beeflow:useContainer support for SquashFS (#990)

* Add beeflow:useContainer support for SquashFS
* Updated coverage.svg

---------

Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>

beeflow/common/crt/charliecloud_driver.py

@@ -97,13 +97,15 @@ def run_text(self, task):  # noqa
                                           main_command=Command([str(arg) for arg in task.command]),
                                           post_commands=[])
 
-        if task_container_name:
-            container_path = '/'.join([self.container_archive, task_container_name]) + '.tar.gz'
-
         # If use_container is specified, no copying is done, the file  path is used
+        squashfs = False
         if use_container:
             task_container_name = self.get_ccname(use_container)
             container_path = os.path.expanduser(use_container)
+            _, ext = os.path.splitext(container_path)
+            # infer if using SquashFS, similar to:
+            # https://hpc.github.io/charliecloud/ch-convert.html#format-inference
+            squashfs = ext in ['.sqfs', '.squash', '.squashfs']
         else:
             container_path = '/'.join([self.container_archive, task_container_name]) + '.tar.gz'
 
@@ -119,12 +121,20 @@ def run_text(self, task):  # noqa
             mpi_opt = ''
         command = ' '.join(task.command)
         env_code = '\n'.join([self.cc_setup if self.cc_setup else '', task_workdir_env])
-        deployed_path = deployed_image_root + '/' + task_container_name
-        pre_commands = [
-            Command(f'mkdir -p {deployed_image_root}\n'.split(), CommandType.ONE_PER_NODE),
-            Command(f'ch-convert -i tar -o dir {container_path} {deployed_path}\n'.split(),
-                    CommandType.ONE_PER_NODE),
-        ]
+        pre_commands = []
+        post_commands = []
+        if squashfs:
+            deployed_path = container_path
+        else:
+            deployed_path = deployed_image_root + '/' + task_container_name
+            pre_commands = [
+                Command(f'mkdir -p {deployed_image_root}\n'.split(), CommandType.ONE_PER_NODE),
+                Command(f'ch-convert -i tar -o dir {container_path} {deployed_path}\n'.split(),
+                        CommandType.ONE_PER_NODE),
+            ]
+            post_commands = [
+                Command(f'rm -rf {deployed_path}\n'.split(), type_=CommandType.ONE_PER_NODE),
+            ]
         # Need to convert the path from inside to outside base on the bind mounts
         extra_opts = ''
         if task.workdir is not None:
@@ -140,9 +150,6 @@ def run_text(self, task):  # noqa
         main_command = (f'ch-run {mpi_opt} {deployed_path} {self.chrun_opts} '
                         f'{extra_opts} {bind_mount_opts} -- {command}\n').split()
         main_command = Command(main_command)
-        post_commands = [
-            Command(f'rm -rf {deployed_path}\n'.split(), type_=CommandType.ONE_PER_NODE),
-        ]
         return ContainerRuntimeResult(env_code, pre_commands, main_command, post_commands)
 
     def build_text(self, userconfig, task):

beeflow/tests/test_charliecloud_driver.py

@@ -0,0 +1,70 @@
+"""Charliecloud driver tests."""
+import pytest
+from beeflow.common.crt.charliecloud_driver import CharliecloudDriver as crt_driver
+from beeflow.common.wf_data import Task, Requirement
+
+
+@pytest.mark.parametrize(
+    "use_container, pre_commands_exp, main_command_exp, post_commands_exp",
+    [
+        ("cont.sqfs", "", "ch-run cont.sqfs env --cd  -b : -- default", ""),
+        (
+            "cont.tar.gz",
+            "mkdir -p env one-per-node ch-convert -i tar -o dir cont.tar.gz env/cont one-per-node",
+            "ch-run env/cont env --cd  -b : -- default",
+            "rm -rf env/cont one-per-node",
+        ),
+    ],
+)
+def test_run_text_use_container(
+    mocker, tmpdir, use_container, pre_commands_exp, main_command_exp, post_commands_exp
+):
+    """Test run_text with different useContainer DockerRequirements."""
+    tmpdir_str = str(tmpdir)
+    mocker.patch("beeflow.common.config_driver.BeeConfig.get", return_value="env")
+    mocker.patch(
+        "beeflow.common.config_driver.BeeConfig.resolve_path", return_value=tmpdir_str
+    )
+    mocker.patch("os.getenv", return_value=str(tmpdir))
+    requirements = [
+        Requirement(
+            "DockerRequirement",
+            {
+                "beeflow:containerName": None,
+                "beeflow:bindMounts": None,
+                "beeflow:copyContainer": None,
+                "dockerPull": None,
+                "beeflow:useContainer": use_container,
+            },
+        )
+    ]
+    task = Task(
+        name="",
+        base_command="",
+        hints=[],
+        requirements=requirements,
+        inputs=[],
+        outputs=[],
+        stdout="",
+        stderr="",
+        workflow_id="",
+        workdir=tmpdir,
+    )
+    driver = crt_driver()
+    res = driver.run_text(task)
+    assert res.env_code.count(tmpdir_str) == 1
+    # simplify results for easier comparison
+    env_code = res.env_code.replace(tmpdir_str, "").replace("\n", " ")
+    pre_commands = " ".join(
+        [f'{" ".join(com.args)} {com.type}' for com in res.pre_commands]
+    ).replace(tmpdir_str, "")
+    main_command = f'{" ".join(res.main_command.args)} {res.main_command.type}'
+    assert main_command.count(tmpdir_str) == 3
+    main_command = main_command.replace(tmpdir_str, "")
+    post_commands = " ".join(
+        [f'{" ".join(com.args)} {com.type}' for com in res.post_commands]
+    )
+    assert env_code == "env cd  "
+    assert pre_commands == pre_commands_exp
+    assert main_command == main_command_exp
+    assert post_commands == post_commands_exp