Merge branch 'develop' into 'master'

Develop

See merge request !92

data_repo_renderer/__init__.py

 """data_repo_renderer."""
 
 import argparse
+import logging
 from pathlib import Path
 from pkg_resources import get_distribution, DistributionNotFound
 import shutil
@@ -8,12 +9,31 @@ import stat
 import textwrap
 import yaml
 
+
+def maybe_get_installed_version(pkg_name):
+    """If `pkg_name` is installed, set version from there.
+
+    Attributes
+    ----------
+    pkg_name : str
+        Package name.
+
+    Returns
+    -------
+    version : str
+        Version number from installed package or 'vX.X.X'
+
+    """
+    try:
+        version = get_distribution(pkg_name).version
+    except DistributionNotFound:
+        # package is not installed
+        version = "vX.X.X"
+    return version
+
+
 # Set version string
-try:
-    __version__ = get_distribution(__name__).version
-except DistributionNotFound:
-    # package is not installed
-    __version__ = "vX.X.X"
+__version__ = maybe_get_installed_version(__name__)
 
 
 class Renderer(object):
@@ -439,6 +459,10 @@ class ReadmeRenderer(Renderer):
         """\
         # {{repo_name}}
 
+        {{repo_description}}
+
+        -----
+
         **Note:**  *This dataset is just a mirror of an external source.
         Please make sure to properly credit the original creators of the data
         set just as you would do if you'd obtained the data directly from
@@ -447,11 +471,6 @@ class ReadmeRenderer(Renderer):
         To learn more about how to use and access the data, check the central
         documentation: <https://git.geomar.de/data/docs/>
 
-        -----
-
-        {{repo_description}}
-
-
         {{maybe_acknowledgements}}
         {{maybe_citations}}
 
@@ -571,6 +590,13 @@ def cli_run_renderer(argvec=None):
     """Run renderer."""
     # parse command line args
     parser = argparse.ArgumentParser(description="Data repo renderer")
+    parser.add_argument("--verbose", action='store_true',
+                        help="Print debugging output.")
+    parser.add_argument("--in-place", action='store_true',
+                        help=(
+                            "Render in place?  This will render everything in "
+                            "the parent directory of `yaml_file`. "
+                            "Incompatible with --prefix and --util."))
     parser.add_argument("--prefix", help=("Custom path to a directory that "
                                           "will contain the rendered repo. "
                                           "Defaults to: './rendered/'"))
@@ -581,10 +607,37 @@ def cli_run_renderer(argvec=None):
                         help="Use this YAML file to render repo.")
     args = parser.parse_args(argvec)
 
-    # extract arguments
-    util_src = Path(args.util if args.util is not None else "./util/")
-    prefix = Path(args.prefix if args.prefix is not None else "./rendered/")
+    # are we verbose?
+    verbose = (args.verbose is True)
+
+    # do we do in-place rerendering?
+    in_place = (args.in_place is True)
+
+    # check for incompatible args
+    if in_place and args.prefix is not None:
+        raise ValueError("--prefix and --in-place are incompatible.")
+    if in_place and args.util is not None:
+        raise ValueError("--util and --in-place are incompatible.")
+
+    # Read paths from cli
     yaml_file = Path(args.yaml_file)
+    if in_place:
+        prefix = yaml_file.parent
+        util_src = prefix / "util"
+    else:
+        util_src = Path(args.util if args.util is not None else "./util/")
+        prefix = Path(args.prefix if args.prefix is not None
+                      else "./rendered/")
+
+    # set up logging
+    logger = logging.getLogger("data_repo_renderer")
+    if verbose:
+        _log_level = logging.DEBUG
+    else:
+        _log_level = logging.INFO
+    logging.basicConfig(
+        level=_log_level,
+        format='%(asctime)s %(name)-16s: %(levelname)-8s %(message)s')
 
