recount3 1.0.0__tar.gz

recount3-1.0.0/LICENSE

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+The Clear BSD License with Extra Clause
+
+Copyright (c) 2026, Alexander A. Alsalihi, Robert M. Flight, Hunter N.B. Moseley
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+* All advertising materials mentioning features or use of this software must display the following acknowledgement: This product includes software developed by the copyright holder.
+* Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+* If the source code is used in a published work, then proper citation of the source code must be included with the published work.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

recount3-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: recount3
+Version: 1.0.0
+Summary: CLI and API for searching, manifesting, and downloading recount3 resources.
+Author: Alexander A. Alsalihi, Robert M. Flight, Hunter N.B. Moseley
+Maintainer: Moseley Bioinformatics Lab
+License-Expression: BSD-3-Clause-Clear
+Project-URL: Homepage, https://github.com/MoseleyBioinformaticsLab/recount3
+Project-URL: Repository, https://github.com/MoseleyBioinformaticsLab/recount3
+Project-URL: Issues, https://github.com/MoseleyBioinformaticsLab/recount3/issues
+Project-URL: Documentation, https://moseleybioinformaticslab.github.io/recount3/
+Keywords: bioinformatics,genomics,recount3,RNA-seq,CLI,data-pipelines,manifests
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+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: Programming Language :: Python :: 3.14
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: numpy<3.0,>=2.0
+Requires-Dist: pandas<3.0,>=2.2
+Requires-Dist: scipy<2.0,>=1.13
+Provides-Extra: bigwig
+Requires-Dist: pybigwig>=0.3.18; extra == "bigwig"
+Provides-Extra: biocpy
+Requires-Dist: biocframe>=0.7; extra == "biocpy"
+Requires-Dist: genomicranges>=0.8; extra == "biocpy"
+Requires-Dist: summarizedexperiment>=0.6; extra == "biocpy"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=2; extra == "docs"
+Provides-Extra: dev
+Requires-Dist: pytest<9,>=8; extra == "dev"
+Requires-Dist: pytest-cov<6,>=5; extra == "dev"
+Requires-Dist: pytest-mock<4,>=3.12; extra == "dev"
+Requires-Dist: pytest-xdist<4,>=3; extra == "dev"
+Requires-Dist: pylint<4,>=3.2; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Requires-Dist: commitizen>=3.29; extra == "dev"
+Provides-Extra: all
+Requires-Dist: recount3[bigwig,biocpy,dev,docs]; extra == "all"
+Dynamic: license-file
+
+recount3
+========
+
+.. image:: https://img.shields.io/pypi/l/recount3.svg
+   :target: https://github.com/MoseleyBioinformaticsLab/recount3/blob/main/LICENSE
+   :alt: Clear BSD License with extra clauses
+
+.. image:: https://img.shields.io/pypi/v/recount3.svg
+   :target: https://pypi.org/project/recount3
+   :alt: Current library version
+
+.. image:: https://img.shields.io/pypi/pyversions/recount3.svg
+   :target: https://pypi.org/project/recount3
+   :alt: Supported Python versions
+
+.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/recount3.svg?style=social&label=Star
+   :target: https://github.com/MoseleyBioinformaticsLab/recount3
+   :alt: GitHub project
+
+|
+
+The ``recount3`` package is a Python library and command-line tool for
+interacting with the `recount3`_ data repository, a uniformly processed
+collection of RNA-seq studies covering human and mouse samples from SRA,
+GTEx, and TCGA.
+
+The package provides a typed API for discovering, downloading, and assembling
+recount3 resources into analysis-ready objects.  A companion CLI implements a
+discover -> manifest -> materialize workflow suitable for use in scripts and
+pipelines.
+
+The ``recount3`` package can be used in two ways:
+
+   * As a Python library for searching, downloading, and assembling
+     recount3 gene/exon/junction count matrices, sample metadata, genome
+     annotations, and BigWig coverage files into
+     ``SummarizedExperiment`` / ``RangedSummarizedExperiment`` objects via
+     the BiocPy stack.
