Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/planemo/ci.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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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 REPO_METADATA_FILES |
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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 diff_path = metadata_file_in_path(diff_dir) |
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33 if diff_path: |
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34 diff_paths.add(diff_path) |
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35 else: |
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36 diff_paths = diff_files |
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37 |
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38 unique_paths = set(os.path.relpath(p, cwd) for p in raw_paths) |
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39 if diff_paths is not None: |
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40 unique_paths = unique_paths.intersection(diff_paths) |
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41 filtered_paths = sorted(io.filter_paths(unique_paths, cwd=cwd, **filter_kwds)) |
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42 excluded_paths = sorted(set(unique_paths) - set(filtered_paths)) |
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43 if excluded_paths: |
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44 ctx.log("List of excluded paths: %s" % excluded_paths) |
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45 |
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46 path_count = len(filtered_paths) |
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47 chunk_size = ((1.0 * path_count) / kwds["chunk_count"]) |
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48 chunk = kwds["chunk"] |
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49 |
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50 chunked_paths = [] |
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51 for i, path in enumerate(filtered_paths): |
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52 if int(math.floor(i / chunk_size)) == chunk: |
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53 chunked_paths.append(path) |
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54 |
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55 return chunked_paths |
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56 |
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57 |
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58 def metadata_file_in_path(diff_dir): |
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59 while diff_dir: |
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60 for metadata_file in REPO_METADATA_FILES: |
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61 if os.path.isfile(os.path.join(diff_dir, metadata_file)): |
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62 return diff_dir |
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63 diff_dir = os.path.dirname(diff_dir) |
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64 |
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65 |
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66 def group_paths(paths): |
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67 repos = {} |
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68 for path in paths: |
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69 repo = os.path.split(path)[0] |
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70 if repo not in repos: |
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71 repos[repo] = [] |
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72 repos[repo].append(path) |
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73 return [" ".join(repos[_]) for _ in repos] |
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74 |
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75 |
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76 def print_path_list(paths, **kwds): |
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77 with io.open_file_or_standard_output(kwds["output"], "w") as f: |
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78 for path in paths: |
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79 print(path, file=f) |
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80 |
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81 |
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82 def print_as_yaml(item, **kwds): |
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83 with io.open_file_or_standard_output(kwds["output"], "w") as f: |
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84 f.write(yaml.safe_dump(item)) |