From 62e283be6558e9abec374d153bfbbaa3ffb8415a Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:50:11 +0200
Subject: [PATCH 01/20] specify ubuntu lts

---
 .github/workflows/python-app.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index f2f4753e..7c93faae 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         # os: [ubuntu-latest, macos-latest, windows-latest]
-        os: [ubuntu-latest, windows-latest]
+        os: [ubuntu-lts-latest, windows-latest]
         python_version: ['3.10', '3.11', '3.12']
     name: Run py eddy tracker build tests
     runs-on: ${{ matrix.os }}

From e6d4ada203bfe29b2a7231428948fcba7bbbcc74 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:56:25 +0200
Subject: [PATCH 02/20] Specify os for readthedocs

---
 .readthedocs.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 1299f38e..ec749526 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -1,6 +1,8 @@
 version: 2
 conda:
   environment: doc/environment.yml
+build:
+  os: ubuntu-lts-latest
 python:
    install:
      - method: setuptools

From 80f8e143adf5ae992286cbe42336730e88a06c9e Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 14:58:56 +0200
Subject: [PATCH 03/20] Add python spec for readthedocs

---
 .readthedocs.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index ec749526..a04495b6 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -3,7 +3,9 @@ conda:
   environment: doc/environment.yml
 build:
   os: ubuntu-lts-latest
+  tools:
+    python: "3.10"
 python:
-   install:
-     - method: setuptools
-       path: .
+  install:
+    - method: setuptools
+      path: .

From 27bafc6d7bb21b02e2ceada0d048a906b4616609 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:08:35 +0200
Subject: [PATCH 04/20] update versionner

---
 src/py_eddy_tracker/__init__.py |  12 +-
 src/py_eddy_tracker/_version.py | 449 ++++++++++++++++++++------------
 2 files changed, 296 insertions(+), 165 deletions(-)

diff --git a/src/py_eddy_tracker/__init__.py b/src/py_eddy_tracker/__init__.py
index 0a98892d..7115bf67 100644
--- a/src/py_eddy_tracker/__init__.py
+++ b/src/py_eddy_tracker/__init__.py
@@ -32,13 +32,13 @@
 del get_versions
 
 
-def start_logger():
+def start_logger(color=True):
     FORMAT_LOG = "%(levelname)-8s %(asctime)s %(module)s.%(funcName)s :\n\t%(message)s"
     logger = logging.getLogger("pet")
     if len(logger.handlers) == 0:
         # set up logging to CONSOLE
         console = logging.StreamHandler()
-        console.setFormatter(ColoredFormatter(FORMAT_LOG))
+        console.setFormatter(ColoredFormatter(FORMAT_LOG, color=color))
         # add the handler to the root logger
         logger.addHandler(console)
     return logger
@@ -53,13 +53,14 @@ class ColoredFormatter(logging.Formatter):
         DEBUG="\033[34m\t",
     )
 
-    def __init__(self, message):
+    def __init__(self, message, color=True):
         super().__init__(message)
+        self.with_color = color
 
     def format(self, record):
         color = self.COLOR_LEVEL.get(record.levelname, "")
         color_reset = "\033[0m"
-        model = color + "%s" + color_reset
+        model = (color + "%s" + color_reset) if self.with_color else "%s"
         record.msg = model % record.msg
         record.funcName = model % record.funcName
         record.module = model % record.module
@@ -696,3 +697,6 @@ def identify_time(str_date):
     VAR_DESCR_inv[VAR_DESCR[key]["nc_name"]] = key
     for key_old in VAR_DESCR[key].get("old_nc_name", list()):
         VAR_DESCR_inv[key_old] = key
+
+from . import _version
+__version__ = _version.get_versions()['version']
diff --git a/src/py_eddy_tracker/_version.py b/src/py_eddy_tracker/_version.py
index 44367e3a..589e706f 100644
--- a/src/py_eddy_tracker/_version.py
+++ b/src/py_eddy_tracker/_version.py
@@ -1,11 +1,13 @@
+
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
 # directories (produced by setup.py build) will contain a much shorter file
 # that just contains the computed version number.
 
-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
+# This file is released into the public domain.
+# Generated by versioneer-0.29
+# https://github.com/python-versioneer/python-versioneer
 
 """Git implementation of _version.py."""
 
@@ -14,9 +16,11 @@
 import re
 import subprocess
 import sys
+from typing import Any, Callable, Dict, List, Optional, Tuple
+import functools
 
 
-def get_keywords():
+def get_keywords() -> Dict[str, str]:
     """Get the keywords needed to look up the version information."""
     # these strings will be replaced by git during git-archive.
     # setup.py/versioneer.py will grep for the variable names, so they must
@@ -32,8 +36,15 @@ def get_keywords():
 class VersioneerConfig:
     """Container for Versioneer configuration parameters."""
 
+    VCS: str
+    style: str
+    tag_prefix: str
+    parentdir_prefix: str
+    versionfile_source: str
+    verbose: bool
+
 
-def get_config():
+def get_config() -> VersioneerConfig:
     """Create, populate and return the VersioneerConfig() object."""
     # these strings are filled in when 'setup.py versioneer' creates
     # _version.py
@@ -51,41 +62,50 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
 
-    def decorate(f):
+def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
+    """Create decorator to mark a method as the handler of a VCS."""
+    def decorate(f: Callable) -> Callable:
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
         HANDLERS[vcs][method] = f
         return f
-
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+def run_command(
+    commands: List[str],
+    args: List[str],
+    cwd: Optional[str] = None,
+    verbose: bool = False,
+    hide_stderr: bool = False,
+    env: Optional[Dict[str, str]] = None,
+) -> Tuple[Optional[str], Optional[int]]:
     """Call the given command(s)."""
     assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+
+    popen_kwargs: Dict[str, Any] = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
+    for command in commands:
         try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen(
-                [c] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None),
-            )
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None), **popen_kwargs)
             break
-        except EnvironmentError:
-            e = sys.exc_info()[1]
+        except OSError as e:
             if e.errno == errno.ENOENT:
                 continue
             if verbose:
@@ -96,18 +116,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
         if verbose:
             print("unable to find command, tried %s" % (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)
             print("stdout was %s" % stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode
 
 
-def versions_from_parentdir(parentdir_prefix, root, verbose):
+def versions_from_parentdir(
+    parentdir_prefix: str,
+    root: str,
+    verbose: bool,
+) -> Dict[str, Any]:
     """Try to determine the version from the parent directory name.
 
     Source tarballs conventionally unpack into a directory that includes both
@@ -116,64 +138,64 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {
-                "version": dirname[len(parentdir_prefix) :],
-                "full-revisionid": None,
-                "dirty": False,
-                "error": None,
-                "date": None,
-            }
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print(
-            "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
-        )
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
 @register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
+def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
     """Extract version information from the given file."""
     # the code embedded in _version.py can just fetch the value of these
     # keywords. When used from setup.py, we don't want to import _version.py,
     # so we do it with a regexp instead. This function is not used from
     # _version.py.
-    keywords = {}
+    keywords: Dict[str, str] = {}
     try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
         pass
     return keywords
 
 
 @register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
+def git_versions_from_keywords(
+    keywords: Dict[str, str],
+    tag_prefix: str,
+    verbose: bool,
+) -> Dict[str, Any]:
     """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
         # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
         # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
         # -like" string, which we must then edit to make compliant), because
@@ -186,11 +208,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         if verbose:
             print("keywords are unexpanded, not using")
         raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -199,7 +221,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r"\d", r)])
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -207,30 +229,33 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix) :]
+            r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %s" % r)
-            return {
-                "version": r,
-                "full-revisionid": keywords["full"].strip(),
-                "dirty": False,
-                "error": None,
-                "date": date,
-            }
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {
-        "version": "0+unknown",
-        "full-revisionid": keywords["full"].strip(),
-        "dirty": False,
-        "error": "no suitable tags",
-        "date": None,
-    }
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(
+    tag_prefix: str,
+    root: str,
+    verbose: bool,
+    runner: Callable = run_command
+) -> Dict[str, Any]:
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -241,7 +266,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
+
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=not verbose)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -249,33 +282,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(
-        GITS,
-        [
-            "describe",
-            "--tags",
-            "--dirty",
-            "--always",
-            "--long",
-            "--match",
-            "%s*" % tag_prefix,
-        ],
-        cwd=root,
-    )
+    describe_out, rc = runner(GITS, [
+        "describe", "--tags", "--dirty", "--always", "--long",
+        "--match", f"{tag_prefix}[[:digit:]]*"
+    ], cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
     describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
     if full_out is None:
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
 
-    pieces = {}
+    pieces: Dict[str, Any] = {}
     pieces["long"] = full_out
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
     # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
     # TAG might have hyphens.
     git_describe = describe_out
@@ -284,16 +341,17 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[: git_describe.rindex("-dirty")]
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            # unparsable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
             return pieces
 
         # tag
@@ -302,12 +360,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
-                full_tag,
-                tag_prefix,
-            )
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -318,26 +374,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
+        out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root)
+        pieces["distance"] = len(out.split())  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
-        0
-    ].strip()
+    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
 
 
-def plus_or_dot(pieces):
+def plus_or_dot(pieces: Dict[str, Any]) -> str:
     """Return a + if we don't already have one, else return a ."""
     if "+" in pieces.get("closest-tag", ""):
         return "."
     return "+"
 
 
-def render_pep440(pieces):
+def render_pep440(pieces: Dict[str, Any]) -> str:
     """Build up version string, with post-release "local version identifier".
 
     Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
@@ -355,29 +412,78 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
 
 
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces: Dict[str, Any]) -> str:
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
         if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%d" % (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
     else:
         # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
+        rendered = "0.post0.dev%d" % pieces["distance"]
     return rendered
 
 
-def render_pep440_post(pieces):
+def render_pep440_post(pieces: Dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]+gHEX] .
 
     The ".dev0" means dirty. Note that .dev0 sorts backwards
@@ -404,12 +510,41 @@ def render_pep440_post(pieces):
     return rendered
 
 
-def render_pep440_old(pieces):
+def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_old(pieces: Dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:
@@ -426,7 +561,7 @@ def render_pep440_old(pieces):
     return rendered
 
 
-def render_git_describe(pieces):
+def render_git_describe(pieces: Dict[str, Any]) -> str:
     """TAG[-DISTANCE-gHEX][-dirty].
 
     Like 'git describe --tags --dirty --always'.
@@ -446,7 +581,7 @@ def render_git_describe(pieces):
     return rendered
 
 
-def render_git_describe_long(pieces):
+def render_git_describe_long(pieces: Dict[str, Any]) -> str:
     """TAG-DISTANCE-gHEX[-dirty].
 
     Like 'git describe --tags --dirty --always -long'.
@@ -466,26 +601,28 @@ def render_git_describe_long(pieces):
     return rendered
 
 
-def render(pieces, style):
+def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {
-            "version": "unknown",
-            "full-revisionid": pieces.get("long"),
-            "dirty": None,
-            "error": pieces["error"],
-            "date": None,
-        }
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
 
     if not style or style == "default":
         style = "pep440"  # the default
 
     if style == "pep440":
         rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
     elif style == "pep440-pre":
         rendered = render_pep440_pre(pieces)
     elif style == "pep440-post":
         rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
     elif style == "pep440-old":
         rendered = render_pep440_old(pieces)
     elif style == "git-describe":
@@ -495,16 +632,12 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {
-        "version": rendered,
-        "full-revisionid": pieces["long"],
-        "dirty": pieces["dirty"],
-        "error": None,
-        "date": pieces.get("date"),
-    }
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
 
 
-def get_versions():
+def get_versions() -> Dict[str, Any]:
     """Get version information or return default if unable to do so."""
     # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
     # __file__, we can work backwards from there to the root. Some
@@ -515,7 +648,8 @@ def get_versions():
     verbose = cfg.verbose
 
     try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
+        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
+                                          verbose)
     except NotThisMethod:
         pass
 
@@ -524,16 +658,13 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split("/"):
+        for _ in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
-        return {
-            "version": "0+unknown",
-            "full-revisionid": None,
-            "dirty": None,
-            "error": "unable to find root of source tree",
-            "date": None,
-        }
+        return {"version": "0+unknown", "full-revisionid": None,
+                "dirty": None,
+                "error": "unable to find root of source tree",
+                "date": None}
 
     try:
         pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
@@ -547,10 +678,6 @@ def get_versions():
     except NotThisMethod:
         pass
 
-    return {
-        "version": "0+unknown",
-        "full-revisionid": None,
-        "dirty": None,
-        "error": "unable to compute version",
-        "date": None,
-    }
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None,
+            "error": "unable to compute version", "date": None}

From 0cb3230e8a97731e25d8e8d65df1e405c1d6406c Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:13:00 +0200
Subject: [PATCH 05/20] versionner file

---
 versioneer.py | 1354 +++++++++++++++++++++++++++++++------------------
 1 file changed, 873 insertions(+), 481 deletions(-)

diff --git a/versioneer.py b/versioneer.py
index 2b545405..1e3753e6 100644
--- a/versioneer.py
+++ b/versioneer.py
@@ -1,4 +1,5 @@
-# Version: 0.18
+
+# Version: 0.29
 
 """The Versioneer - like a rocketeer, but for versions.
 
