Allow custom Python executables

Makefile

@@ -3,36 +3,38 @@
 .PHONY: visual 
 .PHONY: clean
 
+PYTHON = python3
+
 docs:
 	mkdir -p ./documentation
-	pdoc ./pyMBE.py -o ./documentation --docformat google
+	PDOC_ALLOW_EXEC=0 ${PYTHON} -m pdoc ./pyMBE.py -o ./documentation --docformat google
 
 tests:
-	python3 testsuite/lj_tests.py
-	python3 testsuite/set_particle_acidity_test.py
-	python3 testsuite/bond_tests.py
-	python3 testsuite/generate_perpendicular_vectors_test.py
-	python3 testsuite/create_molecule_position_test.py
-	python3 testsuite/seed_test.py
-	python3 testsuite/read-write-df_test.py
-	python3 testsuite/parameter_test.py
-	python3 testsuite/henderson_hasselbalch_tests.py
-	python3 testsuite/cph_ideal_tests.py
-	python3 testsuite/grxmc_ideal_tests.py
-	python3 testsuite/peptide_tests.py
-	python3 testsuite/gcmc_tests.py
-	python3 testsuite/weak_polyelectrolyte_dialysis_test.py
-	python3 testsuite/globular_protein_tests.py
+	${PYTHON} testsuite/lj_tests.py
+	${PYTHON} testsuite/set_particle_acidity_test.py
+	${PYTHON} testsuite/bond_tests.py
+	${PYTHON} testsuite/generate_perpendicular_vectors_test.py
+	${PYTHON} testsuite/create_molecule_position_test.py
+	${PYTHON} testsuite/seed_test.py
+	${PYTHON} testsuite/read-write-df_test.py
+	${PYTHON} testsuite/parameter_test.py
+	${PYTHON} testsuite/henderson_hasselbalch_tests.py
+	${PYTHON} testsuite/cph_ideal_tests.py
+	${PYTHON} testsuite/grxmc_ideal_tests.py
+	${PYTHON} testsuite/peptide_tests.py
+	${PYTHON} testsuite/gcmc_tests.py
+	${PYTHON} testsuite/weak_polyelectrolyte_dialysis_test.py
+	${PYTHON} testsuite/globular_protein_tests.py
 
 sample:
-	python3 samples/peptide.py
+	${PYTHON} samples/peptide.py
 
 visual:
-	python3 visualization/vmd-traj.py
+	${PYTHON} visualization/vmd-traj.py
 	vmd -e visualization.tcl
 
 tutorial:
 	jupyter-lab tutorials/pyMBE_tutorial.ipynb
 
 pylint:
-	pylint pyMBE.py lib/ testsuite/ samples/ maintainer/ visualization/
+	${PYTHON} -m pylint pyMBE.py lib/ testsuite/ samples/ maintainer/ visualization/

samples/Beyer2024/create_paper_data.py

@@ -1,7 +1,8 @@
 # Import pyMBE and other libraries
 import pyMBE
 from lib import analysis
-import os 
+import os
+import sys
 import numpy as np
 import argparse 
 import subprocess
@@ -51,7 +52,7 @@
         raise RuntimeError()
     pH_range = np.linspace(2, 12, num=21)
     for pH in pH_range:
-        run_command=["python3", script_path, "--sequence", sequence, "--pH", str(pH), "--mode", mode]
+        run_command=[sys.executable, script_path, "--sequence", sequence, "--pH", str(pH), "--mode", mode]
         print(subprocess.list2cmdline(run_command))
         subprocess.check_output(run_command)
 
@@ -64,21 +65,22 @@
 
     script_path=pmb.get_resource("samples/Beyer2024/globular_protein.py")
     pH_range = np.linspace(2, 7, num=11)
+    run_command_common=[sys.executable, script_path, "--pdb", protein_pdb, "--path_to_cg", path_to_cg,  "--mode", mode, "--no_verbose"]
 
     if fig_label == "8a":
         protein_pdb = "1f6s"
         path_to_cg = f"parameters/globular_proteins/{protein_pdb}.vtf"
         for pH in pH_range:
 
