Added loguru

poetry.lock

@@ -94,6 +94,21 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "loguru"
+version = "0.6.0"
+description = "Python logging made (stupidly) simple"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+colorama = {version = ">=0.3.4", markers = "sys_platform == \"win32\""}
+win32-setctime = {version = ">=1.0.0", markers = "sys_platform == \"win32\""}
+
+[package.extras]
+dev = ["sphinx-rtd-theme (>=0.4.3)", "sphinx-autobuild (>=0.7.1)", "Sphinx (>=4.1.1)", "isort (>=5.1.1)", "black (>=19.10b0)", "pytest-cov (>=2.7.1)", "pytest (>=4.6.2)", "tox (>=3.9.0)", "flake8 (>=3.7.7)", "docutils (==0.16)", "colorama (>=0.3.4)"]
+
 [[package]]
 name = "mypy-extensions"
 version = "0.4.3"
@@ -248,6 +263,17 @@ category = "main"
 optional = false
 python-versions = ">=3.7"
 
+[[package]]
+name = "win32-setctime"
+version = "1.1.0"
+description = "A small Python utility to set file creation time on Windows"
+category = "main"
+optional = false
+python-versions = ">=3.5"
+
+[package.extras]
+dev = ["black (>=19.3b0)", "pytest (>=4.6.2)"]
+
 [[package]]
 name = "zipp"
 version = "3.8.1"
@@ -263,7 +289,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7"
-content-hash = "c44b5e718866e498815a184650d98fd5e637b07246375d1e9fc4298a0125f0d6"
+content-hash = "6ca131347c47d90f6093f09ad7a6025b55535855e382770019f20e60c07b6c15"
 
 [metadata.files]
 attrs = [
@@ -363,6 +389,10 @@ iniconfig = [
     {file = "iniconfig-1.1.1-py2.py3-none-any.whl", hash = "sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3"},
     {file = "iniconfig-1.1.1.tar.gz", hash = "sha256:bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32"},
 ]
+loguru = [
+    {file = "loguru-0.6.0-py3-none-any.whl", hash = "sha256:4e2414d534a2ab57573365b3e6d0234dfb1d84b68b7f3b948e6fb743860a77c3"},
+    {file = "loguru-0.6.0.tar.gz", hash = "sha256:066bd06758d0a513e9836fd9c6b5a75bfb3fd36841f4b996bc60b547a309d41c"},
+]
 mypy-extensions = [
     {file = "mypy_extensions-0.4.3-py2.py3-none-any.whl", hash = "sha256:090fedd75945a69ae91ce1303b5824f428daf5a028d2f6ab8a299250a846f15d"},
     {file = "mypy_extensions-0.4.3.tar.gz", hash = "sha256:2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8"},
@@ -440,6 +470,10 @@ typing-extensions = [
     {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"},
     {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"},
 ]
+win32-setctime = [
+    {file = "win32_setctime-1.1.0-py3-none-any.whl", hash = "sha256:231db239e959c2fe7eb1d7dc129f11172354f98361c4fa2d6d2d7e278baa8aad"},
+    {file = "win32_setctime-1.1.0.tar.gz", hash = "sha256:15cf5750465118d6929ae4de4eb46e8edae9a5634350c01ba582df868e932cb2"},
+]
 zipp = [
     {file = "zipp-3.8.1-py3-none-any.whl", hash = "sha256:47c40d7fe183a6f21403a199b3e4192cca5774656965b0a4988ad2f8feb5f009"},
     {file = "zipp-3.8.1.tar.gz", hash = "sha256:05b45f1ee8f807d0cc928485ca40a07cb491cf092ff587c0df9cb1fd154848d2"},

pyproject.toml

@@ -8,6 +8,7 @@ authors = ["Jacob Hinkle <jacob.hinkle@jhink.org>"]
 python = "^3.7"
 click = "^8.1.3"
 colorama = "^0.4.5"
+loguru = "^0.6.0"
 
 [tool.poetry.dev-dependencies]
 black = "^22.8.0"

src/nancy/__init__.py

@@ -1,50 +1,4 @@
-import sqlite3
+import sys
 
 from . import store
 from .version import __version__
-
-
-def save_data(
-    destination_mapping,
-    desc=f"Provenance-tracking with nancy v{__version__}",
-):
-    """
-    A command-line interface to compute and save a set of outputs.
-
-    Ex:
-
-    .. code:
-        save_data({
-                "scores.csv": scores,
-                "checkpoints": checkpoint_dir,
-                "plots/learning_curve.pdf": learning_curve_plot,
-                "plots/test_roc.pdf": test_auc_plot,
-                "
-            },
-    """
-    import argparse
-    import os
-    import sys
-
-    parser = argparse.ArgumentParser(description=desc)
-    parser.add_argument(
-        "--out_dir",
-        "-o",
-        required=True,
-        help="Directory (will be created) in which to save all outputs",
-    )
-    args = parser.parse_args()
-
-    if os.path.exists(args.out_dir):
-        print(
-            f"Output directory {args.out_dir} exists. Refusing to overwrite.",
-            file=sys.stderr,
-        )
-        sys.exit(1)
-
-    # Create the output directory, back up the in-memory db to this location, an
-    # switch to it.
-    os.makedirs(args.out_dir, exist_ok=True)
-    persist_db(os.path.join(args.out_dir, "nancy.db"))
-
-    # Now we save the provided roots, and record their locations in _conn.data