@@ -6,18 +7,14 @@
 ==============
 
 * like a rocketeer, but for versions!
-* https://github.com/warner/python-versioneer
+* https://github.com/python-versioneer/python-versioneer
 * Brian Warner
-* License: Public Domain
-* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
-* [![Latest Version]
-(https://pypip.in/version/versioneer/badge.svg?style=flat)
-](https://pypi.python.org/pypi/versioneer/)
-* [![Build Status]
-(https://travis-ci.org/warner/python-versioneer.png?branch=master)
-](https://travis-ci.org/warner/python-versioneer)
-
-This is a tool for managing a recorded version number in distutils-based
+* License: Public Domain (Unlicense)
+* Compatible with: Python 3.7, 3.8, 3.9, 3.10, 3.11 and pypy3
+* [![Latest Version][pypi-image]][pypi-url]
+* [![Build Status][travis-image]][travis-url]
+
+This is a tool for managing a recorded version number in setuptools-based
 python projects. The goal is to remove the tedious and error-prone "update
 the embedded version string" step from your release process. Making a new
 release should be as easy as recording a new tag in your version-control
@@ -26,9 +23,38 @@
 
 ## Quick Install
 
-* `pip install versioneer` to somewhere to your $PATH
-* add a `[versioneer]` section to your setup.cfg (see below)
-* run `versioneer install` in your source tree, commit the results
+Versioneer provides two installation modes. The "classic" vendored mode installs
+a copy of versioneer into your repository. The experimental build-time dependency mode
+is intended to allow you to skip this step and simplify the process of upgrading.
+
+### Vendored mode
+
+* `pip install versioneer` to somewhere in your $PATH
+   * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is
+     available, so you can also use `conda install -c conda-forge versioneer`
+* add a `[tool.versioneer]` section to your `pyproject.toml` or a
+  `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md))
+   * Note that you will need to add `tomli; python_version < "3.11"` to your
+     build-time dependencies if you use `pyproject.toml`
+* run `versioneer install --vendor` in your source tree, commit the results
+* verify version information with `python setup.py version`
+
+### Build-time dependency mode
+
+* `pip install versioneer` to somewhere in your $PATH
+   * A [conda-forge recipe](https://github.com/conda-forge/versioneer-feedstock) is
+     available, so you can also use `conda install -c conda-forge versioneer`
+* add a `[tool.versioneer]` section to your `pyproject.toml` or a
+  `[versioneer]` section to your `setup.cfg` (see [Install](INSTALL.md))
+* add `versioneer` (with `[toml]` extra, if configuring in `pyproject.toml`)
+  to the `requires` key of the `build-system` table in `pyproject.toml`:
+  ```toml
+  [build-system]
+  requires = ["setuptools", "versioneer[toml]"]
+  build-backend = "setuptools.build_meta"
+  ```
+* run `versioneer install --no-vendor` in your source tree, commit the results
+* verify version information with `python setup.py version`
 
 ## Version Identifiers
 
@@ -60,7 +86,7 @@
 for example `git describe --tags --dirty --always` reports things like
 "0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
 0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
-uncommitted changes.
+uncommitted changes).
 
 The version identifier is used for multiple purposes:
 
@@ -165,7 +191,7 @@
 
 Some situations are known to cause problems for Versioneer. This details the
 most significant ones. More can be found on Github
-[issues page](https://github.com/warner/python-versioneer/issues).
+[issues page](https://github.com/python-versioneer/python-versioneer/issues).
 
 ### Subprojects
 
@@ -179,7 +205,7 @@
   `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
   distributions (and upload multiple independently-installable tarballs).
 * Source trees whose main purpose is to contain a C library, but which also
-  provide bindings to Python (and perhaps other langauges) in subdirectories.
+  provide bindings to Python (and perhaps other languages) in subdirectories.
 
 Versioneer will look for `.git` in parent directories, and most operations
 should get the right version string. However `pip` and `setuptools` have bugs
@@ -193,9 +219,9 @@
 Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in
 some later version.
 
-[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking
+[Bug #38](https://github.com/python-versioneer/python-versioneer/issues/38) is tracking
 this issue. The discussion in
-[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the
+[PR #61](https://github.com/python-versioneer/python-versioneer/pull/61) describes the
 issue from the Versioneer side in more detail.
 [pip PR#3176](https://github.com/pypa/pip/pull/3176) and
 [pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve
@@ -223,31 +249,20 @@
 cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into
 a different virtualenv), so this can be surprising.
 
-[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes
+[Bug #83](https://github.com/python-versioneer/python-versioneer/issues/83) describes
 this one, but upgrading to a newer version of setuptools should probably
 resolve it.
 
-### Unicode version strings
-
-While Versioneer works (and is continually tested) with both Python 2 and
-Python 3, it is not entirely consistent with bytes-vs-unicode distinctions.
-Newer releases probably generate unicode version strings on py2. It's not
-clear that this is wrong, but it may be surprising for applications when then
-write these strings to a network connection or include them in bytes-oriented
-APIs like cryptographic checksums.
-
-[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates
-this question.
-
 
 ## Updating Versioneer
 
 To upgrade your project to a new release of Versioneer, do the following:
 
 * install the new Versioneer (`pip install -U versioneer` or equivalent)
-* edit `setup.cfg`, if necessary, to include any new configuration settings
-  indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details.
-* re-run `versioneer install` in your source tree, to replace
+* edit `setup.cfg` and `pyproject.toml`, if necessary,
+  to include any new configuration settings indicated by the release notes.
+  See [UPGRADING](./UPGRADING.md) for details.
+* re-run `versioneer install --[no-]vendor` in your source tree, to replace
   `SRC/_version.py`
 * commit any changed files
 
@@ -264,36 +279,70 @@
 direction and include code from all supported VCS systems, reducing the
 number of intermediate scripts.
 
+## Similar projects
+
+* [setuptools_scm](https://github.com/pypa/setuptools_scm/) - a non-vendored build-time
+  dependency
+* [minver](https://github.com/jbweston/miniver) - a lightweight reimplementation of
+  versioneer
+* [versioningit](https://github.com/jwodder/versioningit) - a PEP 518-based setuptools
+  plugin
 
 ## License
 
 To make Versioneer easier to embed, all its code is dedicated to the public
 domain. The `_version.py` that it creates is also in the public domain.
-Specifically, both are released under the Creative Commons "Public Domain
-Dedication" license (CC0-1.0), as described in
-https://creativecommons.org/publicdomain/zero/1.0/ .
+Specifically, both are released under the "Unlicense", as described in
+https://unlicense.org/.
 
-"""
+[pypi-image]: https://img.shields.io/pypi/v/versioneer.svg
+[pypi-url]: https://pypi.python.org/pypi/versioneer/
+[travis-image]:
+https://img.shields.io/travis/com/python-versioneer/python-versioneer.svg
+[travis-url]: https://travis-ci.com/github/python-versioneer/python-versioneer
 
-from __future__ import print_function
+"""
+# pylint:disable=invalid-name,import-outside-toplevel,missing-function-docstring
+# pylint:disable=missing-class-docstring,too-many-branches,too-many-statements
+# pylint:disable=raise-missing-from,too-many-lines,too-many-locals,import-error
+# pylint:disable=too-few-public-methods,redefined-outer-name,consider-using-with
+# pylint:disable=attribute-defined-outside-init,too-many-arguments
 
-try:
-    import configparser
-except ImportError:
-    import ConfigParser as configparser
+import configparser
 import errno
 import json
 import os
 import re
 import subprocess
 import sys
+from pathlib import Path
+from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union
+from typing import NoReturn
+import functools
+
+have_tomllib = True
+if sys.version_info >= (3, 11):
+    import tomllib
+else:
+    try:
+        import tomli as tomllib
+    except ImportError:
+        have_tomllib = False
 
 
 class VersioneerConfig:
     """Container for Versioneer configuration parameters."""
 
+    VCS: str
+    style: str
+    tag_prefix: str
+    versionfile_source: str
+    versionfile_build: Optional[str]
+    parentdir_prefix: Optional[str]
+    verbose: Optional[bool]
 
-def get_root():
+
+def get_root() -> str:
     """Get the project root directory.
 
     We require that all commands are run from the project root, i.e. the
@@ -301,20 +350,28 @@ def get_root():
     """
     root = os.path.realpath(os.path.abspath(os.getcwd()))
     setup_py = os.path.join(root, "setup.py")
+    pyproject_toml = os.path.join(root, "pyproject.toml")
     versioneer_py = os.path.join(root, "versioneer.py")
-    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
+    if not (
+        os.path.exists(setup_py)
+        or os.path.exists(pyproject_toml)
+        or os.path.exists(versioneer_py)
+    ):
         # allow 'python path/to/setup.py COMMAND'
         root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0])))
         setup_py = os.path.join(root, "setup.py")
+        pyproject_toml = os.path.join(root, "pyproject.toml")
         versioneer_py = os.path.join(root, "versioneer.py")
-    if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
-        err = (
-            "Versioneer was unable to run the project root directory. "
-            "Versioneer requires setup.py to be executed from "
-            "its immediate directory (like 'python setup.py COMMAND'), "
-            "or in a way that lets it use sys.argv[0] to find the root "
-            "(like 'python path/to/setup.py COMMAND')."
-        )
+    if not (
+        os.path.exists(setup_py)
+        or os.path.exists(pyproject_toml)
+        or os.path.exists(versioneer_py)
+    ):
+        err = ("Versioneer was unable to run the project root directory. "
+               "Versioneer requires setup.py to be executed from "
+               "its immediate directory (like 'python setup.py COMMAND'), "
+               "or in a way that lets it use sys.argv[0] to find the root "
+               "(like 'python path/to/setup.py COMMAND').")
         raise VersioneerBadRootError(err)
     try:
         # Certain runtime workflows (setup.py install/develop in a setuptools
@@ -323,46 +380,62 @@ def get_root():
         # module-import table will cache the first one. So we can't use
         # os.path.dirname(__file__), as that will find whichever
         # versioneer.py was first imported, even in later projects.
-        me = os.path.realpath(os.path.abspath(__file__))
-        me_dir = os.path.normcase(os.path.splitext(me)[0])
+        my_path = os.path.realpath(os.path.abspath(__file__))
+        me_dir = os.path.normcase(os.path.splitext(my_path)[0])
         vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
-        if me_dir != vsr_dir:
-            print(
-                "Warning: build in %s is using versioneer.py from %s"
-                % (os.path.dirname(me), versioneer_py)
-            )
+        if me_dir != vsr_dir and "VERSIONEER_PEP518" not in globals():
+            print("Warning: build in %s is using versioneer.py from %s"
+                  % (os.path.dirname(my_path), versioneer_py))
     except NameError:
         pass
     return root
 
 
-def get_config_from_root(root):
+def get_config_from_root(root: str) -> VersioneerConfig:
     """Read the project setup.cfg file to determine Versioneer config."""
-    # This might raise EnvironmentError (if setup.cfg is missing), or
+    # This might raise OSError (if setup.cfg is missing), or
     # configparser.NoSectionError (if it lacks a [versioneer] section), or
     # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
     # the top of versioneer.py for instructions on writing your setup.cfg .
-    setup_cfg = os.path.join(root, "setup.cfg")
-    parser = configparser.SafeConfigParser()
-    with open(setup_cfg, "r") as f:
-        parser.readfp(f)
-    VCS = parser.get("versioneer", "VCS")  # mandatory
-
-    def get(parser, name):
-        if parser.has_option("versioneer", name):
-            return parser.get("versioneer", name)
-        return None
+    root_pth = Path(root)
+    pyproject_toml = root_pth / "pyproject.toml"
+    setup_cfg = root_pth / "setup.cfg"
+    section: Union[Dict[str, Any], configparser.SectionProxy, None] = None
+    if pyproject_toml.exists() and have_tomllib:
+        try:
+            with open(pyproject_toml, 'rb') as fobj:
+                pp = tomllib.load(fobj)
+            section = pp['tool']['versioneer']
+        except (tomllib.TOMLDecodeError, KeyError) as e:
+            print(f"Failed to load config from {pyproject_toml}: {e}")
+            print("Try to load it from setup.cfg")
+    if not section:
+        parser = configparser.ConfigParser()
+        with open(setup_cfg) as cfg_file:
+            parser.read_file(cfg_file)
+        parser.get("versioneer", "VCS")  # raise error if missing
+
+        section = parser["versioneer"]
+
+    # `cast`` really shouldn't be used, but its simplest for the
+    # common VersioneerConfig users at the moment. We verify against
+    # `None` values elsewhere where it matters
 
     cfg = VersioneerConfig()
-    cfg.VCS = VCS
-    cfg.style = get(parser, "style") or ""
-    cfg.versionfile_source = get(parser, "versionfile_source")
-    cfg.versionfile_build = get(parser, "versionfile_build")
-    cfg.tag_prefix = get(parser, "tag_prefix")
-    if cfg.tag_prefix in ("''", '""'):
+    cfg.VCS = section['VCS']
+    cfg.style = section.get("style", "")
+    cfg.versionfile_source = cast(str, section.get("versionfile_source"))
+    cfg.versionfile_build = section.get("versionfile_build")
+    cfg.tag_prefix = cast(str, section.get("tag_prefix"))
+    if cfg.tag_prefix in ("''", '""', None):
         cfg.tag_prefix = ""
-    cfg.parentdir_prefix = get(parser, "parentdir_prefix")
-    cfg.verbose = get(parser, "verbose")
+    cfg.parentdir_prefix = section.get("parentdir_prefix")
+    if isinstance(section, configparser.SectionProxy):
+        # Make sure configparser translates to bool
+        cfg.verbose = section.getboolean("verbose")
+    else:
+        cfg.verbose = section.get("verbose")
+
     return cfg
 
 
@@ -371,41 +444,48 @@ class NotThisMethod(Exception):
 
 
 # these dictionaries contain VCS-specific tools
-LONG_VERSION_PY = {}
-HANDLERS = {}
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
 
-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-
-    def decorate(f):
+def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
+    """Create decorator to mark a method as the handler of a VCS."""
+    def decorate(f: Callable) -> Callable:
         """Store f in HANDLERS[vcs][method]."""
-        if vcs not in HANDLERS:
-            HANDLERS[vcs] = {}
-        HANDLERS[vcs][method] = f
+        HANDLERS.setdefault(vcs, {})[method] = f
         return f
-
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None):
+def run_command(
+    commands: List[str],
+    args: List[str],
+    cwd: Optional[str] = None,
+    verbose: bool = False,
+    hide_stderr: bool = False,
+    env: Optional[Dict[str, str]] = None,
+) -> Tuple[Optional[str], Optional[int]]:
     """Call the given command(s)."""
     assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+
+    popen_kwargs: Dict[str, Any] = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
+    for command in commands:
         try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen(
-                [c] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None),
-            )
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None), **popen_kwargs)
             break
-        except EnvironmentError:
-            e = sys.exc_info()[1]
+        except OSError as e:
             if e.errno == errno.ENOENT:
                 continue
             if verbose:
@@ -416,28 +496,25 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
         if verbose:
             print("unable to find command, tried %s" % (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
         if verbose:
             print("unable to run %s (error)" % dispcmd)
             print("stdout was %s" % stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode
 
 
-LONG_VERSION_PY[
-    "git"
-] = '''
+LONG_VERSION_PY['git'] = r'''
 # This file helps to compute a version number in source trees obtained from
 # git-archive tarball (such as those provided by githubs download-from-tag
 # feature). Distribution tarballs (built by setup.py sdist) and build
 # directories (produced by setup.py build) will contain a much shorter file
 # that just contains the computed version number.
 
