pycopykat 0.2.0__tar.gz

pycopykat-0.2.0/.github/workflows/python-package.yml

@@ -0,0 +1,98 @@
+name: python-package
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test:
+    name: pytest (py${{ matrix.python-version }})
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+
+      - name: Sync project (dev extras)
+        run: uv sync --extra dev
+
+      - name: Tests
+        # tests/test_parity.py and tests/test_rcompat.py compare with stored R results
+        # (tests/data); the two Rscript-backed Kalman tests skip without R.
+        run: uv run pytest tests -v
+
+  build:
+    name: build wheel + twine check
+    runs-on: ubuntu-latest
+    needs: test
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install build + twine
+        run: pip install --upgrade build twine
+
+      - name: Build sdist + wheel
+        run: python -m build
+
+      - name: Twine check
+        run: twine check dist/*
+
+      - name: Assert pure-Python wheel (no binary extensions)
+        run: |
+          python - <<'PY'
+          import glob, sys, zipfile
+          wheels = glob.glob("dist/*.whl")
+          assert len(wheels) == 1, wheels
+          whl = wheels[0]
+          assert whl.endswith("-py3-none-any.whl"), f"non-universal wheel: {whl}"
+          with zipfile.ZipFile(whl) as z:
+              bad = [n for n in z.namelist() if n.endswith((".so", ".pyd", ".dylib"))]
+          assert not bad, f"binary extensions found in wheel: {bad}"
+          print(f"OK pure-Python wheel: {whl}")
+          PY
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: dist-${{ github.sha }}
+          path: dist/*
+          if-no-files-found: error
+
+  lint:
+    # Informational only — ruff has ~190 pre-existing findings; this job
+    # surfaces them without blocking merges. Clean up incrementally and
+    # flip `continue-on-error` off once the baseline is green.
+    name: ruff (non-blocking)
+    runs-on: ubuntu-latest
+    continue-on-error: true
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+      - name: Sync project (dev extras)
+        run: uv sync --extra dev
+      - name: ruff check
+        run: uv run ruff check pycopykat tests

pycopykat-0.2.0/.gitignore

@@ -0,0 +1,57 @@
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+.venv/
+venv/
+env/
+.env
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+.coverage
+htmlcov/
+*.egg-info/
+dist/
+build/
+.ipynb_checkpoints/
+.DS_Store
+*.rds
+*.rda
+!pycopykat/data/**/*.rda
+scratch/
+tmp/
+docs/
+
+
+# ---------------------------------------------------------------------------
+# Raw / sliced datasets (large, regenerable from upstream papers)
+# ---------------------------------------------------------------------------
+/tests/r_out/
+/benchmarks/pilot/
+
+# ---------------------------------------------------------------------------
+# Per-patient sweep artifacts produced by scripts/run_py_sweep.py and
+# scripts/run_all_benchmarks.py. Only top-level aggregates under
+# benchmarks/full/ and benchmarks/scaling/ are kept.
+# ---------------------------------------------------------------------------
+/benchmarks/full/*/
+/benchmarks/scaling/*/
+
+# ---------------------------------------------------------------------------
+# Log rotations from sweep runners. run_all.log.2 is intentionally kept as
+# evidence; everything else is transient.
+# ---------------------------------------------------------------------------
+/benchmarks/**/run_all.log
+/benchmarks/**/run_all.log.[0-9]
+/benchmarks/**/sweep.log
+/benchmarks/**/sweep.log.[0-9]
+!/benchmarks/full/run_all.log.2
+
+# Ad-hoc dev helpers that occasionally appear under benchmarks/
+/benchmarks/**/_compute_report.py
+/benchmarks/**/codex_review.*
+/benchmarks/codex_runs/
+/benchmarks/full/runinfo_pre_*/
+/benchmarks/full/py_logs/

