Add CLI that creates dummy output files and validates input (#934)

 new CLI tool perses-cli that takes in a yaml file and creates dummy output.

.github/workflows/CI.yaml

@@ -11,6 +11,10 @@ on:
     branches:
       - main
 
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
 jobs:
   test:
     name: Test on ubuntu-latest, Python ${{ matrix.python-version }}, OpenMM ${{ matrix.openmm }}
@@ -86,14 +90,12 @@ jobs:
         shell: bash -l {0}
         run: |
           export TRAVIS=true
-          pushd .
-          pytest -v --cov-report xml --cov=perses --durations=0 -a "not advanced" -n auto -m "not gpu_needed"
-          popd
+          pytest -v --cov-report xml --cov=perses --durations=0 -a "not advanced" -n auto -m "not gpu_needed" 
 
       - name: Codecov
         if: ${{ github.repository == 'choderalab/perses'
                 && github.event != 'schedule' }}
         uses: codecov/codecov-action@v1
         with:
           file: ./coverage.xml
-          fail_ci_if_error: true
+          fail_ci_if_error: true

devtools/conda-envs/test_env.yaml

@@ -19,7 +19,7 @@ dependencies:
   - pymbar
   - openmm >=7.6
   - openmoltools # may need to sort out ambermini/ambertools/parmed dependencies (we don't want ambertools)
-  - openmmtools # may need to sort out ambermini/ambertools/parmed dependencies
+  - openmmtools >=0.21.2 # may need to sort out ambermini/ambertools/parmed dependencies
   - numba
   - netcdf4
   - matplotlib
@@ -47,3 +47,4 @@ dependencies:
   - pytest-attrib
   - pytest-xdist
   - arsenic
+  - click

