diff --git a/0.1.31/_modules/index.html b/0.1.31/_modules/index.html index c35c6cb..fd41492 100644 --- a/0.1.31/_modules/index.html +++ b/0.1.31/_modules/index.html @@ -102,7 +102,7 @@

All modules for which code is available

© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein. - Last updated on Jul 08, 2024. + Last updated on Jul 09, 2024.

diff --git a/0.1.31/_modules/mdacli/cli.html b/0.1.31/_modules/mdacli/cli.html index b685f69..82fdad0 100644 --- a/0.1.31/_modules/mdacli/cli.html +++ b/0.1.31/_modules/mdacli/cli.html @@ -247,7 +247,7 @@

Source code for mdacli.cli

 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/_modules/mdacli/colors.html b/0.1.31/_modules/mdacli/colors.html
index 20985d8..d62cd2c 100644
--- a/0.1.31/_modules/mdacli/colors.html
+++ b/0.1.31/_modules/mdacli/colors.html
@@ -314,7 +314,7 @@ 
Source code for mdacli.colors
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/_modules/mdacli/libcli.html b/0.1.31/_modules/mdacli/libcli.html
index d02d39b..3380f62 100644
--- a/0.1.31/_modules/mdacli/libcli.html
+++ b/0.1.31/_modules/mdacli/libcli.html
@@ -958,7 +958,7 @@ 
Source code for mdacli.libcli
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/_modules/mdacli/logger.html b/0.1.31/_modules/mdacli/logger.html
index 68af96d..2759bc5 100644
--- a/0.1.31/_modules/mdacli/logger.html
+++ b/0.1.31/_modules/mdacli/logger.html
@@ -165,7 +165,7 @@ 
Source code for mdacli.logger
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/_modules/mdacli/save.html b/0.1.31/_modules/mdacli/save.html
index 90b2f64..94f00ff 100644
--- a/0.1.31/_modules/mdacli/save.html
+++ b/0.1.31/_modules/mdacli/save.html
@@ -553,7 +553,7 @@ 
Source code for mdacli.save
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/_modules/mdacli/utils.html b/0.1.31/_modules/mdacli/utils.html
index 2637fcc..8888189 100644
--- a/0.1.31/_modules/mdacli/utils.html
+++ b/0.1.31/_modules/mdacli/utils.html
@@ -369,7 +369,7 @@ 
Source code for mdacli.utils
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api.html b/0.1.31/api.html
index 3c8d315..a2bd874 100644
--- a/0.1.31/api.html
+++ b/0.1.31/api.html
@@ -127,7 +127,7 @@ 
API library documentation
     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api/cli.html b/0.1.31/api/cli.html
index 795c5d3..0785451 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='140462186230400'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]

+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140423703360128'>, 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.

@@ -160,7 +160,7 @@
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api/colors.html b/0.1.31/api/colors.html
index e13fc72..b099c97 100644
--- a/0.1.31/api/colors.html
+++ b/0.1.31/api/colors.html
@@ -330,7 +330,7 @@
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api/libcli.html b/0.1.31/api/libcli.html
index eed94c4..dfc82dc 100644
--- a/0.1.31/api/libcli.html
+++ b/0.1.31/api/libcli.html
@@ -427,7 +427,7 @@
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api/logger.html b/0.1.31/api/logger.html
index 12abcfb..cd634da 100644
--- a/0.1.31/api/logger.html
+++ b/0.1.31/api/logger.html
@@ -136,7 +136,7 @@
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api/save.html b/0.1.31/api/save.html
index 5bf2427..93e3dd7 100644
--- a/0.1.31/api/save.html
+++ b/0.1.31/api/save.html
@@ -344,7 +344,7 @@
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/api/utils.html b/0.1.31/api/utils.html
index 8be2bed..d1dfc33 100644
--- a/0.1.31/api/utils.html
+++ b/0.1.31/api/utils.html
@@ -204,7 +204,7 @@
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/authors.html b/0.1.31/authors.html
index ac3ca85..5e87b53 100644
--- a/0.1.31/authors.html
+++ b/0.1.31/authors.html
@@ -110,7 +110,7 @@ 
Authors
 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/changelog.html b/0.1.31/changelog.html
index 9e2edd1..c341651 100644
--- a/0.1.31/changelog.html
+++ b/0.1.31/changelog.html
@@ -352,7 +352,7 @@ 
v0.1.0 (2021-11-18)
     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/contributing.html b/0.1.31/contributing.html
index b2e3f14..bb7816d 100644
--- a/0.1.31/contributing.html
+++ b/0.1.31/contributing.html
@@ -251,7 +251,7 @@ 
Pull Request
     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/genindex.html b/0.1.31/genindex.html
index b59a5a5..ab5cb51 100644
--- a/0.1.31/genindex.html
+++ b/0.1.31/genindex.html
@@ -437,7 +437,7 @@ 
Y

 
   

