Merge pull request #154 from pepkit/dev

Release 0.12.4

Author: khoroshevskyi

.github/workflows/black.yml

@@ -6,6 +6,6 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v6
       - uses: psf/black@stable

.github/workflows/cli-coverage.yml

@@ -25,9 +25,9 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v6
 
-      - uses: actions/setup-python@v1
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.10'
 

.github/workflows/pytest.yml

@@ -26,10 +26,10 @@ jobs:
           - 5432:5432
           options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
 

.github/workflows/python-publish.yml

@@ -11,9 +11,9 @@ jobs:
     permissions:
       id-token: write
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v6
       with:
         python-version: '3.x'
     - name: Install dependencies

README.md

@@ -48,6 +48,7 @@ to increase readability, maintainability, and user experience of pepdbagent, whi
 - <u>Sample</u>: Handles the creation, modification, and deletion of samples, without modification of the entire project.
 - <u>View</u>: Manages the creation, modification, and deletion of views for specific projects.
 - <u>User</u>: Contains user-related information such as favorites and other user-related data.
+- <u>Schema</u>: Provides information and functions related to the user schemas.
 
 ## Example:
 

docs/changelog.md

@@ -2,6 +2,11 @@
 
 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.
 
+## [0.12.4] -- 2026-01-26
+- Added project search by tag in annotation module
+- Updated github actions workflows
+
+
 ## [0.12.3] -- 2025-04-03
 - Fixed models for schema records and versions
 

pepdbagent/_version.py

@@ -1 +1 @@
-__version__ = "0.12.3"
+__version__ = "0.12.4"

pepdbagent/modules/annotation.py

@@ -106,6 +106,7 @@ def get(
             count=self._count_projects(
                 namespace=namespace,
                 search_str=query,
+                tag=tag,
                 admin=admin,
                 filter_by=filter_by,
                 filter_end_date=filter_end_date,
@@ -115,6 +116,7 @@ def get(
             results=self._get_projects(
                 namespace=namespace,
                 search_str=query,
+                tag=tag,
                 admin=admin,
                 offset=offset,
                 limit=limit,
@@ -235,6 +237,7 @@ def _count_projects(
         self,
         namespace: str = None,
         search_str: str = None,
+        tag: str = None,
         admin: Union[str, List[str]] = None,
         filter_by: Optional[Literal["submission_date", "last_update_date"]] = None,
         filter_start_date: Optional[str] = None,
@@ -246,6 +249,7 @@ def _count_projects(
 
         :param namespace: namespace where to search for a project
         :param search_str: search string. will be searched in name, tag and description information
+        :param tag: tag of the projects (find projects with specific tag)
         :param admin: string or list of admins [e.g. "Khoroshevskyi", or ["doc_adin","Khoroshevskyi"]]
         :param filter_by: data to use filter on.
             Options: ["submission_date", "last_update_date"]
@@ -270,6 +274,8 @@ def _count_projects(
         )
         if pep_type:
             statement = statement.where(Projects.pop.is_(pep_type == "pop"))
+        if tag:
+            statement = statement.where(Projects.tag == tag)
         result = self._pep_db_engine.session_execute(statement).first()
 
         try:
@@ -280,6 +286,7 @@ def _count_projects(
     def _get_projects(
         self,
         namespace: str = None,
+        tag: str = None,
         search_str: str = None,
         admin: Union[str, List[str]] = None,
         limit: int = DEFAULT_LIMIT,
@@ -295,6 +302,7 @@ def _get_projects(
         Get projects by providing search string.
 
         :param namespace: namespace where to search for a project
+        :param tag: tag of the projects (find projects with specific tag)
         :param search_str: search string that has to be found in the name or tag
         :param admin: True, if user is admin of the namespace [Default: False]
         :param limit: limit of return results
@@ -322,6 +330,7 @@ def _get_projects(
             namespace=namespace,
             search_str=search_str,
             admin_list=admin,
+            tag=tag,
         )
         statement = self._add_date_filter_if_provided(
             statement, filter_by, filter_start_date, filter_end_date
@@ -406,6 +415,7 @@ def _add_condition(
         namespace: str = None,
         search_str: str = None,
         admin_list: Union[str, List[str]] = None,
+        tag: str = None,
     ) -> Select:
         """
         Add where clause to sqlalchemy statement (in project search)
@@ -414,6 +424,7 @@ def _add_condition(
         :param namespace: project namespace sql:(where namespace = "")
         :param search_str: search string that has to be found in the name or tag
         :param admin_list: list or string of admin rights to namespace
+        :param tag: tag of the projects (find projects with specific tag)
         :return: sqlalchemy representation of a SELECT statement with where clause.
         """
         admin_list = tuple_converter(admin_list)
@@ -428,6 +439,9 @@ def _add_condition(
         if namespace:
             statement = statement.where(Projects.namespace == namespace)
 
+        if tag:
+            statement = statement.where(Projects.tag == tag)
+
         statement = statement.where(
             or_(Projects.private.is_(False), Projects.namespace.in_(admin_list))
         )