diff --git a/cfa/dataops/__init__.py b/cfa/dataops/__init__.py
index 685408f..8466d8b 100644
--- a/cfa/dataops/__init__.py
+++ b/cfa/dataops/__init__.py
@@ -12,12 +12,25 @@
except ImportError:
__version__ = "unknown"
-__all__ = ["__version__", "datacat", "reportcat"]
+__all__ = ["__version__", "datacat"]
def __getattr__(name: str):
- if name in {"datacat", "reportcat"}:
- from .catalog import datacat, reportcat
+ if name == "datacat":
+ from .catalog import datacat
- return datacat if name == "datacat" else reportcat
+ return datacat
+ if name == "reportcat":
+ import warnings
+
+ warnings.warn(
+ "reportcat has been removed from cfa.dataops. "
+ "Reporting support is no longer available.",
+ DeprecationWarning,
+ stacklevel=2,
+ )
+ raise AttributeError(
+ f"module {__name__!r} has no attribute {name!r}: "
+ "reportcat and reporting support have been removed."
+ )
raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
diff --git a/cfa/dataops/catalog.py b/cfa/dataops/catalog.py
index dece429..df5cacd 100644
--- a/cfa/dataops/catalog.py
+++ b/cfa/dataops/catalog.py
@@ -1,6 +1,5 @@
"""building a validated datasource namespace"""
-import json
import logging
import os
import pkgutil
@@ -37,12 +36,9 @@
StorageEndpointValidation,
ValidationError,
)
-from .reporting.catalog import report_dict_to_sn
from .utils import (
get_dataset_dot_path,
- get_date,
get_timestamp,
- get_user,
version_matcher,
)
@@ -89,25 +85,21 @@ def get_all_catalogs() -> list:
return catalogs
-# aggregating all datasets and reports into a single mapping for namespace
+# aggregating all datasets into a single mapping for namespace
# and endpoint construction:
all_catalogs = get_all_catalogs()
all_dataset_ns_map = {}
-all_reports_ns_map = {}
all_defaults = {}
for cns, cat_name, cat_path in all_catalogs:
dataset_mod = import_module(f"{cns}.{cat_name}.datasets")
- report_mod = import_module(f"{cns}.{cat_name}.reports")
all_dataset_ns_map.update(dataset_mod.dataset_ns_map)
- all_reports_ns_map.update(report_mod.report_ns_map)
with open(os.path.join(cat_path, cat_name, "catalog_defaults.toml"), "rb") as f:
defaults = tomli.load(f)
for k in dataset_mod.dataset_ns_map.keys():
all_defaults.update({k: defaults})
dataset_namespaces = get_dataset_dot_path(all_dataset_ns_map)
-report_namespaces = get_dataset_dot_path(all_reports_ns_map)
class CatalogNamespace(SimpleNamespace):
@@ -196,11 +188,7 @@ def __init__(self, config_path: str, defaults: dict, ns: str):
if container == "":
self.config[k]["container"] = self.defaults["storage"]["container"]
self.validate_dataset_config(config_path)
- self._ledger_location = {
- "account": self.defaults["storage"]["account"],
- "container": self.defaults["storage"]["container"],
- "prefix": self.defaults["access_ledger"]["path"],
- }
+
for k, v in self.config.items():
if k in ["load", "extract", "data"] or k.startswith("stage"):
self.__setattr__(
@@ -209,7 +197,6 @@ def __init__(self, config_path: str, defaults: dict, ns: str):
account=self.config[k]["account"],
container=self.config[k]["container"],
prefix=v["prefix"],
- ledger_location=self._ledger_location,
ns=f"{self.__ns_str__}.{k}",
),
)
@@ -243,7 +230,6 @@ def __init__(
account: str,
container: str,
prefix: str,
- ledger_location: dict,
ns: str,
):
"""Basic functionality to interact with blobs to be included
@@ -253,14 +239,11 @@ def __init__(
account (str): the azure storage account to use
container (str): the container in the account to use
prefix (str): the path prefix in the container to use
- ledger_location (dict): the location to write access logs to
ns (str): the current namespace path
"""
self.account = account
self.container = container
self.prefix = prefix if prefix[-1] != "/" else prefix[:-1]
- self.ledger_location = ledger_location
- self.is_ledger = True if ns == "ledger_endpoint" else False
self.__ns_str__ = ns
def _verify_ext_access(self) -> None:
@@ -400,7 +383,6 @@ def write_blob(
container_name=self.container,
append_blob=append,
)
- # self.ledger_entry(action="write")
# print(f"file written to: {full_path}")
def read_blobs(
@@ -429,7 +411,6 @@ def read_blobs(
)
for i in blobs
]
- # self.ledger_entry(action="read")
return blob_bytes
def read_csv(self, suffix: str) -> pd.DataFrame:
@@ -440,7 +421,6 @@ def read_csv(self, suffix: str) -> pd.DataFrame:
container_name=self.container,
)
df = pd.read_csv(blob)
- # self.ledger_entry(action="read")
return df
def get_versions(self) -> list:
@@ -508,21 +488,17 @@ def _get_version_blobs(
# check credential access
self.verify_blob_access()
version = None
- if not self.is_ledger:
- available_versions = self.get_versions()
- version = version_matcher(
- version_spec, available_versions, selection=selection
+ available_versions = self.get_versions()
+ version = version_matcher(version_spec, available_versions, selection=selection)
+ if not version:
+ raise ValueError(
+ f"Version matching {version_spec} not found in available versions: {available_versions}"
)
- if not version:
- raise ValueError(
- f"Version matching {version_spec} not found in available versions: {available_versions}"
- )
- logger.info(f"Using version: {version}")
- if print_version:
- print(f"Using version: {version}")
- walk_path = f"{self.prefix}/{version}/"
- else:
- walk_path = f"{self.prefix.removesuffix('/')}/"
+ logger.info(f"Using version: {version}")
+ if print_version:
+ print(f"Using version: {version}")
+ walk_path = f"{self.prefix}/{version}/"
+
return sorted(
list(
walk_blobs_in_container(
@@ -576,8 +552,6 @@ def download_version_to_local(
with open(local_file_path, "wb") as f:
f.write(file_bytes)
written = True
- # if written:
- # self.ledger_entry(action="read")
return written
@overload
@@ -660,7 +634,6 @@ def get_dataframe(
credential=ManagedIdentityCredential()
),
)
- # self.ledger_entry(action="read")
return df
elif file_ext == "csv":
df = pl.scan_csv(
@@ -671,7 +644,6 @@ def get_dataframe(
credential=ManagedIdentityCredential()
),
)
- ##self.ledger_entry(action="read")
return df
elif file_ext == "ndjson" or file_ext == "jsonl":
df = pl.scan_ndjson(
@@ -682,7 +654,6 @@ def get_dataframe(
credential=ManagedIdentityCredential()
),
)
- ##self.ledger_entry(action="read")
return df
else:
raise ValueError(f"Lazy loading not supported for {file_ext} files.")
@@ -741,32 +712,6 @@ def get_dataframe(
)
return df
- def ledger_entry(self, action: str) -> None:
- """Write an access log entry to the ledger location
-
- Args:
- action (str): the action taken (e.g., 'read', 'write')
- """
- if self.is_ledger:
- return
- log_entry = {
- "timestamp": get_timestamp(make_standard=True),
- "username": get_user(),
- "dataset": self.__ns_str__,
- "action": action,
- }
- log_data = (json.dumps(log_entry) + "\n").encode("utf-8")
- ledger_path = f"{self.ledger_location['prefix']}/{get_date()}.jsonl"
-
- write_blob_stream(
- data=log_data,
- blob_url=ledger_path,
- account_name=self.ledger_location["account"],
- container_name=self.ledger_location["container"],
- append_blob=True,
- overwrite=False,
- )
-
def resolve_version(
self,
version_spec: str | None = None,
@@ -976,18 +921,6 @@ def dict_to_sn(d: Any, defaults: dict | None = None, ns: str = "") -> CatalogNam
)
for k, v in d.items()
]
- if ns != "" and "." not in ns:
- setattr(
- x,
- "_ledger_endpoint",
- BlobEndpoint(
- account=defaults["storage"]["account"],
- container=defaults["storage"]["container"],
- prefix=defaults["access_ledger"]["path"],
- ledger_location={},
- ns="ledger_endpoint",
- ),
- )
return x
@@ -996,15 +929,8 @@ def dict_to_sn(d: Any, defaults: dict | None = None, ns: str = "") -> CatalogNam
dc.append(dict_to_sn({k: all_dataset_ns_map[k]}, all_defaults.get(k, {})))
combined_dict = {key: value for ns in dc for key, value in vars(ns).items()}
-rc = []
-for k in all_reports_ns_map.keys():
- rc.append(report_dict_to_sn({k: all_reports_ns_map[k]}))
-combined_reports_dict = {key: value for ns in rc for key, value in vars(ns).items()}
-
datacat: CatalogNamespace = CatalogNamespace(**combined_dict)
datacat.__setattr__("__namespace_list__", dataset_namespaces)
-reportcat: CatalogNamespace = CatalogNamespace(**combined_reports_dict)
-reportcat.__setattr__("__namespace_list__", report_namespaces)
def _attach_schema_mock_functions(datacat: CatalogNamespace, catalogs: list) -> None:
diff --git a/cfa/dataops/create_catalog/command.py b/cfa/dataops/create_catalog/command.py
index edaf088..5ca33ce 100644
--- a/cfa/dataops/create_catalog/command.py
+++ b/cfa/dataops/create_catalog/command.py
@@ -108,7 +108,7 @@ def main():
)
)
- for mod_i in ["datasets", "reports", "workflows"]:
+ for mod_i in ["datasets", "workflows"]:
shutil.copytree(
os.path.join(repo_files_dirs, mod_i),
os.path.join(library_modules_root, mod_i),
diff --git a/cfa/dataops/create_catalog/repo_files/.gitignore b/cfa/dataops/create_catalog/repo_files/.gitignore
index e4321ca..046d81b 100644
--- a/cfa/dataops/create_catalog/repo_files/.gitignore
+++ b/cfa/dataops/create_catalog/repo_files/.gitignore
@@ -81,7 +81,7 @@ MANIFEST
pip-log.txt
pip-delete-this-directory.txt
-# Unit test / coverage reports
+# Unit test / coverage output
htmlcov/
.tox/
.nox/
diff --git a/cfa/dataops/create_catalog/repo_files/reports/__init__.py b/cfa/dataops/create_catalog/repo_files/reports/__init__.py
deleted file mode 100644
index c9ee9d0..0000000
--- a/cfa/dataops/create_catalog/repo_files/reports/__init__.py
+++ /dev/null
@@ -1,17 +0,0 @@
-"""Initialization for repo_templates datasets."""
-
-from os import path
-
-from cfa.dataops.utils import get_fs_ns_map, remove_ws_and_nonalpha
-
-from .. import _catalog_ns
-
-_here = path.abspath(path.dirname(__file__))
-
-report_ns_map = {
- _catalog_ns: get_fs_ns_map(
- base_dir=_here,
- file_ext="ipynb",
- endpoint_func=lambda p: remove_ws_and_nonalpha(path.split(p)[1]),
- )
-}
diff --git a/cfa/dataops/create_catalog/repo_files/reports/examples/basics.ipynb b/cfa/dataops/create_catalog/repo_files/reports/examples/basics.ipynb
deleted file mode 100644
index fc04689..0000000
--- a/cfa/dataops/create_catalog/repo_files/reports/examples/basics.ipynb
+++ /dev/null
@@ -1,175 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "id": "4dfce678",
- "metadata": {},
- "source": [
- "## Basic Notebook Example\n",
- "\n",
- "The objective of this notebook is to demonstrate the basic necessities and features of notebook based report generation.\n",
- "\n",
- "The first thing to establish is that these notebooks ar parameterizable. This is done by creating a python cell, assigning some default values to variables, and tagging the cell with the tag `parameters`\n",
- "\n",
- "Example:"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "cc6ca370",
- "metadata": {
- "tags": [
- "parameters",
- "remove_input"
- ]
- },
- "outputs": [],
- "source": [
- "# parameters\n",
- "\n",
- "slope: float = 1.2 # adding help text can be achieved with in-line comments\n",
- "intercept: float = 0.5 # y-intercept of the line\n",
- "x_range: tuple = (-5, 5) # range of x values to consider\n",
- "step_size: float = 0.5 # step size for generating x values"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "629f32d8",
- "metadata": {},
- "source": [
- "Now you can create cells that are used to import or compute reporting dependencies or for display. There are three other cell tags that will help with the formatting of your report:\n",
- "\n",
- "- `remove_input`: This cell tag removes the display of any code or markdown input. It is not likely that you will use this for markdown text, but very likely that you will use it on every python cell.\n",
- "- `remove_output`: This cell tag removes the output (including any items from memory that you may have wanted to use later).\n",
- "- `remove_cell`: This cell tag removes the entire cell input and output from the output report. Handy if you want instructions or examples for a report editor that you don't intend to be displayed in the final report.\n",
- "\n",
- "Next we will import a few common items that are often used in reporting, and remove the input so the import statements don't display in the report."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "ddef9fb8",
- "metadata": {
- "tags": [
- "remove_input"
- ]
- },
- "outputs": [],
- "source": [
- "import itables # for pagination and searching tabular data\n",
- "import matplotlib.pyplot as plt # what's a report without a plot or two?\n",
- "import numpy as np # because we all love numpy\n",
- "import pandas as pd # for manipulating and displaying tabular data\n",
- "from IPython.display import ( # for displaying formatted text in python cells\n",
- " Markdown,\n",
- " display,\n",
- ")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "f971af94",
- "metadata": {
- "tags": [
- "remove_input"
- ]
- },
- "outputs": [],
- "source": [
- "display(\n",
- " Markdown(\n",
- " f\"\"\"\n",
- "This is a parameterized markdown example. Here we display all the parameters, defaults and any that were passed by the notebook endpoint in the report catalog.:\n",
- "- Slope: {slope}\n",
- "- Intercept: {intercept}\n",
- "- X Range: {x_range}\n",
- "- Step Size: {step_size}\n",
- "\n",
- "Next we will compute some values and display them in a table.\n",
- "\"\"\"\n",
- " )\n",
- ")"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "d845c8b4",
- "metadata": {
- "tags": [
- "remove_input"
- ]
- },
- "outputs": [],
- "source": [
- "x = np.arange(x_range[0], x_range[1] + step_size, step_size)\n",
- "y = slope * x + intercept\n",
- "df = pd.DataFrame({\"x\": x, \"y\": y})\n",
- "\n",
- "# Display the DataFrame with itables for better interactivity\n",
- "itables.show(\n",
- " df.style.background_gradient(cmap=\"viridis\"),\n",
- " allow_html=True,\n",
- " lengthMenu=[5, 10, 21],\n",
- " pageLength=5,\n",
- ")"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "0e5984e6",
- "metadata": {},
- "source": [
- "Finally, we can display a plot of the values computed using the input parameters."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "27c55442",
- "metadata": {
- "tags": [
- "remove_input"
- ]
- },
- "outputs": [],
- "source": [
- "fig = plt.figure(figsize=(10, 6))\n",
- "plt.plot(x, y, \"c-.\")\n",
- "plt.plot(x, y, \"r.\")\n",
- "plt.title(\"Line Plot of y = mx + b\")\n",
- "plt.xlabel(\"x values\")\n",
- "plt.ylabel(\"y values\")\n",
- "plt.grid(True)\n",
- "plt.axhline(0, color=\"black\", linewidth=1, linestyle=\"--\")\n",
- "plt.axvline(0, color=\"black\", linewidth=1, linestyle=\"--\")\n",
- "plt.show()"
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "venv",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "codemirror_mode": {
- "name": "ipython",
- "version": 3
- },
- "file_extension": ".py",
- "mimetype": "text/x-python",
- "name": "python",
- "nbconvert_exporter": "python",
- "pygments_lexer": "ipython3",
- "version": "3.10.12"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/cfa/dataops/create_catalog/repo_templates/catalog_defaults.toml.mako b/cfa/dataops/create_catalog/repo_templates/catalog_defaults.toml.mako
index 40d3e75..3a2ee1b 100644
--- a/cfa/dataops/create_catalog/repo_templates/catalog_defaults.toml.mako
+++ b/cfa/dataops/create_catalog/repo_templates/catalog_defaults.toml.mako
@@ -2,7 +2,3 @@
account = "cfadatalakeprd"
container = "cfapredict"
-
-[access_ledger]
-
-path = "_access/${unique_name}/ledger/"
diff --git a/cfa/dataops/reporting/__init__.py b/cfa/dataops/reporting/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/cfa/dataops/reporting/catalog.py b/cfa/dataops/reporting/catalog.py
deleted file mode 100644
index caf07e7..0000000
--- a/cfa/dataops/reporting/catalog.py
+++ /dev/null
@@ -1,178 +0,0 @@
-import os
-from pprint import pprint
-from tempfile import TemporaryDirectory
-from types import SimpleNamespace
-from typing import Any
-
-import nbformat
-import papermill as pm
-from cfa.cloudops.blob_helpers import write_blob_stream
-from nbconvert import HTMLExporter
-from traitlets.config import Config
-
-_here_dir = os.path.split(os.path.abspath(__file__))[0]
-
-
-def remove_ws_and_nonalpha(s: str) -> str:
- """Remove whitespace and non-alphanumeric characters from a string.
