Peprs

.github/workflows/black.yml

@@ -1,11 +1,15 @@
 name: Lint
 
-on: [pull_request]
+on: [push, pull_request]
 
 jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6
       - uses: actions/setup-python@v6
-      - uses: psf/black@stable
+        with:
+          python-version: "3.12"
+      - run: pip install ruff
+      - run: ruff check .
+      - run: ruff format --check .

.github/workflows/cli-coverage.yml

@@ -8,7 +8,7 @@ jobs:
   cli-coverage-report:
     strategy:
       matrix:
-        python-version: [ "3.11" ]
+        python-version: [ "3.10" ]
         os: [ ubuntu-latest ] # can't use macOS when using service containers or container jobs
         r: [ release ]
     runs-on: ${{ matrix.os }}
@@ -31,10 +31,8 @@ jobs:
         with:
           python-version: '3.10'
 
-      - name: Install dev dependancies
-        run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
-
-      - run: pip install .
+      - name: Install package with test dependencies
+        run: pip install ".[test]"
 
       - name: Run tests
         run: coverage run -m pytest
@@ -49,4 +47,4 @@ jobs:
           SMOKESHOW_GITHUB_CONTEXT: coverage
           SMOKESHOW_GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           SMOKESHOW_GITHUB_PR_HEAD_SHA: ${{ github.event.pull_request.head.sha }}
-          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}
+          SMOKESHOW_AUTH_KEY: ${{ secrets.SMOKESHOW_AUTH_KEY }}

.github/workflows/pytest.yml

@@ -10,7 +10,7 @@ jobs:
   pytest:
     strategy:
       matrix:
-        python-version: ["3.9", "3.13"]
+        python-version: ["3.10", "3.13"]
         os: [ubuntu-latest] # can't use macOS when using service containers or container jobs
         r: [release]
     runs-on: ${{ matrix.os }}
@@ -33,11 +33,8 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dev dependencies
-      run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
-
-    - name: Install package
-      run: python -m pip install .
+    - name: Install package with test dependencies
+      run: python -m pip install ".[test]"
 
     - name: Run pytest tests
       run: pytest tests -x -vv

.github/workflows/python-publish.yml

@@ -9,19 +9,18 @@ jobs:
     name: upload release to PyPI
     runs-on: ubuntu-latest
     permissions:
+      contents: read
       id-token: write
+
     steps:
     - uses: actions/checkout@v6
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
         python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine
-    - name: Build and publish
-      run: |
-        python setup.py sdist bdist_wheel
+    - name: Install build dependencies
+      run: python -m pip install --upgrade pip build
+    - name: Build package
+      run: python -m build
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1

docs/changelog.md

@@ -2,6 +2,16 @@
 
 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.
 
+
+## [0.13.0] -- 2026-07-01
+- Migrated from `peppy` to `peprs` across all modules (project, sample, view, models, utils)
+- Updated subsample key constant: `SUBSAMPLE_RAW_LIST_KEY` → `SUBSAMPLE_RAW_DICT_KEY`
+- Added alembic database migration support; `run_migrations` parameter added to `PEPDatabaseAgent` and `BaseEngine`
+- Fixed nullable fields in schema models (`SchemaVersionAnnotation`, `SchemaRecordAnnotation`, `UpdateSchemaRecordFields`, `UpdateSchemaVersionFields`)
+- Added support for `"latest"` schema version resolution when uploading/updating projects
+- Moved `SAMPLE_NAME_ATTR` and `SAMPLE_TABLE_INDEX_KEY` constants into `pepdbagent/const.py`
+- Performed code cleanup and refactoring across modules, including modernization of the codestyle, installation and dependencies.
+
 ## [0.12.4] -- 2026-01-26
 - Added project search by tag in annotation module
 - Updated github actions workflows

pepdbagent/__init__.py

@@ -1,6 +1,19 @@
-"""Package-level data"""
+"""Package-level data."""
+
+from importlib.metadata import version
+
+import coloredlogs
+import logmuse
 
-from pepdbagent._version import __version__
 from pepdbagent.pepdbagent import PEPDatabaseAgent
 
+__version__ = version("pepdbagent")
+
 __all__ = ["__version__", "PEPDatabaseAgent"]
+
+_LOGGER = logmuse.init_logger("pepdbagent")
+coloredlogs.install(
+    logger=_LOGGER,
+    datefmt="%H:%M:%S",
+    fmt="[%(levelname)s] [%(asctime)s] %(message)s",
+)

pepdbagent/alembic/env.py

@@ -1,9 +1,7 @@
 from logging.config import fileConfig
 
-from sqlalchemy import engine_from_config
-from sqlalchemy import pool
-
 from alembic import context
+from sqlalchemy import engine_from_config, pool
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.

