Automatically set AMBERHOME so Amber executables produce output files

aiida_amber/helpers.py

@@ -8,6 +8,7 @@
 available in the PATH on almost any UNIX system.
 """
 
+import os
 import shutil
 import tempfile
 
@@ -95,11 +96,14 @@ def get_code(entry_point, computer):
         return codes[0]
 
     path = get_path_to_executable(executable)
+    # AmberTools data files (e.g. dat/leap/parm/*) are looked up relative to AMBERHOME
+    amberhome = os.path.dirname(os.path.dirname(path))
     code = InstalledCode(
         label=executable,
         default_calc_job_plugin=entry_point,
         computer=computer,
         filepath_executable=path,
+        prepend_text=f"export AMBERHOME={amberhome}",
     )
 
     return code.store()

conftest.py

@@ -1,5 +1,8 @@
 """pytest fixtures for simplified testing."""
 
+import os
+import shutil
+
 import pytest
 
 pytest_plugins = "aiida.tools.pytest_fixtures"
@@ -13,55 +16,70 @@ def clear_database_auto(aiida_profile_clean):
 @pytest.fixture(scope="function")
 def sander_code(aiida_code, aiida_localhost):
     """Get sander code."""
+    sander_path = shutil.which("sander")
+    amberhome = os.path.dirname(os.path.dirname(sander_path))
     return aiida_code(
         "core.code.installed",
         label="amber",
         computer=aiida_localhost,
-        filepath_executable="sander",
+        filepath_executable=sander_path,
+        prepend_text=f"export AMBERHOME={amberhome}",
     )
 
 
 @pytest.fixture(scope="function")
 def tleap_code(aiida_code, aiida_localhost):
     """Get tleap code."""
+    tleap_path = shutil.which("tleap")
+    amberhome = os.path.dirname(os.path.dirname(tleap_path))
     return aiida_code(
         "core.code.installed",
         label="amber",
         computer=aiida_localhost,
-        filepath_executable="tleap",
+        filepath_executable=tleap_path,
+        prepend_text=f"export AMBERHOME={amberhome}",
     )
 
 
 @pytest.fixture(scope="function")
 def antechamber_code(aiida_code, aiida_localhost):
     """Get antechamber code."""
+    antechamber_path = shutil.which("antechamber")
+    amberhome = os.path.dirname(os.path.dirname(antechamber_path))
     return aiida_code(
         "core.code.installed",
         label="amber",
         computer=aiida_localhost,
-        filepath_executable="antechamber",
+        filepath_executable=antechamber_path,
+        prepend_text=f"export AMBERHOME={amberhome}",
     )
 
 
 @pytest.fixture(scope="function")
 def pdb4amber_code(aiida_code, aiida_localhost):
     """Get pdb4amber code."""
+    pdb4amber_path = shutil.which("pdb4amber")
+    amberhome = os.path.dirname(os.path.dirname(pdb4amber_path))
     return aiida_code(
         "core.code.installed",
         label="amber",
         computer=aiida_localhost,
-        filepath_executable="pdb4amber",
+        filepath_executable=pdb4amber_path,
+        prepend_text=f"export AMBERHOME={amberhome}",
     )
 
 
 @pytest.fixture(scope="function")
 def parmed_code(aiida_code, aiida_localhost):
     """Get parmed code."""
+    parmed_path = shutil.which("parmed")
+    amberhome = os.path.dirname(os.path.dirname(parmed_path))
     return aiida_code(
         "core.code.installed",
         label="amber",
         computer=aiida_localhost,
-        filepath_executable="parmed",
+        filepath_executable=parmed_path,
+        prepend_text=f"export AMBERHOME={amberhome}",
     )
 
 

tests/cli/test_antechamber.py

@@ -4,7 +4,9 @@
 import subprocess
 
 from aiida.orm.nodes.process.process import ProcessState
+from click.testing import CliRunner
 
+from aiida_amber.cli.antechamber import cli
 from aiida_amber.utils import searchprevious
 
 from .. import TEST_DIR
@@ -13,6 +15,7 @@
 def test_launch_antechamber():
     """
     Run an instance of antechamber.
+    Verify the actual installed console-script entry point (aiida_antechamber) works.
     """
     # get input file paths
     inp = os.path.join(TEST_DIR, "input_files", "antechamber", "LigA.mol2")
@@ -48,3 +51,35 @@ def test_launch_antechamber():
     # check the process has finished and exited correctly
     assert prev_calc.process_state == ProcessState.FINISHED
     assert prev_calc.exit_status == 0
+
+
+def test_cli_launch_antechamber(antechamber_code):
+    """Invoke the antechamber cli in-process to cover cli/antechamber.py."""
+    inp = os.path.join(TEST_DIR, "input_files", "antechamber", "LigA.mol2")
+    result = CliRunner().invoke(
+        cli,
+        [
+            "-i",
+            inp,
+            "-o",
+            "LigandA.mol2",
+            "-fi",
+            "mol2",
+            "-fo",
+            "mol2",
+            "-c",
+            "bcc",
+            "-pf",
+            "yes",
+            "-nc",
+            "-2",
+            "-at",
+            "gaff2",
+            "-j",
+            "5",
+            "-rn",
+            "CHA",
+        ],
+        catch_exceptions=False,
+    )
+    assert result.exit_code == 0

tests/cli/test_parmed.py

@@ -4,7 +4,9 @@
 import subprocess
 
 from aiida.orm.nodes.process.process import ProcessState
+from click.testing import CliRunner
 
