Merge pull request galaxyproject#52 from galaxyproject/bump_versions

Bump all versions

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+ignore = E501

bump_version.py

@@ -0,0 +1,223 @@
+# 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 enum import Enum
+from pathlib import Path
+
+import marko
+from marko.md_renderer import MarkdownRenderer
+from packaging.version import parse as vparse, Version, LegacyVersion
+from planemo.context import PlanemoContext
+from planemo.shed import find_raw_repositories
+from planemo.ci import filter_paths
+
+DATE_FMT = "%Y-%m-%d"
+ENTRY_TYPES = "Added", "Changed", "Fixed"
+NEW_LOG_ENTRY = string.Template("""\
+## [${version}] ${date}
+
+### ${entry_type}
+
+${msg}
+
+""")
+
+
+class Bump(Enum):
+    MAJOR = "major"
+    MINOR = "minor"
+    MICRO = "micro"  # PEP 440
+    PATCH = "micro"  # Semantic Versioning
+
+
+# Allow "PATCH" alias, but leave it out of the help text to avoid confusion
+BUMP_CHOICES = list(Bump.__members__)  # includes aliases
+BUMP_METAVAR = "|".join(_.name for _ in Bump)  # does not include aliases
+
+
+class Renderer(MarkdownRenderer):
+    """\
+    A Markdown renderer that indents all lines in a paragraph.
+    """
+    def render_paragraph(self, element):
+        new_line = False
+        rendered = []
+        for child in element.children:
+            prefix = self._second_prefix if new_line else ""
+            rendered.append(prefix + self.render(child))
+            new_line = isinstance(child, marko.inline.LineBreak)
+        children = "".join(rendered)
+        line = self._prefix + children + "\n"
+        self._prefix = self._second_prefix
+        return line
+
+
+def get_new_release(rel, bump=Bump.MICRO):
+    if len(rel) == 1 and bump is Bump.MINOR or len(rel) == 2 and bump is Bump.MICRO:
+        return rel + (1,)
+    if len(rel) == 1 and bump is Bump.MICRO:
+        return rel + (0, 1)
+    return tuple(r + 1 if bump is b else r for r, b in zip(rel, Bump))
+
+
+def vbump(version, bump=Bump.MICRO):
+    if not isinstance(version, (Version, LegacyVersion)):
+        version = vparse(version)
+    new_release = get_new_release(version.release, bump)
+    # same as packaging.version.Version.__str__, but release is the new one
+    parts = []
+    if version.epoch != 0:
+        parts.append(f"{version.epoch}!")
+    parts.append(".".join(str(x) for x in new_release))
+    if version.pre is not None:
+        parts.append("".join(str(x) for x in version.pre))
+    if version.post is not None:
+        parts.append(f".post{version.post}")
+    if version.dev is not None:
+        parts.append(f".dev{version.dev}")
+    if version.local is not None:
+        parts.append(f"+{version.local}")
+    return "".join(parts)
+
+
+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, date=datetime.date.today(),
+                     entry_type="Changed"):
+    with open(changelog, "rt") as f:
+        tree = md.parse(f.read())
+    date = date.strftime(DATE_FMT)
+    entry = NEW_LOG_ENTRY.substitute(version=version, date=date, msg=msg,
+                                     entry_type=entry_type)
+    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=None, bump=None):
+    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')
+    if not version:
+        if not old_version:
+            raise RuntimeError(f'{workflow}: "release" metadata entry is empty')
+        version = vbump(old_version, bump=bump)
+    # 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))
+    return version
+
+
+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 args.date:
+        args.date = datetime.datetime.strptime(args.date, DATE_FMT)
+    else:
+        args.date = datetime.date.today()
+    args.bump = Bump[args.bump]
+    md = marko.Markdown(renderer=Renderer)
+    for repo in find_repos(args.root, exclude=args.exclude):
+        print(f"processing {repo}")
+        wf_id = get_wf_id(repo)
+        version = update_workflow(repo / wf_id, version=args.version, bump=args.bump)
+        msg = args.msg or f"Update for version {version}."
+        update_changelog(repo / "CHANGELOG.md", md, version, msg, date=args.date,
+                         entry_type=args.entry_type)
+
+
+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",
+                        help="set new workflow version to this value (ignores '-b')")
+    parser.add_argument("-m", "--msg", metavar="STRING", help="log message")
+    parser.add_argument("-d", "--date", metavar="STRING", help="log date as YYYY-MM-DD")
+    parser.add_argument("-t", "--entry-type", metavar="|".join(ENTRY_TYPES),
+                        choices=ENTRY_TYPES, default="Changed", help="log entry type")
+    parser.add_argument("-b", "--bump", metavar=BUMP_METAVAR, choices=BUMP_CHOICES,
+                        default="MICRO", help="version part to bump")
+    main(parser.parse_args())

requirements.txt

@@ -0,0 +1,3 @@
+marko~=1.0
+packaging~=21.0
+planemo>=0.74.5

workflows/data-fetching/parallel-accession-download/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.1.1] 2021-07-23
+
+### Added
+
+Added RO-Crate metadata file. No functional changes.
+
 ## [0.1] - 2021-06-23
 
