repare 0.1.0__tar.gz → 0.1.2__tar.gz

repare-0.1.2/CITATION.cff

@@ -0,0 +1,31 @@
+cff-version: 1.2.0
+type: software
+title: "repare"
+message: "If you use repare in your work, please cite our preprint below!"
+authors:
+  - family-names: Huang
+    given-names: Edward C.
+    orcid: https://orcid.org/0009-0000-2471-0531
+  - family-names: Li
+    given-names: Kevin A.
+    orcid: https://orcid.org/0009-0009-0446-6135
+  - family-names: Narasimhan
+    given-names: Vagheesh M.
+    orcid: https://orcid.org/0000-0001-8651-8844
+repository-code: "https://github.com/ehuangc/repare"
+
+preferred-citation:
+  type: article
+  title: "Fault-tolerant pedigree reconstruction from pairwise kinship relations"
+  authors:
+    - family-names: Huang
+      given-names: Edward C.
+    - family-names: Li
+      given-names: Kevin A.
+    - family-names: Narasimhan
+      given-names: Vagheesh M.
+  journal: "bioRxiv"
+  status: preprint
+  date-published: 2025-08-26
+  doi: 10.1101/2025.08.21.671608
+  url: "https://doi.org/10.1101/2025.08.21.671608"

{repare-0.1.0 → repare-0.1.2}/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.4
 Name: repare
-Version: 0.1.0
+Version: 0.1.2
 Summary: Reconstruct (ancient) pedigrees from pairwise kinship relations.
 Author-email: Edward Huang <edwardhuangc@gmail.com>
 License-Expression: MIT
+Project-URL: Source, https://github.com/ehuangc/repare
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -18,7 +19,7 @@ Provides-Extra: plot
 Requires-Dist: pygraphviz; extra == "plot"
 Dynamic: license-file
 
-:evergreen_tree: **repare** is a Python package for (ancient) pedigree reconstruction.
+🌲 **repare** is a Python package for (ancient) pedigree reconstruction.
 
 ## Installation
 
@@ -28,12 +29,14 @@ conda create -n "repare" -c conda-forge python=3.13 pygraphviz matplotlib networ
 conda activate repare
 pip install repare
 ```
-repare uses PyGraphviz to plot reconstructed pedigrees. Since PyGraphviz relies on Graphviz which cannot be installed using `pip`, we recommend installing repare and its dependencies in a fresh conda environment, as shown above.
+repare uses PyGraphviz to plot reconstructed pedigrees. Since PyGraphviz relies on Graphviz which cannot be installed using `pip`, we recommend installing repare and its dependencies in a fresh conda environment, as shown above. This conda-based installation method automatically installs Graphviz and ensures PyGraphviz is linked to it.
 
-If you don't need to plot reconstructed pedigrees, you can install repare directly with `pip install repare`. If you need to plot reconstructed pedigrees and have your own Graphviz installation, you can install repare and Pygraphviz with `pip install repare[plot]`.
+To install conda, see [this page](https://www.anaconda.com/docs/getting-started/miniconda/install).
 
-To install conda, see [this page](https://www.anaconda.com/docs/getting-started/miniconda/install). To install PyGraphviz and Graphviz (yourself), see [this page](https://pygraphviz.github.io/documentation/stable/install.html).
+### Other
+If you don't need to plot reconstructed pedigrees, you can install repare directly with `pip install repare`. If you need to plot reconstructed pedigrees but have your own Graphviz installation, you can install repare and Pygraphviz (and not Graphviz) with `pip install repare[plot]`.
 
+To install PyGraphviz and Graphviz (yourself), see [this page](https://pygraphviz.github.io/documentation/stable/install.html).
 
 ## Usage
 
@@ -47,7 +50,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
 > ```
 > repare -n nodes.csv -r relations.csv
 > ```
-> For example data inputs, see [examples/nodes.csv](examples/nodes.csv) and [examples/relations.csv](examples/relations.csv).
+> For example data inputs, see [examples/nodes.csv](https://github.com/ehuangc/repare/blob/main/examples/nodes.csv) and [examples/relations.csv](https://github.com/ehuangc/repare/blob/main/examples/relations.csv).
 
 ### Inputs
 **Nodes** (-n) (*required*): Path to a CSV file that contains information about the individuals to be analyzed by repare. 
@@ -99,7 +102,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
 **Verbose** (-v) (*flag*): If set, enable verbose output (INFO-level logging).
 
 <p align="center">
-  <img src="examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" width="600" />
+  <img src="https://raw.githubusercontent.com/ehuangc/repare/main/examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" />
   <br>
   <em>Diagram of repare's pedigree reconstruction process</em>
 </p>
@@ -118,3 +121,20 @@ python benchmarks/published/run_parameter_experiment.py
 exit
 ```
 To install pixi, see [this page](https://pixi.sh/latest/installation/).
+
+## Citation
+If you use repare in your work, please cite our preprint:
+
+> Huang, E. C., Li, K. A., & Narasimhan, V. M. (2025). Fault-tolerant pedigree reconstruction from pairwise kinship relations. bioRxiv. [https://doi.org/10.1101/2025.08.21.671608](https://doi.org/10.1101/2025.08.21.671608)
+
+```
+@article{repare_preprint2025,
+  doi     = {10.1101/2025.08.21.671608},
+  author  = {Huang, Edward C. and Li, Kevin A. and Narasimhan, Vagheesh M.},
+  title   = {Fault-tolerant pedigree reconstruction from pairwise kinship relations},
+  journal = {bioRxiv},
+  month   = {aug},
+  year    = {2025},
+  url     = {https://doi.org/10.1101/2025.08.21.671608},
+}
+```

