#21: Standardize formatting and rebuild template from scratch

gentzkow · Jun 6, 2019 · 0e95dc0 · 0e95dc0
1 parent d4e02d2
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Showing 31 changed files with 241 additions and 146 deletions.
diff --git a/analysis/log/make.log b/analysis/log/make.log
@@ -1,16 +1,16 @@
 --------------------------------------------------------------------------------
-Makelog started: 2019-05-08 12:19:30
-Working directory: /Users/zong/template/analysis
+Makelog started: 2019-06-06 15:09:33
+Working directory: C:\Users\Zong\template\analysis
 --------------------------------------------------------------------------------
 Input links successfully created!
 External links successfully created!
 Source logs successfully written!
 WARNING! The following target files have been modified according to git status:
-/Users/zong/template/data/output/data_graph.csv
-/Users/zong/template/data/output/data_table.csv
-Executing command: `python  "/Users/zong/template/analysis/code/descriptive.py" `
+C:\Users\Zong\template\data\output\data_graph.csv
+C:\Users\Zong\template\data\output\data_table.csv
+Executing command: `python  "C:\Users\Zong\template\analysis\code\descriptive.py" `
 Output logs successfully written!
 --------------------------------------------------------------------------------
-Makelog ended: 2019-05-08 12:19:33
-Working directory: /Users/zong/template/analysis
+Makelog ended: 2019-06-06 15:09:36
+Working directory: C:\Users\Zong\template\analysis
 --------------------------------------------------------------------------------
diff --git a/analysis/log/output_heads.log b/analysis/log/output_heads.log
@@ -1,19 +1,19 @@
 File headers
 --------------------------------------------------------------------------------
-/Users/zong/template/analysis/output/plot.eps
+C:\Users\Zong\template\analysis\output\plot.eps
 --------------------------------------------------------------------------------
 %!PS-Adobe-3.0 EPSF-3.0
 %%Title: output/plot.eps
-%%Creator: matplotlib version 2.2.3, http://matplotlib.org/
-%%CreationDate: Wed May  8 12:19:32 2019
+%%Creator: matplotlib version 2.0.2, http://matplotlib.org/
+%%CreationDate: Thu Jun  6 15:09:35 2019
 %%Orientation: portrait
 %%BoundingBox: 75 223 536 568
 %%EndComments
 %%BeginProlog
 /mpldict 8 dict def
 mpldict begin
 --------------------------------------------------------------------------------
-/Users/zong/template/analysis/output/tables.txt
+C:\Users\Zong\template\analysis\output\tables.txt
 --------------------------------------------------------------------------------
 <tab:table>
 300001.0

diff --git a/analysis/log/output_stats.log b/analysis/log/output_stats.log
@@ -1,3 +1,3 @@
-file name	last modified	file size
-/Users/zong/template/analysis/output/plot.eps	2019-05-08 19:19:32	13305
-/Users/zong/template/analysis/output/tables.txt	2019-05-08 19:19:33	40
+file name | last modified | file size
+C:\Users\Zong\template\analysis\output\plot.eps | 2019-06-06 22:09:36 | 14084
+C:\Users\Zong\template\analysis\output\tables.txt | 2019-06-06 22:09:36 | 44
diff --git a/analysis/log/source_heads.log b/analysis/log/source_heads.log
@@ -1,6 +1,6 @@
 File headers
 --------------------------------------------------------------------------------
-/Users/zong/template/data/output/data_graph.csv
+C:\Users\Zong\template\data\output\data_graph.csv
 --------------------------------------------------------------------------------
 x
 2
@@ -13,7 +13,7 @@ x
 16
 18
 --------------------------------------------------------------------------------
-/Users/zong/template/data/output/data_table.csv
+C:\Users\Zong\template\data\output\data_table.csv
 --------------------------------------------------------------------------------
 "x"
 2

diff --git a/analysis/log/source_map.log b/analysis/log/source_map.log
@@ -1,3 +1,3 @@
 destination | source
-input/data_table.csv | /Users/zong/template/data/output/data_table.csv
-input/data_graph.csv | /Users/zong/template/data/output/data_graph.csv
+input\data_table.csv | C:\Users\Zong\template\data\output\data_table.csv
+input\data_graph.csv | C:\Users\Zong\template\data\output\data_graph.csv
diff --git a/analysis/log/source_stats.log b/analysis/log/source_stats.log
@@ -1,3 +1,3 @@
-file name	last modified	file size
-/Users/zong/template/data/output/data_graph.csv	2019-05-08 19:17:55	2044452
-/Users/zong/template/data/output/data_table.csv	2019-05-08 19:17:54	2044448
+file name | last modified | file size
+C:\Users\Zong\template\data\output\data_graph.csv | 2019-06-06 22:09:19 | 2344453
+C:\Users\Zong\template\data\output\data_table.csv | 2019-06-06 22:09:16 | 2344449
diff --git a/analysis/output/plot.eps b/analysis/output/plot.eps
diff --git a/data/log/make.log b/data/log/make.log
@@ -1,34 +1,35 @@
 --------------------------------------------------------------------------------
-Makelog started: 2019-05-08 12:17:53
-Working directory: /Users/zong/template/data
+Makelog started: 2019-06-06 15:09:14
+Working directory: C:\Users\Zong\template\data
 --------------------------------------------------------------------------------
 Input links successfully created!
 External links successfully created!
 Source logs successfully written!
-Executing command: `Rscript --no-save "/Users/zong/template/data/code/create_table_data.r"`
+Executing command: `Rscript --no-save "C:\Users\Zong\template\data\code\create_table_data.r"`
+Warning message:
+package 'yaml' was built under R version 3.5.2 
+
 
