Merge pull request #29 from pepkit/dev_pipestat_0.9.0

Dev pipestat 0.9.0

docs/eido/code/plugin-api-docs.md

@@ -92,4 +92,4 @@ This filter can save the YAML to file, if kwargs include `path`.
 
 
 
-*Version Information: `eido` v0.2.1, generated by `lucidoc` v0.4.4*
+*Version Information: `eido` v0.2.2, generated by `lucidoc` v0.4.4*

docs/eido/code/python-api.md

@@ -210,4 +210,4 @@ perform actual Sample object validation with jsonschema.
 
 
 
-*Version Information: `eido` v0.2.1, generated by `lucidoc` v0.4.4*
+*Version Information: `eido` v0.2.2, generated by `lucidoc` v0.4.4*

docs/geofetch/code/howto-sra-to-fastq.md

@@ -469,6 +469,8 @@ looper run red_algae/GSE67303_PEP/GSE67303_PEP.yaml -a sra_convert -p local --ou
     *         Peak memory (this run):  0.0793 GB
     *        Pipeline completed time: 2023-08-01 13:06:50
     ## [4 of 4] sample: cm_darkness_rep2; pipeline: sra_convert
+
+
     Writing script to /home/bnt4me/virginia/repos/geofetch/docs_jupyter/submission/sra_convert_cm_darkness_rep2.sub
     Job script (n=1; 0.07Gb): ./submission/sra_convert_cm_darkness_rep2.sub
     Compute node: bnt4me-Precision-5560

docs/geofetch/code/python-api.md

@@ -35,7 +35,7 @@ Class for finding GSE accessions in special period of time. Additionally, user c
 
 
 ```python
-def __init__(self, filters: str = None, retmax: int = 10000000)
+def __init__(self, filters: str=None, retmax: int=10000000)
 ```
 
 
@@ -66,7 +66,7 @@ Compare 2 lists and search for elements that are not in old list
 
 
 ```python
-def generate_file(self, file_path: str, gse_list: list = None)
+def generate_file(self, file_path: str, gse_list: list=None)
 ```
 
 Save the list of GSE accessions stored in this Finder object to a given file
@@ -96,7 +96,7 @@ Get list of all gse accession available in GEO
 
 
 ```python
-def get_gse_by_date(self, start_date: str, end_date: str = None) -> list
+def get_gse_by_date(self, start_date: str, end_date: str=None) -> list
 ```
 
 Search gse accessions by providing start date and end date. By default, the last date is today.
@@ -114,7 +114,7 @@ Search gse accessions by providing start date and end date. By default, the last
 
 
 ```python
-def get_gse_by_day_count(self, n_days: int = 1) -> list
+def get_gse_by_day_count(self, n_days: int=1) -> list
 ```
 
 Get list of gse accessions that were uploaded or updated in last X days
@@ -193,7 +193,7 @@ Class to download or get projects, metadata, data from GEO and SRA
 
 
 ```python
-def __init__(self, name: str = '', metadata_root: str = '', metadata_folder: str = '', just_metadata: bool = False, refresh_metadata: bool = False, config_template: str = None, pipeline_samples: str = None, pipeline_project: str = None, skip: int = 0, acc_anno: bool = False, use_key_subset: bool = False, processed: bool = False, data_source: str = 'samples', filter: str = None, filter_size: str = None, geo_folder: str = '.', split_experiments: bool = False, bam_folder: str = '', fq_folder: str = '', sra_folder: str = '', bam_conversion: bool = False, picard_path: str = '', input: str = None, const_limit_project: int = 50, const_limit_discard: int = 1000, attr_limit_truncate: int = 500, max_soft_size: str = '1GB', discard_soft: bool = False, add_dotfile: bool = False, disable_progressbar: bool = False, add_convert_modifier: bool = False, opts=None, max_prefetch_size=None, **kwargs)
+def __init__(self, name: str='', metadata_root: str='', metadata_folder: str='', just_metadata: bool=False, refresh_metadata: bool=False, config_template: str=None, pipeline_samples: str=None, pipeline_project: str=None, skip: int=0, acc_anno: bool=False, use_key_subset: bool=False, processed: bool=False, data_source: str='samples', filter: str=None, filter_size: str=None, geo_folder: str='.', split_experiments: bool=False, bam_folder: str='', fq_folder: str='', sra_folder: str='', bam_conversion: bool=False, picard_path: str='', input: str=None, const_limit_project: int=50, const_limit_discard: int=1000, attr_limit_truncate: int=500, max_soft_size: str='1GB', discard_soft: bool=False, add_dotfile: bool=False, disable_progressbar: bool=False, add_convert_modifier: bool=False, opts=None, max_prefetch_size=None, **kwargs)
 ```
 