perses/app/cli.py

@@ -0,0 +1,172 @@
+# New cli for testing
+import datetime
+from pathlib import Path
+
+import click
+import openmmtools.utils
+from perses.app.setup_relative_calculation import getSetupOptions
+
+percy = """
+MMMMMMMMMMMMXo:ccldOKNNWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMWxcxOkxdodddxxxk0XWMMMMMMMMMMMMMMMMMMMMMMMMMMMMMWWWWMMWNX0Okk0WMMMMMM
+MMMMMMMMMMMWxlk0OkdddddxkxdoodONWNXK0OOOOOOOOO0KXNWMMMMN0kxxxxxxxxddoddockWMMMMM
+MMMMMMMMMMMMKooOOxooooc;:ldOOxooddddodddddddddodddxxkOkoodkOOkxdodxO000kcxWMMMMM
+MMMMMMMMMMMMMKolk0000OdoddllxOOkkO00000O000000000OkxdookOOdl:cloooxO00kloXMMMMMM
+MMMMMMMMMMMMMMNklokO0OO000OkkO000000000000O000000000O00OdllollxO0000OdldXMMMMMMM
+MMMMMMMMMMMMMMMWXkdodkO00O00O0000OdlxO000000000OxxkO000OxkO00OOO00Odlo0WMMMMMMMM
+MMMMMMMMMMMMMMMMMMWKkdldOOOO00000kdxOO000000000OxldO0000OO000OOxdoox0NMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMXdldOOO0000O000kkO0000000O0OOOOO0O00000Odloxk0NMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMKook00000000000Odlk00000000kooO000O00000OxcxNMMMMMWX0KNMMMMMM
+MMMMMMMMMMMMMMMMMMKloO00000000000O0OkxdooooodxkxkO000000000O0xlkWMMMNkloook0OkxO
+MMMMMMMMMMMMMMMMMNolO000000000000OxlllodddddolloxO00000000O00Odl0MMMOcx0Okooddo:
+MMMMMMMMMMMMMMMMMOcx0OO00000O000kocoxxkO000OOkkocoO0000O0O0000kldWMMxck0000000xc
+MMMMMMMMMMMMMMMMWdlO00O000000OOOo:dd:,:x000xc;cxd:d0000OO000O0OolXMWxck00OO0Oxlx
+MMMMMMMMMMMMMMMMXooOO0000OOOOxkkclkc,,lO000k:,,lxclO00000000000dl0MNdcO0000kolkN
+MMMMMMMMMMMMMMMMXolO00000kolccxOlckxook0000Oxlokx:okdkkxkO00000dl0XxlxO000kloXWM
+MMMMMMMMMMMMMMMMNdlO00000OOd:lO0xclk00000000O0Oxclkkc;loxO0000OocoookO000OolKMMM
+MMMMMMMMMMMMMMMMMOcx00000000xclkOkocldkOOOOOxdlldOOocoOO000000Oc,lxO00000kcxWMMM
+MMMMMMMMMMMMMMMMMNdlO000000O0kocokOkdoooooooooxOkdllxO000O000Od:oO00O000OooXMMMM
+MMMMMMMMMMMMMMMMMMXolk00000O00OkollodxkkkkkkkxdlllxO00000OOOOd:oO000O00OdcOMMMMM
+MMMMMMMMMMMMMMMMMMM0::xO0000000O0OkdooooooooooodkO000000000OocoO000O000xlxWMMMMM
+MMMMMMMMMMMMMMMMMNOoccclxO00O000000000OOOOOOO00000000OO00OdclxO00O0000kldNMMMMMM
+MMMMMMMMMMMMMMMWKdlxOOkolldkO0000000000000000000000000OxolldO0O000000kldNMMMMMMM
+MMMMMMMMMMMMMMWOldO00O00OxollodxOO000000000000000OOkdolloxO000O0000OxlxNMMMMMMMM
+MMMMMMMMMMMMMWkldO000O00000OkdoooooooodddddddoooooooodkO000OO0O000OdlOWMMMMMMMMM
+MMMMMMMMMMMMWOldO00000000000000OOkxxddooooooooddxkO0000O000000O0kdoxKWMMMMMMMMMM
+MMMMMMMMMMMMXooO000000O0000000O0000000000000000OO00000OO000000kooxKWMMMMMMMMMMMM
+MMMMMMMMMMMWxck00000000000000O000000000000000000O00OO000000O00dcOMMMMMMMMMMMMMMM
+MMMWKkkOKWMXooO000000OkkO000000000000000000000000O000000000O00xckMMMMMMMMMMMMMMM
+WMKdlcccldKOcd000000OdcdO0000000000000000000000000000000000000klkMMMMMMMMMMMMMMM
+odccocccdllolk000000d:oO00000000000000000000000000000000000000OlxWMMMMMMMMMMMMMM
+;:;:c::oxllolk00000kclO000000000000000000000000000000000000000OcdWMMMMMMMMMMMMMM
+Oollodxdl;lc:x0000Oo:x0000000000000000000000000000000000000000kcxWMMMMMMMMMMMMMM
+MN0kxxo::odl:d0000Olck000000000000000000000000000000000000O000dcOMMMMMMMMMMMMMMM
+MMMMMMWKkddo;cO000Olck0000000000000000000000000000000000000O0OloNMMMMMMMMMMMMMMM
+MMMMMMMMMWWOcoO000OkclO0000000000000000000000000000000000000Ool0MMMMMMMMMMMMMMMM
+MMMMMMMMMMWxck0OOO0Olck00O00000000000000000000000000000O000Ool0WMMMMMMMMMMMMMMMM
+MMMMMMMMMMM0loxolool:oO000000O000000000000000000000000000OxldKMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMWKkxkKN0o;ck0000O000000000000000000000000OO0OxooONMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMWxck000O000OkkO000000000000000000Oxo:;xNMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMOcx0000000kloO0000000000000Okxoollolc0MMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMKld000O000d;codddddddddoooclooodkO0olKMMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMNolO00000Oll00OOkkkkkkkO0OllO000O0OloNMMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMWxck00000kckMMMMMMMMMMMMMMkcx00000kcxWMMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMMkcx00000dcOMMMMMMMMMMMMMMKld00O00xckMMMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMWdlk00000kckWMMMMMMMMMMMMM0ld0OOO0kldNMMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMKlo0OkkO0OloNMMMMMMMMMMMMWxck0OOOO0dc0MMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMXocdoollxxcdNMMMMMMMMMMMMMkcxOdlloxlc0MMMMMMMMMMMMMMMMMMMMMM
+MMMMMMMMMMMMMMMMMMMMMKolxXXxc:oKMMMMMMMMMMMMMMKl:::x0dcckNMMMMMMMMMMMMMMMMMMMMMM
+"""
+
+
+def _check_openeye_license():
+    import openeye
+
+    assert openeye.oechem.OEChemIsLicensed(), "OpenEye license checks failed!"
+
+
+def _test_platform(platform_name):
+    import openmm.testInstallation
+
+    openmm.testInstallation.main()
+
+    # If a user asks for a platform, try and see if we can use it
+    if platform_name:
+        assert openmmtools.utils.platform_supports_precision(platform_name, 'mixed')
+        click.echo("🎉\t Platform test successful!")
+
+
+def _write_out_files(path, options):
+
+    # Convert path to a pathlib object
+    yaml_path = Path(path)
+
+    # Generate parsed yaml name
+    yaml_name = yaml_path.name
+    time = datetime.datetime.now().strftime("%Y-%m-%d-%H:%M:%S")
+    yaml_parse_name = f"parsed-{time}-{yaml_name}"
+
+    # First make files in same dir as yaml
+    files_next_to_yaml = [
+        "debug.png",
+        "system.xml",
+        yaml_parse_name,
+    ]
+
+    for _file in files_next_to_yaml:
+        with open(_file, "w") as fp:
+            pass
+
+    # Now we make the directory structure
+    trajectory_directory = Path(options["trajectory_directory"])
+    dirs_to_make = trajectory_directory.joinpath("xml")
+    Path(dirs_to_make).mkdir(parents=True, exist_ok=True)
+
+    # Now files that belong in the lower directories
+    files_in_lower_dir = [
+        "atom_mapping.png",
+        "out-complex_checkpoint.nc",
+        "out-complex.nc",
+        "out-complex.pdb",
+        "outhybrid_factory.npy.npz",
+        "out-solvent_checkpoint.nc",
+        "out-solvent.nc",
+        "out-solvent.pdb",
+        "out_topology_proposals.pkl",
+        "out-vacuum_checkpoint.nc",
+        "out-vacuum.nc",
+    ]
+
+    # add the dir prefix
+    files_in_lower_dir = [
+        Path(trajectory_directory).joinpath(_) for _ in files_in_lower_dir
+    ]
+
+    for _file in files_in_lower_dir:
+        with open(_file, "w") as fp:
+            pass
+
+    # Now the files in the 'xml' dir
+    files_in_xml_dir = [
+        "complex-hybrid-system.gz",
+        "complex-new-system.gz",
+        "complex-old-system.gz",
+        "solvent-hybrid-system.gz",
+        "solvent-new-system.gz",
+        "solvent-old-system.gz",
+        "vacuum-hybrid-system.gz",
+        "vacuum-new-system.gz",
+        "vacuum-old-system.gz",
+    ]
+
+    # add the dir prefix
+    files_in_xml_dir = [dirs_to_make.joinpath(_) for _ in files_in_xml_dir]
+
+    for _file in files_in_lower_dir:
+        with open(_file, "w") as fp:
+            pass
+
+
+@click.command()
+@click.option("--yaml", type=click.Path(exists=True, dir_okay=False), required=True)
+@click.option("--platform-name", type=str, default=None)
+def cli(yaml, platform_name):
+    """test"""
+    click.echo(click.style(percy, fg="bright_magenta"))
+    click.echo("📖\t Fetching simulation options ")
+    options = getSetupOptions(yaml)
+    click.echo("🖨️\t Printing options")
+    click.echo(options)
+    click.echo("🕵️\t Checking OpenEye license")
+    _check_openeye_license()
+    click.echo("✅\t OpenEye license good")
+    click.echo("🖥️⚡\t Checking whether requested compute platform is available")
+    _test_platform(platform_name)
+    click.echo("🖨️\t Writing out files")
+    trajectory_directory = options["trajectory_directory"]
+    _write_out_files(trajectory_directory, options)
+    click.echo("🧪\t Simulation over")
+
+
+if __name__ == "__main__":
+    cli()

