Mercurial > repos > shellac > guppy_basecaller
view env/lib/python3.7/site-packages/planemo/ci.py @ 3:758bc20232e8 draft
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author | shellac |
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date | Thu, 14 May 2020 16:20:52 -0400 |
parents | 26e78fe6e8c4 |
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"""Utilities for dealing with continous integration systems.""" from __future__ import print_function import copy import math import os import yaml from planemo import git from planemo import io from planemo.shed import SHED_CONFIG_NAME def filter_paths(ctx, raw_paths, path_type="repo", **kwds): """Filter ``paths``. ``path_type`` is ``repo`` or ``file``. """ cwd = os.getcwd() filter_kwds = copy.deepcopy(kwds) changed_in_commit_range = kwds.get("changed_in_commit_range", None) diff_paths = None if changed_in_commit_range is not None: diff_files = git.diff(ctx, cwd, changed_in_commit_range) if path_type == "repo": diff_dirs = set(os.path.dirname(p) for p in diff_files) diff_paths = set() for diff_dir in diff_dirs: while diff_dir: if os.path.isfile(os.path.join(diff_dir, SHED_CONFIG_NAME)): diff_paths.add(diff_dir) break diff_dir = os.path.dirname(diff_dir) else: diff_paths = diff_files unique_paths = set(os.path.relpath(p, cwd) for p in raw_paths) if diff_paths is not None: new_unique_paths = [] for path in unique_paths: if path in diff_paths: new_unique_paths.append(path) unique_paths = new_unique_paths filtered_paths = sorted(io.filter_paths(unique_paths, cwd=cwd, **filter_kwds)) excluded_paths = sorted(set(unique_paths) - set(filtered_paths)) if excluded_paths: ctx.log("List of excluded paths: %s" % excluded_paths) path_count = len(filtered_paths) chunk_size = ((1.0 * path_count) / kwds["chunk_count"]) chunk = kwds["chunk"] chunked_paths = [] for i, path in enumerate(filtered_paths): if int(math.floor(i / chunk_size)) == chunk: chunked_paths.append(path) return chunked_paths def print_path_list(paths, **kwds): with io.open_file_or_standard_output(kwds["output"], "w") as f: for path in paths: print(path, file=f) def print_as_yaml(item, **kwds): with io.open_file_or_standard_output(kwds["output"], "w") as f: f.write(yaml.safe_dump(item))