 Constructor
@@ -217,7 +217,7 @@ Constructor
 
 
 ```python
-def fetch_all(self, input: str, name: str = None) -> Union[NoReturn, peppy.project.Project]
+def fetch_all(self, input: str, name: str=None) -> Union[NoReturn, peppy.project.Project]
 ```
 
 Main function driver/workflow Function that search, filters, downloads and save data and metadata from  GEO and SRA
@@ -254,7 +254,7 @@ Fetche one processed GSE project and return its metadata
 
 
 ```python
-def get_projects(self, input: str, just_metadata: bool = True, discard_soft: bool = True) -> dict
+def get_projects(self, input: str, just_metadata: bool=True, discard_soft: bool=True) -> dict
 ```
 
 Function for fetching projects from GEO|SRA and receiving peppy project
@@ -275,4 +275,4 @@ Function for fetching projects from GEO|SRA and receiving peppy project
 
 
 
-*Version Information: `geofetch` v0.12.5, generated by `lucidoc` v0.4.4*
+*Version Information: `geofetch` v0.12.6, generated by `lucidoc` v0.4.4*

docs/looper/code/python-api.md

@@ -141,7 +141,7 @@ def description(self)
 
 
 ```python
-def from_dict(pep_dictionary: dict)
+def from_dict(cls, pep_dictionary: dict)
 ```
 
 Init a peppy project instance from a dictionary representation of an already processed PEP.
@@ -153,7 +153,7 @@ Init a peppy project instance from a dictionary representation of an already pro
 
 
 ```python
-def from_pandas(samples_df: pandas.core.frame.DataFrame, sub_samples_df: List[pandas.core.frame.DataFrame] = None, config: dict = None)
+def from_pandas(cls, samples_df: pandas.core.frame.DataFrame, sub_samples_df: List[pandas.core.frame.DataFrame]=None, config: dict=None)
 ```
 
 Init a peppy project instance from a pandas Dataframe
@@ -167,7 +167,7 @@ Init a peppy project instance from a pandas Dataframe
 
 
 ```python
-def from_pep_config(cfg: str = None, amendments: Union[str, Iterable[str]] = None, sample_table_index: Union[str, Iterable[str]] = None, subsample_table_index: Union[str, Iterable[str]] = None, defer_samples_creation: bool = False)
+def from_pep_config(cls, cfg: str=None, amendments: Union[str, Iterable[str]]=None, sample_table_index: Union[str, Iterable[str]]=None, subsample_table_index: Union[str, Iterable[str]]=None, defer_samples_creation: bool=False)
 ```
 
 Init a peppy project instance from a yaml file
@@ -184,7 +184,7 @@ Init a peppy project instance from a yaml file
 
 
 ```python
-def from_sample_yaml(yaml_file: str)
+def from_sample_yaml(cls, yaml_file: str)
 ```
 
 Init a peppy project instance from a yaml file

docs/peppy/code/feature1_append.md

@@ -14,10 +14,10 @@ sample_table_ori = examples_dir + "sample_table_pre.csv"
 %cat $sample_table_ori | column -t -s, | cat
 ```
 
-
-
-
-
+    sample_name  organism  time  read_type
+    pig_0h       pig       0     SINGLE
+    pig_1h       pig       1     SINGLE
+    frog_0h      frog      0     SINGLE
     frog_1h      frog      1     SINGLE
 
 
@@ -48,11 +48,11 @@ sample_table = examples_dir + "sample_table.csv"
 %cat $sample_table | column -t -s, | cat
 ```
 
-
-
-
-
-
+    sample_name  organism  time 
+    pig_0h       pig       0
+    pig_1h       pig       1
+    frog_0h      frog      0
+    frog_1h      frog      1
 
 
 ## Code

docs/peppy/code/feature3_derived.md

@@ -52,10 +52,10 @@ sample_table = examples_dir + "sample_table.csv"
 %cat $sample_table | column -t -s, | cat
 ```
 
-
-
-
-
+    sample_name  protocol  organism  time  file_path
+    pig_0h       RRBS      pig       0     source1
+    pig_1h       RRBS      pig       1     source1
+    frog_0h      RRBS      frog      0     source1
     frog_1h      RRBS      frog      1     source1
 
 

docs/peppy/code/feature5_amend.md

@@ -18,10 +18,10 @@ sample_table = examples_dir + "sample_table.csv"
 %cat $sample_table | column -t -s, | cat
 ```
 
-
-
-
-
+    sample_name  protocol  organism  time  file_path
+    pig_0h       RRBS      pig       0     source1
+    pig_1h       RRBS      pig       1     source1
+    frog_0h      RRBS      frog      0     source1
     frog_1h      RRBS      frog      1     source1
 
 

docs/peppy/code/python-api.md

@@ -60,7 +60,7 @@ A class to model a Project (collection of samples and metadata).
 