+   * As a command-line tool (``recount3``) to search the mirror, produce
+     JSONL manifests, and materialize resources to disk or into a ``.zip``
+     archive.
+
+
+Links
+~~~~~
+
+   * recount3 @ GitHub_
+   * recount3 @ PyPI_
+   * Documentation @ Pages_
+   * Questions & bug reports @ Issues_
+
+
+Installation
+~~~~~~~~~~~~
+
+The core package requires Python 3.10 or newer and depends on NumPy, pandas,
+and SciPy.  Optional extras unlock BiocPy integration and BigWig support.
+
+Install on Linux, Mac OS X
+--------------------------
+
+.. code:: bash
+
+   python3 -m pip install recount3
+
+Install on Windows
+------------------
+
+.. code:: bash
+
+   py -3 -m pip install recount3
+
+Optional extras
+---------------
+
+Install with BiocPy support (``SummarizedExperiment``, ``RangedSummarizedExperiment``,
+``GenomicRanges``):
+
+.. code:: bash
+
+   python3 -m pip install "recount3[biocpy]"
+
+Install with BigWig support (``pybigwig``):
+
+.. code:: bash
+
+   python3 -m pip install "recount3[bigwig]"
+
+Install all optional extras:
+
+.. code:: bash
+
+   python3 -m pip install "recount3[biocpy,bigwig]"
+
+Upgrade on Linux, Mac OS X
+---------------------------
+
+.. code:: bash
+
+   python3 -m pip install recount3 --upgrade
+
+Upgrade on Windows
+------------------
+
+.. code:: bash
+
+   py -3 -m pip install recount3 --upgrade
+
+
+Quickstart
+~~~~~~~~~~
+
+Python API
+----------
+
+Discover all resources for a project, stack the gene-level count matrices
+across samples, and build a ``RangedSummarizedExperiment``:
+
+.. code:: python
+
+   >>> from recount3 import R3ResourceBundle
+   >>>
+   >>> # Discover every resource for a human SRA project.
+   >>> bundle = R3ResourceBundle.discover(
+   ...     organism="human",
+   ...     data_source="sra",
+   ...     project="SRP009615",
+   ... )
+   >>>
+   >>> # Stack raw gene-count matrices across all samples.
+   >>> counts = bundle.only_counts().stack_count_matrices(genomic_unit="gene")
+   >>>
+   >>> # Build a RangedSummarizedExperiment (requires recount3[biocpy]).
+   >>> rse = bundle.to_ranged_summarized_experiment(genomic_unit="gene")
+
+Command-line tool
+-----------------
+
+Discover resources, save a JSONL manifest, and download in parallel:
+
+.. code:: bash
+
+   # Search for gene-level count files and write a manifest.
+   recount3 search gene-exon \
+       organism=human data_source=sra genomic_unit=gene project=SRP009615 \
+       --format=jsonl > manifest.jsonl
+
+   # Materialize all resources from the manifest (8 parallel jobs).
+   recount3 download --from=manifest.jsonl --dest=./downloads --jobs=8
+
+Stream search output directly into download without an intermediate file:
+
+.. code:: bash
+
+   recount3 search annotations \
+       organism=human genomic_unit=gene annotation_extension=G026 \
+       --format=jsonl | \
+   recount3 download --from=- --dest=./annotations
+
+.. note:: Read the full documentation on Pages_ for the complete API reference,
+          CLI guide, and worked examples.
+
+
+Dependencies
+~~~~~~~~~~~~
+
+Core (installed automatically):
+
+.. code:: text
+
+   numpy>=2.0
+   pandas>=2.2
+   scipy>=1.13
+
+Optional: BiocPy integration (``recount3[biocpy]``):
+
+.. code:: text
+
+   biocframe>=0.7
+   genomicranges>=0.8
+   summarizedexperiment>=0.6
+
+Optional: BigWig support (``recount3[bigwig]``):
+
+.. code:: text
+
+   pybigwig>=0.3.18
+
+
+Questions, Feature Requests, and Bug Reports
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Please submit questions, feature requests, and bug reports on Issues_.
+
+
+License
+~~~~~~~
+
+This package is distributed under the BSD_ license.
+
+
+.. _recount3: https://rna.recount.bio
+.. _BiocPy: https://github.com/BiocPy
+.. _GitHub: https://github.com/MoseleyBioinformaticsLab/recount3
+.. _PyPI: https://pypi.org/project/recount3
+.. _Pages: https://moseleybioinformaticslab.github.io/recount3/
+.. _Issues: https://github.com/MoseleyBioinformaticsLab/recount3/issues
+.. _BSD: https://github.com/MoseleyBioinformaticsLab/recount3/blob/main/LICENSE

