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Merge pull request #31 from pepkit/pephub_updates
Pephub updates
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Diff for: ‎autodoc.py

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with open(out, "w") as stream:
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stream.write(md_result)
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else:
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print("Skipping jupyter notebooks")
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print("Skipping jupyter notebooks")

Diff for: ‎docs/pephub/developer/pephubclient/changelog.md

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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.
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## [0.3.0] - 2024-XX-XX
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## [0.4.2] - 2024-04-16
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### Updated
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- View creation, by adding description and no_fail flag
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## [0.4.1] - 2024-03-07
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### Fixed
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- Expired token error handling ([#17](https://github.com/pepkit/pephubclient/issues/17))
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## [0.4.0] - 2024-02-12
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### Added
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- Added param parent dir where peps should be saved
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- Added zip option to save_pep function
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- a parameter that points to where peps should be saved ([#32](https://github.com/pepkit/pephubclient/issues/32))
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- pep zipping option to `save_pep` function ([#34](https://github.com/pepkit/pephubclient/issues/34))
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- API for samples ([#29](https://github.com/pepkit/pephubclient/issues/29))
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- API for projects ([#28](https://github.com/pepkit/pephubclient/issues/28))
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### Changed
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- Transferred save_pep function to helpers
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### Updated
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- Transferred `save_pep` function to helpers
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## [0.3.0] - 2024-01-17
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### Added
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- customization of the base PEPhub URL ([#22](https://github.com/pepkit/pephubclient/issues/22))
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### Updated
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- Updated PEPhub API URL
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- Increased the required pydantic version to >2.5.0
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## [0.2.2] - 2024-01-17
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### Added

Diff for: ‎docs/pephub/developer/pephubclient/phc_samples_usage.md

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<!-- markdownlint-disable -->
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# <kbd>module</kbd> `pephubclient.modules.sample`
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**Global Variables**
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---------------
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- **PEPHUB_SAMPLE_URL**
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---
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## <kbd>class</kbd> `PEPHubSample`
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Class for managing samples in PEPhub and provides methods for getting, creating, updating and removing samples. This class is not related to peppy.Sample class.
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### <kbd>method</kbd> `__init__`
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```python
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__init__(jwt_data: str = None)
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```
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- :param jwt_data: jwt token for authorization
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---
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### <kbd>method</kbd> `create`
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```python
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create(
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namespace: str,
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name: str,
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tag: str,
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sample_name: str,
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sample_dict: dict,
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overwrite: bool = False
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) → None
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```
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Create sample in project in PEPhub.
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- :param namespace: namespace of project
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- :param name: name of project
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- :param tag: tag of project
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- :param sample_dict: sample dict
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- :param sample_name: sample name
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- :param overwrite: overwrite sample if it exists :return: None
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---
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### <kbd>method</kbd> `get`
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```python
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get(namespace: str, name: str, tag: str, sample_name: str = None) → dict
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```
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Get sample from project in PEPhub.
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- :param namespace: namespace of project
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- :param name: name of project
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- :param tag: tag of project
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- :param sample_name: sample name :return: Sample object
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---
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### <kbd>method</kbd> `remove`
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```python
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remove(namespace: str, name: str, tag: str, sample_name: str)
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```
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Remove sample from project in PEPhub.
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- :param namespace: namespace of project
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- :param name: name of project
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- :param tag: tag of project
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- :param sample_name: sample name :return: None
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---
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### <kbd>method</kbd> `update`
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```python
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update(namespace: str, name: str, tag: str, sample_name: str, sample_dict: dict)
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```
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Update sample in project in PEPhub.
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- :param namespace: namespace of project
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- :param name: name of project
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- :param tag: tag of project
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- :param sample_name: sample name
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- :param sample_dict: sample dict, that contain elements to update, or :return: None
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---
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_This file was automatically generated via [lazydocs](https://github.com/ml-tooling/lazydocs)._

