Refactor/Refactor workflow generator

README.md

@@ -186,7 +186,7 @@ Docker, ensure that you upload the PDF file to the OSA folder before building th
 /app/OSA/... or just use volume mounting to access the file.
 
 The --generate-workflows option is intended to create customizable CI/CD pipelines for Python repositories. For detailed
-documentation, see the [Workflow Generator README](./osa_tool/workflow/README.md).
+documentation, see the [Workflow Generator README](./osa_tool/operations/codebase/workflow_generation/README.md).
 
 ### Configuration
 
@@ -208,9 +208,12 @@ documentation, see the [Workflow Generator README](./osa_tool/workflow/README.md
 | `--no-fork`          | Avoid create fork for target repository                                             | `False`                        |
 | `--no-pull-request`  | Avoid create pull request for target repository                                     | `False`                        |
 
-Also OSA supports custom configuration via TOML files. Use the `--config-file` option to specify a path to custom configuration file. If no custom configuration file is provided, OSA will use the default configuration.
+Also OSA supports custom configuration via TOML files. Use the `--config-file` option to specify a path to custom
+configuration file. If no custom configuration file is provided, OSA will use the default configuration.
 
-By default, OSA uses a single model for all tasks (specified via `--model`). If you want to use different models for different types of tasks, disable the `--use-single-model` flag and specify models for each task type (`--model-docstring`, `--model-readme`, `--model-validation`, `--model-general`).
+By default, OSA uses a single model for all tasks (specified via `--model`). If you want to use different models for
+different types of tasks, disable the `--use-single-model` flag and specify models for each task type (
+`--model-docstring`, `--model-readme`, `--model-validation`, `--model-general`).
 
 To learn how to work with the interactive CLI and view descriptions of all available keys, visit
 the [CLI usage guide](./osa_tool/scheduler/README.md).

docs/core/operations/OPERATIONS.md

@@ -6,7 +6,9 @@ This document is auto-generated. Do not edit manually.
 
 | Name | Priority | Intents | Scopes | Args Schema | Executor | Method |
 |------|----------|---------|--------|-------------|----------|--------|
-| `generate_report` | 5 | new_task | full_repo, analysis | — | `ReportGenerator` | `build_pdf` |
+| `generate_report` | 5 | new_task | full_repo, analysis | — | `ReportGenerator` | `run` |
+| `validate_doc` | 10 | new_task | full_repo, analysis | — | `DocValidator` | `run` |
+| `validate_paper` | 15 | new_task | full_repo, analysis | — | `PaperValidator` | `run` |
 | `convert_notebooks` | 30 | new_task | full_repo, codebase | ConvertNotebooksArgs | `NotebookConverter` | `convert_notebooks` |
 | `translate_dirs` | 40 | new_task | full_repo, codebase | — | `RepositoryStructureTranslator` | `rename_directories_and_files` |
 | `generate_docstrings` | 50 | new_task, feedback | full_repo, codebase | GenerateDocstringsArgs | `DocstringsGenerator` | `run` |
@@ -16,4 +18,5 @@ This document is auto-generated. Do not edit manually.
 | `generate_readme` | 70 | new_task, feedback | full_repo, docs | — | `ReadmeAgent` | `generate_readme` |
 | `translate_readme` | 75 | new_task, feedback | full_repo, docs | TranslateReadmeArgs | `ReadmeTranslator` | `translate_readme` |
 | `generate_about` | 80 | new_task | full_repo, docs | — | `AboutGenerator` | `generate_about_content` |
+| `generate_workflows` | 85 | new_task, feedback | full_repo, codebase | GenerateWorkflowsArgs | `WorkflowsExecutor` | `generate` |
 | `organize` | 90 | new_task | full_repo, codebase | — | `RepoOrganizer` | `organize` |

osa_tool/operations/codebase/requirements_generation/requirements_generation.py

@@ -42,6 +42,8 @@ def generate(self) -> dict:
         pyproject_path = self.repo_path / "pyproject.toml"
 
         old_context = self._get_existing_context(req_file_path, pyproject_path)
+        if old_context:
+            self._add_event(EventKind.ANALYZED, mode="existing-context")
 
