add bump_version.py

.flake8

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+[flake8]
+ignore = E501

bump_version.py

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+# Copyright (c) 2021 CRS4
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+"""\
+Bump workflow repository version.
+
+Workflow repositories are searched for starting from the specified root
+directories (the default is to search below the current directory). Uses the
+same searching logic and definition of repository as the ci_find_repos Planemo
+command (any directory with a .shed.yml or .dockstore.yml file).
+
+Workflow repositories are expected to contain:
+
+- the .ga workflow file (e.g., "consensus-from-variation.ga"), which is
+  expected to list its version in the "release" metadata field
+- a CHANGELOG.md file with atx-style Markdown headers (the ones with the
+  leading hash marks), with the convention that:
+  - the top-level header is "# Changelog"
+  - level 2 headers start with ## <VERSION>
+
+Example:
+
+# Changelog
+
+## [0.4] - 2021-06-16
+
+### Changed
+
+- Upgrade multiqc to 1.9+galaxy1
+"""
+
+import argparse
+import datetime
+import json
+import os
+import re
+import string
+from pathlib import Path
+
+import marko
+from marko.md_renderer import MarkdownRenderer
+from planemo.context import PlanemoContext
+from planemo.shed import find_raw_repositories
+from planemo.ci import filter_paths
+
+
+NEW_LOG_ENTRY = string.Template("""\
+## [${version}] ${date}
+
+${msg}
+
+""")
+
+
+def get_wf_id(repo_dir):
+    ids = [_.name for _ in os.scandir(repo_dir) if _.name.endswith(".ga")]
+    if not ids:
+        raise RuntimeError(f".ga workflow file not found in {repo_dir}")
+    return ids[0]
+
+
+def update_changelog(changelog, md, version, msg):
+    with open(changelog, "rt") as f:
+        tree = md.parse(f.read())
+    date = datetime.date.today().strftime("%Y-%m-%d")
+    entry = NEW_LOG_ENTRY.substitute(version=version, date=date, msg=msg)
+    entry_tree = marko.block.Document(entry)
+    for ins_pos, elem in enumerate(tree.children):
+        if isinstance(elem, marko.block.Heading) and elem.level == 2:
+            break
+    else:
+        ins_pos = len(tree.children)
+    tree.children[ins_pos:ins_pos] = entry_tree.children
+    with open(changelog, "wt") as f:
+        f.write(md.render(tree))
+
+
+def update_workflow(workflow, version):
+    with open(workflow, "rt") as f:
+        txt = f.read()
+    code = json.loads(txt)
+    try:
+        old_version = code["release"]
+    except KeyError:
+        raise RuntimeError(f'{workflow} does not have a "release" metadata entry')
+    # no json tools for the update (we'd get a huge diff due to whitespace change)
+    pattern = fr'"release":\s*"{old_version}"'
+    repl = f'"release": "{version}"'
+    with open(workflow, "wt") as f:
+        f.write(re.sub(pattern, repl, txt, 1))
+
+
+def find_repos(paths, exclude=()):
+    """\
+    Find all workflow directories below each path in ``paths``.
+
+    Same as ``planemo ci_find_repos``.
+    """
+    ctx = PlanemoContext()
+    kwargs = dict(recursive=True, fail_fast=True, chunk_count=1, chunk=0, exclude=exclude)
+    raw_repos = [_.path for _ in find_raw_repositories(ctx, paths, **kwargs)]
+    return [Path(_) for _ in filter_paths(ctx, raw_repos, path_type="repo", **kwargs)]
+
+
+def main(args):
+    if not args.msg:
+        args.msg = f"Version {args.version}"
+    md = marko.Markdown(renderer=MarkdownRenderer)
+    for repo in find_repos(args.root, exclude=args.exclude):
+        print(f"processing {repo}")
+        wf_id = get_wf_id(repo)
+        update_workflow(repo / wf_id, args.version)
+        update_changelog(repo / "CHANGELOG.md", md, args.version, args.msg)
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawTextHelpFormatter
+    )
+    parser.add_argument("root", metavar="ROOT_DIR", help="top-level directory",
+                        nargs="*", default=[os.getcwd()])
+    parser.add_argument("--exclude", metavar="PATH", nargs="*", default=(),
+                        help="paths to exclude while searching for workflow repos")
+    parser.add_argument("-v", "--version", metavar="STRING", default="0.1",
+                        help="new workflow version")
+    parser.add_argument("-m", "--msg", metavar="STRING", help="log message")
+    main(parser.parse_args())

requirements.txt

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+marko~=1.0
+planemo>=0.74.5