-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
+# This file is released into the public domain.
+# Generated by versioneer-0.29
+# https://github.com/python-versioneer/python-versioneer
 
 """Git implementation of _version.py."""
 
@@ -446,9 +523,11 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=
 import re
 import subprocess
 import sys
+from typing import Any, Callable, Dict, List, Optional, Tuple
+import functools
 
 
-def get_keywords():
+def get_keywords() -> Dict[str, str]:
     """Get the keywords needed to look up the version information."""
     # these strings will be replaced by git during git-archive.
     # setup.py/versioneer.py will grep for the variable names, so they must
@@ -464,8 +543,15 @@ def get_keywords():
 class VersioneerConfig:
     """Container for Versioneer configuration parameters."""
 
+    VCS: str
+    style: str
+    tag_prefix: str
+    parentdir_prefix: str
+    versionfile_source: str
+    verbose: bool
+
 
-def get_config():
+def get_config() -> VersioneerConfig:
     """Create, populate and return the VersioneerConfig() object."""
     # these strings are filled in when 'setup.py versioneer' creates
     # _version.py
@@ -483,13 +569,13 @@ class NotThisMethod(Exception):
     """Exception raised if a method is not valid for the current scenario."""
 
 
-LONG_VERSION_PY = {}
-HANDLERS = {}
+LONG_VERSION_PY: Dict[str, str] = {}
+HANDLERS: Dict[str, Dict[str, Callable]] = {}
 
 
-def register_vcs_handler(vcs, method):  # decorator
-    """Decorator to mark a method as the handler for a particular VCS."""
-    def decorate(f):
+def register_vcs_handler(vcs: str, method: str) -> Callable:  # decorator
+    """Create decorator to mark a method as the handler of a VCS."""
+    def decorate(f: Callable) -> Callable:
         """Store f in HANDLERS[vcs][method]."""
         if vcs not in HANDLERS:
             HANDLERS[vcs] = {}
@@ -498,22 +584,35 @@ def decorate(f):
     return decorate
 
 
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
-                env=None):
+def run_command(
+    commands: List[str],
+    args: List[str],
+    cwd: Optional[str] = None,
+    verbose: bool = False,
+    hide_stderr: bool = False,
+    env: Optional[Dict[str, str]] = None,
+) -> Tuple[Optional[str], Optional[int]]:
     """Call the given command(s)."""
     assert isinstance(commands, list)
-    p = None
-    for c in commands:
+    process = None
+
+    popen_kwargs: Dict[str, Any] = {}
+    if sys.platform == "win32":
+        # This hides the console window if pythonw.exe is used
+        startupinfo = subprocess.STARTUPINFO()
+        startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
+        popen_kwargs["startupinfo"] = startupinfo
+
+    for command in commands:
         try:
-            dispcmd = str([c] + args)
+            dispcmd = str([command] + args)
             # remember shell=False, so use git.cmd on windows, not just git
-            p = subprocess.Popen([c] + args, cwd=cwd, env=env,
-                                 stdout=subprocess.PIPE,
-                                 stderr=(subprocess.PIPE if hide_stderr
-                                         else None))
+            process = subprocess.Popen([command] + args, cwd=cwd, env=env,
+                                       stdout=subprocess.PIPE,
+                                       stderr=(subprocess.PIPE if hide_stderr
+                                               else None), **popen_kwargs)
             break
-        except EnvironmentError:
-            e = sys.exc_info()[1]
+        except OSError as e:
             if e.errno == errno.ENOENT:
                 continue
             if verbose:
@@ -524,18 +623,20 @@ def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
         if verbose:
             print("unable to find command, tried %%s" %% (commands,))
         return None, None
-    stdout = p.communicate()[0].strip()
-    if sys.version_info[0] >= 3:
-        stdout = stdout.decode()
-    if p.returncode != 0:
+    stdout = process.communicate()[0].strip().decode()
+    if process.returncode != 0:
         if verbose:
             print("unable to run %%s (error)" %% dispcmd)
             print("stdout was %%s" %% stdout)
-        return None, p.returncode
-    return stdout, p.returncode
+        return None, process.returncode
+    return stdout, process.returncode
 
 
-def versions_from_parentdir(parentdir_prefix, root, verbose):
+def versions_from_parentdir(
+    parentdir_prefix: str,
+    root: str,
+    verbose: bool,
+) -> Dict[str, Any]:
     """Try to determine the version from the parent directory name.
 
     Source tarballs conventionally unpack into a directory that includes both
@@ -544,15 +645,14 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
             return {"version": dirname[len(parentdir_prefix):],
                     "full-revisionid": None,
                     "dirty": False, "error": None, "date": None}
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
 
     if verbose:
         print("Tried directories %%s but none started with prefix %%s" %%
@@ -561,41 +661,48 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
 
 
 @register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
+def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
     """Extract version information from the given file."""
     # the code embedded in _version.py can just fetch the value of these
     # keywords. When used from setup.py, we don't want to import _version.py,
     # so we do it with a regexp instead. This function is not used from
     # _version.py.
-    keywords = {}
+    keywords: Dict[str, str] = {}
     try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
         pass
     return keywords
 
 
 @register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
+def git_versions_from_keywords(
+    keywords: Dict[str, str],
+    tag_prefix: str,
+    verbose: bool,
+) -> Dict[str, Any]:
     """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
         # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant
         # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601
         # -like" string, which we must then edit to make compliant), because
@@ -608,11 +715,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         if verbose:
             print("keywords are unexpanded, not using")
         raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %%d
@@ -621,7 +728,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r'\d', r)])
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%%s', no digits" %% ",".join(refs - tags))
     if verbose:
@@ -630,6 +737,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
             r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %%s" %% r)
             return {"version": r,
@@ -645,7 +757,12 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(
+    tag_prefix: str,
+    root: str,
+    verbose: bool,
+    runner: Callable = run_command
+) -> Dict[str, Any]:
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -656,8 +773,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
-                          hide_stderr=True)
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
+
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=not verbose)
     if rc != 0:
         if verbose:
             print("Directory %%s not under git control" %% root)
@@ -665,24 +789,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
-                                          "--always", "--long",
-                                          "--match", "%%s*" %% tag_prefix],
-                                   cwd=root)
+    describe_out, rc = runner(GITS, [
+        "describe", "--tags", "--dirty", "--always", "--long",
+        "--match", f"{tag_prefix}[[:digit:]]*"
+    ], cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
     describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
     if full_out is None:
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
 
-    pieces = {}
+    pieces: Dict[str, Any] = {}
     pieces["long"] = full_out
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
     # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
     # TAG might have hyphens.
     git_describe = describe_out
@@ -699,7 +856,7 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
         # TAG-NUM-gHEX
         mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
+            # unparsable. Maybe git-describe is misbehaving?
             pieces["error"] = ("unable to parse git-describe output: '%%s'"
                                %% describe_out)
             return pieces
@@ -724,26 +881,27 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
-                                    cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
+        out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root)
+        pieces["distance"] = len(out.split())  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"],
-                       cwd=root)[0].strip()
+    date = runner(GITS, ["show", "-s", "--format=%%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
 
 
-def plus_or_dot(pieces):
+def plus_or_dot(pieces: Dict[str, Any]) -> str:
     """Return a + if we don't already have one, else return a ."""
     if "+" in pieces.get("closest-tag", ""):
         return "."
     return "+"
 
 
-def render_pep440(pieces):
+def render_pep440(pieces: Dict[str, Any]) -> str:
     """Build up version string, with post-release "local version identifier".
 
     Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
@@ -768,23 +926,71 @@ def render_pep440(pieces):
     return rendered
 
 
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%%d.g%%s" %% (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces: Dict[str, Any]) -> str:
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
         if pieces["distance"]:
-            rendered += ".post.dev%%d" %% pieces["distance"]
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%%d.dev%%d" %% (post_version + 1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%%d" %% (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
     else:
         # exception #1
-        rendered = "0.post.dev%%d" %% pieces["distance"]
+        rendered = "0.post0.dev%%d" %% pieces["distance"]
     return rendered
 
 
-def render_pep440_post(pieces):
+def render_pep440_post(pieces: Dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]+gHEX] .
 
     The ".dev0" means dirty. Note that .dev0 sorts backwards
@@ -811,12 +1017,41 @@ def render_pep440_post(pieces):
     return rendered
 
 
-def render_pep440_old(pieces):
+def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%%d" %% pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%%s" %% pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%%d" %% pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%%s" %% pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_old(pieces: Dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:
@@ -833,7 +1068,7 @@ def render_pep440_old(pieces):
     return rendered
 
 
-def render_git_describe(pieces):
+def render_git_describe(pieces: Dict[str, Any]) -> str:
     """TAG[-DISTANCE-gHEX][-dirty].
 
     Like 'git describe --tags --dirty --always'.
@@ -853,7 +1088,7 @@ def render_git_describe(pieces):
     return rendered
 
 
-def render_git_describe_long(pieces):
+def render_git_describe_long(pieces: Dict[str, Any]) -> str:
     """TAG-DISTANCE-gHEX[-dirty].
 
     Like 'git describe --tags --dirty --always -long'.
@@ -873,7 +1108,7 @@ def render_git_describe_long(pieces):
     return rendered
 
 
-def render(pieces, style):
+def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
         return {"version": "unknown",
@@ -887,10 +1122,14 @@ def render(pieces, style):
 
     if style == "pep440":
         rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
     elif style == "pep440-pre":
         rendered = render_pep440_pre(pieces)
     elif style == "pep440-post":
         rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
     elif style == "pep440-old":
         rendered = render_pep440_old(pieces)
     elif style == "git-describe":
@@ -905,7 +1144,7 @@ def render(pieces, style):
             "date": pieces.get("date")}
 
 
-def get_versions():
+def get_versions() -> Dict[str, Any]:
     """Get version information or return default if unable to do so."""
     # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
     # __file__, we can work backwards from there to the root. Some
@@ -926,7 +1165,7 @@ def get_versions():
         # versionfile_source is the relative path from the top of the source
         # tree (where the .git directory might live) to this file. Invert
         # this to find the root from __file__.
-        for i in cfg.versionfile_source.split('/'):
+        for _ in cfg.versionfile_source.split('/'):
             root = os.path.dirname(root)
     except NameError:
         return {"version": "0+unknown", "full-revisionid": None,
@@ -953,41 +1192,48 @@ def get_versions():
 
 
 @register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
+def git_get_keywords(versionfile_abs: str) -> Dict[str, str]:
     """Extract version information from the given file."""
     # the code embedded in _version.py can just fetch the value of these
     # keywords. When used from setup.py, we don't want to import _version.py,
     # so we do it with a regexp instead. This function is not used from
     # _version.py.
-    keywords = {}
+    keywords: Dict[str, str] = {}
     try:
-        f = open(versionfile_abs, "r")
-        for line in f.readlines():
-            if line.strip().startswith("git_refnames ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["refnames"] = mo.group(1)
-            if line.strip().startswith("git_full ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["full"] = mo.group(1)
-            if line.strip().startswith("git_date ="):
-                mo = re.search(r'=\s*"(.*)"', line)
-                if mo:
-                    keywords["date"] = mo.group(1)
-        f.close()
-    except EnvironmentError:
+        with open(versionfile_abs, "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith("git_refnames ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["refnames"] = mo.group(1)
+                if line.strip().startswith("git_full ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["full"] = mo.group(1)
+                if line.strip().startswith("git_date ="):
+                    mo = re.search(r'=\s*"(.*)"', line)
+                    if mo:
+                        keywords["date"] = mo.group(1)
+    except OSError:
         pass
     return keywords
 
 
 @register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
+def git_versions_from_keywords(
+    keywords: Dict[str, str],
+    tag_prefix: str,
+    verbose: bool,
+) -> Dict[str, Any]:
     """Get version information from git keywords."""
-    if not keywords:
-        raise NotThisMethod("no keywords at all, weird")
+    if "refnames" not in keywords:
+        raise NotThisMethod("Short version file found")
     date = keywords.get("date")
     if date is not None:
+        # Use only the last line.  Previous lines may contain GPG signature
+        # information.
+        date = date.splitlines()[-1]
+
         # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
         # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
         # -like" string, which we must then edit to make compliant), because
@@ -1000,11 +1246,11 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         if verbose:
             print("keywords are unexpanded, not using")
         raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    refs = set([r.strip() for r in refnames.strip("()").split(",")])
+    refs = {r.strip() for r in refnames.strip("()").split(",")}
     # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
     # just "foo-1.0". If we see a "tag: " prefix, prefer those.
     TAG = "tag: "
-    tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)])
+    tags = {r[len(TAG):] for r in refs if r.startswith(TAG)}
     if not tags:
         # Either we're using git < 1.8.3, or there really are no tags. We use
         # a heuristic: assume all version tags have a digit. The old git %d
@@ -1013,7 +1259,7 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
         # between branches and tags. By ignoring refnames without digits, we
         # filter out many common branch names like "release" and
         # "stabilization", as well as "HEAD" and "master".
-        tags = set([r for r in refs if re.search(r"\d", r)])
+        tags = {r for r in refs if re.search(r'\d', r)}
         if verbose:
             print("discarding '%s', no digits" % ",".join(refs - tags))
     if verbose:
@@ -1021,30 +1267,33 @@ def git_versions_from_keywords(keywords, tag_prefix, verbose):
     for ref in sorted(tags):
         # sorting will prefer e.g. "2.0" over "2.0rc1"
         if ref.startswith(tag_prefix):
-            r = ref[len(tag_prefix) :]
+            r = ref[len(tag_prefix):]
+            # Filter out refs that exactly match prefix or that don't start
+            # with a number once the prefix is stripped (mostly a concern
+            # when prefix is '')
+            if not re.match(r'\d', r):
+                continue
             if verbose:
                 print("picking %s" % r)
-            return {
-                "version": r,
-                "full-revisionid": keywords["full"].strip(),
-                "dirty": False,
-                "error": None,
-                "date": date,
-            }
+            return {"version": r,
+                    "full-revisionid": keywords["full"].strip(),
+                    "dirty": False, "error": None,
+                    "date": date}
     # no suitable tags, so version is "0+unknown", but full hex is still there
     if verbose:
         print("no suitable tags, using unknown + full revision id")
-    return {
-        "version": "0+unknown",
-        "full-revisionid": keywords["full"].strip(),
-        "dirty": False,
-        "error": "no suitable tags",
-        "date": None,
-    }
+    return {"version": "0+unknown",
+            "full-revisionid": keywords["full"].strip(),
+            "dirty": False, "error": "no suitable tags", "date": None}
 
 
 @register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
+def git_pieces_from_vcs(
+    tag_prefix: str,
+    root: str,
+    verbose: bool,
+    runner: Callable = run_command
+) -> Dict[str, Any]:
     """Get version from 'git describe' in the root of the source tree.
 
