Updating the log file documentation

04-01-creating_log_files_manually.md

@@ -52,18 +52,33 @@ close(globallog)
 :::{tab-item} Python
 
 ```python
-% The logging module should achieve this.
-import logging
-logging.warning('Watch out!')
+from datetime import datetime
+def track_calls(func):
+    def wrapper(*args, **kwargs):
+        with open('function_log.txt', 'a') as f:
+            timestamp = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
+            f.write(f"[{timestamp}] Calling {func.__name__} with args: {args}, kwargs: {kwargs}\n")
+        result = func(*args, **kwargs)
+        return result
+    return wrapper
+
+# Usage
+@track_calls
+def my_function(x, y,default="TRUE"):
+    return x + y
+
+my_function(1, 2,default="false")
 ```
+
 will output
 
 ```
-WARNING:root:Watch out!
+[2024-12-15 12:05:37] Calling my_function with args: (1, 2), kwargs: {'default': 'false'}
 ```
 
+See also the [Python logging documentation](https://docs.python.org/3/library/logging.html) for controlled output.
 :::
 
 ::::
 
-While some software (Stata, MATLAB) will create log files that contain commands and output, others (R, Python) will  create log files that contain only output. 
+While some software (Stata, MATLAB) will create log files that contain commands and output, others (R, Python) will (by default) create log files that contain only output.

04-creating_log_files.md

@@ -19,4 +19,10 @@ I do note that we are typically only looking to document what the statistical co
 In almost all cased, the generated log files are simple text files, without any formatting, and can be read by any text editor (e.g., Visual Studio Code, Notepad++, etc.).
 
 
-If not, ensure that they are (avoid *Stata SMCL* files, for example).
+If not, ensure that they are (avoid *Stata SMCL* files, for example).
+
+## Some auxiliary info
+
+> It may be useful at this time to understand how to run code non-interactively. 
+>
+> - [Useful resource for R](https://github.com/gastonstat/tutorial-R-noninteractive/)

index.md

@@ -23,6 +23,8 @@ Content is [![License: CC BY-NC 4.0](https://licensebuttons.net/l/by-nc/4.0/80x1
 
 The table of contents goes initially from easy to more complex. Each section should be seen as one  method of running, with varying levels of "trust" in how robust it is to replicators' environments. Some can be combined, others may not work well together.
 
+> A presentation that may be more up-to-date is available at [presentation/](presentation/).
+
 ## TL;DR
 
 Techy lingo for "too long, didn't read". A summary of the most important takeaways will be at the top of each section.

presentation/04-creating_log_files.md

@@ -114,10 +114,109 @@ log using "`globallog'", name(global) replace text
 :::
 ::::
 
+## Python {auto-animate=true}
+
+:::: {.columns}
+
+::: {.column width=30%}
+
+Create a wrapper that will capture the calls for any function
+
+:::
+
+::: {.column width=70%}
+
+
+```{.python code-line-numbers="2-9"}
+from datetime import datetime
+def track_calls(func):
+    def wrapper(*args, **kwargs):
+        with open('function_log.txt', 'a') as f:
+            timestamp = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
+            f.write(f"[{timestamp}] Calling {func.__name__} with args: {args}, kwargs: {kwargs}\n")
+        result = func(*args, **kwargs)
+        return result
+    return wrapper
+
+# Usage
+@track_calls
+def my_function(x, y,default="TRUE"):
+    return x + y
+
+my_function(1, 2,default="false")
+```
+
+:::
+::::
+
+
+## Python {auto-animate=true}
+
+:::: {.columns}
+
+::: {.column width=30%}
+
+Activate the wrapper
+
+:::
+
+::: {.column width=70%}
+
+```{.python code-line-numbers="12"}
+from datetime import datetime
+def track_calls(func):
+    def wrapper(*args, **kwargs):
+        with open('function_log.txt', 'a') as f:
+            timestamp = datetime.now().strftime('%Y-%m-%d %H:%M:%S')
+            f.write(f"[{timestamp}] Calling {func.__name__} with args: {args}, kwargs: {kwargs}\n")
+        result = func(*args, **kwargs)
+        return result
+    return wrapper
+
+# Usage
+@track_calls
+def my_function(x, y,default="TRUE"):
+    return x + y
+
+my_function(1, 2,default="false")
+```
+
+:::
+::::
+
+## Python {auto-animate=true}
+
+:::: {.columns}
+
+::: {.column width=30%}
+
+Ideally, capture the output
+
+:::
+
+::: {.column width=70%}
+
+
+```{.python code-line-numbers="8"}
+# Usage
+@track_calls
+def my_function(x, y,default="TRUE"):
+    return x + y
+
+my_function(1, 2,default="false")
+# Output
+# [2024-12-15 12:05:37] Calling my_function with args: (1, 2), kwargs: {'default': 'false'}
+
+```
+
+:::
+::::
+
+
 ## Notes
 
 - More examples 
-- While some software (Stata, MATLAB) will create log files that contain **commands and output**, others (R, Python) will create log files that contain **only output**. 
+- While some software (Stata, MATLAB) will create log files that contain **commands and output**, others (R, Python) by default will create log files that contain **only output**. 
 
 
 # Creating log files automatically
@@ -166,13 +265,13 @@ which will create a file `main.log` in the same directory as `main.do`.
 To automatically create a log file, run R from the command line using the `BATCH` functionality, as follows:
 
 ```bash
-R CMD BATCH options infile outfile
+R CMD BATCH infile [outfile]
 ```
 
 > On Windows, you may need to include the full path of R: 
 
 ```
-C:\Program Files\R\R-4.1.0\bin\R.exe CMD BATCH main.R
+C:\Program Files\R\R-4.1.0\bin\R.exe CMD BATCH infile [outfile]
 ```
 
 
@@ -181,10 +280,10 @@ C:\Program Files\R\R-4.1.0\bin\R.exe CMD BATCH main.R
 To automatically create a log file, run R from the command line using the `BATCH` functionality, as follows:
 
 ```bash
-R CMD BATCH options infile outfile
+R CMD BATCH main.R
 ```
 
-This will create a file `main.Rout` in the same directory as `main.R`. 
+`outfile` is omitted. This will create a file `main.Rout` in the same directory as `main.R`. 
 
 ## R {auto-animate=true transition="fade"}
 
@@ -204,6 +303,13 @@ If you want to prevent R from saving or restoring its environment (by default, `
 R CMD BATCH --no-save --no-restore main.R main.$(date +%F-%H:%M:%S).Rout
 ```
 
+## R {auto-animate=true transition="fade"}
+
+The most output, and the least "acquired" information, is obtained by running the following command:
+
+```bash
+R CMD BATCH --debugger --verbose --vanilla main.R main.$(date +%F-%H:%M:%S).Rout
+```
 
 ## R {.smaller}