shexec 2.3.0__tar.gz → 2.4.0__tar.gz

{shexec-2.3.0/shexec.egg-info → shexec-2.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shexec
-Version: 2.3.0
+Version: 2.4.0
 Summary: Run a shell-type command over every file of an input tree: a ChRIS DS plugin on pfdo_run
 Home-page: https://github.com/FNNDSC/pl-shexec
 Author: FNNDSC
@@ -18,8 +18,8 @@ Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: chris_plugin>=0.4.0
-Requires-Dist: pfdo>=6.2.0
-Requires-Dist: pfdo_run>=4.2.0
+Requires-Dist: pfdo>=6.3.0
+Requires-Dist: pfdo_run>=4.3.0
 Requires-Dist: hostlib>=1.2.0
 Requires-Dist: pflog>=2.0.0
 Provides-Extra: dev
@@ -159,7 +159,7 @@ From the command line, with the image:
         fnndsc/pl-shexec shexec --fileFilter txt                                \
         --exec "wc -l %{inputWorkingDir}/%{inputWorkingFile}" /incoming /outgoing
 
-    docker run --rm fnndsc/pl-shexec shexec --man /tmp /tmp
+    docker run --rm fnndsc/pl-shexec shexec --man
 
 With Apptainer, ``apptainer exec docker://fnndsc/pl-shexec shexec ...``. The image carries the coreutils, zip and unzip, bc, perl, tar, ImageMagick and the DCMTK tools.
 

{shexec-2.3.0 → shexec-2.4.0}/README.rst

@@ -130,7 +130,7 @@ From the command line, with the image:
         fnndsc/pl-shexec shexec --fileFilter txt                                \
         --exec "wc -l %{inputWorkingDir}/%{inputWorkingFile}" /incoming /outgoing
 
-    docker run --rm fnndsc/pl-shexec shexec --man /tmp /tmp
+    docker run --rm fnndsc/pl-shexec shexec --man
 
 With Apptainer, ``apptainer exec docker://fnndsc/pl-shexec shexec ...``. The image carries the coreutils, zip and unzip, bc, perl, tar, ImageMagick and the DCMTK tools.
 

{shexec-2.3.0 → shexec-2.4.0}/pyproject.toml

@@ -13,7 +13,7 @@ authors = [{ email = "dev@babyMRI.org" }]
 # fields, which the [project] table does not emit; setup.cfg supplies them, and the
 # author name lives there alone so Author-email stays a bare address.
 requires-python = ">=3.11"
-dependencies = ["chris_plugin>=0.4.0", "pfdo>=6.2.0", "pfdo_run>=4.2.0", "hostlib>=1.2.0", "pflog>=2.0.0"]
+dependencies = ["chris_plugin>=0.4.0", "pfdo>=6.3.0", "pfdo_run>=4.3.0", "hostlib>=1.2.0", "pflog>=2.0.0"]
 classifiers = [
     "Programming Language :: Python :: 3",
     "Programming Language :: Python :: 3.11",

{shexec-2.3.0 → shexec-2.4.0}/shexec/__init__.py

@@ -14,7 +14,7 @@ Dependencies:
 
 from __future__ import annotations
 
-__version__: str = "2.3.0"
+__version__: str = "2.4.0"
 
 from shexec.models import (
     DirNode,

{shexec-2.3.0 → shexec-2.4.0}/shexec/plugin.py

@@ -38,7 +38,7 @@ from pathlib import Path
 from chris_plugin import chris_plugin
 from pfdo_run.__main__ import ARGS_SYNOPSIS_DS, CLI_DS, TAG_HELP, parser_build
 from pflog import timed
-from pftree.manual import Manual, manual_print
+from pftree.manual import Manual, manual_attach
 
 from shexec.models import Plugin, PluginSpec
 from shexec.shexec import plugin_run
@@ -189,11 +189,13 @@ def parser_forSpec(spec: PluginSpec) -> argparse.ArgumentParser:
     The defaults are set on the parser rather than applied afterwards, so the
     description ``chris_plugin_info`` serialises carries them and ChRIS shows them.
     They are set after the omission, so a spec can pin an omitted flag to a value
-    of its own.
+    of its own. ``--man`` and ``--synopsis`` print the plugin's own manual and exit as
+    they are read, so they need no ``inputdir outputdir``.
     """
     parser: argparse.ArgumentParser = parser_build(standalone=False, command=spec.name, version=spec.version)
     parser_omit(parser, spec.omit)
     parser.set_defaults(**spec.defaults)
+    manual_attach(parser, manual_build(spec))
     return parser
 
