CodonAdaptPy 1.0.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

codonadaptpy/__init__.py

@@ -1,10 +1,10 @@
 """
 CodonAdaptPy Package
 
-CodonAdaptPy is an integrated, class-based Python toolkit for validating
+CodonAdaptPy is a Python package for validating
 coding sequences, calculating codon-usage and host-adaptation statistics,
 performing comparative and evolutionary analyses, generating reproducible
-reports, and designing constrained optimized or deoptimized coding sequences.
+reports, and designing synonymous coding sequences under user-defined constraints.
 
 Features:
     - FASTA, GenBank, tabular, pasted-sequence, and batch input workflows
@@ -22,7 +22,7 @@ Scientific interpretation:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from .__version__ import __author__, __email__, __version__

codonadaptpy/__main__.py

@@ -9,7 +9,7 @@ This module makes ``python -m codonadaptpy`` equivalent to the installed
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from .cli import main

codonadaptpy/__version__.py

@@ -13,9 +13,9 @@ Constants:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
-__version__ = "1.0.0"
+__version__ = "1.0.1"
 __author__ = "Naveen Duhan"
 __email__ = ""

codonadaptpy/aggregation.py

@@ -8,12 +8,12 @@ a raw multi-ORF genome as one continuous reading frame.
 
 Classes:
     - IsolateAnalysis: Per-gene, genome-wide, and focus-gene results.
-    - CDSAggregator: Metadata-aware orchestration for isolate collections.
+    - CDSAggregator: Metadata-aware analysis of isolate collections.
 
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/analyzer.py

@@ -1,7 +1,7 @@
 """
-CodonAdaptPy Analysis Orchestration
+CodonAdaptPy Analysis Interface
 
-This module exposes the primary class-based Python API. :class:`CodonAnalyzer`
+This module exposes the primary high-level Python API. :class:`CodonAnalyzer`
 coordinates normalization, validation, intrinsic metrics, optional reference-
 dependent adaptation statistics, multi-host comparisons, simulation, and
 sliding-window profiles while keeping each calculation module independently
@@ -14,7 +14,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -55,7 +55,7 @@ class AnalysisConfig:
 
 
 class CodonAnalyzer:
-    """Run complete codon-usage and adaptation analyses through one API."""
+    """Coordinate codon-usage and adaptation analyses through one interface."""
 
     def __init__(
         self,
@@ -85,7 +85,7 @@ class CodonAnalyzer:
                 )
 
     def analyze(self, record: SequenceRecord) -> AnalysisResult:
-        """Analyze one sequence and return a complete structured result."""
+        """Analyze one sequence and return a structured result."""
 
         validation = self.validator.validate(record, raise_on_error=self.config.strict)
         sequence = validation.normalized_sequence

codonadaptpy/cli.py

@@ -1,12 +1,12 @@
 """
 CodonAdaptPy Command-Line Interface
 
-This module exposes standalone subcommands for complete sequence analysis,
+This module provides commands for coding-sequence analysis,
 multi-host comparison, reference construction/cataloging, and constrained
 optimization or deoptimization. It also exposes MAFFT/trimAL/IQ-TREE/FastTree
 phylogenetics with ETE3-backed static tree and temporal-diagnostic figures.
-CLI workflows call the same class-based API
-used by Python callers and write reproducible, structured output directories.
+CLI workflows use the same public Python API as direct Python calls and write
+reproducible, structured output directories.
 
 Commands:
     - analyze: Analyze one sequence or a batch input file.
@@ -22,7 +22,7 @@ Functions:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -49,7 +49,7 @@ from .visualization import PlotManager
 
 
 def build_parser() -> argparse.ArgumentParser:
-    """Construct the top-level parser and all standalone subcommands."""
+    """Construct the top-level parser and its subcommands."""
 
     parser = argparse.ArgumentParser(
         prog="codonadaptpy",
@@ -62,7 +62,7 @@ def build_parser() -> argparse.ArgumentParser:
     _add_analysis_arguments(analyze)
     analyze.set_defaults(handler=_run_analyze)
 
-    compare = subparsers.add_parser("compare", help="Compare sequences with multiple host references.")
+    compare = subparsers.add_parser("compare", help="Compare sequences against multiple host references.")
     _add_analysis_arguments(compare)
     compare.set_defaults(handler=_run_analyze)
 

codonadaptpy/comparative.py

@@ -13,7 +13,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/exceptions.py

@@ -15,7 +15,7 @@ Exceptions:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 

codonadaptpy/genetic_code.py

@@ -17,7 +17,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/metrics/__init__.py

@@ -8,7 +8,7 @@ pairs, host comparison, and evolutionary diagnostics.
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from .adaptation import AdaptationMetrics

codonadaptpy/metrics/adaptation.py

@@ -12,7 +12,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/metrics/composition.py

@@ -12,7 +12,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/metrics/evolutionary.py

@@ -11,7 +11,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/metrics/host.py

