Initial work on System implementation

It is not clear how to design those classes, though.

pism_ragis/__init__.py

@@ -12,5 +12,6 @@
     "stats",
     "computing",
     "interpolation",
+    "systems",
     "trajectories",
 ]

pism_ragis/systems.py

@@ -0,0 +1,150 @@
+# Copyright (C) 2023 Andy Aschwanden
+#
+# This file is part of pism-ragis.
+#
+# PISM-RAGIS is free software; you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation; either version 3 of the License, or (at your option) any later
+# version.
+#
+# PISM-RAGIS is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PISM; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+"""
+Module provides System class
+"""
+
+from pathlib import Path
+from typing import Union
+
+import toml
+
+
+class System:
+    """
+    Class fo a system
+    """
+
+    def __init__(self, d: Union[dict, Path, str]):
+        if isinstance(d, dict):
+            for key, value in d.items():
+                setattr(self, key, value)
+        elif isinstance(d, Path):
+            for key, value in toml.load(d).items():
+                setattr(self, key, value)
+        elif isinstance(d, str):
+            self._values = toml.loads(d)
+        else:
+            print(f"{d} not recognized")
+
+    def to_dict(self):
+        """
+        Returns self as dictionary
+        """
+        return self.__dict__
+
+    def __repr__(self):
+        repr_str = ""
+
+        repr_str += toml.dumps(self.to_dict())
+
+        return f"""
+
+System
+------------
+
+{repr_str}
+        """
+
+
+class Systems:
+    """
+    Class to hold Systems of base class System
+    """
+
+    def __init__(self):
+        self._default_path: Path = Path("data/")
+        self.add_systems_from_path(self.default_path)
+
+    @property
+    def default_path(self):
+        """
+        Return default path to glob for toml files
+        """
+        return self._default_path
+
+    @default_path.setter
+    def default_path(self, value):
+        self._default_path = value
+
+    def __getitem__(self, name):
+        return self._values[name]
+
+    def __setitem__(self, key, value):
+        setattr(self, key, value)
+
+    def __iter__(self):
+        return iter(self._values)
+
+    def keys(self):
+        """
+        Return keys
+        """
+        return self._values.keys()
+
+    def items(self):
+        """
+        Return items
+        """
+        return self._values.items()
+
+    def values(self):
+        """
+        Return values
+        """
+        return self._values.values()
+
+    def add_system(self, system):
+        """
+        Add a system from a System class
+        """
+        system.to_dict()
+
+    def add_systems_from_path(self, path):
+        """
+
+        Add systems from a pathlib.Path.
+
+        Use glob to add all files with suffix `toml`.
+        """
+        p = Path(path).glob("*.toml")
+        sys = {}
+        for p_ in p:
+            s = toml.load(p_)
+            machine = s["machine"]
+            sys[machine] = s
+        self._values = sys
+
+    # def __len__(self):
+    #     return len(self.systems)
+
+    def dump(self):
+        """
+        Dump class to string
+        """
+        repr_str = ""
+        for s in self.values():
+            repr_str += s["machine"]
+            repr_str += "\n------------\n\n"
+            repr_str += toml.dumps(s)
+            repr_str += "\n"
+        return repr_str
+
+    def __repr__(self):
+        return self.dump()

requirements.txt

@@ -13,3 +13,5 @@ pyogrio>=0.7.2
 pyarrow>=14.0.0
 tqdm>=4.66.1
 openpyxl>=3.1.2
+toml
+types-toml

tests/data/chinook.toml

@@ -0,0 +1,53 @@
+machine = "chinook"
+
+[MPI]
+
+mpido = "mpirun -np {cores} -machinefile ./nodes_$SLURM_JOBID"
+
+[scheduler]
+
+name = "SLRUM"
+submit = "sbatch"
+job_id =  "SLURM_JOBID"
+
+[filesystem]
+
+work_dir = "SLURM_SUBMIT_DIR"
+
+[queues]
+
+t1standard = 24
+t1small = 24
+t2standard =  24
+t2small = 24
+debug = 24
+analysis = 24
+
+[job]
+
+header =  """#!/bin/sh
+#SBATCH --partition={queue}
+#SBATCH --ntasks={cores}
+#SBATCH --tasks-per-node={ppn}
+#SBATCH --time={walltime}
+#SBATCH --mail-type=BEGIN
+#SBATCH --mail-type=END
+#SBATCH --mail-type=FAIL
+#SBATCH --output=pism.%j
+
+module list
+
+umask 007
+
+cd $SLURM_SUBMIT_DIR
+
+# Generate a list of compute node hostnames reserved for this job,
+# this ./nodes file is necessary for slurm to spawn mpi processes
+# across multiple compute nodes
+srun -l /bin/hostname | sort -n | awk '{{print $2}}' > ./nodes_$SLURM_JOBID
+
+ulimit -l unlimited
+ulimit -s unlimited
+ulimit
+
+"""

tests/test_systems.py

@@ -0,0 +1,88 @@
+# Copyright (C) 2023 Andy Aschwanden
+#
+# This file is part of pism-ragis.
+#
+# PISM-RAGIS is free software; you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation; either version 3 of the License, or (at your option) any later
+# version.
+#
+# PISM-RAGIS is distributed in the hope that it will be useful, but WITHOUT ANY
+# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PISM; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
+
+"""
+Tests for Systems class
+
+We need a way to register machine. Maybe the machine list should be its own repo?
+"""
+
+from pathlib import Path
+
+import pytest
+
+from pism_ragis.systems import System
+
+
+@pytest.fixture(name="machine_file")
+def fixture_machine_file():
+    """
+    Return Path to toml file
+    """
+    return Path("tests/data/chinook.toml")
+
+
+@pytest.fixture(name="machine_dict")
+def fixture_machine_dict():
+    """
+    Return system dict
+    """
+    return {
+        "machine": "chinook",
+        "MPI": {"mpido": "mpirun -np {cores} -machinefile ./nodes_$SLURM_JOBID"},
+        "scheduler": {"name": "SLRUM", "submit": "sbatch", "job_id": "SLURM_JOBID"},
+        "filesystem": {"work_dir": "SLURM_SUBMIT_DIR"},
+        "queues": {
+            "t1standard": 24,
+            "t1small": 24,
+            "t2standard": 24,
+            "t2small": 24,
+            "debug": 24,
+            "analysis": 24,
+        },
+    }
+
+
+def test_system_from_dict(machine_dict):
+    """
+    Test creating a System from a dictionary
+    """
+    s = System(machine_dict)
+    assert s.machine == "chinook"  # type: ignore[attr-defined] # pylint: disable=E1101
+
+
+def test_system_from_file(machine_file):
+    """
+    Test creating a System from a toml file
+    """
+    s = System(machine_file)
+    assert s.machine == "chinook"  # type: ignore[attr-defined] # pylint: disable=E1101
+
+
+# @pytest.fixture
+# def systems():
+#     """
+#     Return a basic systems
+#     """
+
+#     p = "tests/data"
+#     return Systems(p)
+
+
+# def test_systems_len(systems):
+#     assert len(systems) == 2