         # Scan with notebooks
         try:

osa_tool/operations/codebase/workflow_generation/workflow_executor.py

@@ -0,0 +1,115 @@
+from typing import List
+
+from osa_tool.config.settings import ConfigManager
+from osa_tool.core.models.event import EventKind, OperationEvent
+from osa_tool.scheduler.workflow_manager import WorkflowManager
+from osa_tool.utils.logger import logger
+
+
+class WorkflowsExecutor:
+    """
+    Executor for CI/CD workflow generation in the agentic pipeline.
+
+    Bridges WorkflowManager to the Operation/Executor pattern,
+    bypassing the legacy Plan-based config path.
+    """
+
+    def __init__(
+        self,
+        config_manager: ConfigManager,
+        workflow_manager: WorkflowManager,
+        include_black: bool = True,
+        include_tests: bool = True,
+        include_pep8: bool = True,
+        include_autopep8: bool = False,
+        include_fix_pep8: bool = False,
+        include_pypi: bool = False,
+        pep8_tool: str = "flake8",
+        use_poetry: bool = False,
+        include_codecov: bool = True,
+        python_versions: List[str] = None,
+        branches: List[str] = None,
+    ):
+        self.config_manager = config_manager
+        self.workflow_manager = workflow_manager
+        self.events: list[OperationEvent] = []
+        self._requested = {
+            "generate_workflows": True,
+            "include_black": include_black,
+            "include_tests": include_tests,
+            "include_pep8": include_pep8,
+            "include_autopep8": include_autopep8,
+            "include_fix_pep8": include_fix_pep8,
+            "include_pypi": include_pypi,
+            "pep8_tool": pep8_tool,
+            "use_poetry": use_poetry,
+            "include_codecov": include_codecov,
+            "python_versions": python_versions or ["3.9", "3.10"],
+            "branches": branches or ["main", "master"],
+        }
+
+    def generate(self) -> dict:
+        if not self.workflow_manager.has_python_code():
+            logger.info("No Python code detected. Skipping workflow generation.")
+            self.events.append(
+                OperationEvent(
+                    kind=EventKind.SKIPPED,
+                    target="workflows",
+                    data={"reason": "no_python_code"},
+                )
+            )
+            return {"result": {"generated": False}, "events": self.events}
+
+        logger.debug("Requested workflow settings: %s", self._requested)
+        effective = self._skip_existing_jobs(self._requested)
+        logger.debug("Effective workflow settings after filtering: %s", effective)
+        WorkflowManager.apply_workflow_settings(self.config_manager, effective)
+        success = self.workflow_manager.generate_workflow(self.config_manager)
+
+        if success:
+            enabled = [k for k, v in effective.items() if k.startswith("include_") and v is True]
+            logger.info("CI/CD workflow generation succeeded. Enabled jobs: %s", enabled)
+            self.events.append(
+                OperationEvent(
+                    kind=EventKind.GENERATED,
+                    target="workflows",
+                    data={
+                        "include_black": effective.get("include_black"),
+                        "include_tests": effective.get("include_tests"),
+                        "include_pep8": effective.get("include_pep8"),
+                        "include_autopep8": effective.get("include_autopep8"),
+                        "include_fix_pep8": effective.get("include_fix_pep8"),
+                        "include_pypi": effective.get("include_pypi"),
+                    },
+                )
+            )
+        else:
+            logger.error("CI/CD workflow generation failed. Check previous log messages for details.")
+            self.events.append(
+                OperationEvent(
+                    kind=EventKind.FAILED,
+                    target="workflows",
+                    data={"reason": "generation_error"},
+                )
+            )
+
+        return {"result": {"generated": success, "settings": effective}, "events": self.events}
+
+    def _skip_existing_jobs(self, settings: dict) -> dict:
+        """Disable generation for jobs that already exist in the repository."""
+        result = dict(settings)
+        for key, job_names in self.workflow_manager.job_name_for_key.items():
+            if key not in result:
+                continue
+            names = [job_names] if isinstance(job_names, str) else job_names
+            if any(job in self.workflow_manager.existing_jobs for job in names):
+                result[key] = False
+                logger.warning("Skipping '%s' workflow: job already exists in the repository.", key)
+                self.events.append(
+                    OperationEvent(
+                        kind=EventKind.SKIPPED,
+                        target=key,
+                        data={"reason": "already_exists"},
+                    )
+                )
+        return result

