From af3b449d95e777289d852335675eff9c9a65038c Mon Sep 17 00:00:00 2001
From: faneshala <fane.shala@epfl.ch>
Date: Wed, 29 May 2024 21:12:52 +0200
Subject: [PATCH] almost lol

---
 src/chembalancer/chembalancer.py | 18 +++++++------
 src/chembalancer/help.py         |  0
 tox.ini                          | 43 --------------------------------
 3 files changed, 11 insertions(+), 50 deletions(-)
 create mode 100644 src/chembalancer/help.py
 delete mode 100644 tox.ini

diff --git a/src/chembalancer/chembalancer.py b/src/chembalancer/chembalancer.py
index e8b5270..34db9bb 100644
--- a/src/chembalancer/chembalancer.py
+++ b/src/chembalancer/chembalancer.py
@@ -17,6 +17,7 @@
 from rdkit import Chem
 import requests
 import base64
+import math
 
 
 def get_smiles_from_name(name):
@@ -93,6 +94,7 @@ def get_molecular_formula(smiles):
         return "Invalid SMILES string"
 
 
+
 def balance_chemical_equation(reactant_smiles, product_smiles):
     reactant_counts = [count_atoms(smiles) for smiles in reactant_smiles]
     product_counts = [count_atoms(smiles) for smiles in product_smiles]
@@ -110,9 +112,16 @@ def balance_chemical_equation(reactant_smiles, product_smiles):
             error_message += f"Elements {missing_in_reactants} are in products but not in reactants."
         raise ValueError(error_message)
 
+    # Use the union of elements from reactants and products
     elements = sorted(reactant_elements.union(product_elements))
+
     A_reactants = setup_matrix(elements, reactant_counts)
     A_products = setup_matrix(elements, product_counts)
+
+    # Debugging: Ensure matrices have the same number of rows
+    if A_reactants.shape[0] != A_products.shape[0]:
+        raise ValueError("Internal error: Reactants and products matrices do not match in row dimension.")
+
     A = np.concatenate([A_reactants, -A_products], axis=1)
 
     integer_coefficients = solve_ilp(A)
@@ -127,20 +136,15 @@ def balance_chemical_equation(reactant_smiles, product_smiles):
 
     return reactant_data, product_data
 
-
-    
 def setup_matrix(elements, counts):
-    # Assuming counts is a list of dictionaries where each dictionary is the atomic count for a molecule
+    # Setup the matrix based on the element order and counts provided
     matrix = []
     for count in counts:
         row = [count.get(element, 0) for element in elements]
         matrix.append(row)
-    
-    # Ensure matrix is 2D
     matrix = np.array(matrix)
     if matrix.ndim == 1:
-        matrix = matrix.reshape(1, -1)  # Reshape to 2D if it's inadvertently 1D
-
+        matrix = matrix.reshape(1, -1)
     return matrix
 
 
diff --git a/src/chembalancer/help.py b/src/chembalancer/help.py
new file mode 100644
index 0000000..e69de29
diff --git a/tox.ini b/tox.ini
deleted file mode 100644
index 810e901..0000000
--- a/tox.ini
+++ /dev/null
@@ -1,43 +0,0 @@
-[tox]
-env_list =
-    check
-    docs
-    {py3}{,-coverage}
-
-[gh-actions]
-python =
-    3.10: check, py310
-    3.11: py311
-    3.12: py312
-
-[testenv]
-basepython =
-    pypy3: pypy3
-    py38: python3.8
-    py39: python3.9
-    py310: python3.10
-    py311: python3.11
-    py312: python3.12
-    {check,docs}: python3
-setenv =
-    PYTHONUNBUFFERED = yes
-    PYTEST_EXTRA_ARGS = -s
-    coverage: PYTEST_EXTRA_ARGS = --cov=src/chembalancer --cov-report xml:.tox/coverage.xml --cov-report term
-passenv =
-    *
-extras =
-    test
-commands =
-    pytest {env:PYTEST_MARKERS:} {env:PYTEST_EXTRA_ARGS:} {posargs:-vv}
-    coverage: genbadge coverage -i .tox/coverage.xml -o assets/coverage-badge.svg
-usedevelop = true
-
-[testenv:docs]
-description = build HTML docs
-setenv =
-    READTHEDOCS_PROJECT = chembalancer
-    READTHEDOCS_VERSION = latest
-extras =
-    doc
-commands =
-    sphinx-build -d "{toxworkdir}/docs_doctree" docs/source "docs/docs_out" --color -vW -bhtml