     This only gets called if the git-archive 'subst' keywords were *not*
@@ -1055,7 +1304,15 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
 
-    out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True)
+    # GIT_DIR can interfere with correct operation of Versioneer.
+    # It may be intended to be passed to the Versioneer-versioned project,
+    # but that should not change where we get our version from.
+    env = os.environ.copy()
+    env.pop("GIT_DIR", None)
+    runner = functools.partial(runner, env=env)
+
+    _, rc = runner(GITS, ["rev-parse", "--git-dir"], cwd=root,
+                   hide_stderr=not verbose)
     if rc != 0:
         if verbose:
             print("Directory %s not under git control" % root)
@@ -1063,33 +1320,57 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
 
     # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
     # if there isn't one, this yields HEX[-dirty] (no NUM)
-    describe_out, rc = run_command(
-        GITS,
-        [
-            "describe",
-            "--tags",
-            "--dirty",
-            "--always",
-            "--long",
-            "--match",
-            "%s*" % tag_prefix,
-        ],
-        cwd=root,
-    )
+    describe_out, rc = runner(GITS, [
+        "describe", "--tags", "--dirty", "--always", "--long",
+        "--match", f"{tag_prefix}[[:digit:]]*"
+    ], cwd=root)
     # --long was added in git-1.5.5
     if describe_out is None:
         raise NotThisMethod("'git describe' failed")
     describe_out = describe_out.strip()
-    full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
+    full_out, rc = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
     if full_out is None:
         raise NotThisMethod("'git rev-parse' failed")
     full_out = full_out.strip()
 
-    pieces = {}
+    pieces: Dict[str, Any] = {}
     pieces["long"] = full_out
     pieces["short"] = full_out[:7]  # maybe improved later
     pieces["error"] = None
 
+    branch_name, rc = runner(GITS, ["rev-parse", "--abbrev-ref", "HEAD"],
+                             cwd=root)
+    # --abbrev-ref was added in git-1.6.3
+    if rc != 0 or branch_name is None:
+        raise NotThisMethod("'git rev-parse --abbrev-ref' returned error")
+    branch_name = branch_name.strip()
+
+    if branch_name == "HEAD":
+        # If we aren't exactly on a branch, pick a branch which represents
+        # the current commit. If all else fails, we are on a branchless
+        # commit.
+        branches, rc = runner(GITS, ["branch", "--contains"], cwd=root)
+        # --contains was added in git-1.5.4
+        if rc != 0 or branches is None:
+            raise NotThisMethod("'git branch --contains' returned error")
+        branches = branches.split("\n")
+
+        # Remove the first line if we're running detached
+        if "(" in branches[0]:
+            branches.pop(0)
+
+        # Strip off the leading "* " from the list of branches.
+        branches = [branch[2:] for branch in branches]
+        if "master" in branches:
+            branch_name = "master"
+        elif not branches:
+            branch_name = None
+        else:
+            # Pick the first branch that is returned. Good or bad.
+            branch_name = branches[0]
+
+    pieces["branch"] = branch_name
+
     # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
     # TAG might have hyphens.
     git_describe = describe_out
@@ -1098,16 +1379,17 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     dirty = git_describe.endswith("-dirty")
     pieces["dirty"] = dirty
     if dirty:
-        git_describe = git_describe[: git_describe.rindex("-dirty")]
+        git_describe = git_describe[:git_describe.rindex("-dirty")]
 
     # now we have TAG-NUM-gHEX or HEX
 
     if "-" in git_describe:
         # TAG-NUM-gHEX
-        mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe)
+        mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
         if not mo:
-            # unparseable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
+            # unparsable. Maybe git-describe is misbehaving?
+            pieces["error"] = ("unable to parse git-describe output: '%s'"
+                               % describe_out)
             return pieces
 
         # tag
@@ -1116,12 +1398,10 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
             if verbose:
                 fmt = "tag '%s' doesn't start with prefix '%s'"
                 print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (
-                full_tag,
-                tag_prefix,
-            )
+            pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
+                               % (full_tag, tag_prefix))
             return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
+        pieces["closest-tag"] = full_tag[len(tag_prefix):]
 
         # distance: number of commits since tag
         pieces["distance"] = int(mo.group(2))
@@ -1132,19 +1412,20 @@ def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
     else:
         # HEX: no tags
         pieces["closest-tag"] = None
-        count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root)
-        pieces["distance"] = int(count_out)  # total number of commits
+        out, rc = runner(GITS, ["rev-list", "HEAD", "--left-right"], cwd=root)
+        pieces["distance"] = len(out.split())  # total number of commits
 
     # commit date: see ISO-8601 comment in git_versions_from_keywords()
-    date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[
-        0
-    ].strip()
+    date = runner(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip()
+    # Use only the last line.  Previous lines may contain GPG signature
+    # information.
+    date = date.splitlines()[-1]
     pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
 
     return pieces
 
 
-def do_vcs_install(manifest_in, versionfile_source, ipy):
+def do_vcs_install(versionfile_source: str, ipy: Optional[str]) -> None:
     """Git-specific installation logic for Versioneer.
 
     For Git, this means creating/changing .gitattributes to mark _version.py
@@ -1153,36 +1434,40 @@ def do_vcs_install(manifest_in, versionfile_source, ipy):
     GITS = ["git"]
     if sys.platform == "win32":
         GITS = ["git.cmd", "git.exe"]
-    files = [manifest_in, versionfile_source]
+    files = [versionfile_source]
     if ipy:
         files.append(ipy)
-    try:
-        me = __file__
-        if me.endswith(".pyc") or me.endswith(".pyo"):
-            me = os.path.splitext(me)[0] + ".py"
-        versioneer_file = os.path.relpath(me)
-    except NameError:
-        versioneer_file = "versioneer.py"
-    files.append(versioneer_file)
+    if "VERSIONEER_PEP518" not in globals():
+        try:
+            my_path = __file__
+            if my_path.endswith((".pyc", ".pyo")):
+                my_path = os.path.splitext(my_path)[0] + ".py"
+            versioneer_file = os.path.relpath(my_path)
+        except NameError:
+            versioneer_file = "versioneer.py"
+        files.append(versioneer_file)
     present = False
     try:
-        f = open(".gitattributes", "r")
-        for line in f.readlines():
-            if line.strip().startswith(versionfile_source):
-                if "export-subst" in line.strip().split()[1:]:
-                    present = True
-        f.close()
-    except EnvironmentError:
+        with open(".gitattributes", "r") as fobj:
+            for line in fobj:
+                if line.strip().startswith(versionfile_source):
+                    if "export-subst" in line.strip().split()[1:]:
+                        present = True
+                        break
+    except OSError:
         pass
     if not present:
-        f = open(".gitattributes", "a+")
-        f.write("%s export-subst\n" % versionfile_source)
-        f.close()
+        with open(".gitattributes", "a+") as fobj:
+            fobj.write(f"{versionfile_source} export-subst\n")
         files.append(".gitattributes")
     run_command(GITS, ["add", "--"] + files)
 
 
-def versions_from_parentdir(parentdir_prefix, root, verbose):
+def versions_from_parentdir(
+    parentdir_prefix: str,
+    root: str,
+    verbose: bool,
+) -> Dict[str, Any]:
     """Try to determine the version from the parent directory name.
 
     Source tarballs conventionally unpack into a directory that includes both
@@ -1191,30 +1476,23 @@ def versions_from_parentdir(parentdir_prefix, root, verbose):
     """
     rootdirs = []
 
-    for i in range(3):
+    for _ in range(3):
         dirname = os.path.basename(root)
         if dirname.startswith(parentdir_prefix):
-            return {
-                "version": dirname[len(parentdir_prefix) :],
-                "full-revisionid": None,
-                "dirty": False,
-                "error": None,
-                "date": None,
-            }
-        else:
-            rootdirs.append(root)
-            root = os.path.dirname(root)  # up a level
+            return {"version": dirname[len(parentdir_prefix):],
+                    "full-revisionid": None,
+                    "dirty": False, "error": None, "date": None}
+        rootdirs.append(root)
+        root = os.path.dirname(root)  # up a level
 
     if verbose:
-        print(
-            "Tried directories %s but none started with prefix %s"
-            % (str(rootdirs), parentdir_prefix)
-        )
+        print("Tried directories %s but none started with prefix %s" %
+              (str(rootdirs), parentdir_prefix))
     raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
 
 
 SHORT_VERSION_PY = """
-# This file was generated by 'versioneer.py' (0.18) from
+# This file was generated by 'versioneer.py' (0.29) from
 # revision-control system data, or from the parent directory name of an
 # unpacked source archive. Distribution tarballs contain a pre-generated copy
 # of this file.
@@ -1231,43 +1509,41 @@ def get_versions():
 """
 
 
-def versions_from_file(filename):
+def versions_from_file(filename: str) -> Dict[str, Any]:
     """Try to determine the version from _version.py if present."""
     try:
         with open(filename) as f:
             contents = f.read()
-    except EnvironmentError:
+    except OSError:
         raise NotThisMethod("unable to read _version.py")
-    mo = re.search(
-        r"version_json = '''\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S
-    )
+    mo = re.search(r"version_json = '''\n(.*)'''  # END VERSION_JSON",
+                   contents, re.M | re.S)
     if not mo:
-        mo = re.search(
-            r"version_json = '''\r\n(.*)'''  # END VERSION_JSON", contents, re.M | re.S
-        )
+        mo = re.search(r"version_json = '''\r\n(.*)'''  # END VERSION_JSON",
+                       contents, re.M | re.S)
     if not mo:
         raise NotThisMethod("no version_json in _version.py")
     return json.loads(mo.group(1))
 
 
-def write_to_version_file(filename, versions):
+def write_to_version_file(filename: str, versions: Dict[str, Any]) -> None:
     """Write the given version number to the given _version.py file."""
-    os.unlink(filename)
-    contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": "))
+    contents = json.dumps(versions, sort_keys=True,
+                          indent=1, separators=(",", ": "))
     with open(filename, "w") as f:
         f.write(SHORT_VERSION_PY % contents)
 
     print("set %s to '%s'" % (filename, versions["version"]))
 
 
-def plus_or_dot(pieces):
+def plus_or_dot(pieces: Dict[str, Any]) -> str:
     """Return a + if we don't already have one, else return a ."""
     if "+" in pieces.get("closest-tag", ""):
         return "."
     return "+"
 
 
-def render_pep440(pieces):
+def render_pep440(pieces: Dict[str, Any]) -> str:
     """Build up version string, with post-release "local version identifier".
 
     Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
@@ -1285,29 +1561,78 @@ def render_pep440(pieces):
                 rendered += ".dirty"
     else:
         # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
+        rendered = "0+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
         if pieces["dirty"]:
             rendered += ".dirty"
     return rendered
 
 
-def render_pep440_pre(pieces):
-    """TAG[.post.devDISTANCE] -- No -dirty.
+def render_pep440_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[[.dev0]+DISTANCE.gHEX[.dirty]] .
+
+    The ".dev0" means not master branch. Note that .dev0 sorts backwards
+    (a feature branch will appear "older" than the master branch).
 
     Exceptions:
-    1: no tags. 0.post.devDISTANCE
+    1: no tags. 0[.dev0]+untagged.DISTANCE.gHEX[.dirty]
     """
     if pieces["closest-tag"]:
         rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0"
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+untagged.%d.g%s" % (pieces["distance"],
+                                          pieces["short"])
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def pep440_split_post(ver: str) -> Tuple[str, Optional[int]]:
+    """Split pep440 version string at the post-release segment.
+
+    Returns the release segments before the post-release and the
+    post-release version number (or -1 if no post-release segment is present).
+    """
+    vc = str.split(ver, ".post")
+    return vc[0], int(vc[1] or 0) if len(vc) == 2 else None
+
+
+def render_pep440_pre(pieces: Dict[str, Any]) -> str:
+    """TAG[.postN.devDISTANCE] -- No -dirty.
+
+    Exceptions:
+    1: no tags. 0.post0.devDISTANCE
+    """
+    if pieces["closest-tag"]:
         if pieces["distance"]:
-            rendered += ".post.dev%d" % pieces["distance"]
+            # update the post release segment
+            tag_version, post_version = pep440_split_post(pieces["closest-tag"])
+            rendered = tag_version
+            if post_version is not None:
+                rendered += ".post%d.dev%d" % (post_version + 1, pieces["distance"])
+            else:
+                rendered += ".post0.dev%d" % (pieces["distance"])
+        else:
+            # no commits, use the tag as the version
+            rendered = pieces["closest-tag"]
     else:
         # exception #1
-        rendered = "0.post.dev%d" % pieces["distance"]
+        rendered = "0.post0.dev%d" % pieces["distance"]
     return rendered
 
 
-def render_pep440_post(pieces):
+def render_pep440_post(pieces: Dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]+gHEX] .
 
