CodonAdaptPy 1.0.0__tar.gz → 1.0.1__tar.gz

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/Dockerfile

@@ -1,7 +1,7 @@
 FROM python:3.12-slim
 
 LABEL org.opencontainers.image.authors="Naveen Duhan"
-LABEL org.opencontainers.image.version="1.0.0"
+LABEL org.opencontainers.image.version="1.0.1"
 LABEL org.opencontainers.image.title="CodonAdaptPy"
 
 WORKDIR /opt/codonadaptpy
@@ -10,4 +10,3 @@ RUN pip install --no-cache-dir ".[all]"
 
 ENTRYPOINT ["codonadaptpy"]
 CMD ["--help"]
-

{codonadaptpy-1.0.0/src/CodonAdaptPy.egg-info → codonadaptpy-1.0.1}/PKG-INFO

@@ -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-1.0.0 → codonadaptpy-1.0.1}/README.md

@@ -2,8 +2,9 @@
 
 [![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)
 
@@ -30,17 +31,17 @@ 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
@@ -51,11 +52,11 @@ 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:
@@ -78,7 +79,7 @@ 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 \
@@ -109,7 +110,7 @@ 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:
 
@@ -153,8 +154,8 @@ 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
@@ -180,7 +181,7 @@ 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
@@ -195,7 +196,7 @@ 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
@@ -231,7 +232,7 @@ 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
 
@@ -260,7 +261,7 @@ 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
@@ -273,5 +274,5 @@ 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-1.0.0 → codonadaptpy-1.0.1}/docs/api.md

@@ -1,14 +1,14 @@
 # Python API and extension guide
 
-`CodonAnalyzer` is the high-level service. Individual calculators in `codonadaptpy.metrics` can be used independently. Inputs and outputs are standard-library dataclasses, making them easy to serialize and stable across optional dependency sets.
+`CodonAnalyzer` is the primary analysis interface. Individual calculators in `codonadaptpy.metrics` can also be used independently. Inputs and outputs are standard-library dataclasses that can be serialized without a framework-specific schema library and remain available regardless of which optional dependencies are installed.
 
-`CDSAggregator` wraps a configured `CodonAnalyzer` to generate per-gene results, boundary-aware genome-wide results for each isolate, and any requested focus genes. Records identify their isolate and gene through metadata; no gene name is hard-coded.
+`CDSAggregator` uses a configured `CodonAnalyzer` to generate per-gene results, boundary-aware genome-wide results for each isolate, and results for any requested focus genes. Records identify their isolate and gene through metadata; no gene name is hard-coded.
 
 Add a metric by implementing a focused calculation class and invoking it from `CodonAnalyzer.analyze`. Add a new input format in `SequenceParser.parse`. Add reference sources by constructing `ReferenceProfile` objects and registering them with `ReferenceManager`. Biological tables should always include database/release provenance, selection criteria, taxonomy, and checksums when available.
 
-`ComparativeAnalyzer.automatic_test(left, right, paired=False, alpha=0.05)` records its normality diagnostic and selects Welch's t test or Mann--Whitney U for independent samples, and a paired t test or Wilcoxon signed-rank test for paired samples. Normality is assessed on within-pair differences for paired designs. The returned dictionary includes the selected test, sample sizes, statistic, p value, effect-size name and value, and the complete selection policy.
+`ComparativeAnalyzer.automatic_test(left, right, paired=False, alpha=0.05)` records its normality diagnostic and selects Welch's t test or Mann--Whitney U for independent samples, and a paired t test or Wilcoxon signed-rank test for paired samples. Normality is assessed on within-pair differences for paired designs. The returned dictionary includes the selected test, sample sizes, statistic, p value, effect-size name and value, and the documented selection policy.
 
-`ComparativeAnalyzer` accepts ordinary numeric records. SciPy is used only for inferential tests and clustering, and NumPy/scikit-learn only for multivariate output. It exposes Welch and Mann-Whitney tests, Hedges' g, FDR correction, PCA, correspondence analysis, stratified LDA with a reproducible train/test split, hierarchical clustering, correlations, and distances.
+`ComparativeAnalyzer` accepts mappings containing numeric metrics and grouping metadata. SciPy is used for inferential tests and clustering, while NumPy and scikit-learn support multivariate analyses. It exposes Welch and Mann-Whitney tests, Hedges' g, FDR correction, PCA, correspondence analysis, stratified LDA with a reproducible train/test split, hierarchical clustering, correlations, and distances.
 
