From 7c39e1755b47e6e46459423b6a50ef2bb3098cb6 Mon Sep 17 00:00:00 2001 From: github-actions Date: Tue, 9 Jul 2024 15:51:08 +0000 Subject: [PATCH] rebuilt html docs for version 0.1.31 from branch main with sphinx at 4543cf1 --- 0.1.31/_modules/mdacli/logger.html | 97 ++++++++++++++++++++++------- 0.1.31/api/cli.html | 2 +- 0.1.31/api/logger.html | 28 +++++++-- 0.1.31/changelog.html | 3 + 0.1.31/genindex.html | 2 + 0.1.31/objects.inv | Bin 1928 -> 1940 bytes 0.1.31/searchindex.js | 2 +- dev/_modules/mdacli/logger.html | 97 ++++++++++++++++++++++------- dev/api/cli.html | 2 +- dev/api/logger.html | 28 +++++++-- dev/changelog.html | 3 + dev/genindex.html | 2 + dev/objects.inv | Bin 1928 -> 1940 bytes dev/searchindex.js | 2 +- stable/_modules/mdacli/logger.html | 97 ++++++++++++++++++++++------- stable/api/cli.html | 2 +- stable/api/logger.html | 28 +++++++-- stable/changelog.html | 3 + stable/genindex.html | 2 + stable/objects.inv | Bin 1928 -> 1940 bytes stable/searchindex.js | 2 +- 21 files changed, 318 insertions(+), 84 deletions(-) diff --git a/0.1.31/_modules/mdacli/logger.html b/0.1.31/_modules/mdacli/logger.html index 2759bc5..700075d 100644 --- a/0.1.31/_modules/mdacli/logger.html +++ b/0.1.31/_modules/mdacli/logger.html @@ -95,20 +95,60 @@

Source code for mdacli.logger

 # Released under the GNU Public Licence, v2 or any higher version
 # SPDX-License-Identifier: GPL-2.0-or-later
 """Logging."""
-
 import contextlib
 import logging
 import sys
+import warnings
+from pathlib import Path
+from typing import List, Optional, Union
 
 from .colors import Emphasise
 
 
+

+[docs]
+def check_suffix(filename: Union[str, Path], suffix: str) -> Union[str, Path]:
+    """Check the suffix of a file name and adds if it not existing.
+
+    If ``filename`` does not end with ``suffix`` the ``suffix`` is added and a
+    warning will be issued.
+
+    Parameters
+    ----------
+    filename : Name of the file to be checked.
+    suffix : Expected file suffix i.e. ``.txt``.
+
+    Returns
+    -------
+    Checked and probably extended file name.
+    """
+    path_filename = Path(filename)
+
+    if path_filename.suffix != suffix:
+        warnings.warn(
+            f"The file name should have a '{suffix}' extension. The user "
+            f"requested the file with name '{filename}', but it will be saved "
+            f"as '{filename}{suffix}'.",
+            stacklevel=1,
+        )
+        path_filename = path_filename.parent / (path_filename.name + suffix)
+
+    if type(filename) is str:
+        return str(path_filename)
+    else:
+        return path_filename

+
+
+
 

 [docs]
 @contextlib.contextmanager
-def setup_logging(logobj, logfile=None, level=logging.WARNING):
-    """
-    Create a logging environment for a given logobj.
+def setup_logging(
+    logobj: logging.Logger,
+    logfile: Optional[Union[str, Path]] = None,
+    level: int = logging.WARNING,
+):
+    """Create a logging environment for a given ``log_obj``.
 
     Parameters
     ----------
@@ -119,39 +159,52 @@ 
Source code for mdacli.logger
     level : int
         Set the root logger level to the specified level. If for example set
         to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
-        function name are displayed. For :py:obj:`logging.INFO only the message
-        logged from errors, warnings and infos will be displayed.
+        function name are displayed. For :py:obj:`logging.INFO` only the
+        message logged from errors, warnings and infos will be displayed.
     """
     try:
+        format = ""
         if level == logging.DEBUG:
-            format = (
-                "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
-                "{message}"
-            )
-        else:
-            format = "{message}"
+            format += "[{levelname}]:{filename}:{funcName}:{lineno} - "
+        format += "{message}"
+
+        formatter = logging.Formatter(format, style="{")
+        handlers: List[Union[logging.StreamHandler, logging.FileHandler]] = []
 
-        logging.basicConfig(format=format,
-                            handlers=[logging.StreamHandler(sys.stdout)],
-                            level=level,
-                            style='{')
+        stream_handler = logging.StreamHandler(sys.stdout)
+        stream_handler.setFormatter(formatter)
+        handlers.append(stream_handler)
 
         if logfile:
-            logfile += ".log" * (not logfile.endswith("log"))
-            handler = logging.FileHandler(filename=logfile, encoding='utf-8')
-            handler.setFormatter(logging.Formatter(format, style='{'))
-            logobj.addHandler(handler)
+            logfile = check_suffix(filename=logfile, suffix=".log")
+            file_handler = logging.FileHandler(
+                filename=str(logfile), encoding="utf-8")
+            file_handler.setFormatter(formatter)
+            handlers.append(file_handler)
         else:
             logging.addLevelName(logging.INFO, Emphasise.info("INFO"))
             logging.addLevelName(logging.DEBUG, Emphasise.debug("DEBUG"))
             logging.addLevelName(logging.WARNING, Emphasise.warning("WARNING"))
             logging.addLevelName(logging.ERROR, Emphasise.error("ERROR"))
-            logobj.info('Logging to file is disabled.')
+
+        logging.basicConfig(
+            format=format, handlers=handlers, level=level, style="{")
+        logging.captureWarnings(True)
+
+        if logfile:
+            abs_path = str(Path(logfile).absolute().resolve())
+            logobj.info(f"This log is also available at '{abs_path}'.")
+        else:
+            logobj.debug("Logging to file is disabled.")
+
+        for handler in handlers:
+            logobj.addHandler(handler)
 