src/nancy/cli/__init__.py

@@ -1,4 +1,5 @@
 import click
+from loguru import logger
 
 from ..version import __version__
 
@@ -30,8 +31,17 @@ def version():
 @click.group(
     cls=AliasedGroup,
     help=f"Composable provenance tracking for scientific data")
-def main():
+@click.option(
-    pass
+    "-L", "--log_level",
+    # https://loguru.readthedocs.io/en/stable/api/logger.html#levels
+    type=click.Choice(['CRITICAL', 'ERROR', 'WARNING', 'SUCCESS', 'INFO', 'DEBUG', 'TRACE']),
+    default='SUCCESS',
+    help='If given, print all output including debugging info.',
+)
+def main(log_level):
+    import sys
+    logger.remove()
+    logger.add(sys.stderr, level=log_level)
 #main.add_command(freeze)
 #main.add_command(thaw)
 main.add_command(diff.diff_cli, name='diff')

src/nancy/cli/diff.py

@@ -1,4 +1,5 @@
 import click
+from loguru import logger
 
 from .. import db, fs, store
 
@@ -91,6 +92,7 @@ def diff(store, filedir_path, show_hashes=False, use_color=True):
     help='If given, do not print any color output.',
 )
 def diff_cli(path, show_hashes, no_color):
+@logger.catch
     """Detect and describe changes to PATH
 
     PATH is a path to a file or directory inside an existing nancy store
@@ -116,4 +118,5 @@ def diff_cli(path, show_hashes, no_color):
     except FileNotFoundError as e:
         print(str(e), file=sys.stderr)
         sys.exit(1)
+    logger.success("Computed diff")
 

src/nancy/cli/record.py

@@ -1,4 +1,5 @@
 import click
+from loguru import logger
 
 from .. import store
 
@@ -10,6 +11,7 @@ import sys
 
 
 def record(directory, message, show_diff=True, show_hashes=False, use_color=True,
+@logger.catch
            skip_confirm=False):
     """Unwrapped record command"""
     if not os.path.isdir(directory):
@@ -26,12 +28,12 @@ def record(directory, message, show_diff=True, show_hashes=False, use_color=True
     if show_diff:
         print_diff(fsdiff, show_hashes=show_hashes, use_color=use_color)
 
-    print('Message:', message)
+    logger.info('Recording with message:', message)
 
     if skip_confirm or confirm("Record the values above into the database?"):
         s.record(fsdiff, message=message)
     else:
-        print("Cancelled!")
+        logger.info("Cancelled!")
         sys.exit(1)
 
 

src/nancy/fs.py

@@ -1,6 +1,7 @@
 """Interaction with the filesystem and with file database entries"""
 
 from dataclasses import dataclass
+from loguru import logger
 import hashlib
 import operator
 import os
@@ -201,6 +202,7 @@ class FSEntry:
 
     @classmethod
     def from_db_index(cls, cursor, root_id=None, root_row=None):
+    @logger.catch
         """Given id of an entry in filedir, recursively fill this object"""
         fields = 'id, filename, filetype, frozen, deleted'
         if root_row is None:

src/nancy/store.py

@@ -1,5 +1,7 @@
 """Utilities for creating new stores and linking between them."""
 
+from loguru import logger
+
 from . import db, environment, fs, machine
 
 import datetime
@@ -22,6 +24,7 @@ class Program:
     def set_start_time(self, t):
         self.start_time = t
 
+    @logger.catch
     def __enter__(self):
         if self._evaluated:
             raise RuntimeError("Cannot re-enter a Program context")
@@ -68,7 +71,7 @@ class Program:
         cur.connection.commit()
         self._evaluated = True  # prevent re-running
         elapsed = end_time - self.start_time
-        print(f"Program [{self.id}] {self.name} (message:{self.message}) ran in {elapsed} seconds.")
+        logger.success(f"Program [{self.id}] {self.name} (message:{self.message}) ran in {elapsed} seconds.")
 
 
 class Store:
@@ -178,7 +181,9 @@ class Store:
     def fs_entries(self, shallow=False):
         """Return recursive structure containing FSEntry objects from db"""
         root_id = self.filedir_root_index()
+        logger.debug('root_id={}', root_id)
         if root_id is None:
+            logger.trace("Empty root")
             return fs.FSEntry.empty_root()
         else:
             return fs.FSEntry.from_db_index(cur, root_id=root_id)
@@ -197,9 +202,12 @@ class Store:
             # provided
             os.path.relpath(os.path.realpath(filepath), os.path.realpath(self.path)),
         )
+        logger.trace("DIFF")
 
         recorded = self.path_to_fsentry(filepath)
+        logger.debug("CURRENT: \n{}", str(current))
 
+        logger.debug("RECORDED: \n{}", str(recorded))
         return fs.FSDiff.compute(recorded, current)
 
     def record(self, diff, message=None):