     The ".dev0" means dirty. Note that .dev0 sorts backwards
@@ -1334,12 +1659,41 @@ def render_pep440_post(pieces):
     return rendered
 
 
-def render_pep440_old(pieces):
+def render_pep440_post_branch(pieces: Dict[str, Any]) -> str:
+    """TAG[.postDISTANCE[.dev0]+gHEX[.dirty]] .
+
+    The ".dev0" means not master branch.
+
+    Exceptions:
+    1: no tags. 0.postDISTANCE[.dev0]+gHEX[.dirty]
+    """
+    if pieces["closest-tag"]:
+        rendered = pieces["closest-tag"]
+        if pieces["distance"] or pieces["dirty"]:
+            rendered += ".post%d" % pieces["distance"]
+            if pieces["branch"] != "master":
+                rendered += ".dev0"
+            rendered += plus_or_dot(pieces)
+            rendered += "g%s" % pieces["short"]
+            if pieces["dirty"]:
+                rendered += ".dirty"
+    else:
+        # exception #1
+        rendered = "0.post%d" % pieces["distance"]
+        if pieces["branch"] != "master":
+            rendered += ".dev0"
+        rendered += "+g%s" % pieces["short"]
+        if pieces["dirty"]:
+            rendered += ".dirty"
+    return rendered
+
+
+def render_pep440_old(pieces: Dict[str, Any]) -> str:
     """TAG[.postDISTANCE[.dev0]] .
 
     The ".dev0" means dirty.
 
-    Eexceptions:
+    Exceptions:
     1: no tags. 0.postDISTANCE[.dev0]
     """
     if pieces["closest-tag"]:
@@ -1356,7 +1710,7 @@ def render_pep440_old(pieces):
     return rendered
 
 
-def render_git_describe(pieces):
+def render_git_describe(pieces: Dict[str, Any]) -> str:
     """TAG[-DISTANCE-gHEX][-dirty].
 
     Like 'git describe --tags --dirty --always'.
@@ -1376,7 +1730,7 @@ def render_git_describe(pieces):
     return rendered
 
 
-def render_git_describe_long(pieces):
+def render_git_describe_long(pieces: Dict[str, Any]) -> str:
     """TAG-DISTANCE-gHEX[-dirty].
 
     Like 'git describe --tags --dirty --always -long'.
@@ -1396,26 +1750,28 @@ def render_git_describe_long(pieces):
     return rendered
 
 
-def render(pieces, style):
+def render(pieces: Dict[str, Any], style: str) -> Dict[str, Any]:
     """Render the given version pieces into the requested style."""
     if pieces["error"]:
-        return {
-            "version": "unknown",
-            "full-revisionid": pieces.get("long"),
-            "dirty": None,
-            "error": pieces["error"],
-            "date": None,
-        }
+        return {"version": "unknown",
+                "full-revisionid": pieces.get("long"),
+                "dirty": None,
+                "error": pieces["error"],
+                "date": None}
 
     if not style or style == "default":
         style = "pep440"  # the default
 
     if style == "pep440":
         rendered = render_pep440(pieces)
+    elif style == "pep440-branch":
+        rendered = render_pep440_branch(pieces)
     elif style == "pep440-pre":
         rendered = render_pep440_pre(pieces)
     elif style == "pep440-post":
         rendered = render_pep440_post(pieces)
+    elif style == "pep440-post-branch":
+        rendered = render_pep440_post_branch(pieces)
     elif style == "pep440-old":
         rendered = render_pep440_old(pieces)
     elif style == "git-describe":
@@ -1425,20 +1781,16 @@ def render(pieces, style):
     else:
         raise ValueError("unknown style '%s'" % style)
 
-    return {
-        "version": rendered,
-        "full-revisionid": pieces["long"],
-        "dirty": pieces["dirty"],
-        "error": None,
-        "date": pieces.get("date"),
-    }
+    return {"version": rendered, "full-revisionid": pieces["long"],
+            "dirty": pieces["dirty"], "error": None,
+            "date": pieces.get("date")}
 
 
 class VersioneerBadRootError(Exception):
     """The project root directory is unknown or missing key files."""
 
 
-def get_versions(verbose=False):
+def get_versions(verbose: bool = False) -> Dict[str, Any]:
     """Get the project version from whatever source is available.
 
     Returns dict with two keys: 'version' and 'full'.
@@ -1453,10 +1805,9 @@ def get_versions(verbose=False):
     assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg"
     handlers = HANDLERS.get(cfg.VCS)
     assert handlers, "unrecognized VCS '%s'" % cfg.VCS
-    verbose = verbose or cfg.verbose
-    assert (
-        cfg.versionfile_source is not None
-    ), "please set versioneer.versionfile_source"
+    verbose = verbose or bool(cfg.verbose)  # `bool()` used to avoid `None`
+    assert cfg.versionfile_source is not None, \
+        "please set versioneer.versionfile_source"
     assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
 
     versionfile_abs = os.path.join(root, cfg.versionfile_source)
@@ -1510,22 +1861,22 @@ def get_versions(verbose=False):
     if verbose:
         print("unable to compute version")
 
-    return {
-        "version": "0+unknown",
-        "full-revisionid": None,
-        "dirty": None,
-        "error": "unable to compute version",
-        "date": None,
-    }
+    return {"version": "0+unknown", "full-revisionid": None,
+            "dirty": None, "error": "unable to compute version",
+            "date": None}
 
 
-def get_version():
+def get_version() -> str:
     """Get the short version string for this project."""
     return get_versions()["version"]
 
 
-def get_cmdclass():
-    """Get the custom setuptools/distutils subclasses used by Versioneer."""
+def get_cmdclass(cmdclass: Optional[Dict[str, Any]] = None):
+    """Get the custom setuptools subclasses used by Versioneer.
+
+    If the package uses a different cmdclass (e.g. one from numpy), it
+    should be provide as an argument.
+    """
     if "versioneer" in sys.modules:
         del sys.modules["versioneer"]
         # this fixes the "python setup.py develop" case (also 'install' and
@@ -1539,25 +1890,25 @@ def get_cmdclass():
         # parent is protected against the child's "import versioneer". By
         # removing ourselves from sys.modules here, before the child build
         # happens, we protect the child from the parent's versioneer too.
-        # Also see https://github.com/warner/python-versioneer/issues/52
+        # Also see https://github.com/python-versioneer/python-versioneer/issues/52
 
-    cmds = {}
+    cmds = {} if cmdclass is None else cmdclass.copy()
 
-    # we add "version" to both distutils and setuptools
-    from distutils.core import Command
+    # we add "version" to setuptools
+    from setuptools import Command
 
     class cmd_version(Command):
         description = "report generated version string"
-        user_options = []
-        boolean_options = []
+        user_options: List[Tuple[str, str, str]] = []
+        boolean_options: List[str] = []
 
-        def initialize_options(self):
+        def initialize_options(self) -> None:
             pass
 
-        def finalize_options(self):
+        def finalize_options(self) -> None:
             pass
 
-        def run(self):
+        def run(self) -> None:
             vers = get_versions(verbose=True)
             print("Version: %s" % vers["version"])
             print(" full-revisionid: %s" % vers.get("full-revisionid"))
@@ -1565,10 +1916,9 @@ def run(self):
             print(" date: %s" % vers.get("date"))
             if vers["error"]:
                 print(" error: %s" % vers["error"])
-
     cmds["version"] = cmd_version
 
-    # we override "build_py" in both distutils and setuptools
+    # we override "build_py" in setuptools
     #
     # most invocation pathways end up running build_py:
     #  distutils/build -> build_py
@@ -1583,30 +1933,68 @@ def run(self):
     #   then does setup.py bdist_wheel, or sometimes setup.py install
     #  setup.py egg_info -> ?
 
+    # pip install -e . and setuptool/editable_wheel will invoke build_py
+    # but the build_py command is not expected to copy any files.
+
     # we override different "build_py" commands for both environments
-    if "setuptools" in sys.modules:
-        from setuptools.command.build_py import build_py as _build_py
+    if 'build_py' in cmds:
+        _build_py: Any = cmds['build_py']
     else:
-        from distutils.command.build_py import build_py as _build_py
+        from setuptools.command.build_py import build_py as _build_py
 
     class cmd_build_py(_build_py):
-        def run(self):
+        def run(self) -> None:
             root = get_root()
             cfg = get_config_from_root(root)
             versions = get_versions()
             _build_py.run(self)
+            if getattr(self, "editable_mode", False):
+                # During editable installs `.py` and data files are
+                # not copied to build_lib
+                return
             # now locate _version.py in the new build/ directory and replace
             # it with an updated value
             if cfg.versionfile_build:
-                target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build)
+                target_versionfile = os.path.join(self.build_lib,
+                                                  cfg.versionfile_build)
                 print("UPDATING %s" % target_versionfile)
                 write_to_version_file(target_versionfile, versions)
-
     cmds["build_py"] = cmd_build_py
 
-    if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
-        from cx_Freeze.dist import build_exe as _build_exe
+    if 'build_ext' in cmds:
+        _build_ext: Any = cmds['build_ext']
+    else:
+        from setuptools.command.build_ext import build_ext as _build_ext
+
+    class cmd_build_ext(_build_ext):
+        def run(self) -> None:
+            root = get_root()
+            cfg = get_config_from_root(root)
+            versions = get_versions()
+            _build_ext.run(self)
+            if self.inplace:
+                # build_ext --inplace will only build extensions in
+                # build/lib<..> dir with no _version.py to write to.
+                # As in place builds will already have a _version.py
+                # in the module dir, we do not need to write one.
+                return
+            # now locate _version.py in the new build/ directory and replace
+            # it with an updated value
+            if not cfg.versionfile_build:
+                return
+            target_versionfile = os.path.join(self.build_lib,
+                                              cfg.versionfile_build)
+            if not os.path.exists(target_versionfile):
+                print(f"Warning: {target_versionfile} does not exist, skipping "
+                      "version update. This can happen if you are running build_ext "
+                      "without first running build_py.")
+                return
+            print("UPDATING %s" % target_versionfile)
+            write_to_version_file(target_versionfile, versions)
+    cmds["build_ext"] = cmd_build_ext
 
+    if "cx_Freeze" in sys.modules:  # cx_freeze enabled?
+        from cx_Freeze.dist import build_exe as _build_exe  # type: ignore
         # nczeczulin reports that py2exe won't like the pep440-style string
         # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
         # setup(console=[{
@@ -1615,7 +2003,7 @@ def run(self):
         #   ...
 
         class cmd_build_exe(_build_exe):
-            def run(self):
+            def run(self) -> None:
                 root = get_root()
                 cfg = get_config_from_root(root)
                 versions = get_versions()
@@ -1627,28 +2015,24 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(
-                        LONG
-                        % {
-                            "DOLLAR": "$",
-                            "STYLE": cfg.style,
-                            "TAG_PREFIX": cfg.tag_prefix,
-                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        }
-                    )
-
+                    f.write(LONG %
+                            {"DOLLAR": "$",
+                             "STYLE": cfg.style,
+                             "TAG_PREFIX": cfg.tag_prefix,
+                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                             })
         cmds["build_exe"] = cmd_build_exe
         del cmds["build_py"]
 
-    if "py2exe" in sys.modules:  # py2exe enabled?
+    if 'py2exe' in sys.modules:  # py2exe enabled?
         try:
-            from py2exe.distutils_buildexe import py2exe as _py2exe  # py3
+            from py2exe.setuptools_buildexe import py2exe as _py2exe  # type: ignore
         except ImportError:
-            from py2exe.build_exe import py2exe as _py2exe  # py2
+            from py2exe.distutils_buildexe import py2exe as _py2exe  # type: ignore
 
         class cmd_py2exe(_py2exe):
-            def run(self):
+            def run(self) -> None:
                 root = get_root()
                 cfg = get_config_from_root(root)
                 versions = get_versions()
@@ -1660,27 +2044,60 @@ def run(self):
                 os.unlink(target_versionfile)
                 with open(cfg.versionfile_source, "w") as f:
                     LONG = LONG_VERSION_PY[cfg.VCS]
-                    f.write(
-                        LONG
-                        % {
-                            "DOLLAR": "$",
-                            "STYLE": cfg.style,
-                            "TAG_PREFIX": cfg.tag_prefix,
-                            "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                            "VERSIONFILE_SOURCE": cfg.versionfile_source,
-                        }
-                    )
-
+                    f.write(LONG %
+                            {"DOLLAR": "$",
+                             "STYLE": cfg.style,
+                             "TAG_PREFIX": cfg.tag_prefix,
+                             "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                             "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                             })
         cmds["py2exe"] = cmd_py2exe
 
+    # sdist farms its file list building out to egg_info
+    if 'egg_info' in cmds:
+        _egg_info: Any = cmds['egg_info']
+    else:
+        from setuptools.command.egg_info import egg_info as _egg_info
+
+    class cmd_egg_info(_egg_info):
+        def find_sources(self) -> None:
+            # egg_info.find_sources builds the manifest list and writes it
+            # in one shot
+            super().find_sources()
+
+            # Modify the filelist and normalize it
+            root = get_root()
+            cfg = get_config_from_root(root)
+            self.filelist.append('versioneer.py')
+            if cfg.versionfile_source:
+                # There are rare cases where versionfile_source might not be
+                # included by default, so we must be explicit
+                self.filelist.append(cfg.versionfile_source)
+            self.filelist.sort()
+            self.filelist.remove_duplicates()
+
+            # The write method is hidden in the manifest_maker instance that
+            # generated the filelist and was thrown away
+            # We will instead replicate their final normalization (to unicode,
+            # and POSIX-style paths)
+            from setuptools import unicode_utils
+            normalized = [unicode_utils.filesys_decode(f).replace(os.sep, '/')
+                          for f in self.filelist.files]
+
+            manifest_filename = os.path.join(self.egg_info, 'SOURCES.txt')
+            with open(manifest_filename, 'w') as fobj:
+                fobj.write('\n'.join(normalized))
+
+    cmds['egg_info'] = cmd_egg_info
+
     # we override different "sdist" commands for both environments
-    if "setuptools" in sys.modules:
-        from setuptools.command.sdist import sdist as _sdist
+    if 'sdist' in cmds:
+        _sdist: Any = cmds['sdist']
     else:
-        from distutils.command.sdist import sdist as _sdist
+        from setuptools.command.sdist import sdist as _sdist
 
     class cmd_sdist(_sdist):
-        def run(self):
+        def run(self) -> None:
             versions = get_versions()
             self._versioneer_generated_versions = versions
             # unless we update this, the command will keep using the old
@@ -1688,7 +2105,7 @@ def run(self):
             self.distribution.metadata.version = versions["version"]
             return _sdist.run(self)
 
