factorforge-cds 3.1.4__tar.gz → 3.1.6__tar.gz

{factorforge_cds-3.1.4/src/factorforge_cds.egg-info → factorforge_cds-3.1.6}/PKG-INFO

@@ -1,13 +1,13 @@
 Metadata-Version: 2.4
 Name: factorforge-cds
-Version: 3.1.4
+Version: 3.1.6
 Summary: FactorForge - open-source constraint-based CDS design engine by Eijex.
 Author-email: Eijex <eijex.lab@gmail.com>
 License-Expression: AGPL-3.0-only
 Project-URL: Homepage, https://factorforge-cds.vercel.app
 Project-URL: Repository, https://github.com/eijex/factorforge-cds
 Project-URL: Issues, https://github.com/eijex/factorforge-cds/issues
-Keywords: codon optimization,CDS design,synthetic biology,bioinformatics,Nicotiana benthamiana,constraint optimization,dynamic programming
+Keywords: codon optimization,CDS design,synthetic biology,bioinformatics,Nicotiana benthamiana,Nicotiana tabacum,Tobacco BY-2,constraint optimization,dynamic programming
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
 Classifier: Programming Language :: Python :: 3
@@ -24,19 +24,24 @@ Requires-Dist: pytest>=7.0; extra == "dev"
 Requires-Dist: pytest-cov>=4.0; extra == "dev"
 Requires-Dist: ruff>=0.1; extra == "dev"
 Requires-Dist: pyyaml>=6.0; extra == "dev"
+Provides-Extra: ml
+Requires-Dist: transformers>=4.40; extra == "ml"
+Requires-Dist: torch>=2.0; extra == "ml"
 Dynamic: license-file
 
 # FactorForge
 
-**Open-source constraint-based CDS design engine for *Nicotiana benthamiana* expression workflows.**
+**Open-source constraint-based CDS design engine for plant expression workflows, with initial focus on *Nicotiana benthamiana* and Tobacco BY-2.**
 
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-3.1.4-green.svg)](https://github.com/eijex/factorforge-cds/releases)
 [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
+[![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407331.svg)](https://doi.org/10.5281/zenodo.20407331)
 [![Web App](https://img.shields.io/badge/web-factorforge--cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
 
-FactorForge optimizes protein sequences into *N. benthamiana*-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs.
+FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports *N. benthamiana* (agroinfiltration) and Tobacco BY-2 (`--host by2`, bioreactor/cGMP workflows).
 
 **→ [Full Documentation](https://eijex.github.io/factorforge-cds/)**
 
@@ -86,7 +91,7 @@ FactorForge has gone through several implementation generations before the curre
 | **v2** — Rule-Based Engine | Internal → Production | Deterministic, constraint-aware design engine; became the foundation for the public release |
 | **v3-alpha** — ML Prototype | Archived | ML-based design attempt; performance was insufficient for production use; preserved under `archive/v3-ml-prototype/` |
 | **v3.0+** — Current release | Public | Open-source release of the matured v2 engine under `factorforge.engines.profile` |
-| **v4** — ML Research Track | Planned | Future ML re-attempt with improved data and architecture |
+| **v3.7+** — ML Engine | Planned | ML-based design as `--engine ml`; added once sufficient wet-lab data is available |
 
 The `archive/` directory preserves all three earlier tracks for provenance. None are installed or exposed by the current package.
 
