From 23697c2279d67d8f03c6cc04bc940d594395ec79 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 27 Feb 2018 13:40:44 -0500
Subject: [PATCH] Print fake shell commands.

A bunch of raw shell scripting was replaced with Python system calls in 953958932384ff7ebd1a09806e6c290c556f9dea, that is great but the cool reporting of the shell commands was lost. This restores the reporting as fake shell commands corresponding to what is happening (sort of).
---
 planemo/commands/cmd_project_init.py |  2 ++
 planemo/io.py                        | 20 ++++++++++++++++++++
 planemo/shed/__init__.py             | 12 +++++++-----
 planemo/tool_builder.py              |  2 +-
 4 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/planemo/commands/cmd_project_init.py b/planemo/commands/cmd_project_init.py
index 7251a0393..4df2b68d8 100644
--- a/planemo/commands/cmd_project_init.py
+++ b/planemo/commands/cmd_project_init.py
@@ -8,6 +8,7 @@
 from planemo import options
 from planemo.cli import command_function
 from planemo.io import (
+    info,
     untar_to,
     warn,
 )
@@ -42,6 +43,7 @@ def cli(ctx, path, template=None, **kwds):
         untar_args = UNTAR_ARGS % (tempdir)
         untar_to(DOWNLOAD_URL, tempdir, untar_args)
         template_dir = os.path.join(tempdir, template)
+        info("mv '%s'/* '%s'" % (template_dir, path))
         for entry in os.listdir(template_dir):
             shutil.move(os.path.join(template_dir, entry), path)
     finally:
diff --git a/planemo/io.py b/planemo/io.py
index 3bfdd070d..0e4608bb9 100644
--- a/planemo/io.py
+++ b/planemo/io.py
@@ -45,6 +45,26 @@ def communicate(cmds, **kwds):
     return output
 
 
+def copy(source, dest):
+    info("cp '%s' '%s'" % (source, dest))
+    shutil.copy(source, dest)
+
+
+def mkdir(path):
+    info("mkdir '%s'" % path)
+    os.mkdir(path)
+
+
+def makedirs(path):
+    info("mkdir -p '%s'" % path)
+    os.makedirs(path)
+
+
+def rm_rf_tree(path):
+    info("rm -rf '%s'" % path)
+    shutil.rmtree(path, ignore_errors=True)
+
+
 def shell(cmds, **kwds):
     if isinstance(cmds, list):
         cmd_string = commands.argv_to_str(cmds)
diff --git a/planemo/shed/__init__.py b/planemo/shed/__init__.py
index 298c4e937..0275e4001 100644
--- a/planemo/shed/__init__.py
+++ b/planemo/shed/__init__.py
@@ -6,7 +6,6 @@
 import json
 import os
 import re
-import shutil
 import sys
 import tarfile
 from collections import namedtuple
@@ -25,9 +24,12 @@
 from planemo.io import (
     can_write_to_path,
     coalesce_return_codes,
+    copy as io_copy,
     error,
     find_matching_directories,
     info,
+    mkdir,
+    rm_rf_tree,
     shell,
     temp_directory,
     warn,
@@ -205,7 +207,7 @@ def shed_init(ctx, path, **kwds):
         workflow_name = os.path.basename(from_workflow)
         workflow_target = os.path.join(path, workflow_name)
         if not os.path.exists(workflow_target):
-            shutil.copyfile(from_workflow, workflow_target)
+            io_copy(from_workflow, workflow_target)
 
         if not can_write_to_path(repo_dependencies_path, **kwds):
             return 1
@@ -287,7 +289,7 @@ def upload_repository(ctx, realized_repository, **kwds):
         tar_path = build_tarball(path, **kwds)
     if kwds.get("tar_only", False):
         name = realized_repository.pattern_to_file_name("shed_upload.tar.gz")
-        shutil.copy(tar_path, name)
+        io_copy(tar_path, name)
         return 0
     shed_context = get_shed_context(ctx, **kwds)
     update_kwds = {}
@@ -393,9 +395,9 @@ def _diff_in(ctx, working, realized_repository, **kwds):
         )
     else:
         tar_path = build_tarball(path)
-        os.mkdir(mine)
+        mkdir(mine)
         shell(['tar', '-xzf', tar_path, '-C', mine])
-        shutil.rmtree(tar_path, ignore_errors=True)
+        rm_rf_tree(tar_path)
 
     output = kwds.get("output", None)
     raw = kwds.get("raw", False)
diff --git a/planemo/tool_builder.py b/planemo/tool_builder.py
index 96bce16c6..3000f9927 100644
--- a/planemo/tool_builder.py
+++ b/planemo/tool_builder.py
@@ -848,7 +848,7 @@ def write_tool_description(ctx, tool_description, **kwds):
     if tool_description.test_files:
         if not os.path.exists("test-data"):
             io.info("No test-data directory, creating one.")
-            os.makedirs('test-data')
+            io.makedirs('test-data')
         for test_file in tool_description.test_files:
             io.info("Copying test-file %s" % test_file)
             try: