Merge pull request #167 from jhlegarreta/AdoptNiprepsMaintenanceAutho…

…rScript

ENH: Adopt the NiPreps author update maintenance script

.maint/update_authors.py

@@ -0,0 +1,302 @@
+#!/usr/bin/env python3
+"""Update and sort the creators list of the zenodo record."""
+
+import json
+import sys
+from pathlib import Path
+
+import click
+from fuzzywuzzy import fuzz, process
+
+
+def read_md_table(md_text):
+    """
+    Extract the first table found in a markdown document as a Python dict.
+
+    Examples
+    --------
+    >>> read_md_table('''
+    ... # Some text
+    ...
+    ... More text
+    ...
+    ... | **Header1** | **Header2** |
+    ... | --- | --- |
+    ... | val1 | val2 |
+    ... |  | val4 |
+    ...
+    ... | **Header3** | **Header4** |
+    ... | --- | --- |
+    ... | val1 | val2 |
+    ... |  | val4 |
+    ... ''')
+    [{'header1': 'val1', 'header2': 'val2'}, {'header2': 'val4'}]
+
+    """
+    prev = None
+    keys = None
+    retval = []
+    for line in md_text.splitlines():
+        if line.strip().startswith("| --- |"):
+            keys = (k.replace("*", "").strip() for k in prev.split("|"))
+            keys = [k.lower() for k in keys if k]
+            continue
+        elif not keys:
+            prev = line
+            continue
+
+        if not line or not line.strip().startswith("|"):
+            break
+
+        values = [v.strip() or None for v in line.split("|")][1:-1]
+        retval.append({k: v for k, v in zip(keys, values) if v})
+
+    return retval
+
+
+def _extract_git_contributor_matches(git_lines, sorted_authors, first_last, first_last_excl):
+    unmatched = []
+    author_matches = []
+    for ele in git_lines:
+        matches = process.extract(ele, first_last, scorer=fuzz.token_sort_ratio, limit=2)
+        # matches is a list [('First match', % Match), ('Second match', % Match)]
+        if matches[0][1] > 80:
+            val = sorted_authors[first_last.index(matches[0][0])]
+        else:
+            # skip unmatched names
+            if ele not in first_last_excl:
+                unmatched.append(ele)
+            continue
+
+        if val not in author_matches:
+            author_matches.append(val)
+
+    return author_matches, unmatched
+
+
+def _get_position_matches(author_matches):
+    position_matches = []
+    for i, item in enumerate(author_matches):
+        pos = item.pop("position", None)
+        if pos is not None:
+            position_matches.append((i, int(pos)))
+
+    return position_matches
+
+
+def sort_contributors(entries, git_lines, exclude=None, last=None):
+    """Return a list of author dictionaries, ordered by contribution."""
+    last = last or []
+    sorted_authors = sorted(entries, key=lambda i: i["name"])
+
+    first_last = [" ".join(val["name"].split(",")[::-1]).strip() for val in sorted_authors]
+    first_last_excl = [" ".join(val["name"].split(",")[::-1]).strip() for val in exclude or []]
+
+    author_matches, unmatched = _extract_git_contributor_matches(
+        git_lines, sorted_authors, first_last, first_last_excl
+    )
+
+    names = {" ".join(val["name"].split(",")[::-1]).strip() for val in author_matches}
+    for missing_name in first_last:
+        if missing_name not in names:
+            missing = sorted_authors[first_last.index(missing_name)]
+            author_matches.append(missing)
+
+    position_matches = _get_position_matches(author_matches)
+
+    for i, pos in position_matches:
+        if pos < 0:
+            pos += len(author_matches) + 1
+        author_matches.insert(pos, author_matches.pop(i))
+
+    return author_matches, unmatched
+
+
+def get_git_lines(fname="line-contributors.txt"):
+    """Run git-line-summary."""
+    import shutil
+    import subprocess as sp
+
+    contrib_file = Path(fname)
+
+    lines = []
+    if contrib_file.exists():
+        print("WARNING: Reusing existing line-contributors.txt file.", file=sys.stderr)
+        lines = contrib_file.read_text().splitlines()
+
+    git_line_summary_path = shutil.which("git-line-summary")
+    if not lines and git_line_summary_path:
+        print("Running git-line-summary on repo")
+        lines = sp.check_output([git_line_summary_path]).decode().splitlines()
+        lines = [ele for ele in lines if "Not Committed Yet" not in ele]
+        contrib_file.write_text("\n".join(lines))
+
+    if not lines:
+        raise RuntimeError(
+            """\
+Could not find line-contributors from git repository.%s"""
+            % """ \
+git-line-summary not found, please install git-extras. """
+            * (git_line_summary_path is None)
+        )
+    return [" ".join(line.strip().split()[1:-1]) for line in lines if "%" in line]
+
+
+def _namelast(inlist):
