Merge branch 'develop' into testing/pixi_extra_tests

Author: jlnav

.github/workflows/basic.yml

@@ -46,7 +46,7 @@ jobs:
         - name: Checkout lockfile
           run: git lfs checkout
 
-        - uses: prefix-dev/setup-pixi@v0.9.3
+        - uses: prefix-dev/setup-pixi@v0.9.4
           with:
             pixi-version: v0.55.0
             frozen: true
@@ -92,4 +92,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.42.2
+        - uses: crate-ci/typos@v1.43.0

.github/workflows/extra.yml

@@ -110,4 +110,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v6
-        - uses: crate-ci/typos@v1.42.2
+        - uses: crate-ci/typos@v1.43.0

.readthedocs.yml

@@ -4,17 +4,31 @@ build:
   os: "ubuntu-22.04"
   tools:
     python: "3.10"
+  commands:
+    # from https://docs.readthedocs.com/platform/stable/build-customization.html#support-git-lfs-large-file-storage
+    # Download and uncompress the binary
+    # https://git-lfs.github.com/
+    - wget https://github.com/git-lfs/git-lfs/releases/download/v3.1.4/git-lfs-linux-amd64-v3.1.4.tar.gz
+    - tar xvfz git-lfs-linux-amd64-v3.1.4.tar.gz git-lfs
+    # Modify LFS config paths to point where git-lfs binary was downloaded
+    - git config filter.lfs.process "`pwd`/git-lfs filter-process"
+    - git config filter.lfs.smudge  "`pwd`/git-lfs smudge -- %f"
+    - git config filter.lfs.clean "`pwd`/git-lfs clean -- %f"
+    # Make LFS available in current repository
+    - ./git-lfs install
+    # Download content from remote
+    - ./git-lfs fetch
+    # Make local files to have the real content on them
+    - ./git-lfs checkout
+    - asdf plugin add pixi
+    - asdf install pixi latest
+    - asdf global pixi latest
+    - pixi run -e docs build-docs
+    - mkdir -p $READTHEDOCS_OUTPUT/html/
+    - cp -r docs/_build/html/** $READTHEDOCS_OUTPUT/html/
 
 sphinx:
     configuration: docs/conf.py
 
 formats:
   - pdf
-
-python:
-    install:
-      - requirements: docs/requirements.txt
-      - method: pip
-        path: .
-        extra_requirements:
-         - docs

docs/conf.py

@@ -101,6 +101,7 @@ class AxParameterWarning(Warning):  # Ensure it's a real warning subclass
     "sphinxcontrib.autodoc_pydantic",
     "sphinx_design",
     "sphinx_copybutton",
+    "sphinx_lfs_content",
 ]
 
 spelling_word_list_filename = "spelling_wordlist.txt"

docs/requirements.txt

@@ -30,6 +30,9 @@
 # To change logging level for just this module
 # logger.setLevel(logging.DEBUG)
 
+# Placeholder for container support - replaced with simulation directory at runtime
+LIBE_SIM_DIR_PLACEHOLDER = "%LIBENSEMBLE_SIM_DIR%"
+
 STATES = """
 UNKNOWN
 CREATED
@@ -431,6 +434,7 @@ def __init__(self) -> None:
         self.workerID = None
         self.comm = None
         self.last_task = 0
+        self.base_dir = os.getcwd()
         Executor.executor = self
 
     def __enter__(self):
@@ -522,6 +526,10 @@ def register_app(
 
         precedent: str, Optional
             Any str that should directly precede the application full path.
+            Supports the placeholder ``%LIBENSEMBLE_SIM_DIR%`` which is replaced
+            at runtime with the simulation directory as a relative path from
+            where the executor was created. This is useful for container exec
+            commands.
         """
 
         if not app_name:
@@ -673,10 +681,26 @@ def set_worker_info(self, comm=None, workerid=None) -> None:
         self.workerID = workerid
         self.comm = comm
 
-    def _check_app_exists(self, full_path: str) -> None:
+    def _check_app_exists(self, app: Application) -> None:
         """Allows submit function to check if app exists and error if not"""
-        if not os.path.isfile(full_path):
-            raise ExecutorException(f"Application does not exist {full_path}")
+        if app.precedent:
+            # Could be a container call in precedent. In that case,
+            # the executable is not available on the host system and
+            # we just forward what the user provided.
+            return
+
+        if not os.path.isfile(app.full_path):
+            raise ExecutorException(f"Application does not exist {app.full_path}")
+
+    def _set_sim_dir_env(self, task: Task, run_cmd: list[str]) -> list[str]:
+        """Replace simulation directory placeholder in run command if present.
+
+        Supports container-based execution where the simulation directory needs to be
+        passed to container exec commands (e.g., podman-hpc exec --workdir).
+        """
+        sim_dir = os.path.relpath(task.workdir, self.base_dir)
+        task._add_to_env("LIBENSEMBLE_SIM_DIR", sim_dir)
+        return [arg.replace(LIBE_SIM_DIR_PLACEHOLDER, sim_dir) for arg in run_cmd]
 
     def submit(
         self,
@@ -745,12 +769,15 @@ def submit(
         task = Task(app, app_args, default_workdir, stdout, stderr, self.workerID, dry_run)
 
         if not dry_run:
-            self._check_app_exists(task.app.full_path)
+            self._check_app_exists(task.app)
 
         runline = task.app.app_cmd.split()
         if task.app_args is not None:
             runline.extend(task.app_args.split())
 