{repare-0.1.0 → repare-0.1.2}/README.md

@@ -1,4 +1,4 @@
-:evergreen_tree: **repare** is a Python package for (ancient) pedigree reconstruction.
+🌲 **repare** is a Python package for (ancient) pedigree reconstruction.
 
 ## Installation
 
@@ -8,12 +8,14 @@ conda create -n "repare" -c conda-forge python=3.13 pygraphviz matplotlib networ
 conda activate repare
 pip install repare
 ```
-repare uses PyGraphviz to plot reconstructed pedigrees. Since PyGraphviz relies on Graphviz which cannot be installed using `pip`, we recommend installing repare and its dependencies in a fresh conda environment, as shown above.
+repare uses PyGraphviz to plot reconstructed pedigrees. Since PyGraphviz relies on Graphviz which cannot be installed using `pip`, we recommend installing repare and its dependencies in a fresh conda environment, as shown above. This conda-based installation method automatically installs Graphviz and ensures PyGraphviz is linked to it.
 
-If you don't need to plot reconstructed pedigrees, you can install repare directly with `pip install repare`. If you need to plot reconstructed pedigrees and have your own Graphviz installation, you can install repare and Pygraphviz with `pip install repare[plot]`.
+To install conda, see [this page](https://www.anaconda.com/docs/getting-started/miniconda/install).
 
-To install conda, see [this page](https://www.anaconda.com/docs/getting-started/miniconda/install). To install PyGraphviz and Graphviz (yourself), see [this page](https://pygraphviz.github.io/documentation/stable/install.html).
+### Other
+If you don't need to plot reconstructed pedigrees, you can install repare directly with `pip install repare`. If you need to plot reconstructed pedigrees but have your own Graphviz installation, you can install repare and Pygraphviz (and not Graphviz) with `pip install repare[plot]`.
 
+To install PyGraphviz and Graphviz (yourself), see [this page](https://pygraphviz.github.io/documentation/stable/install.html).
 
 ## Usage
 
@@ -27,7 +29,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
 > ```
 > repare -n nodes.csv -r relations.csv
 > ```
-> For example data inputs, see [examples/nodes.csv](examples/nodes.csv) and [examples/relations.csv](examples/relations.csv).
+> For example data inputs, see [examples/nodes.csv](https://github.com/ehuangc/repare/blob/main/examples/nodes.csv) and [examples/relations.csv](https://github.com/ehuangc/repare/blob/main/examples/relations.csv).
 
 ### Inputs
 **Nodes** (-n) (*required*): Path to a CSV file that contains information about the individuals to be analyzed by repare. 
@@ -79,7 +81,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
 **Verbose** (-v) (*flag*): If set, enable verbose output (INFO-level logging).
 
 <p align="center">
-  <img src="examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" width="600" />
+  <img src="https://raw.githubusercontent.com/ehuangc/repare/main/examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" />
   <br>
   <em>Diagram of repare's pedigree reconstruction process</em>
 </p>
@@ -98,3 +100,20 @@ python benchmarks/published/run_parameter_experiment.py
 exit
 ```
 To install pixi, see [this page](https://pixi.sh/latest/installation/).
+
+## Citation
+If you use repare in your work, please cite our preprint:
+
+> Huang, E. C., Li, K. A., & Narasimhan, V. M. (2025). Fault-tolerant pedigree reconstruction from pairwise kinship relations. bioRxiv. [https://doi.org/10.1101/2025.08.21.671608](https://doi.org/10.1101/2025.08.21.671608)
+
+```
+@article{repare_preprint2025,
+  doi     = {10.1101/2025.08.21.671608},
+  author  = {Huang, Edward C. and Li, Kevin A. and Narasimhan, Vagheesh M.},
+  title   = {Fault-tolerant pedigree reconstruction from pairwise kinship relations},
+  journal = {bioRxiv},
+  month   = {aug},
+  year    = {2025},
+  url     = {https://doi.org/10.1101/2025.08.21.671608},
+}
+```

