Updated pephubclient with peprs version

docs/changelog.md

@@ -2,6 +2,13 @@
 
 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.
 
+## [0.7.0] - 2026-08-06
+### Changed
+- Replaced the `peppy` dependency with `peprs` (Rust-backed PEP object model).
+  `load_project`, `view.get`, `push`, and `upload` now operate on `peprs.Project`
+  objects instead of `peppy.Project`.
+- Added `pyyaml` as a direct dependency (previously pulled in transitively via peppy).
+
 ## [0.5.1] - 2026-03-18
 ### Fixed
 - Fixed saving project to pephub [#55](https://github.com/pepkit/pephubclient/issues/55)

pephubclient/constants.py

@@ -3,6 +3,12 @@
 
 from pydantic import BaseModel, field_validator
 
+# PEP config/sample keys not exported by peprs.const
+NAME_KEY: str = "name"
+DESC_KEY: str = "description"
+CFG_SAMPLE_TABLE_KEY: str = "sample_table"
+CFG_SUBSAMPLE_TABLE_KEY: str = "subsample_table"
+
 DEFAULT_BASE_URL: str = "https://pephub-api.databio.org/"
 PEPHUB_BASE_URL: str = os.getenv("PEPHUB_BASE_URL", default=DEFAULT_BASE_URL)
 # PEPHUB_BASE_URL = "http://0.0.0.0:8000/"

pephubclient/helpers.py

@@ -5,23 +5,25 @@
 from urllib.parse import urlencode
 
 import pandas as pd
-import peppy
+import peprs
 import requests
 import yaml
-from peppy.const import (
-    CFG_SAMPLE_TABLE_KEY,
-    CFG_SUBSAMPLE_TABLE_KEY,
+from peprs.const import (
     CONFIG_KEY,
-    DESC_KEY,
-    NAME_KEY,
     SAMPLE_RAW_DICT_KEY,
-    SUBSAMPLE_RAW_LIST_KEY,
+    SUBSAMPLE_RAW_DICT_KEY,
 )
 from pydantic import ValidationError
 from requests.exceptions import ConnectionError
 from ubiquerg import parse_registry_path
 
-from pephubclient.constants import RegistryPath
+from pephubclient.constants import (
+    CFG_SAMPLE_TABLE_KEY,
+    CFG_SUBSAMPLE_TABLE_KEY,
+    DESC_KEY,
+    NAME_KEY,
+    RegistryPath,
+)
 from pephubclient.exceptions import (
     BasePephubclientException,
     PEPExistsError,
@@ -227,15 +229,15 @@ def _save_zip_pep(project: dict, zip_filepath: str, force: bool = False) -> None
             project[SAMPLE_RAW_DICT_KEY]
         ).to_csv(index=False)
 
-    if project[SUBSAMPLE_RAW_LIST_KEY] is not None:
-        if not isinstance(project[SUBSAMPLE_RAW_LIST_KEY], list):
+    if project[SUBSAMPLE_RAW_DICT_KEY] is not None:
+        if not isinstance(project[SUBSAMPLE_RAW_DICT_KEY], list):
             config[CFG_SUBSAMPLE_TABLE_KEY] = ["subsample_table1.csv"]
             content_to_zip["subsample_table1.csv"] = pd.DataFrame(
-                project[SUBSAMPLE_RAW_LIST_KEY]
+                project[SUBSAMPLE_RAW_DICT_KEY]
             ).to_csv(index=False)
         else:
             config[CFG_SUBSAMPLE_TABLE_KEY] = []
-            for number, file in enumerate(project[SUBSAMPLE_RAW_LIST_KEY]):
+            for number, file in enumerate(project[SUBSAMPLE_RAW_DICT_KEY]):
                 file_name = f"subsample_table{number + 1}.csv"
                 config[CFG_SUBSAMPLE_TABLE_KEY].append(file_name)
                 content_to_zip[file_name] = pd.DataFrame(file).to_csv(index=False)
@@ -279,7 +281,7 @@ def full_path(fn: str) -> str:
     sample_pandas = pd.DataFrame(project_dict.get(SAMPLE_RAW_DICT_KEY, {}))
 
     subsample_list = [
-        pd.DataFrame(sub_a) for sub_a in project_dict.get(SUBSAMPLE_RAW_LIST_KEY) or []
+        pd.DataFrame(sub_a) for sub_a in project_dict.get(SUBSAMPLE_RAW_DICT_KEY) or []
     ]
 
     filenames = []
@@ -305,8 +307,8 @@ def full_path(fn: str) -> str:
 
 
 def save_pep(
-    project: dict | peppy.Project,
-    reg_path: str = None,
+    project: dict | peprs.Project,
+    reg_path: str | None = None,
     force: bool = False,
     project_path: str | None = None,
     zip: bool = False,
@@ -323,10 +325,10 @@ def save_pep(
             the current directory.
         zip: If True, save project as zip file.
     """
-    if isinstance(project, peppy.Project):
-        project = project.to_dict(extended=True, orient="records")
+    if isinstance(project, peprs.Project):
+        project = project.to_dict(raw=True, by_sample=True)
 