-
- Args:
- s (str): The input string.
-
- Returns:
- str: The cleaned string with whitespace and non-alphanumeric characters removed.
-
- Example:
- >>> remove_ws_and_nonalpha("Hello World! 123.ipynb")
- 'hello_world_123_ipynb'
- """
- s = s.replace(" ", "_").replace(".", "_").lower()
- return "".join(c for c in s if c.isalnum() or c == "_")
-
-
-def retitle_notebook(nb_loc: str, new_title: str) -> None:
- """
- Retitle a notebook by replacing the title in the first cell.
-
- Args:
- nb_loc (str): The path to the notebook file.
- new_title (str): The new title to set for the notebook.
- """
- assert os.path.exists(nb_loc), f"Notebook {nb_loc} does not exist."
- assert nb_loc.endswith(".ipynb"), "Notebook must be a .ipynb file."
-
- with open(nb_loc, encoding="utf-8") as f:
- notebook = nbformat.read(f, as_version=4)
-
- notebook.metadata["title"] = new_title
-
- with open(nb_loc, "w", encoding="utf-8") as f:
- nbformat.write(notebook, f)
-
-
-def nb_to_html(nb_path: str) -> str:
- """Convert the executed notebook to HTML format.
-
- Returns:
- str: The HTML content of the notebook.
- """
- c = Config()
- c.TagRemovePreprocessor.remove_cell_tags = ("remove_cell",)
- c.TagRemovePreprocessor.remove_input_tags = ("remove_input",)
- c.TagRemovePreprocessor.remove_all_outputs_tags = ("remove_outputs",)
- c.TagRemovePreprocessor.enabled = True
- c.HTMLExporter.preprocessors = ["nbconvert.preprocessors.TagRemovePreprocessor"]
- c.TemplateExporter.extra_template_basedirs = os.path.join(
- _here_dir, "jupyter_templates"
- )
- body, _ = HTMLExporter(template_name="lab", config=c).from_filename(nb_path)
- return body
-
-
-class NotebookEndpoint:
- """Class to handle the execution and conversion of Jupyter notebooks to HTML."""
-
- def __init__(self, notebook_path: str):
- self.notebook_path = notebook_path
-
- def get_params(self) -> dict:
- """Get the parameters for the notebook execution."""
- return pm.inspect_notebook(self.notebook_path)
-
- def print_params(self):
- """Pretty print the parameters of the notebook."""
- pprint(self.get_params())
-
- def nb_to_html_str(self, nb_title: str | None = None, **kwargs) -> str:
- """Convert the notebook to HTML format and optionally save it to a file.
-
- Args:
- html_out_path (str): Path to save the HTML output. If None, does not save.
- **kwargs: Parameters to replace defaults in notebook.
-
- Returns:
- str: The HTML content of the notebook.
- """
- with TemporaryDirectory() as temp_dir:
- out_file_path = os.path.join(temp_dir, "output.ipynb")
- pm.execute_notebook(
- input_path=self.notebook_path,
- output_path=out_file_path,
- parameters=kwargs,
- progress_bar=True,
- )
- if nb_title:
- retitle_notebook(out_file_path, nb_title)
- html_content = nb_to_html(out_file_path)
-
- return html_content
-
- def nb_to_html_file(
- self, html_out_path: str, nb_title: str | None = None, **kwargs
- ) -> None:
- """Convert the notebook to HTML format.
-
- Args:
- **kwargs: Parameters to replace defaults in notebook.
-
- Returns:
- None, saves the html content to a file.
- """
- assert html_out_path.endswith(".html"), "Output path must end with .html"
- html_content = self.nb_to_html_str(nb_title=nb_title, **kwargs)
- os.makedirs(os.path.dirname(html_out_path), exist_ok=True)
- with open(html_out_path, "w", encoding="utf-8") as f:
- f.write(html_content)
- print(f"HTML report saved to {os.path.abspath(html_out_path)}")
-
- def nb_to_html_blob(
- self,
- blob_account: str,
- blob_container: str,
- blob_path: str,
- nb_title: str | None = None,
- **kwargs,
- ) -> None:
- """Convert the notebook to HTML format save to blob storage.
-
- Args:
- **kwargs: Parameters to replace defaults in notebook.
-
- Returns:
- None, saves the HTML content to a blob storage.
- """
- assert blob_path.endswith(".html"), "Output path must end with .html"
- html_content = self.nb_to_html_str(nb_title=nb_title, **kwargs)
- write_blob_stream(
- account_name=blob_account,
- container_name=blob_container,
- blob_url=blob_path,
- data=html_content.encode("utf-8"),
- )
-
-
-def report_dict_to_sn(d: Any) -> SimpleNamespace:
- """Simple recursive namespace construction
-
- Args:
- d (Any): a dict, list or other
-
- Returns:
- SimpleNamespace: namespace representation
- """
- x = SimpleNamespace()
- _ = [
- setattr(
- x,
- k,
- NotebookEndpoint(notebook_path=v)
- if k.endswith("ipynb")
- else report_dict_to_sn(v)
- if isinstance(v, dict)
- else [report_dict_to_sn(e) for e in v]
- if isinstance(v, list)
- else v,
- )
- for k, v in d.items()
- ]
- return x
diff --git a/cfa/dataops/reporting/jupyter_templates/base/cell_id_anchor.j2 b/cfa/dataops/reporting/jupyter_templates/base/cell_id_anchor.j2
deleted file mode 100644
index b090895..0000000
--- a/cfa/dataops/reporting/jupyter_templates/base/cell_id_anchor.j2
+++ /dev/null
@@ -1,5 +0,0 @@
-{%- macro cell_id_anchor(cell) -%}
- {% if cell.id | length > 0 -%}
- id="{{ ('cell-id=' ~ cell.id) | escape_html -}}"
- {%- endif %}
-{%- endmacro %}
diff --git a/cfa/dataops/reporting/jupyter_templates/base/celltags.j2 b/cfa/dataops/reporting/jupyter_templates/base/celltags.j2
deleted file mode 100644
index 622a2c6..0000000
--- a/cfa/dataops/reporting/jupyter_templates/base/celltags.j2
+++ /dev/null
@@ -1,7 +0,0 @@
-{%- macro celltags(cell) -%}
- {% if cell.metadata.tags | length > 0 -%}
- {% for tag in (cell.metadata.tags) -%}
- {{ (' celltag_' ~ tag) | escape_html -}}
- {%- endfor -%}
- {%- endif %}
-{%- endmacro %}
diff --git a/cfa/dataops/reporting/jupyter_templates/base/display_priority.j2 b/cfa/dataops/reporting/jupyter_templates/base/display_priority.j2
deleted file mode 100644
index c24639e..0000000
--- a/cfa/dataops/reporting/jupyter_templates/base/display_priority.j2
+++ /dev/null
@@ -1,49 +0,0 @@
-{%- extends 'base/null.j2' -%}
-
-{#display data priority#}
-
-
-{%- block data_priority scoped -%}
- {%- for type in output.data | filter_data_type -%}
- {%- if type == 'application/pdf' -%}
- {%- block data_pdf -%}
- {%- endblock -%}
- {%- elif type == 'image/svg+xml' -%}
- {%- block data_svg -%}
- {%- endblock -%}
- {%- elif type == 'image/png' -%}
- {%- block data_png -%}
- {%- endblock -%}
- {%- elif type == 'text/html' -%}
- {%- block data_html -%}
- {%- endblock -%}
- {%- elif type == 'text/markdown' -%}
- {%- block data_markdown -%}
- {%- endblock -%}
- {%- elif type == 'image/jpeg' -%}
- {%- block data_jpg -%}
- {%- endblock -%}
- {%- elif type == 'text/plain' -%}
- {%- block data_text -%}
- {%- endblock -%}
- {%- elif type == 'text/latex' -%}
- {%- block data_latex -%}
- {%- endblock -%}
- {%- elif type == 'text/vnd.mermaid' -%}
- {%- block data_mermaid -%}
- {%- endblock -%}
- {%- elif type == 'application/javascript' -%}
- {%- block data_javascript -%}
- {%- endblock -%}
- {%- elif type == 'application/vnd.jupyter.widget-view+json' -%}
- {%- block data_widget_view -%}
- {%- endblock -%}
- {%- elif type == resources.output_mimetype -%}
- {%- block data_native -%}
- {%- endblock -%}
- {%- else -%}
- {%- block data_other -%}
- {%- endblock -%}
- {%- endif -%}
- {%- endfor -%}
-{%- endblock data_priority -%}
diff --git a/cfa/dataops/reporting/jupyter_templates/base/jupyter_widgets.html.j2 b/cfa/dataops/reporting/jupyter_templates/base/jupyter_widgets.html.j2
deleted file mode 100644
index 9c66ecf..0000000
--- a/cfa/dataops/reporting/jupyter_templates/base/jupyter_widgets.html.j2
+++ /dev/null
@@ -1,36 +0,0 @@
-{%- macro jupyter_widgets(widgets_cdn_url, html_manager_semver_range, widget_renderer_url='') -%}
-
-
-
-{%- endmacro %}
diff --git a/cfa/dataops/reporting/jupyter_templates/base/mathjax.html.j2 b/cfa/dataops/reporting/jupyter_templates/base/mathjax.html.j2
deleted file mode 100644
index fe7c85c..0000000
--- a/cfa/dataops/reporting/jupyter_templates/base/mathjax.html.j2
+++ /dev/null
@@ -1,38 +0,0 @@
-
-{%- macro mathjax(url="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/latest.js?config=TeX-AMS_CHTML-full,Safe") -%}
-
-
-
-
-
-{%- endmacro %}
diff --git a/cfa/dataops/reporting/jupyter_templates/base/null.j2 b/cfa/dataops/reporting/jupyter_templates/base/null.j2
deleted file mode 100644
index 929b187..0000000
--- a/cfa/dataops/reporting/jupyter_templates/base/null.j2
+++ /dev/null
@@ -1,111 +0,0 @@
-{#
-
-DO NOT USE THIS AS A BASE,
-IF YOU ARE COPY AND PASTING THIS FILE
-YOU ARE PROBABLY DOING THINGS INCORRECTLY.
-
-Null template, does nothing except defining a basic structure
-To layout the different blocks of a notebook.
-
-Subtemplates can override blocks to define their custom representation.
-
-If one of the block you do overwrite is not a leaf block, consider
-calling super.
-
-{%- block nonLeafBlock -%}
- #add stuff at beginning
- {{ super() }}
- #add stuff at end
-{%- endblock nonLeafBlock -%}
-
-consider calling super even if it is a leaf block, we might insert more blocks later.
