py-ruvseq-omicverse 0.1.0__tar.gz

py_ruvseq_omicverse-0.1.0/ATTRIBUTION.md

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+# Attribution
+
+Upstream RUVSeq 1.33.1, commit f560e84eb493f0c2d72279612f9e4ca99493b434.
+Algorithms reconstructed from the upstream source under the accompanying LICENSE.
+Upstream author declarations:
+
+```
+Package: RUVSeq
+Version: 1.33.1
+Title: Remove Unwanted Variation from RNA-Seq Data
+Description: This package implements the remove unwanted variation
+        (RUV) methods of Risso et al. (2014) for the normalization of
+        RNA-Seq read counts between samples.
+Authors@R: c(person("Davide", "Risso", email = "risso.davide@gmail.com",
+	          role = c("aut", "cre", "cph")),
+	     person("Sandrine", "Dudoit", role = "aut"),
+	     person("Lorena", "Pantano", role = "ctb"),
+	     person("Kamil", "Slowikowski", role = "ctb"))
+Author: Davide Risso [aut, cre, cph], Sandrine Dudoit [aut], Lorena Pantano [ctb], Kamil Slowikowski [ctb]
+Maintainer: Davide Risso <risso.davide@gmail.com>
+Date: 04-15-2014
+Imports: methods, MASS
+Depends: Biobase, EDASeq (>= 1.99.1), edgeR
+Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2
+VignetteBuilder: knitr
+License: Artistic-2.0
+LazyLoad: yes
+biocViews: ImmunoOncology, DifferentialExpression, Preprocessing, RNASeq, Software
+URL: https://github.com/drisso/RUVSeq
+BugReports: https://github.com/drisso/RUVSeq/issues
+RoxygenNote: 6.0.1
+
+```

py_ruvseq_omicverse-0.1.0/AUDIT.md

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+# Reviewed R function coverage
+
+AUDIT_AUTO.md is generated by rebuildr. This table also handles exportPattern and comma-separated exportMethods manually.
+
+| R export | Python | Scope |
+|---|---|---|
+| makeGroups | pyruvseq.make_groups | Matrix/default-path subset; see README |
+| RUVg | pyruvseq.ruvg | RUVg, RUVr and RUVs matrix methods plus replicate-index construction. No EDASeq objects, automatic control selection or downstream DE. |
+| RUVr | pyruvseq.ruvr | RUVg, RUVr and RUVs matrix methods plus replicate-index construction. No EDASeq objects, automatic control selection or downstream DE. |
+| RUVs | pyruvseq.ruvs | RUVg, RUVr and RUVs matrix methods plus replicate-index construction. No EDASeq objects, automatic control selection or downstream DE. |

py_ruvseq_omicverse-0.1.0/AUDIT_AUTO.md

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+## R function coverage audit
+
+### Coverage summary
+
+| Category | Ported | Total | % |
+|---|---|---|---|
+| Exported R functions | 0 | 3 | 0.0% |
+| Internal helpers (reachable) | 0 | 0 | 0.0% |
+
+_Python package exposes 0 unique names._
+
+### Exported R functions
+
+| R function | Python equivalent | Status |
+|---|---|---|
+| `RUVg` | `—` | ❌ MISSING |
+| `makeGroups` | `—` | ❌ MISSING |
+| `residuals` | `—` | ❌ MISSING |
+
+### Internal helpers reachable from exports
+
+| R helper | File | Python equivalent | Status |
+|---|---|---|---|

py_ruvseq_omicverse-0.1.0/DISCOVERY.md

@@ -0,0 +1,11 @@
+# Discovery: RUVSeq
+
+Checked omicverse organization repository inventory on 2026-11-11: no standalone target port found.
+Upstream commit: `f560e84eb493f0c2d72279612f9e4ca99493b434`.
+Scope: RUVg, RUVr, RUVs; other package functions are excluded.
+
+Reuse: NumPy/SciPy/pandas for matrix and SVD/NNLS operations. muscat uses existing pyedger and python-limma rather than rewriting either statistical engine.
+RUVg already exists in omicverse PR #1035 and will be extracted with its reference tests rather than independently duplicated.
+Nebulosa and scran pooling have external candidates and are separate reuse audits, not new ports.
+
+Fixed numerical gates are in manifest.yaml, committed before implementation. Synthetic and real public fixtures will be distinguished. No biological accuracy claim follows from fixture-level equivalence.

