pysaysuite 0.2.2__tar.gz

pysaysuite-0.2.2/.github/workflows/publish.yml

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+name: Publish to PyPI
+
+# Publishes to PyPI via Trusted Publishing (OIDC) whenever a GitHub Release
+# is published. No API tokens are stored; the `pypi` environment must be
+# registered as a Trusted Publisher on pypi.org (see README / project notes).
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Build sdist and wheel
+        run: |
+          python -m pip install --upgrade build
+          python -m build
+
+      - name: Check artifacts
+        run: |
+          python -m pip install --upgrade twine
+          python -m twine check dist/*
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+  publish:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/pysaysuite
+    permissions:
+      id-token: write  # required for OIDC trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          name: dist
+          path: dist/
+
+      - name: Publish
+        uses: pypa/gh-action-pypi-publish@release/v1

pysaysuite-0.2.2/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+*.ipynb
+!docs/qpcr_examples/*.ipynb
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# PyPI configuration file
+.pypirc
+
+# Private planning
+internal/*
+.claude/
+# outputs
+pysaysuite_out/*
+

pysaysuite-0.2.2/LICENSE

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pysaysuite-0.2.2/PKG-INFO

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+Metadata-Version: 2.4
+Name: pysaysuite
+Version: 0.2.2
+Summary: Python Assay Suite for quick and reproducible assay analyses in python.
+Project-URL: Homepage, https://github.com/hasanalsharoh/pySaySuite
+Project-URL: Repository, https://github.com/hasanalsharoh/pySaySuite
+Project-URL: Issues, https://github.com/hasanalsharoh/pySaySuite/issues
+Author: Hasan Alsharoh
+License-Expression: Apache-2.0
+License-File: LICENSE
+Keywords: ANCOVA,MIQE,bioinformatics,differential-expression,qPCR
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.10
+Requires-Dist: matplotlib>=3.6
+Requires-Dist: numpy>=1.23
+Requires-Dist: openpyxl>=3.1
+Requires-Dist: pandas>=1.5
+Requires-Dist: patsy>=0.5
+Requires-Dist: scipy>=1.9
+Requires-Dist: seaborn>=0.12
+Requires-Dist: statsmodels>=0.14
+Requires-Dist: tomli>=2.0; python_version < '3.11'
+Requires-Dist: xlrd>=2.0
+Provides-Extra: dev
+Requires-Dist: black>=24.0; extra == 'dev'
+Requires-Dist: ipykernel>=6.0; extra == 'dev'
+Requires-Dist: nbconvert>=7.0; extra == 'dev'
+Requires-Dist: nbformat>=5.9; extra == 'dev'
+Requires-Dist: pytest>=7.0; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Requires-Dist: xlwt>=1.3; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# pySaySuite
+**py**thon as**Say** **Suite** for quick, robust and reproducible assay analyses in python.
+
+# Installation (general)
+The package can be obtained from PyPI:
+```bash
+pip install pySaySuite
+```
+
+## qPCR module
+Standardized, reproducible **qPCR differential-expression analysis** for the lab.
+One canonical, tested implementation of the ANCOVA / multivariable-linear-model method of
+
+> Hampton et al., *Analyzing qPCR data: better practices to facilitate rigor and
+> reproducibility*, **Biochem. Biophys. Rep. 44 (2025) 102356**.
+
+The statistical method is theirs; this package ports it to Python for Applied Biosystems
+**ViiA 7 / QuantStudio** exports. 
+
+### Details
+
+The module is qPCR-focused and reproduces the published *better practices* paper **1:1**
+(Tables 3 & 4 ANCOVA to 3 dp, geNorm conclusion, GAPDH–MMP10 correlation, and the
+amplification efficiencies 1.53/1.57 to ~1e-6 against the `qpcR` R oracle). The whole
+analysis is a short, curated set of functions in two modules:
+
+- **`pysaysuite.qpcr.core`** — the headline pipeline:
+  - `read_plates({name: path}, kind="results"|"amplification", batch_map=None)` — ingest
+    QuantStudio/ViiA 7 exports into a tidy long table, **retaining plate identity** (D9).
+  - `assign_group(long, group)` — configurable sample→group assignment (prefix-dict /
+    callable / layout table), flagging unmatched samples instead of silently grouping them.