osa_tool/operations/docs/community_docs_generation/docs_run.py

@@ -25,54 +25,59 @@ def generate_documentation(config_manager: ConfigManager, metadata: RepositoryMe
     events: list[OperationEvent] = []
     generated_files: list[str] = []
     contributing = ContributingBuilder(config_manager, metadata)
-    contributing.build()
-    events.append(OperationEvent(kind=EventKind.GENERATED, target="CONTRIBUTING"))
-    generated_files.append("CONTRIBUTING.md")
-
     community = CommunityTemplateBuilder(config_manager, metadata)
-    community.build_code_of_conduct()
-    events.append(OperationEvent(kind=EventKind.GENERATED, target="CODE_OF_CONDUCT"))
-    generated_files.append("CODE_OF_CONDUCT.md")
 
-    community.build_security()
-    events.append(OperationEvent(kind=EventKind.GENERATED, target="SECURITY"))
-    generated_files.append("SECURITY.md")
+    try:
+        contributing.build()
+        events.append(OperationEvent(kind=EventKind.GENERATED, target="CONTRIBUTING"))
+        generated_files.append("CONTRIBUTING.md")
+    except Exception as e:
+        logger.error("Failed to generate CONTRIBUTING: %s", repr(e), exc_info=True)
+        events.append(OperationEvent(kind=EventKind.FAILED, target="CONTRIBUTING", data={"error": repr(e)}))
 
-    if config_manager.get_git_settings().host in ["github", "gitlab"]:
-        community.build_pull_request()
-        community.build_bug_issue()
-        community.build_documentation_issue()
-        community.build_feature_issue()
+    try:
+        community.build_code_of_conduct()
+        events.append(OperationEvent(kind=EventKind.GENERATED, target="CODE_OF_CONDUCT"))
+        generated_files.append("CODE_OF_CONDUCT.md")
+    except Exception as e:
+        logger.error("Failed to generate CODE_OF_CONDUCT: %s", repr(e), exc_info=True)
+        events.append(OperationEvent(kind=EventKind.FAILED, target="CODE_OF_CONDUCT", data={"error": repr(e)}))
 
-        events.extend(
-            [
-                OperationEvent(kind=EventKind.GENERATED, target="PULL_REQUEST_TEMPLATE"),
-                OperationEvent(kind=EventKind.GENERATED, target="ISSUE_TEMPLATE:bug"),
-                OperationEvent(kind=EventKind.GENERATED, target="ISSUE_TEMPLATE:documentation"),
-                OperationEvent(kind=EventKind.GENERATED, target="ISSUE_TEMPLATE:feature"),
-            ]
-        )
-        generated_files.extend(
-            [
-                "PULL_REQUEST_TEMPLATE.md",
-                "BUG_ISSUE.md",
-                "DOCUMENTATION_ISSUE.md",
-                "FEATURE_ISSUE.md",
-            ]
-        )
+    try:
+        community.build_security()
+        events.append(OperationEvent(kind=EventKind.GENERATED, target="SECURITY"))
+        generated_files.append("SECURITY.md")
+    except Exception as e:
+        logger.error("Failed to generate SECURITY: %s", repr(e), exc_info=True)
+        events.append(OperationEvent(kind=EventKind.FAILED, target="SECURITY", data={"error": repr(e)}))
 
