PyAntiGen 1.0.13__tar.gz → 1.0.15__tar.gz

{pyantigen-1.0.13 → pyantigen-1.0.15}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyAntiGen
-Version: 1.0.13
+Version: 1.0.15
 Summary: Short one-line description of what PyAntiGen does
 Author: Open Source Contributor
 Author-email: Don <you@example.com>

{pyantigen-1.0.13 → pyantigen-1.0.15}/PyAntiGen.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyAntiGen
-Version: 1.0.13
+Version: 1.0.15
 Summary: Short one-line description of what PyAntiGen does
 Author: Open Source Contributor
 Author-email: Don <you@example.com>

{pyantigen-1.0.13 → pyantigen-1.0.15}/PyAntiGen.egg-info/SOURCES.txt

@@ -39,6 +39,7 @@ framework/template/Example/Model_generate.py
 framework/template/Example/Model_run.py
 framework/template/Example/Engine/Anchor_cache.py
 framework/template/Example/Engine/Deadline.py
+framework/template/Example/Engine/Differential_evolution.py
 framework/template/Example/Engine/Evaluator.py
 framework/template/Example/Engine/Event_times.py
 framework/template/Example/Engine/Fast_profile.py
@@ -46,11 +47,13 @@ framework/template/Example/Engine/Fit_cache.py
 framework/template/Example/Engine/Identifiability.py
 framework/template/Example/Engine/Model_optimize.py
 framework/template/Example/Engine/Model_simulate.py
-framework/template/Example/Engine/Nuisance_sensitivity.py
+framework/template/Example/Engine/Nelder_mead.py
+framework/template/Example/Engine/Noise_floor.py
 framework/template/Example/Engine/Optimize.py
 framework/template/Example/Engine/Petab_export.py
 framework/template/Example/Engine/Preequil_cache.py
 framework/template/Example/Engine/Profile_checkpoint.py
+framework/template/Example/Engine/README.md
 framework/template/Example/Engine/Results.py
 framework/template/Example/Engine/Sensitivity_analysis.py
 framework/template/Example/Engine/Simulate.py

{pyantigen-1.0.13 → pyantigen-1.0.15}/PyAntiGen.egg-info/scm_file_list.json

@@ -27,6 +27,7 @@
     "framework/template/Example/AntiGen_paths.py",
     "framework/template/Example/Engine/Anchor_cache.py",
     "framework/template/Example/Engine/Deadline.py",
+    "framework/template/Example/Engine/Differential_evolution.py",
     "framework/template/Example/Engine/Evaluator.py",
     "framework/template/Example/Engine/Event_times.py",
     "framework/template/Example/Engine/Fast_profile.py",
@@ -34,11 +35,13 @@
     "framework/template/Example/Engine/Identifiability.py",
     "framework/template/Example/Engine/Model_optimize.py",
     "framework/template/Example/Engine/Model_simulate.py",
-    "framework/template/Example/Engine/Nuisance_sensitivity.py",
+    "framework/template/Example/Engine/Nelder_mead.py",
+    "framework/template/Example/Engine/Noise_floor.py",
     "framework/template/Example/Engine/Optimize.py",
     "framework/template/Example/Engine/Petab_export.py",
     "framework/template/Example/Engine/Preequil_cache.py",
     "framework/template/Example/Engine/Profile_checkpoint.py",
+    "framework/template/Example/Engine/README.md",
     "framework/template/Example/Engine/Results.py",
     "framework/template/Example/Engine/Sensitivity_analysis.py",
     "framework/template/Example/Engine/Simulate.py",

pyantigen-1.0.15/PyAntiGen.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "1.0.15",
+  "distance": 0,
+  "node": "gd95e4a4f4c02ea9c4988d93cc24ff19529147f0c",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-09-30"
+}

{pyantigen-1.0.13 → pyantigen-1.0.15}/framework/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '1.0.13'
-__version_tuple__ = version_tuple = (1, 0, 13)
+__version__ = version = '1.0.15'
+__version_tuple__ = version_tuple = (1, 0, 15)
 
-__commit_id__ = commit_id = 'ga5c2cee6b'
+__commit_id__ = commit_id = 'gd95e4a4f4'

