Merge pull request #14 from exabl/enh/snake-nek

More Nek5000 params

.git_archival.txt

@@ -0,0 +1 @@
+ref-names: :%D$

.gitattributes

@@ -0,0 +1 @@
+.git_archival.txt  export-subst

.github/workflows/tests.yml

@@ -24,6 +24,7 @@ jobs:
       uses: actions/checkout@v2
       with:
         submodules: recursive
+        fetch-depth: 0
 
     - name: Install apt packages
       run: |
@@ -44,16 +45,22 @@ jobs:
         restore-keys: |
           ${{ runner.os }}-pip-
 
+    - name: Verify Python environment
+      run: |
+        pip list
+        pip cache list
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel
         pip install .[tests]
 
     - name: Run tests
       run: |
         source activate.sh
-        pytest -s
+        pytest -s --cov-report=xml --cov-report=term-missing
 
     - name: Upload coverage to codecov
       if: ${{ success() }}
-      run: bash <(curl -s https://codecov.io/bash)
+      uses: codecov/codecov-action@v1
+      with:
+        fail_ci_if_error: true

README.md

@@ -1,13 +1,16 @@
-# snek5000
+<div align="center">
+<h1>snek5000</h1>
 
 [![PyPI](https://img.shields.io/pypi/v/snek5000)](https://pypi.org/project/snek5000/)
 [![Tests Status](https://github.com/exabl/snek5000/workflows/Tests/badge.svg)](https://github.com/exabl/snek5000/actions?workflow=Tests)
 [![Documentation Status](https://readthedocs.org/projects/snek5000/badge/?version=latest)](https://snek5000.readthedocs.io/en/latest/?badge=latest)
 [![Maintainability Rating](https://sonarcloud.io/api/project_badges/measure?project=exabl_snek5000&metric=sqale_rating)](https://sonarcloud.io/dashboard?id=exabl_snek5000)
+[![Code coverage](https://codecov.io/gh/exabl/snek5000/branch/master/graph/badge.svg?token=WzGnN0dfbw)](https://codecov.io/gh/exabl/snek5000)
 
-Python framework for Nek5000.
+Python framework for Nek5000
+</div>
 
-**Warning:** This framework is experimental and of beta-quality. The API can also change.
+**Warning:** This framework is experimental and of beta-quality.
 
 **Documentation**: https://snek5000.readthedocs.io/
 
@@ -49,6 +52,13 @@ Check out the
 [tutorials](https://snek5000.readthedocs.io/en/latest/tutorials.html) to learn
 how to use `snek5000`.
 
+<details>
+<summary>
+<b>
+Need more reasons to use snek5000?
+</b>
+</summary>
+
 #### Advantages
 
 - Saves you from the trouble in setting up multiple source files (`.box`, `.par`, `SIZE`)
@@ -95,6 +105,8 @@ how to use `snek5000`.
   templates](https://jinja.palletsprojects.com/en/2.11.x/templates/) (which are
   not so hard, btw)
 
+</details>
+
 ## Contributing
 
 Contributions are welcome! You can help by testing out the code, filing issues

pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["setuptools>=42.0.0", "wheel", "setuptools_scm[toml]>=3.4.2"]
-
+requires = ["setuptools>=49.5.0", "wheel", "setuptools_scm[toml]>=3.4.2", "setuptools_scm_git_archive"]
+build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 write_to = "src/snek5000/_version.py"
 write_to_template = "__version__ = \"{version}\"\n"
 
 [tool.pytest.ini_options]
-addopts = "--cov=src --cov=tests"
+addopts = "--cov=snek5000 --cov=tests"

setup.cfg

@@ -28,11 +28,15 @@ packages=find:
 install_requires =
     snakemake != 5.23.*, != 5.24.*
     fluidsim >= 0.3.3
+    entrypoints
     jinja2
     inflection
     importlib_resources; python_version < "3.7"
-setup_requires =
-    setuptools_scm
+
+[options.entry_points]
+snek5000.solvers =
+    nek = snek5000.solvers.base
+    kth = snek5000.solvers.kth
 
