From 6025b3d9ffe7fab295d605e7ee70c0eaf3e568c3 Mon Sep 17 00:00:00 2001
From: "r.jaepel" <r.jaepel@fz-juelich.de>
Date: Mon, 4 Dec 2023 17:29:57 +0100
Subject: [PATCH] Incorporate jupyter functionality
---
cadetrdm/jupyter_functionality.py | 33 ++++++++++++++-----------------
cadetrdm/repositories.py | 15 ++++++++++++++
2 files changed, 30 insertions(+), 18 deletions(-)
diff --git a/cadetrdm/jupyter_functionality.py b/cadetrdm/jupyter_functionality.py
index d932e73..19b5d43 100644
--- a/cadetrdm/jupyter_functionality.py
+++ b/cadetrdm/jupyter_functionality.py
@@ -14,6 +14,10 @@ class Notebook:
def __init__(self, notebook_path):
self.notebook_path = Path(notebook_path)
+ @property
+ def notebook_name(self):
+ return str(self.notebook_path.name).replace(".", "_")
+
def check_execution_order(self,
check_all_executed=False,
check_top_to_bottom=False,
@@ -96,21 +100,15 @@ class Notebook:
app = JupyterFrontEnd()
app.commands.execute('docmanager:reload')
- def wait_for_user(self, message):
- proceed = input(message + " Y/n")
- if proceed.lower() == "y" or proceed == "":
- return True
- else:
- return False
-
- def clear_and_rerun_notebook(self, force_rerun=False, timeout=600):
+ def check_and_rerun_notebook(self, force_rerun=False, timeout=600):
if "nbconvert_call" in sys.argv:
return
self.save_ipynb()
+ # wait a second for the save process to finish.
time.sleep(1)
- is_in_order = self.check_execution_order(self.notebook_filename, exclude_last_cell=False)
+ is_in_order = self.check_execution_order(exclude_last_cell=False)
if is_in_order and not force_rerun:
print("Notebook was already executed in order.")
@@ -122,27 +120,26 @@ class Notebook:
return
print("Rerunning.")
- with open(self.notebook_filename) as f:
+ with open(self.notebook_path) as f:
nb = nbf.read(f, as_version=4)
ep = ExecutePreprocessor(timeout=timeout, kernel_name='python3', extra_arguments=["nbconvert_call"])
ep.preprocess(nb, )
- with open(self.notebook_filename, 'w', encoding='utf-8') as f:
+ with open(self.notebook_path, 'w', encoding='utf-8') as f:
nbf.write(nb, f)
self.reload_notebook()
- def convert_ipynb(self, formats: list = None):
+ def convert_ipynb(self, output_dir, formats: list = None):
if formats is None:
formats = ["pdf", "python"]
app = NbConvertApp()
app.initialize()
- output_root_directory = os.path.join(r"C:\Users\ronal\PycharmProjects\git_lfs_test_2", "results",
- self.notebook_path.name.replace('.', '_'))
+ output_root_directory = os.path.join(output_dir, self.notebook_name)
for export_format in formats:
app.export_format = export_format
- app.notebooks = [self.notebook_path]
+ app.notebooks = [str(self.notebook_path)]
app.output_base = os.path.join(output_root_directory,
self.notebook_path.name.replace('.ipynb', ''))
if not os.path.exists(output_root_directory):
@@ -151,7 +148,7 @@ class Notebook:
def export_all_figures(self, output_dir):
file_without_extension = self.notebook_path.stem
- images = junix.export_images(filepath=self.notebook_path,
- output_dir=os.path.join(output_dir,
- str(self.notebook_path.name).replace(".", "_")),
+ images = junix.export_images(filepath=str(self.notebook_path),
+ output_dir=os.path.join(output_dir, self.notebook_name),
prefix=file_without_extension)
+
diff --git a/cadetrdm/repositories.py b/cadetrdm/repositories.py
index 7e3452e..d6603f8 100644
--- a/cadetrdm/repositories.py
+++ b/cadetrdm/repositories.py
@@ -1015,6 +1015,21 @@ class ProjectRepo(BaseRepo):
else:
self.exit_context(message=results_commit_message)
+ def commit_notebook(self, notebook_path: str, results_commit_message: str,
+ force_rerun=False, timeout=600, conversion_formats: list = None):
+ if not Path(notebook_path).is_absolute():
+ notebook_path = self.working_dir / notebook_path
+
+ self.enter_context()
+
+ notebook = Notebook(notebook_path)
+ notebook.check_and_rerun_notebook(force_rerun=force_rerun,
+ timeout=timeout)
+ notebook.convert_ipynb(self.output_path, formats=conversion_formats)
+ notebook.export_all_figures(self.output_path)
+
+ self.exit_context(results_commit_message)
+
class OutputRepo(BaseRepo):
pass
--
GitLab