RepoAuditor 0.3.1__tar.gz → 0.4.0__tar.gz

{repoauditor-0.3.1 → repoauditor-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RepoAuditor
-Version: 0.3.1
+Version: 0.4.0
 Summary: Add your description here
 Project-URL: Homepage, https://github.com/gt-sse-center/RepoAuditor
 Project-URL: Documentation, https://github.com/gt-sse-center/RepoAuditor

{repoauditor-0.3.1 → repoauditor-0.4.0}/pyproject.toml

@@ -41,6 +41,7 @@ repoauditor = "RepoAuditor:EntryPoint.app"
 [project.entry-points.RepoAuditor]
 GitHubPlugin = "RepoAuditor.Plugins.GitHubPlugin"
 CommunityStandardsPlugin = "RepoAuditor.Plugins.CommunityStandardsPlugin"
+ScientificSoftwarePlugin = "RepoAuditor.Plugins.ScientificSoftwarePlugin"
 
 [build-system]
 requires = ["hatchling"]

{repoauditor-0.3.1 → repoauditor-0.4.0}/src/RepoAuditor/Plugins/CommunityStandards/CommunityStandardsQuery.py

@@ -23,24 +23,8 @@ from RepoAuditor.Plugins.CommunityStandards.Requirements.SecurityPolicy import S
 from RepoAuditor.Query import ExecutionStyle, Query
 
 
-class CommunityStandardsQuery(Query):
-    """Query with requirements that check for repository Community Standards files."""
-
-    def __init__(self) -> None:
-        super().__init__(
-            "CommunityStandardsQuery",
-            ExecutionStyle.Parallel,
-            [
-                ReadMe(),
-                CodeOfConduct(),
-                Contributing(),
-                LicenseFile(),
-                SecurityPolicy(),
-                IssueTemplates(),
-                PullRequestTemplate(),
-                CodeOwners(),
-            ],
-        )
+class CloneRepositoryMixin:
+    """A mixin class to clone a repository to a temporary directory."""
 
     # ----------------------------------------------------------------------
     @override
@@ -84,9 +68,30 @@ class CommunityStandardsQuery(Query):
 
         return module_data
 
+    # ----------------------------------------------------------------------
     @override
     def Cleanup(self, module_data: dict[str, Any]) -> None:
         """Clean up the cloned repository."""
         repo_dir = module_data["repo_dir"]
         repo_dir.cleanup()
         del module_data
+
+
+class CommunityStandardsQuery(CloneRepositoryMixin, Query):
+    """Query with requirements that check for repository Community Standards files."""
+
+    def __init__(self) -> None:
+        super().__init__(
+            "CommunityStandardsQuery",
+            ExecutionStyle.Parallel,
+            [
+                ReadMe(),
+                CodeOfConduct(),
+                Contributing(),
+                LicenseFile(),
+                SecurityPolicy(),
+                IssueTemplates(),
+                PullRequestTemplate(),
+                CodeOwners(),
+            ],
+        )

{repoauditor-0.3.1 → repoauditor-0.4.0}/src/RepoAuditor/Plugins/GitHubPlugin.py

@@ -14,7 +14,7 @@ from RepoAuditor.Plugins.GitHub.Module import GitHubModule
 
 
 # ----------------------------------------------------------------------
-@pluggy.HookimplMarker(APP_NAME)
+@pluggy.HookimplMarker(APP_NAME)(tryfirst=True)
 def GetModule() -> Module:
     """Return GitHub Module."""
     return GitHubModule()

repoauditor-0.4.0/src/RepoAuditor/Plugins/ScientificSoftware/Module.py

@@ -0,0 +1,26 @@
+# -------------------------------------------------------------------------------
+# |
+# |  Copyright (c) 2024 Scientific Software Engineering Center at Georgia Tech
+# |  Distributed under the MIT License.
+# |
+# -------------------------------------------------------------------------------
+"""Contains the ScientificSoftwareModule object."""
+
+from RepoAuditor.Module import ExecutionStyle
+from RepoAuditor.Plugins.GitHubBase.Module import GitHubBaseModule
+from RepoAuditor.Plugins.ScientificSoftware.ScientificSoftwareQuery import ScientificSoftwareQuery
+
+
+class ScientificSoftwareModule(GitHubBaseModule):
+    """Module that validates existence of repository files for Scientific Software."""
+
+    def __init__(self) -> None:
+        super().__init__(
+            "ScientificSoftware",
+            "Validates existence of repository files for Scientific Software.",
+            ExecutionStyle.Parallel,
+            [
+                ScientificSoftwareQuery(),
+            ],
+            requires_explicit_include=True,
+        )

repoauditor-0.4.0/src/RepoAuditor/Plugins/ScientificSoftware/Requirements/Citation.py