 `PlotManager` returns interactive Plotly figures. `PublicationPlotManager` returns static Matplotlib figures with the Okabe-Ito palette, redundant markers, sample sizes, standard errors, outward-offset axes, and vector-compatible output. Its methods cover grouped PCA and LDA, held-out confusion matrices, exact 59-codon RSCU profiles and heatmaps, composition summaries, ENC-GC3s/neutrality/PR2 diagnostics, all 16 dinucleotide O/E profiles and heatmaps, scalar metric panels, and multi-host CAI/RCDI/SiD comparisons. `save` exports PNG, TIFF, PDF, or SVG.
 
@@ -22,7 +22,7 @@ publication workflows because it prevents silent use of an untrimmed alignment.
 
 `TemporalAnalyzer.temporal_signal` performs a root-to-tip regression and can
 search candidate roots in the style of a rapid TempEst diagnostic. The result
-contains rate, fitted root date, R², p-value, residuals, and the selected
+contains rate, fitted root date, R², p value, residuals, and the selected
 outgroup. `date_tree` applies that deterministic strict-clock mapping while
 anchoring observed tips to their collection dates. `lineage_through_time`
 counts dated branches across a calendar grid. These methods do not implement a
@@ -35,7 +35,7 @@ for quantifying whole-genome versus focus-gene topology discordance.
 
 `ETE3TreePlotter` uses ETE3 for topology parsing, rooting, traversal, pruning,
 and node metadata, then renders headlessly with Matplotlib. It provides ML tree,
-time-tree, temporal-signal, and deterministic LTT figures as 600-DPI raster or
+time-tree, temporal-signal, and deterministic LTT figures as 600 dpi raster or
 vector output without ETE3's optional Qt interface.
 
 ## High-level analysis API

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/docs/cli.md

@@ -17,7 +17,7 @@ codonadaptpy analyze coding_sequences.fasta \
   --output results
 ```
 
-For a table containing isolate and gene metadata, run gene-wise analysis and boundary-aware pooling together:
+For a table containing isolate and gene metadata, run per-gene analysis and boundary-aware pooling together:
 
 ```bash
 codonadaptpy analyze isolate_cds.csv \
@@ -60,7 +60,7 @@ codonadaptpy phylogeny coding_sequences.fasta \
   --output phylogeny_results
 ```
 
-Publication mode requires trimAL unless `--no-trim` is explicitly selected. CodonAdaptPy reports missing executables and does not silently substitute a different method.
+Publication mode requires trimAL unless `--no-trim` is explicitly selected. CodonAdaptPy reports missing executables and does not silently substitute an alternative method.
 
 ## Optimize a coding sequence
 
@@ -73,4 +73,3 @@ codonadaptpy optimize input.fasta \
 ```
 
 Optimized candidates require downstream review for RNA structure, splicing, regulatory elements and experimental performance not represented by the selected constraints.
-

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/docs/conf.py

@@ -7,7 +7,7 @@ public Python API.
 :Created: July 22, 2026
 :Updated: July 22, 2026
 :Author: Naveen Duhan
-:Version: 1.0.0
+:Version: 1.0.1
 """
 
 from __future__ import annotations
@@ -58,4 +58,3 @@ html_context = {
     "github_version": "main",
     "conf_py_path": "/docs/",
 }
-

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/docs/getting_started.md

@@ -2,19 +2,25 @@
 
 ## Choose an installation
 
-The core package has no mandatory third-party Python dependencies. Until a PyPI release is published, install it directly from GitHub:
+The core package has no mandatory third-party Python dependencies. Install the stable release from PyPI:
 
 ```bash
-python -m pip install "git+https://github.com/navduhan/CodonAdaptPy.git"
+python -m pip install CodonAdaptPy
 ```
 
-From a cloned repository, install the full Python feature set with:
+Install all optional Python dependencies with:
 
 ```bash
-python -m pip install ".[all]"
+python -m pip install "CodonAdaptPy[all]"
 ```
 