     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/index.html b/0.1.31/index.html
index b3d061b..8942c4a 100644
--- a/0.1.31/index.html
+++ b/0.1.31/index.html
@@ -198,7 +198,7 @@ 
Available modules
     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/installation.html b/0.1.31/installation.html
index 082e297..e32251c 100644
--- a/0.1.31/installation.html
+++ b/0.1.31/installation.html
@@ -143,7 +143,7 @@ 
conda
     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
       

   

 
diff --git a/0.1.31/philosophy.html b/0.1.31/philosophy.html
index 9c0cb44..e9ac197 100644
--- a/0.1.31/philosophy.html
+++ b/0.1.31/philosophy.html
@@ -155,7 +155,7 @@ 
Philosophy and approach
     
© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein.
-      Last updated on Jul 08, 2024.
+      Last updated on Jul 09, 2024.
diff --git a/0.1.31/py-modindex.html b/0.1.31/py-modindex.html index c7fbb6d..bf4eaca 100644 --- a/0.1.31/py-modindex.html +++ b/0.1.31/py-modindex.html @@ -146,7 +146,7 @@

Python Module Index

© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein. - Last updated on Jul 08, 2024. + Last updated on Jul 09, 2024.

diff --git a/0.1.31/readme.html b/0.1.31/readme.html index d6e7446..8ee2d8b 100644 --- a/0.1.31/readme.html +++ b/0.1.31/readme.html @@ -193,7 +193,7 @@

Available modules

© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein. - Last updated on Jul 08, 2024. + Last updated on Jul 09, 2024.

diff --git a/0.1.31/search.html b/0.1.31/search.html index b27879d..fb8e1f8 100644 --- a/0.1.31/search.html +++ b/0.1.31/search.html @@ -109,7 +109,7 @@

© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein. - Last updated on Jul 08, 2024. + Last updated on Jul 09, 2024.

diff --git a/0.1.31/searchindex.js b/0.1.31/searchindex.js index 74753ae..716e176 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 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"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, "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, "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/0.1.31/usage.html b/0.1.31/usage.html index 7a3459f..729b94b 100644 --- a/0.1.31/usage.html +++ b/0.1.31/usage.html @@ -151,7 +151,7 @@

Usage

© Copyright 2021, Philip Loche, Joao MC Teixeira and Oliver Beckstein. - Last updated on Jul 08, 2024. + Last updated on Jul 09, 2024.

diff --git a/dev/_modules/index.html b/dev/_modules/index.html index a22f018..fd41492 100644 --- a/dev/_modules/index.html +++ b/dev/_modules/index.html @@ -3,7 +3,7 @@ - Overview: module code — mdacli 0.1.32 documentation + Overview: module code — mdacli 0.1.31 documentation @@ -17,13 +17,13 @@ - + @@ -42,7 +42,7 @@
- 0.1.32 + 0.1.31
@@ -129,7 +129,7 @@

All modules for which code is available

aria-label="versions"> - 0.1.32 + 0.1.31 diff --git a/dev/_modules/mdacli/cli.html b/dev/_modules/mdacli/cli.html index 78d6d83..82fdad0 100644 --- a/dev/_modules/mdacli/cli.html +++ b/dev/_modules/mdacli/cli.html @@ -3,7 +3,7 @@ - mdacli.cli — mdacli 0.1.32 documentation + mdacli.cli — mdacli 0.1.31 documentation @@ -17,13 +17,13 @@ - + @@ -42,7 +42,7 @@
- 0.1.32 + 0.1.31
@@ -274,7 +274,7 @@

Source code for mdacli.cli

      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/_modules/mdacli/colors.html b/dev/_modules/mdacli/colors.html
index f7f432e..d62cd2c 100644
--- a/dev/_modules/mdacli/colors.html
+++ b/dev/_modules/mdacli/colors.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.colors — mdacli 0.1.32 documentation
+  mdacli.colors — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -341,7 +341,7 @@ 
Source code for mdacli.colors
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/_modules/mdacli/libcli.html b/dev/_modules/mdacli/libcli.html
index 9ffc26f..3380f62 100644
--- a/dev/_modules/mdacli/libcli.html
+++ b/dev/_modules/mdacli/libcli.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.libcli — mdacli 0.1.32 documentation
+  mdacli.libcli — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -985,7 +985,7 @@ 
Source code for mdacli.libcli
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/_modules/mdacli/logger.html b/dev/_modules/mdacli/logger.html
index 2594940..2759bc5 100644
--- a/dev/_modules/mdacli/logger.html
+++ b/dev/_modules/mdacli/logger.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.logger — mdacli 0.1.32 documentation
+  mdacli.logger — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -95,60 +95,20 @@ 
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 filesuffix 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: logging.Logger,
-    logfile: Optional[Union[str, Path]] = None,
-    level: int = logging.WARNING,
-):
-    """Create a logging environment for a given ``log_obj``.
+def setup_logging(logobj, logfile=None, level=logging.WARNING):
+    """
+    Create a logging environment for a given logobj.
 