{repare-0.1.0 → repare-0.1.2}/benchmarks/simulations/simulator/simulated_pedigree.py

@@ -34,7 +34,7 @@ class SimulatedPedigree:
         self._mean_children_per_mate = 2
         self._sd_children_per_mate = 1
         self._num_generations = 4
-        self._generation_zero_size = 3
+        self._generation_zero_starting_size = 3
 
         # Probability that a node will be masked (i.e., not included in node data)
         self._p_mask_node = p_mask_node
@@ -70,7 +70,7 @@ class SimulatedPedigree:
     def create_pedigree(self) -> None:
         self._create_node(generation=0, sex="M", can_have_children=True)
         self._create_node(generation=0, sex="F", can_have_children=True)
-        for _ in range(self._generation_zero_size - 2):
+        for _ in range(self._generation_zero_starting_size - 2):
             self._create_node(generation=0)
 
         for generation in range(self._num_generations - 1):

{repare-0.1.0 → repare-0.1.2}/pixi.lock

@@ -6292,8 +6292,8 @@ packages:
   timestamp: 1740379663071
 - pypi: ./
   name: repare
-  version: 0.0.3.dev68+gfde66a1.d20250728
-  sha256: e1700c513f524d49dfdcf53a87ece8411d2f51b4b052aa94685704df1eaa73f2
+  version: 0.1.2.dev7+gf68ea5614.d20250828
+  sha256: 0f172b4560db64d24d092d7dbf70afac9f6349e0ba36ef203aa736eedc57ee69
   requires_dist:
   - matplotlib
   - networkx

{repare-0.1.0 → repare-0.1.2}/pyproject.toml

@@ -20,6 +20,9 @@ readme = "README.md"
 license = "MIT"
 license-files = ["LICENSE"]
 
+[project.urls]
+Source = "https://github.com/ehuangc/repare"
+
 [project.optional-dependencies]
 benchmark = ["scikit-learn", "seaborn"]
 plot = ["pygraphviz"]

{repare-0.1.0 → repare-0.1.2}/src/repare/main.py

@@ -1,6 +1,7 @@
 import argparse
 import logging
 import os
+from datetime import datetime
 
 from tqdm.contrib.logging import logging_redirect_tqdm
 
@@ -8,15 +9,17 @@ from repare.pedigree_reconstructor import PedigreeReconstructor
 
 
 def parse_arguments():
-    parser = argparse.ArgumentParser(description="Build and analyze pedigrees.")
+    parser = argparse.ArgumentParser(description="Reconstruct (ancient) pedigrees from pairwise kinship relations.")
     parser.add_argument("-n", "--nodes", type=str, required=True, help="Path to the nodes CSV file.")
     parser.add_argument("-r", "--relations", type=str, required=True, help="Path to the relations CSV file.")
     parser.add_argument(
         "-o",
         "--output",
         type=str,
-        default=".",
-        help="Directory to save the output files. Defaults to the current directory.",
+        default=datetime.now().strftime("repare_output_%Y%m%d_%H%M%S"),
+        help=(
+            "Directory to save the output files. Defaults to repare_output_<YYYYMMDD_HHMMSS> in the current directory."
+        ),
     )
     parser.add_argument(
         "-m",

{repare-0.1.0 → repare-0.1.2}/src/repare.egg-info/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.4
 Name: repare
-Version: 0.1.0
+Version: 0.1.2
 Summary: Reconstruct (ancient) pedigrees from pairwise kinship relations.
 Author-email: Edward Huang <edwardhuangc@gmail.com>
 License-Expression: MIT
+Project-URL: Source, https://github.com/ehuangc/repare
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
@@ -18,7 +19,7 @@ Provides-Extra: plot
 Requires-Dist: pygraphviz; extra == "plot"
 Dynamic: license-file
 
-:evergreen_tree: **repare** is a Python package for (ancient) pedigree reconstruction.
+🌲 **repare** is a Python package for (ancient) pedigree reconstruction.
 