-
-#}
-{%- block header -%}
-{%- endblock header -%}
-{%- block body -%}
- {%- block body_header -%}
- {%- endblock body_header -%}
- {%- block body_loop -%}
- {%- for cell in nb.cells -%}
- {%- block any_cell scoped -%}
- {%- if cell.cell_type == 'code'-%}
- {%- if resources.global_content_filter.include_code -%}
- {%- block codecell scoped -%}
- {%- if resources.global_content_filter.include_input and not cell.metadata.get("transient",{}).get("remove_source", false) -%}
- {%- block input_group -%}
- {%- if resources.global_content_filter.include_input_prompt -%}
- {%- block in_prompt -%}{%- endblock in_prompt -%}
- {%- endif -%}
- {%- block input -%}{%- endblock input -%}
- {%- endblock input_group -%}
- {%- endif -%}
- {%- if cell.outputs and resources.global_content_filter.include_output -%}
- {%- block output_group -%}
- {%- if resources.global_content_filter.include_output_prompt -%}
- {%- block output_prompt -%}{%- endblock output_prompt -%}
- {%- endif -%}
- {%- block outputs scoped -%}
- {%- for output in cell.outputs -%}
- {%- block output scoped -%}
- {%- if output.output_type == 'execute_result' -%}
- {%- block execute_result scoped -%}{%- endblock execute_result -%}
- {%- elif output.output_type == 'stream' -%}
- {%- block stream scoped -%}
- {%- if output.name == 'stdout' -%}
- {%- block stream_stdout scoped -%}
- {%- endblock stream_stdout -%}
- {%- elif output.name == 'stderr' -%}
- {%- block stream_stderr scoped -%}
- {%- endblock stream_stderr -%}
- {%- elif output.name == 'stdin' -%}
- {%- block stream_stdin scoped -%}
- {%- endblock stream_stdin -%}
- {%- endif -%}
- {%- endblock stream -%}
- {%- elif output.output_type == 'display_data' -%}
- {%- block display_data scoped -%}
- {%- block data_priority scoped -%}
- {%- endblock data_priority -%}
- {%- endblock display_data -%}
- {%- elif output.output_type == 'error' -%}
- {%- block error scoped -%}
- {%- for line in output.traceback -%}
- {%- block traceback_line scoped -%}{%- endblock traceback_line -%}
- {%- endfor -%}
- {%- endblock error -%}
- {%- endif -%}
- {%- endblock output -%}
- {%- endfor -%}
- {%- endblock outputs -%}
- {%- endblock output_group -%}
- {%- endif -%}
- {%- endblock codecell -%}
- {%- endif -%}
- {%- elif cell.cell_type in ['markdown'] -%}
- {%- if resources.global_content_filter.include_markdown and not cell.metadata.get("transient",{}).get("remove_source", false) -%}
- {%- block markdowncell scoped-%} {%- endblock markdowncell -%}
- {%- endif -%}
- {%- elif cell.cell_type in ['raw'] -%}
- {%- if resources.global_content_filter.include_raw and not cell.metadata.get("transient",{}).get("remove_source", false) -%}
- {%- block rawcell scoped -%}
- {%- if cell.metadata.get('raw_mimetype', '').lower() in resources.get('raw_mimetypes', ['']) -%}
- {{ cell.source }}
- {%- endif -%}
- {%- endblock rawcell -%}
- {%- endif -%}
- {%- else -%}
- {%- if resources.global_content_filter.include_unknown and not cell.metadata.get("transient",{}).get("remove_source", false) -%}
- {%- block unknowncell scoped-%}
- {%- endblock unknowncell -%}
- {%- endif -%}
- {%- endif -%}
- {%- endblock any_cell -%}
- {%- endfor -%}
- {%- endblock body_loop -%}
- {%- block body_footer -%}
- {%- endblock body_footer -%}
-{%- endblock body -%}
-
-{%- block footer -%}
-{%- endblock footer -%}
diff --git a/cfa/dataops/reporting/jupyter_templates/lab/base.html.j2 b/cfa/dataops/reporting/jupyter_templates/lab/base.html.j2
deleted file mode 100644
index cebe841..0000000
--- a/cfa/dataops/reporting/jupyter_templates/lab/base.html.j2
+++ /dev/null
@@ -1,331 +0,0 @@
-{%- extends 'display_priority.j2' -%}
-{% from 'celltags.j2' import celltags %}
-{% from 'cell_id_anchor.j2' import cell_id_anchor %}
-
-{% block codecell %}
-{%- if not cell.outputs -%}
-{%- set no_output_class="jp-mod-noOutputs" -%}
-{%- endif -%}
-{%- if not resources.global_content_filter.include_input -%}
-{%- set no_input_class="jp-mod-noInput" -%}
-{%- endif -%}
-
-{{ super() }}
-
-{%- endblock codecell %}
-
-{% block input_group -%}
-
-{% endblock input_group %}
-
-{% block input %}
-
-{%- endblock input %}
-
-{% block output_group %}
-
-{% endblock output_group %}
-
-{% block outputs %}
-
-{{ super() }}
-
-{% endblock outputs %}
-
-{% block in_prompt -%}
-
- {%- if cell.execution_count is defined -%}
- In [{{ cell.execution_count|replace(None, " ") }}]:
- {%- else -%}
- In [ ]:
- {%- endif -%}
-
-{%- endblock in_prompt %}
-
-{% block empty_in_prompt -%}
-
-
-{%- endblock empty_in_prompt %}
-
-{#
- output_prompt doesn't do anything in HTML,
- because there is a prompt div in each output area (see output block)
- #}
-{% block output_prompt %}
-{% endblock output_prompt %}
-
-{% block output_area_prompt %}
-
-{%- if output.output_type == 'execute_result' -%}
- {%- if cell.execution_count is defined -%}
- Out[{{ cell.execution_count|replace(None, " ") }}]:
- {%- else -%}
- Out[ ]:
- {%- endif -%}
-{%- endif -%}
-
-{% endblock output_area_prompt %}
-
-{% block output %}
-{%- if output.output_type == 'execute_result' -%}
-
-{%- else -%}
-
-{%- endif -%}
-{% if resources.global_content_filter.include_output_prompt %}
- {{ self.output_area_prompt() }}
-{% endif %}
-{{ super() }}
-
-{% endblock output %}
-
-{% block markdowncell scoped %}
-
-{%- endblock markdowncell %}
-
-{% block rawcell scoped %}
-{%- if cell.metadata.get('raw_mimetype', '').lower() in resources.get('raw_mimetypes', ['']) -%}
-{{ cell.source | clean_html }}
-{%- endif -%}
-{%- endblock rawcell %}
-
-{% block unknowncell scoped %}
-unknown type {{ cell.type }}
-{% endblock unknowncell %}
-
-{% block execute_result -%}
-{%- set extra_class="jp-OutputArea-executeResult" -%}
-{% block data_priority scoped %}
-{{ super() }}
-{% endblock data_priority %}
-{%- set extra_class="" -%}
-{%- endblock execute_result %}
-
-{% block stream_stdout -%}
-
-
-{{- output.text | ansi2html -}}
-
-
-{%- endblock stream_stdout %}
-
-{% block stream_stderr -%}
-
-
-{{- output.text | ansi2html -}}
-
-
-{%- endblock stream_stderr %}
-
-{% block stream_stdin -%}
-{%- if resources.global_content_filter.include_output_stdin -%}
-
-
-{{- output.text | ansi2html -}}
-
-
-{%- endif %}
-{%- endblock stream_stdin %}
-
-{% block data_svg scoped -%}
-
-{%- endblock data_svg %}
-
-{% block data_mermaid scoped -%}
-
-
-{{ output.data['text/vnd.mermaid'].strip() }}
-
-
-{%- endblock data_mermaid %}
-
-{% block data_html scoped -%}
-
-{%- endblock data_html %}
-
-{% block data_markdown scoped -%}
-{%- if resources.should_sanitize_html %}
-{%- set html_value=output.data['text/markdown'] | markdown2html | clean_html -%}
-{%- else %}
-{%- set html_value=output.data['text/markdown'] | markdown2html -%}
-{%- endif %}
-
-{%- endblock data_markdown %}
-
-{% block data_png scoped %}
-
-{%- endblock data_png %}
-
-{% block data_jpg scoped %}
-
-{%- endblock data_jpg %}
-
-{% block data_latex scoped %}
-
-{%- endblock data_latex %}
-
-{% block error -%}
-
-{%- endblock error %}
-
-{%- block traceback_line %}
-{{ line | ansi2html }}
-{%- endblock traceback_line %}
-
-{%- block data_text scoped %}
-
-{%- endblock -%}
-
-{#
- ###############################################################################
- # TODO: how to better handle JavaScript repr? #
- ###############################################################################
- #}
-
-{%- block data_javascript scoped %}
-{% set div_id = uuid4() %}
-
-{%- endblock -%}
-
-{%- block data_widget_view scoped %}
-{% set div_id = uuid4() %}
-{% set datatype_list = output.data | filter_data_type %}
-{% set datatype = datatype_list[0]%}
-
-{%- endblock data_widget_view -%}
-
-{%- block footer %}
-{% set mimetype = 'application/vnd.jupyter.widget-state+json'%}
-{% if mimetype in nb.metadata.get("widgets",{})%}
-
-{% endif %}
-{{ super() }}
-{%- endblock footer-%}
diff --git a/cfa/dataops/reporting/jupyter_templates/lab/conf.json b/cfa/dataops/reporting/jupyter_templates/lab/conf.json
deleted file mode 100644
index fc1a5b8..0000000
--- a/cfa/dataops/reporting/jupyter_templates/lab/conf.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
- "base_template": "base",
- "mimetypes": {
- "text/html": true
- },
- "preprocessors": {
- "100-pygments": {
- "type": "nbconvert.preprocessors.CSSHTMLHeaderPreprocessor",
- "enabled": true
- }
- }
-}
diff --git a/cfa/dataops/reporting/jupyter_templates/lab/index.html.j2 b/cfa/dataops/reporting/jupyter_templates/lab/index.html.j2
deleted file mode 100644
index ad184ca..0000000
--- a/cfa/dataops/reporting/jupyter_templates/lab/index.html.j2
+++ /dev/null
@@ -1,141 +0,0 @@
-{%- extends 'base.html.j2' -%}
-{% from 'mathjax.html.j2' import mathjax %}
-{% from 'mermaidjs.html.j2' import mermaid_js %}
-{% from 'jupyter_widgets.html.j2' import jupyter_widgets %}
-
-{%- block header -%}
-
-
-
-{%- block html_head -%}
-
-
-{% set nb_title = nb.metadata.get('title', resources['metadata']['name']) | escape_html_keep_quotes %}
-
{{nb_title}}
-
-{%- block html_head_js -%}
-{%- block html_head_js_requirejs -%}
-
-{%- endblock html_head_js_requirejs -%}
-{%- endblock html_head_js -%}
-
-{% block jupyter_widgets %}
- {%- if "widgets" in nb.metadata -%}
- {{ jupyter_widgets(resources.jupyter_widgets_base_url, resources.html_manager_semver_range, resources.widget_renderer_url) }}
- {%- endif -%}
-{% endblock jupyter_widgets %}
-
-{% block extra_css %}
-{% endblock extra_css %}
-
-{% for css in resources.inlining.css -%}
-
-{% endfor %}
-
-{% block notebook_css %}
-{{ resources.include_css("static/index.css") }}
-{% if resources.theme == 'dark' %}
- {{ resources.include_css("static/theme-dark.css") }}
-{% elif resources.theme == 'light' %}
- {{ resources.include_css("static/theme-light.css") }}
-{% else %}
- {{ resources.include_lab_theme(resources.theme) }}
-{% endif %}
-
-
-{% endblock notebook_css %}
-
-{%- block html_head_js_mathjax -%}
-{{ mathjax(resources.mathjax_url) }}
-{%- endblock html_head_js_mathjax -%}
-
-{%- block html_head_js_mermaidjs -%}
-{{ mermaid_js(resources.mermaid_js_url) }}
-{%- endblock html_head_js_mermaidjs -%}
-
-{%- block html_head_css -%}
-{%- endblock html_head_css -%}
-
-{%- endblock html_head -%}
-
-{%- endblock header -%}
-
-{%- block body_header -%}
-{% if resources.theme == 'dark' %}
-
-{% else %}
-
-{% endif %}
-
-{%- endblock body_header -%}
-
-{% block body_footer %}
-
-
-{% endblock body_footer %}
-
-{% block footer %}
-{% block footer_js %}
-{% endblock footer_js %}
-{{ super() }}
-
-{% endblock footer %}
diff --git a/cfa/dataops/reporting/jupyter_templates/lab/mermaidjs.html.j2 b/cfa/dataops/reporting/jupyter_templates/lab/mermaidjs.html.j2
deleted file mode 100644
index 0f71588..0000000
--- a/cfa/dataops/reporting/jupyter_templates/lab/mermaidjs.html.j2
+++ /dev/null
@@ -1,188 +0,0 @@
-{%- macro mermaid_js(
-url="https://cdnjs.cloudflare.com/ajax/libs/mermaid/10.7.0/mermaid.esm.min.mjs"
-) -%}
-
-
-
-{%- endmacro %}
diff --git a/cfa/dataops/stub_templates/catalog.pyi.mako b/cfa/dataops/stub_templates/catalog.pyi.mako
index e976dd6..97464df 100644
--- a/cfa/dataops/stub_templates/catalog.pyi.mako
+++ b/cfa/dataops/stub_templates/catalog.pyi.mako
@@ -5,8 +5,6 @@ from typing import Any, Literal, overload
import pandas as pd
import polars as pl
-from .reporting.catalog import NotebookEndpoint
-
def get_all_catalogs() -> list: ...
class CatalogNamespace(SimpleNamespace):
@@ -23,14 +21,11 @@ class DatasetEndpoint:
defaults: dict[str, Any]
config: dict[str, Any]
__ns_str__: str
- _ledger_location: dict[str, Any]
class BlobEndpoint:
account: str
container: str
prefix: str
- ledger_location: dict[str, Any]
- is_ledger: bool
__ns_str__: str
def check_blob_access(self) -> tuple[bool, str]: ...
def verify_blob_access(self) -> None: ...
@@ -89,7 +84,6 @@ class BlobEndpoint:
version_spec: str | None = None,
selection: Literal["newest", "oldest"] = "newest",
) -> VersionMetadata: ...
- def ledger_entry(self, action: str) -> None: ...