-    project = ProjectDict(**project).model_dump(by_alias=True)
+    project = ProjectDict(**project).model_dump()
 
     if not project_path:
         project_path = os.getcwd()

pephubclient/models.py

@@ -1,17 +1,19 @@
 import datetime
 
-from peppy.const import CONFIG_KEY, SAMPLE_RAW_DICT_KEY, SUBSAMPLE_RAW_LIST_KEY
-from pydantic import BaseModel, ConfigDict, Field, field_validator
+from pydantic import BaseModel, ConfigDict, field_validator
 
 
 class ProjectDict(BaseModel):
     """
     Project dict (raw) model.
+
+    Field names match the PEPHub raw-PEP payload and the peprs dialect
+    (``config``/``samples``/``subsamples``), so no aliases are needed.
     """
 
-    config: dict = Field(alias=CONFIG_KEY)
-    subsamples: list | None = Field(alias=SUBSAMPLE_RAW_LIST_KEY)
-    samples: list = Field(alias=SAMPLE_RAW_DICT_KEY)
+    config: dict
+    subsamples: list | None = None
+    samples: list
 
     model_config = ConfigDict(populate_by_name=True, extra="allow")
 

pephubclient/modules/sample.py

@@ -12,7 +12,7 @@ class PEPHubSample(RequestManager):
     Class for managing samples in PEPhub.
 
     Provides methods for getting, creating, updating and removing samples. This class
-    is not related to the peppy.Sample class.
+    is not related to the peprs.Sample class.
     """
 
     def __init__(self, jwt_data: str | None = None) -> None:

pephubclient/modules/view.py

@@ -1,6 +1,6 @@
 import logging
 
-import peppy
+import peprs
 
 from pephubclient.constants import (
     PEPHUB_VIEW_SAMPLE_URL,
@@ -31,7 +31,7 @@ def __init__(self, jwt_data: str | None = None) -> None:
 
     def get(
         self, namespace: str, name: str, tag: str, view_name: str, raw: bool = False
-    ) -> peppy.Project | dict:
+    ) -> peprs.Project | dict:
         """
         Get view from project in PEPhub.
 
@@ -43,7 +43,7 @@ def get(
             raw: If True, return raw response.
 
         Returns:
-            peppy.Project object or dictionary of the project (view).
+            peprs.Project object or dictionary of the project (view).
         """
         url = self._build_view_request_url(
             namespace=namespace, name=name, view_name=view_name
@@ -58,8 +58,8 @@ def get(
             output = self.decode_response(response, output_json=True)
             if raw:
                 return output
-            output = ProjectDict(**output).model_dump(by_alias=True)
-            return peppy.Project.from_dict(output)
+            output = ProjectDict(**output).model_dump()
+            return peprs.Project.from_dict(output)
         elif response.status_code == ResponseStatusCodes.NOT_EXIST:
             raise ResponseError("View does not exist, or you are unauthorized.")
         else:

pephubclient/pephubclient.py

@@ -1,18 +1,14 @@
 from typing import Literal
 
-import peppy
+import peprs
 import urllib3
-from peppy.const import (
-    CONFIG_KEY,
-    NAME_KEY,
-    SAMPLE_RAW_DICT_KEY,
-    SUBSAMPLE_RAW_LIST_KEY,
-)
+from peprs.const import CONFIG_KEY
 from pydantic import ValidationError
 from typing_extensions import deprecated
 from ubiquerg import parse_registry_path
 
 from pephubclient.constants import (
+    NAME_KEY,
     PATH_TO_TOKEN_FILE,
     RegistryPath,
     ResponseStatusCodes,
@@ -119,21 +115,19 @@ def pull(
     def load_project(
         self,
         project_registry_path: str,
-        query_param: dict | None = None,
-    ) -> peppy.Project:
+    ) -> peprs.Project:
         """
-        Load a peppy project from PEPhub as a peppy.Project object.
+        Load a project from PEPhub as a peprs.Project object.
 
         Args:
             project_registry_path: Registry path of the project.
             query_param: Query parameters used in the get request.
 