-        def make_release_tree(self, base_dir, files):
+        def make_release_tree(self, base_dir: str, files: List[str]) -> None:
             root = get_root()
             cfg = get_config_from_root(root)
             _sdist.make_release_tree(self, base_dir, files)
@@ -1697,10 +2114,8 @@ def make_release_tree(self, base_dir, files):
             # updated value
             target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
             print("UPDATING %s" % target_versionfile)
-            write_to_version_file(
-                target_versionfile, self._versioneer_generated_versions
-            )
-
+            write_to_version_file(target_versionfile,
+                                  self._versioneer_generated_versions)
     cmds["sdist"] = cmd_sdist
 
     return cmds
@@ -1743,25 +2158,28 @@ def make_release_tree(self, base_dir, files):
 
 """
 
-INIT_PY_SNIPPET = """
+OLD_SNIPPET = """
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
 """
 
+INIT_PY_SNIPPET = """
+from . import {0}
+__version__ = {0}.get_versions()['version']
+"""
+
 
-def do_setup():
-    """Main VCS-independent setup function for installing Versioneer."""
+def do_setup() -> int:
+    """Do main VCS-independent setup function for installing Versioneer."""
     root = get_root()
     try:
         cfg = get_config_from_root(root)
-    except (
-        EnvironmentError,
-        configparser.NoSectionError,
-        configparser.NoOptionError,
-    ) as e:
-        if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
-            print("Adding sample versioneer config to setup.cfg", file=sys.stderr)
+    except (OSError, configparser.NoSectionError,
+            configparser.NoOptionError) as e:
+        if isinstance(e, (OSError, configparser.NoSectionError)):
+            print("Adding sample versioneer config to setup.cfg",
+                  file=sys.stderr)
             with open(os.path.join(root, "setup.cfg"), "a") as f:
                 f.write(SAMPLE_CONFIG)
         print(CONFIG_ERROR, file=sys.stderr)
@@ -1770,76 +2188,46 @@ def do_setup():
     print(" creating %s" % cfg.versionfile_source)
     with open(cfg.versionfile_source, "w") as f:
         LONG = LONG_VERSION_PY[cfg.VCS]
-        f.write(
-            LONG
-            % {
-                "DOLLAR": "$",
-                "STYLE": cfg.style,
-                "TAG_PREFIX": cfg.tag_prefix,
-                "PARENTDIR_PREFIX": cfg.parentdir_prefix,
-                "VERSIONFILE_SOURCE": cfg.versionfile_source,
-            }
-        )
-
-    ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py")
+        f.write(LONG % {"DOLLAR": "$",
+                        "STYLE": cfg.style,
+                        "TAG_PREFIX": cfg.tag_prefix,
+                        "PARENTDIR_PREFIX": cfg.parentdir_prefix,
+                        "VERSIONFILE_SOURCE": cfg.versionfile_source,
+                        })
+
+    ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
+                       "__init__.py")
+    maybe_ipy: Optional[str] = ipy
     if os.path.exists(ipy):
         try:
             with open(ipy, "r") as f:
                 old = f.read()
-        except EnvironmentError:
+        except OSError:
             old = ""
-        if INIT_PY_SNIPPET not in old:
+        module = os.path.splitext(os.path.basename(cfg.versionfile_source))[0]
+        snippet = INIT_PY_SNIPPET.format(module)
+        if OLD_SNIPPET in old:
+            print(" replacing boilerplate in %s" % ipy)
+            with open(ipy, "w") as f:
+                f.write(old.replace(OLD_SNIPPET, snippet))
+        elif snippet not in old:
             print(" appending to %s" % ipy)
             with open(ipy, "a") as f:
-                f.write(INIT_PY_SNIPPET)
+                f.write(snippet)
         else:
             print(" %s unmodified" % ipy)
     else:
         print(" %s doesn't exist, ok" % ipy)
-        ipy = None
-
-    # Make sure both the top-level "versioneer.py" and versionfile_source
-    # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
-    # they'll be copied into source distributions. Pip won't be able to
-    # install the package without this.
-    manifest_in = os.path.join(root, "MANIFEST.in")
-    simple_includes = set()
-    try:
-        with open(manifest_in, "r") as f:
-            for line in f:
-                if line.startswith("include "):
-                    for include in line.split()[1:]:
-                        simple_includes.add(include)
-    except EnvironmentError:
-        pass
-    # That doesn't cover everything MANIFEST.in can do
-    # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
-    # it might give some false negatives. Appending redundant 'include'
-    # lines is safe, though.
-    if "versioneer.py" not in simple_includes:
-        print(" appending 'versioneer.py' to MANIFEST.in")
-        with open(manifest_in, "a") as f:
-            f.write("include versioneer.py\n")
-    else:
-        print(" 'versioneer.py' already in MANIFEST.in")
-    if cfg.versionfile_source not in simple_includes:
-        print(
-            " appending versionfile_source ('%s') to MANIFEST.in"
-            % cfg.versionfile_source
-        )
-        with open(manifest_in, "a") as f:
-            f.write("include %s\n" % cfg.versionfile_source)
-    else:
-        print(" versionfile_source already in MANIFEST.in")
+        maybe_ipy = None
 
     # Make VCS-specific changes. For git, this means creating/changing
     # .gitattributes to mark _version.py for export-subst keyword
     # substitution.
-    do_vcs_install(manifest_in, cfg.versionfile_source, ipy)
+    do_vcs_install(cfg.versionfile_source, maybe_ipy)
     return 0
 
 
-def scan_setup_py():
+def scan_setup_py() -> int:
     """Validate the contents of setup.py against Versioneer's expectations."""
     found = set()
     setters = False
@@ -1876,10 +2264,14 @@ def scan_setup_py():
     return errors
 
 
+def setup_command() -> NoReturn:
+    """Set up Versioneer and exit with appropriate error code."""
+    errors = do_setup()
+    errors += scan_setup_py()
+    sys.exit(1 if errors else 0)
+
+
 if __name__ == "__main__":
     cmd = sys.argv[1]
     if cmd == "setup":
-        errors = do_setup()
-        errors += scan_setup_py()
-        if errors:
-            sys.exit(1)
+        setup_command()

From 4afa5f14b082b5faebce21feb4abe7b246286fb0 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:22:27 +0200
Subject: [PATCH 06/20] update for documentation

---
 .github/workflows/python-app.yml | 2 +-
 .readthedocs.yml                 | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
index 7c93faae..f2f4753e 100644
--- a/.github/workflows/python-app.yml
+++ b/.github/workflows/python-app.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         # os: [ubuntu-latest, macos-latest, windows-latest]
-        os: [ubuntu-lts-latest, windows-latest]
+        os: [ubuntu-latest, windows-latest]
         python_version: ['3.10', '3.11', '3.12']
     name: Run py eddy tracker build tests
     runs-on: ${{ matrix.os }}
diff --git a/.readthedocs.yml b/.readthedocs.yml
index a04495b6..4b698a62 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -4,8 +4,10 @@ conda:
 build:
   os: ubuntu-lts-latest
   tools:
-    python: "3.10"
+    python: "mambaforge-latest"
 python:
   install:
     - method: setuptools
       path: .
+sphinx:
+  configuration: docs/conf.py
\ No newline at end of file

From 3a54bbb6e50ebc38dcb334539dcb5b456a408127 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 29 Jul 2024 15:24:56 +0200
Subject: [PATCH 07/20] again doc

---
 .readthedocs.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 4b698a62..ddfbb747 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -9,5 +9,3 @@ python:
   install:
     - method: setuptools
       path: .
-sphinx:
-  configuration: docs/conf.py
\ No newline at end of file

From d5d3aed5f4ac51b361697638144fc19410f04093 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Tue, 12 Nov 2024 17:02:22 +0100
Subject: [PATCH 08/20] correction on lagerloef uv

---
 src/py_eddy_tracker/dataset/grid.py | 67 +++++++++++++----------------
 1 file changed, 29 insertions(+), 38 deletions(-)

diff --git a/src/py_eddy_tracker/dataset/grid.py b/src/py_eddy_tracker/dataset/grid.py
index edb96bac..d8a48f69 100644
--- a/src/py_eddy_tracker/dataset/grid.py
+++ b/src/py_eddy_tracker/dataset/grid.py
@@ -1670,7 +1670,7 @@ def spectrum_lonlat(self, grid_name, area=None, ref=None, **kwargs):
                 (lat_content[0], lat_content[1] / ref_lat_content[1]),
             )
 
-    def compute_finite_difference(self, data, schema=1, mode="reflect", vertical=False):
+    def compute_finite_difference(self, data, schema=1, mode="reflect", vertical=False, second=False):
         if not isinstance(schema, int) and schema < 1:
             raise Exception("schema must be a positive int")
 
@@ -1694,13 +1694,16 @@ def compute_finite_difference(self, data, schema=1, mode="reflect", vertical=Fal
                 data2[:schema] = nan
 
         # Distance for one degree
-        d = self.EARTH_RADIUS * 2 * pi / 360
+        d = self.EARTH_RADIUS * 2 * pi / 360 * 2 * schema
         # Mulitply by 2 step
         if vertical:
-            d *= self.ystep * 2 * schema
+            d *= self.ystep 
         else:
-            d *= self.xstep * cos(deg2rad(self.y_c)) * 2 * schema
-        return (data1 - data2) / d
+            d *= self.xstep * cos(deg2rad(self.y_c))
+        if second:
+            return (data1 + data2 - 2 * data) / (d ** 2 / 4)
+        else:
+            return (data1 - data2) / d
 
     def compute_stencil(
         self, data, stencil_halfwidth=4, mode="reflect", vertical=False
@@ -1787,13 +1790,14 @@ def compute_stencil(
         )
         return ma.array(g, mask=m)
 
-    def add_uv_lagerloef(self, grid_height, uname="u", vname="v", schema=15):
-        self.add_uv(grid_height, uname, vname)
+    def add_uv_lagerloef(self, grid_height, uname="u", vname="v", schema=15, **kwargs):
+        self.add_uv(grid_height, uname, vname, **kwargs)
         latmax = 5
-        _, (i_start, i_end) = self.nearest_grd_indice((0, 0), (-latmax, latmax))
+        _, i_start = self.nearest_grd_indice(0, -latmax)
+        _, i_end = self.nearest_grd_indice(0, latmax)
         sl = slice(i_start, i_end)
         # Divide by sideral day
-        lat = self.y_c[sl]
+        lat = self.y_c
         gob = (
             cos(deg2rad(lat))
             * ones((self.x_c.shape[0], 1))
@@ -1807,39 +1811,26 @@ def add_uv_lagerloef(self, grid_height, uname="u", vname="v", schema=15):
         mode = "wrap" if self.is_circular() else "reflect"
 
         # fill data to compute a finite difference on all point
-        data = self.convolve_filter_with_dynamic_kernel(
-            grid_height,
-            self.kernel_bessel,
-            lat_max=10,
-            wave_length=500,
-            order=1,
-            extend=0.1,
-        )
-        data = self.convolve_filter_with_dynamic_kernel(
-            data, self.kernel_bessel, lat_max=10, wave_length=500, order=1, extend=0.1
-        )
-        data = self.convolve_filter_with_dynamic_kernel(
-            data, self.kernel_bessel, lat_max=10, wave_length=500, order=1, extend=0.1
-        )
+        kw_filter = dict(kernel_func=self.kernel_bessel, order=1, extend=.1)
+        data = self.convolve_filter_with_dynamic_kernel(grid_height, wave_length=500, **kw_filter, lat_max=6+5+2+3)
         v_lagerloef = (
             self.compute_finite_difference(
-                self.compute_finite_difference(data, mode=mode, schema=schema),
-                mode=mode,
-                schema=schema,
-            )[:, sl]
-            * gob
-        )
-        u_lagerloef = (
-            -self.compute_finite_difference(
-                self.compute_finite_difference(data, vertical=True, schema=schema),
-                vertical=True,
-                schema=schema,
-            )[:, sl]
+                self.compute_finite_difference(data, mode=mode, schema=1),
+                vertical=True, schema=1
+            )
             * gob
         )
-        w = 1 - exp(-((lat / 2.2) ** 2))
-        self.vars[vname][:, sl] = self.vars[vname][:, sl] * w + v_lagerloef * (1 - w)
-        self.vars[uname][:, sl] = self.vars[uname][:, sl] * w + u_lagerloef * (1 - w)
+        u_lagerloef = -self.compute_finite_difference(data, vertical=True, schema=schema, second=True) * gob
+
+        v_lagerloef = self.convolve_filter_with_dynamic_kernel(v_lagerloef, wave_length=195, **kw_filter, lat_max=6 + 5 +2)
+        v_lagerloef = self.convolve_filter_with_dynamic_kernel(v_lagerloef, wave_length=416, **kw_filter, lat_max=6 + 5)
+        v_lagerloef = self.convolve_filter_with_dynamic_kernel(v_lagerloef, wave_length=416, **kw_filter, lat_max=6)
+        u_lagerloef = self.convolve_filter_with_dynamic_kernel(u_lagerloef, wave_length=195, **kw_filter, lat_max=6 + 5 +2)
+        u_lagerloef = self.convolve_filter_with_dynamic_kernel(u_lagerloef, wave_length=416, **kw_filter, lat_max=6 + 5)
+        u_lagerloef = self.convolve_filter_with_dynamic_kernel(u_lagerloef, wave_length=416, **kw_filter, lat_max=6)
+        w = 1 - exp(-((lat[sl] / 2.2) ** 2))
+        self.vars[vname][:, sl] = self.vars[vname][:, sl] * w + v_lagerloef[:, sl] * (1 - w)
+        self.vars[uname][:, sl] = self.vars[uname][:, sl] * w + u_lagerloef[:, sl] * (1 - w)
 
     def add_uv(self, grid_height, uname="u", vname="v", stencil_halfwidth=4):
         r"""Compute a u and v grid

From f6ae4ee6d6d21e70dd75344e85617978b6306637 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Fri, 15 Nov 2024 16:14:20 +0100
Subject: [PATCH 09/20] fix matplotlib and zarr version