+        runline = self._set_sim_dir_env(task, runline)
+        task.runline = " ".join(runline)
+
         if dry_run:
             logger.info(f"Test (No submit) Runline: {' '.join(runline)}")
         else:

libensemble/executors/executor.py

@@ -71,8 +71,6 @@ class MPIExecutor(Executor):
 
         from libensemble.executors.mpi_executor import MPIExecutor
         exctr = MPIExecutor(custom_info=customizer)
-
-
     """
 
     def __init__(self, custom_info: dict = {}) -> None:
@@ -317,7 +315,7 @@ def submit(
         task = Task(app, app_args, default_workdir, stdout, stderr, self.workerID, dry_run)
 
         if not dry_run:
-            self._check_app_exists(task.app.full_path)
+            self._check_app_exists(task.app)
 
         if stage_inout is not None:
             logger.warning("stage_inout option ignored in this " "executor - runs in-place")
@@ -363,7 +361,8 @@ def submit(
         if task.app_args is not None:
             runline.extend(task.app_args.split())
 
-        task.runline = " ".join(runline)  # Allow to be queried
+        runline = self._set_sim_dir_env(task, runline)
+        task.runline = " ".join(runline)
 
         if env_script is not None:
             run_cmd = Executor._process_env_script(task, runline, env_script)

libensemble/executors/mpi_executor.py

@@ -936,6 +936,25 @@ def test_non_existent_app_mpi():
         assert 0
 
 
+def test_non_existent_app_precedent():
+    """Tests exception on non-existent app is not thrown if precedent is set.
+    This is common when running apps in containers, where the executable is not
+    check-able from the host system."""
+    from libensemble.executors.executor import Executor
+
+    print(f"\nTest: {sys._getframe().f_code.co_name}\n")
+
+    exctr = Executor()
+
+    # Can register a non-existent app in case created as part of workflow.
+    exctr.register_app(full_path=non_existent_app, app_name="nonexist")
+
+    w_exctr = Executor.executor  # simulate on worker
+
+    # all should be ok
+    w_exctr.submit(app_name="nonexist", dry_run=True)
+
+
 def test_man_signal_unrec_tag():
     print(f"\nTest: {sys._getframe().f_code.co_name}\n")
 
@@ -990,5 +1009,6 @@ def test_man_signal_unrec_tag():
     test_dry_run()
     test_non_existent_app()
     test_non_existent_app_mpi()
+    test_non_existent_app_precedent()
     test_man_signal_unrec_tag()
     teardown_module(__file__)

libensemble/tests/unit_tests/test_executor.py

@@ -118,7 +118,9 @@ def run_check(exp_env, exp_cmd, **kwargs):
         args_for_sim = "sleep 0"
         exp_runline = exp_cmd + " simdir/my_simtask.x sleep 0"
         task = exctr.submit(calc_type="sim", app_args=args_for_sim, dry_run=True, **kwargs)
-        assert task.env == exp_env, f"Task env does not match expected:\n Received: {task.env}\n Expected: {exp_env}"
+        for key, value in exp_env.items():
+            assert key in task.env, f"Expected env key '{key}' not found in task.env: {task.env}"
+            assert task.env[key] == value, f"Env key '{key}' has value '{task.env[key]}', expected '{value}'"
         assert (
             task.runline == exp_runline
         ), f"Run line  does not match expected.\n Received: {task.runline}\n Expected: {exp_runline}"

libensemble/tests/unit_tests/test_executor_gpus.py

@@ -242,6 +242,16 @@ def check_gpu_setting(task, assert_setting=True, print_setting=False, resources=
         print(f"Worker {task.workerID}: {desc}GPU setting ({stype}): {gpu_setting} {addon}", flush=True)
 
     if assert_setting:
-        assert (
-            gpu_setting == expected
-        ), f"Worker {task.workerID}: Found GPU setting: {gpu_setting}, Expected: {expected}"
+        if isinstance(expected, dict):
+            for key, value in expected.items():
+                assert key in gpu_setting, (
+                    f"Worker {task.workerID}: Expected env key '{key}' not found in GPU setting: {gpu_setting}"
+                )
+                assert gpu_setting[key] == value, (
+                    f"Worker {task.workerID}: GPU setting key '{key}' has value '{gpu_setting[key]}', "
+                    f"expected '{value}'"
+                )
+        else:
+            assert (
+                gpu_setting == expected
+            ), f"Worker {task.workerID}: Found GPU setting: {gpu_setting}, Expected: {expected}"