@@ -101,7 +106,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
 ## Citing
 
 ```
-FactorForge v3.1.4 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.1.6 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.1.4 → factorforge_cds-3.1.6}/README.md

@@ -1,14 +1,16 @@
 # FactorForge
 
-**Open-source constraint-based CDS design engine for *Nicotiana benthamiana* expression workflows.**
+**Open-source constraint-based CDS design engine for plant expression workflows, with initial focus on *Nicotiana benthamiana* and Tobacco BY-2.**
 
 [![License](https://img.shields.io/badge/license-AGPL--3.0-blue.svg)](LICENSE)
 [![Python](https://img.shields.io/badge/python-3.10%2B-blue.svg)](https://www.python.org/)
-[![Version](https://img.shields.io/badge/version-3.1.4-green.svg)](https://github.com/eijex/factorforge-cds/releases)
 [![PyPI](https://img.shields.io/pypi/v/factorforge-cds.svg)](https://pypi.org/project/factorforge-cds/)
+[![CI](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml/badge.svg)](https://github.com/eijex/factorforge-cds/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/eijex/factorforge-cds/branch/main/graph/badge.svg)](https://codecov.io/gh/eijex/factorforge-cds)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20407331.svg)](https://doi.org/10.5281/zenodo.20407331)
 [![Web App](https://img.shields.io/badge/web-factorforge--cds.vercel.app-brightgreen.svg)](https://factorforge-cds.vercel.app)
 
-FactorForge optimizes protein sequences into *N. benthamiana*-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs.
+FactorForge optimizes protein sequences into host-compatible CDS by maximizing CAI, controlling GC content, eliminating PolyA signals, and producing MoClo/Golden Gate-ready constructs. Supports *N. benthamiana* (agroinfiltration) and Tobacco BY-2 (`--host by2`, bioreactor/cGMP workflows).
 
 **→ [Full Documentation](https://eijex.github.io/factorforge-cds/)**
 
@@ -58,7 +60,7 @@ FactorForge has gone through several implementation generations before the curre
 | **v2** — Rule-Based Engine | Internal → Production | Deterministic, constraint-aware design engine; became the foundation for the public release |
 | **v3-alpha** — ML Prototype | Archived | ML-based design attempt; performance was insufficient for production use; preserved under `archive/v3-ml-prototype/` |
 | **v3.0+** — Current release | Public | Open-source release of the matured v2 engine under `factorforge.engines.profile` |
-| **v4** — ML Research Track | Planned | Future ML re-attempt with improved data and architecture |
+| **v3.7+** — ML Engine | Planned | ML-based design as `--engine ml`; added once sufficient wet-lab data is available |
 
 The `archive/` directory preserves all three earlier tracks for provenance. None are installed or exposed by the current package.
 
@@ -73,7 +75,7 @@ FactorForge predictions are **in-silico only** and have not been experimentally
 ## Citing
 