     Parameters
     ----------
@@ -159,52 +119,39 @@ 
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}:{funcName}:{lineno} - "
-        format += "{message}"
-
-        formatter = logging.Formatter(format, style="{")
-        handlers: List[Union[logging.StreamHandler, logging.FileHandler]] = []
+            format = (
+                "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
+                "{message}"
+            )
+        else:
+            format = "{message}"
 
-        stream_handler = logging.StreamHandler(sys.stdout)
-        stream_handler.setFormatter(formatter)
-        handlers.append(stream_handler)
+        logging.basicConfig(format=format,
+                            handlers=[logging.StreamHandler(sys.stdout)],
+                            level=level,
+                            style='{')
 
         if logfile:
-            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)
+            logfile += ".log" * (not logfile.endswith("log"))
+            handler = logging.FileHandler(filename=logfile, encoding='utf-8')
+            handler.setFormatter(logging.Formatter(format, style='{'))
+            logobj.addHandler(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"))
-
-        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!r}.")
-        else:
-            logobj.debug("Logging to file is disabled.")
-
-        for handler in handlers:
-            logobj.addHandler(handler)
+            logobj.info('Logging to file is disabled.')
 
         yield
-
     finally:
+        handlers = logobj.handlers[:]
         for handler in handlers:
-            handler.flush()
             handler.close()
             logobj.removeHandler(handler)

 
@@ -245,7 +192,7 @@ 
Source code for mdacli.logger
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/_modules/mdacli/save.html b/dev/_modules/mdacli/save.html
index d68e06c..94f00ff 100644
--- a/dev/_modules/mdacli/save.html
+++ b/dev/_modules/mdacli/save.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.save — mdacli 0.1.32 documentation
+  mdacli.save — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -580,7 +580,7 @@ 
Source code for mdacli.save
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/_modules/mdacli/utils.html b/dev/_modules/mdacli/utils.html
index 8863210..8888189 100644
--- a/dev/_modules/mdacli/utils.html
+++ b/dev/_modules/mdacli/utils.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.utils — mdacli 0.1.32 documentation
+  mdacli.utils — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -396,7 +396,7 @@ 
Source code for mdacli.utils
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js
index e673888..ef6aebe 100644
--- a/dev/_static/documentation_options.js
+++ b/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.32',
+    VERSION: '0.1.31',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/dev/_static/opensearch.xml b/dev/_static/opensearch.xml
index 479fda6..82ff9e2 100644
--- a/dev/_static/opensearch.xml
+++ b/dev/_static/opensearch.xml
@@ -1,11 +1,11 @@
 
 
   mdacli
-  Search mdacli 0.1.32 documentation
+  Search mdacli 0.1.31 documentation
   utf-8
   
-  mdacli 0.1.32 documentation
+  mdacli 0.1.31 documentation
   https://mdacli.mdanalysis.org//_static/mdanalysis-logo.ico
   
 
\ No newline at end of file
diff --git a/dev/api.html b/dev/api.html
index 4f06a71..a2bd874 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -4,7 +4,7 @@
   
 
   
-  API library documentation — mdacli 0.1.32 documentation
+  API library documentation — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -154,7 +154,7 @@ 
API library documentation
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/api/cli.html b/dev/api/cli.html
index 2f4db5b..0785451 100644
--- a/dev/api/cli.html
+++ b/dev/api/cli.html
@@ -4,7 +4,7 @@
   
 
   
-  High-Level API — mdacli 0.1.32 documentation
+  High-Level API — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -106,7 +106,7 @@
 
The toplevel command line interface.

 

 

-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='139825847530112'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]

+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140423703360128'>, 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.

@@ -187,7 +187,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/api/colors.html b/dev/api/colors.html
index 2e90659..b099c97 100644
--- a/dev/api/colors.html
+++ b/dev/api/colors.html
@@ -4,7 +4,7 @@
   
 
   
-  Coloring — mdacli 0.1.32 documentation
+  Coloring — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -357,7 +357,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/api/libcli.html b/dev/api/libcli.html
index 93f94d6..dfc82dc 100644
--- a/dev/api/libcli.html
+++ b/dev/api/libcli.html
@@ -4,7 +4,7 @@
   
 
   
-  Support functions for CLI — mdacli 0.1.32 documentation
+  Support functions for CLI — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -454,7 +454,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/api/logger.html b/dev/api/logger.html
index 30a96b9..cd634da 100644
--- a/dev/api/logger.html
+++ b/dev/api/logger.html
@@ -4,7 +4,7 @@
   
 
   
-  Logging — mdacli 0.1.32 documentation
+  Logging — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               

-                0.1.32
+                0.1.31
               

 

   
@@ -66,7 +66,6 @@
 
  • Results Saving
    • 
 
  • Coloring
    • 
 
  • Logging
 
    • 
@@ -105,29 +104,10 @@
   
    
 
    Logging
    
 
    Logging.
    
