Mercurial > repos > shellac > guppy_basecaller

comparison env/lib/python3.7/site-packages/planemo/ci.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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-1:000000000000 0:26e78fe6e8c4
1 """Utilities for dealing with continous integration systems."""
2
3 from __future__ import print_function
4
5 import copy
6 import math
7 import os
8
9 import yaml
10
11 from planemo import git
12 from planemo import io
13 from planemo.shed import SHED_CONFIG_NAME
14
15
16 def filter_paths(ctx, raw_paths, path_type="repo", **kwds):
17 """Filter ``paths``.
18
19 ``path_type`` is ``repo`` or ``file``.
20 """
21 cwd = os.getcwd()
22
23 filter_kwds = copy.deepcopy(kwds)
24 changed_in_commit_range = kwds.get("changed_in_commit_range", None)
25 diff_paths = None
26 if changed_in_commit_range is not None:
27 diff_files = git.diff(ctx, cwd, changed_in_commit_range)
28 if path_type == "repo":
29 diff_dirs = set(os.path.dirname(p) for p in diff_files)
30 diff_paths = set()
31 for diff_dir in diff_dirs:
32 while diff_dir:
33 if os.path.isfile(os.path.join(diff_dir, SHED_CONFIG_NAME)):
34 diff_paths.add(diff_dir)
35 break
36 diff_dir = os.path.dirname(diff_dir)
37 else:
38 diff_paths = diff_files
39
40 unique_paths = set(os.path.relpath(p, cwd) for p in raw_paths)
41 if diff_paths is not None:
42 new_unique_paths = []
43 for path in unique_paths:
44 if path in diff_paths:
45 new_unique_paths.append(path)
46 unique_paths = new_unique_paths
47 filtered_paths = sorted(io.filter_paths(unique_paths, cwd=cwd, **filter_kwds))
48 excluded_paths = sorted(set(unique_paths) - set(filtered_paths))
49 if excluded_paths:
50 ctx.log("List of excluded paths: %s" % excluded_paths)
51
52 path_count = len(filtered_paths)
53 chunk_size = ((1.0 * path_count) / kwds["chunk_count"])
54 chunk = kwds["chunk"]
55
56 chunked_paths = []
57 for i, path in enumerate(filtered_paths):
58 if int(math.floor(i / chunk_size)) == chunk:
59 chunked_paths.append(path)
60
61 return chunked_paths
62
63
64 def print_path_list(paths, **kwds):
65 with io.open_file_or_standard_output(kwds["output"], "w") as f:
66 for path in paths:
67 print(path, file=f)
68
69
70 def print_as_yaml(item, **kwds):
71 with io.open_file_or_standard_output(kwds["output"], "w") as f:
72 f.write(yaml.safe_dump(item))