pycopykat-0.2.0/LICENSE

@@ -0,0 +1,338 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
+source code.  And you must show them these terms so they know their
+rights.
+
+  We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software.  If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+  Finally, any free program is threatened constantly by software
+patents.  We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary.  To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                    GNU GENERAL PUBLIC LICENSE
+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+  0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License.  The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language.  (Hereinafter, translation is included without limitation in
+the term "modification".)  Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope.  The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+  1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+  2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+    a) You must cause the modified files to carry prominent notices
+    stating that you changed the files and the date of any change.
+
+    b) You must cause any work that you distribute or publish, that in
+    whole or in part contains or is derived from the Program or any
+    part thereof, to be licensed as a whole at no charge to all third
+    parties under the terms of this License.
+
+    c) If the modified program normally reads commands interactively
+    when run, you must cause it, when started running for such
+    interactive use in the most ordinary way, to print or display an
+    announcement including an appropriate copyright notice and a
+    notice that there is no warranty (or else, saying that you provide
+    a warranty) and that users may redistribute the program under
+    these conditions, and telling the user how to view a copy of this
+    License.  (Exception: if the Program itself is interactive but
+    does not normally print such an announcement, your work based on
+    the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole.  If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works.  But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+  3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+    a) Accompany it with the complete corresponding machine-readable
+    source code, which must be distributed under the terms of Sections
+    1 and 2 above on a medium customarily used for software interchange; or,
+
+    b) Accompany it with a written offer, valid for at least three
+    years, to give any third party, for a charge no more than your
+    cost of physically performing source distribution, a complete
+    machine-readable copy of the corresponding source code, to be
+    distributed under the terms of Sections 1 and 2 above on a medium
+    customarily used for software interchange; or,
+
+    c) Accompany it with the information you received as to the offer
+    to distribute corresponding source code.  (This alternative is
+    allowed only for noncommercial distribution and only if you
+    received the program in object code or executable form with such
+    an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it.  For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable.  However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+  4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License.  Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+  5. You are not required to accept this License, since you have not
+signed it.  However, nothing else grants you permission to modify or
+distribute the Program or its derivative works.  These actions are
+prohibited by law if you do not accept this License.  Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+  6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions.  You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+  7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all.  For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices.  Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Moe Ghoul>, 1 April 1989
+  Moe Ghoul, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

pycopykat-0.2.0/NAMESPACE_PARITY.md

@@ -0,0 +1,17 @@
+# R copykat 1.2.5 exports and their pycopykat counterparts
+
+| R export | pycopykat | parity |
+|---|---|---|
+| `copykat` | `pycopykat.copykat` (+ `CopykatConfig`, `CopykatResult`) | same breakpoints, baseline cells and calls; CNA to ~1e-10 |
+| `annotateGenes.hg20`, `annotateGenes.mm10` | `pycopykat.core.annotate` | identical rows and order |
+| `baseline.norm.cl` | `pycopykat.core.baseline_norm_cl` | identical clusters, sigmas (EM iterations), baseline cells |
+| `baseline.GMM` | `pycopykat.core.baseline_gmm` | identical calls (same EM) |
+| `baseline.synthetic` | `pycopykat.core.baseline_synthetic` | identical (R's `set.seed(123)` + `rnorm`) |
+| `CNA.MCMC` | `pycopykat.core.cna_mcmc` | identical draws (R's `rgamma` stream) |
+| `convert.all.bins.hg20` | `pycopykat.core.convert_bins_hg20` | identical bin membership and fill |
+| `heatmap.3` | `pycopykat.viz.heatmap.plot_cna_heatmap` | matplotlib heatmap (not a copy) |
+| `cal_dist` | — | not ported (`test.emd` option) |
+
+R pieces reproduced in `pycopykat._rcompat`: Mersenne-Twister `set.seed`/`unif_rand`, `norm_rand` (inversion),
+`rnorm`, `rgamma` (GD/GS with `exp_rand`), `hclust` (`ward.D`, `ward.D2`) and `cutree`, mixtools `normalmixEM`
+(three components, common sigma), `mean`/`sd`/`median` with R's long-double sums, and `ks.test`'s statistic.