-
    
-
    
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-
    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 filesuffix i.e. .txt.)
      • 
-
    
-
    
-
    Returns:
    
-
    Checked and probably extended file name.
    
-
    
-
    
-
    
-
 
    
 
    
-mdacli.logger.setup_logging(logobj: Logger, logfile: str | Path | None = None, level: int = 30)[source]
    
-
    Create a logging environment for a given log_obj.
    
+mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
+
    Create a logging environment for a given logobj.
    
 
    
 
    Parameters:
    
 
      
@@ -135,8 +115,8 @@
 
    • 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 logging.INFO only the
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      • 
+function name are displayed. For :py:obj:`logging.INFO only the message
+logged from errors, warnings and infos will be displayed.
      
 
    
 
    
 
    
@@ -183,7 +163,7 @@
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+        0.1.31
       
     
 
diff --git a/dev/api/save.html b/dev/api/save.html
index d62ebdc..93e3dd7 100644
--- a/dev/api/save.html
+++ b/dev/api/save.html
@@ -4,7 +4,7 @@
   
 
   
-  Results Saving — mdacli 0.1.32 documentation
+  Results Saving — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
    
-                0.1.32
+                0.1.31
               
    
 
    
   
@@ -371,7 +371,7 @@
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-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/api/utils.html b/dev/api/utils.html
index a25a90b..d1dfc33 100644
--- a/dev/api/utils.html
+++ b/dev/api/utils.html
@@ -4,7 +4,7 @@
   
 
   
-  Utilities — mdacli 0.1.32 documentation
+  Utilities — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
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+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
    
-                0.1.32
+                0.1.31
               
    
 
    
   
@@ -231,7 +231,7 @@
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-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/authors.html b/dev/authors.html
index 5cbb4d6..5e87b53 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -4,7 +4,7 @@
   
 
   
-  Authors — mdacli 0.1.32 documentation
+  Authors — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
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+        
         
         
         
     
     
     
     
@@ -44,7 +44,7 @@
               
           
               
    
-                0.1.32
+                0.1.31
               
    
 
    
   
@@ -137,7 +137,7 @@ 
    Authors
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-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/changelog.html b/dev/changelog.html
index 1304834..c341651 100644
--- a/dev/changelog.html
+++ b/dev/changelog.html
@@ -4,7 +4,7 @@
   
 
   
-  Changelog — mdacli 0.1.32 documentation
+  Changelog — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
    
-                0.1.32
+                0.1.31
               
    
 
    
   
@@ -62,7 +62,6 @@
 
  • Contributing
    • 
 
  • API library documentation
    • 
 
  • Changelog
      
-
    • v0.1.32 (2024-07-09)
      • 
 
    • v0.1.31 (2024-07-08)
      • 
 
    • v0.1.30 (2024-04-03)
      • 
 
    • v0.1.29 (2024-03-21)
      • 
@@ -126,12 +125,6 @@
              
   
      
 
      Changelog
      
-
      
-
      v0.1.32 (2024-07-09)
      
-
        
-
      • Cleanup logger function
        • 
-
      
-
      
 
      
 
      v0.1.31 (2024-07-08)
      
 
        
@@ -386,7 +379,7 @@ 
        v0.1.0 (2021-11-18)
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/contributing.html b/dev/contributing.html
index e511b69..bb7816d 100644
--- a/dev/contributing.html
+++ b/dev/contributing.html
@@ -4,7 +4,7 @@
   
 
   
-  Contributing — mdacli 0.1.32 documentation
+  Contributing — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
        
-                0.1.32
+                0.1.31
               
        
 
        
   
@@ -278,7 +278,7 @@ 
        Pull Request
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/genindex.html b/dev/genindex.html
index 64f94d1..ab5cb51 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Index — mdacli 0.1.32 documentation
+  Index — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
        
-                0.1.32
+                0.1.31
               
        
 
        
   
@@ -139,8 +139,6 @@ 
        B
        
 
        C
        
 
        
   
          
-      
        • check_suffix() (in module mdacli.logger)
-
          • 
       
        • cli() (in module mdacli.cli)
 
          • 
       
        • convert_analysis_parameters() (in module mdacli.libcli)
@@ -466,7 +464,7 @@ 
          Y
          
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-        0.1.32
+        0.1.31
       
     
 
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index aaeeece..8942c4a 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -4,7 +4,7 @@
   
 
   
-  MDAnalysis command line interface — mdacli 0.1.32 documentation
+  MDAnalysis command line interface — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -44,7 +44,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -225,7 +225,7 @@ 
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-        0.1.32
+        0.1.31
       
     
 
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index ad87670..e32251c 100644
--- a/dev/installation.html
+++ b/dev/installation.html
@@ -4,7 +4,7 @@
   