         yield
+
     finally:
-        handlers = logobj.handlers[:]
         for handler in handlers:
+            handler.flush()
             handler.close()
             logobj.removeHandler(handler)

 
diff --git a/0.1.31/api/cli.html b/0.1.31/api/cli.html
index 0785451..5e7f1b1 100644
--- a/0.1.31/api/cli.html
+++ b/0.1.31/api/cli.html
@@ -106,7 +106,7 @@
 
The toplevel command line interface.

 

 

-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140423703360128'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]

+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='139831459525248'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
 
Create the command-line interface.

 
This function creates a command line interface with a given name based
 on a module list.

diff --git a/0.1.31/api/logger.html b/0.1.31/api/logger.html
index cd634da..2e48aae 100644
--- a/0.1.31/api/logger.html
+++ b/0.1.31/api/logger.html
@@ -66,6 +66,7 @@
 
  • Results Saving
    • 
 
  • Coloring
    • 
 
  • Logging
 
    • 
@@ -104,10 +105,29 @@
   
    
 
    Logging
    
 
    Logging.
    
+
    
+
    
+mdacli.logger.check_suffix(filename: str | Path, suffix: str) → str | Path[source]
    
+
    Check the suffix of a file name and adds if it not existing.
    
+
    If filename does not end with suffix the suffix is added and a
+warning will be issued.
    
+
    
+
    Parameters:
    
+
      
+
    • filename (Name of the file to be checked.)
      • 
+
    • suffix (Expected file suffix i.e. .txt.)
      • 
+
    
+
    
+
    Returns:
    
+
    Checked and probably extended file name.
    
+
    
+
    
+
    
+
 
    
 
    
-mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
    
-
    Create a logging environment for a given logobj.
    
+mdacli.logger.setup_logging(logobj: Logger, logfile: str | Path | None = None, level: int = 30)[source]
+
    Create a logging environment for a given log_obj.
    
 
    
 
    Parameters:
    
 
      
@@ -115,8 +135,8 @@
 
    • logfile (str) – Name of the log file
      • 
 
    • level (int) – Set the root logger level to the specified level. If for example set
 to logging.DEBUG detailed debug logs inludcing filename and
-function name are displayed. For :py:obj:`logging.INFO only the message
-logged from errors, warnings and infos will be displayed.
      • 
+function name are displayed. For logging.INFO only the
+message logged from errors, warnings and infos will be displayed.
      
 
    
 
    
 
    
diff --git a/0.1.31/changelog.html b/0.1.31/changelog.html
index c341651..0b137ec 100644
--- a/0.1.31/changelog.html
+++ b/0.1.31/changelog.html
@@ -125,6 +125,9 @@
              
   
    
 
    Changelog
    
+
      
+
    • Cleanup logger function
      • 
+
    
 
    
 
    v0.1.31 (2024-07-08)
    
 
      
diff --git a/0.1.31/genindex.html b/0.1.31/genindex.html
index ab5cb51..9b826a5 100644
--- a/0.1.31/genindex.html
+++ b/0.1.31/genindex.html
@@ -139,6 +139,8 @@ 
      B
      
 
      C
      
 
      
   
        
+      
      • check_suffix() (in module mdacli.logger)
+
        • 
       
      • cli() (in module mdacli.cli)
 
