hyphaeon-core 0.1.0__tar.gz

hyphaeon_core-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Sergei L. Kosakovsky Pond and HyphAeon Contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

hyphaeon_core-0.1.0/PKG-INFO

@@ -0,0 +1,51 @@
+Metadata-Version: 2.4
+Name: hyphaeon-core
+Version: 0.1.0
+Summary: Aeon-Core: Shared bioinformatics infrastructure for Aeon-family packages
+Author-email: "Sergei L. Kosakovsky Pond" <spond@temple.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/veg/HyphAeon
+Project-URL: Bug Tracker, https://github.com/veg/HyphAeon/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.0.0
+Requires-Dist: biopython>=1.80
+Requires-Dist: numpy>=1.22.0
+Requires-Dist: scipy>=1.9.0
+Requires-Dist: pandas>=1.5.0
+Requires-Dist: huggingface-hub>=0.20.0
+Requires-Dist: safetensors>=0.4.0
+Provides-Extra: tn93
+Requires-Dist: tn93>=1.2.0; extra == "tn93"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Dynamic: license-file
+
+# aeon-core
+
+Shared infrastructure for the HyphAeon family of packages (HyphAeon, ChronAeon).
+
+Contains the `PhyloAxialTransformer` foundation model, pretrained weight resolution (HuggingFace Hub), and core utilities for alignment processing, inference, spectral splits, temporal parsing, I/O, and statistics.
+
+## Installation
+
+```bash
+pip install hyphaeon-core
+```
+
+## Components
+
+- **`model`** — `PhyloAxialTransformer`, `BustedMultiTaskHead`, `decode_soft_ordinal_lrt`
+- **`weights`** — Weight resolution from HuggingFace Hub (`datamonkey/hyphaeon`), safetensors loading
+- **`inference`** — Device management, adaptive batch sizing, model loading, alignment preparation
+- **`dataset`** — Alignment parsing, TN93 distance matrices, tree handling, MDS coordinates
+- **`splits`** — Cross-taxa attention extraction, fused affinity matrices
+- **`temporal`** — Date parsing utilities (`parse_date_to_decimal`, `extract_date_from_string`)
+- **`io`** — JSON/CSV writers, directory helpers
+- **`stats`** — LRT p-value computation, Benjamini-Hochberg, Cauchy combination
+- **`_progress`** — `ChunkProgress` progress bar utility

hyphaeon_core-0.1.0/README.md

@@ -0,0 +1,23 @@
+# aeon-core
+
+Shared infrastructure for the HyphAeon family of packages (HyphAeon, ChronAeon).
+
+Contains the `PhyloAxialTransformer` foundation model, pretrained weight resolution (HuggingFace Hub), and core utilities for alignment processing, inference, spectral splits, temporal parsing, I/O, and statistics.
+
+## Installation
+
+```bash
+pip install hyphaeon-core
+```
+
+## Components
+
+- **`model`** — `PhyloAxialTransformer`, `BustedMultiTaskHead`, `decode_soft_ordinal_lrt`
+- **`weights`** — Weight resolution from HuggingFace Hub (`datamonkey/hyphaeon`), safetensors loading
+- **`inference`** — Device management, adaptive batch sizing, model loading, alignment preparation
+- **`dataset`** — Alignment parsing, TN93 distance matrices, tree handling, MDS coordinates
+- **`splits`** — Cross-taxa attention extraction, fused affinity matrices
+- **`temporal`** — Date parsing utilities (`parse_date_to_decimal`, `extract_date_from_string`)
+- **`io`** — JSON/CSV writers, directory helpers
+- **`stats`** — LRT p-value computation, Benjamini-Hochberg, Cauchy combination
+- **`_progress`** — `ChunkProgress` progress bar utility

hyphaeon_core-0.1.0/pyproject.toml

@@ -0,0 +1,43 @@
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "hyphaeon-core"
+version = "0.1.0"
+authors = [
+  { name="Sergei L. Kosakovsky Pond", email="spond@temple.edu" },
+]
+description = "Aeon-Core: Shared bioinformatics infrastructure for Aeon-family packages"
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "MIT" }
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: OS Independent",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+]
+dependencies = [
+    "torch>=2.0.0",
+    "biopython>=1.80",
+    "numpy>=1.22.0",
+    "scipy>=1.9.0",
+    "pandas>=1.5.0",
+    "huggingface-hub>=0.20.0",
+    "safetensors>=0.4.0",
+]
+
+[project.optional-dependencies]
+tn93 = ["tn93>=1.2.0"]
+dev = ["pytest>=7.0"]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+
+[project.urls]
+"Homepage" = "https://github.com/veg/HyphAeon"
+"Bug Tracker" = "https://github.com/veg/HyphAeon/issues"