pyantigen-1.0.15/framework/template/Example/Engine/Deadline.py

@@ -0,0 +1,262 @@
+"""An optional wall-clock stop time, and nothing that tries to predict the future.
+
+What this is *not* for. It is not what keeps a run alive on a preemptible
+partition. Hyak's ``ckpt`` partitions stop a job without notice and with no
+grace period, and the time limit Slurm reports (``SLURM_JOB_END_TIME``) is not
+when that happens, so no amount of watching the clock can say when the job will
+die. What makes a kill survivable is that the optimizers write their state as
+they go -- see :mod:`Engine.Nelder_mead` -- so at any instant the copy on disk
+is at most a couple of evaluations old. Given that, there is nothing left for a
+deadline to protect against on ckpt, and this module deliberately does nothing
+there.
+
+What it is for. Two cases where the end *is* known and stopping tidily is worth
+a little:
+
+* ``--wall-time`` (or ``PROFILE_WALL_TIME``), an explicit budget, which is how
+  one asks for a shorter run than the allocation on a laptop or in a test.
+* A partition that runs to its ``--time`` limit and is never preempted, where
+  ``SLURM_JOB_END_TIME`` really is the end.
+
+In both, the point of stopping a little early is the write-up: the trace
+assembly, the plots and the results file take real time, and a run that is
+killed in the middle of them has computed everything and reported nothing.
+So the run stops handing out work ``margin_s`` before the end, lets every point
+in flight save its state at its next evaluation and return, and reports what it
+has as ``INCOMPLETE``.
+
+A wrong answer here is cheap by construction. A stop time that comes out too
+early makes the run end early and say so; one that comes out too late means the
+job is killed while working, which the state on disk already survives. Neither
+loses a computed point, which is why none of the source-ranking, staleness
+detection or fallback logic this file used to carry is needed any more.
+
+Off a scheduler with no flag, :func:`resolve_deadline` returns ``None``, every
+check passes, and the run behaves exactly as it always did.
+"""
+
+import os
+import time
+
+# How long before the end the run stops handing out work. It has to cover what
+# happens *after* the last point lands: the pool shutdown, trace assembly,
+# plotting and the results write, none of which are instant on a large spec.
+DEFAULT_MARGIN_S = 600.0
+
+# Set by Model_run.py from --wall-time. An environment variable rather than a
+# threaded argument because the only consumer sits at the bottom of a call chain
+# that would otherwise need the flag added to a dozen signatures for it.
+WALL_TIME_ENV = "PROFILE_WALL_TIME"
+MARGIN_ENV = "PROFILE_DEADLINE_MARGIN"
+
+
+class DeadlineReached(RuntimeError):
+    """Raised when the wall budget stopped a batch before its jobs were done.
+
+    Carries how much work was left so the caller can say so plainly. This is a
+    normal, successful outcome of a run with a stop time -- not a failure -- and
+    callers are expected to catch it, finish reporting on what they have, and
+    exit 0.
+    """
+
+    def __init__(self, n_remaining, label=None):
+        self.n_remaining = int(n_remaining)
+        self.label = label
+        where = f" in {label}" if label else ""
+        super().__init__(
+            f"wall-clock budget reached with {self.n_remaining} point(s) "
+            f"not started{where}"
+        )
+
+
+# ---------------------------------------------------------------------------
+# Parsing and discovery
+# ---------------------------------------------------------------------------
+
+def parse_duration(text):
+    """Seconds from ``4h``, ``3.5h``, ``90m``, ``45s``, ``4:00:00`` or ``1-12:00:00``.
+
+    A bare number is seconds. That differs from ``sbatch --time``, where a bare
+    number is minutes, so prefer an explicit suffix when writing one by hand.
+    Returns None for anything unparseable, which the callers treat as "no
+    budget" rather than as an error -- a malformed value must not take down a
+    run that would otherwise have completed.
+    """
+    if text is None:
+        return None
+    if isinstance(text, (int, float)):
+        return float(text) if text > 0 else None
+
+    s = str(text).strip().lower()
+    if not s:
+        return None
+
+    days = 0.0
+    if "-" in s:
+        head, _, s = s.partition("-")
+        try:
+            days = float(head)
+        except ValueError:
+            return None
+
+    try:
+        if ":" in s:
+            parts = [float(p) for p in s.split(":")]
+            if len(parts) > 3:
+                return None
+            while len(parts) < 3:
+                parts.insert(0, 0.0)
+            h, m, sec = parts
+            total = h * 3600.0 + m * 60.0 + sec
+        elif s[-1] in "smhd":
+            mult = {"s": 1.0, "m": 60.0, "h": 3600.0, "d": 86400.0}[s[-1]]
+            total = float(s[:-1]) * mult
+        else:
+            total = float(s)
+    except (ValueError, IndexError):
+        return None
+
+    total += days * 86400.0
+    return total if total > 0 else None
+
+
+def partition_is_preemptible():
+    """Whether this job can be evicted before its time limit.
+
+    On Hyak the checkpoint partitions -- ``ckpt``, ``ckpt-g2``, ``ckpt-all`` --
+    run on other groups' idle nodes and are stopped without notice when an owner
+    reclaims them. Every other partition runs to its ``--time`` and is not
+    preempted. Read from the partition name because that is the only thing Slurm