-For alignment and phylogenetic inference, use the supplied Conda environment so MAFFT, trimAL, IQ-TREE and FastTree are installed as real executables:
+From a cloned repository, install an editable development environment with:
+
+```bash
+python -m pip install --editable ".[dev,all]"
+```
+
+For alignment and phylogenetic inference, use the supplied Conda environment so MAFFT, trimAL, IQ-TREE and FastTree are available on the command line:
 
 ```bash
 conda env create -f environment.yml
@@ -58,7 +64,7 @@ Supported inputs include pasted DNA or RNA, FASTA, GenBank, CSV, TSV and ZIP arc
 
 ## Boundary-aware per-isolate analysis
 
-Genome-wide codon analysis should pool validated CDS-level counts within each isolate. It should not concatenate complete genomes or create artificial codons across adjacent gene boundaries.
+Genome-wide codon analysis should pool counts from validated CDSs within each isolate. A raw genome sequence should not be treated as one continuous CDS, and adjacent genes should not create artificial codons or codon pairs.
 
 ```python
 from codonadaptpy import CDSAggregator, CodonAnalyzer

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/docs/index.md

@@ -1,6 +1,6 @@
 # CodonAdaptPy
 
-CodonAdaptPy is a standalone, class-based Python package for validated coding-sequence analysis, codon-usage and host-adaptation metrics, comparative statistics, evolutionary diagnostics, phylogenetic context, reproducible reporting, and constrained synonymous sequence design.
+CodonAdaptPy is a Python package for validated coding-sequence analysis, codon-usage and host-adaptation metrics, comparative statistics, evolutionary diagnostics, phylogenetic context, reproducible reporting, and constrained synonymous sequence design.
 
 ```{image} assets/codonadaptpy_graphical_abstract.png
 :alt: CodonAdaptPy workflow from validated coding sequences through four analytical lenses to auditable molecular-evolution evidence
@@ -12,21 +12,27 @@ CodonAdaptPy treats codon-usage similarity as descriptive evidence rather than d
 
 ## Installation
 
-Install the dependency-free analysis core directly from GitHub:
+Install the dependency-free analysis core and command-line interface from PyPI:
 
 ```bash
-python -m pip install "git+https://github.com/navduhan/CodonAdaptPy.git"
+python -m pip install CodonAdaptPy
 ```
 
-Or clone the repository and install all optional Python functionality:
+Install all optional Python dependencies with:
+
+```bash
+python -m pip install "CodonAdaptPy[all]"
+```
+
+For development, clone the repository and use an editable installation:
 
 ```bash
 git clone https://github.com/navduhan/CodonAdaptPy.git
 cd CodonAdaptPy
-python -m pip install ".[all]"
+python -m pip install --editable ".[dev,all]"
 ```
 
-Phylogenetic workflows additionally require MAFFT, trimAL, IQ-TREE or FastTree. The supplied `environment.yml` installs these external programs explicitly.
+Phylogenetic workflows also require MAFFT, trimAL, IQ-TREE or FastTree. The supplied `environment.yml` installs these external programs together with CodonAdaptPy.
 
 ```{toctree}
 :maxdepth: 2
@@ -49,7 +55,8 @@ api
 ## Project information
 
 - **Author:** Naveen Duhan
-- **Version:** 1.0.0
+- **Version:** 1.0.1
 - **License:** GNU General Public License v3 or later
+- **PyPI:** [pypi.org/project/CodonAdaptPy](https://pypi.org/project/CodonAdaptPy/)
 - **Source code:** [github.com/navduhan/CodonAdaptPy](https://github.com/navduhan/CodonAdaptPy)
 - **Issue tracker:** [GitHub Issues](https://github.com/navduhan/CodonAdaptPy/issues)

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/docs/input_validation.md

@@ -4,8 +4,8 @@ FASTA identifiers must be unique. CSV/TSV input requires `identifier` (or `id`/`
 
 Per-isolate aggregation requires an isolate field and a gene field. These can be columns in the sequence table, key/value tokens in FASTA descriptions, GenBank CDS annotations, or a separate CSV/TSV joined with `--metadata`. A typical metadata table contains `identifier,isolate,gene,genotype,host,collection_date,country,accession`.
 