        • 
       
      • convert_analysis_parameters() (in module mdacli.libcli)
diff --git a/0.1.31/objects.inv b/0.1.31/objects.inv
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diff --git a/0.1.31/searchindex.js b/0.1.31/searchindex.js
index 716e176..cdb9308 100644
--- a/0.1.31/searchindex.js
+++ b/0.1.31/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {"API library documentation": [[0, "api-library-documentation"]], "Add your fork as remote": [[9, "add-your-fork-as-remote"]], "Authors": [[7, "authors"]], "Available modules": [[10, "available-modules"], [13, "available-modules"]], "Changelog": [[8, "changelog"]], "Clone the main project to your computer": [[9, "clone-the-main-project-to-your-computer"]], "Coloring": [[2, "module-mdacli.colors"]], "Contributing": [[9, "contributing"]], "Create a new branch and start developing": [[9, "create-a-new-branch-and-start-developing"]], "Fork this repository": [[9, "fork-this-repository"]], "High-Level API": [[1, "module-mdacli.cli"]], "Install for developers": [[9, "install-for-developers"]], "Installation": [[11, "installation"]], "Logging": [[4, "module-mdacli.logger"]], "MDAnalysis command line interface": [[10, "mdanalysis-command-line-interface"], [13, "mdanalysis-command-line-interface"]], "Philosophy and approach": [[12, "philosophy-and-approach"]], "Pull Request": [[9, "pull-request"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Results Saving": [[5, "module-mdacli.save"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Update CHANGELOG": [[9, "update-changelog"]], "Usage": [[14, "usage"]], "Utilities": [[6, "module-mdacli.utils"]], "conda": [[11, "conda"]], "pip": [[11, "pip"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.18 (2022-04-12)": [[8, 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"madcli": 9, "mai": [3, 9], "maico": 12, "main": [3, 6], "make": [8, 9, 12], "manag": 5, "mandatori": 3, "mandatory_analysis_paramet": 3, "mani": 12, "manual": 8, "map": 5, "mass": 3, "matrix": 8, "md": [10, 13], "mda": [8, 10, 12, 13, 14], "mdacli": [0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14], "mdacli_result": 5, "mdanalysi": [1, 3, 5, 8, 9, 11, 12, 14], "mean": [10, 13], "member": 3, "merg": 9, "messag": [2, 4, 9, 10, 13], "metavar": 3, "method": [6, 9], "might": 0, "min_ndim": 5, "mock": 1, "mod": 3, "mode": 3, "modul": [1, 3, 8, 14], "module_list": 1, "module_nam": 3, "moment": [10, 13], "more": [8, 10, 12, 13, 14], "most": 9, "move": 8, "multidimension": 5, "must": 3, "my": [2, 9], "myfork": 9, "namd": 3, "name": [1, 3, 4, 5, 6, 8, 9, 10, 13, 14], "namespac": 3, "narg": 3, "ndarrai": [3, 5], "ndim": 5, "need": [0, 3, 8, 9], "new": [3, 8, 12], "next": 9, "nice": 9, "no_entry_sign": 9, "non": 5, "none": [1, 3, 4, 5, 8], "nor": 3, "note": [3, 5], "now": 9, "np": [3, 5], "nt": 8, "num": 5, "number": [5, 6, 8, 14], "numpi": [3, 5], "numpydocstr": 6, "o": 14, "object": [3, 5, 6, 12], "observ": [10, 13], "ok": 2, "oliv": 7, "ommit": 1, "onc": 9, "one": [3, 5], "onli": [0, 3, 4, 9, 10, 13], "onlin": [9, 14], "open": [9, 14], "oper": 5, "option": [3, 5, 8, 14], "option_str": 3, "optional_analysis_paramet": 3, "order": 3, "org": 8, "organ": 5, "origin": 5, "other": 14, "our": [9, 12], "out_extra": 5, "out_list": 5, "output": [3, 14], "output_directori": 3, "output_paramet": 3, "output_prefix": 3, "overview": [10, 13], "ow": 14, "own": [9, 14], "oxygen": 14, "p": 6, "packag": [8, 9], "page": [0, 8, 10, 13, 14], "pair": [10, 13], "pairwis": [10, 13], "paramet": [1, 2, 3, 4, 5, 6, 8, 12, 14], "parent": [3, 12], "pars": [3, 6, 8], "parsabl": 8, "parse_callable_signatur": 6, "parse_doc": 6, "parser": [3, 6, 12], "partial": 3, "pass": [3, 9], "path": 4, "pca": [10, 13], "pdb": 3, "peopl": 12, "per": 3, "perform": [3, 9, 10, 13], "permiss": 8, "persistencelength": 1, "phase": 9, "philip": 7, "pink": 2, "pip": 9, "pipelin": 9, "pkg": 3, "place": 9, "pleas": [9, 11], "pluge": 11, "point": 3, "popul": 3, "posit": 8, "possibl": 3, "possibli": 9, "potenti": 2, "power": 9, "pr": 9, "pre": 14, "prefix": [5, 14], "present": [3, 6, 9], "previou": 9, "princip": [10, 13], "print": [2, 3], "pro": 9, "probabl": [3, 4], "problem": 12, "procedur": 14, "process": [3, 9, 12], "profil": [10, 13], "program": [3, 10, 13], "progress": [10, 13], "project": [10, 12, 13], "proper": 5, "protoread": 3, "provid": [3, 12, 14], "psf": 3, "pullrequest": 9, "push": 9, "py": [8, 9, 11], "py3": 8, "pyproject": 8, "python": [8, 9, 11, 12], "question": 3, "r": 6, "radial": 14, "rais": [3, 6], "ramachandran": [10, 13], "rdf": 14, "read": [3, 9], "reader": 3, "readm": 8, "real": 9, "red": 2, "reenabl": 8, "refer": [0, 3, 8, 9, 10, 13], "reference_univers": 3, "reference_universe_paramet": 3, "reflect": 9, "regex": [6, 8], "regex101": 6, "regular": 0, "regularli": 12, "rel": 3, "relat": [10, 13], "relax": 9, "releas": 8, "remov": [5, 8], "remove_fil": 5, "renam": 8, "replac": 8, "repositori": 11, "requir": [3, 6, 8, 14], "result": [0, 12, 14], "return": [2, 3, 4, 5, 6], "return_with_remov": 5, "review": 9, "right": 9, "rigid": 14, "rm": [10, 13], "rmsd": [10, 13], "rmsf": [10, 13], "root": 4, "routin": 12, "row": [5, 14], "rst": [8, 9], "run": [3, 6, 8, 10, 13, 14], "run_analsi": 8, "run_analysi": [3, 8], "run_paramet": 3, "safe": 9, "same": [3, 5, 9, 11, 12], "sampl": 14, "save": [0, 3, 8, 12, 