Remove temporary allocations

pyproject.toml

@@ -14,9 +14,11 @@ dev = [
     "pre-commit>=4.2.0",
     "ruff>=0.11.4",
     "pytest>=7.0",
+    "pytest-profiling",
+    "flameprof",
 ]
 
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 python_files = "test_*.py"
-addopts = "-v"
+addopts = "-v -m 'not profiling'"

src/dementpy.py

@@ -103,4 +103,5 @@ def main():
     os.chdir('../'+output_folder)
     export(Output_init, site, outname)
 
-main()
+if __name__ == '__main__':
+    main()

src/grid.py

@@ -420,8 +420,8 @@ def metabolism(self,day):
         # Update Substrates pools with dead enzymes
         DeadEnz_df = pd.concat(
             [Enzyme_Loss,
-            Enzyme_Loss.mul(self.Enz_Attrib['N_cost'].tolist()*self.gridsize,axis=0),
-            Enzyme_Loss.mul(self.Enz_Attrib['P_cost'].tolist()*self.gridsize,axis=0)],
+            Enzyme_Loss.mul(np.repeat(self.Enz_Attrib['N_cost'].values, self.gridsize), axis=0),
+            Enzyme_Loss.mul(np.repeat(self.Enz_Attrib['P_cost'].values, self.gridsize), axis=0)],
             axis=1
         )
         DeadEnz_df.index = [np.arange(self.gridsize).repeat(self.n_enzymes), DeadEnz_df.index] # create a multi-index
@@ -713,5 +713,5 @@ def reinitialization(self,initialization,microbes_pp,output,mode,pulse,*args):
         # last: assign microbes to each grid box randomly based on prior densities
         choose_taxa = np.zeros((self.n_taxa,self.gridsize), dtype='int8')
         for i in range(self.n_taxa):
-            choose_taxa[i,:] = np.random.choice([1,0], self.gridsize, replace=True, p=[frequencies[i], 1-frequencies[i]])
+            choose_taxa[i,:] = np.random.binomial(1, frequencies[i], self.gridsize)
         self.Microbes.loc[np.ravel(choose_taxa,order='F')==0] = np.float32(0) # NOTE order='F'

tests/profiling/test_profiling.py

@@ -0,0 +1,18 @@
+"""Test(s) to use with pytest-profiling to identify bottlenecks in the code."""
+import pytest
+
+@pytest.mark.profiling
+def test_profiling(monkeypatch):
+
+    # Define the command line arguments
+    import sys
+    argv = ['dementpy.py', 'grassland', 'output', '20250402', 'scrubland']
+    monkeypatch.setattr(sys, 'argv', argv)
+
+    # Move to subfolder so input and output folders will be correct
+    import os
+    os.chdir('src')
+
+    # Run dementpy
+    import dementpy
+    dementpy.main()