 ```
-FactorForge v3.1.4 (2026). Open-source constraint-based CDS design engine.
+FactorForge v3.1.6 (2026). Open-source constraint-based CDS design engine.
 Eijex. https://github.com/eijex/factorforge-cds
 ```
 

{factorforge_cds-3.1.4 → factorforge_cds-3.1.6}/pyproject.toml

@@ -4,14 +4,14 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "factorforge-cds"
-version = "3.1.4"
+version = "3.1.6"
 description = "FactorForge - open-source constraint-based CDS design engine by Eijex."
 readme = "README.md"
 license = "AGPL-3.0-only"
 license-files = ["LICENSE"]
 requires-python = ">=3.10"
 authors = [{ name = "Eijex", email = "eijex.lab@gmail.com" }]
-keywords = ["codon optimization", "CDS design", "synthetic biology", "bioinformatics", "Nicotiana benthamiana", "constraint optimization", "dynamic programming"]
+keywords = ["codon optimization", "CDS design", "synthetic biology", "bioinformatics", "Nicotiana benthamiana", "Nicotiana tabacum", "Tobacco BY-2", "constraint optimization", "dynamic programming"]
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Science/Research",
@@ -33,6 +33,10 @@ dev = [
     "ruff>=0.1",
     "pyyaml>=6.0",
 ]
+ml = [
+    "transformers>=4.40",
+    "torch>=2.0",
+]
 
 [project.urls]
 Homepage = "https://factorforge-cds.vercel.app"
@@ -46,6 +50,9 @@ factorforge-validate = "factorforge.validation.cli:main"
 [tool.setuptools.packages.find]
 where = ["src"]
 
+[tool.setuptools.package-data]
+"factorforge" = ["data/*.json", "data/templates/*.json", "schemas/*.json"]
+
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 norecursedirs = ["archive"]

{factorforge_cds-3.1.4 → factorforge_cds-3.1.6}/src/factorforge/__init__.py

@@ -4,7 +4,7 @@ FactorForge - Codon Optimization Platform
 profile: constraint-aware rule/profile engine
 """
 
-__version__ = "3.1.4"
+__version__ = "3.1.6"
 __author__ = "Eijex"
 
 # Auto-register engines (safe when running from source tree)

{factorforge_cds-3.1.4 → factorforge_cds-3.1.6}/src/factorforge/analysis/metrics.py

@@ -9,6 +9,8 @@ from dataclasses import dataclass
 from pathlib import Path
 from typing import Any
 
+from factorforge.engines.profile.utils import get_data_path
+
 
 STANDARD_GENETIC_CODE: dict[str, str] = {
     "TTT": "F",
@@ -90,7 +92,7 @@ class CodonUsageTable:
 
 
 def _default_codon_table_path() -> Path:
-    return Path(__file__).resolve().parents[3] / "data" / "nbenthamiana_codons.json"
+    return get_data_path() / "nbenthamiana_codons.json"
 
 
 def load_codon_usage_table(path: Path | None = None) -> CodonUsageTable:

{factorforge_cds-3.1.4 → factorforge_cds-3.1.6}/src/factorforge/cli/main.py

@@ -16,6 +16,8 @@ from factorforge import __version__
 from factorforge.engines.registry import EngineRegistry
 from factorforge.engines.profile.utils import parse_fasta_records
 
+HOST_MAP = {"nbenthamiana": "nbenthamiana", "by2": "ntabacum"}
+
 
 def _configure_stdio() -> None:
     """Best-effort UTF-8 for Windows consoles."""
@@ -79,6 +81,49 @@ def _format_dp_fasta(sequence_id: str, dna_sequence: str, cai: float, gc: float)
     return f"{header}\n{_wrap_sequence(dna_sequence)}\n"
 
 
+def _option_was_explicitly_set(option_name: str) -> bool:
+    """Return whether an option was provided on the command line."""
+    ctx = click.get_current_context(silent=True)
+    if ctx is None:
+        return False
+    get_parameter_source = getattr(ctx, "get_parameter_source", None)
+    if not callable(get_parameter_source):
+        return False
+    return get_parameter_source(option_name) == click.core.ParameterSource.COMMANDLINE
+
+
+def _engine_option_was_explicitly_set() -> bool:
+    """Return whether --engine/-e was provided on the command line."""
+    return _option_was_explicitly_set("engine")
+
+
+def _format_profile_fasta(sequence_id: str, profile: str, result) -> str:
+    """Format a profile optimization result as FASTA."""
+    cai = float(result.metrics.get("cai", 0.0))
+    gc = float(result.metrics.get("gc_percent", result.metrics.get("gc_content", 0.0)))
+    score = float(result.metrics.get("score", 0.0))
+    header = f">{sequence_id}|profile={profile}|cai={cai:.3f}|gc={gc:.2f}|score={score:.3f}"
+    return f"{header}\n{_wrap_sequence(result.sequence)}\n"
+
+
+def _format_profile_comparison_table(profile_results) -> str:
+    """Format profile optimization metrics as a comparison table."""
+    divider = "─" * 45
+    lines = [
+        "Profile comparison results:",
+        divider,
+        f"{'Profile':<18}{'CAI':>7} {'GC%':>7} {'Score':>8}",
+        divider,
+    ]
+    for profile_name, result in profile_results:
+        cai = float(result.metrics.get("cai", 0.0))
+        gc = float(result.metrics.get("gc_percent", result.metrics.get("gc_content", 0.0)))
+        score = float(result.metrics.get("score", 0.0))
+        lines.append(f"{profile_name:<18}{cai:>7.3f} {gc:>7.2f} {score:>8.3f}")
+    lines.append(divider)
+    return "\n".join(lines)
+
+
 @click.group()
 @click.version_option(version=__version__)
 def cli():
@@ -106,6 +151,12 @@ def list_engines():
     type=click.Choice(["dp", "profile"], case_sensitive=False),
     help="Engine (dp, profile)",
 )
+@click.option(
+    "--host",
+    default="nbenthamiana",
+    type=click.Choice(["nbenthamiana", "by2"], case_sensitive=False),
+    help="Expression host: nbenthamiana (default) or by2 (Tobacco BY-2 / N. tabacum)",