 ## Installation
 
@@ -28,12 +29,14 @@ conda create -n "repare" -c conda-forge python=3.13 pygraphviz matplotlib networ
 conda activate repare
 pip install repare
 ```
-repare uses PyGraphviz to plot reconstructed pedigrees. Since PyGraphviz relies on Graphviz which cannot be installed using `pip`, we recommend installing repare and its dependencies in a fresh conda environment, as shown above.
+repare uses PyGraphviz to plot reconstructed pedigrees. Since PyGraphviz relies on Graphviz which cannot be installed using `pip`, we recommend installing repare and its dependencies in a fresh conda environment, as shown above. This conda-based installation method automatically installs Graphviz and ensures PyGraphviz is linked to it.
 
-If you don't need to plot reconstructed pedigrees, you can install repare directly with `pip install repare`. If you need to plot reconstructed pedigrees and have your own Graphviz installation, you can install repare and Pygraphviz with `pip install repare[plot]`.
+To install conda, see [this page](https://www.anaconda.com/docs/getting-started/miniconda/install).
 
-To install conda, see [this page](https://www.anaconda.com/docs/getting-started/miniconda/install). To install PyGraphviz and Graphviz (yourself), see [this page](https://pygraphviz.github.io/documentation/stable/install.html).
+### Other
+If you don't need to plot reconstructed pedigrees, you can install repare directly with `pip install repare`. If you need to plot reconstructed pedigrees but have your own Graphviz installation, you can install repare and Pygraphviz (and not Graphviz) with `pip install repare[plot]`.
 
+To install PyGraphviz and Graphviz (yourself), see [this page](https://pygraphviz.github.io/documentation/stable/install.html).
 
 ## Usage
 
@@ -47,7 +50,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
 > ```
 > repare -n nodes.csv -r relations.csv
 > ```
-> For example data inputs, see [examples/nodes.csv](examples/nodes.csv) and [examples/relations.csv](examples/relations.csv).
+> For example data inputs, see [examples/nodes.csv](https://github.com/ehuangc/repare/blob/main/examples/nodes.csv) and [examples/relations.csv](https://github.com/ehuangc/repare/blob/main/examples/relations.csv).
 
 ### Inputs
 **Nodes** (-n) (*required*): Path to a CSV file that contains information about the individuals to be analyzed by repare. 
@@ -99,7 +102,7 @@ repare -n NODES -r RELATIONS [-o OUTPUT] [-m MAX_CANDIDATE_PEDIGREES] [-e EPSILO
 **Verbose** (-v) (*flag*): If set, enable verbose output (INFO-level logging).
 
 <p align="center">
-  <img src="examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" width="600" />
+  <img src="https://raw.githubusercontent.com/ehuangc/repare/main/examples/algorithm_diagram.svg" alt="Reconstruction Process Diagram" />
   <br>
   <em>Diagram of repare's pedigree reconstruction process</em>
 </p>
@@ -118,3 +121,20 @@ python benchmarks/published/run_parameter_experiment.py
 exit
 ```
 To install pixi, see [this page](https://pixi.sh/latest/installation/).
+
+## Citation
+If you use repare in your work, please cite our preprint:
+
+> Huang, E. C., Li, K. A., & Narasimhan, V. M. (2025). Fault-tolerant pedigree reconstruction from pairwise kinship relations. bioRxiv. [https://doi.org/10.1101/2025.08.21.671608](https://doi.org/10.1101/2025.08.21.671608)
+
+```
+@article{repare_preprint2025,
+  doi     = {10.1101/2025.08.21.671608},
+  author  = {Huang, Edward C. and Li, Kevin A. and Narasimhan, Vagheesh M.},
+  title   = {Fault-tolerant pedigree reconstruction from pairwise kinship relations},
+  journal = {bioRxiv},
+  month   = {aug},
+  year    = {2025},
+  url     = {https://doi.org/10.1101/2025.08.21.671608},
+}
+```

{repare-0.1.0 → repare-0.1.2}/src/repare.egg-info/SOURCES.txt

@@ -1,6 +1,7 @@
 .gitattributes
 .gitignore
 .pre-commit-config.yaml
+CITATION.cff
 LICENSE
 README.md
 pixi.lock