 ### Added

workflows/data-fetching/parallel-accession-download/parallel-accession-download.ga

@@ -15,7 +15,7 @@
     ],
     "format-version": "0.1",
     "license": "MIT",
-    "release": "0.1",
+    "release": "0.1.1",
     "name": "Parallel Accession Download",
     "steps": {
         "0": {

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/CHANGELOG.md

@@ -1,5 +1,11 @@
 # Changelog
 
+## [0.2.1] 2021-07-23
+
+### Added
+
+Added RO-Crate metadata file. No functional changes.
+
 ## [0.2] - 2021-04-30
 ### Changed
 - Lower the default for consensus variant allele frequency threshold to 0.7
@@ -24,7 +30,6 @@
   variants of its samples as stated in the README, independent of it residing
   in low-coverage regions or not.
 
-
 ## [0.1]
 
 - Initial version of COVID-19: consensus construction

workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: consensus construction",
-    "release": "0.2",
+    "release": "0.2.1",
     "steps": {
         "0": {
             "annotation": "Collection of VCFs produced by upstream workflows for variation analysis",

workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/CHANGELOG.md

@@ -1,9 +1,17 @@
-0.2
----------
+# Changelog
+
+## [0.2.1] 2021-07-23
+
+### Added
+
+Added RO-Crate metadata file. No functional changes.
+
+## [0.2]
+
 - Apply the strand-bias filter only after variant annotation with snpEff. By
   producing fully annotated VCFs with and without filtering, downstream
   workflows can easily be switched between filtered/unfiltered input data
 
-0.1
----------
+## [0.1]
+
 - Initial version of COVID-19: variation analysis on ARTIC ONT data workflow

workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/ont-artic-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis of ARTIC ONT data",
-    "release": "0.2",
+    "release": "0.2.1",
     "steps": {
         "0": {
             "annotation": "ONT reads from ARTIC assay with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/CHANGELOG.md

@@ -1,12 +1,17 @@
 # Changelog
 
+## [0.4.1] 2021-07-23
+
+### Added
+
+Added RO-Crate metadata file. No functional changes.
+
 ## [0.4] - 2021-06-16
 
 ### Changed
 
 - Upgrade multiqc to 1.9+galaxy1
 
-
 ## [0.3] - 2021-05-19
 
 ### Changed

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on ARTIC PE data",
-    "release": "0.4",
+    "release": "0.4.1",
     "steps": {
         "0": {
             "annotation": "Illumina reads from ARTIC assay with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/CHANGELOG.md

@@ -1,13 +1,17 @@
 # Changelog
 
+## [0.2.1] 2021-07-23
+
+### Added
+
+Added RO-Crate metadata file. No functional changes.
+
 ## [0.2] 2021-06-17
 
 ### Changed
 
 - Upgrade multiqc to 1.9+galaxy1
 
-
 ## [0.1]
 
-
 - Initial version of COVID-19: variation analysis on WGS PE data workflow

workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on WGS PE data",
-    "release": "0.2",
+    "release": "0.2.1",
     "steps": {
         "0": {
             "annotation": "Illumina reads with fastqsanger encoding",

workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/CHANGELOG.md

@@ -1,3 +1,17 @@
-0.1
----------
+# Changelog
+
+## [0.1.2] 2021-07-23
+
+### Added
+
+Added RO-Crate metadata file. No functional changes.
+
+## [0.1.1] 2021-06-14
+
+### Fixed
+
+Fix reference to test file in .dockstore.yml
+
+## [0.1]
+
 - Initial version of COVID-19: variation analysis on WGS SE data workflow

workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation.ga

@@ -11,7 +11,7 @@
     "format-version": "0.1",
     "license": "MIT",
     "name": "COVID-19: variation analysis on WGS SE data",
-    "release": "0.1",
+    "release": "0.1.2",
     "steps": {
         "0": {
             "annotation": "Illumina reads with fastqsanger encoding",