@@ -0,0 +1,63 @@
+# -------------------------------------------------------------------------------
+# |
+# |  Copyright (c) 2024 Scientific Software Engineering Center at Georgia Tech
+# |  Distributed under the MIT License.
+# |
+# -------------------------------------------------------------------------------
+"""Contains the Citation requirement."""
+
+import textwrap
+
+from RepoAuditor.Plugins.CommunityStandards.Impl.ExistsRequirementImpl import ExistsRequirementImpl
+
+
+class Citation(ExistsRequirementImpl):
+    """Validates that a CITATION file is present which is used to make the repository citable.
+
+    Details of how GitHub looks for citation files can be found here: https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
+    """
+
+    def __init__(self) -> None:
+        super().__init__(
+            "Citation",
+            filename="CITATION",
+            possible_locations=[
+                # GitHub requires the citation file be in the root directory
+                "CITATION.cff",
+                "CITATION",
+                "CITATIONS",
+                "CITATION.bib",
+                "CITATIONS.bib",
+                "CITATION.md",
+                "CITATIONS.md",
+                "citation.cff",
+                "citation",
+                "citations",
+                "citation.bib",
+                "citations.bib",
+                "citation.md",
+                "citations.md",
+                # R packages are located in the `inst` directory
+                "inst/CITATION",
+            ],
+            resolution=textwrap.dedent(
+                """\
+                1) Create a CITATION/CITATIONS file in in the root directory.
+
+                2) It can have any of the following extensions:
+                   - [blank] e.g. `CITATION`
+                   - CITATION.cff
+                   - CITATION.md
+                   - CITATION.bib
+                """
+            ),
+            rationale=textwrap.dedent(
+                """\
+                A citation file helps users correctly cite your software.
+
+                For more details, please see
+                https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repository/about-citation-files
+                """
+            ),
+            dynamic_arg_name="unrequired",
+        )

repoauditor-0.4.0/src/RepoAuditor/Plugins/ScientificSoftware/ScientificSoftwareQuery.py

@@ -0,0 +1,24 @@
+# -------------------------------------------------------------------------------
+# |
+# |  Copyright (c) 2024 Scientific Software Engineering Center at Georgia Tech
+# |  Distributed under the MIT License.
+# |
+# -------------------------------------------------------------------------------
+"""Contains the ScientificSoftwareQuery object."""
+
+from RepoAuditor.Plugins.CommunityStandards.CommunityStandardsQuery import CloneRepositoryMixin
+from RepoAuditor.Plugins.ScientificSoftware.Requirements.Citation import Citation
+from RepoAuditor.Query import ExecutionStyle, Query
+
+
+class ScientificSoftwareQuery(CloneRepositoryMixin, Query):
+    """Query with requirements that check the repository for Scientific Software specific files."""
+
+    def __init__(self) -> None:
+        super().__init__(
+            "ScientificSoftwareQuery",
+            ExecutionStyle.Parallel,
+            [
+                Citation(),
+            ],
+        )

repoauditor-0.4.0/src/RepoAuditor/Plugins/ScientificSoftwarePlugin.py

@@ -0,0 +1,20 @@
+# -------------------------------------------------------------------------------
+# |
+# |  Copyright (c) 2024 Scientific Software Engineering Center at Georgia Tech
+# |  Distributed under the MIT License.
+# |
+# -------------------------------------------------------------------------------
+"""Contains Plugin functionality."""
+
+import pluggy
+
+from RepoAuditor import APP_NAME
+from RepoAuditor.Module import Module
+from RepoAuditor.Plugins.ScientificSoftware.Module import ScientificSoftwareModule
+
+
+# ----------------------------------------------------------------------
+@pluggy.HookimplMarker(APP_NAME)
+def GetModule() -> Module:
+    """Return Scientific Software Module."""
+    return ScientificSoftwareModule()

{repoauditor-0.3.1 → repoauditor-0.4.0}/src/RepoAuditor/Query.py

@@ -8,6 +8,7 @@
 
 import threading
 from abc import ABC, abstractmethod
+from collections.abc import Sequence
 from dataclasses import dataclass
 from typing import Any, Optional, Protocol
 