pepdbagent/alembic/versions/44cb1e7a80de_initial_migration.py

@@ -8,8 +8,8 @@
 
 from typing import Sequence, Union
 
-from alembic import op
 import sqlalchemy as sa
+from alembic import op
 from sqlalchemy.dialects import postgresql
 from sqlalchemy.schema import FetchedValue
 
@@ -64,7 +64,9 @@ def upgrade() -> None:
         sa.UniqueConstraint("namespace", "name"),
     )
     op.create_index(op.f("ix_schema_groups_id"), "schema_groups", ["id"], unique=False)
-    op.create_index(op.f("ix_schema_groups_name"), "schema_groups", ["name"], unique=False)
+    op.create_index(
+        op.f("ix_schema_groups_name"), "schema_groups", ["name"], unique=False
+    )
     op.create_index(
         op.f("ix_schema_groups_namespace"), "schema_groups", ["namespace"], unique=False
     )
@@ -87,7 +89,9 @@ def upgrade() -> None:
         sa.PrimaryKeyConstraint("id"),
         sa.UniqueConstraint("namespace", "name"),
     )
-    op.create_index(op.f("ix_schemas_description"), "schemas", ["description"], unique=False)
+    op.create_index(
+        op.f("ix_schemas_description"), "schemas", ["description"], unique=False
+    )
     op.create_index(op.f("ix_schemas_id"), "schemas", ["id"], unique=False)
     op.create_index(op.f("ix_schemas_name"), "schemas", ["name"], unique=False)
     op.create_table(
@@ -113,7 +117,9 @@ def upgrade() -> None:
         sa.Column("schema_id", sa.Integer(), nullable=True),
         sa.Column("pop", sa.Boolean(), nullable=True),
         sa.Column("forked_from_id", sa.Integer(), nullable=True),
-        sa.ForeignKeyConstraint(["forked_from_id"], ["projects.id"], ondelete="SET NULL"),
+        sa.ForeignKeyConstraint(
+            ["forked_from_id"], ["projects.id"], ondelete="SET NULL"
+        ),
         sa.ForeignKeyConstraint(["namespace"], ["users.namespace"], ondelete="CASCADE"),
         sa.ForeignKeyConstraint(["schema_id"], ["schemas.id"], ondelete="SET NULL"),
         sa.PrimaryKeyConstraint("id"),
@@ -225,7 +231,9 @@ def upgrade() -> None:
             sa.Enum("UPDATE", "INSERT", "DELETE", name="updatetypes"),
             nullable=False,
         ),
-        sa.ForeignKeyConstraint(["history_id"], ["project_history.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(
+            ["history_id"], ["project_history.id"], ondelete="CASCADE"
+        ),
         sa.PrimaryKeyConstraint("id"),
     )
     op.create_table(
@@ -249,8 +257,12 @@ def downgrade() -> None:
     op.drop_table("stars")
     op.drop_table("samples")
     op.drop_table("project_history")
-    op.drop_index(op.f("ix_schema_group_relations_schema_id"), table_name="schema_group_relations")
-    op.drop_index(op.f("ix_schema_group_relations_group_id"), table_name="schema_group_relations")
+    op.drop_index(
+        op.f("ix_schema_group_relations_schema_id"), table_name="schema_group_relations"
+    )
+    op.drop_index(
+        op.f("ix_schema_group_relations_group_id"), table_name="schema_group_relations"
+    )
     op.drop_table("schema_group_relations")
     op.drop_table("projects")
     op.drop_index(op.f("ix_schemas_name"), table_name="schemas")

pepdbagent/alembic/versions/8a037f13b4e5_upgrading_schemas.py

@@ -8,8 +8,8 @@
 
 from typing import Sequence, Union
 
-from alembic import op
 import sqlalchemy as sa
+from alembic import op
 from sqlalchemy.dialects import postgresql
 from sqlalchemy.schema import FetchedValue
 