@@ -12,7 +12,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -64,7 +64,7 @@ class HostComparator:
         self.adaptation = AdaptationMetrics(self.genetic_code)
 
     def compare(self, codons: list[str], reference: Mapping[str, float]) -> dict[str, float]:
-        """Calculate a complete host-comparison result for one reference."""
+        """Calculate a structured host-comparison result for one reference."""
 
         keys = sorted(codon for codon, aa in self.genetic_code.forward_table.items() if aa != "*")
         query_frequency = self.usage.frequencies(codons)

codonadaptpy/metrics/pairs.py

@@ -11,7 +11,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/metrics/usage.py

@@ -12,7 +12,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -32,7 +32,7 @@ class CodonUsageMetrics:
         self.genetic_code = genetic_code or GeneticCode.from_ncbi(1)
 
     def counts(self, codons: Iterable[str], *, include_stops: bool = False) -> dict[str, int]:
-        """Count unambiguous recognized codons and return a complete 64-codon map."""
+        """Count unambiguous recognized codons and return a 64-codon map."""
 
         observed = Counter(codon.upper().replace("U", "T") for codon in codons)
         return {

codonadaptpy/models.py

@@ -11,12 +11,12 @@ Classes:
     - ValidationConfig: User-selected validation policy.
     - ValidationIssue: One structured validation observation.
     - ValidationReport: Validation outcome and normalized sequence.
-    - AnalysisResult: Complete metrics for a single sequence.
+    - AnalysisResult: Metrics and metadata for a single sequence.
 
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/optimizer.py

@@ -16,7 +16,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/parsers.py

@@ -18,7 +18,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/phylo_visualization.py

@@ -17,7 +17,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/phylogenetics.py

@@ -1,7 +1,7 @@
 """
 CodonAdaptPy Phylogenetic and Temporal Analysis
 
-This module provides class-based wrappers for reproducible nucleotide or
+This module provides reusable interfaces for reproducible nucleotide or
 protein phylogenetics and lightweight temporal exploration. External programs
 are invoked with argument lists rather than shell strings, their commands and
 outputs are retained, and failures include captured diagnostic text.
@@ -23,7 +23,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/references.py

@@ -14,7 +14,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

codonadaptpy/reporting.py

@@ -12,7 +12,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -33,7 +33,7 @@ class ReportGenerator:
     """Export package results to machine-readable and publication-friendly files."""
 
     def write_json(self, results: list[AnalysisResult], path: str | Path) -> Path:
-        """Write complete nested analysis results as indented JSON."""
+        """Write nested analysis results as indented JSON."""
 
         destination = Path(path)
         destination.write_text(

codonadaptpy/validation.py

@@ -18,7 +18,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -166,4 +166,3 @@ class SequenceValidator:
         if raise_on_error and not report.is_valid:
             raise SequenceValidationError("; ".join(issue.message for issue in report.errors))
         return report
-

codonadaptpy/visualization.py

@@ -13,7 +13,7 @@ Classes:
 :Created: July 20, 2026
 :Updated: July 20, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations

{codonadaptpy-1.0.0.dist-info → codonadaptpy-1.0.1.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: CodonAdaptPy
-Version: 1.0.0
-Summary: Integrated codon-usage, host-adaptation, evolutionary analysis, and sequence optimization
+Version: 1.0.1
+Summary: Codon usage, host adaptation, evolutionary analysis, phylogenetics, and sequence design
 Author: Naveen Duhan
 License-Expression: GPL-3.0-or-later
 Project-URL: Homepage, https://github.com/navduhan/CodonAdaptPy
@@ -71,8 +71,9 @@ Dynamic: license-file
 
 [![CI](https://github.com/navduhan/CodonAdaptPy/actions/workflows/ci.yml/badge.svg)](https://github.com/navduhan/CodonAdaptPy/actions/workflows/ci.yml)
 [![Documentation Status](https://readthedocs.org/projects/codonadaptpy/badge/?version=latest)](https://codonadaptpy.readthedocs.io/en/latest/?badge=latest)
+[![PyPI version](https://img.shields.io/pypi/v/CodonAdaptPy.svg)](https://pypi.org/project/CodonAdaptPy/)
 
-CodonAdaptPy 1.0.0 is a standalone, class-based Python package for coding-sequence validation, codon-usage analysis, multi-host comparison, evolutionary diagnostics, reproducible reporting, and constrained codon optimization or deoptimization.
+CodonAdaptPy 1.0.1 is a Python package for coding-sequence validation, codon-usage analysis, multi-host comparison, evolutionary diagnostics, reproducible reporting, and constrained codon optimization or deoptimization.
 
