Merge pull request #208 from snek5000/snek-make

snek-make command

Makefile

@@ -21,6 +21,9 @@ coverage_html:
 black:
 	black src tests docs
 
+isort:
+	isort src tests docs
+
 list-sessions:
 	@nox --version 2>/dev/null || pip install nox
 	@$(NOX) -l

pyproject.toml

@@ -42,12 +42,14 @@ show_missing = true
 exclude_lines = [
     "if __name__ == .__main__.:",
     'if "sphinx" in sys.modules:',
-    "raise ValueError",
+    "raise FileNotFoundError",
     "raise NotImplementedError",
+    "raise ValueError",
     "except KeyError:",
     "except ImportError:",
     "except AttributeError:",
-    "except NotImplementedError:"
+    "except NotImplementedError:",
+    "except StopIteration:",
 ]
 
 [tool.coverage.html]

setup.cfg

@@ -48,6 +48,7 @@ console_scripts =
   snek-generate-config = snek5000.config:ensure_config_file
   snek-info = snek5000.util.console:print_versions
   snek-ipy-load = snek5000.util.console:start_ipython_load_sim
+  snek-make = snek5000.make:snek_make
 
 [options.extras_require]
 docs =

src/snek5000/clusters.py

@@ -54,5 +54,5 @@ def nproc_available():
         var = "os.cpu_count()"
         nproc = os.cpu_count()
 
-    logger.info(f"Using {var} to detect maximum number of processors available")
+    logger.debug(f"Using {var} to detect maximum number of processors available")
     return nproc

src/snek5000/make.py

@@ -2,6 +2,8 @@
 ======================
 
 """
+import argparse
+import sys
 from pathlib import Path
 from typing import Iterable
 from warnings import warn
@@ -27,15 +29,30 @@ class Make:
 
     """
 
-    def __init__(self, sim):
-        self.sim = sim
-        self.path_run = sim.output.path_run
-        try:
-            self.file = next(f for f in sim.output.get_paths() if f.name == "Snakefile")
-        except AttributeError:
-            raise AttributeError("Unable to get path of Snakefile via Output class")
-        except StopIteration:
-            raise FileNotFoundError(f"No Snakefile in {self.path_run}")
+    def __init__(self, sim=None, path_run=None):
+
+        if (sim is None and path_run is None) or (
+            sim is not None and path_run is not None
+        ):
+            raise ValueError("Either sim of path_run has to be given.")
+
+        if path_run is None:
+            self.path_run = sim.output.path_run
+            try:
+                self.file = next(
+                    f for f in sim.output.get_paths() if f.name == "Snakefile"
+                )
+            except AttributeError:
+                raise AttributeError("Unable to get path of Snakefile via Output class")
+            except StopIteration:
+                raise FileNotFoundError(f"No Snakefile in {self.path_run}")
+        else:
+            if not path_run.exists():
+                raise FileNotFoundError(f"{path_run} does not exist.")
+            self.path_run = Path(path_run)
+            self.file = self.path_run / "Snakefile"
+            if not self.file.exists():
+                raise FileNotFoundError(f"No Snakefile in {path_run}")
 
         self.log_handler = []
 
@@ -97,6 +114,8 @@ def exec(
         It is also possible to do the same directly from command line
         by changing to the simulation directory and executing::
 
+          snek-make -h
+          snek-make compile
           snakemake -j1 compile
           snakemake -j1 --set-resources='run:nproc=4' run
 
@@ -109,6 +128,7 @@ def exec(
 
         or from command line with::
 
+          snek-make -l
           snakemake --list-target-rules
 
         .. seealso:: Useful Snakemake `command line arguments`_
@@ -255,3 +275,61 @@ def build(self, config):
                 return self.exec(*self.targets, config=config, force_incomplete=True)
             else:
                 return True
+
+
+def snek_make():
+    """Used for the command snek-make"""
+    parser = argparse.ArgumentParser(
+        prog="snek-make",
+        description="Execute Snakemake rules",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+    )
+
+    parser.add_argument(
+        "rule",
+        nargs="?",
+        default=None,
+        help="Snakemake rule to be executed.",
+    )
+    parser.add_argument(
+        "-l",
+        "--list-rules",
+        action="store_true",
+        help="List rules and exit.",
+    )
+    parser.add_argument(
+        "-d",
+        "--dry-run",
+        action="store_true",
+        help="Dry run snakemake rules without executing.",
+    )
+    parser.add_argument(
+        "-np",
+        "--nproc",
+        type=int,
+        default=None,
+        help="Number of MPI processes.",
+    )
+    parser.add_argument(
+        "--clean-after-fail",
+        action="store_true",
+        help="Keep incomplete output files of failed jobs.",
+    )
+
+    args = parser.parse_args()
+
+    make = Make(path_run=Path.cwd())
+
+    if args.rule is None:
+        print("You need to specify a rule to be executed")
+
+    if args.list_rules or args.rule is None:
+        make.list()
+        sys.exit(0)
+
+    make.exec(
+        args.rule,
+        dryrun=args.dry_run,
+        keep_incomplete=not args.clean_after_fail,
+        nproc=args.nproc,
+    )

tests/test_make.py

@@ -1,11 +1,17 @@
+import os
+import sys
 from concurrent.futures import ProcessPoolExecutor as Pool
 from concurrent.futures import as_completed
+from contextlib import contextmanager
 from pathlib import Path
+from unittest.mock import patch
 
+import pytest
+
+from snek5000.make import _Nek5000Make, snek_make
 
-def nek5000_build(config):
-    from snek5000.make import _Nek5000Make
 
+def nek5000_build(config):
     nm = _Nek5000Make()
     return nm.build(config)
 
@@ -28,3 +34,32 @@ def test_nek5000_make(pytestconfig):
         ]
         for future in as_completed(simultaneous_builds):
             assert future.result()
+
+
+def test_snek_make_help():
+    with patch.object(sys, "argv", ["snek-make", "-h"]):
+        with pytest.raises(SystemExit):
+            snek_make()
+
+
+@contextmanager
+def current_dir_changed_to(path):
+    cwd = Path.cwd()
+    os.chdir(path)
+    try:
+        yield
+    finally:
+        os.chdir(cwd)
+
+
+def test_snek_make_no_rule(sim_data):
+    with patch.object(sys, "argv", ["snek-make"]):
+        with pytest.raises(SystemExit):
+            with current_dir_changed_to(sim_data):
+                snek_make()
+
+
+def test_snek_make_clean(sim_data):
+    with patch.object(sys, "argv", ["snek-make", "clean"]):
+        with current_dir_changed_to(sim_data):
+            snek_make()