Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/ci.py @ 3:758bc20232e8 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 """Utilities for dealing with continous integration systems."""
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2
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3 from __future__ import print_function
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4
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5 import copy
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6 import math
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7 import os
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8
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9 import yaml
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10
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11 from planemo import git
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12 from planemo import io
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13 from planemo.shed import SHED_CONFIG_NAME
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14
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15
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16 def filter_paths(ctx, raw_paths, path_type="repo", **kwds):
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17 """Filter ``paths``.
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18
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19 ``path_type`` is ``repo`` or ``file``.
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20 """
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21 cwd = os.getcwd()
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22
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23 filter_kwds = copy.deepcopy(kwds)
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24 changed_in_commit_range = kwds.get("changed_in_commit_range", None)
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25 diff_paths = None
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26 if changed_in_commit_range is not None:
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27 diff_files = git.diff(ctx, cwd, changed_in_commit_range)
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28 if path_type == "repo":
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29 diff_dirs = set(os.path.dirname(p) for p in diff_files)
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30 diff_paths = set()
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31 for diff_dir in diff_dirs:
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32 while diff_dir:
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33 if os.path.isfile(os.path.join(diff_dir, SHED_CONFIG_NAME)):
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34 diff_paths.add(diff_dir)
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35 break
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36 diff_dir = os.path.dirname(diff_dir)
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37 else:
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38 diff_paths = diff_files
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39
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40 unique_paths = set(os.path.relpath(p, cwd) for p in raw_paths)
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41 if diff_paths is not None:
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42 new_unique_paths = []
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43 for path in unique_paths:
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44 if path in diff_paths:
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45 new_unique_paths.append(path)
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46 unique_paths = new_unique_paths
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47 filtered_paths = sorted(io.filter_paths(unique_paths, cwd=cwd, **filter_kwds))
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48 excluded_paths = sorted(set(unique_paths) - set(filtered_paths))
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49 if excluded_paths:
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50 ctx.log("List of excluded paths: %s" % excluded_paths)
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51
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52 path_count = len(filtered_paths)
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53 chunk_size = ((1.0 * path_count) / kwds["chunk_count"])
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54 chunk = kwds["chunk"]
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55
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56 chunked_paths = []
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57 for i, path in enumerate(filtered_paths):
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58 if int(math.floor(i / chunk_size)) == chunk:
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59 chunked_paths.append(path)
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60
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61 return chunked_paths
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62
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63
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64 def print_path_list(paths, **kwds):
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65 with io.open_file_or_standard_output(kwds["output"], "w") as f:
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66 for path in paths:
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67 print(path, file=f)
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68
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69
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70 def print_as_yaml(item, **kwds):
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71 with io.open_file_or_standard_output(kwds["output"], "w") as f:
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72 f.write(yaml.safe_dump(item))