Add phase 1 GitHub repo sampling pipeline

.gitignore

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+# Secrets and API Keys
+.env
+
+# Python compilation files
+__pycache__/
+*.pyc
+.pytest_cache
+
+# Downloaded Data
+output/
+run*/
+seen_repo_ids.json

plan.md

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+# GitHub Commit Pipeline Plan
+
+## Summary
+Build a Python pipeline with two separate CLI commands:
+
+- `sample-repos`: collect repositories from GitHub Search using config-backed defaults and optional runtime query overrides, then save repository metadata.
+- `fetch-commits`: read the saved repositories and fetch commit history from each repository’s current default branch.
+
+Randomized sampling stays out of scope for v1, but phase 1 should preserve enough metadata and modularity to support future sampling improvements without changing phase 2 behavior.
+
+## Key Changes
+### Phase 1 behavior
+- Use `GET /search/repositories` as the primary discovery endpoint.
+- Build the effective search query from:
+  - default search constants stored outside the CLI
+  - optional runtime `--query` override supplied by the user
+- Start with default filters equivalent to:
+  - `is:public`
+  - `stars:>10`
+  - `size:>1000`
+  - `archived:false`
+  - exclude forks by default
+- Keep repository selection deterministic/simple for v1:
+  - fetch search results with normal pagination
+  - save accepted repositories in returned order
+  - no randomization logic in v1
+- Deduplicate repositories by GitHub `repo_id`.
+- Persist:
+  - raw repo dataset
+  - seen-repo index keyed by `repo_id`
+  - run metadata containing the final resolved search query and CLI inputs
+- Default repo count for phase 1 is `n=10` when the user does not provide a count.
+
+### Phase 2 behavior
+- Refresh repository metadata with `GET /repos/{owner}/{repo}` before commit extraction.
+- Fetch commits only from the repository’s current default branch using `GET /repos/{owner}/{repo}/commits`.
+- Treat storage identity for commit records as `repo_id + sha` so the same SHA in different repository contexts is not accidentally collapsed.
+- Write one normalized commit record per JSONL line.
+- Prototype with a default truncation cap of `1` page per repository:
+  - default `per_page=100`
+  - default `max_pages_per_repo=1`
+- If a repository hits the page cap:
+  - mark it `success_with_warning`
+  - set `truncated=true`
+  - record `truncation_reason=max_pages`
+- If a repository becomes inaccessible or repeatedly fails:
+  - log the repo and failure reason
+  - mark it failed in run state
+  - continue processing remaining repositories
+- Support rerun policy via flag:
+  - default: refresh from scratch
+  - optional resume mode: skip repos already marked complete
+
+### CLI and storage
+- Expose two commands:
+  - `sample-repos`
+  - `fetch-commits`
+- Keep v1 flags focused:
+  - `sample-repos`: `--count` defaulting to `10`, output root, rerun/dedupe mode, optional `--query`
+  - `fetch-commits`: input repo dataset or run folder, output root, refresh-vs-resume mode, `--max-pages-per-repo`, retry settings
+- Organize outputs under a `run_id` folder with separate phase 1 and phase 2 subfolders.
+- Keep phase 1 and phase 2 datasets separate.
+- Write phase 2 output as chunked or partitioned JSONL files rather than one monolithic file.
+- Include runnable test commands in project docs/help output so phase 1 and phase 2 can be exercised from the terminal immediately after setup.
+
+## Public Interfaces / Data Shape
+### CLI examples to include for testing
+- Default phase 1 run:
+  - `python main.py sample-repos`
+- Phase 1 with explicit repo count:
+  - `python main.py sample-repos --count 25`
+- Phase 1 with runtime search override:
+  - `python main.py sample-repos --count 25 --query "is:public stars:>50 size:>5000 archived:false"`
+- Default phase 2 run against a run folder:
+  - `python main.py fetch-commits --run-id <run_id>`
+- Phase 2 with resume and higher page cap:
+  - `python main.py fetch-commits --run-id <run_id> --resume --max-pages-per-repo 3`
+
+### Phase 1 repo record
+Each repo record should include at minimum:
+- `run_id`
+- `repo_id`
+- `full_name`
+- `html_url`
+- `api_url`
+- `default_branch`
+- `language`
+- `description`
+- `stargazers_count`
+- `size_kb`
+- `fork`
+- `archived`
+- `visibility`
+- `sample_query`
+- `sample_page`
+- `sampled_at`
+
+### Phase 2 commit record
+Each commit record should include at minimum:
+- `run_id`
+- `repo_id`
+- `repo_full_name`
+- `repo_html_url`
+- `default_branch_at_fetch`
+- `sha`
+- `parent_shas`
+- `author_name`
+- `author_email`
+- `author_date`
+- `committer_name`
+- `committer_email`
+- `committer_date`
+- `message`
+- `html_url`
+- `fetched_at`
+- `source_endpoint`
+- `page_number`
+- `truncated`
+
+### Run state / config shape
+Persist lightweight state to support resume and future extensibility:
+- resolved search query after merging defaults and runtime override
+- per-run repo status: pending, complete, failed, success_with_warning
+- failure reason if failed
+- seen repo index keyed by `repo_id`
+
+## Test Plan
+- Phase 1 uses default `count=10` when no repo count is supplied.
+- Phase 1 accepts an explicit repo count and stops after collecting that many unique repos.
+- Phase 1 resolves the effective search query correctly from config defaults plus optional `--query`.
+- Phase 1 calls GitHub Search with the expected final filters.
+- Phase 1 deduplicates repositories by `repo_id` within a run and across reruns.
+- Phase 1 persists repo records and seen-index state correctly.
+- Phase 2 refreshes repo metadata before commit extraction.
+- Phase 2 fetches only default-branch history.
+- Phase 2 stops after 1 page by default and marks capped repos as `success_with_warning`.
+- Phase 2 writes one commit per JSONL line with truncation metadata when capped.
+- Phase 2 logs and skips inaccessible repositories without failing the whole run.
+- Resume mode skips repos already marked complete.
+- Refresh mode re-fetches repos from scratch.
+- The documented CLI example commands run successfully with defaults and with explicit overrides.
+
+## Assumptions and Defaults
+- Randomized sampling is out of scope for v1.
+- V1 phase 1 is a search-and-save workflow, not a statistically rigorous sampler.
+- Search defaults live outside the CLI in a config/constants source.
+- `--query` is supported at runtime for phase 1 and is treated as the user-supplied search query input.
+- Default phase 2 behavior is refresh from scratch; resume is opt-in.
+- Default phase 2 truncation is `1` page per repository for prototyping and storage control.
+- JSONL is the raw storage format for v1.
+- Future sampling improvements should be additive and should not require changing the repo dataset schema, commit dataset schema, or phase 2 contract.
+- Remaining CLI clarification to lock before implementation: whether `--query` should fully replace the default search query or be appended on top of the default filters. If unspecified, the implementation should default to replacing the search query entirely and record the resolved final query in run metadata.