 
   
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+                0.1.31
               
          
 
          
   
@@ -170,7 +170,7 @@ 
          conda
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/dev/objects.inv b/dev/objects.inv
index b58dabf..6986add 100644
Binary files a/dev/objects.inv and b/dev/objects.inv differ
diff --git a/dev/philosophy.html b/dev/philosophy.html
index 6661305..e9ac197 100644
--- a/dev/philosophy.html
+++ b/dev/philosophy.html
@@ -4,7 +4,7 @@
   
 
   
-  Philosophy and approach — mdacli 0.1.32 documentation
+  Philosophy and approach — mdacli 0.1.31 documentation
       
       
       
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+        
         
         
         
     
     
     
     
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+                0.1.31
               
          
 
          
   
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-        0.1.32
+        0.1.31
       
     
 
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index 5f598d1..bf4eaca 100644
--- a/dev/py-modindex.html
+++ b/dev/py-modindex.html
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+        0.1.31
       
     
 
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index 1eb9da0..8ee2d8b 100644
--- a/dev/readme.html
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+  MDAnalysis command line interface — mdacli 0.1.31 documentation
       
       
       
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index 94b66dd..fb8e1f8 100644
--- a/dev/search.html
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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, "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, "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/sitemap.xml b/dev/sitemap.xml
index 40091ea..deecdff 100644
--- a/dev/sitemap.xml
+++ b/dev/sitemap.xml
@@ -1,2 +1,2 @@
 
-https://mdacli.mdanalysis.org/en/0.1.32/api.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/authors.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/changelog.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/contributing.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/installation.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/philosophy.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/readme.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/usage.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/genindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/py-modindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/search.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/opensearch.html
\ No newline at end of file
+https://mdacli.mdanalysis.org/en/0.1.31/api.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/authors.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/changelog.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/contributing.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/installation.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/philosophy.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/readme.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/usage.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/genindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/py-modindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/search.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/opensearch.html
\ No newline at end of file
diff --git a/dev/usage.html b/dev/usage.html
index b727c33..729b94b 100644
--- a/dev/usage.html
+++ b/dev/usage.html
@@ -4,7 +4,7 @@
   
 
   
-  Usage — mdacli 0.1.32 documentation
+  Usage — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -178,7 +178,7 @@ 
          Usage
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/latest/index.html b/latest/index.html
index 5b99a32..c038085 100644
--- a/latest/index.html
+++ b/latest/index.html
@@ -1,6 +1,6 @@
 
 
 
-Redirecting to https://mdacli.mdanalysis.org/0.1.32/index.html
-
-
+Redirecting to https://mdacli.mdanalysis.org/0.1.31/index.html
+
+
diff --git a/sitemap_index.xml b/sitemap_index.xml
index a7654a2..f12455e 100644
--- a/sitemap_index.xml
+++ b/sitemap_index.xml
@@ -1,2 +1,2 @@
 
-https://mdacli.mdanalysis.org/0.1.32/sitemap.xmlhttps://mdacli.mdanalysis.org/stable/sitemap.xmlhttps://mdacli.mdanalysis.org/dev/sitemap.xml
\ No newline at end of file
+https://mdacli.mdanalysis.org/0.1.31/sitemap.xmlhttps://mdacli.mdanalysis.org/stable/sitemap.xmlhttps://mdacli.mdanalysis.org/dev/sitemap.xml
\ No newline at end of file
diff --git a/stable/_modules/index.html b/stable/_modules/index.html
index a22f018..fd41492 100644
--- a/stable/_modules/index.html
+++ b/stable/_modules/index.html
@@ -3,7 +3,7 @@
 
   
   
-  Overview: module code — mdacli 0.1.32 documentation
+  Overview: module code — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -129,7 +129,7 @@ 
          All modules for which code is available
          
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_modules/mdacli/cli.html b/stable/_modules/mdacli/cli.html
index 78d6d83..82fdad0 100644
--- a/stable/_modules/mdacli/cli.html
+++ b/stable/_modules/mdacli/cli.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.cli — mdacli 0.1.32 documentation
+  mdacli.cli — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -274,7 +274,7 @@ 
          Source code for mdacli.cli
                aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_modules/mdacli/colors.html b/stable/_modules/mdacli/colors.html
index f7f432e..d62cd2c 100644
--- a/stable/_modules/mdacli/colors.html
+++ b/stable/_modules/mdacli/colors.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.colors — mdacli 0.1.32 documentation
+  mdacli.colors — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -341,7 +341,7 @@ 
          Source code for mdacli.colors
                aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_modules/mdacli/libcli.html b/stable/_modules/mdacli/libcli.html
index 9ffc26f..3380f62 100644
--- a/stable/_modules/mdacli/libcli.html
+++ b/stable/_modules/mdacli/libcli.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.libcli — mdacli 0.1.32 documentation
+  mdacli.libcli — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -985,7 +985,7 @@ 
          Source code for mdacli.libcli
                aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_modules/mdacli/logger.html b/stable/_modules/mdacli/logger.html
index 2594940..2759bc5 100644
--- a/stable/_modules/mdacli/logger.html
+++ b/stable/_modules/mdacli/logger.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.logger — mdacli 0.1.32 documentation
+  mdacli.logger — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -95,60 +95,20 @@ 
          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 filesuffix 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: logging.Logger,
-    logfile: Optional[Union[str, Path]] = None,
-    level: int = logging.WARNING,
-):
-    """Create a logging environment for a given ``log_obj``.
+def setup_logging(logobj, logfile=None, level=logging.WARNING):
+    """
+    Create a logging environment for a given logobj.
 