perses/tests/conftest.py

@@ -20,3 +20,8 @@ def pytest_collection_modifyitems(config, items):
         for item in items:
             if "slow" in item.keywords:
                 item.add_marker(skip_slow)
+
+@pytest.fixture
+def in_tmpdir(tmpdir):
+    with tmpdir.as_cwd():
+        yield

perses/tests/test_cli.py

@@ -0,0 +1,49 @@
+from click.testing import CliRunner
+from perses.app.cli import cli
+
+test_yaml = """
+protein_pdb: Tyk2_protein.pdb
+ligand_file: Tyk2_ligands_shifted.sdf
+old_ligand_index: 0
+new_ligand_index: 3
+forcefield_files:
+  - amber/ff14SB.xml
+  - amber/tip3p_standard.xml
+  - amber/tip3p_HFE_multivalent.xml
+  - amber/phosaa10.xml
+small_molecule_forcefield: openff-1.0.0
+pressure: 1
+temperature: 300
+solvent_padding: 9
+atom_expression:
+  - IntType
+bond_expession:
+  - DefaultBonds
+n_steps_per_move_application: 1
+fe_type: repex
+checkpoint_interval: 50
+n_cycles: 1
+n_states: 3
+n_equilibration_iterations: 0
+trajectory_directory: temp/offlig10to24
+trajectory_prefix: out
+atom_selection: not water
+phases:
+  - complex
+  - solvent
+  - vacuum
+timestep: 4
+h_constraints: true
+"""
+
+
+def test_dummy_cli(in_tmpdir):
+    runner = CliRunner()
+    with runner.isolated_filesystem():
+        with open("test.yaml", "w") as f:
+            f.write(test_yaml)
+
+        result = runner.invoke(cli, ["--yaml", "test.yaml"])
+        print(result)
+        print(result.output)
+        assert result.exit_code == 0

setup.py

@@ -90,6 +90,7 @@ def find_package_data(data_root, package_root):
         "console_scripts": [
             "perses-relative = perses.app.setup_relative_calculation:run",
             "perses-fah = perses.app.fah_generator:run",
+            "perses-cli = perses.app.cli:cli",
         ],
     },
     ext_modules=extensions,