 [options.extras_require]
 docs =

src/snek5000/__init__.py

@@ -30,6 +30,7 @@
     import importlib_resources as resources
 
 import os
+from pathlib import Path
 
 from fluiddyn.util import mpi  # noqa: F401
 
@@ -66,3 +67,36 @@ def get_asset(asset_name):
     """Fetches path of an asset from subpackage ``snek5000.assets``."""
     asset = next(resources.path("snek5000.assets", asset_name).gen)
     return asset
+
+
+def load_simul(path_dir):
+    path_dir = Path(path_dir)
+
+    from warnings import warn
+
+    info_solver_xml = path_dir / "info_solver.xml"
+    if info_solver_xml.exists():
+        from snek5000.info import InfoSolverNek
+
+        info_solver = InfoSolverNek(path_file=info_solver_xml)
+        solver = info_solver.short_name
+    else:
+        warn(f"The {info_solver_xml} file is missing!")
+        solver = path_dir.name.split("_")[0]
+
+    # Load simulation class
+    from snek5000.solvers import import_solver
+
+    Simul = import_solver(solver)
+
+    # Load parameters
+    params_xml = path_dir / "params.xml"
+    try:
+        params_par = next(path_dir.glob("*.par"))
+    except StopIteration:
+        warn(f"The {path_dir}/*.par file is missing!")
+        params_par = None
+
+    params = Simul.load_params_from_file(path_xml=params_xml, path_par=params_par)
+    sim = Simul(params, existing_path_run=path_dir)
+    return sim

src/snek5000/make.py

@@ -28,13 +28,17 @@ def list(self):
         with change_dir(self.path_run):
             return snakemake(self.file, listrules=True, log_handler=self.log_handler)
 
-    def exec(self, rules=("run",), dryrun=False):
+    def exec(self, rules=("run",), dryrun=False, **kwargs):
         """Execute snakemake rules in sequence.
 
         :returns: True if workflow execution was successful.
 
         """
         with change_dir(self.path_run):
             return snakemake(
-                self.file, targets=rules, dryrun=dryrun, log_handler=self.log_handler
+                self.file,
+                targets=rules,
+                dryrun=dryrun,
+                log_handler=self.log_handler,
+                **kwargs
             )

src/snek5000/solvers/__init__.py

@@ -8,3 +8,22 @@
    kth
 
 """
+
+
+def available_solvers():
+    """Returns a dictionary of all registered solvers registered as an
+    entrypoint_.
+
+    _entrypoint: https://packaging.python.org/guides/creating-and-discovering-plugins/#using-package-metadata
+
+    """
+    import entrypoints
+
+    return entrypoints.get_group_named("snek5000.solvers")
+
+
+def import_solver(name):
+    """Import the Simul class of a solver."""
+    solvers = available_solvers()
+    module = solvers[name].load()
+    return module.Simul

src/snek5000/solvers/base.py

@@ -20,11 +20,19 @@
 class SimulNek(SimulBase):
     """Simulation class
 
-    .. code-block:: python
-
-       from snek5000.solvers.base import Simul
-       params = Simul.create_default_params()
-       sim = Simul(params)
+    Parameters
+    ----------
+    params: Parameters
+        Input parameters for the simulation run.
+    write_files: bool, optional
+        Write simulation files, including usr, box, SIZE files. By default
+        all files are written.
+
+    Example
+    -------
+    >>> from snek5000.solvers.base import Simul
+    >>> params = Simul.create_default_params()
+    >>> sim = Simul(params)
 
     """
 
@@ -115,6 +123,7 @@ def _complete_params_with_default(params):
                 write_control="timeStep",
                 write_interval=10,
                 filtering=None,
+                filter_modes=2,
                 filter_cutoff_ratio=0.65,
                 filter_weight=12.0,
                 write_double_precision=True,
@@ -134,17 +143,32 @@ def _complete_params_with_default(params):
                 stress_formulation=False,
             )
         )
-        common = dict(residual_tol=math.nan, residual_proj=False)
+        common = dict(
+            residual_tol=math.nan, residual_proj=False, write_to_field_file=True
+        )
         params_nek.velocity._set_attribs(common)
         params_nek.pressure._set_attribs(common)
         params_nek.temperature._set_attribs(common)
         params_nek.scalar01._set_attribs(common)
 
+        common_ts = dict(solver="helm", advection=True, absolute_tol=math.nan)
+        params_nek.temperature._set_attribs(common_ts)
+        params_nek.scalar01._set_attribs(common_ts)
+
+        params_nek.mesh._set_attrib("write_to_field_file", True)
         params_nek.velocity._set_attribs(dict(viscosity=math.nan, density=math.nan))
         params_nek.pressure._set_attrib("preconditioner", "semg_xxt")
+        params_nek.temperature._set_attribs(
+            dict(
+                conjugate_heat_transfer=False,
+                conductivity=math.nan,
+                rho_cp=math.nan,
+            )
+        )
+        params_nek.scalar01._set_attribs(dict(density=math.nan, diffusivity=math.nan))
         return params
 
-    def __init__(self, params):
+    def __init__(self, params, existing_path_run=None):
         np.seterr(all="warn")
         np.seterr(under="ignore")
 
