[4/6] Modernise pyproject.toml; expand .gitignore

.gitignore

@@ -1,4 +1,8 @@
 *.egg-info
 dist/
 build/
-.DS_Store
+.DS_Store
+__pycache__/
+.pytest_cache/
+.venv/
+Influence/

InfluenceCalculator/__init__.py

@@ -1,3 +1,4 @@
 from .InfluenceCalculator import InfluenceCalculator
+from .InfluenceCalculator import adjust_influence
 
-__all__ = ["InfluenceCalculator"]
+__all__ = ["InfluenceCalculator", "adjust_influence"]

InfluenceCalculator/data/__init__.py

@@ -0,0 +1,65 @@
+"""Bundled connectome datasets for ConnectomeInfluenceCalculator.
+
+C. elegans
+----------
+celegans_edgelist() and celegans_meta() return the C. elegans
+hermaphrodite chemical connectome (300 cells, 3,539 edges, 20,672
+synapses) as pandas DataFrames.
+
+The CSVs were taken from the OpenWorm project distribution
+(https://openworm.org/, accessed February 2026), which aggregates the
+original electron-microscopy reconstructions of White et al. 1986 and
+Cook et al. 2019.  Neurotransmitter and cell-class annotations follow
+WormAtlas (https://www.wormatlas.org/) and CenGen (Taylor et al. 2021,
+https://cengen.shinyapps.io/CengenApp/).
+
+If you publish results computed from these CSVs, please cite the
+OpenWorm aggregation alongside the underlying connectome papers:
+
+    @article{szigeti2014openworm,
+      title   = {{OpenWorm}: an open-science approach to modeling
+                 Caenorhabditis elegans},
+      author  = {Szigeti, Bal{\\'a}zs and Gleeson, Padraig and
+                 Vella, Michael and others},
+      journal = {Frontiers in Computational Neuroscience},
+      volume  = {8}, pages = {137}, year = 2014,
+      doi     = {10.3389/fncom.2014.00137}}
+
+    @article{white1986structure,
+      title   = {The structure of the nervous system of the nematode
+                 Caenorhabditis elegans},
+      author  = {White, J. G. and Southgate, E. and
+                 Thomson, J. N. and Brenner, S.},
+      journal = {Philosophical Transactions of the Royal Society B},
+      volume  = {314}, number = {1165}, pages = {1--340}, year = 1986,
+      doi     = {10.1098/rstb.1986.0056}}
+
+    @article{cook2019whole,
+      title   = {Whole-animal connectomes of both Caenorhabditis
+                 elegans sexes},
+      author  = {Cook, Steven J. and Jarrell, Travis A. and
+                 Brittin, Christopher A. and others},
+      journal = {Nature}, volume = {571}, number = {7763},
+      pages   = {63--71}, year = 2019,
+      doi     = {10.1038/s41586-019-1352-7}}
+"""
+import pandas as pd
+from importlib.resources import files
+
+
+def celegans_edgelist():
+    """Load the bundled C. elegans synaptic edge list as a pandas
+    DataFrame with columns 'pre', 'post', 'count', and 'norm'.
+    """
+    return pd.read_csv(files(__package__) / "celegans_edgelist.csv")
+
+
+def celegans_meta():
+    """Load the bundled C. elegans neuron metadata as a pandas
+    DataFrame with columns 'root_id', 'top_nt', 'super_class',
+    'neuron_class', and 'body_part'.
+    """
+    return pd.read_csv(files(__package__) / "celegans_meta.csv")
+
+
+__all__ = ["celegans_edgelist", "celegans_meta"]