fix(options): fix --singularity flag

docs/md/usage.md

@@ -31,9 +31,9 @@ slappt --image docker://alpine \
        --entrypoint "echo 'hello world'"
 ```
 
-## Parallelism
+## Multiple jobs
 
-`slappt` is convenient not only for one-off container jobs, but for running multiple copies of a workflow in parallel (e.g. for Monte Carlo simulations), or mapping a workflow over a list of inputs. These use cases are accomplished with job arrays and can be configured via the `--iterations` and the `--inputs` options.
+`slappt` is convenient not only for one-off container jobs, but for running multiple copies of a workflow, possibly in parallel (e.g. for Monte Carlo simulations), or mapping a workflow over a list of inputs. These use cases are accomplished with job arrays and can be configured via the `--iterations` and the `--inputs` options.
 
 **Note:** your job remains limited by the number of nodes allocated to it by the scheduler. To run containers in parallel, you must request multiple nodes.
 
@@ -74,10 +74,15 @@ Assuming we have permission to submit to the `batch` partition, we can generate
 ```shell
 slappt --image docker://alpine \
        --shell sh \
-       --nodes 2 \
        --partition batch \
        --entrypoint "cat \$SLAPPT_INPUT" \
-       --inputs inputs.txt
+       --inputs inputs.txt > job.sh
 ```
 
-This script will request 2 nodes, spawning a container on each with the `SLAPPT_INPUT` environment variable set one of the input files.
+This will generate a script to spawn a container, reading the input from the `SLAPPT_INPUT` environment variable.
+
+It can be then submitted with, for instance:
+
+```shell
+sbatch --array=1-2 job.sh
+```

slappt/scripts.py

@@ -17,7 +17,6 @@
 )
 
 SHEBANG = "#!/bin/bash"
-LAUNCHER_SCRIPT_NAME = "launch"  # TODO make configurable
 
 
 class ScriptGenerator:
@@ -105,23 +104,11 @@ def gen_job_headers(self) -> List[str]:
         return headers
 
     def gen_job_command(self) -> List[str]:
-        if self.config.parallelism == Parallelism.LAUNCHER:
-            commands = self.gen_launcher_entrypoint()
-        elif self.config.parallelism == Parallelism.JOBARRAY:
-            commands = self.gen_job_array_script()
-        else:
-            raise ValueError(
-                f"Unsupported parallelism strategy {self.config.parallelism}"
-            )
-
-        self.logger.debug(f"Using run commands: {linesep.join(commands)}")
-        return commands
-
-    def gen_job_array_script(self) -> List[str]:
         commands = []
+
         if self.config.inputs:
             commands.append(
-                f"file=$(head -n $SLURM_ARRAY_TASK_ID {self.config.inputs} | tail -1)"
+                f"SLAPPT_INPUT=$(head -n $SLURM_ARRAY_TASK_ID {self.config.inputs} | tail -1)"
             )
 
         commands = commands + ScriptGenerator.generate_invocation(
@@ -135,44 +122,10 @@ def gen_job_array_script(self) -> List[str]:
             shell=self.config.shell,
             singularity=self.config.singularity,
         )
-        return commands
 
-    def gen_launcher_entrypoint(self) -> List[str]:
-        commands = []
-        commands.append(f"export LAUNCHER_WORKDIR={self.config.workdir}")
-        commands.append(
-            f"export LAUNCHER_JOB_FILE={environ.get(LAUNCHER_SCRIPT_NAME)}"
-        )
-        commands.append("$LAUNCHER_DIR/paramrun")
+        self.logger.debug(f"Using run commands: {linesep.join(commands)}")
         return commands
 
-    def gen_launcher_script(self) -> List[str]:
-        lines: List[str] = []
-        files = []  # TODO: read from inputs.list
-
-        for i in range(0, self.config.iterations):
-            for file_name in files:
-                env = (
-                    self.config.environment if self.config.environment else []
-                )