+    retval = []
+    for i in inlist:
+        i["name"] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
+        retval.append(i)
+    return retval
+
+
+@click.group()
+def cli():
+    """Generate authorship boilerplates."""
+    pass
+
+
+@cli.command()
+@click.option("-z", "--zenodo-file", type=click.Path(exists=True), default=".zenodo.json")
+@click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
+@click.option(
+    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+)
+@click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
+@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
+def zenodo(
+    zenodo_file,
+    maintainers,
+    contributors,
+    pi,
+    former_file,
+):
+    """Generate a new Zenodo payload file."""
+    data = get_git_lines()
+
+    zenodo = json.loads(Path(zenodo_file).read_text())
+
+    former = _namelast(read_md_table(Path(former_file).read_text()))
+    zen_creators, miss_creators = sort_contributors(
+        _namelast(read_md_table(Path(maintainers).read_text())),
+        data,
+        exclude=former,
+    )
+
+    zen_contributors, miss_contributors = sort_contributors(
+        _namelast(read_md_table(Path(contributors).read_text())), data, exclude=former
+    )
+
+    zen_pi = _namelast(
+        sorted(
+            read_md_table(Path(pi).read_text()),
+            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
+        )
+    )
+
+    zenodo["creators"] = zen_creators
+    zenodo["contributors"] = zen_contributors + zen_pi
+
+    misses = set(miss_creators).intersection(miss_contributors)
+    if misses:
+        print(
+            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            file=sys.stderr,
+        )
+
+    # Remove position
+    for creator in zenodo["creators"]:
+        creator.pop("position", None)
+        creator.pop("handle", None)
+        if isinstance(creator["affiliation"], list):
+            creator["affiliation"] = creator["affiliation"][0]
+
+    for creator in zenodo["contributors"]:
+        creator.pop("handle", None)
+        creator["type"] = "Researcher"
+        creator.pop("position", None)
+
+        if isinstance(creator["affiliation"], list):
+            creator["affiliation"] = creator["affiliation"][0]
+
+    Path(zenodo_file).write_text("%s\n" % json.dumps(zenodo, indent=2))
+
+
+@cli.command()
+@click.option("-m", "--maintainers", type=click.Path(exists=True), default=".maint/MAINTAINERS.md")
+@click.option(
+    "-c", "--contributors", type=click.Path(exists=True), default=".maint/CONTRIBUTORS.md"
+)
+@click.option("--pi", type=click.Path(exists=True), default=".maint/PIs.md")
+@click.option("-f", "--former-file", type=click.Path(exists=True), default=".maint/FORMER.md")
+def publication(
+    maintainers,
+    contributors,
+    pi,
+    former_file,
+):
+    """Generate the list of authors and affiliations for papers."""
+    members = _namelast(read_md_table(Path(maintainers).read_text())) + _namelast(
+        read_md_table(Path(contributors).read_text())
+    )
+
+    hits, misses = sort_contributors(
+        members,
+        get_git_lines(),
+        exclude=_namelast(read_md_table(Path(former_file).read_text())),
+    )
+
+    pi_hits = _namelast(
+        sorted(
+            read_md_table(Path(pi).read_text()),
+            key=lambda v: (int(v.get("position", -1)), v.get("lastname")),
+        )
+    )
+
+    pi_names = [pi["name"] for pi in pi_hits]
+    hits = [hit for hit in hits if hit["name"] not in pi_names] + pi_hits
+
+    def _aslist(value):
+        if isinstance(value, (list, tuple)):
+            return value
+        return [value]
+
+    # Remove position
+    affiliations = []
+    for item in hits:
+        item.pop("position", None)
+        for a in _aslist(item.get("affiliation", "Unaffiliated")):
+            if a not in affiliations:
+                affiliations.append(a)
+
+    aff_indexes = [
+        ", ".join(
+            [
+                "%d" % (affiliations.index(a) + 1)
+                for a in _aslist(author.get("affiliation", "Unaffiliated"))
+            ]
+        )
+        for author in hits
+    ]
+
+    if misses:
+        print(
+            "Some people made commits, but are missing in .maint/ " f"files: {', '.join(misses)}",
+            file=sys.stderr,
+        )
+
+    print("Authors (%d):" % len(hits))
+    print(
+        "%s."
+        % "; ".join(["%s \\ :sup:`%s`\\ " % (i["name"], idx) for i, idx in zip(hits, aff_indexes)])
+    )
+
+    print(
+        "\n\nAffiliations:\n%s"
+        % "\n".join(["{0: >2}. {1}".format(i + 1, a) for i, a in enumerate(affiliations)])
+    )
+
+
+if __name__ == "__main__":
+    """ Install entry-point """
+    cli()