Add rerun script (#264)

* Add script for automatically re-running notebooks

Co-authored-by: Thomas Wiecki <[email protected]>

* Re-run lasso_block_update.ipynb notebook

Co-authored-by: Thomas Wiecki <[email protected]>

Author: michaelosthege

examples/pymc3_howto/lasso_block_update.ipynb

@@ -0,0 +1,171 @@
+"""
+This script/module may be used to re-run, commit & push notebooks
+from the CLI or from another Python script (via `import rerun`).
+
+Run `python rerun.py -h` to show the CLI help.
+
+The example below does the following:
+1. Re-runs the BEST notebook
+2. Commits changes to a branch "rerun-best"
+3. Push that branch to a remote named "mine"
+   Assuming you did something like: `git add remote mine https://github.com/yourgithubusername/pymc-examples`
+
+```
+python scripts/rerun.py --fp_notebook=examples/case_studies/BEST.ipynb --commit_to=rerun-best --push_to=mine
+```
+"""
+import argparse
+import logging
+import pathlib
+import subprocess
+
+
+logging.basicConfig(level=logging.INFO)
+_log = logging.getLogger(__file__)
+DP_REPO = pathlib.Path(__file__).absolute().parent.parent
+
+REPLACEMENTS = {
+    "az.from_pymc3": "pm.to_inference_data",
+    "arviz.from_pymc3": "pm.to_inference_data",
+    "pymc3": "pymc",
+    "PyMC3": "PyMC",
+    "pymc3": "pymc",
+    "PyMC3": "PyMC",
+    "from theano import tensor as tt": "import aesara.tensor as at",
+    "import theano.tensor as tt": "import aesara.tensor as at",
+    "tt.": "at.",
+    "aet": "at",
+    "studenat": "studentt",
+    "theano": "aesara",
+    "Theano": "Aesara",
+    "pm.sample()": "pm.sample(return_inferencedata=False)",
+    ", return_inferencedata=True": "",
+    "return_inferencedata=True, ": "",
+    "return_inferencedata=True,": "",
+    "return_inferencedata=True": "",
+}
+
+
+def apply_replacements(fp: pathlib.Path) -> bool:
+    try:
+        _log.info("⏳ Running API migration")
+        with open(fp, "r", encoding="utf-8") as file:
+            lines = file.read()
+
+        for pattern, substitute in REPLACEMENTS.items():
+            lines = lines.replace(pattern, substitute)
+
+        with open(fp, "w", encoding="utf-8") as file:
+            file.write(lines)
+        return True
+    except Exception as ex:
+        _log.exception("❌ Failed to apply replacements.", exc_info=ex)
+        return False
+
+
+def run_precommit(fp: pathlib.Path, attempts: int = 2):
+    try:
+        for a in range(attempts):
+            _log.info("⏳ Running pre-commit attempt %i on %s", a, fp)
+            try:
+                subprocess.check_call(["pre-commit", "run", "--files", str(fp)])
+            except subprocess.CalledProcessError:
+                if a == attempts - 1:
+                    raise
+        return True
+    except Exception as ex:
+        _log.exception("❌ Failed to run pre-commit.", exc_info=ex)
+        return False
+
+
+def execute_notebook(fp: pathlib.Path) -> bool:
+    try:
+        _log.info("⏳ Executing notebook %s", fp)
+        subprocess.check_call(
+            [
+                "jupyter",
+                "nbconvert",
+                "--ExecutePreprocessor.kernel_name=python3",
+                "--ExecutePreprocessor.timeout=14000",
+                "--execute",
+                "--inplace",
+                str(fp),
+            ]
+        )
+        _log.info("✔ Notebook executed successfully.")
+        return True
+    except subprocess.CalledProcessError as ex:
+        _log.exception("❌ Failed to commit.", exc_info=ex)
+        return False
+
+
+def commit(fp: pathlib.Path, branch: str) -> bool:
+    try:
+        _log.info("Switching to branch %s", branch)
+        if branch not in subprocess.check_output(["git", "branch"]).decode("ascii"):
+            subprocess.check_call(["git", "checkout", "-b", branch])
+        else:
+            subprocess.check_call(["git", "checkout", branch])
+
+        _log.info("⏳ Committing changes in %s to %s", fp, branch)
+        subprocess.check_call(["git", "stage", str(fp)])
+        subprocess.check_call(["git", "commit", "-m", f"Re-run {fp.name} notebook"])
+        _log.info("✔ Changes in %s were commited to branch %s.", fp, branch)
+        return True
+    except subprocess.CalledProcessError as ex:
+        _log.exception("❌ Failed to commit.", exc_info=ex)
+        return False
+
+
+def push(branch, remote: str) -> bool:
+    try:
+        _log.info("⏳ Pushing %s to %s", branch, remote)
+        subprocess.check_call(["git", "push", "-u", remote, f"{branch}:{branch}"])
+        _log.info("✔ Pushed %s to %s/%s.", branch, remote, branch)
+        return True
+    except subprocess.CalledProcessError as ex:
+        _log.exception("❌ Failed push.", exc_info=ex)
+        return False
+
+
+def get_args():
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--fp_notebook",
+        type=str,
+        help=f"Absolute or relative path to a Jupyter notebook in {str(DP_REPO)}.",
+        required=True,
+    )
+    parser.add_argument(
+        "--commit_to",
+        type=str,
+        help="Name of a git branch to commit to on success.",
+        required=False,
+    )
+    parser.add_argument(
+        "--push_to", type=str, help="Name of a git remote to push to on success.", required=False
+    )
+    return parser.parse_args()
+
+
+if __name__ == "__main__":
+    args = get_args()
+
+    fp = pathlib.Path(args.fp_notebook)
+    if not fp.exists():
+        raise FileNotFoundError(f"Notebook file {fp} does not exist.")
+
+    success = True
+    success = success and apply_replacements(fp)
+    success = success and run_precommit(fp)
+    success = success and execute_notebook(fp)
+    if args.commit_to:
+        success = success and run_precommit(fp)
+        success = success and commit(fp, args.commit_to)
+        if success and args.push_to:
+            success = success and push(args.commit_to, args.push_to)
+
+    if success:
+        _log.info("✔ All steps succeeded.")
+    else:
+        _log.error("❌ Manual investigation needed.")