py_ruvseq_omicverse-0.1.0/LICENSE

@@ -0,0 +1,197 @@
+Artistic License 2.0
+
+Copyright (c) 2000-2006, The Perl Foundation.
+
+Everyone is permitted to copy and distribute verbatim copies of this
+license document, but changing it is not allowed.
+
+Preamble
+********
+
+This license establishes the terms under which a given free software
+Package may be copied, modified, distributed, and/or redistributed.  The
+intent is that the Copyright Holder maintains some artistic control over
+the development of that Package while still keeping the Package
+available as open source and free software.
+
+You are always permitted to make arrangements wholly outside of this
+license directly with the Copyright Holder of a given Package.  If the
+terms of this license do not permit the full use that you propose to
+make of the Package, you should contact the Copyright Holder and seek a
+different licensing arrangement.
+
+Definitions
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+"Copyright Holder" means the individual(s) or organization(s) named in
+the copyright notice for the entire Package.
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+"Contributor" means any party that has contributed code or other
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+"Distributor Fee" means any fee that you charge for Distributing this
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+"Standard Version" refers to the Package if it has not been modified, or
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+"Modified Version" means the Package, if it has been changed, and such
+changes were not explicitly requested by the Copyright Holder.
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+"Original License" means this Artistic License as Distributed with the
+Standard Version of the Package, in its current version or as it may be
+modified by The Perl Foundation in the future.
+
+"Source" form means the source code, documentation source, and
+configuration files for the Package.
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+"Compiled" form means the compiled bytecode, object code, binary, or any
+other form resulting from mechanical transformation or translation of
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+********************************************************
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+Modified Versions for any purpose without restriction, provided that you
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+(3) You may apply any bug fixes, portability changes, and other
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+works, to embed the Package in a larger work of your own, or to build
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+Package, and Distribute the result without restriction, provided the
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+********************************************************
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+(9) Works (including, but not limited to, modules and scripts) that
+merely extend or make use of the Package, do not, by themselves, cause
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+******************
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+Versions is governed by this Artistic License.  By using, modifying or
+distributing the Package, you accept this license.  Do not use, modify,
+or distribute the Package, if you do not accept this license.
+
+(11) If your Modified Version has been derived from a Modified Version
+made by someone other than you, you are nevertheless required to ensure
+that your Modified Version complies with the requirements of this
+license.
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+(12) This license does not grant you the right to use any trademark,
+service mark, tradename, or logo of the Copyright Holder.
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+(13) This license includes the non-exclusive, worldwide, free-of-charge
+patent license to make, have made, use, offer to sell, sell, import and
+otherwise transfer the Package with respect to any patent claims
+licensable by the Copyright Holder that are necessarily infringed by the
+Package.  If you institute patent litigation (including a cross-claim or
+counterclaim) against any party alleging that the Package constitutes
+direct or contributory patent infringement, then this Artistic License
+to you shall terminate on the date that such litigation is filed.
+
+(14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
+HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
+WARRANTIES.  THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
+PERMITTED BY YOUR LOCAL LAW.  UNLESS REQUIRED BY LAW, NO COPYRIGHT
+HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT,
+INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE
+OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

py_ruvseq_omicverse-0.1.0/MANIFEST.in

@@ -0,0 +1,4 @@
+include *.md *.yaml LICENSE
+recursive-include tests *.py *.R
+recursive-include data *.csv *.txt *.json *.npz
+recursive-include scripts *.py