@@ -177,10 +201,14 @@ def __init__(self, params):
                 setattr(self, cls_name.lower(), Class(self))
 
         if "Output" in dict_classes:
-            # path_run would be initialized by the Output instance if available
-            # See self.output._init_name_run()
-            self.path_run = Path(self.output.path_run)
-            self.output.copy(self.path_run)
+            if existing_path_run:
+                self.path_run = self.output.path_run = Path(existing_path_run)
+            else:
+                # path_run would be initialized by the Output instance if available
+                # See self.output._init_name_run()
+                self.path_run = Path(self.output.path_run)
+                if mpi.rank == 0:
+                    self.output.copy(self.path_run)
         else:
             par_file = None
             self.path_run = None
@@ -193,14 +221,15 @@ def __init__(self, params):
             logger.info(f"solver: {self.__class__}")
             logger.info(f"path_run: {self.path_run}")
             logger.info("*" * _banner_length)
-            if self.path_run:
+            if self.path_run and not existing_path_run:
                 par_file = self.path_run / f"{self.output.name_pkg}.par"
                 logger.info(f"Writing params files... {par_file}, params.xml")
                 with open(par_file, "w") as fp:
                     params.nek._write_par(fp)
 
                 params._save_as_xml(
-                    self.path_run / "params.xml", f"eTurb version {__version__}"
+                    self.path_run / "params.xml",
+                    f"snek5000 version {__version__}",
                 )
 
 

src/snek5000/solvers/kth.py

@@ -2,16 +2,30 @@
 ==================
 
 """
-from ..info import InfoSolverMake
+# FIXME: This breaks because a different layout is used?
+# from ..info import InfoSolverMake as _InfoSolver
+from ..info import InfoSolverNek as _InfoSolver
 from ..util import docstring_params
 from .base import SimulNek
 
 
+class InfoSolverKTH(_InfoSolver):
+    """Contain the information on a :class:`snek5000.solvers.kth.SimulKTH`
+    instance.
+
+    """
+
+    def _init_root(self):
+        super()._init_root()
+        self.module_name = "snek5000.solvers.kth"
+        self.class_name = "Simul"
+        self.short_name = "kth"
+
+
 class SimulKTH(SimulNek):
     """A base class which incorporates parameters for KTH toolbox also."""
 
-    # FIXME: This breaks because a different layout is used?
-    # InfoSolver = InfoSolverMake
+    InfoSolver = InfoSolverKTH
 
     @staticmethod
     def _complete_params_with_default(params):

src/snek5000/util/archive.py

@@ -103,9 +103,7 @@ def exec_tar(tarball, items, remove):
     else:
         output = tar
 
-    main = shlex.split(
-        tar_cmd(compress_format, remove=remove, append=output.exists())
-    )
+    main = shlex.split(tar_cmd(compress_format, remove=remove, append=output.exists()))
 
     # run command
     items = [str(i) for i in items]
@@ -152,7 +150,7 @@ def parse_args_from_filename(tarball):
 
 def compress_cmd(compress_format):
     compress_program = {
-        ".gz": "pigz",
+        ".gz": "pigz" if shutil.which("pigz") else "gzip",
         ".xz": "xz",
         ".lz4": "lz4",
         ".zst": "zstdmt --rm",
@@ -164,7 +162,7 @@ def compress_cmd(compress_format):
 def tar_cmd(compress_format="", remove=False, append=False):
     archive_program = {
         "": "tar",
-        ".gz": "tar --use-compress-program pigz",
+        ".gz": f"tar --use-compress-program {compress_cmd('.gz')}",
         ".xz": "tar",
         ".lz4": "tar --use-compress-program lz4",
         ".zst": "tar --use-compress-program zstdmt",

tests/test_solver.py

@@ -1,3 +1,13 @@
+from snek5000 import load_simul
+from snek5000.solvers import available_solvers, import_solver
+
+
+def test_entrypoints():
+    solvers = available_solvers()
+    assert "nek" in solvers
+    assert "kth" in solvers
+    assert "phill" in solvers
+
 
 def test_init_base():
     from snek5000.solvers.base import Simul
@@ -11,3 +21,13 @@ def test_init_kth():
 
     params = Simul.create_default_params()
     Simul(params)
+
+
+def test_import_solver():
+    from phill.solver import Simul
+
+    assert Simul is import_solver("phill")
+    params = Simul.create_default_params()
+    sim1 = Simul(params)
+    sim2 = load_simul(sim1.path_run)
+    assert isinstance(sim1, Simul) and isinstance(sim2, Simul)