+  - `build_wide(long, ...)` — collapse technical replicates to mean CT; flag noisy
+    replicate groups (`wide.attrs["noisy_replicates"]`, D11).
+  - `run_ancova(wide, targets, refs, ...)` — per-target ANCOVA on raw CT, returning a
+    **tidy coefficient DataFrame** (one row per model term). Supports a `formula=` override
+    and `reference="gmean"` (default) / a gene name / `"separate"` (D3); BH-FDR across the
+    panel (D5) and an observations-per-parameter guard (D8).
+  - `check_identifiability(...)` — Group⊥plate separability (D6); `run_ancova` also warns
+    on confounded designs automatically.
+- **`pysaysuite.qpcr.qc`** — quality screens and efficiency-based cross-checks:
+  - `genorm2` — geNorm *M* reference selection, a 1:1 port of `ctrlGene::geNorm2` (D14).
+  - `reference_stability`, `target_reference_correlation` — reference QC.
+  - `estimate_eff(amp, design=..., method="spline")` — per-gene efficiency; the optional
+    `design=` metadata join restricts the screen to real sample wells (drops NTC/water),
+    which is what makes the published 1.53/1.57 reproduce exactly. Two estimators are kept
+    and never conflated (D15): `well_efficiency_spline` (qpcR-faithful) and `well_efficiency`
+    (a robust, baseline-subtracted LinRegPCR screen).
+  - `run_ancova_efficiency` — ANCOVA on efficiency-weighted CT (robustness variant).
+  - `pfaffl_compare` — Pfaffl / 2^-ΔΔCt efficiency-corrected cross-check (D7).
+- **`pysaysuite.qpcr.plot`** / **`pysaysuite.qpcr.report`** — figures (forest, efficiency,
+  reference stability, diagnostics, covariate, Pfaffl) and the methods-stamp / output writers (D10).
+- **`pysaysuite.Config`** — typed analysis config, loadable from TOML.
+- **`pysaysuite.core`** — intentionally **empty** for now; a shared cross-assay layer is
+  premature with only the qPCR module present (each assay's input differs), and is deferred
+  until a second assay lands (D12).
+
+The headline functions are also re-exported at the top level:
+`from pysaysuite import read_plates, build_wide, run_ancova, genorm2, estimate_eff, ...`.
+
+### Quickstart
+
+```python
+import pysaysuite as ps
+
+# 1. Ingest QuantStudio exports (one entry per plate) and assign groups.
+long = ps.read_plates({"Plate1": "plate1.xls", "Plate2": "plate2.xls"})
+long = ps.assign_group(long, {"N": "Control", "T": "Case"})   # by sample-name prefix
+
+# 2. Reference-gene QC and selection.
+wide = ps.build_wide(long)
+stability = ps.genorm2(wide, ["RNU48", "U6", "GAPDH"])         # geNorm M ranking
+
+# 3. Headline differential expression (ANCOVA on raw CT, geometric-mean reference).
+result = ps.run_ancova(wide, targets=["MIR-21", "MIR-331"], refs=["RNU48", "U6"])
+groups = result[result["is_group_effect"]]                    # one row per target
+print(groups[["target", "estimate", "p_value", "p_fdr", "direction"]])
+
+# 4. (Optional) efficiency screen + Pfaffl cross-check.
+amp  = ps.read_plates({"Plate1": "plate1.xls"}, kind="amplification")
+eff  = ps.estimate_eff(amp, design=long[["well"]].drop_duplicates())
+xchk = ps.pfaffl_compare(wide, ["MIR-21"], ["RNU48", "U6"], eff, result)
+```
+
+`run_ancova` returns a tidy table with columns `target, term, estimate, se, t, p_value,
+is_group_effect, p_fdr, direction, n, n_params, obs_per_param, r2_adj`; the analysis
+parameters for the methods stamp live in `result.attrs["params"]`.
+
+### Reproduce the paper, 1:1
+
+`docs/qpcr_examples/qpcr_paper_replication_pysaysuite.ipynb` runs the **package** end-to-end on
+Hampton et al.'s own data (`docs/qpcr_examples/data/`) and asserts, in-notebook, that every
+result matches the published values: Tables 3 & 4 (ANCOVA), the geNorm conclusion, the
+GAPDH–MMP10 correlation, and the GAPDH/MMP10 amplification efficiencies. Execute it with:
+
+```bash
+conda run -n pysaysuite jupyter nbconvert --to notebook --execute --inplace \
+  docs/testfiles/qpcr_paper_replication_pysaysuite.ipynb
+```
+
+## Install (for development)
+
+The package is developed in its own conda environment:
+
+```bash
+conda create -n pysaysuite python=3.12 -y
+conda activate pysaysuite
+pip install -e ".[dev]"
+```