-            run_command=["python3", script_path, "--pdb", protein_pdb, "--pH", str(pH), "--path_to_cg", path_to_cg,  "--mode", mode, "--no_verbose", "--metal_ion_name", "Ca", "--metal_ion_charge", str(2)]
+            run_command=run_command_common + ["--pH", str(pH), "--metal_ion_name", "Ca", "--metal_ion_charge", str(2)]
             print(subprocess.list2cmdline(run_command))
             subprocess.check_output(run_command)
 
     elif fig_label == "8b":
         protein_pdb = "1beb"
         path_to_cg = f"parameters/globular_proteins/{protein_pdb}.vtf"
         for pH in pH_range:
-            run_command=["python3", script_path, "--pdb", protein_pdb, "--pH", str(pH), "--path_to_cg", path_to_cg,  "--mode", mode, "--no_verbose"]
+            run_command=run_command_common + ["--pH", str(pH)]
             print(subprocess.list2cmdline(run_command))
             subprocess.check_output(run_command)
     else:
@@ -91,7 +93,7 @@
     pH_range = np.linspace(1, 13, num=13)
     c_salt_res = 0.01 * pmb.units.mol/pmb.units.L
     for pH in pH_range:
-        run_command=["python3", script_path, "--c_salt_res", str(0.01), "--c_mon_sys", str(0.435), "--pH_res", str(pH), "--pKa_value", str(4.0), "--mode", mode]
+        run_command=[sys.executable, script_path, "--c_salt_res", str(0.01), "--c_mon_sys", str(0.435), "--pH_res", str(pH), "--pKa_value", str(4.0), "--mode", mode]
         print(subprocess.list2cmdline(run_command))
         subprocess.check_output(run_command)
 

testsuite/cph_ideal_tests.py

@@ -1,5 +1,6 @@
 # Import pyMBE and other libraries
 import pyMBE
+import sys
 import subprocess
 import numpy as np
 import pandas as pd
@@ -13,7 +14,7 @@
 print("*** Constant pH (cpH) implementation tests ***\n")
 print("*** Test that our implementation of the cpH method reproduces the Henderson Hasselbalch equation for an ideal polyampholyte ***\n")
 
-run_command = ["python3", script_path, "--test"]
+run_command = [sys.executable, script_path, "--test"]
 subprocess.check_output(run_command)
 
 data = pd.read_csv(data_path)

testsuite/gcmc_tests.py

@@ -1,21 +1,22 @@
 # Import pyMBE and other libraries
-import pyMBE
-from lib import analysis
+import sys
 import tempfile
 import subprocess
+import pyMBE
+from lib import analysis
 import numpy as np
 
 # Template of the test
 
-def gcmc_test(mode, script_path):
+def gcmc_test(script_path, mode):
     if mode == "ideal":
         print("*** Running test for GCMC of salt solution (ideal). ***")
     elif mode == "interacting":
         print("*** Running test for GCMC of salt solution (interacting). ***")
     with tempfile.TemporaryDirectory() as time_series_path:
         for c_salt_res in salt_concentrations:
             print(f"c_salt_res = {c_salt_res}")
-            run_command=["python3", script_path, "--c_salt_res", str(c_salt_res), "--output", time_series_path, "--mode", mode, "--no_verbose"]
+            run_command=[sys.executable, script_path, "--c_salt_res", str(c_salt_res), "--output", time_series_path, "--mode", mode, "--no_verbose"]
             print(subprocess.list2cmdline(run_command))
             subprocess.check_output(run_command)
         # Analyze all time series
@@ -37,7 +38,7 @@ def gcmc_test(mode, script_path):
 atol=0.0 # absolute tolerance
 
 # Ideal test
-gcmc_test("ideal", script_path)
+gcmc_test(script_path, "ideal")
 
 # Interacting test
-gcmc_test("interacting", script_path)
+gcmc_test(script_path, "interacting")

testsuite/globular_protein_tests.py

@@ -1,6 +1,7 @@
 # Import pyMBE and other libraries
 import pyMBE
 from lib import analysis
+import sys
 import tempfile
 import subprocess
 import numpy as np
@@ -22,13 +23,13 @@ def run_protein_test(script_path, test_pH_values, protein_pdb, rtol, atol,mode="
 