def save_dataframe(
self,
df: pd.DataFrame | pl.DataFrame,
@@ -128,4 +122,3 @@ class ${cls.name}(${cls.base}):
% endfor
datacat: DataCatalog
-reportcat: ReportCatalog
diff --git a/cfa/dataops/stub_templates/init.pyi.mako b/cfa/dataops/stub_templates/init.pyi.mako
index a25070b..ed453a0 100644
--- a/cfa/dataops/stub_templates/init.pyi.mako
+++ b/cfa/dataops/stub_templates/init.pyi.mako
@@ -1,4 +1,4 @@
-from .catalog import datacat as datacat, reportcat as reportcat
+from .catalog import datacat as datacat
__version__: str
__all__: list[str]
diff --git a/cfa/dataops/type_stubs.py b/cfa/dataops/type_stubs.py
index 38655c8..e36a1c3 100644
--- a/cfa/dataops/type_stubs.py
+++ b/cfa/dataops/type_stubs.py
@@ -20,7 +20,6 @@
class _Node:
children: dict[str, "_Node"] = field(default_factory=dict)
dataset_config_path: str | None = None
- report_path: str | None = None
@dataclass(frozen=True)
@@ -64,13 +63,11 @@ def _insert_node(
path: tuple[str, ...],
*,
dataset_config_path: str | None = None,
- report_path: str | None = None,
) -> None:
node = root
for segment in path:
node = node.children.setdefault(segment, _Node())
node.dataset_config_path = dataset_config_path
- node.report_path = report_path
def _walk_dataset_map(
@@ -92,25 +89,6 @@ def _walk_dataset_map(
return datasets
-def _walk_report_map(
- mapping: Mapping[str, Any],
- namespace: tuple[str, ...] = (),
-) -> list[tuple[tuple[str, ...], str]]:
- reports: list[tuple[tuple[str, ...], str]] = []
- for key, value in mapping.items():
- segment = _ensure_identifier(str(key), namespace)
- path = (*namespace, segment)
- if isinstance(value, str) and value.endswith(".ipynb"):
- reports.append((path, value))
- elif isinstance(value, Mapping):
- reports.extend(_walk_report_map(value, path))
- elif isinstance(value, list):
- for item in value:
- if isinstance(item, Mapping):
- reports.extend(_walk_report_map(item, path))
- return reports
-
-
def _dataset_stage_names(config_path: str) -> list[str]:
with open(config_path, "rb") as f:
config = tomli.load(f)
@@ -134,10 +112,6 @@ def _dataset_class(class_name: str, config_path: str) -> _StubClass:
)
-def _report_class(class_name: str) -> _StubClass:
- return _StubClass(name=class_name, base="NotebookEndpoint")
-
-
def _namespace_classes(
node: _Node,
*,
@@ -153,9 +127,6 @@ def _namespace_classes(
if child.dataset_config_path is not None:
child_class = _class_name(prefix, child_path, "Dataset")
classes.append(_dataset_class(child_class, child.dataset_config_path))
- elif child.report_path is not None:
- child_class = _class_name(prefix, child_path, "Report")
- classes.append(_report_class(child_class))
else:
child_classes, child_class = _namespace_classes(
child,
@@ -173,8 +144,6 @@ def _namespace_classes(
]
if not path:
attributes.append(_StubAttribute("__namespace_list__", "list[str]"))
- elif is_dataset_catalog and len(path) == 1:
- attributes.append(_StubAttribute("_ledger_endpoint", "BlobEndpoint"))
classes.append(
_StubClass(
@@ -193,16 +162,8 @@ def _build_dataset_tree(dataset_ns_map: Mapping[str, Any]) -> _Node:
return root
-def _build_report_tree(report_ns_map: Mapping[str, Any]) -> _Node:
- root = _Node()
- for path, report_path in _walk_report_map(report_ns_map):
- _insert_node(root, path, report_path=report_path)
- return root
-
-
def _build_stub_model(
dataset_ns_map: Mapping[str, Any],
- report_ns_map: Mapping[str, Any],
) -> _StubModel:
dataset_classes, _ = _namespace_classes(
_build_dataset_tree(dataset_ns_map),
@@ -211,14 +172,7 @@ def _build_stub_model(
root_name="DataCatalog",
is_dataset_catalog=True,
)
- report_classes, _ = _namespace_classes(
- _build_report_tree(report_ns_map),
- prefix="ReportCatalog",
- path=(),
- root_name="ReportCatalog",
- is_dataset_catalog=False,
- )
- return _StubModel(classes=tuple([*dataset_classes, *report_classes]))
+ return _StubModel(classes=tuple(dataset_classes))
def _render_template(template_name: str, **context: Any) -> str:
@@ -230,13 +184,12 @@ def _render_template(template_name: str, **context: Any) -> str:
def render_catalog_stub(
dataset_ns_map: Mapping[str, Any],
- report_ns_map: Mapping[str, Any],
) -> str:
"""Render a precise ``cfa.dataops.catalog`` stub for installed catalogs."""
return _render_template(
"catalog.pyi.mako",
- model=_build_stub_model(dataset_ns_map, report_ns_map),
+ model=_build_stub_model(dataset_ns_map),
)
@@ -248,7 +201,6 @@ def write_catalog_stubs(
output_root: str | Path = DEFAULT_STUB_ROOT,
*,
dataset_ns_map: Mapping[str, Any],
- report_ns_map: Mapping[str, Any],
) -> list[Path]:
output_root = Path(output_root)
package_root = output_root / "cfa" / "dataops"
@@ -257,7 +209,7 @@ def write_catalog_stubs(
catalog_stub = package_root / "catalog.pyi"
init_stub = package_root / "__init__.pyi"
catalog_stub.write_text(
- render_catalog_stub(dataset_ns_map, report_ns_map),
+ render_catalog_stub(dataset_ns_map),
encoding="utf-8",
)
init_stub.write_text(render_init_stub(), encoding="utf-8")
@@ -276,12 +228,11 @@ def main() -> None:
)
args = parser.parse_args()
- from .catalog import all_dataset_ns_map, all_reports_ns_map
+ from .catalog import all_dataset_ns_map
written = write_catalog_stubs(
args.output_root,
dataset_ns_map=all_dataset_ns_map,
- report_ns_map=all_reports_ns_map,
)
for path in written:
print(path)
diff --git a/changelog.md b/changelog.md
index f36a5bf..4497cd9 100644
--- a/changelog.md
+++ b/changelog.md
@@ -127,7 +127,7 @@ This release marks a significant milestone for the CFA DataOps project, providin
**Key Highlights:**
- **Unified Data Access**: `datacat` interface for seamless dataset access.
-- **Automated Reporting**: `reportcat` for generating interactive HTML reports from Jupyter notebooks.
+- **Automated Reporting**: `reportcat` for generating interactive HTML reports from Jupyter notebooks. *(Note: `reportcat` and reporting support were removed in a later release.)*
- **Robust CLI Tools**: Manage catalogs and datasets effortlessly.
- **Flexible Data Loading**: Advanced version filtering for Pandas and Polars DataFrames.
diff --git a/docs/catalog_creation.md b/docs/catalog_creation.md
index 96ef458..3ec4705 100644
--- a/docs/catalog_creation.md
+++ b/docs/catalog_creation.md
@@ -4,7 +4,7 @@ This guide explains how to create a new dataops data catalog repository using th
## Overview
-The `dataops_catalog_init` command creates a structured repository for managing data catalogs within the CFA DataOps framework. It generates a complete Python package with predefined templates for datasets, workflows, and reports.
+The `dataops_catalog_init` command creates a structured repository for managing data catalogs within the CFA DataOps framework. It generates a complete Python package with predefined templates for datasets and workflows.
## Prerequisites
@@ -78,10 +78,6 @@ When you run the command, it creates the following structure:
│ │ ├── experiment_tracking_example.toml
│ │ ├── multistage_example.toml
│ │ └── reference_data_example.toml
-│ ├── reports/
-│ │ ├── __init__.py
-│ │ └── examples/
-│ │ └── basics.ipynb
│ └── workflows/
│ ├── __init__.py
│ ├── etl/
@@ -112,15 +108,12 @@ When you run the command, it creates the following structure:
### 1. Catalog Defaults (`catalog_defaults.toml`)
-Contains default configuration for storage and access:
+Contains default configuration for storage:
```toml
[storage]
account = "cfadatalakeprd"
container = "cfapredict"
-
-[access_ledger]
-path = "_access/
/ledger/"
```
### 2. Dataset Examples
@@ -193,7 +186,7 @@ After creating your catalog repository:
pip install -e .[dev]
```
-3. **Start developing your datasets, workflows, and reports**
+3. **Start developing your datasets and workflows**
## Interactive Confirmation
@@ -242,7 +235,7 @@ After creating your catalog repository:
1. Review and customize the example dataset configurations
2. Add your actual data sources and configurations
3. Develop custom workflows for your data processing needs
-4. Create reports and visualizations using the provided templates
+4. Add project-specific processing logic in the generated workflow packages
5. Set up automated testing and validation
## Troubleshooting
diff --git a/docs/index.md b/docs/index.md
index f3bcda8..7f1d27f 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,6 +1,6 @@
# CFA DataOps Documentation
-Welcome to the CFA DataOps system - a catalog-based approach to data management, ETL, and reporting.
+Welcome to the CFA DataOps system - a catalog-based approach to data management and ETL.
## Getting Started
@@ -12,21 +12,18 @@ Welcome to the CFA DataOps system - a catalog-based approach to data management,
3. **[CLI Tools Reference](cli_tools.md)** - Command-line tools for exploring and downloading datasets
4. **[Data User Guide](data_user_guide.md)** - Access and work with datasets using `datacat`
5. **[Data Developer Guide](data_developer_guide.md)** - Add datasets and ETL processes to catalogs
-6. **[Report Generation](report_generation.md)** - Create and generate reports using `reportcat`
## Quick Reference
```python
# Essential imports
-from cfa.dataops import datacat, reportcat
+from cfa.dataops import datacat
# List available resources
print("Datasets:", datacat.__namespace_list__)
-print("Reports:", reportcat.__namespace_list__)
-# Access data and reports (example)
+# Access data (example)
df = datacat.private.scenarios.covid19vax_trends.load.get_dataframe()
-report_html = reportcat.private.examples.basics_ipynb.nb_to_html_str()
```
When you need to preview the version that a dataframe load will use, call `resolve_version()` on the same dataset endpoint with the same `version_spec` and `selection` values you plan to pass to `get_dataframe()`.
diff --git a/docs/managing_catalogs.md b/docs/managing_catalogs.md
index ecb7700..200cf39 100644
--- a/docs/managing_catalogs.md
+++ b/docs/managing_catalogs.md
@@ -4,7 +4,7 @@ This guide explains how to work with multiple catalog repositories in the CFA Da
## Overview
-The DataOps system is designed around catalog repositories that you create using `dataops_catalog_init`. Multiple catalogs can be installed in the same Python environment, providing unified access to all datasets and reports through `datacat` and `reportcat`.
+The DataOps system is designed around catalog repositories that you create using `dataops_catalog_init`. Multiple catalogs can be installed in the same Python environment, providing unified access to datasets through `datacat`.
## Creating Your First Catalog
@@ -21,10 +21,9 @@ The DataOps system is designed around catalog repositories that you create using
3. **Verify installation**:
```python
- from cfa.dataops import datacat, reportcat
+ from cfa.dataops import datacat
print(datacat.__namespace_list__)
- print(reportcat.__namespace_list__)
```
## Working with Multiple Catalogs
@@ -47,11 +46,10 @@ cd /path/to/my-project-catalog && pip install -e .[dev]
### Unified Access
-All datasets and reports become accessible through unified interfaces:
+Datasets become accessible through a unified interface:
```python
from cfa.dataops import datacat
-from cfa.dataops.reporting import reportcat
# Access datasets from any installed catalog
datacat.private.scenarios.covid19vax_trends.load.get_dataframe()
@@ -65,10 +63,6 @@ df_meta = datacat.private.scenarios.covid19vax_trends.load.resolve_version(
)
print(df_meta.version)
-# Access reports from any installed catalog
-reportcat.private.scenarios.examples.basics_ipynb
-reportcat.private.surveillance.weekly.summary_ipynb
-reportcat.private.my_project.analysis.trend_report_ipynb
```
### Listing Available Resources
@@ -77,12 +71,8 @@ reportcat.private.my_project.analysis.trend_report_ipynb
# List all datasets across all catalogs
print("Available datasets:", datacat.__namespace_list__)
-# List all reports across all catalogs
-print("Available reports:", reportcat.__namespace_list__)
-
# Explore specific catalog namespaces
print("Scenarios datasets:", dir(datacat.scenarios))
-print("Surveillance reports:", dir(reportcat.surveillance))
```
## Catalog Repository Structure
@@ -99,9 +89,6 @@ my-catalog/
│ ├── datasets/ # Dataset configurations (TOML files)
│ │ ├── dataset1.toml
│ │ └── dataset2.toml
-│ ├── reports/ # Jupyter notebook templates
-│ │ ├── examples/
-│ │ └── analysis/
│ └── workflows/ # ETL and processing scripts
│ ├── etl/
│ ├── multistage/
@@ -122,13 +109,12 @@ my-catalog/
### Naming Conventions
- Use descriptive catalog names that reflect their purpose
- Keep dataset names consistent within each catalog
-- Use clear, hierarchical organization for reports
### Development Workflow
1. Create separate catalogs for different data domains
2. Install all relevant catalogs in your development environment
-3. Use `datacat` and `reportcat` for unified access
-4. Develop datasets and reports within their appropriate catalog repositories
+3. Use `datacat` for unified access
+4. Develop datasets within their appropriate catalog repositories
### Sharing Catalogs
- Catalog repositories can be shared via Git repositories
@@ -147,16 +133,6 @@ surveillance_data = datacat.surveillance.flu_trends.load.get_dataframe()
combined_analysis = analyze_trends(scenarios_data, surveillance_data)
```
-### Catalog-Specific Reports
-```python
-# Generate reports using data from specific catalogs
-report = reportcat.private.scenarios.analysis.trend_analysis_ipynb
-report.nb_to_html_file(
- html_out_path="trend_report.html",
- dataset_namespace="scenarios.covid19vax_trends"
-)
-```
-
## Troubleshooting
### Catalog Not Found
diff --git a/docs/release_notes/v2025.12.10.md b/docs/release_notes/v2025.12.10.md
index 56da63f..0ce240c 100644
--- a/docs/release_notes/v2025.12.10.md
+++ b/docs/release_notes/v2025.12.10.md
@@ -5,7 +5,7 @@ We're thrilled to announce the first official release of the **CFA DataOps** pro
## 🚀 Highlights
* **Unified Data Access**: Seamlessly access datasets across multiple catalogs using the `datacat` interface.
-* **Automated Reporting**: Generate client-side rendering interactive HTML reports from Jupyter notebooks with `reportcat`.
+* **Automated Reporting**: Generate client-side rendering interactive HTML reports from Jupyter notebooks with `reportcat`. *(Note: `reportcat` and reporting support were removed in a later release.)*
* **Robust CLI Tools**: Manage catalogs, datasets, stages, and versions directly from the command line.
* **Flexible Data Loading**: Load data into Pandas or Polars DataFrames with advanced version filtering and selection.
* **Azure Blob Storage Integration**: Built-in support for reading/writing raw and transformed data to Azure Blob Storage.
@@ -72,9 +72,9 @@ from cfa.dataops import datacat
df = datacat.public.my_dataset.load.get_dataframe(version=">2024.12.01,<2025.08")
```
-**Generate a Report:**
+**Generate a Report** *(removed in a later release)*:
```python
-from cfa.dataops.reporting import reportcat
+from cfa.dataops import reportcat # removed in a later release
reportcat.examples.dataset_report_ipynb.nb_to_html_file('report.html')
```
@@ -84,7 +84,6 @@ For more detailed information, please refer to our comprehensive documentation:
* [Data User Guide](https://cdcgov.github.io/cfa-dataops/data_user_guide/)
* [Data Developer Guide](https://cdcgov.github.io/cfa-dataops/data_developer_guide/)
* [Managing Catalogs](https://cdcgov.github.io/cfa-dataops/managing_catalogs/)
-* [Report Generation](https://cdcgov.github.io/cfa-dataops/report_generation/)
* [CLI Tools](https://cdcgov.github.io/cfa-dataops/cli_tools/)
---
diff --git a/docs/report_generation.md b/docs/report_generation.md
deleted file mode 100644
index 278d170..0000000
--- a/docs/report_generation.md
+++ /dev/null
@@ -1,130 +0,0 @@
-# Report Generation
-
-Generate parameterized reports from Jupyter notebooks stored in your catalog repositories.
-
-> **Prerequisites**: You need to have catalog repositories with report templates created and installed. See [Managing Catalogs](managing_catalogs.md) for setup instructions.