---
 environment.yml  | 1 -
 requirements.txt | 4 ++--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/environment.yml b/environment.yml
index 12ce70e7..e9a05ac0 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,7 +1,6 @@
 name: binder-pyeddytracker
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - python=3.10
   - pip
diff --git a/requirements.txt b/requirements.txt
index 4c8af099..556cabbf 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,11 +1,11 @@
-matplotlib
+matplotlib < 3.8 # need an update of contour management
 opencv-python
 pint
 polygon3
 pyyaml
 requests
 scipy
-zarr
+zarr < 3.0
 netCDF4
 numpy
 numba
\ No newline at end of file

From 66f2f313187dd30920db8d80a0444aff04259443 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Fri, 15 Nov 2024 16:18:09 +0100
Subject: [PATCH 10/20] add requirement on environement doc

---
 doc/environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/doc/environment.yml b/doc/environment.yml
index 89fcbe9c..065c1027 100644
--- a/doc/environment.yml
+++ b/doc/environment.yml
@@ -1,11 +1,11 @@
 channels:
   - conda-forge
-  - defaults
 dependencies:
   - python=3.10
   - ffmpeg
   - pip
   - pip:
+    - -r ../requirements.txt
     - sphinx-gallery
     - sphinx_rtd_theme
     - sphinx>=3.1

From 449b7f87292adbcbd9fb4c2b71a4890176282066 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Tue, 19 Nov 2024 10:09:53 +0100
Subject: [PATCH 11/20] update python version condition

---
 doc/environment.yml | 2 +-
 environment.yml     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/environment.yml b/doc/environment.yml
index 065c1027..7cf02b76 100644
--- a/doc/environment.yml
+++ b/doc/environment.yml
@@ -1,7 +1,7 @@
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python>=3.10
   - ffmpeg
   - pip
   - pip:
diff --git a/environment.yml b/environment.yml
index e9a05ac0..819d28d7 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: binder-pyeddytracker
 channels:
   - conda-forge
 dependencies:
-  - python=3.10
+  - python>=3.10
   - pip
   - ffmpeg
   - pip:

From 99a848fa0cd38693ee5d62ac6a2e6a2324996cdb Mon Sep 17 00:00:00 2001
From: Antoine Delepoulle <36040805+AntSimi@users.noreply.github.com>
Date: Wed, 20 Nov 2024 15:24:34 +0100
Subject: [PATCH 12/20] solve doc problem (#255)

* reject python 3.13
* use pip instead of setuptools
* add sample id to install
---
 .readthedocs.yml                              |  2 +-
 doc/environment.yml                           |  3 ++-
 environment.yml                               |  2 +-
 .../pet_eddy_detection_ACC.py                 |  3 ++-
 src/py_eddy_tracker/data/__init__.py          | 19 +++++++++++++------
 5 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index ddfbb747..5ac02e12 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -7,5 +7,5 @@ build:
     python: "mambaforge-latest"
 python:
   install:
-    - method: setuptools
+    - method: pip
       path: .
diff --git a/doc/environment.yml b/doc/environment.yml
index 7cf02b76..063a60de 100644
--- a/doc/environment.yml
+++ b/doc/environment.yml
@@ -1,11 +1,12 @@
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10
+  - python>=3.10, <3.13
   - ffmpeg
   - pip
   - pip:
     - -r ../requirements.txt
+    - git+https://github.com/AntSimi/py-eddy-tracker-sample-id.git
     - sphinx-gallery
     - sphinx_rtd_theme
     - sphinx>=3.1
diff --git a/environment.yml b/environment.yml
index 819d28d7..e94c7bc1 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: binder-pyeddytracker
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10
+  - python>=3.10, <3.13
   - pip
   - ffmpeg
   - pip:
diff --git a/examples/02_eddy_identification/pet_eddy_detection_ACC.py b/examples/02_eddy_identification/pet_eddy_detection_ACC.py
index 3d3d4ac1..d12c62f3 100644
--- a/examples/02_eddy_identification/pet_eddy_detection_ACC.py
+++ b/examples/02_eddy_identification/pet_eddy_detection_ACC.py
@@ -7,6 +7,7 @@
 Two detections are provided : with a filtered ADT and without filtering
 
 """
+
 from datetime import datetime
 
 from matplotlib import pyplot as plt, style
@@ -80,7 +81,7 @@ def set_fancy_labels(fig, ticklabelsize=14, labelsize=14, labelweight="semibold"
 # Identification
 # ^^^^^^^^^^^^^^
 # Run the identification step with slices of 2 mm
-date = datetime(2016, 5, 15)
+date = datetime(2019, 2, 23)
 kw_ident = dict(
     date=date, step=0.002, shape_error=70, sampling=30, uname="u", vname="v"
 )
diff --git a/src/py_eddy_tracker/data/__init__.py b/src/py_eddy_tracker/data/__init__.py
index f14fee87..bf062983 100644
--- a/src/py_eddy_tracker/data/__init__.py
+++ b/src/py_eddy_tracker/data/__init__.py
@@ -8,6 +8,7 @@
     20160515 adt None None longitude latitude . \
     --cut 800 --fil 1
 """
+
 import io
 import lzma
 from os import path
@@ -26,14 +27,20 @@ def get_remote_demo_sample(path):
         if path.endswith(".nc"):
             return io.BytesIO(content)
     else:
-        if path.endswith(".nc"):
+        try:
+            import py_eddy_tracker_sample_id
+            if path.endswith(".nc"):
+                return py_eddy_tracker_sample_id.get_remote_demo_sample(path)
+            content = open(py_eddy_tracker_sample_id.get_remote_demo_sample(f"{path}.tar.xz"), "rb").read()
+        except:
+            if path.endswith(".nc"):
+                content = requests.get(
+                    f"https://github.com/AntSimi/py-eddy-tracker-sample-id/raw/master/{path}"
+                ).content
+                return io.BytesIO(content)
             content = requests.get(
-                f"https://github.com/AntSimi/py-eddy-tracker-sample-id/raw/master/{path}"
+                f"https://github.com/AntSimi/py-eddy-tracker-sample-id/raw/master/{path}.tar.xz"
             ).content
-            return io.BytesIO(content)
-        content = requests.get(
-            f"https://github.com/AntSimi/py-eddy-tracker-sample-id/raw/master/{path}.tar.xz"
-        ).content
 
     # Tar module could manage lzma tar, but it will apply uncompress for each extractfile
     tar = tarfile.open(mode="r", fileobj=io.BytesIO(lzma.decompress(content)))

From 0a4ed708d87cc4073634beac8fb88a4b16747f0e Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Mon, 6 Jan 2025 16:18:47 +0100
Subject: [PATCH 13/20] bug correction toward direction #252

---
 src/py_eddy_tracker/appli/network.py         |  2 +-
 src/py_eddy_tracker/dataset/grid.py          | 13 ++++++-------
 src/py_eddy_tracker/observations/tracking.py |  2 +-
 3 files changed, 8 insertions(+), 9 deletions(-)

diff --git a/src/py_eddy_tracker/appli/network.py b/src/py_eddy_tracker/appli/network.py
index b8c2da51..0a3d06ca 100644
--- a/src/py_eddy_tracker/appli/network.py
+++ b/src/py_eddy_tracker/appli/network.py
@@ -283,7 +283,7 @@ def previous_obs(d, i_seg):
 def display_compare(ref, others):
     def display(value, ref=None):
         if ref:
-            outs = [f"{v/ref[k] * 100:.1f}% ({v})" for k, v in value.items()]
+            outs = [f"{v / ref[k] * 100:.1f}% ({v})" for k, v in value.items()]
         else:
             outs = value
         return "".join([f"{v:^18}" for v in outs])
diff --git a/src/py_eddy_tracker/dataset/grid.py b/src/py_eddy_tracker/dataset/grid.py
index d8a48f69..f15503b2 100644
--- a/src/py_eddy_tracker/dataset/grid.py
+++ b/src/py_eddy_tracker/dataset/grid.py
@@ -9,6 +9,7 @@
 from matplotlib.path import Path as BasePath
 from netCDF4 import Dataset
 from numba import njit, prange, types as numba_types
+import numpy as np
 from numpy import (
     arange,
     array,
@@ -35,7 +36,6 @@
     percentile,
     pi,
     radians,
-    round_,
     sin,
     sinc,
     sqrt,
@@ -2251,12 +2251,11 @@ def compute_pixel_path(x0, y0, x1, y1, x_ori, y_ori, x_step, y_step, nb_x):
     i_x1 = empty(nx, dtype=numba_types.int_)
     i_y0 = empty(nx, dtype=numba_types.int_)
     i_y1 = empty(nx, dtype=numba_types.int_)
-    # Because round_ is not accepted with array in numba
     for i in range(nx):
-        i_x0[i] = round_(((x0[i] - x_ori) % 360) / x_step)
-        i_x1[i] = round_(((x1[i] - x_ori) % 360) / x_step)
-        i_y0[i] = round_((y0[i] - y_ori) / y_step)
-        i_y1[i] = round_((y1[i] - y_ori) / y_step)
+        i_x0[i] = np.round(((x0[i] - x_ori) % 360) / x_step)
+        i_x1[i] = np.round(((x1[i] - x_ori) % 360) / x_step)
+        i_y0[i] = np.round((y0[i] - y_ori) / y_step)
+        i_y1[i] = np.round((y1[i] - y_ori) / y_step)
     # Delta index of x
     d_x = i_x1 - i_x0
     d_x = (d_x + nb_x // 2) % nb_x - (nb_x // 2)
@@ -2941,7 +2940,7 @@ def compute_stencil(x, y, h, m, earth_radius, vertical=False, stencil_halfwidth=
             h_3, h_2, h_1, h0 = h[-4, j], h[-3, j], h[-2, j], h[-1, j]
             m_3, m_2, m_1, m0 = m[-4, j], m[-3, j], m[-2, j], m[-1, j]
         else:
-            m_3, m_2, m_1, m0 = False, False, False, False
+            m_3, m_2, m_1, m0 = True, True, True, True
         h1, h2, h3, h4 = h[0, j], h[1, j], h[2, j], h[3, j]
         m1, m2, m3, m4 = m[0, j], m[1, j], m[2, j], m[3, j]
         for i in range(nb_x):
diff --git a/src/py_eddy_tracker/observations/tracking.py b/src/py_eddy_tracker/observations/tracking.py
index 164f9724..fa1c1f93 100644
--- a/src/py_eddy_tracker/observations/tracking.py
+++ b/src/py_eddy_tracker/observations/tracking.py
@@ -380,7 +380,7 @@ def extract_toward_direction(self, west=True, delta_lon=None):
         d_lon = lon[i1] - lon[i0]
         m = d_lon < 0 if west else d_lon > 0
         if delta_lon is not None:
-            m *= delta_lon < d_lon
+            m *= delta_lon < abs(d_lon)
         m = m.repeat(nb)
         return self.extract_with_mask(m)
 

From c069878e3f69cd908c8bef6906f05ca4f015ef0e Mon Sep 17 00:00:00 2001
From: Antoine Delepoulle <36040805+AntSimi@users.noreply.github.com>
Date: Wed, 20 Nov 2024 15:24:34 +0100
Subject: [PATCH 14/20] Add method to get period information for each network

---
 src/py_eddy_tracker/observations/network.py | 34 +++++++++++++++++----
 1 file changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/py_eddy_tracker/observations/network.py b/src/py_eddy_tracker/observations/network.py
index a2e2daed..87ef4a78 100644
--- a/src/py_eddy_tracker/observations/network.py
+++ b/src/py_eddy_tracker/observations/network.py
@@ -9,6 +9,7 @@
 import netCDF4
 from numba import njit, types as nb_types
 from numba.typed import List
+import numpy as np
 from numpy import (
     arange,
     array,
@@ -124,7 +125,7 @@ def __repr__(self):
             f"Atlas with {self.nb_network} networks ({self.nb_network / period:0.0f} networks/year),"
             f" {self.nb_segment} segments ({self.nb_segment / period:0.0f} segments/year), {len(self)} observations ({len(self) / period:0.0f} observations/year)",
             f"    {m_event.size} merging ({m_event.size / period:0.0f} merging/year), {s_event.size} splitting ({s_event.size / period:0.0f} splitting/year)",
-            f"    with {(nb_by_network > big).sum()} network with more than {big} obs and the biggest have {nb_by_network.max()} observations ({nb_by_network[nb_by_network> big].sum()} observations cumulate)",
+            f"    with {(nb_by_network > big).sum()} network with more than {big} obs and the biggest have {nb_by_network.max()} observations ({nb_by_network[nb_by_network > big].sum()} observations cumulate)",
             f"    {nb_trash} observations in trash",
         ]
         return "\n".join(infos)
@@ -225,6 +226,12 @@ def network_size(self, id_networks=None):
             i = id_networks - self.index_network[2]
             return self.index_network[1][i] - self.index_network[0][i]
 
+    def networks_period(self):
+        """
+        Return period for each network
+        """
+        return get_period_with_index(self.time, *self.index_network[:2])
+
     def unique_segment_to_id(self, id_unique):
         """Return id network and id segment for a unique id
 
@@ -1788,8 +1795,8 @@ def date2file(julian_day):
             )
             logger.info(
                 (
-                    f"coherence {_t} / {range_end-1} ({(_t - range_start) / (range_end - range_start-1):.1%})"
-                    f" : {time.time()-_timestamp:5.2f}s"
+                    f"coherence {_t} / {range_end - 1} ({(_t - range_start) / (range_end - range_start - 1):.1%})"
+                    f" : {time.time() - _timestamp:5.2f}s"
                 )
             )
 
@@ -1865,8 +1872,8 @@ def date2file(julian_day):
             )
             logger.info(
                 (
-                    f"coherence {_t} / {range_end-1} ({(_t - range_start) / (range_end - range_start-1):.1%})"
-                    f" : {time.time()-_timestamp:5.2f}s"
+                    f"coherence {_t} / {range_end - 1} ({(_t - range_start) / (range_end - range_start - 1):.1%})"
+                    f" : {time.time() - _timestamp:5.2f}s"
                 )
             )
         return itf_final, ptf_final
@@ -2065,7 +2072,7 @@ def group_observations(self, min_overlap=0.2, minimal_area=False, **kwargs):
         nb_alone, nb_obs, nb_gr = (gr == self.NOGROUP).sum(), len(gr), len(unique(gr))
         logger.info(
             f"{nb_alone} alone / {nb_obs} obs, {nb_gr} groups, "
-            f"{nb_alone *100./nb_obs:.2f} % alone, {(nb_obs - nb_alone) / (nb_gr - 1):.1f} obs/group"
+            f"{nb_alone * 100. / nb_obs:.2f} % alone, {(nb_obs - nb_alone) / (nb_gr - 1):.1f} obs/group"
         )
         return gr
 