14], "save_1d_arrai": 5, "save_2d_arrai": 5, "save_3d_arrai": 5, "save_3d_array_to_2d_csv": 5, "save_files_to_zip": 5, "save_higher_dim_arrai": 5, "save_json_serializ": 5, "save_result": 8, "save_result_arrai": 5, "save_results_object": 5, "save_to_json": 5, "savetxt_w_command": 5, "scientist": 12, "script": 12, "search": 3, "see": [2, 3, 6, 9, 14], "select": [3, 10, 12, 13, 14], "select_atom": 3, "seri": 3, "serializ": 5, "serv": 5, "set": [3, 4, 8, 9, 14], "setup": [8, 9, 11], "setup_cli": 3, "setup_log": [4, 8], "sever": 12, "shape": 3, "shortest": 5, "shortli": 9, "should": [1, 3, 9, 11], "show": 12, "signatur": 6, "similar": 14, "simpl": [10, 12, 13, 14], "simplifi": 8, "simul": 12, "sinc": [3, 9, 12], "singl": [3, 5, 8], "skip_mod": 1, "skip_modul": 1, "slightli": 11, "smile": 9, "smile_cat": 9, "so": [6, 9, 11, 12, 14], "solv": 12, "some": [9, 12, 14], "sometim": 12, "sort_kei": 5, "sourc": [1, 2, 3, 4, 5, 6], "spc": 14, "special": 3, "specif": [0, 9], "specifi": [4, 10, 13], "split": [3, 5, 6], "split_argparse_into_group": 3, "split_time_unit": 6, "squar": [10, 13], "squeez": 5, "stack": 5, "stack_1d_arrays_list": 5, "stackoverflow": 3, "stage": [10, 13], "stai": 12, "start": [3, 6, 8, 12], "static": 2, "step": [3, 6, 9], "stop": [3, 8], "storage_dict": 6, "store": [3, 5, 12, 14], "str": [1, 2, 3, 4, 5, 6], "stream": 3, "strict": 6, "string": [1, 2, 3, 5, 6, 14], "structur": [10, 12, 13], "student": 12, "style": [2, 8, 9], "sub": 3, "sub_pars": 3, "subclass": 3, "subdictinari": 6, "submit": 9, "subpars": 3, "subset": 5, "subtitl": 9, "suffix": [3, 4], "suitabl": 3, "summari": 6, "suppli": 3, "support": [0, 8, 10, 13], "syntax": 12, "t": [9, 11], "tabl": [3, 5], "taken": [2, 5], "task": 9, "taurenmd": 12, "teixeira": 7, "term": 3, "termin": 14, "test": 8, "thei": [5, 12], "them": [9, 12], "therefor": 12, "thezip": 5, "thi": [1, 2, 3, 6, 10, 12, 13, 14], "thread": 8, "through": [10, 12, 13], "time": [3, 6, 8, 9], "titl": [3, 9], "togeth": [5, 11, 14], "toml": 8, "tool": [10, 11, 13], "top": 11, "toplevel": 1, "topol": 14, "topolgi": 14, "topologi": [3, 12], "topology_format": 3, "topologyreaderbas": 3, "tox": 8, "tox_": 9, "tpr": 14, "traj": 14, "trajectori": [3, 8, 10, 12, 13, 14], "trajectory_format": 3, "translat": 8, "trr": [3, 14], "true": [1, 5], "try": 5, "try_to_squeeze_m": 5, "tupl": 6, "turquois": 2, "tuvokki": 2, "twice": 9, "two": 14, "txt": 4, "type": [3, 5, 6, 8, 12], "typo": 8, "u": [9, 11], "under": 9, "underlin": 2, "unit": [3, 6], "univers": [3, 12], "up": [1, 3, 9, 12], "updat": [8, 11], "upgrad": 11, "upload": 8, "upstream": 9, "url": 8, "us": [0, 3, 6, 8, 9, 10, 11, 12, 13, 14], "usag": 0, "user": [0, 12], "usernam": 9, "util": 0, "v": 14, "v2": 9, "valu": [5, 6, 8], "valueerror": [3, 6], "variabl": [2, 12], "vebos": 3, "vector": 3, "verbos": [3, 14], "veri": [0, 9, 12], "verifi": 9, "version": [1, 3, 9], "vertic": 5, "via": 9, "volumetr": [10, 13], "vx": 9, "wai": [3, 9, 12], "wang": 7, "want": [0, 11], "warn": [1, 2, 3, 4, 14], "water": 14, "waterbridgeanalysi": 1, "we": [5, 9, 12], "webpag": 7, "welcom": [9, 10, 13], "well": 9, "were": 12, "what": 3, "when": [1, 6, 9], "where": [3, 5, 6], "which": [1, 3, 5, 6, 11, 12], "whole": 9, "window": 8, "wish": 9, "within": 12, "without": [5, 12], "work": [3, 10, 13], "workflow": 9, "wrapper": 12, "write": 12, "x": [5, 6, 9], "x1b": 2, "xdarr": 5, "xplor": 3, "xtc": 3, "xyz": 3, "yai": 2, "yellow": 2, "yet": 6, "you": [9, 11, 14], "your": [10, 11, 13, 14], "zip": [5, 12, 14], "zipit": 5, "zipnam": 5, "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "\u03c8": [10, 13], "\u03d5": [10, 13]}, "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "titleterms": {"0": 8, "01": 8, "02": 8, "03": 8, "04": 8, "06": 8, "07": 8, "08": 8, "09": 8, "1": 8, "10": 8, "11": 8, "12": 8, "13": 8, "14": 8, "15": 8, "16": 8, "17": 8, "18": 8, "19": 8, "2": 8, "20": 8, "2021": 8, "2022": 8, "2023": 8, "2024": 8, "21": 8, "22": 8, "23": 8, "24": 8, "25": 8, "26": 8, "27": 8, "28": 8, "29": 8, "3": 8, "30": 8, "31": 8, "4": 8, "5": 8, "6": 8, "7": 8, "8": 8, "9": 8, "add": 9, "api": [0, 1], "approach": 12, "author": 7, "avail": [10, 13], "branch": 9, "chang": 9, "changelog": [8, 9], "cli": 3, "clone": 9, "color": 2, "command": [10, 13], "comput": 9, "conda": 11, "contribut": 9, "creat": 9, "develop": 9, "document": 0, "fork": 9, "function": 3, "high": 1, "instal": [9, 11], "interfac": [10, 13], "level": 1, "librari": 0, "line": [10, 13], "log": 4, "main": 9, "mdanalysi": [10, 13], "modul": [10, 13], "new": 9, "philosophi": 12, "pip": 11, "project": 9, "pull": 9, "remot": 9, "repositori": 9, "request": 9, "result": 5, "run": 9, "save": 5, "start": 9, "support": 3, "test": 9, "thi": 9, "tox": 9, "updat": 9, "usag": 14, "util": 6, "v0": 8, "your": 9}})
\ No newline at end of file
diff --git a/dev/_modules/mdacli/logger.html b/dev/_modules/mdacli/logger.html
index 2759bc5..700075d 100644
--- a/dev/_modules/mdacli/logger.html
+++ b/dev/_modules/mdacli/logger.html
@@ -95,20 +95,60 @@ 
        Source code for mdacli.logger
         # Released under the GNU Public Licence, v2 or any higher version
 # SPDX-License-Identifier: GPL-2.0-or-later
 """Logging."""
-
 import contextlib
 import logging
 import sys
+import warnings
+from pathlib import Path
+from typing import List, Optional, Union
 