poetry.lock

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+# This file is automatically @generated by Poetry 2.3.4 and should not be changed by hand.
+
+[[package]]
+name = "certifi"
+version = "2026.2.25"
+description = "Python package for providing Mozilla's CA Bundle."
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+groups = ["main"]
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+six = ">=1.5"
+
+[[package]]
+name = "python-dotenv"
+version = "1.2.2"
+description = "Read key-value pairs from a .env file and set them as environment variables"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "python_dotenv-1.2.2-py3-none-any.whl", hash = "sha256:1d8214789a24de455a8b8bd8ae6fe3c6b69a5e3d64aa8a8e5d68e694bbcb285a"},
+    {file = "python_dotenv-1.2.2.tar.gz", hash = "sha256:2c371a91fbd7ba082c2c1dc1f8bf89ca22564a087c2c287cd9b662adde799cf3"},
+]
+
+[package.extras]
+cli = ["click (>=5.0)"]
+
+[[package]]
+name = "requests"
+version = "2.33.1"
+description = "Python HTTP for Humans."
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+files = [
+    {file = "requests-2.33.1-py3-none-any.whl", hash = "sha256:4e6d1ef462f3626a1f0a0a9c42dd93c63bad33f9f1c1937509b8c5c8718ab56a"},
+    {file = "requests-2.33.1.tar.gz", hash = "sha256:18817f8c57c6263968bc123d237e3b8b08ac046f5456bd1e307ee8f4250d3517"},
+]
+
+[package.dependencies]
+certifi = ">=2023.5.7"
+charset_normalizer = ">=2,<4"
+idna = ">=2.5,<4"
+urllib3 = ">=1.26,<3"
+
+[package.extras]
+socks = ["PySocks (>=1.5.6,!=1.5.7)"]
+use-chardet-on-py3 = ["chardet (>=3.0.2,<8)"]
+
+[[package]]
+name = "requests-mock"
+version = "1.12.1"
+description = "Mock out responses from the requests package"
+optional = false
+python-versions = ">=3.5"
+groups = ["main"]
+files = [
+    {file = "requests-mock-1.12.1.tar.gz", hash = "sha256:e9e12e333b525156e82a3c852f22016b9158220d2f47454de9cae8a77d371401"},
+    {file = "requests_mock-1.12.1-py2.py3-none-any.whl", hash = "sha256:b1e37054004cdd5e56c84454cc7df12b25f90f382159087f4b6915aaeef39563"},
+]
+
+[package.dependencies]
+requests = ">=2.22,<3"
+
+[package.extras]
+fixture = ["fixtures"]
+
+[[package]]
+name = "six"
+version = "1.17.0"
+description = "Python 2 and 3 compatibility utilities"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+groups = ["main"]
+files = [
+    {file = "six-1.17.0-py2.py3-none-any.whl", hash = "sha256:4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274"},
+    {file = "six-1.17.0.tar.gz", hash = "sha256:ff70335d468e7eb6ec65b95b99d3a2836546063f63acc5171de367e834932a81"},
+]
+
+[[package]]
+name = "tzdata"
+version = "2026.1"
+description = "Provider of IANA time zone data"
+optional = false
+python-versions = ">=2"
+groups = ["main"]
+markers = "sys_platform == \"win32\" or sys_platform == \"emscripten\""
+files = [
+    {file = "tzdata-2026.1-py2.py3-none-any.whl", hash = "sha256:4b1d2be7ac37ceafd7327b961aa3a54e467efbdb563a23655fbfe0d39cfc42a9"},
+    {file = "tzdata-2026.1.tar.gz", hash = "sha256:67658a1903c75917309e753fdc349ac0efd8c27db7a0cb406a25be4840f87f98"},
+]
+
+[[package]]
+name = "urllib3"
+version = "2.6.3"
+description = "HTTP library with thread-safe connection pooling, file post, and more."
+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
+files = [
+    {file = "urllib3-2.6.3-py3-none-any.whl", hash = "sha256:bf272323e553dfb2e87d9bfd225ca7b0f467b919d7bbd355436d3fd37cb0acd4"},
+    {file = "urllib3-2.6.3.tar.gz", hash = "sha256:1b62b6884944a57dbe321509ab94fd4d3b307075e0c2eae991ac71ee15ad38ed"},
+]
+
+[package.extras]
+brotli = ["brotli (>=1.2.0) ; platform_python_implementation == \"CPython\"", "brotlicffi (>=1.2.0.0) ; platform_python_implementation != \"CPython\""]
+h2 = ["h2 (>=4,<5)"]
+socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"]
+zstd = ["backports-zstd (>=1.0.0) ; python_version < \"3.14\""]
+
+[metadata]
+lock-version = "2.1"
+python-versions = ">=3.12"
+content-hash = "3c8765a0ae32ec30eec764e892bef0c0e87524d351f88387e91b78c4b604d112"

pyproject.toml

@@ -0,0 +1,27 @@
+[project]
+name = "github_datapipe"
+version = "0.1.0"
+description = "This project extracts github data."
+authors = [
+    {name = "HirBrahmbhatt"}
+]
+requires-python = ">=3.12"
+dependencies = [
+    "requests (>=2.33.1,<3.0.0)",
+    "pandas (>=3.0.2,<4.0.0)",
+    "pyarrow (>=23.0.1,<24.0.0)",
+    "python-dotenv (>=1.2.2,<2.0.0)",
+    "pytest (>=9.0.3,<10.0.0)",
+    "requests-mock (>=1.12.1,<2.0.0)"
+]
+
+[project.scripts]
+github-datapipe = "github_datapipe.extract_repos:main"
+
+
+[build-system]
+requires = ["poetry-core>=2.0.0,<3.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]

