From c5b057e4dea214b7c290c4da59a53cf5bea9eb5a Mon Sep 17 00:00:00 2001
From: SimonBoothroyd <simon.boothroyd@hotmail.com>
Date: Sun, 20 Oct 2024 09:11:51 -0400
Subject: [PATCH] Update template

---
 .gitattributes              |   2 +-
 .github/workflows/ci.yaml   |   5 +-
 .github/workflows/docs.yaml |   6 -
 Makefile                    |   8 +-
 absolv/__init__.py          |   8 +-
 absolv/_version.py          | 717 ------------------------------------
 absolv/config.py            |  12 +
 absolv/runner.py            |   2 +
 absolv/tests/test_fep.py    |   3 -
 devtools/envs/base.yaml     |   7 +-
 mkdocs.yml                  |   4 +-
 pyproject.toml              |  21 +-
 12 files changed, 36 insertions(+), 759 deletions(-)
 delete mode 100644 absolv/_version.py

diff --git a/.gitattributes b/.gitattributes
index c2ec006..00a7b00 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -1 +1 @@
-absolv/_version.py export-subst
\ No newline at end of file
+.git_archival.txt  export-subst
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 014bc3e..83eaa16 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -24,10 +24,11 @@ jobs:
         make env
         make lint
         make test
-        make docs-build
+        make docs
 
     - name: CodeCov
-      uses: codecov/codecov-action@v3.1.1
+      uses: codecov/codecov-action@v4.1.1
       with:
         file: ./coverage.xml
         flags: unittests
+        token: ${{ secrets.CODECOV_TOKEN }}
diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
index 543aee0..c6ace56 100644
--- a/.github/workflows/docs.yaml
+++ b/.github/workflows/docs.yaml
@@ -35,8 +35,6 @@ jobs:
         fi
 
     - name: Build and Deploy Documentation
-      env:
-        INSIDER_DOCS_TOKEN: ${{ secrets.INSIDER_DOCS_TOKEN }}
       run: |
         git config --global user.name 'GitHub Actions'
         git config --global user.email 'actions@github.com'
@@ -46,8 +44,4 @@ jobs:
         git fetch --all --prune
 
         make env
-
-        sed -i 's/# extensions/extensions/' mkdocs.yml
-
-        make docs-insiders INSIDER_DOCS_TOKEN="${INSIDER_DOCS_TOKEN}"
         make docs-deploy VERSION="$VERSION"
diff --git a/Makefile b/Makefile
index 7cbf5d3..ca10431 100644
--- a/Makefile
+++ b/Makefile
@@ -4,7 +4,7 @@ CONDA_ENV_RUN=conda run --no-capture-output --name $(PACKAGE_NAME)
 
 TEST_ARGS := -v --cov=$(PACKAGE_NAME) --cov-report=term --cov-report=xml --junitxml=unit.xml --color=yes
 
-.PHONY: env lint format test docs-build docs-deploy docs-insiders
+.PHONY: env lint format test docs docs-deploy
 
 env:
 	mamba create     --name $(PACKAGE_NAME)
@@ -22,7 +22,7 @@ format:
 test:
 	$(CONDA_ENV_RUN) pytest -v $(TEST_ARGS) $(PACKAGE_NAME)/tests/
 
-docs-build:
+docs:
 	$(CONDA_ENV_RUN) mkdocs build
 
 docs-deploy:
@@ -30,7 +30,3 @@ ifndef VERSION
 	$(error VERSION is not set)
 endif
 	$(CONDA_ENV_RUN) mike deploy --push --update-aliases $(VERSION)
-
-docs-insiders:
-	$(CONDA_ENV_RUN) pip install git+https://$(INSIDER_DOCS_TOKEN)@github.com/SimonBoothroyd/mkdocstrings-python.git \
-                    			 git+https://$(INSIDER_DOCS_TOKEN)@github.com/SimonBoothroyd/griffe-pydantic.git@fix-inheritence-static
diff --git a/absolv/__init__.py b/absolv/__init__.py
index c600522..2851d95 100755
--- a/absolv/__init__.py
+++ b/absolv/__init__.py
@@ -1,6 +1,10 @@
 """Absolute solvation free energy calculations using OpenMM"""
 
-from . import _version
+import importlib.metadata
+
+try:
+    __version__ = importlib.metadata.version("absolv")
+except importlib.metadata.PackageNotFoundError:
+    __version__ = "0+unknown"
 