-Genome-wide codon analysis pools annotated CDSs; it does not analyze a raw multi-ORF genome as one reading frame. Each CDS must be oriented 5′→3′ in its coding direction. Reading frames restart independently, terminal stops are removed, and word/pair calculations respect gene boundaries.
+Genome-wide codon analysis pools annotated CDSs; it does not analyze a raw multi-ORF genome as one reading frame. Each CDS must be oriented 5′→3′ in its coding direction. Reading frames restart independently, terminal stops are removed, and nucleotide-word and codon-pair calculations respect gene boundaries.
 
-RNA `U` is converted to DNA `T` by default and recorded as a warning. IUPAC ambiguous nucleotides are recognized and handled according to `reject`, `skip`, or `allow`. Unsupported symbols are errors. The reading frame is a zero-based offset. Partial mode changes missing start/stop and trailing incomplete codons from strict errors where appropriate, but internal stops remain errors.
+RNA `U` is converted to DNA `T` by default and recorded as a warning. IUPAC ambiguous nucleotides are recognized and handled according to `reject`, `skip`, or `allow`. Unsupported symbols are errors. The reading frame is a zero-based offset. In partial mode, missing start or stop codons and trailing incomplete codons may be downgraded from errors; internal stops remain errors.
 
 Strict mode raises on invalid sequences. Lenient mode returns a `ValidationReport` so a batch workflow can inspect problems. Metrics exclude ambiguous codons because assigning them probabilistically would introduce an undocumented model assumption.

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/docs/interpretation.md

@@ -4,7 +4,7 @@ Codon usage reflects interacting effects of mutation, selection, drift, gene exp
 
 Reference construction is often the largest source of avoidable bias. Use curated complete CDSs, document whether highly expressed genes were selected, avoid mixing genetic codes, preserve database releases, and compare sensitivity across reference definitions. Very short genes and compositionally unusual proteins provide few independent synonymous observations.
 
-Optimization modifies nucleotide sequence and may affect RNA structure, splicing, transcription, innate immune recognition, synthesis, and regulatory motifs not included in a chosen constraint set. CodonAdaptPy therefore returns multiple candidates and explicit violations. Candidates require downstream in-silico review and experimental validation.
+Optimization modifies nucleotide sequences and may affect RNA structure, splicing, transcription, innate immune recognition, synthesis, and regulatory motifs not included in the selected constraint set. CodonAdaptPy therefore returns multiple candidates and explicit constraint violations. Candidates require downstream in silico review and experimental validation.
 
 Root-to-tip regression and deterministic lineage-through-time output are rapid
 temporal diagnostics. A fitted root date is sensitive to rooting, recombination,

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1}/pyproject.toml

@@ -4,8 +4,8 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "CodonAdaptPy"
-version = "1.0.0"
-description = "Integrated codon-usage, host-adaptation, evolutionary analysis, and sequence optimization"
+version = "1.0.1"
+description = "Codon usage, host adaptation, evolutionary analysis, phylogenetics, and sequence design"
 readme = "README.md"
 requires-python = ">=3.10"
 license = "GPL-3.0-or-later"

{codonadaptpy-1.0.0 → codonadaptpy-1.0.1/src/CodonAdaptPy.egg-info}/PKG-INFO

@@ -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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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-1.0.0 → codonadaptpy-1.0.1}/src/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 → codonadaptpy-1.0.1}/tests/test_analyzer.py

@@ -1,4 +1,4 @@
-"""Integration tests for the high-level class-based analysis API."""
+"""Integration tests for the high-level analysis API."""
 
 from codonadaptpy import CodonAnalyzer, SequenceRecord
 from codonadaptpy.references import ReferenceManager
@@ -11,7 +11,7 @@ def test_complete_analysis_with_reference() -> None:
     assert result.metrics["cai"] == 1.0
     assert result.metrics["sense_codons"] == 4
     assert len(result.codon_counts) == 61
-    assert result.metadata["software_version"] == "1.0.0"
+    assert result.metadata["software_version"] == "1.0.1"
     assert len(result.metadata["input_sha256"]) == 64