src/github_datapipe/config.py

@@ -0,0 +1,21 @@
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+
+
+@dataclass(frozen=True) # This makes the class immutable so in the process, we do not accidently change the variable values of this
+class GithubConfig:
+    base_url: str = "https://api.github.com"
+    api_version: str = "2022-11-28"
+    search_repositories_endpoint: str = "/search/repositories"
+    default_repo_count: int = 10
+    default_per_page: int = 100
+    default_output_root: str = "runs"
+    default_query: str = "is:public stars:>10 size:>1000 archived:false fork:false created:>2025-07-15"
+    user_agent: str = "github-datapipe/0.1.0"
+
+
+
+
+ROOT_DIR = Path(__file__).resolve().parent

src/github_datapipe/extract_repos.py

@@ -0,0 +1,286 @@
+from __future__ import annotations
+
+import json
+import os
+from dataclasses import dataclass
+from datetime import UTC, datetime
+from pathlib import Path
+from typing import Any
+from uuid import uuid4
+
+import requests
+from dotenv import load_dotenv
+
+from github_datapipe.config import GithubConfig
+
+load_dotenv()
+
+
+class GithubApiError(RuntimeError):
+    """Raised when GitHub responds with an error payload."""
+
+
+@dataclass(frozen=True)
+class SampleReposOptions:
+    """
+        To set configuration options for the GitHub repository sampling run.
+        Attributes:
+            1. count (int): The total number of unique repositories to collect. Must be > 0. Defaults to GithubConfig.default_repo_count
+            2. output_root: The base directory where the run folder will be created to store the search repository data.
+            3. query: The github search string using github offered query params.
+            4. per_page: The number of results to fetch per API call. Max is 100.
+            5. mode: 'fresh' (starting a fresh run) or "append-deduped" (if you want to resume half-done previous run and avoid duplicates).
+            6. run_id: To keep a trace of current run by giving it a unique id.
+    """
+    count: int = GithubConfig.default_repo_count
+    output_root: Path = Path(GithubConfig.default_output_root)
+    query: str = GithubConfig.default_query
+    per_page: int = GithubConfig.default_per_page
+    mode: str = "append-deduped"
+    run_id: str | None = None
+
+
+def resolve_query(query_override: str | None) -> str:
+    """ To override default query params with user inserted query params. """
+    return query_override.strip() if query_override else GithubConfig.default_query
+
+
+class GithubRepoSampler:
+    def __init__(self, token: str, session: requests.Session | None = None) -> None:
+        """
+            Everytime an instance of GithubRepoSampler is created, this method will be called first to open a session and set headers.
+            Args:
+                token (str): A valid GitHub Personal Access Token (PAT).
+                session (requests.Session | None, optional): An existing session to use. If None, a new session is created.
+        """
+        self._session = session or requests.Session()
+        self._session.headers.update(
+            {
+                "Accept": "application/vnd.github+json",
+                "Authorization": f"Bearer {token}",
+                "X-GitHub-Api-Version": GithubConfig.api_version,
+                "User-Agent": GithubConfig.user_agent,
+            }
+        )
+
+    def search_repositories(self, query: str, page: int, per_page: int) -> dict[str, Any]:
+        """
+            Calls github's /search/repositories endpoint passing query params and other.
+
+            Args:
+                query (str): The GitHub-formatted search query string.
+                page (int): The specific page of results to fetch.
+                per_page (int): The number of items to return per page (max 100).
+
+            Returns:
+                dict[str, Any]: The raw JSON payload returned by the GitHub API.
+
+            Raises:
+                GithubApiError: If the API responds with an HTTP status code >= 400 
+        """
+        response = self._session.get(
+            f"{GithubConfig.base_url}{GithubConfig.search_repositories_endpoint}",