-__version__ = _version.get_versions()["version"]
 __all__ = ["__version__"]
diff --git a/absolv/_version.py b/absolv/_version.py
deleted file mode 100644
index bbe89ee..0000000
--- a/absolv/_version.py
+++ /dev/null
@@ -1,717 +0,0 @@
-# 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-0.29
-# https://github.com/python-versioneer/python-versioneer
-
-"""Git implementation of _version.py."""
-
-import errno
-import functools
-import os
-import re
-import subprocess
-import sys
-from collections.abc import Callable
-from typing import Any
-
-
-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
-    # each be defined on a line of their own. _version.py will just call
-    # get_keywords().
-    git_refnames = "$Format:%d$"
-    git_full = "$Format:%H$"
-    git_date = "$Format:%ci$"
-    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
-    return 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() -> VersioneerConfig:
-    """Create, populate and return the VersioneerConfig() object."""
-    # these strings are filled in when 'setup.py versioneer' creates
-    # _version.py
-    cfg = VersioneerConfig()
-    cfg.VCS = "git"
-    cfg.style = "pep440"
-    cfg.tag_prefix = ""
-    cfg.parentdir_prefix = "absolv-"
-    cfg.versionfile_source = "absolv/_version.py"
-    cfg.verbose = False
-    return cfg
-
-
-class NotThisMethod(Exception):
-    """Exception raised if a method is not valid for the current scenario."""
-
-
-LONG_VERSION_PY: dict[str, str] = {}
-HANDLERS: dict[str, dict[str, Callable]] = {}
-
-
-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: list[str],
-    args: list[str],
-    cwd: str | None = None,
-    verbose: bool = False,
-    hide_stderr: bool = False,
-    env: dict[str, str] | None = None,
-) -> tuple[str | None, int | None]:
-    """Call the given command(s)."""
-    assert isinstance(commands, list)
-    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([command] + args)
-            # remember shell=False, so use git.cmd on windows, not just git
-            process = subprocess.Popen(
-                [command] + args,
-                cwd=cwd,
-                env=env,
-                stdout=subprocess.PIPE,
-                stderr=(subprocess.PIPE if hide_stderr else None),
-                **popen_kwargs,
-            )
-            break
-        except OSError as e:
-            if e.errno == errno.ENOENT:
-                continue
-            if verbose:
-                print("unable to run %s" % dispcmd)
-                print(e)
-            return None, None
-    else:
-        if verbose:
-            print("unable to find command, tried {}".format(commands))
-        return None, None
-    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, process.returncode
-    return stdout, process.returncode
-
-
-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
-    the project name and a version string. We will also support searching up
-    two directory levels for an appropriately named parent directory
-    """
-    rootdirs = []
-
-    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,
-            }
-        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)
-        )
-    raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
-@register_vcs_handler("git", "get_keywords")
-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: dict[str, str] = {}
-    try:
-        with open(versionfile_abs) 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: dict[str, str],
-    tag_prefix: str,
-    verbose: bool,
-) -> dict[str, Any]:
-    """Get version information from git keywords."""
-    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
-        # it's been around since git-1.5.3, and it's too difficult to
-        # discover which version we're using, or to work around using an
-        # older one.
-        date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-    refnames = keywords["refnames"].strip()
-    if refnames.startswith("$Format"):
-        if verbose:
-            print("keywords are unexpanded, not using")
-        raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
-    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 = {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
-        # expansion behaves like git log --decorate=short and strips out the
-        # refs/heads/ and refs/tags/ prefixes that would let us distinguish
-        # 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 = {r for r in refs if re.search(r"\d", r)}
-        if verbose:
-            print("discarding '%s', no digits" % ",".join(refs - tags))
-    if verbose:
-        print("likely tags: %s" % ",".join(sorted(tags)))
-    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) :]
-            # 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,
-            }
-    # 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,
-    }
-
-
-@register_vcs_handler("git", "pieces_from_vcs")
-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*
-    expanded, and _version.py hasn't already been rewritten with a short
-    version string, meaning we're inside a checked out source tree.
-    """
-    GITS = ["git"]
-    if sys.platform == "win32":
-        GITS = ["git.cmd", "git.exe"]
-
-    # 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)
-        raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
-    # 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 = 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 = runner(GITS, ["rev-parse", "HEAD"], cwd=root)
-    if full_out is None:
-        raise NotThisMethod("'git rev-parse' failed")
-    full_out = full_out.strip()
-
-    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
-
-    # look for -dirty suffix
-    dirty = git_describe.endswith("-dirty")
-    pieces["dirty"] = dirty
-    if 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)
-        if not mo:
-            # unparsable. Maybe git-describe is misbehaving?
-            pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out
-            return pieces
-
-        # tag
-        full_tag = mo.group(1)
-        if not full_tag.startswith(tag_prefix):
-            if verbose:
-                fmt = "tag '%s' doesn't start with prefix '%s'"
-                print(fmt % (full_tag, tag_prefix))
-            pieces["error"] = "tag '{}' doesn't start with prefix '{}'".format(
-                full_tag,
-                tag_prefix,
-            )
-            return pieces
-        pieces["closest-tag"] = full_tag[len(tag_prefix) :]
-
-        # distance: number of commits since tag
-        pieces["distance"] = int(mo.group(2))
-
-        # commit: short hex revision ID
-        pieces["short"] = mo.group(3)
-
-    else:
-        # HEX: no tags
-        pieces["closest-tag"] = None
-        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 = 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: 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: dict[str, Any]) -> str:
-    """Build up version string, with post-release "local version identifier".
-
-    Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
-    get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
-    Exceptions:
-    1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += plus_or_dot(pieces)
-            rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
-            if pieces["dirty"]:
-                rendered += ".dirty"
-    else:
-        # exception #1
-        rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"])
-        if pieces["dirty"]:
-            rendered += ".dirty"
-    return rendered
-
-
-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[.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, int | None]:
-    """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"]:
-            # 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.post0.dev%d" % pieces["distance"]
-    return rendered
-
-
-def render_pep440_post(pieces: dict[str, Any]) -> str:
-    """TAG[.postDISTANCE[.dev0]+gHEX] .
-
-    The ".dev0" means dirty. Note that .dev0 sorts backwards
-    (a dirty tree will appear "older" than the corresponding clean one),
-    but you shouldn't be releasing software with -dirty anyways.
-
-    Exceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%d" % pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-            rendered += plus_or_dot(pieces)
-            rendered += "g%s" % pieces["short"]
-    else:
-        # exception #1
-        rendered = "0.post%d" % pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-        rendered += "+g%s" % pieces["short"]
-    return rendered
-
-
-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.
-
-    Exceptions:
-    1: no tags. 0.postDISTANCE[.dev0]
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"] or pieces["dirty"]:
-            rendered += ".post%d" % pieces["distance"]
-            if pieces["dirty"]:
-                rendered += ".dev0"
-    else:
-        # exception #1
-        rendered = "0.post%d" % pieces["distance"]
-        if pieces["dirty"]:
-            rendered += ".dev0"
-    return rendered
-
-
-def render_git_describe(pieces: dict[str, Any]) -> str:
-    """TAG[-DISTANCE-gHEX][-dirty].
-
-    Like 'git describe --tags --dirty --always'.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        if pieces["distance"]:
-            rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-def render_git_describe_long(pieces: dict[str, Any]) -> str:
-    """TAG-DISTANCE-gHEX[-dirty].
-
-    Like 'git describe --tags --dirty --always -long'.
-    The distance/hash is unconditional.
-
-    Exceptions:
-    1: no tags. HEX[-dirty]  (note: no 'g' prefix)
-    """
-    if pieces["closest-tag"]:
-        rendered = pieces["closest-tag"]
-        rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
-    else:
-        # exception #1
-        rendered = pieces["short"]
-    if pieces["dirty"]:
-        rendered += "-dirty"
-    return rendered
-
-
-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,
-        }
-
-    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":
-        rendered = render_git_describe(pieces)
-    elif style == "git-describe-long":
-        rendered = render_git_describe_long(pieces)
-    else:
-        raise ValueError("unknown style '%s'" % style)
-
-    return {
-        "version": rendered,
-        "full-revisionid": pieces["long"],
-        "dirty": pieces["dirty"],
-        "error": None,
-        "date": pieces.get("date"),
-    }
-
-
-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
-    # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
-    # case we can only use expanded keywords.
-
-    cfg = get_config()
-    verbose = cfg.verbose
-
-    try:
-        return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose)
-    except NotThisMethod:
-        pass
-
-    try:
-        root = os.path.realpath(__file__)
-        # 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 _ 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,
-        }
-
-    try:
-        pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
-        return render(pieces, cfg.style)
-    except NotThisMethod:
-        pass
-
-    try:
-        if cfg.parentdir_prefix:
-            return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
-    except NotThisMethod:
-        pass
-
-    return {
-        "version": "0+unknown",
-        "full-revisionid": None,
-        "dirty": None,
-        "error": "unable to compute version",
-        "date": None,
-    }
diff --git a/absolv/config.py b/absolv/config.py
index 0d0af12..6b6267a 100644
--- a/absolv/config.py
+++ b/absolv/config.py
@@ -172,6 +172,18 @@ class HREMDProtocol(pydantic.BaseModel):
         "'propagate the system' -> 'exchange replicas' to run.",
     )
 