 
 ```python
-def __init__(self, cfg: str = None, amendments: Union[str, Iterable[str]] = None, sample_table_index: Union[str, Iterable[str]] = None, subsample_table_index: Union[str, Iterable[str]] = None, defer_samples_creation: bool = False)
+def __init__(self, cfg: str=None, amendments: Union[str, Iterable[str]]=None, sample_table_index: Union[str, Iterable[str]]=None, subsample_table_index: Union[str, Iterable[str]]=None, defer_samples_creation: bool=False)
 ```
 
 Initialize self.  See help(type(self)) for accurate signature.
@@ -203,7 +203,7 @@ Copy self to a new object.
 
 
 ```python
-def create_samples(self, modify: bool = False)
+def create_samples(self, modify: bool=False)
 ```
 
 Populate Project with Sample objects
@@ -234,7 +234,7 @@ def description(self)
 
 
 ```python
-def from_dict(pep_dictionary: dict)
+def from_dict(cls, pep_dictionary: dict)
 ```
 
 Init a peppy project instance from a dictionary representation of an already processed PEP.
@@ -246,7 +246,7 @@ Init a peppy project instance from a dictionary representation of an already pro
 
 
 ```python
-def from_pandas(samples_df: pandas.core.frame.DataFrame, sub_samples_df: List[pandas.core.frame.DataFrame] = None, config: dict = None)
+def from_pandas(cls, samples_df: pandas.core.frame.DataFrame, sub_samples_df: List[pandas.core.frame.DataFrame]=None, config: dict=None)
 ```
 
 Init a peppy project instance from a pandas Dataframe
@@ -260,7 +260,7 @@ Init a peppy project instance from a pandas Dataframe
 
 
 ```python
-def from_pep_config(cfg: str = None, amendments: Union[str, Iterable[str]] = None, sample_table_index: Union[str, Iterable[str]] = None, subsample_table_index: Union[str, Iterable[str]] = None, defer_samples_creation: bool = False)
+def from_pep_config(cls, cfg: str=None, amendments: Union[str, Iterable[str]]=None, sample_table_index: Union[str, Iterable[str]]=None, subsample_table_index: Union[str, Iterable[str]]=None, defer_samples_creation: bool=False)
 ```
 
 Init a peppy project instance from a yaml file
@@ -277,7 +277,7 @@ Init a peppy project instance from a yaml file
 
 
 ```python
-def from_sample_yaml(yaml_file: str)
+def from_sample_yaml(cls, yaml_file: str)
 ```
 
 Init a peppy project instance from a yaml file
@@ -413,7 +413,7 @@ def name(self)
 
 
 ```python
-def parse_config_file(self, cfg_path: str = None, amendments: Iterable[str] = None)
+def parse_config_file(self, cfg_path: str=None, amendments: Iterable[str]=None)
 ```
 
 Parse provided yaml config file and check required fields exist.
@@ -556,7 +556,7 @@ That's the subsample table indexes selection priority order:
 
 
 ```python
-def to_dict(self, extended: bool = False, orient: Literal['dict', 'list', 'series', 'split', 'tight', 'records', 'index'] = 'dict') -> dict
+def to_dict(self, extended: bool=False, orient: Literal['dict', 'list', 'series', 'split', 'tight', 'records', 'index']='dict') -> dict
 ```
 
 Convert the Project object to a dictionary.

docs/pipestat/changelog.md

@@ -2,6 +2,21 @@
 
 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.
 
+## [0.9.0] - 2024-04-19
+### Fixed
+- Bug with rm_record for filebackend
+- Bug when using record_identifier via env variable and the CLI
+### Added
+- Added results history and history retrieval for both file and db backends via `retrieve_history` [#177](https://github.com/pepkit/pipestat/issues/177).
+- Added `remove_record` to Pipestat manager object (it is no longer only on backend classes)
+- Added `meta` key to each record for the file backend
+- db backend will now create an additional sql history table
+- Reporting history is toggleable
+### Changed
+- Removing the last result no longer removes the entire record.
+- `pipestat_created_time, and `pipestat_modified_time` now live under the `meta` key.
+- `history` lives under the `meta` key for the filebackend.
+
 ## [0.8.2] - 2024-02-22
 ### Changed
 - Changed yacman requirement and using FutureYamlConfigManager.