+from aiida_amber.cli.parmed import cli
 from aiida_amber.utils import searchprevious
 
 from .. import TEST_DIR
@@ -13,6 +15,7 @@
 def test_launch_parmed():
     """
     Run an instance of parmed.
+    Verify the actual installed console-script entry point (aiida_parmed) works.
     """
     # get input file paths
     parmed_in = os.path.join(TEST_DIR, "input_files", "parmed", "parmed_1264_na.in")
@@ -37,3 +40,12 @@ def test_launch_parmed():
     # check the process has finished and exited correctly
     assert prev_calc.process_state == ProcessState.FINISHED
     assert prev_calc.exit_status == 0
+
+
+def test_cli_launch_parmed(parmed_code):
+    """Invoke the parmed cli in-process to cover cli/parmed.py."""
+    parmed_in = os.path.join(TEST_DIR, "input_files", "parmed", "parmed_1264_na.in")
+    prmtop = os.path.join(TEST_DIR, "input_files", "parmed", "1D23_tip4pew.prmtop")
+    inpcrd = os.path.join(TEST_DIR, "input_files", "parmed", "1D23_tip4pew.inpcrd")
+    result = CliRunner().invoke(cli, ["-i", parmed_in, "-p", prmtop, "-c", inpcrd], catch_exceptions=False)
+    assert result.exit_code == 0

tests/cli/test_pdb4amber.py

@@ -9,12 +9,16 @@
 
 from aiida_amber.utils import searchprevious
 
+from click.testing import CliRunner
+from aiida_amber.cli.pdb4amber import cli
+
 from .. import TEST_DIR
 
 
 def test_launch_pdb4amber():
     """
     Run an instance of pdb4amber.
+    Verify the actual installed console-script entry point (aiida_pdb4amber) works.
     """
     # get input file paths
     inp = os.path.join(TEST_DIR, "input_files", "pdb4amber", "Protein.pdb")
@@ -35,4 +39,16 @@ def test_launch_pdb4amber():
     prev_calc = qb.first()[0]
     # check the process has finished and exited correctly
     assert prev_calc.process_state == ProcessState.FINISHED
-    assert prev_calc.exit_status == 0
+    assert prev_calc.exit_status == 0
+
+
+def test_cli_launch_pdb4amber(pdb4amber_code):
+    """Invoke the pdb4amber cli in-process to cover cli/pdb4amber.py."""
+    inp = os.path.join(TEST_DIR, "input_files", "pdb4amber", "Protein.pdb")
+    result = CliRunner().invoke(
+        cli,
+        ["-i", inp, "--out", "test.pdb", "--dry", "--reduce",
+         "--logfile", "test.log", "--leap-template"],
+        catch_exceptions=False,
+    )
+    assert result.exit_code == 0

tests/cli/test_sander.py

@@ -4,7 +4,9 @@
 import subprocess
 
 from aiida.orm.nodes.process.process import ProcessState
+from click.testing import CliRunner
 
+from aiida_amber.cli.sander import cli
 from aiida_amber.utils import searchprevious
 
 from .. import TEST_DIR
@@ -13,6 +15,7 @@
 def test_launch_sander():
     """
     Run an instance of sander.
+    Verify the actual installed console-script entry point (aiida_sander) works.
     """
     # get input file paths
     mdin = os.path.join(TEST_DIR, "input_files", "sander", "01_Min.in")
@@ -42,3 +45,16 @@ def test_launch_sander():
     # check the process has finished and exited correctly
     assert prev_calc.process_state == ProcessState.FINISHED
     assert prev_calc.exit_status == 0
+
+
+def test_cli_launch_sander(sander_code):
+    """Invoke the sander cli in-process to cover cli/sander.py."""
+    mdin = os.path.join(TEST_DIR, "input_files", "sander", "01_Min.in")
+    prmtop = os.path.join(TEST_DIR, "input_files", "sander", "parm7")
+    inpcrd = os.path.join(TEST_DIR, "input_files", "sander", "rst7")
+    result = CliRunner().invoke(
+        cli,
+        ["-i", mdin, "-p", prmtop, "-c", inpcrd, "-o", "01_Min.out", "-r", "01_Min.ncrst", "-inf", "01_Min.mdinfo"],
+        catch_exceptions=False,
+    )
+    assert result.exit_code == 0

tests/cli/test_tleap.py

@@ -4,7 +4,9 @@
 import subprocess
 
 from aiida.orm.nodes.process.process import ProcessState
+from click.testing import CliRunner
 
+from aiida_amber.cli.tleap import cli
 from aiida_amber.utils import searchprevious
 
 from .. import TEST_DIR
@@ -13,6 +15,7 @@
 def test_launch_tleap():
     """
     Run an instance of tleap.
+    Verify the actual installed console-script entry point (aiida_tleap) works.
     """
     # get input file paths
     tleap_in = os.path.join(TEST_DIR, "input_files", "tleap", "tleap.in")
@@ -30,3 +33,10 @@ def test_launch_tleap():
     # check the process has finished and exited correctly
     assert prev_calc.process_state == ProcessState.FINISHED
     assert prev_calc.exit_status == 0
+
+
+def test_cli_launch_tleap(tleap_code):
+    """Invoke the tleap cli in-process to cover cli/tleap.py."""
+    tleap_in = os.path.join(TEST_DIR, "input_files", "tleap", "tleap.in")
+    result = CliRunner().invoke(cli, ["-f", tleap_in], catch_exceptions=False)
+    assert result.exit_code == 0