-    if config_manager.get_git_settings().host == "gitlab":
-        community.build_vulnerability_disclosure()
+    if config_manager.get_git_settings().host in ["github", "gitlab"]:
+        for method, target, filename in [
+            (community.build_pull_request, "PULL_REQUEST_TEMPLATE", "PULL_REQUEST_TEMPLATE.md"),
+            (community.build_bug_issue, "ISSUE_TEMPLATE:bug", "BUG_ISSUE.md"),
+            (community.build_documentation_issue, "ISSUE_TEMPLATE:documentation", "DOCUMENTATION_ISSUE.md"),
+            (community.build_feature_issue, "ISSUE_TEMPLATE:feature", "FEATURE_ISSUE.md"),
+        ]:
+            try:
+                method()
+                events.append(OperationEvent(kind=EventKind.GENERATED, target=target))
+                generated_files.append(filename)
+            except Exception as e:
+                logger.error("Failed to generate %s: %s", target, repr(e), exc_info=True)
+                events.append(OperationEvent(kind=EventKind.FAILED, target=target, data={"error": repr(e)}))
 
-        events.append(
-            OperationEvent(
-                kind=EventKind.GENERATED,
-                target="VULNERABILITY_DISCLOSURE",
+    if config_manager.get_git_settings().host == "gitlab":
+        try:
+            community.build_vulnerability_disclosure()
+            events.append(OperationEvent(kind=EventKind.GENERATED, target="VULNERABILITY_DISCLOSURE"))
+            generated_files.append("Vulnerability_Disclosure.md")
+        except Exception as e:
+            logger.error("Failed to generate VULNERABILITY_DISCLOSURE: %s", repr(e), exc_info=True)
+            events.append(
+                OperationEvent(kind=EventKind.FAILED, target="VULNERABILITY_DISCLOSURE", data={"error": repr(e)})
             )
-        )
-        generated_files.append("Vulnerability_Disclosure.md")
 
-    logger.info("All additional documentation successfully generated.")
+    logger.info("Additional documentation generation completed.")
 
     return {
         "result": {

osa_tool/operations/operations_catalog.py

@@ -12,6 +12,7 @@
 from osa_tool.operations.codebase.notebook_conversion.notebook_converter import NotebookConverter
 from osa_tool.operations.codebase.organization.repo_organizer import RepoOrganizer
 from osa_tool.operations.codebase.requirements_generation.requirements_generation import RequirementsGenerator
+from osa_tool.operations.codebase.workflow_generation.workflow_executor import WorkflowsExecutor
 from osa_tool.operations.docs.about_generation.about_generator import AboutGenerator
 from osa_tool.operations.docs.community_docs_generation.docs_run import generate_documentation
 from osa_tool.operations.docs.community_docs_generation.license_generation import LicenseCompiler
@@ -229,6 +230,42 @@ class GenerateAboutOperation(Operation):
     executor_dependencies = ["config_manager", "git_agent"]
 