recount3-1.0.0/README.rst

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+recount3
+========
+
+.. image:: https://img.shields.io/pypi/l/recount3.svg
+   :target: https://github.com/MoseleyBioinformaticsLab/recount3/blob/main/LICENSE
+   :alt: Clear BSD License with extra clauses
+
+.. image:: https://img.shields.io/pypi/v/recount3.svg
+   :target: https://pypi.org/project/recount3
+   :alt: Current library version
+
+.. image:: https://img.shields.io/pypi/pyversions/recount3.svg
+   :target: https://pypi.org/project/recount3
+   :alt: Supported Python versions
+
+.. image:: https://img.shields.io/github/stars/MoseleyBioinformaticsLab/recount3.svg?style=social&label=Star
+   :target: https://github.com/MoseleyBioinformaticsLab/recount3
+   :alt: GitHub project
+
+|
+
+The ``recount3`` package is a Python library and command-line tool for
+interacting with the `recount3`_ data repository, a uniformly processed
+collection of RNA-seq studies covering human and mouse samples from SRA,
+GTEx, and TCGA.
+
+The package provides a typed API for discovering, downloading, and assembling
+recount3 resources into analysis-ready objects.  A companion CLI implements a
+discover -> manifest -> materialize workflow suitable for use in scripts and
+pipelines.
+
+The ``recount3`` package can be used in two ways:
+
+   * As a Python library for searching, downloading, and assembling
+     recount3 gene/exon/junction count matrices, sample metadata, genome
+     annotations, and BigWig coverage files into
+     ``SummarizedExperiment`` / ``RangedSummarizedExperiment`` objects via
+     the BiocPy stack.
+   * As a command-line tool (``recount3``) to search the mirror, produce
+     JSONL manifests, and materialize resources to disk or into a ``.zip``
+     archive.
+
+
+Links
+~~~~~
+
+   * recount3 @ GitHub_
+   * recount3 @ PyPI_
+   * Documentation @ Pages_
+   * Questions & bug reports @ Issues_
+
+
+Installation
+~~~~~~~~~~~~
+
+The core package requires Python 3.10 or newer and depends on NumPy, pandas,
+and SciPy.  Optional extras unlock BiocPy integration and BigWig support.
+
+Install on Linux, Mac OS X
+--------------------------
+
+.. code:: bash
+
+   python3 -m pip install recount3
+
+Install on Windows
+------------------
+
+.. code:: bash
+
+   py -3 -m pip install recount3
+
+Optional extras
+---------------
+
+Install with BiocPy support (``SummarizedExperiment``, ``RangedSummarizedExperiment``,
+``GenomicRanges``):
+
+.. code:: bash
+
+   python3 -m pip install "recount3[biocpy]"
+
+Install with BigWig support (``pybigwig``):
+
+.. code:: bash
+
+   python3 -m pip install "recount3[bigwig]"
+
+Install all optional extras:
+
+.. code:: bash
+
+   python3 -m pip install "recount3[biocpy,bigwig]"
+
+Upgrade on Linux, Mac OS X
+---------------------------
+
+.. code:: bash
+
+   python3 -m pip install recount3 --upgrade
+
+Upgrade on Windows
+------------------
+
+.. code:: bash
+
+   py -3 -m pip install recount3 --upgrade
+
+
+Quickstart
+~~~~~~~~~~
+
+Python API
+----------
+
+Discover all resources for a project, stack the gene-level count matrices
+across samples, and build a ``RangedSummarizedExperiment``:
+
+.. code:: python
+
+   >>> from recount3 import R3ResourceBundle
+   >>>
+   >>> # Discover every resource for a human SRA project.
+   >>> bundle = R3ResourceBundle.discover(
+   ...     organism="human",
+   ...     data_source="sra",
+   ...     project="SRP009615",
+   ... )
+   >>>
+   >>> # Stack raw gene-count matrices across all samples.
+   >>> counts = bundle.only_counts().stack_count_matrices(genomic_unit="gene")
+   >>>
+   >>> # Build a RangedSummarizedExperiment (requires recount3[biocpy]).
+   >>> rse = bundle.to_ranged_summarized_experiment(genomic_unit="gene")
+
+Command-line tool
+-----------------
+
+Discover resources, save a JSONL manifest, and download in parallel:
+
+.. code:: bash
+
+   # Search for gene-level count files and write a manifest.
+   recount3 search gene-exon \
+       organism=human data_source=sra genomic_unit=gene project=SRP009615 \
+       --format=jsonl > manifest.jsonl
+
+   # Materialize all resources from the manifest (8 parallel jobs).
+   recount3 download --from=manifest.jsonl --dest=./downloads --jobs=8
+
+Stream search output directly into download without an intermediate file:
+
+.. code:: bash
+
+   recount3 search annotations \
+       organism=human genomic_unit=gene annotation_extension=G026 \
+       --format=jsonl | \
+   recount3 download --from=- --dest=./annotations
+
+.. note:: Read the full documentation on Pages_ for the complete API reference,
+          CLI guide, and worked examples.
+
+
+Dependencies
+~~~~~~~~~~~~
+
+Core (installed automatically):
+
+.. code:: text
+
+   numpy>=2.0
+   pandas>=2.2
+   scipy>=1.13
+
+Optional: BiocPy integration (``recount3[biocpy]``):
+
+.. code:: text
+
+   biocframe>=0.7
+   genomicranges>=0.8
+   summarizedexperiment>=0.6
+
+Optional: BigWig support (``recount3[bigwig]``):
+
+.. code:: text
+
+   pybigwig>=0.3.18
+
+
+Questions, Feature Requests, and Bug Reports
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Please submit questions, feature requests, and bug reports on Issues_.
+
+
+License
+~~~~~~~
+
+This package is distributed under the BSD_ license.
+
+
+.. _recount3: https://rna.recount.bio
+.. _BiocPy: https://github.com/BiocPy
+.. _GitHub: https://github.com/MoseleyBioinformaticsLab/recount3
+.. _PyPI: https://pypi.org/project/recount3
+.. _Pages: https://moseleybioinformaticslab.github.io/recount3/
+.. _Issues: https://github.com/MoseleyBioinformaticsLab/recount3/issues
+.. _BSD: https://github.com/MoseleyBioinformaticsLab/recount3/blob/main/LICENSE

