Update usage style. See #145, #148, #73

pepkit · Jul 13, 2017 · 17fb841 · 17fb841
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diff --git a/doc/source/usage.rst b/doc/source/usage.rst
@@ -14,13 +14,16 @@ Each task is controlled by one of the five main commands ``run``, ``summarize``,
 - ``looper destroy``: Deletes all output results for this project.
 
 
+Command-line usage:
+******************************
 
 Here you can see the command-line usage instructions for the main looper command and for each subcommand:
 
 
-.. code-block:: shell
+``looper --help``
+----------------------------------
 
-	>looper --help
+.. code-block:: shell
 
 	version: 0.6.0-dev
 	usage: looper [-h] [-V] {run,summarize,destroy,check,clean} ...
@@ -43,9 +46,12 @@ Here you can see the command-line usage instructions for the main looper command
 	For subcommand-specific options, type: 'looper <subcommand> -h'
 	https://github.com/epigen/looper For debug options, type: 'looper -h
 	--details'
-	
-	
-	>looper run --help
+
+``looper run --help``
+----------------------------------
+
+.. code-block:: shell
+
 	version: 0.6.0-dev
 	usage: looper run [-h] [-t TIME_DELAY] [--ignore-flags] [--compute COMPUTE]
 	                  [--env ENV] [--limit LIMIT] [--file-checks] [-d]
@@ -71,9 +77,12 @@ Here you can see the command-line usage instructions for the main looper command
 	  -d, --dry-run         Don't actually submit the project/subproject.
 	  --sp SUBPROJECT       Name of subproject to use, as designated in the
 	                        project's configuration file
-	
-	
-	>looper summarize --help
+
+``looper summarize --help``
+----------------------------------
+
+.. code-block:: shell
+
 	version: 0.6.0-dev
 	usage: looper summarize [-h] [--file-checks] [-d] [--sp SUBPROJECT]
 	                        config_file
@@ -87,9 +96,12 @@ Here you can see the command-line usage instructions for the main looper command
 	  -d, --dry-run    Don't actually submit the project/subproject.
 	  --sp SUBPROJECT  Name of subproject to use, as designated in the project's
 	                   configuration file
-	
-	
-	>looper destroy --help
+
+``looper destroy --help``
+----------------------------------
+
+.. code-block:: shell
+
 	version: 0.6.0-dev
 	usage: looper destroy [-h] [--file-checks] [-d] [--sp SUBPROJECT] config_file
 	
@@ -102,9 +114,12 @@ Here you can see the command-line usage instructions for the main looper command
 	  -d, --dry-run    Don't actually submit the project/subproject.
 	  --sp SUBPROJECT  Name of subproject to use, as designated in the project's
 	                   configuration file
-	
-	
-	>looper check --help
+
+``looper check --help``
+----------------------------------
+
+.. code-block:: shell
+
 	version: 0.6.0-dev
 	usage: looper check [-h] [--file-checks] [-d] [--sp SUBPROJECT] config_file
 	
@@ -117,9 +132,12 @@ Here you can see the command-line usage instructions for the main looper command
 	  -d, --dry-run    Don't actually submit the project/subproject.
 	  --sp SUBPROJECT  Name of subproject to use, as designated in the project's
 	                   configuration file
-	
-	
-	>looper clean --help
+
+``looper clean --help``
+----------------------------------
+
+.. code-block:: shell
+
 	version: 0.6.0-dev
 	usage: looper clean [-h] [--file-checks] [-d] [--sp SUBPROJECT] config_file
 	
@@ -132,9 +150,12 @@ Here you can see the command-line usage instructions for the main looper command
 	  -d, --dry-run    Don't actually submit the project/subproject.
 	  --sp SUBPROJECT  Name of subproject to use, as designated in the project's
 	                   configuration file
-	
-	
-	>looper --details --help
+
+``looper --help --details``
+----------------------------------
+
+.. code-block:: shell
+
 	version: 0.6.0-dev
 	usage: looper [-h] [-V] [--logfile LOGFILE] [--verbosity {0,1,2,3,4}]
 	              [--logging-level LOGGING_LEVEL] [--dbg]

diff --git a/doc/source/usage.template b/doc/source/usage.template
@@ -14,10 +14,8 @@ Each task is controlled by one of the five main commands ``run``, ``summarize``,
 - ``looper destroy``: Deletes all output results for this project.
 
 
+Command-line usage:
+******************************
 
 Here you can see the command-line usage instructions for the main looper command and for each subcommand:
 
-
-.. code-block:: shell
-
-	>looper --help
diff --git a/update-usage-docs.sh b/update-usage-docs.sh
@@ -1,12 +1,18 @@
-looper --help > USAGE.temp 2>&1
+cp doc/source/usage.template usage.template
+#looper --help > USAGE.temp 2>&1
 
-for cmd in run summarize destroy check clean "--details"; do
+for cmd in "--help" "run --help" "summarize --help" "destroy --help" "check --help" "clean --help" "--help --details"; do
 	echo $cmd
-	echo -e "\n\n>looper $cmd --help" >> USAGE.temp
-	looper $cmd --help >> USAGE.temp 2>&1
+	echo -e "\n\`\`looper $cmd\`\`" > USAGE_header.temp
+	echo -e "----------------------------------" >> USAGE_header.temp
+	looper $cmd --help > USAGE.temp 2>&1
+	sed -i 's/^/\t/' USAGE.temp
+	sed -i '1s/^/\n.. code-block:: shell\n\n/' USAGE.temp
+	#sed -i -e "/\`looper $cmd\`/r USAGE.temp" -e '$G' usage.template  # for -in place inserts
+	cat USAGE_header.temp USAGE.temp >> usage.template # to append to the end
 done
-
-sed -i 's/^/\t/' USAGE.temp
-sed -e '/>looper --help/r USAGE.temp' -e '$G' doc/source/usage.template > doc/source/usage.rst
-cat doc/source/usage.rst
 rm USAGE.temp
+rm USAGE_header.temp
+mv usage.template  doc/source/usage.rst
+cat doc/source/usage.rst
+#rm USAGE.temp