+            params={"q": query, "page": page, "per_page": per_page},
+            timeout=30,
+        )
+        if response.status_code >= 400:
+            try:
+                payload = response.json()
+            except ValueError:
+                payload = {"message": response.text}
+            message = payload.get("message", "GitHub API request failed")
+            raise GithubApiError(f"GitHub search failed ({response.status_code}): {message}")
+        return response.json()
+
+
+def sample_repositories(options: SampleReposOptions) -> dict[str, Any]:
+    """
+        Orchestrates the end-to-end execution of a GitHub repository data pull.
+
+        This function handles the complete lifecycle of a sampling run: validating credentials,
+        setting up the local file system for the run, managing state to prevent duplicate 
+        downloads, paginating through the GitHub Search API, and saving the normalized data.
+
+        Effects:
+            - Creates a timestamped run directory inside `options.output_root`.
+            - Writes newly fetched repository data to `repos.jsonl`.
+            - Writes or updates a global `seen_repo_ids.json` tracker file.
+            - Writes a `manifest.json` logging the run's parameters and results.
+
+        Args:
+            options (SampleReposOptions): The configuration parameters for the run.
+
+        Returns:
+            dict[str, Any]: A summary dictionary containing the `run_id`, the total 
+                `count_collected`, and the absolute paths to the generated output files.
+    """
+    # 1. SETUP: Validate the token and creds
+    github_token = os.getenv("github_token")
+    if not github_token:
+        raise ValueError("GitHub token is not available in .env as `github_token`.")
+
+    if options.count <= 0:
+        raise ValueError("`count` must be greater than 0.")
+
+    # 2. FILE SYSTEM: Create isolated folders for this specific run
+    run_id = options.run_id or build_run_id()
+    output_root = options.output_root.resolve() # returns an absolute path
+    run_root = output_root / run_id # isolated folder created for one single execution (or "run") of this script.
+    phase1_root = run_root / "phase1" # the search phase is phase 1
+    phase1_root.mkdir(parents=True, exist_ok=True) 
+
+    # Define exact file paths for where data will live
+    seen_index_path = output_root / "seen_repo_ids.json" # Notes the last seen repo's id
+    repos_path = phase1_root / "repos.jsonl" # Actual repo metadata
+    manifest_path = phase1_root / "manifest.json" # log entry
+
+    # 3. STATE MGMT: seen_repo_ids will make sure that duplicated data doesn't end up in the result
+    seen_repo_ids = set() if options.mode == "fresh" else load_seen_repo_ids(seen_index_path)
+    current_run_seen_repo_ids: set[int] = set()
+
+    # 4. NETWORK SETUP: Initialize the session wrapper
+    sampler = GithubRepoSampler(token=github_token)
+    accepted_repos: list[dict[str, Any]] = []
+    page = 1
+    total_count: int | None = None
+
+    # 5. THE MAIN LOOP: Keep fetching until the requested target count is hit
+    while len(accepted_repos) < options.count:
+        payload = sampler.search_repositories(
+            query=options.query,
+            page=page,
+            per_page=options.per_page,
+        )
+        # Github Search API response = JSON Object containing { search metadata, items: [{ repo obj1 }, { repo obj 2} ...] }
+        items = payload.get("items", []) 
+        total_count = payload.get("total_count", total_count) # the number of the repos matching your query at exact moment in time
+        
+        # Break safety: If GitHub returns an empty list, we've exhausted all results of current api call
+        if not items:
+            break
+
+        sampled_at = utc_now() # to keep note of current time incase we need to revise it
+
+        # Process each repository in the current result present in items
+        for repo in items:
+            repo_id = int(repo["id"])
+            if repo_id in seen_repo_ids or repo_id in current_run_seen_repo_ids:
+                continue
+
+            normalized_repo = normalize_repo_record(
+                repo=repo,
+                run_id=run_id,
+                sample_query=options.query,
+                sample_page=page,
+                sampled_at=sampled_at,
+            )
+            accepted_repos.append(normalized_repo)
+            current_run_seen_repo_ids.add(repo_id)
+
+            if len(accepted_repos) >= options.count:
+                break
+
+        page += 1
+
+    write_jsonl(repos_path, accepted_repos)
+    if options.mode != "fresh":
+        seen_repo_ids.update(current_run_seen_repo_ids)
+        write_json(seen_index_path, sorted(seen_repo_ids))
+
+    # manifest is a log object that denotes what kind of input was given to achieve certain output.
+    manifest = {
+        "run_id": run_id,
+        "command": "sample-repos",
+        "resolved_query": options.query,
+        "count_requested": options.count,
+        "count_collected": len(accepted_repos),
+        "per_page": options.per_page,
+        "mode": options.mode,
+        "page_count_scanned": max(page - 1, 0),
+        "github_total_count": total_count,
+        "output_files": {
+            "repos_jsonl": str(repos_path),
+            "seen_repo_ids_json": str(seen_index_path) if options.mode != "fresh" else None,
+        },
+        "sampled_at": utc_now(),
+    }
+    write_json(manifest_path, manifest)
+
+    return {
+        "run_id": run_id,
+        "count_collected": len(accepted_repos),
+        "repos_path": repos_path,
+        "manifest_path": manifest_path,
+        "seen_index_path": seen_index_path if options.mode != "fresh" else None,
+    }
+
+
+def normalize_repo_record(
+    repo: dict[str, Any],
+    run_id: str,
+    sample_query: str,
+    sample_page: int,
+    sampled_at: str,
+) -> dict[str, Any]:
+    
+    """
+        Extracts and flattens relevant fields from a raw GitHub repository payload.
+
+        Args:
+            repo (dict[str, Any]): The raw JSON dictionary for a single repository 
+                as returned by the GitHub API.
+            run_id (str): The unique identifier for the current sampling run.
+            sample_query (str): The search string used to find this repository.
+            sample_page (int): The pagination page number this repository was found on.
+            sampled_at (str): ISO-8601 formatted timestamp of when the record was fetched.
+
+        Returns:
+            dict[str, Any]: A flat dictionary containing the filtered repository metrics 
+            (e.g., repo_id, language, stargazers_count, size_kb) and traceability data.
+    """
+    return {
+        "run_id": run_id,
+        "repo_id": repo["id"],
+        "full_name": repo["full_name"],
+        "html_url": repo["html_url"],
+        "api_url": repo["url"],
+        "default_branch": repo.get("default_branch"),
+        "language": repo.get("language"),
+        "description": repo.get("description"),
+        "stargazers_count": repo.get("stargazers_count"),
+        "size_kb": repo.get("size"),
+        "fork": repo.get("fork"),
+        "archived": repo.get("archived"),
+        "visibility": repo.get("visibility"),
+        "sample_query": sample_query,
+        "sample_page": sample_page,
+        "sampled_at": sampled_at,
+    }
+
+
+def load_seen_repo_ids(path: Path) -> set[int]:
+    if not path.exists():
+        return set()
+    payload = json.loads(path.read_text(encoding="utf-8"))
+    return {int(repo_id) for repo_id in payload}
+
+
+def write_json(path: Path, payload: Any) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(json.dumps(payload, indent=2), encoding="utf-8")
+
+
+def write_jsonl(path: Path, rows: list[dict[str, Any]]) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    with path.open("w", encoding="utf-8") as handle:
+        for row in rows:
+            handle.write(json.dumps(row))
+            handle.write("\n")
+
+
+def build_run_id() -> str:
+    return f"run-{datetime.now(tz=UTC).strftime('%Y%m%dT%H%M%SZ')}-{uuid4().hex[:8]}"
+
+
+def utc_now() -> str:
+    return datetime.now(tz=UTC).isoformat()