recount3-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "recount3"
+dynamic = ["version"]
+description = "CLI and API for searching, manifesting, and downloading recount3 resources."
+dependencies = [
+  "numpy>=2.0,<3.0",
+  "pandas>=2.2,<3.0",
+  "scipy>=1.13,<2.0",
+]
+readme = { file = "README.rst", content-type = "text/x-rst" }
+requires-python = ">=3.10"
+license = "BSD-3-Clause-Clear"
+license-files = ["LICENSE"]
+authors = [
+  { name = "Alexander A. Alsalihi" },
+  { name = "Robert M. Flight" },
+  { name = "Hunter N.B. Moseley" }
+]
+maintainers = [
+  { name = "Moseley Bioinformatics Lab" }
+]
+keywords = [
+  "bioinformatics",
+  "genomics",
+  "recount3",
+  "RNA-seq",
+  "CLI",
+  "data-pipelines",
+  "manifests",
+]
+classifiers = [
+  "Development Status :: 5 - Production/Stable",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Programming Language :: Python :: 3.14",
+  "Typing :: Typed",
+]
+
+# Console entry point: `recount3`
+[project.scripts]
+recount3 = "recount3.cli:main"
+
+[project.urls]
+Homepage = "https://github.com/MoseleyBioinformaticsLab/recount3"
+Repository = "https://github.com/MoseleyBioinformaticsLab/recount3"
+Issues = "https://github.com/MoseleyBioinformaticsLab/recount3/issues"
+Documentation = "https://moseleybioinformaticslab.github.io/recount3/"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["recount3*"]
+
+[tool.setuptools.package-data]
+recount3 = ["py.typed"]
+
+[tool.setuptools.dynamic]
+version = { attr = "recount3.version.__version__" }
+
+[project.optional-dependencies]
+bigwig = [
+  "pybigwig>=0.3.18",
+]
+biocpy = [
+  "biocframe>=0.7",
+  "genomicranges>=0.8",
+  "summarizedexperiment>=0.6",
+]
+docs = [
+  "sphinx>=7",
+  "sphinx-rtd-theme>=2",
+]
+dev = [
+  "pytest>=8,<9",
+  "pytest-cov>=5,<6",
+  "pytest-mock>=3.12,<4",
+  "pytest-xdist>=3,<4",
+  "pylint>=3.2,<4",
+  "build>=1.2",
+  "twine>=5",
+  "commitizen>=3.29",
+]
+
+all = [
+  "recount3[bigwig,biocpy,docs,dev]"
+]
+
+[tool.pytest.ini_options]
+minversion = "8.0"
+addopts = "-ra"
+testpaths = ["tests"]
+pythonpath = ["src"]
+
+[tool.coverage.run]
+branch = true
+source = ["src"]
+
+[tool.coverage.report]
+show_missing = true
+skip_covered = true
+exclude_lines = [
+  "pragma: no cover",
+  "if __name__ == .__main__.:",
+]
+
+[tool.commitizen]
+name = "cz_conventional_commits"
+version = "1.0.0"
+version_files = ["src/recount3/version.py:__version__"]
+tag_format = "v$version"
+changelog_file = "CHANGELOG.rst"
+update_changelog_on_bump = true

recount3-1.0.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+