     print(f"Running tests for {protein_pdb}")
     with tempfile.TemporaryDirectory() as time_series_path:
-
         for pH in test_pH_values:
             print(f"pH = {pH}")
-            run_command=["python3", script_path, "--pdb", protein_pdb, "--pH", str(pH), "--path_to_cg", f"parameters/globular_proteins/{protein_pdb}.vtf"]
+            run_command=[sys.executable, script_path, "--pdb", protein_pdb, "--pH", str(pH),
+                         "--path_to_cg", f"parameters/globular_proteins/{protein_pdb}.vtf",
+                         "--mode", "test", "--no_verbose", "--output", time_series_path]
             if protein_pdb == '1f6s':
                 run_command+=["--metal_ion_name","Ca", "--metal_ion_charge", "2"]
-            run_command+=["--mode", "test", "--no_verbose", "--output", time_series_path]
             print(subprocess.list2cmdline(run_command))
             subprocess.check_output(run_command)
         # Analyze all time series

testsuite/grxmc_ideal_tests.py

@@ -1,5 +1,6 @@
 # Import pyMBE and other libraries
 import pyMBE
+import sys
 import subprocess
 import numpy as np
 import pandas as pd
@@ -12,7 +13,7 @@
 print("*** Grand reaction (G-RxMC) implementation tests ***\n")
 print("*** Test that our implementation of the original G-RxMC method reproduces the Henderson-Hasselbalch equation corrected with the Donnan potential (HH+Don) for an ideal mixture of peptides ***")
 
-run_command = ["python3", script_path, "--mode", "standard", "--test"]
+run_command = [sys.executable, script_path, "--mode", "standard", "--test"]
 subprocess.check_output(run_command)
 
 data = pd.read_csv(data_path)
@@ -26,7 +27,7 @@
 
 print("*** Test that our implementation of the G-RxMC method with unified ion types reproduces HH+Don for an ideal mixture of peptides ***")
 
-run_command = ["python3", script_path, "--mode", "unified", "--test"]
+run_command = [sys.executable, script_path, "--mode", "unified", "--test"]
 subprocess.check_output(run_command)
 
 data = pd.read_csv(data_path)

testsuite/peptide_tests.py

@@ -1,8 +1,9 @@
 # Import pyMBE and other libraries
-import pyMBE
-from lib import analysis
+import sys
 import tempfile
 import subprocess
+import pyMBE
+from lib import analysis
 import numpy as np
 import pandas as pd
 
@@ -24,7 +25,7 @@ def run_peptide_test(script_path,test_pH_values,sequence,rtol,atol,mode="test"):
     with tempfile.TemporaryDirectory() as time_series_path:
         for pH in test_pH_values:
             print(f"pH = {pH}")
-            run_command=["python3", script_path, "--sequence", sequence, "--pH", str(pH), "--mode", "test", "--no_verbose", "--output", time_series_path]
+            run_command=[sys.executable, script_path, "--sequence", sequence, "--pH", str(pH), "--mode", "test", "--no_verbose", "--output", time_series_path]
             print(subprocess.list2cmdline(run_command))
             subprocess.check_output(run_command)
         # Analyze all time series

testsuite/weak_polyelectrolyte_dialysis_test.py

@@ -1,6 +1,7 @@
 # Import pyMBE and other libraries
 import pyMBE
 from lib import analysis
+import sys
 import tempfile
 import subprocess
 import numpy as np
@@ -21,7 +22,7 @@
 with tempfile.TemporaryDirectory() as time_series_path:
     for pH in test_pH_values:
         print(f"pH = {pH}")
-        run_command=["python3", script_path, "--c_salt_res", str(c_salt_res), "--c_mon_sys", str(c_mon_sys), "--pKa_value", str(pKa_value), "--pH_res", str(pH), "--mode", "test", "--output", time_series_path, "--no_verbose"]
+        run_command=[sys.executable, script_path, "--c_salt_res", str(c_salt_res), "--c_mon_sys", str(c_mon_sys), "--pKa_value", str(pKa_value), "--pH_res", str(pH), "--mode", "test", "--output", time_series_path, "--no_verbose"]
         print(subprocess.list2cmdline(run_command))
         subprocess.check_output(run_command)
     # Analyze all time series