py_ruvseq_omicverse-0.1.0/PKG-INFO

@@ -0,0 +1,260 @@
+Metadata-Version: 2.4
+Name: py-ruvseq-omicverse
+Version: 0.1.0
+Summary: Reference-validated py-RUVSeq algorithm subset
+License: Artistic License 2.0
+        
+        Copyright (c) 2000-2006, The Perl Foundation.
+        
+        Everyone is permitted to copy and distribute verbatim copies of this
+        license document, but changing it is not allowed.
+        
+        Preamble
+        ********
+        
+        This license establishes the terms under which a given free software
+        Package may be copied, modified, distributed, and/or redistributed.  The
+        intent is that the Copyright Holder maintains some artistic control over
+        the development of that Package while still keeping the Package
+        available as open source and free software.
+        
+        You are always permitted to make arrangements wholly outside of this
+        license directly with the Copyright Holder of a given Package.  If the
+        terms of this license do not permit the full use that you propose to
+        make of the Package, you should contact the Copyright Holder and seek a
+        different licensing arrangement.
+        
+        Definitions
+        ***********
+        
+        "Copyright Holder" means the individual(s) or organization(s) named in
+        the copyright notice for the entire Package.
+        
+        "Contributor" means any party that has contributed code or other
+        material to the Package, in accordance with the Copyright Holder's
+        procedures.
+        
+        "You" and "your" means any person who would like to copy, distribute, or
+        modify the Package.
+        
+        "Package" means the collection of files distributed by the Copyright
+        Holder, and derivatives of that collection and/or of those files.  A
+        given Package may consist of either the Standard Version, or a Modified
+        Version.
+        
+        "Distribute" means providing a copy of the Package or making it
+        accessible to anyone else, or in the case of a company or organization,
+        to others outside of your company or organization.
+        
+        "Distributor Fee" means any fee that you charge for Distributing this
+        Package or providing support for this Package to another party.  It does
+        not mean licensing fees.
+        
+        "Standard Version" refers to the Package if it has not been modified, or
+        has been modified only in ways explicitly requested by the Copyright
+        Holder.
+        
+        "Modified Version" means the Package, if it has been changed, and such
+        changes were not explicitly requested by the Copyright Holder.
+        
+        "Original License" means this Artistic License as Distributed with the
+        Standard Version of the Package, in its current version or as it may be
+        modified by The Perl Foundation in the future.
+        
+        "Source" form means the source code, documentation source, and
+        configuration files for the Package.
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+        other form resulting from mechanical transformation or translation of
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+        ********************************************************
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+        (1) You are permitted to use the Standard Version and create and use
+        Modified Versions for any purpose without restriction, provided that you
+        do not Distribute the Modified Version.
+        
+        Permissions for Redistribution of the Standard Version
+        ******************************************************
+        
+        (2) You may Distribute verbatim copies of the Source form of the
+        Standard Version of this Package in any medium without restriction,
+        either gratis or for a Distributor Fee, provided that you duplicate all
+        of the original copyright notices and associated disclaimers.  At your
+        discretion, such verbatim copies may or may not include a Compiled form
+        of the Package.
+        
+        (3) You may apply any bug fixes, portability changes, and other
+        modifications made available from the Copyright Holder.  The resulting
+        Package will still be considered the Standard Version, and as such will
+        be subject to the Original License.
+        
+        Distribution of Modified Versions of the Package as Source
+        **********************************************************
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+        (4) You may Distribute your Modified Version as Source (either gratis or
+        for a Distributor Fee, and with or without a Compiled form of the
+        Modified Version) provided that you clearly document how it differs from
+        the Standard Version, including, but not limited to, documenting any
+        non-standard features, executables, or modules, and provided that you do
+        at least ONE of the following:
+        
+        (a) make the Modified Version available to the Copyright Holder of the
+        Standard Version, under the Original License, so that the Copyright
+        Holder may include your modifications in the Standard Version.
+        
+        (b) ensure that installation of your Modified Version does not prevent
+        the user installing or running the Standard Version.  In addition, the
+        Modified Version must bear a name that is different from the name of the
+        Standard Version.
+        
+        (c) allow anyone who receives a copy of the Modified Version to make the
+        Source form of the Modified Version available to others under
+        
+        (i) the Original License or
+        
+        (ii) a license that permits the licensee to freely copy, modify and
+        redistribute the Modified Version using the same licensing terms that
+        apply to the copy that the licensee received, and requires that the
+        Source form of the Modified Version, and of any works derived from it,
+        be made freely available in that license fees are prohibited but
+        Distributor Fees are allowed.
+        
+        Distribution of Compiled Forms of the Standard Version or Modified
+        ******************************************************************
+        Versions without the Source
+        ***************************
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+        (5) You may Distribute Compiled forms of the Standard Version without
+        the Source, provided that you include complete instructions on how to
+        get the Source of the Standard Version.  Such instructions must be valid
+        at the time of your distribution.  If these instructions, at any time
+        while you are carrying out such distribution, become invalid, you must
+        provide new instructions on demand or cease further distribution.  If
