repare 0.1.1__py3-none-any.whl → 0.1.2__py3-none-any.whl

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-0.1.1.dist-info → repare-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: repare
-Version: 0.1.1
+Version: 0.1.2
 Summary: Reconstruct (ancient) pedigrees from pairwise kinship relations.
 Author-email: Edward Huang <edwardhuangc@gmail.com>
 License-Expression: MIT
@@ -29,12 +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
 
@@ -48,7 +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. 
@@ -119,3 +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-0.1.2.dist-info/RECORD

@@ -0,0 +1,10 @@
+repare/__init__.py,sha256=esYDcCYXwJUJVVpWQFFpocPwCZzL5xo_Hxihbknfunc,138
+repare/main.py,sha256=ExmfZyE3yEW-IeS0w8rvIHRI3n3jk4Z_cxijNRbEsck,2804
+repare/pedigree.py,sha256=0YXNz2qeML63pgOyX6izaf0zcYIm61N5GU29816P1kg,70547
+repare/pedigree_reconstructor.py,sha256=zbkc9uyd5uqKM9HCZVg6rvvEEo28i65PN-RybrQxILE,49359
+repare-0.1.2.dist-info/licenses/LICENSE,sha256=uqhB_C7lgd3rOQU5SLtWeu_tVc_L0zGGdN488GCrtmY,1063
+repare-0.1.2.dist-info/METADATA,sha256=vCybfDcxQ-29s0gPQrEza41YP9iFVSgriWwpXp6qtow,7493
+repare-0.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+repare-0.1.2.dist-info/entry_points.txt,sha256=tWRppCTqmNN8n4hJ_ShCgO8dJFU4PKTQsexMZS-PFHw,44
+repare-0.1.2.dist-info/top_level.txt,sha256=MBgnP6OarsEmlqLXjKcPqKFIMIdpwADg5vt6eMPVA0M,7
+repare-0.1.2.dist-info/RECORD,,

repare-0.1.1.dist-info/RECORD

@@ -1,10 +0,0 @@
-repare/__init__.py,sha256=esYDcCYXwJUJVVpWQFFpocPwCZzL5xo_Hxihbknfunc,138
-repare/main.py,sha256=Jmdzzc2_XxBzQ5vU5l0Q0Sh_M714-EWpYCBPOqnng_k,2628
-repare/pedigree.py,sha256=0YXNz2qeML63pgOyX6izaf0zcYIm61N5GU29816P1kg,70547
-repare/pedigree_reconstructor.py,sha256=zbkc9uyd5uqKM9HCZVg6rvvEEo28i65PN-RybrQxILE,49359
-repare-0.1.1.dist-info/licenses/LICENSE,sha256=uqhB_C7lgd3rOQU5SLtWeu_tVc_L0zGGdN488GCrtmY,1063
-repare-0.1.1.dist-info/METADATA,sha256=Rwk4p3XZDOCPYsnbHMuinKM1juRbSf1iB-C1ClFwYZg,6608
-repare-0.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-repare-0.1.1.dist-info/entry_points.txt,sha256=tWRppCTqmNN8n4hJ_ShCgO8dJFU4PKTQsexMZS-PFHw,44
-repare-0.1.1.dist-info/top_level.txt,sha256=MBgnP6OarsEmlqLXjKcPqKFIMIdpwADg5vt6eMPVA0M,7
-repare-0.1.1.dist-info/RECORD,,