     # load YAML file
     with yaml_file.open() as stream:
@@ -602,6 +655,7 @@ def cli_run_renderer(argvec=None):
             try:
                 f.unlink()
             except Exception as e:
+                logger.debug("failed to unlink {} with: {}".format(f, e))
                 pass
     _unlink_files([update_script, init_script, readme_file])
 
@@ -635,18 +689,30 @@ def cli_run_renderer(argvec=None):
     ReadmeRenderer(yaml_dict, output_file=readme_file)
 
     # copy yaml file
-    try:
-        shutil.copy(str(yaml_file), str(prefix / "meta.yaml"))
-    except shutil.SameFileError as e:
-        pass
+    if not in_place:
+        try:
+            shutil.copy(str(yaml_file), str(prefix / "meta.yaml"))
+        except shutil.SameFileError as e:
+            logger.debug("failed to copy `meta.yaml` with: {}".format(e))
+            pass
 
-    # copy util scripts (if any)
-    try:
-        shutil.copytree(str(util_src), str(util_dst))
-    except Exception as e:
-        pass
+    # copy util scripts (if any):  First, remove targed util, and then copy
+    # source util directory.
+    if not in_place:
+        try:
+            shutil.rmtree(str(util_dst))
+        except Exception as e:
+            logger.debug("failed to unlink {} with: {}".format(util_dst, e))
+            pass
+        try:
+            shutil.copytree(str(util_src), str(util_dst))
+        except Exception as e:
+            logger.debug("failed to copy {} to {} with: {}".format(
+                util_src, util_dst, e))
+            pass
 
     # make scripts executable
     _make_file_executable(update_script)
     _make_file_executable(init_script)
-    list(map(_make_file_executable, util_dst.glob("*.*")))
+    if not in_place:
+        list(map(_make_file_executable, util_dst.glob("*.*")))

tests/test_full_yaml_file_and_cli.py

@@ -236,8 +236,10 @@ def util(tmp_path):
     return util_path
 
 
+@pytest.mark.parametrize("cli_args_verbose", [[], ["--verbose"]])
 @pytest.mark.parametrize("util_after", [True, False])
-def test_full_yaml_example_01(util, yaml_example, tmp_path, util_after):
+def test_full_yaml_example_01(util, yaml_example, tmp_path, util_after,
+                              cli_args_verbose):
 
     # Set up command line args
     cli_args = ["--prefix", str(tmp_path / "rendered"),
@@ -248,6 +250,9 @@ def test_full_yaml_example_01(util, yaml_example, tmp_path, util_after):
     if util_after:
         cli_args.insert(2, cli_args.pop(-1))
 
+    # cycle over verbose flag
+    cli_args = cli_args_verbose + cli_args
+
     # and run the renderer
     data_repo_renderer.cli_run_renderer(cli_args)
 
@@ -260,3 +265,15 @@ def test_full_yaml_example_01(util, yaml_example, tmp_path, util_after):
     assert all(
         (tmp_path / "rendered" / "util" / file_name).exists()
         for file_name in ["postprocessing_01.sh", "postprocessing_02.sh"])
+
+
+@pytest.mark.parametrize("cli_args_verbose", [[], ["--verbose"]])
+@pytest.mark.parametrize(
+    "cli_args_i_p_u",
+    [["--in-place", "--prefix", "some_prefix"],
+     ["--in-place", "--util", "some_util"],
+     ["--in-place", "--prefix", "some_prefix", "--util", "some_util"]])
+def test_incompatible_cli_args(cli_args_i_p_u, cli_args_verbose):
+    cli_args = cli_args_verbose + cli_args_i_p_u + ["meta.yaml"]
+    with pytest.raises(ValueError):
+        data_repo_renderer.cli_run_renderer(cli_args)

tests/test_install.py

+# -*- coding:utf-8 -*-
+
+import data_repo_renderer
+import pytest
+
+
+def test_generic_version_if_not_installed():
+    vers = data_repo_renderer.maybe_get_installed_version("datareporenderer")
+    assert vers == "vX.X.X"