-
-## Quick Start
-
-```python
-from cfa.dataops import reportcat
-
-# List all available reports
-print("Available reports:", reportcat.__namespace_list__)
-
-# Generate a report
-report = reportcat.examples.basics_ipynb
-report.nb_to_html_file(html_out_path="my_report.html")
-```
-
-## Available Reports
-
-Reports are organized in a namespace structure. You can explore available reports using reportcat:
-
-```python
-from cfa.dataops import reportcat
-
-# List all available reports
-available_reports = reportcat.__namespace_list__
-print(available_reports)
-
-# Or explore the reportcat namespace directly
-print(dir(reportcat)) # Shows top-level catalog namespaces
-
-# Access specific reports
-reportcat.examples.basics_ipynb
-reportcat.examples.dataset_report_ipynb
-```
-
-## Using Report Templates
-
-Each report is represented by a `NotebookEndpoint` object that provides methods for:
-
-- Getting report parameters (`get_params()`)
-- Generating HTML output (`nb_to_html_str()`, `nb_to_html_file()`, `nb_to_html_blob()`)
-
-### Example: Dataset Report
-
-The dataset_report.ipynb template demonstrates a basic report that:
-
-1. Takes a dataset namespace as a parameter
-2. Shows dataset configuration
-3. Displays available versions
-4. Provides data summaries and samples
-5. Creates visualizations
-
-Example usage:
-
-```python
-# Get the report endpoint
-report = reportcat.examples.dataset_report_ipynb
-
-# View available parameters
-report.print_params()
-
-# Generate HTML report
-report.nb_to_html_file(
- html_out_path="my_report.html",
- dataset_namespace="scenarios.covid19vax_trends"
-)
-
-# Or save directly to blob storage
-report.nb_to_html_blob(
- blob_account="myaccount",
- blob_container="mycontainer",
- blob_path="reports/dataset_report.html",
- dataset_namespace="scenarios.covid19vax_trends"
-)
-```
-
-## Creating Custom Reports
-
-To create a new report in your catalog repository:
-
-1. Create a Jupyter notebook in your catalog's `reports/` directory (e.g., `{your_catalog}/reports/my_report.ipynb`)
-2. Use cell tags `parameters` and `remove_input` for parameter cells
-3. Add help text as comments for parameters
-4. Use markdown cells for documentation
-5. The report will automatically be available in the `reportcat` namespace after installing your catalog
-
-### Report Organization
-
-Reports can be organized within subdirectories in your catalog's `reports/` folder:
-
-```
-{your_catalog}/reports/
-├── examples/
-│ └── basics.ipynb
-├── analysis/
-│ └── trend_analysis.ipynb
-└── summary/
- └── monthly_report.ipynb
-```
-
-These will be accessible as:
-- `reportcat.{catalog_name}.examples.basics_ipynb`
-- `reportcat.{catalog_name}.analysis.trend_analysis_ipynb`
-- `reportcat.{catalog_name}.summary.monthly_report_ipynb`
-
-### Report Parameters
-
-Parameters are defined in cells tagged with "parameters":
-
-```python
-dataset_namespace: str = "scenarios.covid19vax_trends" # help string
-```
-
-### Template Best Practices
-
-- Use cell tags to control input/output visibility
-- Add clear markdown documentation
-- Handle errors gracefully
-- Include data validation
-- Use consistent styling
-- Test with different parameter
-
-## Screenshot Example of a Report
-
-Below is a screenshot for the basics report highlighting just a few of the things you can do with this reporting functionality. In addition to the myriad of jupyter compatible libraries that embed JavaScript (like ITables), authoring new functionality is also pretty simple, using `IPython.display` submodule, to author all sorts of add-ons that can be included in reports (e.g., a floating table of contents, or a temporary annotation layer).
-
-
diff --git a/docs/reportcat_publish_example.md b/docs/reportcat_publish_example.md
deleted file mode 100644
index cb6af16..0000000
--- a/docs/reportcat_publish_example.md
+++ /dev/null
@@ -1,103 +0,0 @@
-# Publishing Reports with Reportcat
-
-This guide demonstrates how to generate a **parameterized notebook report** and publish it to **Azure Blob Storage** using `NotebookEndpoint`.
-
-This example builds on the **Reportcat Quickstart** and shows how to automate report publishing.
-
----
-
-## Example Location
-
-Example files in this repository:
-
- examples/reportcat/
- ├── minimal_report.ipynb
- ├── run_minimal_report.py
- └── publish_report.py
-
-
-The `publish_report.py` example demonstrates how to execute a notebook and upload the resulting HTML report directly to Azure Blob Storage.
-
----
-
-## Prerequisites
-
-From the repository root:
-
-```powershell
-python -m venv venv
-venv\Scripts\activate
-pip install -e .
-```
-You must also have Azure access to a storage account.
-
----
-
-## Azure Configuration
-
-Set the required environment variables before running the example.
-
-PowerShell:
-
-```powershell
-$env:REPORTCAT_BLOB_ACCOUNT="storage_account_name"
-$env:REPORTCAT_BLOB_CONTAINER="container"
-$env:REPORTCAT_BLOB_PATH="TID/Test_Data/minimal_report.html"
-```
-
-These values specify where the generated report will be uploaded.
-
----
-
-## Running the Publishing Example
-
-Execute the script:
-
- python examples/reportcat/publish_report.py
-
-
-During execution the workflow performs:
-
-- Notebook parameter injection
-- Notebook execution via papermill
-- Conversion to HTML
-- Upload to Azure Blob Storage
-
----
-
-Example Script:
-
- examples/reportcat/publish_report.py
-
-Expected Result
-
-After successful execution:
-- The notebook runs with injected parameters
-- An HTML report is generated
-- The report is uploaded to Azure Blob Storage
-
-Example output location:
-
- https://.blob.core.windows.net//TID/Test_Data/minimal_report.html
-
----
-
-## When to Use This Pattern
-
-This workflow is useful when:
-
-- generating scheduled reports
-- publishing automated analytics outputs
-- creating reproducible reporting pipelines
-- integrating notebook reports into cloud storage workflows
-
----
-
-## Next Steps
-
-Teams can extend this pattern by:
-
-- integrating report generation into GitHub Actions
-- scheduling report execution
-- publishing reports to shared storage locations
-- parameterizing reports with pipeline inputs
diff --git a/docs/reportcat_quickstart.md b/docs/reportcat_quickstart.md
deleted file mode 100644
index 0fd13a2..0000000
--- a/docs/reportcat_quickstart.md
+++ /dev/null
@@ -1,158 +0,0 @@
-# Reportcat Quickstart
-
-This guide demonstrates how to use `cfa.dataops.reporting.catalog.NotebookEndpoint` to execute a **parameterized Jupyter notebook** and generate an **HTML report**.
-
-The example in this repository provides a minimal workflow that users can adapt for automated reporting.
-
----
-
-## What reportcat provides
-
-`NotebookEndpoint` enables:
-
-- Parameterized notebook execution using **papermill**
-- Report rendering using **nbconvert**
-- Exporting results to **HTML reports**
-- Optional publishing to **Azure Blob Storage**
-
-This approach is useful for teams that want to:
-
-- Standardize notebook-based reporting
-- Automate periodic report generation
-- Run reproducible notebook pipelines
-
----
-
-## Repository example
-
-This repository includes a minimal working example located at:
-
-examples/reportcat/
-
- ### Files included
- examples/reportcat/
- ├── minimal_report.ipynb
- └── run_minimal_report.py
-
-
----
-
-## `minimal_report.ipynb`
-
-A simple notebook that:
-
-- Accepts parameters
-- Performs a small computation
-- Outputs results for the report
-
----
-
-## `run_minimal_report.py`
-
-A script that:
-
-- Executes the notebook
-- Injects parameters
-- Generates an HTML report
-
----
-
-## Prerequisites
-
-From the **cfa-dataops** repository root:
-
-```powershell
-python -m venv venv
-venv\Scripts\activate
-pip install -e .
-```
-This installs the cfa-dataops package in editable mode.
-
----
-
-## Running the example
-
-Execute the example report generation script:
-
- python examples/reportcat/run_minimal_report.py
-
-During execution, NotebookEndpoint will:
-
-- Inject parameters into the notebook
-- Execute the notebook via papermill
-- Convert the executed notebook to HTML
-
-Example console output:
-
- Executing: 100%
- HTML report saved to out/minimal_report.html
- Report generated: out/minimal_report.html
-
----
-
-## Output
-
-The generated report will appear in:
-
- out/minimal_report.html
-
-Opening the file will show the executed notebook results rendered as an HTML report.
-
-Example output:
- x = 10
- y = 20
- result = 30
-
-## Understanding parameters
-
-The notebook defines parameters in a dedicated cell:
-
- # parameters
- x = 1
- y = 2
-
-The execution script injects new values:
-
- ep.nb_to_html_file(
- html_out_path="out/minimal_report.html",
- nb_title="Minimal Report",
- kernel_name="python3",
- x=10,
- y=20
- )
-
-These values override the defaults during notebook execution.
-
----
-
-## When to use reportcat
-
-Reportcat is useful when:
-
-- notebooks are used to produce repeatable reports
-- reports must be generated programmatically
-- teams want parameterized notebook pipelines
-- outputs need to be published as HTML artifacts
-
----
-
-## Troubleshooting
-
-Notebook kernel not found
-
-List available kernels:
-
- python -m jupyter kernelspec list
-
-Ensure your script uses the correct kernel:
-
- kernel_name="python3"
-
----
-
-## Editable install issues
-
-Reinstall the package:
-
-
- pip install -e .
diff --git a/examples/reportcat/minimal_report.ipynb b/examples/reportcat/minimal_report.ipynb
deleted file mode 100644
index a1aeebb..0000000
--- a/examples/reportcat/minimal_report.ipynb
+++ /dev/null
@@ -1,73 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "markdown",
- "id": "206ed9cf",
- "metadata": {},
- "source": [
- "# Minimal report example\n",
- "\n",
- "This notebook demonstrates a simple parameterized report using reportcat."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "6e65b765",
- "metadata": {},
- "outputs": [],
- "source": [
- "# parameters\n",
- "x = 1\n",
- "y = 2"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "c391d43b",
- "metadata": {},
- "source": [
- "## Example calculation\n",
- "\n",
- "This cell uses the injected parameters to produce a simple output."
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "2bbbd117",
- "metadata": {},
- "outputs": [],
- "source": [
- "result = x + y\n",
- "\n",
- "print(\"Injected parameter values:\")\n",
- "print(\"-------------------------\")\n",
- "print(f\"x = {x}\")\n",
- "print(f\"y = {y}\")\n",
- "print(f\"result = {result}\")"
- ]
- },
- {
- "cell_type": "markdown",
- "id": "81a0501c",
- "metadata": {},
- "source": [
- "This output confirms that papermill parameters were injected successfully and the notebook was rendered as an HTML report using reportcat."
- ]
- }
- ],
- "metadata": {
- "kernelspec": {
- "display_name": "venv (3.13.5)",
- "language": "python",
- "name": "python3"
- },
- "language_info": {
- "name": "python",
- "version": "3.13.5"
- }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}
diff --git a/examples/reportcat/publish_report.py b/examples/reportcat/publish_report.py
deleted file mode 100644
index ffec2d9..0000000
--- a/examples/reportcat/publish_report.py
+++ /dev/null
@@ -1,38 +0,0 @@
-import os
-from pathlib import Path
-
-from cfa.dataops.reporting.catalog import NotebookEndpoint
-
-
-def must_get(name: str) -> str:
- value = os.getenv(name)
- if not value:
- raise ValueError(f"Missing required environment variable: {name}")
- return value
-
-
-def main() -> None:
- """Generate and publish a minimal HTML report to Azure Blob Storage."""
- repo_root = Path(__file__).resolve().parents[2]
- notebook_path = repo_root / "examples" / "reportcat" / "minimal_report.ipynb"
-
- blob_account = must_get("REPORTCAT_BLOB_ACCOUNT")
- blob_container = must_get("REPORTCAT_BLOB_CONTAINER")
- blob_path = must_get("REPORTCAT_BLOB_PATH")
-
- ep = NotebookEndpoint(str(notebook_path))
- ep.nb_to_html_blob(
- blob_account=blob_account,
- blob_container=blob_container,
- blob_path=blob_path,
- nb_title="Minimal Report",
- kernel_name="python3",
- x=10,
- y=20,
- )
-
- print("Report published to Azure Blob Storage.")
-
-
-if __name__ == "__main__":
- main()
diff --git a/examples/reportcat/run_minimal_report.py b/examples/reportcat/run_minimal_report.py
deleted file mode 100644
index b243c5f..0000000
--- a/examples/reportcat/run_minimal_report.py
+++ /dev/null
@@ -1,25 +0,0 @@
-from pathlib import Path
-
-from cfa.dataops.reporting.catalog import NotebookEndpoint
-
-
-def main() -> None:
- """Generate a minimal HTML report from a parameterized notebook."""
- repo_root = Path(__file__).resolve().parents[2]
- notebook_path = repo_root / "examples" / "reportcat" / "minimal_report.ipynb"
- output_path = repo_root / "out" / "minimal_report.html"
-
- ep = NotebookEndpoint(str(notebook_path))
- ep.nb_to_html_file(
- html_out_path=str(output_path),
- nb_title="Minimal Report",
- kernel_name="python3",
- x=10,
- y=20,
- )
-
- print(f"Report generated: {output_path}")
-
-
-if __name__ == "__main__":
- main()
diff --git a/mkdocs.yaml b/mkdocs.yaml
index 6e9d97c..070e585 100644
--- a/mkdocs.yaml
+++ b/mkdocs.yaml
@@ -6,7 +6,6 @@ nav:
- managing_catalogs.md
- data_user_guide.md
- data_developer_guide.md
- - report_generation.md
- cli_tools.md
repo_url: https://github.com/cdcgov/cfa-dataops
diff --git a/pyproject.toml b/pyproject.toml
index c0cdebd..ecf3245 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[project]
name = "cfa.dataops"
-version = "2026.08.07.0"
+version = "2026.08.26.0"
description = "Data cataloging, ETL, modeling, verification, and validation for CFA"
authors = [
{ name = "Ryan Raasch", email = "xng3@cdc.gov" },
@@ -17,15 +17,8 @@ dependencies = [
"tqdm (>=4.67.1)",
"pyarrow (>=19.0.1)",
"fastparquet (>=2025.12.0)",
- "matplotlib (~=3.9)",
"pandas (>=2.2.3)",
- "altair (>=5.5.0)",
- "vl-convert-python (>=1.7.0)",
"pandera[pandas] (>=0.24.0)",
- "papermill (>=2.6.0)",
- "ipywidgets (>=8.1.7)",
- "itables (>=2.4.4)",
- "nbconvert (>=7.16.6)",
"jupyter (>=1.1.1)",
"jupyterlab>=4.5.10",
"rich (>=14.1.0)",
diff --git a/tests/conftest.py b/tests/conftest.py
index c3eb3c3..0e847bd 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -186,7 +186,6 @@ def dataset_ns_map():
def dataset_defaults():
return {
"storage": {"account": "account_test", "container": "container_test"},
- "access_ledger": {"path": "_access/test/ledger/"},
}
diff --git a/tests/fixtures/expected_catalog_stub.pyi b/tests/fixtures/expected_catalog_stub.pyi
deleted file mode 100644
index a1e89ad..0000000
--- a/tests/fixtures/expected_catalog_stub.pyi
+++ /dev/null
@@ -1,135 +0,0 @@
-from collections.abc import Sequence
-from types import SimpleNamespace
-from typing import Any, Literal, overload
-
-import pandas as pd
-import polars as pl
-
-from .reporting.catalog import NotebookEndpoint
-
-def get_all_catalogs() -> list[tuple[str, str, str]]: ...