@@ -52,7 +52,9 @@ def upgrade() -> None:
         sa.Column("last_update_date", sa.TIMESTAMP(timezone=True), nullable=True),
         sa.Column("contributors", sa.String(), nullable=True),
         sa.Column("release_notes", sa.String(), nullable=True),
-        sa.ForeignKeyConstraint(["schema_id"], ["schema_records.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(
+            ["schema_id"], ["schema_records.id"], ondelete="CASCADE"
+        ),
         sa.PrimaryKeyConstraint("id"),
         sa.UniqueConstraint("schema_id", "version"),
     )
@@ -62,7 +64,9 @@ def upgrade() -> None:
         sa.Column("tag_name", sa.String(), nullable=False),
         sa.Column("tag_value", sa.String(), nullable=True),
         sa.Column("schema_version_id", sa.Integer(), nullable=False),
-        sa.ForeignKeyConstraint(["schema_version_id"], ["schema_versions.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(
+            ["schema_version_id"], ["schema_versions.id"], ondelete="CASCADE"
+        ),
         sa.PrimaryKeyConstraint("id"),
     )
     op.drop_index("ix_schemas_description", table_name="schemas")
@@ -76,16 +80,22 @@ def upgrade() -> None:
     op.drop_index("ix_schema_groups_namespace", table_name="schema_groups")
     # op.drop_table('schema_groups')
     op.execute("DROP TABLE schema_groups CASCADE;")
-    op.drop_index("ix_schema_group_relations_group_id", table_name="schema_group_relations")
-    op.drop_index("ix_schema_group_relations_schema_id", table_name="schema_group_relations")
+    op.drop_index(
+        "ix_schema_group_relations_group_id", table_name="schema_group_relations"
+    )
+    op.drop_index(
+        "ix_schema_group_relations_schema_id", table_name="schema_group_relations"
+    )
     op.drop_table("schema_group_relations")
 
     op.execute("UPDATE projects SET schema_id = NULL;")
     op.create_foreign_key(
         None, "projects", "schema_versions", ["schema_id"], ["id"], ondelete="SET NULL"
     )
     op.drop_column("projects", "pep_schema")
-    op.add_column("users", sa.Column("number_of_schemas", sa.Integer(), nullable=True, default=0))
+    op.add_column(
+        "users", sa.Column("number_of_schemas", sa.Integer(), nullable=True, default=0)
+    )
     # ### end Alembic commands ###
 
 
@@ -94,7 +104,8 @@ def downgrade() -> None:
     # ### commands auto generated by Alembic - please adjust! ###
     op.drop_column("users", "number_of_schemas")
     op.add_column(
-        "projects", sa.Column("pep_schema", sa.VARCHAR(), autoincrement=False, nullable=True)
+        "projects",
+        sa.Column("pep_schema", sa.VARCHAR(), autoincrement=False, nullable=True),
     )
     op.drop_constraint(None, "projects", type_="foreignkey")
     op.create_foreign_key(
@@ -121,7 +132,9 @@ def downgrade() -> None:
             name="schema_group_relations_schema_id_fkey",
             ondelete="CASCADE",
         ),
-        sa.PrimaryKeyConstraint("schema_id", "group_id", name="schema_group_relations_pkey"),
+        sa.PrimaryKeyConstraint(
+            "schema_id", "group_id", name="schema_group_relations_pkey"
+        ),
     )
     op.create_index(
         "ix_schema_group_relations_schema_id",
@@ -130,7 +143,10 @@ def downgrade() -> None:
         unique=False,
     )
     op.create_index(
-        "ix_schema_group_relations_group_id", "schema_group_relations", ["group_id"], unique=False
+        "ix_schema_group_relations_group_id",
+        "schema_group_relations",
+        ["group_id"],
+        unique=False,
     )
     op.create_table(
         "schema_groups",
@@ -145,9 +161,13 @@ def downgrade() -> None:
             ondelete="CASCADE",
         ),
         sa.PrimaryKeyConstraint("id", name="schema_groups_pkey"),
-        sa.UniqueConstraint("namespace", "name", name="schema_groups_namespace_name_key"),
+        sa.UniqueConstraint(
+            "namespace", "name", name="schema_groups_namespace_name_key"
+        ),
+    )
+    op.create_index(
+        "ix_schema_groups_namespace", "schema_groups", ["namespace"], unique=False
     )
-    op.create_index("ix_schema_groups_namespace", "schema_groups", ["namespace"], unique=False)
     op.create_index("ix_schema_groups_name", "schema_groups", ["name"], unique=False)
     op.create_index("ix_schema_groups_id", "schema_groups", ["id"], unique=False)
     op.create_table(
@@ -176,7 +196,10 @@ def downgrade() -> None:
             nullable=True,
         ),
         sa.ForeignKeyConstraint(
-            ["namespace"], ["users.namespace"], name="schemas_namespace_fkey", ondelete="CASCADE"
+            ["namespace"],
+            ["users.namespace"],
+            name="schemas_namespace_fkey",
+            ondelete="CASCADE",
         ),
         sa.PrimaryKeyConstraint("id", name="schemas_pkey"),
         sa.UniqueConstraint("namespace", "name", name="schemas_namespace_name_key"),