   ___  ____  ____  ____  ____ (R)
  /__    /   ____/   /   ____/
-___/   /   /___/   /   /___/   15.1   Copyright 1985-2017 StataCorp LLC
+___/   /   /___/   /   /___/   13.1   Copyright 1985-2013 StataCorp LP
   Statistics/Data Analysis            StataCorp
                                       4905 Lakeway Drive
      MP - Parallel Edition            College Station, Texas 77845 USA
                                       800-STATA-PC        http://www.stata.com
                                       979-696-4600        stata@stata.com
                                       979-696-4601 (fax)
 
-Unlimited-user 4-core Stata network license expires 21 Jul 2019:
-       Serial number:  501509201134
-         Licensed to:  Zong Huang
-                       Stanford University
+3-user 8-core Stata network perpetual license:
+       Serial number:  501306208483
+         Licensed to:  IDRE-UCLA
+                       IDRE-UCLA
 
 Notes:
-      1.  Stata is running in batch mode.
-      2.  Unicode is supported; see help unicode_advice.
-      3.  More than 2 billion observations are allowed; see help obs_advice.
-      4.  Maximum number of variables is set to 5000; see help set_maxvar.
+      1.  (/v# option or -set maxvar-) 5000 maximum variables
+      2.  Stata running in batch mode
 
-. do "/Users/zong/template/data/code/create_graph_data.do" 
+. do "C:\Users\Zong\template\data\code\create_graph_data.do" 
 
 . clear all
 
@@ -44,8 +45,8 @@ Notes:
 . 
 . * EXECUTE
 . main
-(1 var, 300,000 obs)
-(300,000 real changes made)
+(1 var, 300000 obs)
+(300000 real changes made)
 (note: file output/data_graph.csv not found)
 file output/data_graph.csv saved
 
@@ -54,6 +55,6 @@ end of do-file
 
 Output logs successfully written!
 --------------------------------------------------------------------------------
-Makelog ended: 2019-05-08 12:17:55
-Working directory: /Users/zong/template/data
+Makelog ended: 2019-06-06 15:09:18
+Working directory: C:\Users\Zong\template\data
 --------------------------------------------------------------------------------
diff --git a/data/log/output_heads.log b/data/log/output_heads.log
@@ -1,8 +1,8 @@
 File headers
 --------------------------------------------------------------------------------
-/Users/zong/template/data/output/data_graph.csv
+C:\Users\Zong\template\data\output\data_table.csv
 --------------------------------------------------------------------------------
-x
+"x"
 2
 4
 6
@@ -13,9 +13,9 @@ x
 16
 18
 --------------------------------------------------------------------------------
-/Users/zong/template/data/output/data_table.csv
+C:\Users\Zong\template\data\output\data_graph.csv
 --------------------------------------------------------------------------------
-"x"
+x
 2
 4
 6

diff --git a/data/log/output_stats.log b/data/log/output_stats.log
@@ -1,3 +1,3 @@
-file name	last modified	file size
-/Users/zong/template/data/output/data_graph.csv	2019-05-08 19:17:55	2044452
-/Users/zong/template/data/output/data_table.csv	2019-05-08 19:17:54	2044448
+file name | last modified | file size
+C:\Users\Zong\template\data\output\data_table.csv | 2019-06-06 22:09:16 | 2344449
+C:\Users\Zong\template\data\output\data_graph.csv | 2019-06-06 22:09:19 | 2344453
diff --git a/data/log/source_heads.log b/data/log/source_heads.log
@@ -1,6 +1,6 @@
 File headers
 --------------------------------------------------------------------------------
-/Users/zong/template/raw/data.csv
+C:\Users\Zong\template\raw\data.csv
 --------------------------------------------------------------------------------
 x
 1

diff --git a/data/log/source_map.log b/data/log/source_map.log
@@ -1,2 +1,2 @@
 destination | source
-input/data.csv | /Users/zong/template/raw/data.csv
+input\data.csv | C:\Users\Zong\template\raw\data.csv
diff --git a/data/log/source_stats.log b/data/log/source_stats.log
@@ -1,2 +1,2 @@
-file name	last modified	file size
-/Users/zong/template/raw/data.csv	2019-05-07 19:45:55	1988897
+file name | last modified | file size
+C:\Users\Zong\template\raw\data.csv | 2019-05-09 23:44:32 | 1988897
diff --git a/data/output/data_graph.csv b/data/output/data_graph.csv
diff --git a/data/output/data_table.csv b/data/output/data_table.csv
diff --git a/lib/gslab_make/private/exceptionclasses.py b/lib/gslab_make/private/exceptionclasses.py
@@ -11,6 +11,8 @@ class CritError(Exception):
     pass
 