-
-class CatalogNamespace(SimpleNamespace):
- pass
-
-class DatasetEndpoint:
- config_path: str
- defaults: dict[str, Any]
- config: dict[str, Any]
- __ns_str__: str
- _ledger_location: dict[str, Any]
-
-class BlobEndpoint:
- account: str
- container: str
- prefix: str
- ledger_location: dict[str, Any]
- is_ledger: bool
- __ns_str__: str
- def write_blob(
- self,
- file_buffer: bytes | Sequence[bytes],
- path_after_prefix: str,
- auto_version: bool = False,
- append: bool = False,
- ) -> None: ...
- def read_blobs(
- self,
- version_spec: str | None = None,
- selection: Literal["newest", "oldest"] = "newest",
- print_version: bool = True,
- ) -> list[bytes]: ...
- def read_csv(self, suffix: str) -> pd.DataFrame: ...
- def get_versions(self) -> list[str]: ...
- def get_file_ext(
- self,
- version_spec: str | None = None,
- selection: Literal["newest", "oldest"] = "newest",
- ) -> str: ...
- def download_version_to_local(
- self,
- local_path: str,
- version_spec: str | None = None,
- force: bool = False,
- selection: Literal["newest", "oldest"] = "newest",
- ) -> bool: ...
- @overload
- def get_dataframe(
- self,
- output: Literal["pandas", "pd"] = "pandas",
- version_spec: str | None = None,
- selection: Literal["newest", "oldest"] = "newest",
- ) -> pd.DataFrame: ...
- @overload
- def get_dataframe(
- self,
- output: Literal["polars", "pl"],
- version_spec: str | None = None,
- selection: Literal["newest", "oldest"] = "newest",
- ) -> pl.DataFrame: ...
- @overload
- def get_dataframe(
- self,
- output: Literal["pl_lazy", "lazy"],
- version_spec: str | None = None,
- selection: Literal["newest", "oldest"] = "newest",
- ) -> pl.LazyFrame: ...
- def ledger_entry(self, action: str) -> None: ...
- def save_dataframe(
- self,
- df: pd.DataFrame | pl.DataFrame,
- path_after_prefix: str,
- file_format: str = "parquet",
- auto_version: bool = False,
- ) -> None: ...
- def save_file_to_blob(
- self,
- file_path: str,
- path_after_prefix: str,
- auto_version: bool = False,
- ) -> None: ...
- def save_dir_to_blob(
- self,
- dir_path: str,
- path_after_prefix: str,
- auto_version: bool = False,
- ) -> None: ...
-
-def dict_to_sn(
- d: Any,
- defaults: dict[str, Any] | None = None,
- ns: str = "",
-) -> CatalogNamespace: ...
-
-class _DataCatalogPublicStfNhsnHrdPrelimDataset(DatasetEndpoint):
- config: dict[str, Any]
- extract: BlobEndpoint
- stage_01: BlobEndpoint
- load: BlobEndpoint
-
-class _DataCatalogPublicStfNamespace(CatalogNamespace):
- nhsn_hrd_prelim: _DataCatalogPublicStfNhsnHrdPrelimDataset
-
-class _DataCatalogPublicNamespace(CatalogNamespace):
- stf: _DataCatalogPublicStfNamespace
- _ledger_endpoint: BlobEndpoint
-
-class DataCatalog(CatalogNamespace):
- public: _DataCatalogPublicNamespace
- __namespace_list__: list[str]
-
-class _ReportCatalogPublicExamplesBasicReportReport(NotebookEndpoint):
- pass
-
-class _ReportCatalogPublicExamplesNamespace(CatalogNamespace):
- basic_report: _ReportCatalogPublicExamplesBasicReportReport
-
-class _ReportCatalogPublicNamespace(CatalogNamespace):
- examples: _ReportCatalogPublicExamplesNamespace
-
-class ReportCatalog(CatalogNamespace):
- public: _ReportCatalogPublicNamespace
- __namespace_list__: list[str]
-
-datacat: DataCatalog
-reportcat: ReportCatalog
diff --git a/tests/test_blob_access_check.py b/tests/test_blob_access_check.py
index 9de58ad..c350a63 100644
--- a/tests/test_blob_access_check.py
+++ b/tests/test_blob_access_check.py
@@ -3,6 +3,11 @@
from unittest.mock import patch
import pytest
+from azure.core.exceptions import (
+ ClientAuthenticationError,
+ HttpResponseError,
+ ResourceNotFoundError,
+)
from cfa.dataops.catalog import BlobEndpoint
@@ -10,16 +15,10 @@
@pytest.fixture
def blob_endpoint():
"""Create a BlobEndpoint instance for testing."""
- ledger_location = {
- "account": "account_test",
- "container": "container_test",
- "prefix": "_access/test/ledger/",
- }
return BlobEndpoint(
account="myaccount",
container="mycontainer",
prefix="test/prefix",
- ledger_location=ledger_location,
ns="test.endpoint",
)
@@ -38,13 +37,12 @@ def test_check_blob_access_success(self, blob_endpoint):
assert "mycontainer" in message
def test_check_blob_access_401_unauthorized(self, blob_endpoint):
- class Err401(Exception):
- status_code = 401
+ error = HttpResponseError(message="Unauthorized")
+ error.status_code = 401
- with patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- side_effect=Err401("Unauthorized"),
- ):
+ with patch("cfa.dataops.catalog.BlobServiceClient") as mock_bsc:
+ mock_container = mock_bsc.return_value.get_container_client.return_value
+ mock_container.get_container_properties.side_effect = error
has_access, message = blob_endpoint.check_blob_access()
assert has_access is False
@@ -52,13 +50,12 @@ class Err401(Exception):
assert "credentials" in message.lower()
def test_check_blob_access_403_forbidden(self, blob_endpoint):
- class Err403(Exception):
- status_code = 403
+ error = HttpResponseError(message="Access denied")
+ error.status_code = 403
- with patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- side_effect=Err403("Access denied"),
- ):
+ with patch("cfa.dataops.catalog.BlobServiceClient") as mock_bsc:
+ mock_container = mock_bsc.return_value.get_container_client.return_value
+ mock_container.get_container_properties.side_effect = error
has_access, message = blob_endpoint.check_blob_access()
assert has_access is False
@@ -66,13 +63,11 @@ class Err403(Exception):
assert "permissions" in message.lower()
def test_check_blob_access_resource_not_found(self, blob_endpoint):
- class Err404(Exception):
- status_code = 404
-
- with patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- side_effect=Err404("Container not found"),
- ):
+ with patch("cfa.dataops.catalog.BlobServiceClient") as mock_bsc:
+ mock_container = mock_bsc.return_value.get_container_client.return_value
+ mock_container.get_container_properties.side_effect = ResourceNotFoundError(
+ "Container not found"
+ )
has_access, message = blob_endpoint.check_blob_access()
assert has_access is False
@@ -80,20 +75,22 @@ class Err404(Exception):
assert "mycontainer" in message
def test_check_blob_access_authentication_error(self, blob_endpoint):
- with patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- side_effect=Exception("credential unavailable"),
- ):
+ with patch("cfa.dataops.catalog.BlobServiceClient") as mock_bsc:
+ mock_container = mock_bsc.return_value.get_container_client.return_value
+ mock_container.get_container_properties.side_effect = (
+ ClientAuthenticationError("credential unavailable")
+ )
has_access, message = blob_endpoint.check_blob_access()
assert has_access is False
assert "Authentication failed" in message
def test_check_blob_access_generic_exception(self, blob_endpoint):
- with patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- side_effect=Exception("Something went wrong"),
- ):
+ with patch("cfa.dataops.catalog.BlobServiceClient") as mock_bsc:
+ mock_container = mock_bsc.return_value.get_container_client.return_value
+ mock_container.get_container_properties.side_effect = Exception(
+ "Something went wrong"
+ )
has_access, message = blob_endpoint.check_blob_access()
assert has_access is False
@@ -215,28 +212,22 @@ def test_get_dataframe_fails_without_access(self, blob_endpoint, mocker):
class TestGetVersionBlobsWithAccessCheck:
"""Tests for _get_version_blobs with access checks."""
- def test_get_version_blobs_ledger_fails_without_access(self, mocker):
- ledger_location = {
- "account": "account_test",
- "container": "container_test",
- "prefix": "_access/test/ledger/",
- }
- ledger_endpoint = BlobEndpoint(
+ def test_get_version_blobs_fails_without_access(self, mocker):
+ endpoint = BlobEndpoint(
account="myaccount",
container="mycontainer",
- prefix="_access/test/ledger",
- ledger_location=ledger_location,
- ns="ledger_endpoint",
+ prefix="test/prefix",
+ ns="test.endpoint",
)
mocker.patch.object(
- ledger_endpoint,
+ endpoint,
"verify_blob_access",
side_effect=RuntimeError("Cannot access Blob storage. Access denied"),
)
mock_walk = mocker.patch("cfa.dataops.catalog.walk_blobs_in_container")
with pytest.raises(RuntimeError) as exc_info:
- ledger_endpoint._get_version_blobs()
+ endpoint._get_version_blobs()
assert "Cannot access Blob storage" in str(exc_info.value)
mock_walk.assert_not_called()
diff --git a/tests/test_blob_endpoint_download.py b/tests/test_blob_endpoint_download.py
index b8673e8..6e6f543 100644
--- a/tests/test_blob_endpoint_download.py
+++ b/tests/test_blob_endpoint_download.py
@@ -15,60 +15,14 @@ def blob_endpoint(mocker, mock_write_blob_stream):
"cfa.dataops.catalog.write_blob_stream",
mock_write_blob_stream,
)
- ledger_location = {
- "account": "account_test",
- "container": "container_test",
- "prefix": "_access/test/ledger/",
- }
return BlobEndpoint(
account="account_test",
container="container_test",
prefix="test/prefix",
- ledger_location=ledger_location,
ns="test.endpoint",
)
-def test_get_version_blobs_ledger_returns_none_version(mocker, mock_write_blob_stream):
- """Ledger endpoints should not fail when no resolved version is set."""
- mocker.patch(
- "cfa.dataops.catalog.write_blob_stream",
- mock_write_blob_stream,
- )
- ledger_endpoint = BlobEndpoint(
- account="account_test",
- container="container_test",
- prefix="_access/test/ledger",
- ledger_location={
- "account": "account_test",
- "container": "container_test",
- "prefix": "_access/test/ledger/",
- },
- ns="ledger_endpoint",
- )
- mocker.patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- return_value=[
- {
- "name": "_access/test/ledger/older.json",
- "creation_time": "2025-01-01T12:00:00",
- },
- {
- "name": "_access/test/ledger/newer.json",
- "creation_time": "2025-01-02T12:00:00",
- },
- ],
- )
-
- blobs, version = ledger_endpoint._get_version_blobs()
-
- assert version is None
- assert [blob["name"] for blob in blobs] == [
- "_access/test/ledger/older.json",
- "_access/test/ledger/newer.json",
- ]
-
-
class TestDownloadVersionToLocal:
"""Tests for the download_version_to_local method"""
@@ -401,53 +355,6 @@ def mock_read_blob_stream(blob_url, account_name, container_name):
assert os.path.exists(expected_file)
assert os.path.isfile(expected_file)
- def test_download_version_to_local_no_ledger_entry_when_not_written(
- self, mocker, blob_endpoint
- ):
- """Test that no ledger entry is created when no files are written"""
- test_content = b"test content"
-
- def mock_read_blob_stream(blob_url, account_name, container_name):
- return test_content
-
- mocker.patch(
- "cfa.dataops.catalog.read_blob_stream",
- side_effect=mock_read_blob_stream,
- )
-
- mocker.patch.object(
- blob_endpoint,
- "_get_version_blobs",
- return_value=(
- [
- {
- "name": "test/prefix/2025-01-01T12-00-00/data.csv",
- "creation_time": "2025-01-01T12:00:00",
- }
- ],
- "2025-01-01T12-00-00",
- ),
- )
-
- # Mock ledger_entry to track if it was called
- mock_ledger = mocker.patch.object(blob_endpoint, "ledger_entry")
-
- with tempfile.TemporaryDirectory() as tmpdir:
- # Create the file beforehand
- expected_file = os.path.join(tmpdir, "2025-01-01T12-00-00", "data.csv")
- os.makedirs(os.path.dirname(expected_file), exist_ok=True)
- with open(expected_file, "wb") as f:
- f.write(b"existing content")
-
- blob_endpoint.download_version_to_local(
- local_path=tmpdir,
- version_spec="==2025-01-01T12-00-00",
- force=False,
- )
-
- # Verify ledger entry was NOT called
- mock_ledger.assert_not_called()
-
def test_download_version_to_local_mixed_new_and_existing_files(
self, mocker, blob_endpoint
):
diff --git a/tests/test_blob_endpoint_save_methods.py b/tests/test_blob_endpoint_save_methods.py
index 216f51c..6ef30a6 100644
--- a/tests/test_blob_endpoint_save_methods.py
+++ b/tests/test_blob_endpoint_save_methods.py
@@ -18,16 +18,10 @@ def blob_endpoint(mocker, mock_write_blob_stream):
"cfa.dataops.catalog.write_blob_stream",
mock_write_blob_stream,
)
- ledger_location = {
- "account": "account_test",
- "container": "container_test",
- "prefix": "_access/test/ledger/",
- }
return BlobEndpoint(
account="account_test",
container="container_test",
prefix="test/prefix",
- ledger_location=ledger_location,
ns="test.endpoint",
)
diff --git a/tests/test_catalog_additional.py b/tests/test_catalog_additional.py
index 92e9d0f..b73645a 100644
--- a/tests/test_catalog_additional.py
+++ b/tests/test_catalog_additional.py
@@ -23,7 +23,6 @@ def _make_blob_endpoint(ns: str = "tests.example.load") -> BlobEndpoint:
account="acct",
container="container",
prefix="base/prefix/",
- ledger_location={"account": "lacct", "container": "lcont", "prefix": "_access"},
ns=ns,
)
@@ -72,13 +71,10 @@ def test_get_all_catalogs_reraises_non_namespace_import_error(mocker):
get_all_catalogs()
-def test_blob_endpoint_strips_trailing_slash_and_ledger_flag():
+def test_blob_endpoint_strips_trailing_slash():
normal = _make_blob_endpoint(ns="tests.example.load")
- ledger = _make_blob_endpoint(ns="ledger_endpoint")
assert normal.prefix == "base/prefix"
- assert normal.is_ledger is False
- assert ledger.is_ledger is True
def test_write_blob_splits_partitions_with_suffix(mocker):
@@ -120,24 +116,6 @@ def test_get_versions_returns_desc_sorted_names(mocker):
assert versions == ["2026-01-01T00-00-00", "2025-01-01T00-00-00"]
-def test_get_version_blobs_for_ledger_uses_prefix_without_version(mocker):
- endpoint = _make_blob_endpoint(ns="ledger_endpoint")
- mocker.patch("cfa.dataops.catalog.check_ext_env", return_value=True)
- walk_mock = mocker.patch(
- "cfa.dataops.catalog.walk_blobs_in_container",
- return_value=[
- {"name": "_access/2026-01-01.jsonl", "creation_time": 2},
- {"name": "_access/2025-12-31.jsonl", "creation_time": 1},
- ],
- )
-
- blobs, version = endpoint._get_version_blobs(print_version=False)
-
- assert version is None
- assert [b["creation_time"] for b in blobs] == [1, 2]
- assert walk_mock.call_args.kwargs["name_starts_with"] == "base/prefix/"
-
-
def test_get_dataframe_raises_for_invalid_output(mocker):
endpoint = _make_blob_endpoint()
mocker.patch("cfa.dataops.catalog.check_ext_env", return_value=True)
@@ -146,15 +124,6 @@ def test_get_dataframe_raises_for_invalid_output(mocker):
endpoint.get_dataframe(output="arrow")
-def test_ledger_entry_noop_for_ledger_endpoint(mocker):
- endpoint = _make_blob_endpoint(ns="ledger_endpoint")
- write_mock = mocker.patch("cfa.dataops.catalog.write_blob_stream")
-
- endpoint.ledger_entry(action="read")
-
- write_mock.assert_not_called()
-
-
def test_resolve_version_returns_empty_metadata_when_no_match(mocker):
endpoint = _make_blob_endpoint()
mocker.patch.object(
diff --git a/tests/test_command.py b/tests/test_command.py
index 7de7f85..a8d48b0 100644
--- a/tests/test_command.py
+++ b/tests/test_command.py
@@ -37,7 +37,6 @@ def mock_datacat(mocker):
extract=mock_extract,
load=mock_load,
stage_01=mock_stage_01,
- _ledger_endpoint=MagicMock(),
)
# Create test namespace
@@ -85,8 +84,6 @@ def test_get_stages_list_valid_dataset(self, mock_datacat, capsys):
assert "extract" in result
assert "load" in result
assert "stage_01" in result
- assert "_ledger_endpoint" not in result # Should be filtered out
-
# Verify stages are sorted
assert result == sorted(result)
@@ -268,8 +265,8 @@ def test_save_data_locally_prints_tree_on_download(self, mock_datacat, mocker):
assert "/tmp/downloads" in output
assert "tree output" in output
- def test_save_data_locally_reports_existing_download(self, mock_datacat, mocker):
- """Test save_data_locally reports when the dataset already exists"""
+ def test_save_data_locally_notifies_existing_download(self, mock_datacat, mocker):
+ """Test save_data_locally notifies when the dataset already exists"""
mock_datacat.test.dataset1.load.download_version_to_local.return_value = False
mocker.patch(
"cfa.dataops.command.ArgumentParser.parse_args",
diff --git a/tests/test_create_catalog.py b/tests/test_create_catalog.py
index 8e0e39b..b3396aa 100644
--- a/tests/test_create_catalog.py
+++ b/tests/test_create_catalog.py
@@ -86,7 +86,7 @@ def create_catalog_programmatically(
)
# Copy module directories
- for mod_i in ["datasets", "reports", "workflows"]:
+ for mod_i in ["datasets", "workflows"]:
shutil.copytree(
os.path.join(repo_files_dirs, mod_i),
os.path.join(library_modules_root, mod_i),
@@ -156,7 +156,6 @@ def test_create_basic_catalog(catalog_parent):
# Check module directories
assert catalog_module_path.join("datasets").check(dir=True)
- assert catalog_module_path.join("reports").check(dir=True)
assert catalog_module_path.join("workflows").check(dir=True)
@@ -282,29 +281,6 @@ def test_datasets_directory_structure(catalog_parent):
)
-def test_reports_directory_structure(catalog_parent):
- """Test that the reports directory is properly created."""
- unique_name = "reports_test"
- catalog_location = catalog_parent.join("reports_test")
-
- success = create_catalog_programmatically(
- unique_name=unique_name,
- location=str(catalog_location),
- expanded_repo_for_cfa=False,
- )
-
- assert success is True
-
- reports_path = catalog_location.join("cfa", "catalog", unique_name, "reports")
- assert reports_path.check(dir=True)
- assert reports_path.join("__init__.py").check(file=True)
-
- # Check for examples directory
- examples_path = reports_path.join("examples")
- assert examples_path.check(dir=True)
- assert examples_path.join("basics.ipynb").check(file=True)
-
-
def test_workflows_directory_structure(catalog_parent):
"""Test that the workflows directory is properly created."""
unique_name = "workflows_test"
@@ -457,7 +433,7 @@ def test_file_copying_operations(catalog_parent):
assert gitignore_path.check(file=True)
# Verify module directories were copied with their contents
- for module_dir in ["datasets", "reports", "workflows"]:
+ for module_dir in ["datasets", "workflows"]:
module_path = catalog_module_path.join(module_dir)
assert module_path.check(dir=True)
assert module_path.join("__init__.py").check(file=True)
diff --git a/tests/test_datasets_catalog.py b/tests/test_datasets_catalog.py
index eaf360e..46a8ad1 100644
--- a/tests/test_datasets_catalog.py
+++ b/tests/test_datasets_catalog.py
@@ -25,7 +25,6 @@ def content_as_bytes(self):
def test_dict_to_sn(simple_dataset_ns_map):
defaults = {
"storage": {"account": "account", "container": "container"},
- "access_ledger": {"path": "some/path/"},
}
result = dict_to_sn(simple_dataset_ns_map, defaults)
print(result.space.example.config)
@@ -381,12 +380,6 @@ def test_datasets_catalog_get_dataframe_pl_lazy(
"2025-06-03T17-56-50",
),
)
- mocker.patch.object(
- datacat.tests.etl_test.load,
- "ledger_entry",
- return_value=None,
- )
-
# Avoid real auth wiring during test
mocker.patch("cfa.dataops.catalog.ManagedIdentityCredential", return_value=object())
mocker.patch(
diff --git a/tests/test_reporting_catalog.py b/tests/test_reporting_catalog.py
deleted file mode 100644
index f0b6656..0000000
--- a/tests/test_reporting_catalog.py
+++ /dev/null
@@ -1,477 +0,0 @@
-from types import SimpleNamespace
-
-import pytest
-
-from cfa.dataops.reporting.catalog import (
- NotebookEndpoint,
- nb_to_html,
- remove_ws_and_nonalpha,
- report_dict_to_sn,
- retitle_notebook,
-)
-
-
-class TestRemoveWsAndNonalpha:
- """Test the remove_ws_and_nonalpha function."""
-
- def test_remove_whitespace_and_special_chars(self):
- """Test removing whitespace and special characters."""
- result = remove_ws_and_nonalpha("Hello World! 123.ipynb")
- assert result == "hello_world_123_ipynb"
-
- def test_remove_spaces_and_dots(self):
- """Test removing spaces and dots."""
- result = remove_ws_and_nonalpha("test file.name.ipynb")
- assert result == "test_file_name_ipynb"
-
- def test_empty_string(self):
- """Test with empty string."""
- result = remove_ws_and_nonalpha("")
- assert result == ""
-
- def test_only_alphanumeric(self):
- """Test with only alphanumeric characters."""
- result = remove_ws_and_nonalpha("test123")
- assert result == "test123"
-
- def test_underscores_preserved(self):
- """Test that underscores are preserved."""
- result = remove_ws_and_nonalpha("test_file_name")
- assert result == "test_file_name"
-
-
-class TestRetitleNotebook:
- """Test the retitle_notebook function."""
-
- def test_retitle_notebook_success(self, mocker):
- """Test successfully retitling a notebook."""
- # Mock notebook content - create a proper notebook object with metadata attribute
- mock_notebook = SimpleNamespace()
- mock_notebook.metadata = {"title": "Old Title"}
- mock_notebook.cells = []
-
- # Mock file operations
- mock_exists = mocker.patch("os.path.exists", return_value=True)
- mock_nbformat_read = mocker.patch("nbformat.read", return_value=mock_notebook)
- mock_nbformat_write = mocker.patch("nbformat.write")
- _ = mocker.patch(
- "builtins.open", mocker.mock_open(read_data="notebook_content")
- )
-
- # Test the function
- retitle_notebook("test.ipynb", "New Title")
-
- # Verify calls
- mock_exists.assert_called_once_with("test.ipynb")
- mock_nbformat_read.assert_called_once()
- mock_nbformat_write.assert_called_once()
- assert mock_notebook.metadata["title"] == "New Title"
-
- def test_retitle_notebook_file_not_exists(self, mocker):
- """Test retitle_notebook with non-existent file."""
- mocker.patch("os.path.exists", return_value=False)
-
- with pytest.raises(AssertionError, match="does not exist"):
- retitle_notebook("nonexistent.ipynb", "New Title")
-
- def test_retitle_notebook_wrong_extension(self, mocker):
- """Test retitle_notebook with wrong file extension."""
- mocker.patch("os.path.exists", return_value=True)
-
- with pytest.raises(AssertionError, match="must be a .ipynb file"):
- retitle_notebook("test.txt", "New Title")
-
-
-class TestNbToHtml:
- """Test the nb_to_html function."""
-
- def test_nb_to_html_success(self, mocker):
- """Test successful notebook to HTML conversion."""
- mock_html_content = "Test HTML"
- mock_exporter = mocker.MagicMock()
- mock_exporter.from_filename.return_value = (mock_html_content, {})
-
- mocker.patch(
- "cfa.dataops.reporting.catalog.HTMLExporter",
- return_value=mock_exporter,
- )
-
- result = nb_to_html("test.ipynb")
-
- assert result == mock_html_content
- mock_exporter.from_filename.assert_called_once_with("test.ipynb")
-
-
-class TestNotebookEndpoint:
- """Test the NotebookEndpoint class."""
-
- @pytest.fixture
- def notebook_endpoint(self):
- """Create a NotebookEndpoint instance for testing."""
- return NotebookEndpoint("test_notebook.ipynb")
-
- def test_init(self, notebook_endpoint):
- """Test NotebookEndpoint initialization."""
- assert notebook_endpoint.notebook_path == "test_notebook.ipynb"
-
- def test_get_params(self, mocker, notebook_endpoint):
- """Test getting notebook parameters."""
- mock_params = {"param1": "value1", "param2": "value2"}
- mock_inspect = mocker.patch(
- "papermill.inspect_notebook", return_value=mock_params
- )
-
- result = notebook_endpoint.get_params()
-
- assert result == mock_params
- mock_inspect.assert_called_once_with("test_notebook.ipynb")
-
- def test_print_params(self, mocker, notebook_endpoint):
- """Test printing notebook parameters."""
- mock_params = {"param1": "value1", "param2": "value2"}
- mocker.patch("papermill.inspect_notebook", return_value=mock_params)
- mock_pprint = mocker.patch("cfa.dataops.reporting.catalog.pprint")
-
- notebook_endpoint.print_params()
-
- mock_pprint.assert_called_once_with(mock_params)
-
- def test_nb_to_html_str(self, mocker, notebook_endpoint):
- """Test converting notebook to HTML string."""
- mock_html_content = "Test HTML"
-
- # Mock TemporaryDirectory
- mock_temp_dir = mocker.patch("cfa.dataops.reporting.catalog.TemporaryDirectory")
- mock_temp_dir.return_value.__enter__.return_value = "/tmp/test"
-
- # Mock papermill execution
- mock_execute = mocker.patch("papermill.execute_notebook")
-
- # Mock nb_to_html function
- mock_nb_to_html = mocker.patch(
- "cfa.dataops.reporting.catalog.nb_to_html",
- return_value=mock_html_content,
- )
-
- # Mock os.path.join
- mocker.patch("os.path.join", return_value="/tmp/test/output.ipynb")
-
- result = notebook_endpoint.nb_to_html_str(param1="value1")
-
- assert result == mock_html_content
- mock_execute.assert_called_once_with(
- input_path="test_notebook.ipynb",
- output_path="/tmp/test/output.ipynb",
- parameters={"param1": "value1"},
- progress_bar=True,
- )
- mock_nb_to_html.assert_called_once_with("/tmp/test/output.ipynb")
-
- def test_nb_to_html_str_with_retitle(self, mocker, notebook_endpoint):
- """Test converting notebook to HTML string with retitling."""
- mock_html_content = "Test HTML"
-
- # Mock TemporaryDirectory
- mock_temp_dir = mocker.patch("cfa.dataops.reporting.catalog.TemporaryDirectory")
- mock_temp_dir.return_value.__enter__.return_value = "/tmp/test"
-
- # Mock papermill execution
- _ = mocker.patch("papermill.execute_notebook")
-
- # Mock retitle_notebook
- mock_retitle = mocker.patch("cfa.dataops.reporting.catalog.retitle_notebook")
-
- # Mock nb_to_html function
- _ = mocker.patch(
- "cfa.dataops.reporting.catalog.nb_to_html",
- return_value=mock_html_content,
- )
-
- # Mock os.path.join
- mocker.patch("os.path.join", return_value="/tmp/test/output.ipynb")
-
- result = notebook_endpoint.nb_to_html_str(nb_title="New Title")
-
- assert result == mock_html_content
- mock_retitle.assert_called_once_with("/tmp/test/output.ipynb", "New Title")
-
- def test_nb_to_html_file(self, mocker, notebook_endpoint):
- """Test converting notebook to HTML file."""
- mock_html_content = "Test HTML"
-
- # Mock the nb_to_html_str method
- mock_nb_to_html_str = mocker.patch.object(
- notebook_endpoint, "nb_to_html_str", return_value=mock_html_content
- )
-
- # Mock file operations
- mock_makedirs = mocker.patch("os.makedirs")
- _ = mocker.patch("os.path.dirname", return_value="/path/to")
- _ = mocker.patch(
- "os.path.abspath", return_value="/absolute/path/to/output.html"
- )
- mock_file_open = mocker.patch("builtins.open", mocker.mock_open())
- mock_print = mocker.patch("builtins.print")
-
- # Test the function
- notebook_endpoint.nb_to_html_file(
- "/path/to/output.html", nb_title="Test Title", param1="value1"
- )
-
- # Verify calls
- mock_nb_to_html_str.assert_called_once_with(
- nb_title="Test Title", param1="value1"
- )
- mock_makedirs.assert_called_once_with("/path/to", exist_ok=True)
- mock_file_open.assert_called_once_with(
- "/path/to/output.html", "w", encoding="utf-8"
- )
- mock_print.assert_called_once_with(
- "HTML report saved to /absolute/path/to/output.html"
- )
-
- def test_nb_to_html_file_wrong_extension(self, notebook_endpoint):
- """Test nb_to_html_file with wrong file extension."""
