Add saving of the beautification diff to the test server. (#204)

We should be able to save the full diff of the beautification test output, and present it on the benchmark server in the `Test files: 「file-tree-view」「file-list-view」` entries.

Additionally, beautify main.

source/src/core/simple_metrics/metrics/RMSDMetric.hh

@@ -32,12 +32,12 @@ namespace core {
 namespace simple_metrics {
 namespace metrics {
 
-///@brief A metric to calculate the RMSD between two poses. 
+///@brief A metric to calculate the RMSD between two poses.
 /// Please note that by default it doesn't align poses. You need to set set_run_superimpose() to True for performing alignment.
 /// You Can set a subset of residues to calculate via ResidueSelector.
 ///
-/// By default RMSD is calcualted between all atoms other than hydrogens (all_heavy). This can be changed via **set_rmsd_type**  
-/// 
+/// By default RMSD is calcualted between all atoms other than hydrogens (all_heavy). This can be changed via **set_rmsd_type**
+///
 /// @details We match all corresponding atoms and do not fail if a residue does not match up.
 ///
 class RMSDMetric : public core::simple_metrics::RealMetric{
@@ -131,19 +131,19 @@ public:
 	set_run_superimpose( bool super );
 
 	///@brief Set what we will be calculating the RMSD on.
-        ///
+	///
 	/// By default RMSD is calcualted between all atoms other than hydrogens (all_heavy).
 	///
 	/// You can look up core/rms/rms_enum.hh for available options. Right now the available options are:
-	/// rmsd_protein_bb_heavy: backbone heavy atoms N,CA,C 
-	/// rmsd_protein_bb_heavy_including_O: backbone heavy atoms N,CA,C,O 
+	/// rmsd_protein_bb_heavy: backbone heavy atoms N,CA,C
+	/// rmsd_protein_bb_heavy_including_O: backbone heavy atoms N,CA,C,O
 	/// rmsd_protein_bb_ca: CA (C-alpha)
 	/// rmsd_sc_heavy: side chain heavy atoms
-        /// rmsd_sc: all side chain atoms (including H)
+	/// rmsd_sc: all side chain atoms (including H)
 	/// rmsd_all_heavy: all heavy atoms
 	/// rmsd_all: all atoms
-        ///
-	/// Example: 
+	///
+	/// Example:
 	/// metric = rosetta.core.simple_metrics.metrics.RMSDMetric(pose_1)
 	/// metric.set_rmsd_type(rosetta.core.scoring.rmsd_protein_bb_heavy)
 	/// metric.set_run_superimpose(True)

tests/benchmark/tests/code_quality.py

@@ -470,6 +470,9 @@ def run_beautification_test(rosetta_dir, working_dir, platform, config, hpc_driv
 
     if res:
         state, output = _S_failed_, 'Some of the source code looks ugly!!! Script test_all_files_already_beautiful.py output:\n' + o
+        res_diff, diff = execute('Generating patch file for changes', 'cd {}/source && git --no-pager diff --no-color'.format(rosetta_dir), return_="tuple")
+        with open(working_dir+'/full_diff.patch', 'w') as f: f.write(diff)
+        output += "\n\nSee full_diff.patch in the `Test files` for the full list of changes\n"
     else:
         state = _S_passed_