Added colab build script

build_scripts/colab_nb_builder.py

@@ -0,0 +1,134 @@
+#!/bin/env python
+
+import json
+from pathlib import Path
+import argparse
+import logging
+
+log = logging.getLogger(__name__)
+
+
+def get_requirements_cell(requirements_path: str | Path) -> dict:
+    """turns a requirements.txt into jupyter cell data"""
+    with open(requirements_path, "r") as f:
+        cell_data = f.readlines()
+    for i, line in enumerate(cell_data):
+        # Check for comments or empty lines, append !pip install to everything else
+        if (len(line.strip()) == 0) or (line.strip()[0] in ["#", "\n"]):
+            continue
+        cell_data[i] = "!pip install " + line
+
+    extra_lines = [
+        "# This cell has been automatically inserted from build/google_colab_cell.py\n",
+        "# It should make this notebook google-colab compatible!\n",
+        "\n" "!pip install --upgrade pip \n",
+    ]
+
+    for i, line in enumerate(extra_lines):
+        cell_data.insert(i, extra_lines)
+
+    jupyter_cell = {
+        "cell_type": "code",
+        "execution_count": None,
+        "metadata": {},
+        "source": cell_data,  # readlines' output format is the jupyter format
+    }
+    return jupyter_cell
+
+
+def colabify_notebooks(
+    input_notebook_path: str | Path,
+    output_notebook_path: str | Path = None,
+    requirements_path: str | Path = "requirements.txt",
+) -> None:
+    """Adds cell(s) to a jupyter notebook for it to work in google colab
+
+    Parameters
+    ----------
+    input_notebook_path
+        the notebook you want to use as a template
+    output_notebook_path : optional
+        the path to where you wish to save the notebook.
+        If left out this will be in colab_notebooks/name_colab.ipynb
+    requirements_path : optional
+        the path to the requirements file to be inserted
+    """
+    normal_nb_path = Path(input_notebook_path)
+    if output_notebook_path is None:
+        output_notebook_path = Path("colab_notebooks") / (
+            normal_nb_path.with_suffix("").name + "_colab.ipynb"
+        )
+
+    with open(normal_nb_path, "r") as normal_nb_f:
+        notebook_json = json.load(normal_nb_f)
+
+    colab_cell = get_requirements_cell(requirements_path)
+    notebook_json["cells"].insert(0, colab_cell)
+
+    output_notebook_path.parent.mkdir(parents=True, exist_ok=True)
+    with open(output_notebook_path, "w") as colab_nb_f:
+        json.dump(notebook_json, colab_nb_f)
+    return
+
+
+# TODO DELME
+colabify_notebooks("notebooks/2_Analysing_Patient_Data.ipynb")
+
+
+def main():
+    """CLI function for this script"""
+    logging.basicConfig(level=logging.INFO)
+    log.info("Starting CLI script")
+
+    parser = argparse.ArgumentParser(
+        prog="colabifier",
+        description="Adds a cell to the top of a jupyter notebook for clab",
+    )
+    parser.add_argument(
+        "-f",
+        "--fpath",
+        help="File path of a single jupyter notebook to operate on",
+        default=None,
+    )
+    parser.add_argument(
+        "-d",
+        "--directory",
+        help="Directory path of jupyter notebooks to operate on",
+        default=None,
+    )
+    parser.add_argument(
+        "-r",
+        "--requirements",
+        help="requirements file path",
+        default="requirements.txt",
+    )
+    args = parser.parse_args()
+    fpath = args.fpath
+    directory = args.directory
+    requirements = args.requirements
+    # Sanity check
+    no_inputs = (fpath is None) and (directory is None)
+    too_many_inputs = (fpath is not None) and (directory is not None)
+    if no_inputs or too_many_inputs:
+        raise ValueError("Need only one of fpath or directory")
+    log.info("CLI loaded. Starting processing")
+
+    if fpath:
+        log.info(f"Single file input {fpath}, colabifying")
+        colabify_notebooks(fpath, requirements_path=requirements)
+    elif directory:
+        # TODO make file glob below be case insensitive
+        files = list(Path(directory).glob("*.ipynb"))
+        log.info(f"Directory input: {directory}, colabifying {len(files)} ipynb files")
+        for file in files:
+            log.info(f"Processing file {file}")
+            colabify_notebooks(file, requirements_path=requirements)
+    log.info("Done! Exiting")
+    return
+
+
+log.info("AA")
+log.info(f"{__name__}")
+if __name__ == "__main__":
+    log.info("AA")
+    main()