@@ -53,7 +54,7 @@ class Query(ABC):
         self,
         name: str,
         style: ExecutionStyle,
-        requirements: list[Requirement],
+        requirements: Sequence[Requirement],
     ) -> None:
         self.name = name
         self.style = style
@@ -75,7 +76,7 @@ class Query(ABC):
         status_func: OnStatusFunc,
         *,
         max_num_threads: Optional[int] = None,
-    ) -> list["Query.EvaluateInfo"]:
+    ) -> Sequence["Query.EvaluateInfo"]:
         """Evaluate the Query given the query data and the data from the requirements."""
         status_info = StatusInfo()
         status_info_lock = threading.Lock()

{repoauditor-0.3.1 → repoauditor-0.4.0}/src/RepoAuditor/__init__.py

@@ -2,4 +2,4 @@ APP_NAME = "RepoAuditor"
 
 # Note that the default value below will be used until the value
 # here is explicitly updated by the Continuous Integration system.
-__version__ = "0.3.1"
+__version__ = "0.4.0"

{repoauditor-0.3.1 → repoauditor-0.4.0}/tests/Plugins/CommunityStandards/CommunityStandardsQuery_UnitTest.py

@@ -36,6 +36,8 @@ def patch_temp_directory(monkeypatch):
 class TestCommunityStandardsQuery:
     """Tests for CommunityStandardsQuery class."""
 
+    query = CommunityStandardsQuery()
+
     def test_GetData(self, module_data, monkeypatch):
         """Test the GetData method."""
         monkeypatch.setattr(
@@ -53,8 +55,7 @@ class TestCommunityStandardsQuery:
             mock_clone_from,
         )
 
-        query = CommunityStandardsQuery()
-        query_data = query.GetData(module_data)
+        query_data = self.query.GetData(module_data)
 
         assert query_data["repo_dir"].name == "test_temp_directory"
 
@@ -77,8 +78,7 @@ class TestCommunityStandardsQuery:
 
         monkeypatch.setattr(Repo, "clone_from", mock_clone_from)
 
-        query = CommunityStandardsQuery()
-        _ = query.GetData(module_data)
+        _ = self.query.GetData(module_data)
 
     def test_GetData_does_not_add_pat(self, module_data, monkeypatch):
         """Test the GetData method preserves the URL when no PAT is provided"""
@@ -97,8 +97,7 @@ class TestCommunityStandardsQuery:
 
         monkeypatch.setattr(Repo, "clone_from", mock_clone_from)
 
-        query = CommunityStandardsQuery()
-        _ = query.GetData(module_data)
+        _ = self.query.GetData(module_data)
 
     def test_GetData_handles_gitpython_errors(self, module_data, monkeypatch):
         """Test the GetData method handles errors raised by the gitpyhon module"""
@@ -115,15 +114,13 @@ class TestCommunityStandardsQuery:
 
         monkeypatch.setattr(Repo, "clone_from", mock_clone_from)
 
-        query = CommunityStandardsQuery()
         with pytest.raises(RuntimeError) as e_info:
-            _ = query.GetData(module_data)
+            _ = self.query.GetData(module_data)
         assert gitpython_error_msg in str(e_info)
 
     def test_Cleanup(self, module_data):
         """Test the Cleanup method."""
-        query = CommunityStandardsQuery()
         module_data["repo_dir"] = MockTemporaryDirectory()
-        result = query.Cleanup(module_data)
+        result = self.query.Cleanup(module_data)
 
         assert result is None

repoauditor-0.4.0/tests/Plugins/ScientificSoftware/ScientificSoftwareQuery_UnitTest.py

@@ -0,0 +1,16 @@
+# -------------------------------------------------------------------------------
+# |
+# |  Copyright (c) 2024 Scientific Software Engineering Center at Georgia Tech
+# |  Distributed under the MIT License.
+# |
+# -------------------------------------------------------------------------------
+"""Unit tests for ScientificSoftwareQuery.py"""
+
+from RepoAuditor.Plugins.ScientificSoftware.ScientificSoftwareQuery import ScientificSoftwareQuery
+from CommunityStandards.CommunityStandardsQuery_UnitTest import TestCommunityStandardsQuery
+
+
+class TestScientificSoftwareQuery(TestCommunityStandardsQuery):
+    """Tests for ScientificSoftwareQuery class."""
+
+    query = ScientificSoftwareQuery()

