Revert "PR #21: Review and test template (#25)"

This reverts commit 5f1d277.
gentzkow · Aug 13, 2019 · d72c23f · d72c23f
1 parent 5f1d277
commit d72c23f
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diff --git a/.gitignore b/.gitignore
@@ -24,7 +24,6 @@
 *.lyx.emergency
 *.Rhistory
 *.Rapp.history
-*Rplots.pdf
 *.DS_Store
 *.aux
 *.fls

diff --git a/README.md b/README.md
@@ -13,7 +13,7 @@ To build the repository as-is, the following applications are additionally requi
 * R
 * Stata
 
-These software are used by the scripts contained in the repository. By default, the **Setup** and **Build** instructions below will assume their usage.
+These software are used by the scripts contained in the repository. By default, the **Setup** instructions below will assume their usage.
 
 ## Setup
 **If you are using Windows, you may need to run certain bash commands in administrator mode due to permission errors. To do so, open your terminal by right clicking and selecting `Run as administrator`. To set administrator mode on permanently, refer to the [RA manual](https://github.com/gentzkow/template/wiki/Repository-Usage#Administrator-Mode).**
@@ -51,16 +51,6 @@ These software are used by the scripts contained in the repository. By default,
    Rscript setup_r.r
    ```
 
-## Build
-**If you are using Windows, you may need to run certain bash commands in administrator mode due to permission errors. To do so, open your terminal by right clicking and selecting `Run as administrator`. To set administrator mode on permanently, refer to the [RA manual](https://github.com/gentzkow/template/wiki/Repository-Usage#Administrator-Mode).**
-
-1. Follow the *Setup* instructions above.
-
-2. From the root of repository, run the following bash command:
-   ```
-   python run_all.py
-   ```
-
 ## Command Line Usage
 
 For specific instructions on how to set up command line usage for an application, refer to the [RA manual](https://github.com/gentzkow/template/wiki/Command-Line-Usage).

diff --git a/analysis/external.txt b/analysis/external.txt
diff --git a/analysis/externals.txt b/analysis/externals.txt
@@ -0,0 +1,17 @@
+# Each line of instruction in this `externals.txt` file should contain a destination and source delimited by a `|`.
+# Lines beginning with # are ignored.
+# 
+# For example, suppose your `externals.txt` file contains the following lines of text:
+# > destination | source
+#
+# Now suppose you run the following line of code:
+# > link_externals(paths, ['externals.txt'])
+# 
+# This will create a link in `paths['external_dir']` named `destination` that links to `source`.
+# 
+# Alternative, suppose you run the following line of code:
+# > copy_externals(paths, ['externals.txt'])
+# 
+# This will create a file in `paths['eternal_dir']` named `destination` that is a copy of `source`.
+
+# Destination | Source
diff --git a/analysis/input.txt → analysis/inputs.txt b/analysis/input.txt → analysis/inputs.txt
diff --git a/analysis/log/make.log b/analysis/log/make.log
@@ -1,13 +1,16 @@
 --------------------------------------------------------------------------------
-Makelog started: 2019-07-29 17:06:01
+Makelog started: 2019-05-08 12:19:30
 Working directory: /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" `
 Output logs successfully written!
 --------------------------------------------------------------------------------
-Makelog ended: 2019-07-29 17:06:04
+Makelog ended: 2019-05-08 12:19:33
 Working directory: /Users/zong/template/analysis
 --------------------------------------------------------------------------------
diff --git a/analysis/log/output_heads.log b/analysis/log/output_heads.log
@@ -5,7 +5,7 @@ File headers
 %!PS-Adobe-3.0 EPSF-3.0
 %%Title: output/plot.eps
 %%Creator: matplotlib version 2.2.3, http://matplotlib.org/
-%%CreationDate: Mon Jul 29 17:06:03 2019
+%%CreationDate: Wed May  8 12:19:32 2019
 %%Orientation: portrait
 %%BoundingBox: 75 223 536 568
 %%EndComments

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 | 2019-07-30 00:06:03 | 13305
-/Users/zong/template/analysis/output/tables.txt | 2019-07-30 00:06:04 | 40
+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
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 | 2019-07-30 00:06:00 | 2044452
-/Users/zong/template/data/output/data_table.csv | 2019-07-30 00:05:59 | 2044448
+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
diff --git a/analysis/make.py b/analysis/make.py
@@ -1,24 +1,20 @@
-###################
-### ENVIRONMENT ###
-###################
+### ENVIRONMENT
 import git
 import imp
 import os
 import yaml
 
