Make ase,mdtraj and MDAnalysis optional extras

.github/workflows/tests.yml

@@ -29,7 +29,7 @@ jobs:
 
       - name: Install MDANSE
         working-directory: MDANSE
-        run: python -m pip install --group test .
+        run: python -m pip install --group test --group external .
 
       - name: Run unit tests
         working-directory: MDANSE
@@ -66,7 +66,7 @@ jobs:
 
       - name: Install MDANSE
         working-directory: MDANSE
-        run: python -m pip install --group test .
+        run: python -m pip install --group test --group external .
 
       - name: Install MDANSE_GUI
         working-directory: MDANSE_GUI

MDANSE/Src/MDANSE/Framework/Configurable.py

@@ -15,6 +15,8 @@
 #
 from __future__ import annotations
 
+from typing import Any, ClassVar
+
 from more_itertools import value_chain
 
 from MDANSE.MLogging import LOG
@@ -40,9 +42,10 @@ class Configurable:
             #.. 2-value is the dictionary of the keywords used when initializing the configurator.
     """
 
-    enabled = True
+    enabled: ClassVar[bool] = True
+    visible: ClassVar[bool] = True
 
-    settings = {}
+    settings: ClassVar[dict[str, tuple[str, dict[str, Any]]]] = {}
 
     def __init__(self, settings=None, trajectory_input="mdanse"):
         """

MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py

@@ -15,13 +15,16 @@
 #
 from __future__ import annotations
 
-from ase.io.formats import all_formats
-
 from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 from MDANSE.Framework.Configurators.InputFileConfigurator import InputFileConfigurator
 from MDANSE.MLogging import LOG
 
+try:
+    from ase.io.formats import all_formats
+except ImportError:
+    all_formats = []
+
 
 @IConfigurator.register("AseInputFileConfigurator")
 class AseInputFileConfigurator(InputFileConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisCoordinateFileConfigurator.py

@@ -15,12 +15,15 @@
 #
 from __future__ import annotations
 
-import MDAnalysis as mda
+from contextlib import suppress
 
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
 from .MultiInputFileConfigurator import MultiInputFileConfigurator
 
+with suppress(ImportError):
+    import MDAnalysis as mda
+
 
 @IConfigurator.register("MDAnalysisCoordinateFileConfigurator")
 class MDAnalysisCoordinateFileConfigurator(MultiInputFileConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTimeStepConfigurator.py

@@ -17,11 +17,12 @@
 
 from contextlib import suppress
 
-import MDAnalysis as mda
-
 from MDANSE.Framework.Configurators.FloatConfigurator import FloatConfigurator
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
+with suppress(ImportError):
+    import MDAnalysis as mda
+
 
 @IConfigurator.register("MDAnalysisTimeStepConfigurator")
 class MDAnalysisTimeStepConfigurator(FloatConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/MDAnalysisTopologyFileConfigurator.py

@@ -16,14 +16,16 @@
 from __future__ import annotations
 
 from collections.abc import Iterable
-
-import MDAnalysis as mda
+from contextlib import suppress
 
 from MDANSE.Framework.AtomMapping import AtomLabel
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
 from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator
 
+with suppress(ImportError):
+    import MDAnalysis as mda
+
 
 @IConfigurator.register("MDAnalysisTopologyFileConfigurator")
 class MDAnalysisTopologyFileConfigurator(FileWithAtomDataConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTimeStepConfigurator.py

@@ -17,11 +17,12 @@
 
 from contextlib import suppress
 
-import mdtraj as md
-
 from MDANSE.Framework.Configurators.FloatConfigurator import FloatConfigurator
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
+with suppress(ImportError):
+    import mdtraj as md
+
 
 @IConfigurator.register("MDTrajTimeStepConfigurator")
 class MDTrajTimeStepConfigurator(FloatConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTopologyFileConfigurator.py

@@ -17,16 +17,18 @@
 
 import traceback
 from collections.abc import Iterable
+from contextlib import suppress
 from pathlib import Path
 
-import mdtraj as md
-from mdtraj.core.trajectory import _TOPOLOGY_EXTS
-
 from MDANSE.Framework.AtomMapping import AtomLabel
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
 from .FileWithAtomDataConfigurator import FileWithAtomDataConfigurator
 
+with suppress(ImportError):
+    import mdtraj as md
+    from mdtraj.core.trajectory import _TOPOLOGY_EXTS
+
 