pycopykat-0.2.0/PKG-INFO

@@ -0,0 +1,128 @@
+Metadata-Version: 2.5
+Name: pycopykat
+Version: 0.2.0
+Summary: A Python implementation of CopyKAT (Gao et al., Nat Biotechnol 2021) that reproduces R copykat 1.2.5: copy-number profiles and aneuploid/diploid calls of single cells from scRNA-seq counts.
+Project-URL: Homepage, https://github.com/omicverse/py-CopyKAT
+Project-URL: Repository, https://github.com/omicverse/py-CopyKAT
+Project-URL: Issues, https://github.com/omicverse/py-CopyKAT/issues
+Project-URL: Upstream R reference, https://github.com/navinlabcode/copykat
+Author-email: Jieshen Xian <lucyagune3@gmail.com>, OmicVerse Team <contact@omicos.cn>
+License-Expression: GPL-2.0-or-later
+License-File: LICENSE
+Keywords: CNA,aneuploidy,bioinformatics,copy-number,copykat,scRNA-seq,single-cell,tumor
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
+Classifier: Operating System :: OS Independent
+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: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: <3.13,>=3.10
+Requires-Dist: anndata>=0.10
+Requires-Dist: joblib>=1.3
+Requires-Dist: matplotlib>=3.8
+Requires-Dist: numba>=0.59
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: pandas>=2.1
+Requires-Dist: pyarrow>=14
+Requires-Dist: scikit-learn>=1.4
+Requires-Dist: scipy>=1.11
+Requires-Dist: threadpoolctl>=3
+Requires-Dist: typer>=0.9
+Provides-Extra: dev
+Requires-Dist: hypothesis>=6; extra == 'dev'
+Requires-Dist: mypy>=1.9; extra == 'dev'
+Requires-Dist: pytest-benchmark>=4; extra == 'dev'
+Requires-Dist: pytest>=8; extra == 'dev'
+Requires-Dist: ruff>=0.4; extra == 'dev'
+Description-Content-Type: text/markdown
+
+# pycopykat
+
+A Python implementation of [CopyKAT](https://github.com/navinlabcode/copykat) (Gao et al., *Nat Biotechnol* 2021): copy-number profiles of single cells in 220 kb bins and the call of each cell as aneuploid (tumour) or diploid (normal) from scRNA-seq UMI counts.
+
+**Status:** v0.2.0 — reproduces R copykat 1.2.5. With the same seed pycopykat gives R's breakpoints, R's baseline cells and R's call for every cell; the copy-number matrices agree to about 1e-10. On six breast tumours of the CopyKAT paper it ran 4.7 to 17 times faster than R on one thread. See *Reproducing R* below and [`report/`](report/).
+
+## Installation
+
+```bash
+pip install pycopykat
+```
+
+Python 3.10–3.12. The wheel bundles R copykat's reference tables (hg20 and mm10 gene positions, the 220 kb bins, the cell-cycle genes), identical to the package's `sysdata.rda`.
+
+## Usage
+
+```python
+import pandas as pd
+from pycopykat import CopykatConfig, copykat
+
+counts = pd.read_csv("counts.tsv", sep="\t", index_col=0)     # genes x cells, raw UMI counts
+res = copykat(counts, CopykatConfig(id_type="Symbol", genome="hg20", n_jobs=8))
+
+res.prediction        # cell.names, copykat.pred  (as R's res$prediction)
+res.cna_mat           # bins x cells, index (chrom, chrompos, abspos)  (R's res$CNAmat)
+res.hclustering       # R hclust of the cells (merge, height, order)
+res.to_txt("out/", "sample")
+```
+
+`copykat` also takes an `AnnData` (cells x genes, counts in `X`). The arguments of `CopykatConfig` are those of R `copykat()` with the same defaults: `id_type` (`"Symbol"`/`"Ensembl"`), `genome` (`"hg20"`/`"mm10"`), `cell_line`, `ngene_chr`, `min_gene_per_cell`, `low_dr`, `up_dr`, `win_size`, `ks_cut`, `distance` (`"euclidean"`, `"pearson"`, `"spearman"`) and `norm_cell_names` (known normal cells); `seed` is the value R copykat passes to `set.seed` (1234), and `n_jobs` sets the threads of the steps without random numbers (results do not depend on it).
+
+Per patient on an AnnData:
+
+```python
+from pycopykat import copykat_by_batch
+adata = copykat_by_batch(adata, batch_key="patient", config=CopykatConfig(n_jobs=8))
+# adata.obs["copykat_pred"], adata.obsm["copykat_cna"], adata.uns["copykat_bins"]
+```
