fastapi