- with pytest.raises(AssertionError, match="must end with .html"):
- notebook_endpoint.nb_to_html_file("/path/to/output.txt")
-
- def test_nb_to_html_blob(self, mocker, notebook_endpoint):
- """Test converting notebook to HTML blob."""
- mock_html_content = "Test HTML"
-
- # Mock the nb_to_html_str method
- mock_nb_to_html_str = mocker.patch.object(
- notebook_endpoint, "nb_to_html_str", return_value=mock_html_content
- )
-
- # Mock write_blob_stream
- mock_write_blob = mocker.patch(
- "cfa.dataops.reporting.catalog.write_blob_stream"
- )
-
- # Test the function
- notebook_endpoint.nb_to_html_blob(
- blob_account="test_account",
- blob_container="test_container",
- blob_path="reports/output.html",
- nb_title="Test Title",
- param1="value1",
- )
-
- # Verify calls
- mock_nb_to_html_str.assert_called_once_with(
- nb_title="Test Title", param1="value1"
- )
- mock_write_blob.assert_called_once_with(
- account_name="test_account",
- container_name="test_container",
- blob_url="reports/output.html",
- data=mock_html_content.encode("utf-8"),
- )
-
- def test_nb_to_html_blob_wrong_extension(self, notebook_endpoint):
- """Test nb_to_html_blob with wrong file extension."""
- with pytest.raises(AssertionError, match="must end with .html"):
- notebook_endpoint.nb_to_html_blob(
- blob_account="test_account",
- blob_container="test_container",
- blob_path="reports/output.txt",
- )
-
-
-class TestReportDictToSn:
- """Test the report_dict_to_sn function."""
-
- def test_simple_dict_conversion(self):
- """Test converting a simple dictionary to SimpleNamespace."""
- test_dict = {"key1": "value1", "key2": "value2"}
- result = report_dict_to_sn(test_dict)
-
- assert isinstance(result, SimpleNamespace)
- assert result.key1 == "value1"
- assert result.key2 == "value2"
-
- def test_nested_dict_conversion(self):
- """Test converting nested dictionaries to SimpleNamespace."""
- test_dict = {
- "level1": {
- "level2": {"key": "value"},
- "simple_key": "simple_value",
- }
- }
- result = report_dict_to_sn(test_dict)
-
- assert isinstance(result, SimpleNamespace)
- assert isinstance(result.level1, SimpleNamespace)
- assert isinstance(result.level1.level2, SimpleNamespace)
- assert result.level1.level2.key == "value"
- assert result.level1.simple_key == "simple_value"
-
- def test_notebook_endpoint_creation(self):
- """Test that .ipynb files create NotebookEndpoint instances."""
- test_dict = {
- "reports": {
- "example_ipynb": "/path/to/notebook.ipynb",
- "regular_key": "regular_value",
- }
- }
- result = report_dict_to_sn(test_dict)
-
- assert isinstance(result, SimpleNamespace)
- assert isinstance(result.reports, SimpleNamespace)
- assert isinstance(result.reports.example_ipynb, NotebookEndpoint)
- assert result.reports.example_ipynb.notebook_path == "/path/to/notebook.ipynb"
- assert result.reports.regular_key == "regular_value"
-
- def test_list_conversion(self):
- """Test converting lists within dictionaries."""
- # The report_dict_to_sn function only processes dictionaries at the top level
- # Lists are processed recursively only if they contain dictionaries
- test_dict = {
- "list_key": [
- {"nested_key": "nested_value"},
- ]
- }
- result = report_dict_to_sn(test_dict)
-
- assert isinstance(result, SimpleNamespace)
- assert isinstance(result.list_key, list)
- assert len(result.list_key) == 1
- assert isinstance(result.list_key[0], SimpleNamespace)
- assert result.list_key[0].nested_key == "nested_value"
-
- def test_mixed_content_conversion(self):
- """Test converting mixed content types."""
- test_dict = {
- "notebook_example_ipynb": "/path/to/example.ipynb",
- "nested_dict": {
- "inner_notebook_ipynb": "/path/to/inner.ipynb",
- "inner_list": [
- {"dict_in_list": "value"},
- ],
- },
- "simple_value": "test",
- "number_value": 42,
- }
- result = report_dict_to_sn(test_dict)
-
- # Check notebook endpoint creation
- assert isinstance(result.notebook_example_ipynb, NotebookEndpoint)
- assert result.notebook_example_ipynb.notebook_path == "/path/to/example.ipynb"
-
- # Check nested structure
- assert isinstance(result.nested_dict, SimpleNamespace)
- assert isinstance(result.nested_dict.inner_notebook_ipynb, NotebookEndpoint)
- assert (
- result.nested_dict.inner_notebook_ipynb.notebook_path
- == "/path/to/inner.ipynb"
- )
-
- # Check list handling
- assert isinstance(result.nested_dict.inner_list, list)
- assert isinstance(result.nested_dict.inner_list[0], SimpleNamespace)
- assert result.nested_dict.inner_list[0].dict_in_list == "value"
-
- # Check simple values
- assert result.simple_value == "test"
- assert result.number_value == 42
-
- def test_empty_dict_conversion(self):
- """Test converting an empty dictionary."""
- result = report_dict_to_sn({})
- assert isinstance(result, SimpleNamespace)
- assert len(vars(result)) == 0
-
-
-class TestReportingCatalogIntegration:
- """Integration tests for the reporting catalog functionality."""
-
- def test_report_namespace_creation(self, mocker):
- """Test creating a report namespace similar to dataset catalog."""
- # Mock the glob.glob to return some test notebook paths
- mock_glob = mocker.patch("glob.glob")
- mock_glob.return_value = [
- "/path/to/reporting/reports/examples/basic_ipynb",
- "/path/to/reporting/reports/analysis/advanced_ipynb",
- ]
-
- # Mock os.path.split and os.path.join
- mocker.patch(
- "os.path.split",
- return_value=("/path/to/reporting", "catalog.py"),
- )
- mocker.patch("os.path.join")
-
- # Test that we can create a namespace structure
- test_report_map = {
- "examples": {
- "basic_ipynb": "/path/to/basic.ipynb",
- "tutorial_ipynb": "/path/to/tutorial.ipynb",
- },
- "analysis": {
- "advanced_ipynb": "/path/to/advanced.ipynb",
- },
- }
-
- result = report_dict_to_sn(test_report_map)
-
- # Verify structure
- assert isinstance(result, SimpleNamespace)
- assert isinstance(result.examples, SimpleNamespace)
- assert isinstance(result.analysis, SimpleNamespace)
-
- # Verify notebook endpoints
- assert isinstance(result.examples.basic_ipynb, NotebookEndpoint)
- assert isinstance(result.examples.tutorial_ipynb, NotebookEndpoint)
- assert isinstance(result.analysis.advanced_ipynb, NotebookEndpoint)
-
- # Verify paths
- assert result.examples.basic_ipynb.notebook_path == "/path/to/basic.ipynb"
- assert result.examples.tutorial_ipynb.notebook_path == "/path/to/tutorial.ipynb"
- assert result.analysis.advanced_ipynb.notebook_path == "/path/to/advanced.ipynb"
-
- def test_end_to_end_notebook_execution(self, mocker):
- """Test end-to-end notebook execution workflow."""
- # Create a test notebook endpoint
- notebook_endpoint = NotebookEndpoint("/path/to/test.ipynb")
-
- # Mock all the dependencies
- mock_temp_dir = mocker.patch("cfa.dataops.reporting.catalog.TemporaryDirectory")
- mock_temp_dir.return_value.__enter__.return_value = "/tmp/test"
-
- mock_execute = mocker.patch("papermill.execute_notebook")
- mock_retitle = mocker.patch("cfa.dataops.reporting.catalog.retitle_notebook")
- mock_nb_to_html = mocker.patch(
- "cfa.dataops.reporting.catalog.nb_to_html",
- return_value="Test Report",
- )
- mock_write_blob = mocker.patch(
- "cfa.dataops.reporting.catalog.write_blob_stream"
- )
- mocker.patch("os.path.join", return_value="/tmp/test/output.ipynb")
-
- # Execute the workflow
- notebook_endpoint.nb_to_html_blob(
- blob_account="test_account",
- blob_container="reports",
- blob_path="test_report.html",
- nb_title="Test Report",
- param1="test_value",
- param2=42,
- )
-
- # Verify the workflow
- mock_execute.assert_called_once_with(
- input_path="/path/to/test.ipynb",
- output_path="/tmp/test/output.ipynb",
- parameters={"param1": "test_value", "param2": 42},
- progress_bar=True,
- )
- mock_retitle.assert_called_once_with("/tmp/test/output.ipynb", "Test Report")
- mock_nb_to_html.assert_called_once_with("/tmp/test/output.ipynb")
- mock_write_blob.assert_called_once_with(
- account_name="test_account",
- container_name="reports",
- blob_url="test_report.html",
- data=b"Test Report",
- )
diff --git a/tests/test_type_stubs.py b/tests/test_type_stubs.py
index 2f71bc9..d7a765c 100644
--- a/tests/test_type_stubs.py
+++ b/tests/test_type_stubs.py
@@ -49,13 +49,6 @@ def _representative_catalog_stub(dataset_config: Path) -> str:
},
},
},
- report_ns_map={
- "public": {
- "examples": {
- "basic_report": "/reports/basic_report.ipynb",
- },
- },
- },
)
@@ -80,7 +73,6 @@ def test_render_catalog_stub_uses_real_dataset_paths_and_stages(tmp_path):
},
},
},
- report_ns_map={},
)
assert "class _DataCatalogPublicStfNhsnHrdPrelimDataset(DatasetEndpoint):" in stub
@@ -96,24 +88,6 @@ def test_render_catalog_stub_uses_real_dataset_paths_and_stages(tmp_path):
assert "load: BlobEndpoint" not in public_namespace
-def test_render_catalog_stub_uses_real_report_paths():
- stub = render_catalog_stub(
- dataset_ns_map={},
- report_ns_map={
- "public": {
- "examples": {
- "basic_report": "/reports/basic_report.ipynb",
- },
- },
- },
- )
-
- assert (
- "class _ReportCatalogPublicExamplesBasicReportReport(NotebookEndpoint):" in stub
- )
- assert "basic_report: _ReportCatalogPublicExamplesBasicReportReport" in stub
-
-
def test_render_init_stub_outputs_parseable_python_syntax():
ast.parse(render_init_stub())
@@ -124,7 +98,6 @@ def test_render_catalog_stub_rejects_non_identifier_segments(tmp_path):
with pytest.raises(ValueError, match="not a valid Python identifier"):
render_catalog_stub(
dataset_ns_map={"public-data": {"example": str(dataset_config)}},
- report_ns_map={},
)
@@ -135,7 +108,6 @@ def test_write_catalog_stubs_creates_project_local_stub_tree(tmp_path):
written = write_catalog_stubs(
output_root,
dataset_ns_map={"public": {"example": str(dataset_config)}},
- report_ns_map={},
)
assert written == [
diff --git a/tests/test_utils_misc.py b/tests/test_utils_misc.py
index e112b7c..7a87fc8 100644
--- a/tests/test_utils_misc.py
+++ b/tests/test_utils_misc.py
@@ -14,24 +14,6 @@ def test_remove_ws_and_nonalpha_normalizes_text():
)
-def test_get_fs_ns_map_basic_without_endpoint_func(tmp_path):
- reports = tmp_path / "reports"
- reports.mkdir()
- top = reports / "My Notebook.ipynb"
- nested_dir = reports / "Team Alpha"
- nested_dir.mkdir()
- nested = nested_dir / "Quarterly.Report.ipynb"
- top.write_text("{}")
- nested.write_text("{}")
-
- fs_map = utils.get_fs_ns_map(str(reports), "ipynb")
-
- assert "my_notebook" in fs_map
- assert fs_map["my_notebook"] == str(top)
- assert "team_alpha" in fs_map
- assert fs_map["team_alpha"]["quarterly_report"] == str(nested)
-
-
def test_get_fs_ns_map_with_endpoint_func(tmp_path):
datasets = tmp_path / "datasets"
datasets.mkdir()
@@ -57,24 +39,6 @@ def test_get_fs_ns_map_endpoint_func_must_return_string(tmp_path):
utils.get_fs_ns_map(str(datasets), "toml", endpoint_func=lambda _: 123)
-def test_get_dataset_dot_path_flattens_nested_map():
- endpoint_map = {
- "space": {
- "example": "configs/example.toml",
- "nested": {"report": "reports/q1.ipynb"},
- "skip": "not_a_dataset.txt",
- },
- "root": "configs/root.toml",
- }
-
- paths = utils.get_dataset_dot_path(endpoint_map)
-
- assert "space.example" in paths
- assert "space.nested.report" in paths
- assert "root" in paths
- assert "space.skip" not in paths
-
-
def test_get_timestamp_formats(mocker):
fixed = datetime(2026, 7, 24, 10, 11, 12)
dt_cls = mocker.patch("cfa.dataops.utils.datetime")
diff --git a/typings/cfa/dataops/__init__.pyi b/typings/cfa/dataops/__init__.pyi
index 1b8bd48..ed453a0 100644
--- a/typings/cfa/dataops/__init__.pyi
+++ b/typings/cfa/dataops/__init__.pyi
@@ -1,5 +1,4 @@
from .catalog import datacat as datacat
-from .catalog import reportcat as reportcat
__version__: str
__all__: list[str]
diff --git a/typings/cfa/dataops/catalog.pyi b/typings/cfa/dataops/catalog.pyi
index 05efca0..3d2cbc4 100644
--- a/typings/cfa/dataops/catalog.pyi
+++ b/typings/cfa/dataops/catalog.pyi
@@ -21,14 +21,11 @@ class DatasetEndpoint:
defaults: dict[str, Any]
config: dict[str, Any]
__ns_str__: str
- _ledger_location: dict[str, Any]
class BlobEndpoint:
account: str
container: str
prefix: str
- ledger_location: dict[str, Any]
- is_ledger: bool
__ns_str__: str
def check_blob_access(self) -> tuple[bool, str]: ...
def verify_blob_access(self) -> None: ...
@@ -87,7 +84,6 @@ class BlobEndpoint:
version_spec: str | None = None,
selection: Literal["newest", "oldest"] = "newest",
) -> VersionMetadata: ...
- def ledger_entry(self, action: str) -> None: ...
def save_dataframe(
self,
df: pd.DataFrame | pl.DataFrame,
@@ -117,8 +113,4 @@ def dict_to_sn(
class DataCatalog(CatalogNamespace):
__namespace_list__: list[str]
-class ReportCatalog(CatalogNamespace):
- __namespace_list__: list[str]
-
datacat: DataCatalog
-reportcat: ReportCatalog
diff --git a/uv.lock b/uv.lock
index 9676b98..cc5e95b 100644
--- a/uv.lock
+++ b/uv.lock
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