+    exposes that distinguishes the two; off a scheduler there is nothing to be
+    preempted by, so the answer is False.
+    """
+    partition = (os.environ.get("SLURM_JOB_PARTITION") or "").lower()
+    return "ckpt" in partition
+
+
+def resolve_deadline(wall_time=None, now=None, verbose=True):
+    """Absolute epoch time this process should be finished by, or None.
+
+    In order:
+
+    1. *wall_time*, else ``PROFILE_WALL_TIME`` -- an explicit budget measured
+       from now. It wins over the scheduler because it is how someone asks for a
+       shorter run than the allocation allows, and because it is the only source
+       that exists on a laptop.
+    2. ``SLURM_JOB_END_TIME``, but only on a partition that is not preempted.
+       On ckpt the job's real end is an eviction that this cannot see, the
+       reported limit is days away, and on a requeued job the variable has been
+       seen to carry a value left over from an earlier attempt. Nothing is lost
+       by ignoring it there -- state is written as the run goes -- and a
+       plausible-looking wrong end time is the one thing here that could make
+       a healthy run stop early.
+
+    None means no stop time, which turns every downstream check into a no-op.
+    """
+    now = time.time() if now is None else now
+
+    budget = parse_duration(wall_time)
+    label = None
+    if budget is None:
+        raw_env = os.environ.get(WALL_TIME_ENV)
+        budget = parse_duration(raw_env)
+        if raw_env:
+            label = f"{WALL_TIME_ENV}={raw_env!r}"
+    elif wall_time:
+        label = f"--wall-time {wall_time!r}"
+    if budget is not None:
+        end = now + budget
+        if verbose:
+            print(f"[deadline] stop time from {label}: {_fmt_epoch(end)} "
+                  f"({budget / 60.0:.0f} min from now)", flush=True)
+        return end
+
+    if partition_is_preemptible():
+        if verbose:
+            print("[deadline] preemptible partition: no stop time. Nothing "
+                  "here can predict an eviction, and every optimizer saves "
+                  "its state as it goes, so a kill costs a couple of "
+                  "evaluations either way.", flush=True)
+        return None
+
+    raw = os.environ.get("SLURM_JOB_END_TIME")
+    try:
+        end = float(raw) if raw else None
+    except ValueError:
+        end = None
+    if end is not None and end > now:
+        if verbose:
+            print(f"[deadline] stop time from SLURM_JOB_END_TIME: "
+                  f"{_fmt_epoch(end)} ({(end - now) / 60.0:.0f} min from now)",
+                  flush=True)
+        return end
+    return None
+
+
+def _fmt_epoch(t):
+    """Local-time rendering of an epoch float, for a human reading a log."""
+    try:
+        return time.strftime("%Y-%m-%dT%H:%M:%S", time.localtime(t))
+    except (OSError, OverflowError, ValueError):
+        return repr(t)
+
+
+def _default_margin():
+    return parse_duration(os.environ.get(MARGIN_ENV)) or DEFAULT_MARGIN_S
+
+
+class RunBudget:
+    """How much of this run's wall clock is left before it should stop.
+
+    Deliberately small: a stop time and a margin, and the two questions worth
+    asking of them -- "may another point start?" and "when must a running point
+    stop?". An unset deadline makes both permissive, so the same object can be
+    constructed unconditionally and passed everywhere.
+
+    There is no estimate of what a point costs. The old admission rule refused a
+    point that would not fit, which is exactly what made it wrong: a point can
+    be resumed from wherever it is stopped, so starting one with ten minutes to
+    spare is not a loss, and refusing it on a guess is.
+    """
+
+    def __init__(self, deadline=None, margin_s=None):
+        self.deadline = deadline
+        self.margin_s = _default_margin() if margin_s is None else float(margin_s)
+        # Set once a batch has been cut short, so the run can report honestly
+        # that it stopped for time rather than because the work was done.
+        self.stopped_early = False
+
+    @property
+    def is_limited(self):
+        return self.deadline is not None
+
+    def remaining(self, now=None):
+        """Seconds left before the deadline; ``inf`` when there is none."""
+        if self.deadline is None:
+            return float("inf")
+        return self.deadline - (time.time() if now is None else now)
+
+    def work_deadline(self):
+        """The last moment this run may still be computing, or None.
+
+        Leaves the margin for trace assembly, plotting and the results write.
+        Running points are told to stop here; None means run to convergence.
+        """
+        if self.deadline is None:
+            return None
+        return self.deadline - self.margin_s
+
+    def admits(self, now=None):
+        """Whether another point may be started."""
+        if self.deadline is None:
+            return True
+        return self.remaining(now) > self.margin_s
+
+    def describe(self):
+        """One line for the log, saying what the budget will actually do."""
+        if self.deadline is None:
+            return "no wall-clock stop time; running until the work is done"
+        return (f"{self.remaining() / 60.0:.0f} min left, "
+                f"{self.margin_s / 60.0:.0f} min of it reserved for the "
+                f"write-up; no new point starts after that, and running points "
+                f"save their state and stop at it")