 @IConfigurator.register("MDTrajTopologyFileConfigurator")
 class MDTrajTopologyFileConfigurator(FileWithAtomDataConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/MDTrajTrajectoryFileConfigurator.py

@@ -15,14 +15,16 @@
 #
 from __future__ import annotations
 
+from contextlib import suppress
 from pathlib import Path
 
-from mdtraj.formats.registry import FormatRegistry
-
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
 from .MultiInputFileConfigurator import MultiInputFileConfigurator
 
+with suppress(ImportError):
+    from mdtraj.formats.registry import FormatRegistry
+
 
 @IConfigurator.register("MDTrajTrajectoryFileConfigurator")
 class MDTrajTrajectoryFileConfigurator(MultiInputFileConfigurator):

MDANSE/Src/MDANSE/Framework/Configurators/OutputStructureConfigurator.py

@@ -17,11 +17,14 @@
 
 from pathlib import Path
 
-from ase.io.formats import ioformats
-
 from MDANSE import PLATFORM
 from MDANSE.Framework.Configurators.IConfigurator import IConfigurator
 
+try:
+    from ase.io.formats import ioformats
+except ImportError:
+    ioformats = []
+
 
 @IConfigurator.register("OutputStructureConfigurator")
 class OutputStructureConfigurator(IConfigurator):

MDANSE/Src/MDANSE/Framework/Converters/ASE.py

@@ -20,15 +20,12 @@
 from math import sqrt
 
 import numpy as np
-from ase import Atoms
-from ase.io.trajectory import Trajectory as ASETrajectory
 from more_itertools import ilen
 
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
 from MDANSE.Framework.AtomMapping import get_element_from_mapping
 from MDANSE.Framework.Converters.Converter import Converter
 from MDANSE.Framework.Jobs.IJob import IJob
-from MDANSE.Framework.Parsers import ASEParser
 from MDANSE.Framework.Units import INTERNAL_UNITS, UnitError, measure
 from MDANSE.MLogging import LOG
 from MDANSE.MolecularDynamics.Configuration import (
@@ -38,6 +35,17 @@
 from MDANSE.MolecularDynamics.Trajectory import TrajectoryWriter
 from MDANSE.MolecularDynamics.UnitCell import UnitCell
 
+try:
+    from ase import Atoms
+    from ase.io.trajectory import Trajectory as ASETrajectory
+
+    from MDANSE.Framework.Parsers import ASEParser
+
+    ase_available = True
+except ImportError:
+    ASEParser = object()
+    ase_available = False
+
 
 class ASETrajectoryFileError(Exception):
     pass
@@ -56,6 +64,8 @@ class ASE(Converter):
     standard input file names.
     """
 
+    enabled = ase_available
+    requires_extras = ("ase",)
     category = ("Converters", "General")
     label = "ASE"
 

MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py

@@ -18,8 +18,6 @@
 from pathlib import Path
 
 import numpy as np
-from mdtraj.formats.trr import TRRTrajectoryFile
-from mdtraj.formats.xtc import XTCTrajectoryFile
 
 from MDANSE.Framework.Converters.Converter import Converter
 from MDANSE.Framework.Jobs.IJob import IJob
@@ -28,6 +26,14 @@
 from MDANSE.MolecularDynamics.Trajectory import TrajectoryWriter
 from MDANSE.MolecularDynamics.UnitCell import UnitCell
 
+try:
+    from mdtraj.formats.trr import TRRTrajectoryFile
+    from mdtraj.formats.xtc import XTCTrajectoryFile
+
+    mdtraj_available = True
+except ImportError:
+    mdtraj_available = False
+
 
 class GromacsConverterError(Exception):
     pass
@@ -38,6 +44,8 @@ class GromacsConverterError(Exception):
 class Gromacs(Converter):
     """Converts a Gromacs trajectory to an MDT trajectory."""
 