 from .colors import Emphasise
 
 
+
        
+[docs]
+def check_suffix(filename: Union[str, Path], suffix: str) -> Union[str, Path]:
+    """Check the suffix of a file name and adds if it not existing.
+
+    If ``filename`` does not end with ``suffix`` the ``suffix`` is added and a
+    warning will be issued.
+
+    Parameters
+    ----------
+    filename : Name of the file to be checked.
+    suffix : Expected file suffix i.e. ``.txt``.
+
+    Returns
+    -------
+    Checked and probably extended file name.
+    """
+    path_filename = Path(filename)
+
+    if path_filename.suffix != suffix:
+        warnings.warn(
+            f"The file name should have a '{suffix}' extension. The user "
+            f"requested the file with name '{filename}', but it will be saved "
+            f"as '{filename}{suffix}'.",
+            stacklevel=1,
+        )
+        path_filename = path_filename.parent / (path_filename.name + suffix)
+
+    if type(filename) is str:
+        return str(path_filename)
+    else:
+        return path_filename
        
+
+
+
 
        
 [docs]
 @contextlib.contextmanager
-def setup_logging(logobj, logfile=None, level=logging.WARNING):
-    """
-    Create a logging environment for a given logobj.
+def setup_logging(
+    logobj: logging.Logger,
+    logfile: Optional[Union[str, Path]] = None,
+    level: int = logging.WARNING,
+):
+    """Create a logging environment for a given ``log_obj``.
 
     Parameters
     ----------
@@ -119,39 +159,52 @@ 
        Source code for mdacli.logger
             level : int
         Set the root logger level to the specified level. If for example set
         to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
-        function name are displayed. For :py:obj:`logging.INFO only the message
-        logged from errors, warnings and infos will be displayed.
+        function name are displayed. For :py:obj:`logging.INFO` only the
+        message logged from errors, warnings and infos will be displayed.
     """
     try:
+        format = ""
         if level == logging.DEBUG:
-            format = (
-                "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
-                "{message}"
-            )
-        else:
-            format = "{message}"
+            format += "[{levelname}]:{filename}:{funcName}:{lineno} - "
+        format += "{message}"
+
+        formatter = logging.Formatter(format, style="{")
+        handlers: List[Union[logging.StreamHandler, logging.FileHandler]] = []
 
-        logging.basicConfig(format=format,
-                            handlers=[logging.StreamHandler(sys.stdout)],
-                            level=level,
-                            style='{')
+        stream_handler = logging.StreamHandler(sys.stdout)
+        stream_handler.setFormatter(formatter)
+        handlers.append(stream_handler)
 