     Parameters
     ----------
@@ -159,52 +119,39 @@ 
          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}:{funcName}:{lineno} - "
-        format += "{message}"
-
-        formatter = logging.Formatter(format, style="{")
-        handlers: List[Union[logging.StreamHandler, logging.FileHandler]] = []
+            format = (
+                "[{levelname}] {filename}:{name}:{funcName}:{lineno}: "
+                "{message}"
+            )
+        else:
+            format = "{message}"
 
-        stream_handler = logging.StreamHandler(sys.stdout)
-        stream_handler.setFormatter(formatter)
-        handlers.append(stream_handler)
+        logging.basicConfig(format=format,
+                            handlers=[logging.StreamHandler(sys.stdout)],
+                            level=level,
+                            style='{')
 
         if logfile:
-            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)
+            logfile += ".log" * (not logfile.endswith("log"))
+            handler = logging.FileHandler(filename=logfile, encoding='utf-8')
+            handler.setFormatter(logging.Formatter(format, style='{'))
+            logobj.addHandler(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"))
-
-        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!r}.")
-        else:
-            logobj.debug("Logging to file is disabled.")
-
-        for handler in handlers:
-            logobj.addHandler(handler)
+            logobj.info('Logging to file is disabled.')
 
         yield
-
     finally:
+        handlers = logobj.handlers[:]
         for handler in handlers:
-            handler.flush()
             handler.close()
             logobj.removeHandler(handler)
          
 
@@ -245,7 +192,7 @@ 
          Source code for mdacli.logger
                aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_modules/mdacli/save.html b/stable/_modules/mdacli/save.html
index d68e06c..94f00ff 100644
--- a/stable/_modules/mdacli/save.html
+++ b/stable/_modules/mdacli/save.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.save — mdacli 0.1.32 documentation
+  mdacli.save — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -580,7 +580,7 @@ 
          Source code for mdacli.save
                aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_modules/mdacli/utils.html b/stable/_modules/mdacli/utils.html
index 8863210..8888189 100644
--- a/stable/_modules/mdacli/utils.html
+++ b/stable/_modules/mdacli/utils.html
@@ -3,7 +3,7 @@
 
   
   
-  mdacli.utils — mdacli 0.1.32 documentation
+  mdacli.utils — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -396,7 +396,7 @@ 
          Source code for mdacli.utils
                aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/_static/documentation_options.js b/stable/_static/documentation_options.js
index e673888..ef6aebe 100644
--- a/stable/_static/documentation_options.js
+++ b/stable/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.32',
+    VERSION: '0.1.31',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/stable/_static/opensearch.xml b/stable/_static/opensearch.xml
index 479fda6..82ff9e2 100644
--- a/stable/_static/opensearch.xml
+++ b/stable/_static/opensearch.xml
@@ -1,11 +1,11 @@
 
 
   mdacli
-  Search mdacli 0.1.32 documentation
+  Search mdacli 0.1.31 documentation
   utf-8
   
-  mdacli 0.1.32 documentation
+  mdacli 0.1.31 documentation
   https://mdacli.mdanalysis.org//_static/mdanalysis-logo.ico
   
 
\ No newline at end of file
diff --git a/stable/api.html b/stable/api.html
index 4f06a71..a2bd874 100644
--- a/stable/api.html
+++ b/stable/api.html
@@ -4,7 +4,7 @@
   
 
   
-  API library documentation — mdacli 0.1.32 documentation
+  API library documentation — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -154,7 +154,7 @@ 
          API library documentation
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/api/cli.html b/stable/api/cli.html
index 2f4db5b..0785451 100644
--- a/stable/api/cli.html
+++ b/stable/api/cli.html
@@ -4,7 +4,7 @@
   
 
   
-  High-Level API — mdacli 0.1.32 documentation
+  High-Level API — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -106,7 +106,7 @@
 
          The toplevel command line interface.
          
 
          
 
          
-mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='139825847530112'>, version='', description='', skip_modules=None, ignore_warnings=False)[source]
          
+mdacli.cli.cli(name, module_list, base_class=<Mock name='mock.AnalysisBase' id='140423703360128'>, 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.
          