@@ -2316,3 +2323,18 @@ def mask_follow_obs(m, next_obs, time, indexs, dt=3):
             m[i_next] = True
             i_next = next_obs[i_next]
             dt_ = abs(time[i_next] - t0)
+
+
+@njit(cache=True)
+def get_period_with_index(t, i0, i1):
+    """Return peek to peek cover by each slice define by i0 and i1
+
+    :param array t: array which contain values to estimate spread
+    :param array i0: index which determine start of slice
+    :param array i1: index which determine end of slice
+    :return array: Peek to peek of t
+    """
+    periods = np.empty(i0.size, t.dtype)
+    for i in range(i0.size):
+        periods[i] = t[i0[i] : i1[i]].ptp()
+    return periods

From 7ad635def9c26d02f2b00cf4f8c71ff4af449e98 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Fri, 10 Jan 2025 15:46:10 +0100
Subject: [PATCH 15/20] In cas of empty slice continue and set period to 0

---
 src/py_eddy_tracker/observations/network.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/py_eddy_tracker/observations/network.py b/src/py_eddy_tracker/observations/network.py
index 87ef4a78..393dae78 100644
--- a/src/py_eddy_tracker/observations/network.py
+++ b/src/py_eddy_tracker/observations/network.py
@@ -2336,5 +2336,8 @@ def get_period_with_index(t, i0, i1):
     """
     periods = np.empty(i0.size, t.dtype)
     for i in range(i0.size):
+        if i1[i] == i0[i]:
+            periods[i] = 0
+            continue
         periods[i] = t[i0[i] : i1[i]].ptp()
     return periods

From 1c42ae3358e62055646c11df1d2916de8c3dd941 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Tue, 28 Jan 2025 15:52:09 +0100
Subject: [PATCH 16/20] add docs conf.py

---
 .readthedocs.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.readthedocs.yml b/.readthedocs.yml
index 5ac02e12..ba36f8ea 100644
--- a/.readthedocs.yml
+++ b/.readthedocs.yml
@@ -9,3 +9,5 @@ python:
   install:
     - method: pip
       path: .
+sphinx:
+  configuration: doc/conf.py
\ No newline at end of file

From a39435dd2a02b0f313765452bdaebe39203769cf Mon Sep 17 00:00:00 2001
From: "J. Gamot" <jgamot@groupcls.com>
Date: Thu, 16 Jan 2025 17:07:06 +0100
Subject: [PATCH 17/20] modifications network file

---
 src/py_eddy_tracker/appli/gui.py            |  7 ++-
 src/py_eddy_tracker/observations/network.py | 63 ++++++++++++++++++---
 2 files changed, 60 insertions(+), 10 deletions(-)

diff --git a/src/py_eddy_tracker/appli/gui.py b/src/py_eddy_tracker/appli/gui.py
index 4a8cdeb0..c3d7619b 100644
--- a/src/py_eddy_tracker/appli/gui.py
+++ b/src/py_eddy_tracker/appli/gui.py
@@ -11,7 +11,7 @@
 from matplotlib.animation import FuncAnimation
 from matplotlib.axes import Axes
 from matplotlib.collections import LineCollection
-from numpy import arange, where
+from numpy import arange, where, nan
 
 from .. import EddyParser
 from ..gui import GUI
@@ -58,7 +58,10 @@ def setup(
         self.kw_label["fontweight"] = kwargs.pop("fontweight", "demibold")
         # To text each visible eddy
         if field_txt:
-            self.field_txt = self.eddy[field_txt]
+            if isinstance(field_txt,str):
+                self.field_txt = self.eddy[field_txt]
+            else :
+                self.field_txt=field_txt
         if field_color:
             # To color each visible eddy
             self.field_color = self.eddy[field_color].astype("f4")
diff --git a/src/py_eddy_tracker/observations/network.py b/src/py_eddy_tracker/observations/network.py
index 393dae78..ef0b02b4 100644
--- a/src/py_eddy_tracker/observations/network.py
+++ b/src/py_eddy_tracker/observations/network.py
@@ -5,7 +5,8 @@
 from glob import glob
 import logging
 import time
-
+from datetime import timedelta, datetime
+import os
 import netCDF4
 from numba import njit, types as nb_types
 from numba.typed import List
@@ -16,6 +17,7 @@
     bincount,
     bool_,
     concatenate,
+
     empty,
     nan,
     ones,
@@ -120,6 +122,7 @@ def __repr__(self):
         period = (self.period[1] - self.period[0]) / 365.25
         nb_by_network = self.network_size()
         nb_trash = 0 if self.ref_index != 0 else nb_by_network[0]
+        lifetime=self.lifetime
         big = 50_000
         infos = [
             f"Atlas with {self.nb_network} networks ({self.nb_network / period:0.0f} networks/year),"
@@ -127,6 +130,7 @@ def __repr__(self):
             f"    {m_event.size} merging ({m_event.size / period:0.0f} merging/year), {s_event.size} splitting ({s_event.size / period:0.0f} splitting/year)",
             f"    with {(nb_by_network > big).sum()} network with more than {big} obs and the biggest have {nb_by_network.max()} observations ({nb_by_network[nb_by_network > big].sum()} observations cumulate)",
             f"    {nb_trash} observations in trash",
+            f" {lifetime.max()} days max of lifetime",
         ]
         return "\n".join(infos)
 
@@ -201,6 +205,13 @@ def ref_segment_track_index(self):
     @property
     def ref_index(self):
         return self.index_network[2]
+    
+    @property
+    def lifetime(self):
+        """Return lifetime for each observation"""
+        lt=self.networks_period.astype("int")
+        nb_by_network=self.network_size()
+        return lt.repeat(nb_by_network)
 
     def network_segment_size(self, id_networks=None):
         """Get number of segment by network
@@ -226,12 +237,15 @@ def network_size(self, id_networks=None):
             i = id_networks - self.index_network[2]
             return self.index_network[1][i] - self.index_network[0][i]
 
+    @property
     def networks_period(self):
         """
         Return period for each network
         """
         return get_period_with_index(self.time, *self.index_network[:2])
 
+    
+    
     def unique_segment_to_id(self, id_unique):
         """Return id network and id segment for a unique id
 
@@ -281,7 +295,7 @@ def astype(self, cls):
                 new[k][:] = self[k][:]
         new.sign_type = self.sign_type
         return new
-
+    
     def longer_than(self, nb_day_min=-1, nb_day_max=-1):
         """
         Select network on time duration
@@ -1132,23 +1146,29 @@ def segment_track_array(self):
             self._segment_track_array = build_unique_array(self.segment, self.track)
         return self._segment_track_array
 
-    def birth_event(self):
+    def birth_event(self, only_index=False):
         """Extract birth events."""
         i_start, _, _ = self.index_segment_track
         indices = i_start[self.previous_obs[i_start] == -1]
         if self.first_is_trash():
             indices = indices[1:]
-        return self.extract_event(indices)
-
+        if only_index: 
+            return indices
+        else : 
+            return self.extract_event(indices)
+        
     generation_event = birth_event
 
-    def death_event(self):
+    def death_event(self, only_index=False):
         """Extract death events."""
         _, i_stop, _ = self.index_segment_track
         indices = i_stop[self.next_obs[i_stop - 1] == -1] - 1
         if self.first_is_trash():
             indices = indices[1:]
-        return self.extract_event(indices)
+        if only_index: 
+            return indices
+        else : 
+            return self.extract_event(indices)
 
     dissipation_event = death_event
 
@@ -1459,7 +1479,7 @@ def plot(self, ax, ref=None, color_cycle=None, **kwargs):
             j += 1
         return mappables
 
-    def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None):
+    def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None, return_mask=False):
         """
         Remove short segments that don't connect several segments
 
@@ -1485,6 +1505,8 @@ def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None):
             )
         # get mask for selected obs
         m = ~self.segment_mask(segments_keep)
+        if return_mask:
+            return ~m
         self.track[m] = 0
         self.segment[m] = 0
         self.previous_obs[m] = -1
@@ -1502,6 +1524,8 @@ def remove_dead_end(self, nobs=3, ndays=0, recursive=0, mask=None):
         self.sort()
         if recursive > 0:
             self.remove_dead_end(nobs, ndays, recursive - 1)
+        
+        
 
     def extract_segment(self, segments, absolute=False):
         """Extract given segments
@@ -2042,6 +2066,29 @@ def group_observations(self, min_overlap=0.2, minimal_area=False, **kwargs):
         results, nb_obs = list(), list()
         # To display print only in INFO
         display_iteration = logger.getEffectiveLevel() == logging.INFO
+        
+        
+        # Trier les fichiers par date
+        def extract_date(file):
+            filename = os.path.basename(file)
+            date_str = filename.split('_')[-1].split('.')[0]  # Extraire la partie date (ex : "20180101")
+            return datetime.strptime(date_str, "%Y%m%d")  # Convertir en objet datetime
+        self.filenames = sorted(self.filenames, key=extract_date)
+
+        # Detect missing date and print them to inform the user which files are missing
+        missing_dates = []
+        dates_list = [extract_date(self.filenames[i]) for i in range(len(self.filenames))]
+        for i in range(len(dates_list) - 1):
+            expected_date = dates_list[i] + timedelta(days=1)
+            while expected_date < dates_list[i + 1]:  
+                missing_dates.append(expected_date)
+                expected_date += timedelta(days=1)
+        if missing_dates:
+            missing_str = ', '.join(date.strftime("%Y-%m-%d") for date in missing_dates)
+            raise Exception(f"Following files missing : {missing_str}")
+        else:
+            print("No missing files")
+
         for i, filename in enumerate(self.filenames):
             if display_iteration:
                 print(f"{filename} compared to {self.window} next", end="\r")

From f7f820d3746cc137f14ccb5853599c26dd80cf93 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Wed, 29 Jan 2025 16:17:44 +0100
Subject: [PATCH 18/20] Move out argsort from numba to speed up

---
 src/py_eddy_tracker/generic.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/py_eddy_tracker/generic.py b/src/py_eddy_tracker/generic.py
index 612def68..2fdb737a 100644
--- a/src/py_eddy_tracker/generic.py
+++ b/src/py_eddy_tracker/generic.py
@@ -615,7 +615,6 @@ def build_circle(x0, y0, r):
     return x_norm * r + x0, y_norm * r + y0
 
 
-@njit(cache=True)
 def window_index(x, x0, half_window=1):
     """
     Give for a fixed half_window each start and end index for each x0, in
@@ -626,7 +625,12 @@ def window_index(x, x0, half_window=1):
     :param float half_window: half window
     """
     # Sort array, bounds will be sort also
-    i_ordered = x.argsort()
+    i_ordered = x.argsort(kind="mergesort")
+    return window_index_(x, i_ordered, x0, half_window)
+
+
+@njit(cache=True)
+def window_index_(x, i_ordered, x0, half_window=1):
     nb_x, nb_pt = x.size, x0.size
     first_index = empty(nb_pt, dtype=i_ordered.dtype)
     last_index = empty(nb_pt, dtype=i_ordered.dtype)

From 8fe5bf10e1bc973c83dd114b12e19c37b2f27edc Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Thu, 30 Jan 2025 11:59:41 +0100
Subject: [PATCH 19/20] Remove  check on missing file, code was build with bad
 hypothesis

---
 src/py_eddy_tracker/observations/network.py | 22 ---------------------
 1 file changed, 22 deletions(-)

diff --git a/src/py_eddy_tracker/observations/network.py b/src/py_eddy_tracker/observations/network.py
index ef0b02b4..f0b9d7cc 100644
--- a/src/py_eddy_tracker/observations/network.py
+++ b/src/py_eddy_tracker/observations/network.py
@@ -2067,28 +2067,6 @@ def group_observations(self, min_overlap=0.2, minimal_area=False, **kwargs):
         # To display print only in INFO
         display_iteration = logger.getEffectiveLevel() == logging.INFO
         
-        
-        # Trier les fichiers par date
-        def extract_date(file):
-            filename = os.path.basename(file)
-            date_str = filename.split('_')[-1].split('.')[0]  # Extraire la partie date (ex : "20180101")
-            return datetime.strptime(date_str, "%Y%m%d")  # Convertir en objet datetime
-        self.filenames = sorted(self.filenames, key=extract_date)
-
-        # Detect missing date and print them to inform the user which files are missing
-        missing_dates = []
-        dates_list = [extract_date(self.filenames[i]) for i in range(len(self.filenames))]
-        for i in range(len(dates_list) - 1):
-            expected_date = dates_list[i] + timedelta(days=1)
-            while expected_date < dates_list[i + 1]:  
-                missing_dates.append(expected_date)
-                expected_date += timedelta(days=1)
-        if missing_dates:
-            missing_str = ', '.join(date.strftime("%Y-%m-%d") for date in missing_dates)
-            raise Exception(f"Following files missing : {missing_str}")
-        else:
-            print("No missing files")
-
         for i, filename in enumerate(self.filenames):
             if display_iteration:
                 print(f"{filename} compared to {self.window} next", end="\r")

From 229543fdf7d0a8a3e1de6c40d769185cd85ca1b7 Mon Sep 17 00:00:00 2001
From: "A. Delepoulle" <36040805+AntSimi@users.noreply.github.com>
Date: Fri, 6 Jun 2025 10:33:16 +0200
Subject: [PATCH 20/20] update changelog

---
 CHANGELOG.rst | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f8eee72f..6d6d6a30 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -11,14 +11,23 @@ and this project adheres to `Semantic Versioning <https://semver.org/spec/v2.0.0
 Changed
 ^^^^^^^
 
-- Remove dead end method for network will move dead end to the trash and not remove observations
-
 Fixed
 ^^^^^
 
 Added
 ^^^^^
 
+[3.6.2] - 2025-06-06
+--------------------
+Changed
+^^^^^^^
+
+- Remove dead end method for network will move dead end to the trash and not remove observations
+
+Fixed
+^^^^^
+
+- Fix matplotlib version
 
 [3.6.1] - 2022-10-14
 --------------------