         if logfile:
-            logfile += ".log" * (not logfile.endswith("log"))
-            handler = logging.FileHandler(filename=logfile, encoding='utf-8')
-            handler.setFormatter(logging.Formatter(format, style='{'))
-            logobj.addHandler(handler)
+            logfile = check_suffix(filename=logfile, suffix=".log")
+            file_handler = logging.FileHandler(
+                filename=str(logfile), encoding="utf-8")
+            file_handler.setFormatter(formatter)
+            handlers.append(file_handler)
         else:
             logging.addLevelName(logging.INFO, Emphasise.info("INFO"))
             logging.addLevelName(logging.DEBUG, Emphasise.debug("DEBUG"))
             logging.addLevelName(logging.WARNING, Emphasise.warning("WARNING"))
             logging.addLevelName(logging.ERROR, Emphasise.error("ERROR"))
-            logobj.info('Logging to file is disabled.')
+
+        logging.basicConfig(
+            format=format, handlers=handlers, level=level, style="{")
+        logging.captureWarnings(True)
+
+        if logfile:
+            abs_path = str(Path(logfile).absolute().resolve())
+            logobj.info(f"This log is also available at '{abs_path}'.")
+        else:
+            logobj.debug("Logging to file is disabled.")
+
+        for handler in handlers:
+            logobj.addHandler(handler)
 
         yield
+
     finally:
-        handlers = logobj.handlers[:]
         for handler in handlers:
+            handler.flush()
             handler.close()
             logobj.removeHandler(handler)
        
 
diff --git a/dev/api/cli.html b/dev/api/cli.html
index 0785451..5e7f1b1 100644
--- a/dev/api/cli.html
+++ b/dev/api/cli.html
@@ -106,7 +106,7 @@
 
        The toplevel command line interface.
        
 
        
 
        
-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140423703360128'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
        
+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='139831459525248'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
 
        Create the command-line interface.
        
 
        This function creates a command line interface with a given name based
 on a module list.
        
diff --git a/dev/api/logger.html b/dev/api/logger.html
index cd634da..2e48aae 100644
--- a/dev/api/logger.html
+++ b/dev/api/logger.html
@@ -66,6 +66,7 @@
 
      • Results Saving
        • 
 
      • Coloring
        • 
 
      • Logging
 
        • 
@@ -104,10 +105,29 @@
   
        
 
        Logging
        
 
        Logging.
        
+
        
+
        
+mdacli.logger.check_suffix(filename: str | Path, suffix: str) → str | Path[source]
        
+
        Check the suffix of a file name and adds if it not existing.
        
+
        If filename does not end with suffix the suffix is added and a
+warning will be issued.
        
+
        
+
        Parameters:
        
+
          
+
        • filename (Name of the file to be checked.)
          • 
+
        • suffix (Expected file suffix i.e. .txt.)
          • 
+
        
+
        
+
        Returns:
        
+
        Checked and probably extended file name.
        
+
        
+
        
+
        
+
 
        
 
        
-mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
        
-
        Create a logging environment for a given logobj.
        
+mdacli.logger.setup_logging(logobj: Logger, logfile: str | Path | None = None, level: int = 30)[source]
+
        Create a logging environment for a given log_obj.
        
 
        
 
        Parameters:
        
 
          
@@ -115,8 +135,8 @@
 
        • logfile (str) – Name of the log file
          • 
 
        • level (int) – Set the root logger level to the specified level. If for example set
 to logging.DEBUG detailed debug logs inludcing filename and
-function name are displayed. For :py:obj:`logging.INFO only the message
-logged from errors, warnings and infos will be displayed.
          • 
+function name are displayed. For logging.INFO only the
+message logged from errors, warnings and infos will be displayed.
          
 
        
 
        
 
        
diff --git a/dev/changelog.html b/dev/changelog.html
index c341651..0b137ec 100644
--- a/dev/changelog.html
+++ b/dev/changelog.html
@@ -125,6 +125,9 @@
              
   
        
 
        Changelog
        
+
          
+
        • Cleanup logger function
          • 
+
        
 
        
 
        v0.1.31 (2024-07-08)
        
 
          
diff --git a/dev/genindex.html b/dev/genindex.html
index ab5cb51..9b826a5 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -139,6 +139,8 @@ 
          B
          
 
          C
          
 
          
   
            
+      
          • check_suffix() (in module mdacli.logger)
+
            • 
       
          • cli() (in module mdacli.cli)
 