+        you provide valid instructions or cease distribution within thirty days
+        after you become aware that the instructions are invalid, then you do
+        not forfeit any of your rights under this license.
+        
+        (6) You may Distribute a Modified Version in Compiled form without the
+        Source, provided that you comply with Section 4 with respect to the
+        Source of the Modified Version.
+        
+        Aggregating or Linking the Package
+        **********************************
+        
+        (7) You may aggregate the Package (either the Standard Version or
+        Modified Version) with other packages and Distribute the resulting
+        aggregation provided that you do not charge a licensing fee for the
+        Package.  Distributor Fees are permitted, and licensing fees for other
+        components in the aggregation are permitted.  The terms of this license
+        apply to the use and Distribution of the Standard or Modified Versions
+        as included in the aggregation.
+        
+        (8) You are permitted to link Modified and Standard Versions with other
+        works, to embed the Package in a larger work of your own, or to build
+        stand-alone binary or bytecode versions of applications that include the
+        Package, and Distribute the result without restriction, provided the
+        result does not expose a direct interface to the Package.
+        
+        Items That are Not Considered Part of a Modified Version
+        ********************************************************
+        
+        (9) Works (including, but not limited to, modules and scripts) that
+        merely extend or make use of the Package, do not, by themselves, cause
+        the Package to be a Modified Version.  In addition, such works are not
+        considered parts of the Package itself, and are not subject to the terms
+        of this license.
+        
+        General Provisions
+        ******************
+        
+        (10) Any use, modification, and distribution of the Standard or Modified
+        Versions is governed by this Artistic License.  By using, modifying or
+        distributing the Package, you accept this license.  Do not use, modify,
+        or distribute the Package, if you do not accept this license.
+        
+        (11) If your Modified Version has been derived from a Modified Version
+        made by someone other than you, you are nevertheless required to ensure
+        that your Modified Version complies with the requirements of this
+        license.
+        
+        (12) This license does not grant you the right to use any trademark,
+        service mark, tradename, or logo of the Copyright Holder.
+        
+        (13) This license includes the non-exclusive, worldwide, free-of-charge
+        patent license to make, have made, use, offer to sell, sell, import and
+        otherwise transfer the Package with respect to any patent claims
+        licensable by the Copyright Holder that are necessarily infringed by the
+        Package.  If you institute patent litigation (including a cross-claim or
+        counterclaim) against any party alleging that the Package constitutes
+        direct or contributory patent infringement, then this Artistic License
+        to you shall terminate on the date that such litigation is filed.
+        
+        (14) Disclaimer of Warranty: THE PACKAGE IS PROVIDED BY THE COPYRIGHT
+        HOLDER AND CONTRIBUTORS "AS IS' AND WITHOUT ANY EXPRESS OR IMPLIED
+        WARRANTIES.  THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+        PARTICULAR PURPOSE, OR NON-INFRINGEMENT ARE DISCLAIMED TO THE EXTENT
+        PERMITTED BY YOUR LOCAL LAW.  UNLESS REQUIRED BY LAW, NO COPYRIGHT
+        HOLDER OR CONTRIBUTOR WILL BE LIABLE FOR ANY DIRECT, INDIRECT,
+        INCIDENTAL, OR CONSEQUENTIAL DAMAGES ARISING IN ANY WAY OUT OF THE USE
+        OF THE PACKAGE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Repository, https://github.com/omicverse/py-RUVSeq
+Project-URL: Issues, https://github.com/omicverse/py-RUVSeq/issues
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: ATTRIBUTION.md
+Requires-Dist: numpy>=1.23
+Requires-Dist: scipy>=1.10
+Requires-Dist: pandas>=1.5
+Provides-Extra: test
+Requires-Dist: pytest>=7; extra == "test"
+Dynamic: license-file
+
+# py-RUVSeq
+
+Review-stage Python reconstruction of a **subset** of RUVSeq, following the discovery, preregistration and reference-validation workflow in [omicverse-rebuildr](https://github.com/omicverse/omicverse-rebuildr).
+
+RUVg, RUVr and RUVs matrix methods plus replicate-index construction. No EDASeq objects, automatic control selection or downstream DE.
+
+## Install and test
+
+This project has not been published on PyPI. From this checkout:
+
+```bash
+python -m pip install ".[test]"
+python -m pytest -q
+```
+
+## Usage and function map
+
+See [the executed tutorial](examples/tutorial_fixture.ipynb), [R-to-Python parameter dictionary](examples/function_by_function_R_parity.ipynb), and [complete upstream export audit](AUDIT.md).
+Inputs, orientations and unsupported modes are documented in function docstrings. No R process is used at runtime.
+
+## Reproduce the R oracle
+
+```bash
+git clone https://github.com/drisso/RUVSeq.git ../RUVSeq-ref
+git -C ../RUVSeq-ref checkout f560e84eb493f0c2d72279612f9e4ca99493b434
+Rscript tests/reference.R ../RUVSeq-ref
+python -m pytest -q
+```
+
+The runner sources the pinned upstream functions, not a rewritten R approximation. RUVSeq S4 registration is intercepted to execute only matrix methods. SPARK sparse sum/mean helpers are supplied by Matrix, with unchanged statistical functions. MuSiC and muscat functions are sourced with their R dependencies loaded. muscat's source declares R >=4.6; this selected function subset was executed on R 4.5.2, not installed as the full package.
+
+muscat's public fixture additionally uses `Rscript tests/public_reference.R ../muscat-ref`.
+All other primary fixtures are synthetic and do not establish biological accuracy. Numerical gates were committed before implementation and have not been widened.
+
+## Validation and limitations
+
+28 focused tests passed locally without skips. See [reconstruction report](RECONSTRUCTION_REPORT.md) for scope and remaining release checks. This is fixture-level equivalence, not full-domain or full-package equivalence. Runtime objects and failure messages are Python-native.
+
+## Citation and license
+
+Upstream [RUVSeq](https://github.com/drisso/RUVSeq) at `f560e84eb493f0c2d72279612f9e4ca99493b434`; see ATTRIBUTION.md for upstream authors and package citation context, and LICENSE for terms.
+
+## Distribution preparation
+
+The intended PyPI distribution is `py-ruvseq-omicverse`; the import remains `pyruvseq`. See [release preparation](RELEASE.md) for installed-wheel validation and the manual Trusted Publishing procedure. This preparation does not mean a PyPI release is available.