 
+class GenerateWorkflowsArgs(BaseModel):
+    include_black: bool = Field(True, description="Generate Black code formatter workflow.")
+    include_tests: bool = Field(True, description="Generate unit tests workflow.")
+    include_pep8: bool = Field(True, description="Generate PEP 8 compliance check workflow.")
+    include_autopep8: bool = Field(False, description="Generate autopep8 auto-fix workflow.")
+    include_fix_pep8: bool = Field(False, description="Generate fix-pep8 slash-command workflow.")
+    include_pypi: bool = Field(False, description="Generate PyPI publish workflow.")
+    pep8_tool: Literal["flake8", "pylint"] = Field("flake8", description="Tool for PEP 8 checking.")
+    use_poetry: bool = Field(False, description="Use Poetry for PyPI packaging.")
+    include_codecov: bool = Field(True, description="Include Codecov coverage upload step.")
+    python_versions: List[str] = Field(
+        default_factory=lambda: ["3.9", "3.10"],
+        description="Python versions to test against. Example: ['3.10', '3.11', '3.12']",
+    )
+    branches: List[str] = Field(
+        default_factory=lambda: ["main", "master"],
+        description="Git branches to trigger workflows on.",
+    )
+
+
+class GenerateWorkflowsOperation(Operation):
+    name = "generate_workflows"
+    description = "Generate CI/CD workflow files (GitHub Actions / GitLab CI) for the repository."
+
+    supported_intents = ["new_task", "feedback"]
+    supported_scopes = ["full_repo", "codebase"]
+    priority = 85
+
+    args_schema = GenerateWorkflowsArgs
+    args_policy = "auto"
+
+    executor = WorkflowsExecutor
+    executor_method = "generate"
+    executor_dependencies = ["config_manager", "workflow_manager"]
+
+
 class OrganizeRepositoryOperation(Operation):
     name = "organize"
     description = (

osa_tool/scheduler/workflow_manager.py

@@ -1,17 +1,21 @@
 import os
 from abc import ABC, abstractmethod
+from pathlib import Path
 from typing import Optional
 
 import yaml
 
 from osa_tool.config.settings import ConfigManager
-from osa_tool.scheduler.plan import Plan
 from osa_tool.core.git.metadata import RepositoryMetadata
+from osa_tool.operations.codebase.workflow_generation.workflow_generator import (
+    GitHubWorkflowGenerator,
+    GitLabWorkflowGenerator,
+)
+from osa_tool.scheduler.plan import Plan
 from osa_tool.tools.repository_analysis.sourcerank import SourceRank
 from osa_tool.utils.arguments_parser import get_keys_from_group_in_yaml
 from osa_tool.utils.logger import logger
 from osa_tool.utils.utils import parse_folder_name
-from osa_tool.workflow.workflow_generator import GitHubWorkflowGenerator, GitLabWorkflowGenerator
 
 
 class WorkflowManager(ABC):
@@ -71,12 +75,21 @@ def has_python_code(self) -> bool:
         """
         Checks whether the repository contains Python code.
 
+        First checks the repository metadata language field. If that is absent or
+        does not mention Python, falls back to counting ``.py`` files on disk.
+
         Returns:
             True if Python code is present, False otherwise.
         """
-        if not self.metadata.language:
-            return False
-        return "Python" in self.metadata.language
+        if self.metadata.language and "Python" in self.metadata.language:
+            return True
+
+        py_count = sum(1 for _ in Path(self.base_path).rglob("*.py"))
+        if py_count > 0:
+            logger.info("Metadata did not report Python, but found %d .py file(s) on disk.", py_count)
+            return True
+
+        return False
 
     def build_actual_plan(self, sourcerank: SourceRank) -> dict:
         """
@@ -122,6 +135,19 @@ def build_actual_plan(self, sourcerank: SourceRank) -> dict:
 
         return result_plan
 
+    @staticmethod
+    def apply_workflow_settings(config_manager: ConfigManager, settings: dict) -> None:
+        """
+        Apply workflow settings directly from a dict, bypassing the legacy Plan.
+        Used by the agentic pipeline.
+
+        Args:
+            config_manager: Configuration manager to update.
+            settings: Dict of workflow settings keys and values.
+        """
+        config_manager.config.workflows = config_manager.config.workflows.model_copy(update=settings)
+        logger.info("Config successfully updated with workflow settings")
+
     def update_workflow_config(self, config_manager: ConfigManager, plan: Plan) -> None:
         """
         Update workflow configuration settings in the config loader based on the given plan.

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "osa_tool"
-version = "0.2.8"
+version = "0.2.9"
 description = "Tool that just makes your open source project better!"
 requires-python = ">=3.11,<4.0"
 authors = [