+    enabled = mdtraj_available
+    requires_extras = ("mdtraj",)
     label = "Gromacs"
 
     settings = {}

MDANSE/Src/MDANSE/Framework/Converters/MDAnalysis.py

@@ -15,8 +15,6 @@
 #
 from __future__ import annotations
 
-import MDAnalysis as mda
-
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
 from MDANSE.Framework.AtomMapping import get_element_from_mapping
 from MDANSE.Framework.Converters.Converter import Converter
@@ -29,6 +27,13 @@
 from MDANSE.MolecularDynamics.Trajectory import TrajectoryWriter
 from MDANSE.MolecularDynamics.UnitCell import UnitCell
 
+try:
+    import MDAnalysis as mda
+
+    mda_available = True
+except ImportError:
+    mda_available = False
+
 
 @IJob.register("MDAnalysis")
 @Converter.register("MDAnalysis")
@@ -45,6 +50,8 @@ class MDAnalysis(Converter):
     <a href="https://userguide.mdanalysis.org/stable/formats/index.html#formats">formats</a>.
     """
 
+    enabled = mda_available
+    requires_extras = ("mdanalysis",)
     category = ("Converters", "General")
     label = "MDAnalysis"
     settings = {}

MDANSE/Src/MDANSE/Framework/Converters/MDTraj.py

@@ -17,8 +17,6 @@
 
 from math import isclose
 
-import mdtraj as md
-
 from MDANSE.Chemistry.ChemicalSystem import ChemicalSystem
 from MDANSE.Framework.AtomMapping import get_element_from_mapping
 from MDANSE.Framework.Converters.Converter import Converter
@@ -30,6 +28,13 @@
 from MDANSE.MolecularDynamics.Trajectory import TrajectoryWriter
 from MDANSE.MolecularDynamics.UnitCell import UnitCell
 
+try:
+    import mdtraj as md
+
+    mdtraj_available = True
+except ImportError:
+    mdtraj_available = False
+
 
 @IJob.register("MDTraj")
 @Converter.register("MDTraj")
@@ -41,6 +46,8 @@ class MDTraj(Converter):
     trajectories will be stitched together.
     """
 
+    enabled = mdtraj_available
+    requires_extras = ("mdtraj",)
     category = ("Converters", "General")
     label = "MDTraj"
     settings = {}

MDANSE/Src/MDANSE/Framework/Jobs/AverageStructure.py

@@ -18,13 +18,19 @@
 from pathlib import Path
 
 import numpy as np
-from ase.atoms import Atom, Atoms
-from ase.io import write as ase_write
 
 from MDANSE import PLATFORM
 from MDANSE.Framework.Jobs.IJob import IJob
 from MDANSE.Framework.Units import measure
 
+try:
+    from ase.atoms import Atom, Atoms
+    from ase.io import write as ase_write
+
+    ase_available = True
+except ImportError:
+    ase_available = False
+
 
 @IJob.register("AverageStructure")
 class AverageStructure(IJob):
@@ -41,6 +47,8 @@ class AverageStructure(IJob):
     you can output just the crystalline part using a corresponding atom selection.
     """
 
+    enabled = ase_available
+    requires_extras = ("ase",)
     label = "Average Structure"
 
     category = ("Trajectory",)

MDANSE/Src/MDANSE/Framework/Jobs/CartesianCorrelationFunction.py

@@ -29,6 +29,7 @@
 
 class CartesianCorrelationFunction(IJob):
     enabled = False
+    visible = False
 
     category = (
         "Analysis",

MDANSE/Src/MDANSE/Framework/Jobs/DistanceHistogram.py

@@ -41,6 +41,7 @@ class DistanceHistogram(IJob):
     type = None
 
     enabled = False
+    visible = False
 
     category = (
         "Analysis",

MDANSE/Src/MDANSE/Framework/Jobs/IJob.py

@@ -200,11 +200,13 @@ class IJob(Configurable, RegisterFactory, ABC):
     """
 
     registry: ClassVar[UCDict[str, type[IJob]]] = UCDict()
+    requires_extras: ClassVar[tuple[str, ...]] = ()
 
     section = "job"
     key_gen = key_generator(6)
     ancestor: ClassVar[list[str]] = []
     PREDICTORS: ClassVar[tuple[str, ...]] = ()
+
     runscript_import_line = "from MDANSE.Framework.Jobs.IJob import IJob"
 
     def __init__(self, trajectory_input="mdanse"):

MDANSE/Src/MDANSE/Framework/Jobs/RotationAutocorrelation.py

@@ -34,6 +34,7 @@ class RotationAutocorrelation(IJob):
     """
 
     enabled = False
+    visible = False
 
     label = "Rotation Autocorrelation"
 

MDANSE/Src/MDANSE/Framework/Parsers/CASTEP_MD.py

@@ -22,7 +22,6 @@
 from typing import Any
 
 import numpy as np
-from ase.io.trajectory import Trajectory as ASETrajectory
 from more_itertools import first, one, split_at
 
 from MDANSE.Framework.AtomMapping import AtomLabel