 ![CodonAdaptPy workflow from validated coding sequences through modular codon analysis to auditable molecular-evolution evidence](docs/assets/codonadaptpy_graphical_abstract.png)
 
@@ -99,17 +100,17 @@ Codon-usage similarity is descriptive. It is not direct proof of increased expre
 Install the dependency-free core and CLI:
 
 ```bash
-python -m pip install .
+python -m pip install CodonAdaptPy
 ```
 
-Install every standalone analysis, input, plot, and reporting feature:
+Install all optional analysis, input, plotting, and reporting dependencies:
 
 ```bash
-python -m pip install ".[all]"
+python -m pip install "CodonAdaptPy[all]"
 ```
 
-Phylogenetic workflows additionally require command-line programs. The
-recommended complete environment installs them explicitly:
+Phylogenetic workflows also require external command-line programs. The
+supplied Conda environment installs them together with CodonAdaptPy:
 
 ```bash
 conda env create -f environment.yml
@@ -120,11 +121,11 @@ For an existing environment such as `ngs`:
 
 ```bash
 conda install -n ngs -c bioconda -c conda-forge mafft trimal iqtree fasttree ete3
-python -m pip install ".[phylo]"
+python -m pip install "CodonAdaptPy[phylo]"
 ```
 
-CodonAdaptPy reports a missing executable instead of silently substituting a
-different method. Publication mode requires trimAL unless `--no-trim` is
+CodonAdaptPy reports a missing executable instead of silently substituting an
+alternative method. Publication mode requires trimAL unless `--no-trim` is
 explicitly selected.
 
 For development:
@@ -147,7 +148,7 @@ codonadaptpy analyze coding_sequences.fasta \
   --output results
 ```
 
-Compare the same sequences with multiple hosts:
+Compare the same sequences against multiple host reference profiles:
 
 ```bash
 codonadaptpy compare coding_sequences.fasta \
@@ -178,7 +179,7 @@ ATG...TAA
 ATG...TAA
 ```
 
-For a FASTA plus a separate metadata file, pass `--metadata metadata.csv`. During genome-wide aggregation every CDS is validated independently, its reading frame starts again at position zero, its terminal stop is removed, and no nucleotide or codon pair is counted across gene boundaries.
+For a FASTA plus a separate metadata file, pass `--metadata metadata.csv`. During genome-wide aggregation, every CDS is validated independently, its reading frame restarts at position zero, its terminal stop is removed, and no nucleotide word or codon pair is counted across gene boundaries.
 
 Build a versioned reference profile from highly expressed coding sequences:
 
@@ -222,8 +223,8 @@ codonadaptpy phylogeny f_gene_sequences.fasta \
 ```
 
 This produces ML and time-tree figures, a root-to-tip regression, dated Newick,
-lineage-through-time output, and JSON provenance. The deterministic time tree
-and LTT curve are rapid deterministic diagnostics—not relaxed-clock posterior
+lineage-through-time output, and JSON provenance. The time tree and LTT curve
+are rapid, deterministic diagnostics—not relaxed-clock posterior
 dating, effective population-size inference, or 95% HPD intervals.
 
 ## Python API
@@ -249,7 +250,7 @@ print(result.metrics["enc"])
 print(result.metrics["gc3"])
 ```
 
-Create a publication-ready figure through the package:
+Create a publication-ready figure with CodonAdaptPy:
 
 ```python
 from codonadaptpy import PublicationPlotManager
@@ -264,7 +265,7 @@ plots.save(figure, "f_gene_diagnostics.pdf")
 plots.save(figure, "f_gene_diagnostics.png", dpi=600)
 ```
 
-Run phylogenetics through the class-based API:
+Run phylogenetics through the Python API:
 
 ```python
 from codonadaptpy import ETE3TreePlotter, PhylogeneticAnalyzer, TemporalAnalyzer
@@ -300,7 +301,7 @@ JSON profiles preserve provenance and versioning:
 }
 ```
 
-Missing sense codons are completed with zero counts during validation. CSV/TSV profiles use `codon,count` or `codon,frequency` columns. The only bundled profile is `uniform_standard`, an explicitly non-biological testing baseline; real host tables must retain a documented source and release.
+Missing sense codons are represented by zero counts during validation. CSV/TSV profiles use `codon,count` or `codon,frequency` columns. The only bundled profile is `uniform_standard`, an explicitly non-biological testing baseline; biological host profiles must retain a documented source and release.
 
 ## CAI edge-case policy
 
@@ -329,7 +330,7 @@ Every analysis captures CodonAdaptPy and Python versions, UTC analysis time, gen
 ```text
 src/codonadaptpy/
 ├── aggregation.py       # Per-isolate gene and genome-wide CDS scopes
-├── analyzer.py          # Main class-based API
+├── analyzer.py          # Main analysis API
 ├── comparative.py       # Group and multivariate analysis
 ├── genetic_code.py      # Translation tables and codon families
 ├── metrics/             # Adaptation, usage, composition, pair, host, evolution
@@ -342,5 +343,5 @@ src/codonadaptpy/
 ├── reporting.py         # JSON/CSV/Excel/HTML/PDF/FASTA output
 ├── validation.py        # Coding-sequence quality control
 ├── visualization.py     # Interactive and static plots
-└── cli.py               # Standalone subcommands
+└── cli.py               # Command-line subcommands
 ```

codonadaptpy-1.0.1.dist-info/RECORD

@@ -0,0 +1,32 @@
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codonadaptpy-1.0.0.dist-info/RECORD

@@ -1,32 +0,0 @@
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