+    trajectory_interval: int | None = pydantic.Field(
+        None,
+        description="The number of cycles to run before saving the current replica "
+        "states to DCD trajectory files. If ``None``, no trajectories will be saved.",
+    )
+    trajectory_enforce_pbc: bool = pydantic.Field(
+        False,
+        description="Whether to apply periodic boundary conditions when retrieving "
+        "coordinates for writing to trajectory files.",
+    )
+
+
 
 class EquilibriumProtocol(pydantic.BaseModel):
     """Configure how an equilibrium (e.g. TI, MBAR) alchemical free energy
diff --git a/absolv/runner.py b/absolv/runner.py
index ab2754f..5a8b7bc 100644
--- a/absolv/runner.py
+++ b/absolv/runner.py
@@ -218,6 +218,8 @@ def _run_phase_hremd(
         n_warmup_steps=protocol.production_protocol.n_warmup_steps,
         n_steps_per_cycle=protocol.production_protocol.n_steps_per_cycle,
         n_cycles=protocol.production_protocol.n_cycles,
+        trajectory_interval=protocol.production_protocol.trajectory_interval,
+        trajectory_enforce_pbc=protocol.production_protocol.trajectory_enforce_pbc
     )
 
     with tempfile.TemporaryDirectory() as tmp_dir:
diff --git a/absolv/tests/test_fep.py b/absolv/tests/test_fep.py
index 431d388..a4786dc 100644
--- a/absolv/tests/test_fep.py
+++ b/absolv/tests/test_fep.py
@@ -56,9 +56,6 @@ def test_find_nonbonded_forces_lj_only(aq_nacl_lj_system):
     assert custom_bond_force is None
 
 
-@pytest.mark.xfail(
-    reason="interchange splits electrostatic force when plugins are present"
-)
 def test_find_nonbonded_forces_custom(aq_meoh_de_system):
     expected_types = (
         openmm.NonbondedForce,
diff --git a/devtools/envs/base.yaml b/devtools/envs/base.yaml
index 47f8b00..75a611c 100644
--- a/devtools/envs/base.yaml
+++ b/devtools/envs/base.yaml
@@ -49,10 +49,9 @@ dependencies:
   - mkdocs-gen-files
   - mkdocs-literate-nav
   - mkdocs-jupyter
+  - mkdocs-bibtex
   - mkdocstrings
-  - mkdocstrings-python
+  - mkdocstrings-python >=1.10.8
+  - griffe-pydantic
   - black
   - mike
-
-  - pip:
-      - mkdocs-bibtex
diff --git a/mkdocs.yml b/mkdocs.yml
index a1c8ec7..3f2ea16 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -102,13 +102,12 @@ plugins:
           - http://docs.openmm.org/latest/api-python/objects.inv
           - https://www.mdtraj.org/1.9.6/objects.inv
         options:
-          # extensions: [ griffe_pydantic ]
+          extensions: [ griffe_pydantic ]
           docstring_options:
             ignore_init_summary: true
             returns_multiple_items: false
             returns_named_value: false
           docstring_section_style: list
-          filters: ["!^_", "!^model_dump_yaml$", "!^model_config$"]
           heading_level: 1
           inherited_members: true
           merge_init_into_class: true
@@ -118,7 +117,6 @@ plugins:
           show_signature_annotations: true
           show_symbol_type_heading: true
           show_symbol_type_toc: true
-          show_if_no_docstring: false
           signature_crossrefs: true
           summary: true
           members_order: source
diff --git a/pyproject.toml b/pyproject.toml
index 8852f43..21ac86b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,30 +1,21 @@
 [build-system]
-requires = ["setuptools>=61.0", "wheel", "versioneer"]
+requires = ["setuptools>=61.0", "setuptools_scm>=8", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "absolv"
 description = "Absolute solvation free energy calculations using OpenMM"
+authors = [ {name = "Simon Boothroyd"} ]
+license = { text = "MIT" }
 dynamic = ["version"]
 readme = "README.md"
 requires-python = ">=3.10"
 classifiers = ["Programming Language :: Python :: 3"]
 
-[tool.setuptools]
-zip-safe = false
-include-package-data = false
-
 [tool.setuptools.packages.find]
-namespaces = true
-where = ["."]
+include = ["absolv*"]
 
-[tool.versioneer]
-VCS = "git"
-style = "pep440"
-versionfile_source = "absolv/_version.py"
-versionfile_build = "absolv/_version.py"
-tag_prefix = ""
-parentdir_prefix = "absolv-"
+[tool.setuptools_scm]
 
 [tool.ruff.lint]
 ignore = ["C901", "E501"]
@@ -32,7 +23,7 @@ select = ["B","C","E","F","W","B9"]
 ignore-init-module-imports = true
 
 [tool.coverage.run]
-omit = ["**/tests/*", "**/_version.py"]
+omit = ["**/tests/*"]
 
 [tool.coverage.report]
 exclude_lines = [