Merge pull request #110 from hanjinliu/fix-run

fix some CLI

cylindra/cli/config.py

@@ -64,6 +64,7 @@ def __call__(self, parser, namespace, values, option_string=None):
         with open(save_path, mode="w") as f:
             json.dump(cfg.asdict(), f, indent=4, separators=(", ", ": "))
         print(f"Config file imported: {save_path.as_posix()}")
+        parser.exit()
 
 
 class ParserConfig(ParserBase):

cylindra/cli/run.py

@@ -11,7 +11,7 @@ class ParserRun(ParserBase):
     cylindra run [bold green]path[/bold green] [bold cyan]options[/bold cyan]
 
     [u bold green]path[/u bold green]
-        Path to the project/image file.
+        Path to the project/python file.
 
     [u bold cyan]options[/u bold cyan]
         [bold]--headless[/bold]
@@ -33,17 +33,21 @@ def run_action(
         from runpy import run_path
 
         ui = start(viewer=self.viewer, headless=headless)
+        project_path = None
         if Path(path).suffix in ("", ".tar", ".zip", ".json"):
             prj = read_project(path)
             with prj.open_project() as d:
                 py_path = str(prj._script_py_path(d))
                 out_globs = run_path(py_path, {"ui": ui})
             is_project = True
+            project_path = prj.project_path
         else:
             out_globs = run_path(path, {"ui": ui})
             is_project = False
         if callable(main := out_globs.get("main")):
             main(ui)  # script.py style
+        if project_path is not None:
+            ui._project_dir = project_path
         if output is None:
             if is_project:
                 ui.overwrite_project()

cylindra_builtins/_pytest_fixtures.py

@@ -1,3 +1,4 @@
+import sys
 from contextlib import suppress
 
 import pytest
@@ -33,3 +34,29 @@ def ui(make_napari_viewer, request: "pytest.FixtureRequest"):
             sv.close()
         StaParameters._viewer = None
     viewer.close()
+
+
+@pytest.fixture
+def run_cli(make_napari_viewer, monkeypatch):
+    from magicclass.utils import thread_worker
+    from magicgui.application import use_app
+
+    from cylindra.__main__ import main
+    from cylindra.cli import set_testing
+    from cylindra.core import ACTIVE_WIDGETS
+
+    viewer = make_napari_viewer()
+    set_testing(True)
+    monkeypatch.setattr("builtins.input", lambda *_: "")
+
+    def _run_cli(*args):
+        sys.argv = [str(a) for a in args]
+        main(viewer, ignore_sys_exit=True)
+
+    with thread_worker.blocking_mode():
+        yield _run_cli
+
+    for widget in ACTIVE_WIDGETS:
+        widget.close()
+    ACTIVE_WIDGETS.clear()
+    use_app().process_events()

pyproject.toml

@@ -42,7 +42,7 @@ dependencies = [
     "qt-command-palette>=0.0.7",
     "matplotlib>=3.8.1",
     "rich>=13.6.0",
-    "dask>=2023.12.1",
+    "dask>=2023.12.1,!=2024.8.1",
 ]
 authors = [
     { email = "liuha@med.kobe-u.ac.jp" },

tests/test_gui_0.py

@@ -18,9 +18,7 @@
 
 from cylindra import _config, cylmeasure, view_project
 from cylindra._config import get_config
-from cylindra.const import (
-    MoleculesHeader as Mole,
-)
+from cylindra.const import MoleculesHeader as Mole
 from cylindra.const import PropertyNames as H
 from cylindra.widgets import CylindraMainWidget
 from cylindra.widgets.sta import MaskChoice, TemplateChoice
@@ -1260,79 +1258,6 @@ def test_spline_fitter(ui: CylindraMainWidget):
     ui.macro.redo()
 
 
-def test_cli(make_napari_viewer, monkeypatch):
-    import sys
-
-    from cylindra.__main__ import main
-    from cylindra.cli import set_testing
-    from cylindra.core import ACTIVE_WIDGETS
-
-    viewer: napari.Viewer = make_napari_viewer()
-    set_testing(True)
-
-    def run_cli(*args):
-        sys.argv = [str(a) for a in args]
-        main(viewer, ignore_sys_exit=True)
-
-    # test help
-    for cmd in [
-        "average",
-        "config",
-        "find",
-        "new",
-        "open",
-        "plugin",
-        "preview",
-        "run",
-        "workflow",
-    ]:
-        run_cli("cylindra", cmd, "--help")
-    with thread_worker.blocking_mode():
-        run_cli("cylindra")
-        run_cli("cylindra", "preview", PROJECT_DIR_14PF / "project.json")
-        run_cli("cylindra", "preview", PROJECT_DIR_14PF / "project.json", "--gui")
-        run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_tar.tar")
-        run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_zip.zip")
-        run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_tar.tar::project.json")
-        run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_tar.tar::Mole-0.csv")
-
-        with tempfile.TemporaryDirectory() as dirpath:
-            run_cli(
-                "cylindra", "new",
-                Path(dirpath) / "test-project",
-                "--image", TEST_DIR / "14pf_MT.tif",
-                "--multiscales", "1", "2",
-                "--missing_wedge", "-60", "50",
-                "--molecules", PROJECT_DIR_14PF / "Mole-*",
-            )  # fmt: skip
-            run_cli("cylindra", "open", Path(dirpath) / "test-project")
-        run_cli("cylindra", "config", "--list")
-        run_cli("cylindra", "config", PROJECT_DIR_14PF, "--remove")
-        run_cli("cylindra", "workflow", "--list")
-        with tempfile.TemporaryDirectory() as dirpath:
-            run_cli(
-                "cylindra", "average",
-                TEST_DIR / "test_project_*",
-                "--molecules", "Mole-*",
-                "--size", "10.0",
-                "--output", Path(dirpath) / "test.tif",
-                "--filter", "col('nth') % 2 == 0",
-                "--split", "--seed", "123",
-            )  # fmt: skip
-        run_cli("cylindra", "find", "**/*.zip")
-        run_cli("cylindra", "find", "**/*.zip", "--called", "register_path")
-
-    for widget in ACTIVE_WIDGETS:
-        widget.close()
-    ACTIVE_WIDGETS.clear()
-    use_app().process_events()
-
-    run_cli("cylindra plugin list")
-    monkeypatch.setattr("builtins.input", lambda _: "")
-    with tempfile.TemporaryDirectory() as dirpath:
-        run_cli(f"cylindra plugin new {dirpath}")
-
-
 def test_function_menu(make_napari_viewer):
     from cylindra.widgets.subwidgets import Volume
 