repoauditor-0.4.0/tests/Plugins/ScientificSoftware_EndToEndTest.py

@@ -0,0 +1,35 @@
+# -------------------------------------------------------------------------------
+# |
+# |  Copyright (c) 2024 Scientific Software Engineering Center at Georgia Tech
+# |  Distributed under the MIT License.
+# |
+# -------------------------------------------------------------------------------
+"""End-to-end tests for the ScientificSoftware plugin."""
+
+import pytest
+from dbrownell_Common.TestHelpers.StreamTestHelpers import (
+    InitializeStreamCapabilities,
+)
+from typer.testing import CliRunner
+from utilities import ScrubDurationGithuburlAndSpaces
+
+from RepoAuditor.EntryPoint import app
+
+# ----------------------------------------------------------------------
+pytest.fixture(InitializeStreamCapabilities(), scope="session", autouse=True)
+
+
+# ----------------------------------------------------------------------
+class TestScientificSoftware:
+    """End-to-end tests for files in a GitHub repository which implements scientific software."""
+
+    # ----------------------------------------------------------------------
+    def test_NoCitation(self, pat_args, snapshot):
+        """Test if no CITATION file exists in the repository."""
+        result = CliRunner().invoke(
+            app,
+            pat_args,
+        )
+
+        assert result.exit_code == -1, result.output
+        assert ScrubDurationGithuburlAndSpaces(result.stdout) == snapshot

repoauditor-0.4.0/tests/Plugins/__snapshots__/ScientificSoftware_EndToEndTest.ambr

@@ -0,0 +1,65 @@
+# serializer version: 1
+# name: TestScientificSoftware.test_NoCitation
+  '''
+  Processing 1 module...
+    Processing 'ScientificSoftware' (1 of 1)...
+  
+  
+  
+  
+    DONE! (-1, <scrubbed duration>)
+  DONE! (-1, <scrubbed duration>)
+  
+  
+  ╭───────────────────────────────────────────────── ScientificSoftware ─────────────────────────────────────────────────╮
+  │                                                                                                                      │
+  │ Validates existence of repository files for Scientific Software.                                                     │
+  │                                                                                                                      │
+  │                                                                                                                      │
+  │ Successful:     0 (0.00%)                                                                                            │
+  │ Warnings:       0 (0.00%)                                                                                            │
+  │ Errors:         1 (100.00%)                                                                                          │
+  │ Skipped:        0 (0.00%)                                                                                            │
+  │                                                                                                                      │
+  │ ╭─ [Error] Citation ───────────────────────────────────────────────────────────────────────────────────────────────╮ │
+  │ │                                                                                                                  │ │
+  │ │ Validates that CITATION file exists.                                                                             │ │
+  │ │                                                                                                                  │ │
+  │ │ ERROR: No CITATION file found.                                                                                   │ │
+  │ │                                                                                                                  │ │
+  │ │ Resolution                                                                                                       │ │
+  │ │ ----------                                                                                                       │ │
+  │ │   1) Create a CITATION/CITATIONS file in in the root directory.                                                  │ │
+  │ │                                                                                                                  │ │
+  │ │   2) It can have any of the following extensions:                                                                │ │
+  │ │      -  e.g. `CITATION`                                                                                          │ │
+  │ │      - CITATION.cff                                                                                              │ │
+  │ │      - CITATION.md                                                                                               │ │
+  │ │      - CITATION.bib                                                                                              │ │
+  │ │                                                                                                                  │ │
+  │ │ Rationale                                                                                                        │ │
+  │ │ ---------                                                                                                        │ │
+  │ │   A citation file helps users correctly cite your software.                                                      │ │
+  │ │                                                                                                                  │ │
+  │ │   For more details, please see                                                                                   │ │
+  │ │   https://docs.github.com/en/repositories/managing-your-repositorys-settings-and-features/customizing-your-repos │ │
+  │ │ itory/about-citation-files                                                                                       │ │
+  │ │                                                                                                                  │ │
+  │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ │
+  │ ╭─ Metrics ────────────────────────────────────────────────────────────────────────────────────────────────────────╮ │
+  │ │                                                                                                                  │ │
+  │ │                                                                                                                  │ │
+  │ │ Successful:     0 (0.00%)                                                                                        │ │
+  │ │ Warnings:       0 (0.00%)                                                                                        │ │
+  │ │ Errors:         1 (100.00%)                                                                                      │ │
+  │ │ Skipped:        0 (0.00%)                                                                                        │ │
+  │ │                                                                                                                  │ │
+  │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯ │
+  │                                                                                                                      │
+  ╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
+  
+  Results: DONE! (-1, <scrubbed duration>)
+  
+  
+  '''
+# ---