         Returns:
-            The peppy project.
+            The peprs project.
         """
-        raw_pep = self.load_raw_pep(project_registry_path, query_param)
-        peppy_project = peppy.Project().from_dict(raw_pep)
-        return peppy_project
+
+        return peprs.Project.from_pephub(project_registry_path)
 
     def push(
         self,
@@ -156,9 +150,9 @@ def push(
             is_private: Specifies whether the project should be private.
             force: Force push to the database. Use it to update, or upload a project.
         """
-        peppy_project = peppy.Project(cfg=cfg)
+        peprs_project = peprs.Project(cfg)
         self.upload(
-            project=peppy_project,
+            project=peprs_project,
             namespace=namespace,
             name=name,
             tag=tag,
@@ -168,15 +162,15 @@ def push(
 
     def upload(
         self,
-        project: peppy.Project,
+        project: peprs.Project,
         namespace: str,
         name: str = None,
         tag: str = None,
         is_private: bool = False,
         force: bool = True,
     ) -> None:
         """
-        Upload a peppy project to PEPhub.
+        Upload a peprs project to PEPhub.
 
         Args:
             project: Project object that has to be uploaded to the DB.
@@ -186,17 +180,14 @@ def upload(
             is_private: Make project private.
             force: Overwrite project if it exists.
         """
+        # peprs already emits config/samples/subsamples keys, so no remapping is needed.
         pep_dict = project.to_dict(
-            extended=True,
-            orient="records",
+            raw=True,
+            by_sample=True,
         )
         if name:
             pep_dict[CONFIG_KEY][NAME_KEY] = name
 
-        pep_dict["config"] = pep_dict.pop(CONFIG_KEY)
-        pep_dict["samples"] = pep_dict.pop(SAMPLE_RAW_DICT_KEY)
-        pep_dict["subsamples"] = pep_dict.pop(SUBSAMPLE_RAW_LIST_KEY)
-        print(pep_dict)
         upload_data = ProjectUploadData(
             pep_dict=pep_dict,
             tag=tag,
@@ -243,13 +234,13 @@ def find_project(
         self,
         namespace: str,
         query_string: str = "",
-        tag: str = None,
+        tag: str | None = None,
         limit: int = 100,
         offset: int = 0,
-        filter_by: Literal["submission_date", "last_update_date"] = None,
-        start_date: str = None,
-        end_date: str = None,
-    ) -> SearchReturnModel:
+        filter_by: Literal["submission_date", "last_update_date"] | None = None,
+        start_date: str | None = None,
+        end_date: str | None = None,
+    ) -> SearchReturnModel | None:
         """
         Find projects in a specific namespace and return a list of PEP annotations.
 
@@ -303,9 +294,9 @@ def _load_raw_pep(
         registry_path: str,
         jwt_data: str | None = None,
         query_param: dict | None = None,
-    ) -> dict:
+    ) -> dict | None:
         """
-        Request PEPhub and return the requested project as a peppy.Project object.
+        Request PEPhub and return the requested project as a raw project dict.
 
         !!! This method is deprecated. Use load_raw_pep instead. !!!
 
@@ -323,9 +314,9 @@ def load_raw_pep(
         self,
         registry_path: str,
         query_param: dict | None = None,
-    ) -> dict:
+    ) -> dict | None:
         """
-        Request PEPhub and return the requested project as a peppy.Project object.
+        Request PEPhub and return the requested project as a raw project dict.
 
         Args:
             registry_path: Project namespace, eg. "geo/GSE124224:tag".
@@ -349,7 +340,7 @@ def load_raw_pep(
             correct_proj_dict = ProjectDict(**decoded_response)
 
             # This step is necessary because of this issue: https://github.com/pepkit/pephub/issues/124
-            return correct_proj_dict.model_dump(by_alias=True)
+            return correct_proj_dict.model_dump()
 
         if pephub_response.status_code == ResponseStatusCodes.NOT_EXIST:
             raise ResponseError("File does not exist, or you are unauthorized.")
@@ -392,7 +383,7 @@ def _build_pull_request_url(self, query_param: dict = None) -> str:
         return f"{self.__base_url}api/v1/projects/" + endpoint
 
     def _build_project_search_url(
-        self, namespace: str, query_param: dict = None
+        self, namespace: str, query_param: dict | None = None
     ) -> str:
         """
         Build the request for searching projects from pephub.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "pephubclient"
-version = "0.6.1"
+version = "0.7.0"
 description = "PEPhub command line interface."
 readme = "README.md"
 license = "BSD-2-Clause"
@@ -22,10 +22,11 @@ classifiers = [
 ]
 dependencies = [
     "typer>=0.7.0",
-    "peppy>=0.40.5",
+    "peprs>=0.2.4",
     "requests>=2.28.2",
     "pydantic>2.5.0",
     "pandas>=2.0.0",
+    "pyyaml>=6.0",
     "ubiquerg>=0.6.3",
     "coloredlogs>=15.0.1",
     "toml>=0.10.2",

tests/conftest.py

@@ -16,6 +16,7 @@ def device_code_return():
 def test_raw_pep_return():
     sample_prj = {
         "config": {
+            "pep_version": "2.1.0",
             "This": "is config",
             "description": "desc",
             "name": "sample name",