hyphaeon_core-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

hyphaeon_core-0.1.0/src/aeon_core/__init__.py

@@ -0,0 +1,51 @@
+"""
+Aeon-Core: Shared model and bioinformatics infrastructure for Aeon-family packages.
+"""
+
+from .model import PhyloAxialTransformer, BustedMultiTaskHead, decode_soft_ordinal_lrt
+from .weights import (
+    resolve_weights_path, load_arch_config, load_weights,
+    load_model_config, list_available_variants, print_available_variants, get_variant_filename,
+    HF_REPO_ID, DEFAULT_VARIANT, CACHE_DIR,
+)
+from .inference import (
+    get_device, get_device_memory_budget,
+    get_live_available_memory, compute_live_adaptive_chunk_sizes,
+    compute_adaptive_safe_batch_size,
+    load_model, prepare_alignment,
+)
+from .splits import (
+    extract_cross_taxa_attentions_and_embeddings,
+    compute_fused_affinity_matrix,
+)
+from .dataset import (
+    GENETIC_CODE, CODON_TO_AA, AA_MAP,
+    get_codon_token, get_aa_token,
+    parse_alignment_sequences,
+    compute_tn93_distance_matrix,
+    compute_tn93_cross_distance_matrix,
+    parse_beast_xml,
+    extract_tree_from_string_or_file,
+    has_nonzero_branch_lengths,
+    estimate_tree_branch_lengths_hyphy,
+    enforce_nonzero_branch_lengths,
+    compute_fast_dist_matrix,
+    compute_mds_coordinates,
+    downsample_taxa_faith_pd,
+    prune_identical_sequences,
+    load_alignment_and_tree,
+)
+from .temporal import (
+    parse_date_to_decimal,
+    parse_dates_from_auspice_json,
+    extract_date_from_string,
+)
+from .io import ensure_parent_directory, write_json, write_csv, format_pq
+from .stats import (
+    pvals_from_lrt_meme,
+    pvals_from_lrt_self_liang,
+    benjamini_hochberg,
+    cauchy_combination_p,
+)
+
+__version__ = "0.1.0"

hyphaeon_core-0.1.0/src/aeon_core/_progress.py

@@ -0,0 +1,81 @@
+"""
+Shared live progress bar for model-running subcommands.
+
+A single reusable carriage-return progress bar lifted faithfully from the
+filter baseline/re-eval bars (filter.py) and the DMS bar (epistasis.py). Every
+per-chunk inference loop that just needs the plain "codon x/n, %, rate,
+elapsed, ETA" bar should construct a ``ChunkProgress`` and call ``.update()``
+per chunk and ``.finish()`` at the end.
+
+The richer DMS-specific bar (adds mut/s + running mean plasticity Phi) stays
+in ``run_insilico_selection_dms`` as-is; this generic helper covers the plain
+inference loops (predict, busted single-file, disease, phenotype/epistasis
+attribution).
+
+TTY vs non-TTY behaviour mirrors the DMS bar:
+  * on a TTY it rewrites a single line via carriage-return + clear-to-EOL;
+  * otherwise it prints a fresh (flushed) line so progress is visible under
+    SLURM logs / pipes.
+"""
+
+import sys
+import time
+
+
+class ChunkProgress:
+    """Reusable per-chunk live progress bar.
+
+    Parameters
+    ----------
+    total : int
+        Total number of units to process (e.g. number of variable codons).
+    label : str
+        Bracketed label shown at the start of the bar, e.g. ``"Predict"``.
+    unit : str
+        Unit name printed in the bar (default ``"codon"``).
+    enabled : bool
+        When False, all methods are no-ops (mirrors the ``progress`` flag).
+    """
+
+    def __init__(self, total, label, unit="codon", enabled=True):
+        self.total = int(total)
+        self.label = label
+        self.unit = unit
+        self.enabled = bool(enabled)
+        self.t_start = time.time()
+        self.is_tty = sys.stdout.isatty()
+
+    def update(self, done):
+        """Report ``done`` units completed; throttled to >=0.5s or completion."""
+        if not self.enabled:
+            return
+        now = time.time()
+        # Throttle refreshes to avoid flooding logs; always emit on completion.
+        last = getattr(self, "_last_update", None)
+        if last is not None and done < self.total and (now - last) < 0.5:
+            return
+        self._last_update = now
+
+        done = int(done)
+        pct = (done / max(1, self.total)) * 100.0
+        elapsed = now - self.t_start
+        rate = done / max(1e-3, elapsed)
+        eta = (self.total - done) / max(1e-3, rate)
+        line = (
+            f"[{self.label}] {self.unit} {done:5d}/{self.total:5d} "
+            f"({pct:5.1f}%) | {rate:6.1f} {self.unit}/s | "
+            f"Elapsed: {elapsed:5.1f}s | ETA: {eta:5.1f}s"
+        )
+        if self.is_tty:
+            sys.stdout.write("\r\033[K" + line)
+            sys.stdout.flush()
+        else:
+            print(line, flush=True)
+
+    def finish(self):
+        """Emit the trailing newline on a TTY so the bar line is not overwritten."""
+        if not self.enabled:
+            return
+        if self.is_tty:
+            sys.stdout.write("\n")
+            sys.stdout.flush()