+
+Command line: `pycopykat run --input counts.tsv --output-dir out/ --sam-name sample`, or `pycopykat run-h5ad --adata data.h5ad --batch-key patient --output out.h5ad`.
+
+In OmicVerse: `ov.single.CNV(adata, method="copykat").run()`.
+
+## Reproducing R
+
+pycopykat follows R copykat 1.2.5 (`copykat()` and its helpers) step by step, in R's order of genes and cells:
+
+* **Filters and annotation** — the cell and gene filters, the annotation (first entry per symbol, data order, then stably by `abspos`), the removal of HLA and cell-cycle genes and the per-cell chromosome-coverage test (runs of chromosomes over the expressed genes) are R's.
+* **Smoothing** — `log(sqrt(x) + sqrt(x + 1))`, centring, and the local-level Kalman smoother of `dlm` (`dlmModPoly(1, dV = 0.16, dW = 0.001)`); dlm computes on SVD factors, which shifts the first genes of each cell by about 1e-10.
+* **Baseline** — `hclust(ward.D2)` and `cutree` are ported from R's Fortran and C (nearest-neighbour list, tie order, cluster numbering); mixtools' `normalmixEM` (three components, common sigma) is ported with its `normpost` routine, so the EM takes the same iterations; the silhouette, the F test and the GMM fallback (`baseline.GMM`) follow R. Known normal cells and the cell-line mode (`baseline.synthetic`, `set.seed(123)` and `rnorm` per cluster) are supported.
+* **Segmentation** — `CNA.MCMC` draws `MCpoissongamma`, i.e. `rgamma(1000, shape, rate)`, for every window of the cluster medians and for every segment of every cell. R's Mersenne-Twister, `norm_rand` (inversion) and `rgamma` (Ahrens–Dieter GD and GS, `exp_rand`) are ported (`pycopykat._rcompat`); the draws are produced in vectorised form and are identical to R's, so the KS breakpoints and the posterior means are R's. `ks.test` uses R's cumulative sum, and the KS cut-off is lowered as in R when fewer than 25 breakpoints are found.
+* **Bins and calls** — `convert.all.bins.hg20` (gene centres in `[start, end]` with the start taken from the previous bin, empty bins filled from the nearest bin), the v1.2 classification (`ward.D` trees cut at k = 4, 3 or 2, the clusters holding the pre-defined diploid cells, the baseline re-adjustment, the correlation rule and the Wasserstein assignment) and the low-confidence labels are R's.
+
+R copykat with `n.cores > 1` does not repeat its own results (`mclapply` children start from unseeded generators); pycopykat always follows the `n.cores = 1` stream.
+
+Comparison with R copykat 1.2.5 (same seed, `n.cores = 1`):
+
+| sample (GSE148673) | cells | breakpoints | calls identical | max \|ΔCNA\| | pycopykat, 1 thread (s) | R (s) |
+|---|---|---|---|---|---|---|
+| DCIS1 | 1,480 | 231 = 231 | yes | 4.3e-11 | 80 | 730 |
+| TNBC1 | 1,097 | 291 = 291 | yes | 5.2e-11 | 72 | 496 |
+| TNBC2 | 1,034 | 267 = 267 | yes | 5.5e-11 | 62 | 437 |
+| TNBC3 | 532 | 326 = 326 | yes | 5.3e-11 | 46 | 220 |
+| TNBC4 | 3,056 | 252 = 252 | yes | 6.2e-11 | 177 | 2,478 |
+| TNBC5 | 3,225 | 219 = 219 | yes | 1.3e-11 | 165 | 2,759 |
+
+Times are the faster of two runs, each on one idle core ([`report/`](report/)). Most of the time goes to the
+segmentation's gamma draws, which come from one sequential random stream; more threads (`n_jobs`) speed up
+only the other steps.
+
+The known-normal, cell-line and Pearson-distance modes were checked the same way on TNBC3. `tests/test_parity.py` checks copykat's example data (`exp.rawdata`) against stored R results, and `tests/test_rcompat.py` the R pieces against stored R values; `tests/r_reference.R` and `tests/r_components.R` regenerate them.
+
+## Testing
+
+```bash
+pip install -e '.[dev]'
+pytest
+```
+
+## Citation
+
+Gao R, Bai S, Henderson YC, et al. Delineating copy number and clonal substructure in human tumors from single-cell transcriptomes. *Nat Biotechnol* 39, 599–608 (2021).
+
+## License
+
+GPL-2.0-or-later, as R copykat (GPL-2).