@@ -187,7 +187,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/api/colors.html b/stable/api/colors.html
index 2e90659..b099c97 100644
--- a/stable/api/colors.html
+++ b/stable/api/colors.html
@@ -4,7 +4,7 @@
   
 
   
-  Coloring — mdacli 0.1.32 documentation
+  Coloring — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -357,7 +357,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/api/libcli.html b/stable/api/libcli.html
index 93f94d6..dfc82dc 100644
--- a/stable/api/libcli.html
+++ b/stable/api/libcli.html
@@ -4,7 +4,7 @@
   
 
   
-  Support functions for CLI — mdacli 0.1.32 documentation
+  Support functions for CLI — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -454,7 +454,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/api/logger.html b/stable/api/logger.html
index 30a96b9..cd634da 100644
--- a/stable/api/logger.html
+++ b/stable/api/logger.html
@@ -4,7 +4,7 @@
   
 
   
-  Logging — mdacli 0.1.32 documentation
+  Logging — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -66,7 +66,6 @@
 
        • Results Saving
          • 
 
        • Coloring
          • 
 
        • Logging
 
          • 
@@ -105,29 +104,10 @@
   
          
 
          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 filesuffix i.e. .txt.)
            • 
-
          
-
          
-
          Returns:
          
-
          Checked and probably extended file name.
          
-
          
-
          
-
          
-
 
          
 
          
-mdacli.logger.setup_logging(logobj: Logger, logfile: str | Path | None = None, level: int = 30)[source]
          
-
          Create a logging environment for a given log_obj.
          
+mdacli.logger.setup_logging(logobj, logfile=None, level=30)[source]
+
          Create a logging environment for a given logobj.
          
 
          
 
          Parameters:
          
 
            
@@ -135,8 +115,8 @@
 
          • 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 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.
            
 
          
 
          
 
          
@@ -183,7 +163,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/api/save.html b/stable/api/save.html
index d62ebdc..93e3dd7 100644
--- a/stable/api/save.html
+++ b/stable/api/save.html
@@ -4,7 +4,7 @@
   
 
   
-  Results Saving — mdacli 0.1.32 documentation
+  Results Saving — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -371,7 +371,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/api/utils.html b/stable/api/utils.html
index a25a90b..d1dfc33 100644
--- a/stable/api/utils.html
+++ b/stable/api/utils.html
@@ -4,7 +4,7 @@
   
 
   
-  Utilities — mdacli 0.1.32 documentation
+  Utilities — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -231,7 +231,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/authors.html b/stable/authors.html
index 5cbb4d6..5e87b53 100644
--- a/stable/authors.html
+++ b/stable/authors.html
@@ -4,7 +4,7 @@
   
 
   
-  Authors — mdacli 0.1.32 documentation
+  Authors — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -44,7 +44,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -137,7 +137,7 @@ 
          Authors
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/changelog.html b/stable/changelog.html
index 1304834..c341651 100644
--- a/stable/changelog.html
+++ b/stable/changelog.html
@@ -4,7 +4,7 @@
   
 
   
-  Changelog — mdacli 0.1.32 documentation
+  Changelog — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
          
-                0.1.32
+                0.1.31
               
          
 
          
   
@@ -62,7 +62,6 @@
 
        • Contributing
          • 
 
        • API library documentation
          • 
 
        • Changelog
            
-
          • v0.1.32 (2024-07-09)
            • 
 
          • v0.1.31 (2024-07-08)
            • 
 
          • v0.1.30 (2024-04-03)
            • 
 
          • v0.1.29 (2024-03-21)
            • 
@@ -126,12 +125,6 @@
              
   
            
 
            Changelog
            
-
            
-
            v0.1.32 (2024-07-09)
            
-
              
-
            • Cleanup logger function
              • 
-
            
-
            
 
            
 
            v0.1.31 (2024-07-08)
            
 
              
@@ -386,7 +379,7 @@ 
              v0.1.0 (2021-11-18)
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/contributing.html b/stable/contributing.html
index e511b69..bb7816d 100644
--- a/stable/contributing.html
+++ b/stable/contributing.html
@@ -4,7 +4,7 @@
   
 
   
-  Contributing — mdacli 0.1.32 documentation
+  Contributing — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
              
-                0.1.32
+                0.1.31
               
              
 
              
   
@@ -278,7 +278,7 @@ 
              Pull Request
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/genindex.html b/stable/genindex.html
index 64f94d1..ab5cb51 100644
--- a/stable/genindex.html
+++ b/stable/genindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Index — mdacli 0.1.32 documentation
+  Index — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -42,7 +42,7 @@
               
           
               
              
-                0.1.32
+                0.1.31
               
              
 
              
   
@@ -139,8 +139,6 @@ 
              B
              
 
              C
              
 
              
   
                
-      
              • check_suffix() (in module mdacli.logger)
-
                • 
       
              • cli() (in module mdacli.cli)
 