-# LOAD GSLAB MAKE
 ROOT = git.Repo('.', search_parent_directories = True).working_tree_dir 
 f, path, desc = imp.find_module('gslab_make', [os.path.join(ROOT, 'lib')]) 
-gs = imp.load_module('gslab_make', f, path, desc)
+gs = imp.load_module('gslab_make', f, path, desc) # Load `gslab_make`
 
-# SET DEFAULT PATHS
-PATHS = {
+PATHS = { # Set default paths; used by `gslab_make` functions
     'config'          : '../config.yaml',
     'config_user'     : '../config_user.yaml',
     'input_dir'       : 'input', 
     'external_dir'    : 'external',
     'output_dir'      : 'output/',
-    'output_local_dir': ['output_local'],       # Optional; include any local directories with outputs
+	'output_local_dir': [],                     # Optional; include any local directories with outputs
     'pdf_dir'         : 'output/',
     'makelog'         : 'log/make.log',         # Set to '' to avoid writing log
     'output_statslog' : 'log/output_stats.log', # Set to '' to avoid writing log
@@ -28,27 +24,25 @@
     'source_headslog' : 'log/source_heads.log'  # Set to '' to avoid writing log
 }
 
-### SET PATH MAPPINGS
-PATH_MAPPINGS = { 
+PATH_MAPPINGS = { # Set path mappings; used by `move_sources` functions
     'root': ROOT
 }
 
-### LOAD CONFIG USER 
-gs.update_executables(PATHS)
-PATH_MAPPINGS = gs.update_mappings(PATHS, PATH_MAPPINGS)
+### CONFIG USER 
+config_user = yaml.load(open(PATHS['config_user'], 'rb'))
+if config_user['local']['executables']: # Update executables; used by `run_program` functions
+    gs.private.metadata.default_executables[os.name].update(config_user['local']['executables'])
+if config_user['external']: # Update path mappings; used by `create_links` functions
+    PATH_MAPPINGS.update(config_user['external'])
 
-############
-### MAKE ###
-############
-
-### START MAKE
+### START 
 gs.remove_dir(['input', 'external'])
 gs.clear_dir(['output', 'log'])
 gs.start_makelog(PATHS)
 
 ### GET INPUT FILES 
-inputs = gs.link_inputs(PATHS, ['input.txt'], PATH_MAPPINGS)
-externals = gs.link_externals(PATHS, ['external.txt'], PATH_MAPPINGS)
+inputs = gs.link_inputs(PATHS, ['inputs.txt'], PATH_MAPPINGS)
+externals = gs.link_externals(PATHS, ['externals.txt'], PATH_MAPPINGS)
 gs.write_source_logs(PATHS, inputs + externals)
 gs.get_modified_sources(PATHS, inputs + externals)
 
@@ -61,5 +55,5 @@
 ### CHECK FILE SIZES
 gs.check_module_size(PATHS)
 
-### END MAKE
+### END
 gs.end_makelog(PATHS)
diff --git a/analysis/output/plot.eps b/analysis/output/plot.eps
diff --git a/config.yaml b/config.yaml
@@ -23,9 +23,9 @@ software_required:
 # Maximum allowed file sizes
 #####################################################################
 max_file_sizes:
-  file_MB_limit_lfs: 100         # Soft limit on file size (w/ LFS)
-  total_MB_limit_lfs: 500        # Soft limit on total size (w/ LFS)  
-  file_MB_limit: 0.5             # Soft limit on file size (w/o LFS)
-  total_MB_limit: 100            # Soft limit on total size (w/o LFS)
+  file_MB_limit_lfs: 100             # Soft limit on file size (w/ LFS)
+  total_MB_limit_lfs: 500            # Soft limit on total size (w/ LFS)  
+  file_MB_limit: 0.5                 # Soft limit on file size (w/o LFS)
+  total_MB_limit: 100                # Soft limit on total size (w/o LFS)
 
 
diff --git a/data/external.txt b/data/external.txt
diff --git a/data/externals.txt b/data/externals.txt
@@ -0,0 +1,17 @@
+# Each line of instruction in this `externals.txt` file should contain a destination and source delimited by a `|`.
+# Lines beginning with # are ignored.
+# 
+# For example, suppose your `externals.txt` file contains the following lines of text:
+# > destination | source
+#
+# Now suppose you run the following line of code:
+# > link_externals(paths, ['externals.txt'])
+# 
+# This will create a link in `paths['external_dir']` named `destination` that links to `source`.
+# 
+# Alternative, suppose you run the following line of code:
+# > copy_externals(paths, ['externals.txt'])
+# 
+# This will create a file in `paths['eternal_dir']` named `destination` that is a copy of `source`.
+
+# Destination | Source
diff --git a/data/input.txt → data/inputs.txt b/data/input.txt → data/inputs.txt
diff --git a/data/log/make.log b/data/log/make.log
@@ -1,5 +1,5 @@
 --------------------------------------------------------------------------------
-Makelog started: 2019-07-29 17:05:58
+Makelog started: 2019-05-08 12:17:53
 Working directory: /Users/zong/template/data
 --------------------------------------------------------------------------------
 Input links successfully created!
@@ -17,8 +17,8 @@ ___/   /   /___/   /   /___/   15.1   Copyright 1985-2017 StataCorp LLC
                                       979-696-4600        stata@stata.com
                                       979-696-4601 (fax)
 