            • 
       
          • convert_analysis_parameters() (in module mdacli.libcli)
diff --git a/dev/objects.inv b/dev/objects.inv
index 6986add58b972c3d2fe0ce0523a9081d6bdc2cc0..c66b93d28b0ae47887f925ffbbe1c46d5124c098 100644
GIT binary patch
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index 716e176..cdb9308 100644
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"your": [10, 11, 13, 14], "zip": [5, 12, 14], "zipit": 5, "zipnam": 5, "\u03c7_1": [10, 13], "\u03c7_2": [10, 13], "\u03c8": [10, 13], "\u03d5": [10, 13]}, "titles": ["API library documentation", "High-Level API", "Coloring", "Support functions for CLI", "Logging", "Results Saving", "Utilities", "Authors", "Changelog", "Contributing", "MDAnalysis command line interface", "Installation", "Philosophy and approach", "MDAnalysis command line interface", "Usage"], "titleterms": {"0": 8, "01": 8, "02": 8, "03": 8, "04": 8, "06": 8, "07": 8, "08": 8, "09": 8, "1": 8, "10": 8, "11": 8, "12": 8, "13": 8, "14": 8, "15": 8, "16": 8, "17": 8, "18": 8, "19": 8, "2": 8, "20": 8, "2021": 8, "2022": 8, "2023": 8, "2024": 8, "21": 8, "22": 8, "23": 8, "24": 8, "25": 8, "26": 8, "27": 8, "28": 8, "29": 8, "3": 8, "30": 8, "31": 8, "4": 8, "5": 8, "6": 8, "7": 8, "8": 8, "9": 8, "add": 9, "api": [0, 1], "approach": 12, "author": 7, "avail": [10, 13], "branch": 9, "chang": 9, "changelog": [8, 9], "cli": 3, "clone": 9, "color": 2, "command": [10, 13], "comput": 9, "conda": 11, "contribut": 9, "creat": 9, "develop": 9, "document": 0, "fork": 9, "function": 3, "high": 1, "instal": [9, 11], "interfac": [10, 13], "level": 1, "librari": 0, "line": [10, 13], "log": 4, "main": 9, "mdanalysi": [10, 13], "modul": [10, 13], "new": 9, "philosophi": 12, "pip": 11, "project": 9, "pull": 9, "remot": 9, "repositori": 9, "request": 9, "result": 5, "run": 9, "save": 5, "start": 9, "support": 3, "test": 9, "thi": 9, "tox": 9, "updat": 9, "usag": 14, "util": 6, "v0": 8, "your": 9}})
\ No newline at end of file
diff --git a/stable/_modules/mdacli/logger.html b/stable/_modules/mdacli/logger.html
index 2759bc5..700075d 100644
--- a/stable/_modules/mdacli/logger.html
+++ b/stable/_modules/mdacli/logger.html
@@ -95,20 +95,60 @@ 
            Source code for mdacli.logger
             # Released under the GNU Public Licence, v2 or any higher version
 # SPDX-License-Identifier: GPL-2.0-or-later
 """Logging."""
-
 import contextlib
 import logging
 import sys
+import warnings
+from pathlib import Path
+from typing import List, Optional, Union
 
 from .colors import Emphasise
 
 
+
            
+[docs]
+def check_suffix(filename: Union[str, Path], suffix: str) -> Union[str, Path]:
+    """Check the suffix of a file name and adds if it not existing.
+
+    If ``filename`` does not end with ``suffix`` the ``suffix`` is added and a
+    warning will be issued.
+
+    Parameters
+    ----------
+    filename : Name of the file to be checked.
+    suffix : Expected file suffix i.e. ``.txt``.
+
+    Returns
+    -------
+    Checked and probably extended file name.
+    """
+    path_filename = Path(filename)
+
+    if path_filename.suffix != suffix:
+        warnings.warn(
+            f"The file name should have a '{suffix}' extension. The user "
+            f"requested the file with name '{filename}', but it will be saved "
+            f"as '{filename}{suffix}'.",
+            stacklevel=1,
+        )
+        path_filename = path_filename.parent / (path_filename.name + suffix)
+
+    if type(filename) is str:
+        return str(path_filename)
+    else:
+        return path_filename
            
+
+
+
 
            
 [docs]
 @contextlib.contextmanager
-def setup_logging(logobj, logfile=None, level=logging.WARNING):
-    """
-    Create a logging environment for a given logobj.
+def setup_logging(
+    logobj: logging.Logger,
+    logfile: Optional[Union[str, Path]] = None,
+    level: int = logging.WARNING,
+):
+    """Create a logging environment for a given ``log_obj``.
 
     Parameters
     ----------
@@ -119,39 +159,52 @@ 
            Source code for mdacli.logger
                 level : int
         Set the root logger level to the specified level. If for example set
         to :py:obj:`logging.DEBUG` detailed debug logs inludcing filename and
-        function name are displayed. For :py:obj:`logging.INFO only the message
-        logged from errors, warnings and infos will be displayed.
+        function name are displayed. For :py:obj:`logging.INFO` only the
+        message logged from errors, warnings and infos will be displayed.
     """
     try:
+        format = ""
         if level == logging.DEBUG:
-            format = (
-                "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
-                "{message}"
-            )
-        else:
-            format = "{message}"
+            format += "[{levelname}]:{filename}:{funcName}:{lineno} - "
+        format += "{message}"
+
+        formatter = logging.Formatter(format, style="{")
+        handlers: List[Union[logging.StreamHandler, logging.FileHandler]] = []
 
-        logging.basicConfig(format=format,
-                            handlers=[logging.StreamHandler(sys.stdout)],
-                            level=level,
-                            style='{')
+        stream_handler = logging.StreamHandler(sys.stdout)
+        stream_handler.setFormatter(formatter)
+        handlers.append(stream_handler)
 
         if logfile:
-            logfile += ".log" * (not logfile.endswith("log"))
-            handler = logging.FileHandler(filename=logfile, encoding='utf-8')
-            handler.setFormatter(logging.Formatter(format, style='{'))
-            logobj.addHandler(handler)
+            logfile = check_suffix(filename=logfile, suffix=".log")
+            file_handler = logging.FileHandler(
+                filename=str(logfile), encoding="utf-8")
+            file_handler.setFormatter(formatter)
+            handlers.append(file_handler)
         else:
             logging.addLevelName(logging.INFO, Emphasise.info("INFO"))
             logging.addLevelName(logging.DEBUG, Emphasise.debug("DEBUG"))
             logging.addLevelName(logging.WARNING, Emphasise.warning("WARNING"))
             logging.addLevelName(logging.ERROR, Emphasise.error("ERROR"))
-            logobj.info('Logging to file is disabled.')
+
+        logging.basicConfig(
+            format=format, handlers=handlers, level=level, style="{")
+        logging.captureWarnings(True)
+
+        if logfile:
+            abs_path = str(Path(logfile).absolute().resolve())
+            logobj.info(f"This log is also available at '{abs_path}'.")
+        else:
+            logobj.debug("Logging to file is disabled.")
+
+        for handler in handlers:
+            logobj.addHandler(handler)
 
         yield
+
     finally:
-        handlers = logobj.handlers[:]
         for handler in handlers:
+            handler.flush()
             handler.close()
             logobj.removeHandler(handler)
            
 
diff --git a/stable/api/cli.html b/stable/api/cli.html
index 0785451..5e7f1b1 100644
--- a/stable/api/cli.html
+++ b/stable/api/cli.html
@@ -106,7 +106,7 @@
 
            The toplevel command line interface.
            