Diff for: ‎docs/pephub/developer/pephubclient/phc_usage.md

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<!-- markdownlint-disable -->
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# <kbd>module</kbd> `pephubclient.pephubclient`
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---
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## <kbd>class</kbd> `PEPHubClient`
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---
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#### <kbd>property</kbd> sample
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view represents the PHCSample class which contains all samples API
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---
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#### <kbd>property</kbd> view
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view represents the PHCView class which contains all views API
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---
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### <kbd>method</kbd> `find_project`
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```python
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find_project(
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namespace: str,
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query_string: str = '',
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limit: int = 100,
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offset: int = 0,
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filter_by: Literal['submission_date', 'last_update_date'] = None,
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start_date: str = None,
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end_date: str = None
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) → SearchReturnModel
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```
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Find project in specific namespace and return list of PEP annotation
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- :param namespace: Namespace where to search for projects
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- :param query_string: Search query
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- :param limit: Return limit
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- :param offset: Return offset
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- :param filter_by: Use filter date. Option: [submission_date, last_update_date]
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- :param start_date: filter beginning date
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- :param end_date: filter end date (if none today's date is used) :return:
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---
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### <kbd>method</kbd> `load_project`
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```python
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load_project(
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project_registry_path: str,
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query_param: Optional[dict] = None
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) → Project
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```
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Load peppy project from PEPhub in peppy.Project object
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- :param project_registry_path: registry path of the project
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- :param query_param: query parameters used in get request :return Project: peppy project.
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---
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### <kbd>method</kbd> `load_raw_pep`
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```python
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load_raw_pep(registry_path: str, query_param: Optional[dict] = None) → dict
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```
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Request PEPhub and return the requested project as peppy.Project object.
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- :param registry_path: Project namespace, eg. "geo/GSE124224:tag"
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- :param query_param: Optional variables to be passed to PEPhub :return: Raw project in dict.
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---
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### <kbd>method</kbd> `login`
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```python
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login() → NoReturn
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```
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Log in to PEPhub
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---
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### <kbd>method</kbd> `logout`
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```python
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logout() → NoReturn
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```
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Log out from PEPhub
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---
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### <kbd>method</kbd> `pull`
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```python
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pull(
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project_registry_path: str,
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force: Optional[bool] = False,
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zip: Optional[bool] = False,
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output: Optional[str] = None
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) → None
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```
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Download project locally
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- :param str project_registry_path: Project registry path in PEPhub (e.g. databio/base:default)
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- :param bool force: if project exists, overwrite it.
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- :param bool zip: if True, save project as zip file
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- :param str output: path where project will be saved :return: None
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---
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### <kbd>method</kbd> `push`
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```python
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push(
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cfg: str,
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namespace: str,
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name: Optional[str] = None,
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tag: Optional[str] = None,
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is_private: Optional[bool] = False,
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force: Optional[bool] = False
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) → None
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```
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Push (upload/update) project to Pephub using config/csv path
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- :param str cfg: Project config file (YAML) or sample table (CSV/TSV) with one row per sample to constitute project
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- :param str namespace: namespace
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- :param str name: project name
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- :param str tag: project tag
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- :param bool is_private: Specifies whether project should be private [Default= False]
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- :param bool force: Force push to the database. Use it to update, or upload project. [Default= False] :return: None
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---
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### <kbd>method</kbd> `upload`
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```python
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upload(
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project: Project,
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namespace: str,
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name: str = None,
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tag: str = None,
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is_private: bool = False,
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force: bool = True
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) → None
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```
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Upload peppy project to the PEPhub.
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- :param peppy.Project project: Project object that has to be uploaded to the DB
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- :param namespace: namespace
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- :param name: project name
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- :param tag: project tag
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- :param force: Force push to the database. Use it to update, or upload project.
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- :param is_private: Make project private
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- :param force: overwrite project if it exists :return: None
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---
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_This file was automatically generated via [lazydocs](https://github.com/ml-tooling/lazydocs)._

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