 class ColoredError(Exception):
+    """ Colorized error messages. """
+
     def __init__(self, message, trace = ''):
         message = '\n\n' + colored(message, color = 'red')
         if trace:
@@ -20,4 +22,5 @@ def __init__(self, message, trace = ''):
             super(ColoredError, self).__init__(message)
 
 class ProgramError(ColoredError):
+    """ Program execution exception. """
     pass
diff --git a/lib/gslab_make/private/messages.py b/lib/gslab_make/private/messages.py
@@ -3,11 +3,11 @@
 from builtins import (bytes, str, open, super, range,
                       zip, round, input, int, pow, object)
 
-######################################################
-# Define Messages
-######################################################      
+# ~~~~~~~~~~~~~~~ #
+# Define messages #
+# ~~~~~~~~~~~~~~~ #  
 
-# 1) Critical Errors
+# Critical errors
 crit_error_unknown_system = '\nERROR! `gslab_make` only supports the following operating systems: `POSIX`, `NT`.' 
 crit_error_no_makelog = '\nERROR! Makelog `%s` not found. Makelog either not started (via `start_makelog`) or deleted after started.' 
 crit_error_no_program_output = '\nERROR! Certain applications (`matlab`, `sas`, `stata`) automatically create program outputs when ran using system command. Program output `%s` is expected from `%s` but cannot be not found or opened. Traceback can be found below.'
@@ -23,15 +23,15 @@
 crit_error_path_mapping = '\nERROR! `{%s}` found in linking/copying instructions but not in path mapping. Traceback can be found below.'
 crit_error_no_repo = '\nERROR! Current working directory is not part of a git repository.'
 
-# 2) Syntax Errors
+# Syntax errors
 syn_error_wildcard = '\nERROR! Destination and source must have same number of wildcards (`*`).' 
 
-# 3) Type errors
+# Type errors
 type_error_file_list = '\nERROR! Files `%s` must be specified in a list.' 
 type_error_dir_list = '\nERROR! Directories `%s` must be specified in a list.' 
 type_error_not_dir = '\nERROR! Path `%s` is not a directory.' 
 
-# 4) Warnings
+# Warnings
 warning_glob = 'WARNING! No files were returned by `glob_recursive` for path `%s` when walking to a depth of `%s`.'
 warning_lyx_type = 'WARNING! Document type `%s` unrecognized. Reverting to default of no special document type.'
 warning_modified_files = "WARNING! The following target files have been modified according to git status:\n%s"
@@ -42,7 +42,7 @@
 warning_git_lfs_file_log = "\nWARNING! Certain files tracked by git lfs exceed config limit (%s MB). See below for list of files."
 warning_git_lfs_repo = "\nWARNING! Total size of files tracked by git lfs exceed config limitt (%s MB)."
 
-# 5) Notes
+# Notes
 note_makelog_start = 'Makelog started: '
 note_makelog_end = 'Makelog ended: '
 note_working_directory = 'Working directory: '

diff --git a/lib/gslab_make/private/metadata.py b/lib/gslab_make/private/metadata.py
@@ -3,13 +3,12 @@
 from builtins import (bytes, str, open, super, range,
                       zip, round, input, int, pow, object)
 
-######################################################
-# Define metadata
-######################################################  
+# ~~~~~~~~~~~~~~~ #
+# Define metadata #
+# ~~~~~~~~~~~~~~~ #
 
 makelog_started = False
 
-# Commands
 commands = {
     'posix': 
         {'makelink'  : 'ln -s \"%s\" \"%s\"', 

diff --git a/lib/gslab_make/private/utility.py b/lib/gslab_make/private/utility.py
@@ -102,7 +102,22 @@ def file_to_array(file_name):
 
 
 def format_traceback(trace = ''):
-    """ Format error message. """
+    """ Format traceback message.
+
+    Parameters
+    ----------
+    trace : str
+        Traceback to format. Defaults to `traceback.format_exc()`.
+
+    Notes
+    -----
+    Format trackback for readability to pass into user messages. 
+
+    Returns
+    -------
+    formatted : str
+        Formatted traceback.
+    """
 
     if not trace:
         trace = traceback.format_exc()
@@ -134,7 +149,7 @@ def format_list(list):
 
     Notes
     -----
-    Format list for readability to pass into user messages 
+    Format list for readability to pass into user messages.
 
     Returns
     -------
@@ -147,9 +162,10 @@ def format_list(list):
 
     return(formatted)
 
-
-# Following functions are not currently actively used in code base
-
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
+# Following functions are not currently actively used in code base #
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ #
+
 def check_duplicate(original, copy): 
     """ Check duplicate.
 

diff --git a/paper_slides/input/plot.eps b/paper_slides/input/plot.eps