src/github_datapipe/main.py

@@ -0,0 +1,86 @@
+from __future__ import annotations
+
+import argparse
+from pathlib import Path
+
+from github_datapipe.config import GithubConfig
+from github_datapipe.extract_repos import SampleReposOptions, resolve_query, sample_repositories
+
+### parser that unpacks the command line args passed as queries and 
+def build_parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description="GitHub data pipeline CLI")
+    subparsers = parser.add_subparsers(dest="command", required=True)
+
+    sample_parser = subparsers.add_parser(
+        "sample-repos",
+        help="Collect repositories from GitHub Search and save phase 1 outputs.",
+    )
+    sample_parser.add_argument(
+        "--count",
+        type=int,
+        default=GithubConfig.default_repo_count,
+        help=f"Number of repositories to sample. Defaults to {GithubConfig.default_repo_count}.",
+    )
+    sample_parser.add_argument(
+        "--query",
+        type=str,
+        default=None,
+        help="Optional raw GitHub repository search query. Replaces config defaults when provided.",
+    )
+    sample_parser.add_argument(
+        "--output-root",
+        type=Path,
+        default=Path(GithubConfig.default_output_root),
+        help=f"Directory where run outputs are stored. Defaults to `{GithubConfig.default_output_root}`.",
+    )
+    sample_parser.add_argument(
+        "--mode",
+        choices=("append-deduped", "fresh"),
+        default="append-deduped",
+        help="Whether to dedupe against the persisted seen-repo index or start a fresh phase-1 run.",
+    )
+    sample_parser.add_argument(
+        "--per-page",
+        type=int,
+        default=GithubConfig.default_per_page,
+        help=f"GitHub Search page size. Defaults to {GithubConfig.default_per_page}.",
+    )
+    sample_parser.add_argument(
+        "--run-id",
+        type=str,
+        default=None,
+        help="Optional run identifier. If omitted, a run id is generated automatically.",
+    )
+
+    return parser
+
+
+def main() -> int:
+    parser = build_parser()
+    args = parser.parse_args()
+
+    if args.command == "sample-repos":
+        options = SampleReposOptions(
+            count=args.count,
+            output_root=args.output_root,
+            query=resolve_query(args.query),
+            per_page=args.per_page,
+            mode=args.mode,
+            run_id=args.run_id,
+        )
+        # result will return output from the extract repo's sample_repositories
+        result = sample_repositories(options)
+        print(f"Run ID: {result['run_id']}")
+        print(f"Collected repositories: {result['count_collected']}")
+        print(f"Repositories file: {result['repos_path']}")
+        print(f"Manifest file: {result['manifest_path']}")
+        if result["seen_index_path"] is not None:
+            print(f"Seen repo index: {result['seen_index_path']}")
+        return 0
+
+    parser.error(f"Unsupported command: {args.command}")
+    return 1
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())