+)
 @click.option("--profile", "-p", default="balanced", help="Optimization profile")
 @click.option(
     "--objective",
@@ -118,6 +169,13 @@ def list_engines():
 @click.option("--template", "construct_template", help="Construct template name")
 @click.option("--output", "-o", help="Output file")
 @click.option("--format", "output_format", default="fasta", help="Output format (fasta, genbank)")
+@click.option(
+    "--compare-profiles",
+    help=(
+        "Comma-separated profiles to compare "
+        "(e.g. balanced,high_cai,gc_target). Implies --engine profile."
+    ),
+)
 @click.option(
     "--scan-mode",
     default="full",
@@ -129,6 +187,7 @@ def list_engines():
 def optimize(
     input_file,
     engine,
+    host,
     profile,
     objective,
     gc_min,
@@ -136,11 +195,28 @@ def optimize(
     construct_template,
     output,
     output_format,
+    compare_profiles,
     scan_mode,
     scan_include,
     scan_exclude,
 ):
     """Optimize protein sequence"""
+    compare_profile_list = _parse_csv_option(compare_profiles)
+    engine = engine.lower()
+    host_value = host.lower()
+    internal_host = HOST_MAP[host_value]
+    host_was_explicit = _option_was_explicitly_set("host")
+
+    if host_was_explicit and engine == "dp" and _engine_option_was_explicitly_set():
+        raise click.UsageError("--host is only supported with --engine profile")
+    if host_was_explicit and engine == "dp" and internal_host != "nbenthamiana":
+        engine = "profile"
+
+    if compare_profile_list:
+        if engine == "dp" and _engine_option_was_explicitly_set():
+            raise click.UsageError("--compare-profiles cannot be used with --engine dp.")
+        engine = "profile"
+
     try:
         # Read file
         with open(input_file, encoding="utf-8") as f:
@@ -156,6 +232,38 @@ def optimize(
             if len(fasta_records) == 1:
                 sequence = fasta_records[0][1]
 
+        if compare_profile_list:
+            if fasta_records is not None and len(fasta_records) > 1:
+                raise ValueError("Profile comparison requires a single input sequence.")
+            if construct_template:
+                raise ValueError("Profile comparison does not support --template mode.")
+            if output_format.lower() != "fasta":
+                raise ValueError("Profile comparison only supports FASTA output.")
+
+            optimizer = EngineRegistry.get("profile")
+            profile_results = []
+            for profile_name in compare_profile_list:
+                result = optimizer.optimize(
+                    sequence,
+                    profile=profile_name,
+                    host=internal_host,
+                    scan_mode=scan_mode,
+                    scan_include=scan_include_list,
+                    scan_exclude=scan_exclude_list,
+                )
+                profile_results.append((profile_name, result))
+
+            if output:
+                first_profile, first_result = profile_results[0]
+                sequence_id = Path(input_file).stem or "factorforge_profile"
+                fasta = _format_profile_fasta(sequence_id, first_profile, first_result)
+                with open(output, "w", encoding="utf-8") as f:
+                    f.write(fasta)
+                click.echo(f"Saved to: {output}")
+
+            click.echo(_format_profile_comparison_table(profile_results))
+            return
+
         if fasta_records is not None and len(fasta_records) > 1:
             if engine == "dp":
                 raise ValueError("Multi-FASTA input requires --engine profile.")
@@ -170,6 +278,7 @@ def optimize(
                 results = optimizer.optimize_batch(
                     payload,
                     profile=profile,
+                    host=internal_host,
                     scan_mode=scan_mode,
                     scan_include=scan_include_list,
                     scan_exclude=scan_exclude_list,
@@ -179,6 +288,7 @@ def optimize(
                     optimizer.optimize(
                         seq,
                         profile=profile,
+                        host=internal_host,
                         scan_mode=scan_mode,
                         scan_include=scan_include_list,
                         scan_exclude=scan_exclude_list,
@@ -246,9 +356,14 @@ def optimize(
         if engine == "profile" and construct_template:
             from factorforge.engines.profile.pipeline import OptimizationPipeline
 
-            pipeline = OptimizationPipeline(profile=profile, construct_template=construct_template)
+            pipeline = OptimizationPipeline(
+                profile=profile,
+                construct_template=construct_template,
+                host=internal_host,
+            )
             result = pipeline.run(
                 sequence,
+                host=internal_host,
                 scan_mode=scan_mode,
                 scan_include=scan_include_list,
                 scan_exclude=scan_exclude_list,
@@ -278,6 +393,7 @@ def optimize(
             result = optimizer.optimize(
                 sequence,
                 profile=profile,
+                host=internal_host,
                 scan_mode=scan_mode,
                 scan_include=scan_include_list,
                 scan_exclude=scan_exclude_list,