py_ruvseq_omicverse-0.1.0/README.md

@@ -0,0 +1,45 @@
+# py-RUVSeq
+
+Review-stage Python reconstruction of a **subset** of RUVSeq, following the discovery, preregistration and reference-validation workflow in [omicverse-rebuildr](https://github.com/omicverse/omicverse-rebuildr).
+
+RUVg, RUVr and RUVs matrix methods plus replicate-index construction. No EDASeq objects, automatic control selection or downstream DE.
+
+## Install and test
+
+This project has not been published on PyPI. From this checkout:
+
+```bash
+python -m pip install ".[test]"
+python -m pytest -q
+```
+
+## Usage and function map
+
+See [the executed tutorial](examples/tutorial_fixture.ipynb), [R-to-Python parameter dictionary](examples/function_by_function_R_parity.ipynb), and [complete upstream export audit](AUDIT.md).
+Inputs, orientations and unsupported modes are documented in function docstrings. No R process is used at runtime.
+
+## Reproduce the R oracle
+
+```bash
+git clone https://github.com/drisso/RUVSeq.git ../RUVSeq-ref
+git -C ../RUVSeq-ref checkout f560e84eb493f0c2d72279612f9e4ca99493b434
+Rscript tests/reference.R ../RUVSeq-ref
+python -m pytest -q
+```
+
+The runner sources the pinned upstream functions, not a rewritten R approximation. RUVSeq S4 registration is intercepted to execute only matrix methods. SPARK sparse sum/mean helpers are supplied by Matrix, with unchanged statistical functions. MuSiC and muscat functions are sourced with their R dependencies loaded. muscat's source declares R >=4.6; this selected function subset was executed on R 4.5.2, not installed as the full package.
+
+muscat's public fixture additionally uses `Rscript tests/public_reference.R ../muscat-ref`.
+All other primary fixtures are synthetic and do not establish biological accuracy. Numerical gates were committed before implementation and have not been widened.
+
+## Validation and limitations
+
+28 focused tests passed locally without skips. See [reconstruction report](RECONSTRUCTION_REPORT.md) for scope and remaining release checks. This is fixture-level equivalence, not full-domain or full-package equivalence. Runtime objects and failure messages are Python-native.
+
+## Citation and license
+
+Upstream [RUVSeq](https://github.com/drisso/RUVSeq) at `f560e84eb493f0c2d72279612f9e4ca99493b434`; see ATTRIBUTION.md for upstream authors and package citation context, and LICENSE for terms.
+
+## Distribution preparation
+
+The intended PyPI distribution is `py-ruvseq-omicverse`; the import remains `pyruvseq`. See [release preparation](RELEASE.md) for installed-wheel validation and the manual Trusted Publishing procedure. This preparation does not mean a PyPI release is available.