tests/test_gui_2_cli.py

@@ -0,0 +1,111 @@
+import tempfile
+from pathlib import Path
+
+from cylindra import _config
+
+from ._const import PROJECT_DIR_13PF, PROJECT_DIR_14PF, TEST_DIR
+
+
+def test_help(run_cli):
+    # test help
+    for cmd in [
+        "average",
+        "config",
+        "find",
+        "new",
+        "open",
+        "plugin",
+        "preview",
+        "run",
+        "workflow",
+    ]:
+        run_cli("cylindra", cmd, "--help")
+
+
+def test_start_gui(run_cli):
+    run_cli("cylindra")
+
+
+def test_preview(run_cli):
+    run_cli("cylindra", "preview", PROJECT_DIR_14PF / "project.json")
+    run_cli("cylindra", "preview", PROJECT_DIR_14PF / "project.json", "--gui")
+    run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_tar.tar")
+    run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_zip.zip")
+    run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_tar.tar::project.json")
+    run_cli("cylindra", "preview", PROJECT_DIR_14PF / "test_tar.tar::Mole-0.csv")
+
+
+def test_new_and_open(run_cli):
+    with tempfile.TemporaryDirectory() as dirpath:
+        run_cli(
+            "cylindra", "new",
+            Path(dirpath) / "test-project",
+            "--image", TEST_DIR / "14pf_MT.tif",
+            "--multiscales", "1", "2",
+            "--missing_wedge", "-60", "50",
+            "--molecules", PROJECT_DIR_14PF / "Mole-*",
+        )  # fmt: skip
+        run_cli("cylindra", "open", Path(dirpath) / "test-project")
+
+
+def test_config(run_cli):
+    run_cli("cylindra", "config", "--list")
+    run_cli("cylindra", "config", PROJECT_DIR_13PF)
+    run_cli("cylindra", "config", PROJECT_DIR_14PF / "script.py", "--remove")
+    run_cli("cylindra", "config", PROJECT_DIR_14PF, "--remove")
+
+    with tempfile.TemporaryDirectory() as tempdir, _config.patch_config_dir(tempdir):
+        from cylindra.components.spline._config import SplineConfig
+
+        d = Path(tempdir) / "temp"
+        d.mkdir()
+        config_path = d / "temp-config.json"
+        SplineConfig().to_file(config_path)
+        run_cli("cylindra", "config", config_path, "--import")
+
+
+def test_average(run_cli):
+    with tempfile.TemporaryDirectory() as dirpath:
+        dirpath = Path(dirpath)
+        run_cli(
+            "cylindra", "average",
+            TEST_DIR / "test_project_*",
+            "--molecules", "Mole-*",
+            "--size", "10.0",
+            "--output", dirpath / "test.tif",
+            "--filter", "col('nth') % 2 == 0",
+            "--split", "--seed", "123",
+        )  # fmt: skip
+
+
+def test_run(run_cli):
+    run_cli("cylindra", "run", PROJECT_DIR_14PF, "--headless")
+    run_cli(
+        "cylindra",
+        "run",
+        PROJECT_DIR_14PF,
+        "--headless",
+        "-o",
+        Path("test.tar"),
+    )
+
+
+def test_find(run_cli):
+    run_cli("cylindra", "find", "**/*.zip")
+    run_cli("cylindra", "find", "**/*.zip", "--called", "register_path")
+
+
+def test_workflow(run_cli):
+    code = "import numpy as np\ndef main(ui):\n    print(ui.default_config)\n"
+
+    with tempfile.TemporaryDirectory() as tempdir, _config.patch_workflow_path(tempdir):
+        Path(tempdir).joinpath("test-cli.py").write_text(code)
+        run_cli("cylindra", "workflow")
+        run_cli("cylindra", "workflow", "test-cli.py")
+    run_cli("cylindra", "workflow", "--list")
+
+
+def test_plugin(run_cli):
+    run_cli("cylindra", "plugin", "list")
+    with tempfile.TemporaryDirectory() as dirpath:
+        run_cli("cylindra", "plugin", "new", dirpath)