-Unlimited-user 4-core Stata network license expires 21 Jul 2020:
-       Serial number:  501609000313
+Unlimited-user 4-core Stata network license expires 21 Jul 2019:
+       Serial number:  501509201134
          Licensed to:  Zong Huang
                        Stanford University
 
@@ -54,6 +54,6 @@ end of do-file
 
 Output logs successfully written!
 --------------------------------------------------------------------------------
-Makelog ended: 2019-07-29 17:06:00
+Makelog ended: 2019-05-08 12:17:55
 Working directory: /Users/zong/template/data
 --------------------------------------------------------------------------------
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 | 2019-07-30 00:06:00 | 2044452
-/Users/zong/template/data/output/data_table.csv | 2019-07-30 00:05:59 | 2044448
+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
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 | 2019-07-12 17:24:17 | 1988897
+file name	last modified	file size
+/Users/zong/template/raw/data.csv	2019-05-07 19:45:55	1988897
diff --git a/data/make.py b/data/make.py
@@ -1,24 +1,20 @@
-###################
-### ENVIRONMENT ###
-###################
+### ENVIRONMENT
 import git
 import imp
 import os
 import yaml
 
-# LOAD GSLAB MAKE
 ROOT = git.Repo('.', search_parent_directories = True).working_tree_dir 
 f, path, desc = imp.find_module('gslab_make', [os.path.join(ROOT, 'lib')]) 
-gs = imp.load_module('gslab_make', f, path, desc)
+gs = imp.load_module('gslab_make', f, path, desc) # Load `gslab_make`
 
-# SET DEFAULT PATHS
-PATHS = {
+PATHS = { # Set default paths; used by `gslab_make` functions
     'config'          : '../config.yaml',
     'config_user'     : '../config_user.yaml',
     'input_dir'       : 'input', 
     'external_dir'    : 'external',
     'output_dir'      : 'output/',
-    'output_local_dir': ['output_local'],       # Optional; include any local directories with outputs
+    'output_local_dir': [],                     # Optional; include any local directories with outputs
     'pdf_dir'         : 'output/',
     'makelog'         : 'log/make.log',         # Set to '' to avoid writing log
     'output_statslog' : 'log/output_stats.log', # Set to '' to avoid writing log
@@ -28,27 +24,25 @@
     'source_headslog' : 'log/source_heads.log'  # Set to '' to avoid writing log
 }
 
-### SET PATH MAPPINGS
-PATH_MAPPINGS = { 
+PATH_MAPPINGS = { # Set path mappings; used by `move_sources` functions
     'root': ROOT
 }
 
-### LOAD CONFIG USER 
-gs.update_executables(PATHS)
-PATH_MAPPINGS = gs.update_mappings(PATHS, PATH_MAPPINGS)
+### CONFIG USER 
+config_user = yaml.load(open(PATHS['config_user'], 'rb'))
+if config_user['local']['executables']: # Update executables; used by `run_program` functions
+    gs.private.metadata.default_executables[os.name].update(config_user['local']['executables'])
+if config_user['external']: # Update path mappings; used by `create_links` functions
+    PATH_MAPPINGS.update(config_user['external'])
 
-############
-### MAKE ###
-############
-
-### START MAKE
+### START 
 gs.remove_dir(['input', 'external'])
 gs.clear_dir(['output', 'log'])
 gs.start_makelog(PATHS)
 
 ### GET INPUT FILES 
-inputs = gs.link_inputs(PATHS, ['input.txt'], PATH_MAPPINGS)
-externals = gs.link_externals(PATHS, ['external.txt'], PATH_MAPPINGS)
+inputs = gs.link_inputs(PATHS, ['inputs.txt'], PATH_MAPPINGS)
+externals = gs.link_externals(PATHS, ['externals.txt'], PATH_MAPPINGS)
 gs.write_source_logs(PATHS, inputs + externals)
 gs.get_modified_sources(PATHS, inputs + externals)
 
@@ -62,5 +56,5 @@
 ### CHECK FILE SIZES
 gs.check_module_size(PATHS)
 
-### END MAKE
+### END
 gs.end_makelog(PATHS)