 
            
 
            
-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140423703360128'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
            
+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='139831459525248'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
 
            Create the command-line interface.
            
 
            This function creates a command line interface with a given name based
 on a module list.
            
diff --git a/stable/api/logger.html b/stable/api/logger.html
index cd634da..2e48aae 100644
--- a/stable/api/logger.html
+++ b/stable/api/logger.html
@@ -66,6 +66,7 @@
 
          • Results Saving
            • 
 
          • Coloring
            • 
 
          • Logging
 
            • 
@@ -104,10 +105,29 @@
   
            
 
            Logging
            
 
            Logging.
            
+
            
+
            
+mdacli.logger.check_suffix(filename: str | Path, suffix: str) → str | Path[source]
            
+
            Check the suffix of a file name and adds if it not existing.
            
+
            If filename does not end with suffix the suffix is added and a
+warning will be issued.
            
+
            
+
            Parameters:
            
+
              
+
            • filename (Name of the file to be checked.)
              • 
+
            • suffix (Expected file suffix i.e. .txt.)
              • 
+
            
+
            
+
            Returns:
            
+
            Checked and probably extended file name.
            
+
            
+
            
+
            
+
 
            
 
            
-mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
            
-
            Create a logging environment for a given logobj.
            
+mdacli.logger.setup_logging(logobj: Logger, logfile: str | Path | None = None, level: int = 30)[source]
+
            Create a logging environment for a given log_obj.
            
 
            
 
            Parameters:
            
 
              
@@ -115,8 +135,8 @@
 
            • logfile (str) – Name of the log file
              • 
 
            • level (int) – Set the root logger level to the specified level. If for example set
 to logging.DEBUG detailed debug logs inludcing filename and
-function name are displayed. For :py:obj:`logging.INFO only the message
-logged from errors, warnings and infos will be displayed.
              • 
+function name are displayed. For logging.INFO only the
+message logged from errors, warnings and infos will be displayed.
              
 
            
 
            
 
            
diff --git a/stable/changelog.html b/stable/changelog.html
index c341651..0b137ec 100644
--- a/stable/changelog.html
+++ b/stable/changelog.html
@@ -125,6 +125,9 @@
              
   
            
 
            Changelog
            
+
              
+
            • Cleanup logger function
              • 
+
            
 
            
 
            v0.1.31 (2024-07-08)
            
 
              
diff --git a/stable/genindex.html b/stable/genindex.html
index ab5cb51..9b826a5 100644
--- a/stable/genindex.html
+++ b/stable/genindex.html
@@ -139,6 +139,8 @@ 
              B
              
 
              C
              
 
              
   
                
+      
              • check_suffix() (in module mdacli.logger)
+
                • 
       
              • cli() (in module mdacli.cli)
 
                • 
       
              • convert_analysis_parameters() (in module mdacli.libcli)
diff --git a/stable/objects.inv b/stable/objects.inv
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diff --git a/stable/searchindex.js b/stable/searchindex.js
index 716e176..cdb9308 100644
--- a/stable/searchindex.js
+++ b/stable/searchindex.js
@@ -1 +1 @@
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"Pull Request": [[9, "pull-request"]], "Pull Request your changes": [[9, "pull-request-your-changes"]], "Results Saving": [[5, "module-mdacli.save"]], "Running tests with tox": [[9, "running-tests-with-tox"]], "Support functions for CLI": [[3, "module-mdacli.libcli"]], "Update CHANGELOG": [[9, "update-changelog"]], "Usage": [[14, "usage"]], "Utilities": [[6, "module-mdacli.utils"]], "conda": [[11, "conda"]], "pip": [[11, "pip"]], "v0.1.0 (2021-11-18)": [[8, "v0-1-0-2021-11-18"]], "v0.1.1 (2021-11-18)": [[8, "v0-1-1-2021-11-18"]], "v0.1.10 (2022-01-18)": [[8, "v0-1-10-2022-01-18"]], "v0.1.11 (2022-01-19)": [[8, "v0-1-11-2022-01-19"]], "v0.1.12 (2022-01-19)": [[8, "v0-1-12-2022-01-19"]], "v0.1.13 (2022-02-16)": [[8, "v0-1-13-2022-02-16"]], "v0.1.14 (2022-02-17)": [[8, "v0-1-14-2022-02-17"]], "v0.1.15 (2022-02-25)": [[8, "v0-1-15-2022-02-25"]], "v0.1.16 (2022-02-25)": [[8, "v0-1-16-2022-02-25"]], "v0.1.17 (2022-04-07)": [[8, "v0-1-17-2022-04-07"]], "v0.1.18 (2022-04-12)": [[8, 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