tests/test_phase1.py

@@ -0,0 +1,99 @@
+from __future__ import annotations
+
+import json
+from pathlib import Path
+
+import requests
+
+from github_datapipe.config import GithubConfig
+from github_datapipe.extract_repos import SampleReposOptions, resolve_query, sample_repositories
+
+
+def test_resolve_query_uses_default_when_missing() -> None:
+    """ Verifies that an empty or missing query string falls back to the config default. """
+    assert resolve_query(None) == GithubConfig.default_query
+
+
+def test_resolve_query_uses_override_when_present() -> None:
+    """ Verifies that a user-provided query overrides the config default. """
+    assert resolve_query("stars:>50") == "stars:>50"
+
+
+def test_sample_repositories_dedupes_and_persists(monkeypatch, tmp_path: Path) -> None:
+    """
+    Tests the core data pipeline: ensures pagination works, duplicates are 
+    ignored across pages, and data is correctly saved to the file system.
+    """
+
+    # ==========================================
+    # ARRANGE
+    # ==========================================
+    monkeypatch.setenv("github_token", "token")
+
+    # Create a mock GitHub API that returns 3 total repos across 2 pages.
+    # Notice that 'repo-one' (ID 100) is returned twice to test deduplication.
+    class FakeSampler:
+        def __init__(self, token: str, session: requests.Session | None = None) -> None:
+            self.token = token
+
+        def search_repositories(self, query: str, page: int, per_page: int) -> dict:
+            if page == 1:
+                return {
+                    "total_count": 3,
+                    "items": [
+                        fake_repo(100, "owner/repo-one"),
+                        fake_repo(100, "owner/repo-one"),
+                        fake_repo(101, "owner/repo-two"),
+                    ],
+                }
+            return {"total_count": 3, "items": [fake_repo(102, "owner/repo-three")]}
+
+    # Inject the mock sampler into the main code
+    monkeypatch.setattr("github_datapipe.extract_repos.GithubRepoSampler", FakeSampler)
+
+    options = SampleReposOptions(
+        count=3,
+        output_root=tmp_path, # Safely write files to a temporary test folder
+        query="stars:>10",
+        mode="append-deduped",
+        run_id="run-test",
+    )
+
+    # ==========================================
+    # ACT
+    # ==========================================
+
+    result = sample_repositories(options)
+
+    # ==========================================
+    # ASSERT
+    # ==========================================
+    repos_path = Path(result["repos_path"])
+    rows = [json.loads(line) for line in repos_path.read_text(encoding="utf-8").splitlines()]
+    assert len(rows) == 3
+    assert [row["repo_id"] for row in rows] == [100, 101, 102]
+
+    seen_path = tmp_path / "seen_repo_ids.json"
+    seen_payload = json.loads(seen_path.read_text(encoding="utf-8"))
+    assert seen_payload == [100, 101, 102]
+
+
+def fake_repo(repo_id: int, full_name: str) -> dict:
+    """
+    Helper function to generate a mock GitHub repository payload.
+    Provides only the fields required by the `normalize_repo_record` function.
+    """
+    return {
+        "id": repo_id,
+        "full_name": full_name,
+        "html_url": f"https://github.com/{full_name}",
+        "url": f"https://api.github.com/repos/{full_name}",
+        "default_branch": "main",
+        "language": "Python",
+        "description": f"Description for {full_name}",
+        "stargazers_count": 42,
+        "size": 2048,
+        "fork": False,
+        "archived": False,
+        "visibility": "public",
+    }