py_ruvseq_omicverse-0.1.0/RECONSTRUCTION_REPORT.md

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+# Reconstruction report: py-RUVSeq
+
+Date: 2026-11-11. Upstream commit: `f560e84eb493f0c2d72279612f9e4ca99493b434`. Review-stage algorithm subset, not a full release.
+
+## Coverage
+RUVg, RUVr and RUVs matrix methods plus replicate-index construction. No EDASeq objects, automatic control selection or downstream DE.
+See AUDIT.md and port.yaml for exported-function coverage, including skipped entries. No unimplemented export is marked complete.
+
+## Evidence
+Frozen gates: manifest.yaml (committed before code). R oracle: tests/reference.R. Offline reference fixtures: data/. Focused tests: 28 passed, no skips. All four notebooks have executed outputs. Windows wheel builds succeeded. Installed-wheel tests in a fresh Python 3.12 environment passed with no skips; see fresh-validation.log.
+
+## Iterations
+Baseline: pinned source and predetermined comparison class. Follow-up: Python candidate and invalid-input tests. SPARK-X's initial analytical-CDF shortcut failed the default R numerical gate and was replaced by Davies. muscat's initial default backend call differed in dispersion selection and was corrected from the R namespace evidence. No tolerance was relaxed. No acceleration or biological-accuracy claim is made.
+
+![Validation evolution](examples/evolution.png)
+
+## Limitations and release status
+This covers the listed paths only. RUVSeq objects, SPARK GLMMs, MuSiC2 and muscat mixed models remain excluded. Synthetic fixtures are identified as such; muscat additionally runs the public Kang subset distributed by its pinned source. PyPI publication and a full rebuildr release are not claimed. The notebook parameter dictionary and coverage audit support review; installed-R full-package testing is distinct from executing selected upstream R functions.

py_ruvseq_omicverse-0.1.0/RELEASE.md

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+# Release preparation
+
+Distribution: `py-ruvseq-omicverse`. Python import: `pyruvseq`. Candidate: `0.1.0`.
+These names intentionally differ. Preparation does not establish a PyPI release.
+
+## Validation
+
+`python -m build` produces a source archive and builds the wheel from that archive.
+The source archive includes reference fixtures, R runners, attribution and scope documentation.
+CI installs the wheel and executes the existing reference tests outside the checkout:
+
+```bash
+python -m pip install build twine
+python -m build
+python -m twine check --strict dist/*
+python -m pip install dist/*.whl pytest
+python -m pip check
+python -I scripts/test_installed.py --sdist dist/*.tar.gz --module pyruvseq --distribution py-ruvseq-omicverse
+```
+
+## First publication
+
+1. Review and merge the implementation and release-preparation changes into `main`.
+2. In the intended PyPI account, configure a pending Trusted Publisher:
+   project `py-ruvseq-omicverse`, GitHub owner `omicverse`, repository `py-RUVSeq`,
+   workflow `publish.yml`, environment `pypi`.
+3. Configure the corresponding GitHub `pypi` environment. GitHub repository
+   access alone does not establish PyPI project ownership. Do not share tokens in issues.
+4. Explicitly dispatch **Publish to PyPI** on `main`, with version `0.1.0`.
+   Pushes, pull requests and tags do not trigger publication. The workflow checks
+   the version, rebuilds and tests distributions before publishing via OIDC.
+5. In a new environment, install `py-ruvseq-omicverse==0.1.0` from PyPI, verify the
+   downloaded artifact and rerun the reference tests. Only then update OmicVerse
+   installation hints and tested version pins.
+
+A successful build is not a public release. No full-package R equivalence or
+biological accuracy claim is added by these packaging checks.

py_ruvseq_omicverse-0.1.0/data/groups_r.csv

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+1,2,3,4
+5,6,7,8
+9,10,11,12
+13,14,15,16