 
@@ -217,9 +219,6 @@ def plugin_build(spec: PluginSpec, singleton: bool = True) -> Plugin:
     manual: Manual = manual_build(spec)
 
     def body(options: argparse.Namespace, inputdir: Path, outputdir: Path) -> int:
-        if options.man or options.synopsis:
-            manual_print(manual, shortOnly=not options.man)
-            return 0
         return plugin_run(options, inputdir, outputdir)
 
     body.__name__ = spec.name

{shexec-2.3.0 → shexec-2.4.0/shexec.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shexec
-Version: 2.3.0
+Version: 2.4.0
 Summary: Run a shell-type command over every file of an input tree: a ChRIS DS plugin on pfdo_run
 Home-page: https://github.com/FNNDSC/pl-shexec
 Author: FNNDSC
@@ -18,8 +18,8 @@ Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: chris_plugin>=0.4.0
-Requires-Dist: pfdo>=6.2.0
-Requires-Dist: pfdo_run>=4.2.0
+Requires-Dist: pfdo>=6.3.0
+Requires-Dist: pfdo_run>=4.3.0
 Requires-Dist: hostlib>=1.2.0
 Requires-Dist: pflog>=2.0.0
 Provides-Extra: dev
@@ -159,7 +159,7 @@ From the command line, with the image:
         fnndsc/pl-shexec shexec --fileFilter txt                                \
         --exec "wc -l %{inputWorkingDir}/%{inputWorkingFile}" /incoming /outgoing
 
-    docker run --rm fnndsc/pl-shexec shexec --man /tmp /tmp
+    docker run --rm fnndsc/pl-shexec shexec --man
 
 With Apptainer, ``apptainer exec docker://fnndsc/pl-shexec shexec ...``. The image carries the coreutils, zip and unzip, bc, perl, tar, ImageMagick and the DCMTK tools.
 

{shexec-2.3.0 → shexec-2.4.0}/shexec.egg-info/requires.txt

@@ -1,6 +1,6 @@
 chris_plugin>=0.4.0
-pfdo>=6.2.0
-pfdo_run>=4.2.0
+pfdo>=6.3.0
+pfdo_run>=4.3.0
 hostlib>=1.2.0
 pflog>=2.0.0
 

{shexec-2.3.0 → shexec-2.4.0}/tests/test_cli.py

@@ -17,11 +17,15 @@ from shexec.plugin import synopsis_build
 
 
 def test_manual_andSynopsis(tmp_path: Path, capsys: pytest.CaptureFixture[str]) -> None:
-    assert main(parser.parse_args(["--man"]), tmp_path, tmp_path) == 0
+    with pytest.raises(SystemExit) as exc:
+        parser.parse_args(["--man"])
+    assert exc.value.code == 0
     out: str = capsys.readouterr().out
     body: str = out.split("DESCRIPTION", 1)[1]
     assert "`" not in body and "TAGS" in body and "<inputDir>" in body and "shexec" in body
-    assert main(parser.parse_args(["--synopsis"]), tmp_path, tmp_path) == 0
+    with pytest.raises(SystemExit) as exc:
+        parser.parse_args(["--synopsis"])
+    assert exc.value.code == 0
     assert "TAGS" not in capsys.readouterr().out
 
 
@@ -62,3 +66,13 @@ def test_chris_plugin_info_describesThePlugin() -> None:
     assert description["documentation"] == "https://github.com/FNNDSC/pl-shexec"
     assert description["authors"] == "FNNDSC <dev@babyMRI.org>"
     assert any(p["name"] == "exec" for p in description["parameters"])
+
+
+def test_consoleScript_manNeedsNoDirectories(
+    monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture[str]
+) -> None:
+    monkeypatch.setattr("sys.argv", ["shexec", "--man"])
+    with pytest.raises(SystemExit) as exc:
+        main()
+    assert exc.value.code == 0
+    assert "TAGS" in capsys.readouterr().out

{shexec-2.3.0 → shexec-2.4.0}/tests/test_plugin.py

@@ -76,7 +76,9 @@ def test_derivedPlugin_describesItself_forChris() -> None:
 
 def test_derivedPlugin_manualAndVersion_areItsOwn(tmp_path: Path, capsys: pytest.CaptureFixture[str]) -> None:
     plugin: Plugin = plugin_build(spec_make(), singleton=False)
-    assert plugin.main(plugin.parser.parse_args(["--man"]), tmp_path, tmp_path) == 0
+    with pytest.raises(SystemExit) as exc:
+        plugin.parser.parse_args(["--man"])
+    assert exc.value.code == 0
     out: str = capsys.readouterr().out
     assert "linecount" in out and "Counts lines." in out and "9.9.9" in out and "TAGS" in out
     with pytest.raises(SystemExit):
@@ -105,7 +107,8 @@ def test_omittedFlags_absentFromParserDescriptionAndManual_valuePinned(
         plugin.parser.parse_args(["--threads", "4"])
     assert raised.value.code == 2
     capsys.readouterr()
-    assert plugin.main(plugin.parser.parse_args(["--man"]), Path("/tmp"), Path("/tmp")) == 0
+    with pytest.raises(SystemExit):
+        plugin.parser.parse_args(["--man"])
     manual: str = capsys.readouterr().out
     assert "[--threads" not in manual and "[--threadsSplit" not in manual
     assert "[--verbosity" in manual