ebi-eva-common-pyutils 0.7.0__tar.gz → 0.7.2__tar.gz

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/CHANGELOG.md

@@ -2,6 +2,19 @@
 Changelog for ebi_eva_common_pyutils
 ===========================
 
+## 0.7.2 (2025-06-19)
+---------------------
+
+- Enable overwrite on existing config path.
+- Update lxml
+
+
+## 0.7.1 (2025-05-21)
+---------------------
+
+- Make sure all loggers are debug by default
+
+
 ## 0.7.0 (2025-04-14)
 ----------------------
 

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi_eva_common_pyutils
-Version: 0.7.0
+Version: 0.7.2
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/ebi_eva_common_pyutils/config.py

@@ -2,6 +2,9 @@ import os
 
 import yaml
 
+from ebi_eva_common_pyutils.logger import logging_config as log_cfg
+
+logger = log_cfg.get_logger(__name__)
 
 class Configuration:
     """
@@ -120,6 +123,9 @@ class WritableConfig(Configuration):
         for p in path[:-1]:
             if p not in top_level:
                 top_level[p] = {}
+            elif not isinstance(top_level[p], dict):
+                logger.warning(f'Overwriting existing config path {".".join(path)}')
+                top_level[p] = {}
             top_level = top_level[p]
         top_level[path[-1]] = value
 

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/ebi_eva_common_pyutils/logger.py

@@ -17,17 +17,28 @@ import logging.handlers
 from sys import stdout, stderr
 from cached_property import cached_property
 
+# The way Logger/Handler/Formatter works
+#  - Logger create the log message
+#  - Formatter describe what is included in the lo message
+#  - Handler Propagate them to where they should go (file/screen, ...)
+# Logger are part of hierarchy and always have parent up to the root logger.
+# The root logger is usually set to WARNING level
+# When a log is emitted to a logger, the logger checks it own level and propagate to its handler.
+# If it does not have any handlers it propagates to its parent (unless propagate is set to false)
+#
+# SPECIAL CASE: When a logger has a level set to NOTSET (0) it inherit the level from its parent
+
 
 class LoggingConfiguration:
     """
-    This class provides an all in one management of all loggers in the stack. By default it pulls existing loggers,
+    This class provides an all in one management of all loggers in the stack. By default, it pulls existing loggers,
     stores additional ones along with handlers and formatters.
     """
 
     default_fmt = '[%(asctime)s][%(name)s][%(levelname)s] %(message)s'
     default_datefmt = '%Y-%b-%d %H:%M:%S'
 
-    def __init__(self, use_existing_logger=True, log_level=logging.INFO):
+    def __init__(self, use_existing_logger=True, log_level=logging.DEBUG):
         self.blank_formatter = logging.Formatter()
         self.handlers = set()
         if use_existing_logger:
@@ -38,6 +49,8 @@ class LoggingConfiguration:
         else:
             self.loggers = {}
         self._log_level = log_level
+        if log_level is not None:
+            self.set_log_level(log_level)
 
     @cached_property
     def formatter(self):
@@ -61,8 +74,8 @@ class LoggingConfiguration:
         else:
             logger = logging.getLogger(name)
             self.loggers[name] = logger
-
-        logger.setLevel(level or self._log_level)
+        log_level = level if level > self._log_level else self._log_level
+        logger.setLevel(log_level)
         for h in self.handlers:
             logger.addHandler(h)
 
@@ -74,19 +87,20 @@ class LoggingConfiguration:
         :param logging.Handler handler:
         :param int level: Log level to assign to the created handler
         """
-        handler.setLevel(level or self._log_level)
+        log_level = level if level > self._log_level else self._log_level
+        handler.setLevel(log_level)
         handler.setFormatter(self.formatter)
         for name in self.loggers:
             self.loggers[name].addHandler(handler)
         self.handlers.add(handler)
 
-    def add_stdout_handler(self, level=None):
+    def add_stdout_handler(self, level=logging.INFO):
         self.add_handler(logging.StreamHandler(stdout), level=level or self._log_level)
 
-    def add_stderr_handler(self, level=None):
+    def add_stderr_handler(self, level=logging.INFO):
         self.add_handler(logging.StreamHandler(stderr), level=level or self._log_level)
 
-    def add_file_handler(self, filename, level=None):
+    def add_file_handler(self, filename, level=logging.INFO):
         self.add_handler(logging.FileHandler(filename=filename), level=level or self._log_level)
 
     def set_log_level(self, level):

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/ebi_eva_common_pyutils/reference/assembly.py

@@ -236,8 +236,12 @@ class NCBIAssembly(AppLogger):
         urllib.request.urlretrieve(url, output_file)
 
     def download_or_construct(self, genbank_only=False, overwrite=False):
-        """First download the assembly report and fasta from the FTP, then append any missing contig from
-        the assembly report to the assembly fasta."""
+        """
+        First download the assembly report and fasta from the FTP, then append any missing contig from
+        the assembly report to the assembly fasta.
+        Setting genbank_only = True ensure that only contigs that have genbank accession will be added to the assembly fasta.
+        Setting overwrite = True delete any existing fasta file and assembly report. then download them again.
+        """
         self.download_assembly_report(overwrite)
         try:
             self.download_assembly_fasta(overwrite)

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/ebi_eva_common_pyutils.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ebi-eva-common-pyutils
-Version: 0.7.0
+Version: 0.7.2
 Summary: EBI EVA - Common Python Utilities
 Home-page: https://github.com/EBIVariation/eva-common-pyutils
 License: Apache

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/ebi_eva_common_pyutils.egg-info/requires.txt

@@ -1,5 +1,5 @@
 requests==2.*
-lxml==4.*,>4.9
+lxml==5.*
 pyyaml==6.*
 cached-property==1.5.*
 retry==0.*,>0.9

{ebi_eva_common_pyutils-0.7.0 → ebi_eva_common_pyutils-0.7.2}/setup.py

@@ -1,19 +1,22 @@
 import os
 from distutils.core import setup
+from os.path import abspath, dirname, join
 
 from setuptools import find_packages
+base_dir = abspath(dirname(__file__))
+requirements_txt = join(base_dir, 'requirements.txt')
+requirements = [l.strip() for l in open(requirements_txt) if l and not l.startswith('#')]
 
 setup(
     name='ebi_eva_common_pyutils',
     scripts=[os.path.join(os.path.dirname(__file__), 'ebi_eva_internal_pyutils', 'archive_directory.py')],
     packages=find_packages(),
-    version='0.7.0',
+    version='0.7.2',
     license='Apache',
     description='EBI EVA - Common Python Utilities',
     url='https://github.com/EBIVariation/eva-common-pyutils',
     keywords=['EBI', 'EVA', 'PYTHON', 'UTILITIES'],
-    install_requires=['requests==2.*', 'lxml>4.9,==4.*', 'pyyaml==6.*', 'cached-property==1.5.*', 'retry>0.9,==0.*',
-                      'openpyxl==3.*'],
+    install_requires=requirements,
     extras_require={'eva-internal': ['psycopg2-binary', 'pymongo', 'networkx<=2.5']},
     classifiers=[
         'Development Status :: 5 - Production/Stable',