-                env.append(EnvironmentVariable("SLAPPT_ITERATION", str(i + 1)))
-                path = join(self.config.workdir, file_name)
-                lines = lines + ScriptGenerator.generate_invocation(
-                    work_dir=self.config.workdir,
-                    image=self.config.image,
-                    commands=self.config.entrypoint.replace(
-                        "$SLAPPT_INPUT", path
-                    ),
-                    env=env,
-                    bind_mounts=self.config.bind_mounts,
-                    no_cache=self.config.no_cache,
-                    gpus=self.config.gpus,
-                    shell=self.config.shell,
-                    singularity=self.config.singularity,
-                )
-
-        return lines
-
     def gen_job_script(self) -> List[str]:
         headers = self.gen_job_headers()
         command = self.gen_job_command()

slappt/slappt.py

@@ -54,7 +54,7 @@ def generate_script(config: SlapptConfig):
 @click.option("--cores", required=False, type=int, default=1)
 @click.option("--tasks", required=False, type=int, default=1)
 @click.option("--header_skip", required=False)
-@click.option("--singularity", required=False, type=bool, default=False)
+@click.option("--singularity", is_flag=True, default=False)
 def cli(
     ctx,
     file,

slappt/sshlurm.py

@@ -191,7 +191,6 @@ def read_stderr():
         return job_id
 
 
-# @click.group(invoke_without_command=True)
 @click.command()
 @click.argument("file", required=True)
 @click.option("--host", required=False, type=str)
@@ -202,7 +201,7 @@ def read_stderr():
 @click.option("--pkey", required=False, type=str, default="~/.ssh/id_rsa")
 @click.option("--allow_stderr", required=False, type=bool, default=False)
 @click.option("--timeout", required=False, type=int, default=15)
-@click.option("--verbose", required=False, type=bool, default=False)
+@click.option("--verbose", is_flag=True, default=False)
 def cli(
     file,
     workdir,

slappt/tests/scripts/test_slappt.py

@@ -13,10 +13,8 @@
 
 
 # todo parametrize with optional params (e.g. account)
-@pytest.mark.parametrize("file", [None, "job.sh"])
-def test_script_hello_world(tmp_path, file):
+def test_script_hello_world(tmp_path):
     config = SlapptConfig(
-        file=str(tmp_path / file) if file else None,
         name=str(uuid4()),
         image="alpine",
         entrypoint="echo 'hello world'",
@@ -30,8 +28,7 @@ def test_script_hello_world(tmp_path, file):
     assert script[0].startswith("#!/bin/bash")
 
 
-@pytest.mark.parametrize("file", [None, "job.sh"])
-def test_script_with_inputs_file(tmp_path, file):
+def test_script_with_inputs_file(tmp_path):
     input_file_1 = tmp_path / "input_1.txt"
     input_file_2 = tmp_path / "input_2.txt"
     inputs_file = tmp_path / "inputs.txt"
@@ -47,7 +44,6 @@ def test_script_with_inputs_file(tmp_path, file):
         f.write(str(input_file_2))
 
     config = SlapptConfig(
-        file=str(tmp_path / file) if file else None,
         name=str(uuid4()),
         image="alpine",
         entrypoint="cat $SLAPPT_INPUT",
@@ -60,3 +56,22 @@ def test_script_with_inputs_file(tmp_path, file):
     script = generate_script(config)
     pprint(script)
     assert script[0].startswith("#!/bin/bash")
+    assert script[-2].startswith("SLAPPT_INPUT=")
+
+
+def test_singularity_flag(tmp_path):
+    config = SlapptConfig(
+        name=str(uuid4()),
+        image="alpine",
+        entrypoint="echo 'hello world'",
+        workdir=str(tmp_path),
+        email=email,
+        partition=partition,
+        singularity=True,
+    )
+
+    script = generate_script(config)
+    pprint(script)
+    assert script[0].startswith("#!/bin/bash")
+    assert any(s.startswith("singularity exec") for s in script)
+    assert not any(s.startswith("apptainer exec") for s in script)