                • 
       
              • convert_analysis_parameters() (in module mdacli.libcli)
@@ -466,7 +464,7 @@ 
                Y
                
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/index.html b/stable/index.html
index aaeeece..8942c4a 100644
--- a/stable/index.html
+++ b/stable/index.html
@@ -4,7 +4,7 @@
   
 
   
-  MDAnalysis command line interface — mdacli 0.1.32 documentation
+  MDAnalysis command line interface — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -44,7 +44,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -225,7 +225,7 @@ 
                Available modules
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/installation.html b/stable/installation.html
index ad87670..e32251c 100644
--- a/stable/installation.html
+++ b/stable/installation.html
@@ -4,7 +4,7 @@
   
 
   
-  Installation — mdacli 0.1.32 documentation
+  Installation — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -170,7 +170,7 @@ 
                conda
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/objects.inv b/stable/objects.inv
index b58dabf..6986add 100644
Binary files a/stable/objects.inv and b/stable/objects.inv differ
diff --git a/stable/philosophy.html b/stable/philosophy.html
index 6661305..e9ac197 100644
--- a/stable/philosophy.html
+++ b/stable/philosophy.html
@@ -4,7 +4,7 @@
   
 
   
-  Philosophy and approach — mdacli 0.1.32 documentation
+  Philosophy and approach — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -182,7 +182,7 @@ 
                Philosophy and approach
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/py-modindex.html b/stable/py-modindex.html
index 5f598d1..bf4eaca 100644
--- a/stable/py-modindex.html
+++ b/stable/py-modindex.html
@@ -3,7 +3,7 @@
 
   
   
-  Python Module Index — mdacli 0.1.32 documentation
+  Python Module Index — mdacli 0.1.31 documentation
       
       
       
@@ -17,13 +17,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -173,7 +173,7 @@ 
                Python Module Index
                
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/readme.html b/stable/readme.html
index 1eb9da0..8ee2d8b 100644
--- a/stable/readme.html
+++ b/stable/readme.html
@@ -4,7 +4,7 @@
   
 
   
-  MDAnalysis command line interface — mdacli 0.1.32 documentation
+  MDAnalysis command line interface — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
      
@@ -43,7 +43,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -220,7 +220,7 @@ 
                Available modules
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/search.html b/stable/search.html
index 94b66dd..fb8e1f8 100644
--- a/stable/search.html
+++ b/stable/search.html
@@ -3,7 +3,7 @@
 
   
   
-  Search — mdacli 0.1.32 documentation
+  Search — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -136,7 +136,7 @@
      aria-label="versions">
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/stable/searchindex.js b/stable/searchindex.js
index ea96ba2..716e176 100644
--- a/stable/searchindex.js
+++ b/stable/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/stable/sitemap.xml b/stable/sitemap.xml
index 40091ea..deecdff 100644
--- a/stable/sitemap.xml
+++ b/stable/sitemap.xml
@@ -1,2 +1,2 @@
 
-https://mdacli.mdanalysis.org/en/0.1.32/api.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/api/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/authors.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/changelog.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/contributing.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/installation.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/philosophy.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/readme.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/usage.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/genindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/py-modindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/mdacli/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/_modules/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/search.htmlhttps://mdacli.mdanalysis.org/en/0.1.32/opensearch.html
\ No newline at end of file
+https://mdacli.mdanalysis.org/en/0.1.31/api.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/api/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/authors.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/changelog.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/contributing.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/installation.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/philosophy.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/readme.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/usage.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/genindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/py-modindex.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/cli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/colors.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/libcli.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/logger.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/save.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/mdacli/utils.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/_modules/index.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/search.htmlhttps://mdacli.mdanalysis.org/en/0.1.31/opensearch.html
\ No newline at end of file
diff --git a/stable/usage.html b/stable/usage.html
index b727c33..729b94b 100644
--- a/stable/usage.html
+++ b/stable/usage.html
@@ -4,7 +4,7 @@
   
 
   
-  Usage — mdacli 0.1.32 documentation
+  Usage — mdacli 0.1.31 documentation
       
       
       
@@ -18,13 +18,13 @@
   
         
         
-        
+        
         
         
         
     
     
     
     
@@ -45,7 +45,7 @@
               
           
               
                
-                0.1.32
+                0.1.31
               
                
 
                
   
@@ -178,7 +178,7 @@ 
                Usage
     
       
-        0.1.32
+        0.1.31
       
     
 
diff --git a/versions.json b/versions.json
index e9f4a59..937a963 100644
--- a/versions.json
+++ b/versions.json
@@ -1,8 +1,8 @@
 [
   {
-    "version": "0.1.32",
-    "display": "0.1.32",
-    "url": "https://mdacli.mdanalysis.org/0.1.32",
+    "version": "0.1.31",
+    "display": "0.1.31",
+    "url": "https://mdacli.mdanalysis.org/0.1.31",
     "latest": true
   },
   {