[WIP] Review code and user interface for Versionix

test/conftest.py

@@ -0,0 +1,15 @@
+import pytest
+import versionix.registry as _registry
+
+
+@pytest.fixture(autouse=True)
+def _inject_test_registry_entries():
+    """Inject test-only entries into the registry for the duration of each test."""
+    test_entries = {
+        "for_testing_empty_parsers": {"options": "", "parsers": []},
+        "for_testing_no_parsers": {"options": ""},
+    }
+    _registry.metadata.update(test_entries)
+    yield
+    for key in test_entries:
+        _registry.metadata.pop(key, None)

test/test_parser.py

@@ -105,7 +105,6 @@ def test_script(fp, mocker):
     print(result)
 
     runner.invoke(main, ["--registered"])
-    runner.invoke(main, ["--stats"])
     runner.invoke(
         main,
     )
@@ -121,6 +120,19 @@ def test_DESeq2_error(fp, mocker):
         assert True
 
 
+def test_DESeq2_uses_rscript_caller(fp, mocker):
+    # DESeq2 is registered with a Rscript caller; the PATH check should look for Rscript, not DESeq2
+    def which_side_effect(cmd):
+        return "/usr/bin/Rscript" if cmd == "Rscript" else None
+
+    mocker.patch("versionix.parser.shutil.which", side_effect=which_side_effect)
+    fp.register(
+        'Rscript -e "library(DESeq2);packageVersion(\'DESeq2\')"',
+        stdout=["[1] '1.42.0'"],
+    )
+    assert get_version("DESeq2") == "1.42.0"
+
+
 def test_empty_parsers(fp, mocker):
     try:
         mocker.patch("shutil.which", return_value=True)

versionix/parser.py

@@ -122,7 +122,7 @@ def _get_container_runner(container):
             sys.exit(1)
 
 
-def get_version(standalone, verbose=True, R=False, container=None):
+def get_version(standalone, verbose=True, container=None):
     """Main entry point that returns the version of an existing executable"""
     # we should use check_output in case the standalone opens a GUI (e.g. fastqc --WRONG pops up the GUI)
 
@@ -135,10 +135,18 @@ def get_version(standalone, verbose=True, R=False, container=None):
         standalone.startswith("singularity") or standalone.startswith("apptainer") or standalone.startswith("docker")
     ):  # pragma: no cover
         pass
-    elif shutil.which(standalone) is None:
-        if verbose:
-            logger.error(f"{standalone} command not found in your environment")
-        sys.exit(1)
+    else:
+        # For registered tools with a custom caller, check the caller binary rather than
+        # the standalone name (e.g. DESeq2 is invoked via `Rscript`, not a `DESeq2` binary).
+        if standalone in metadata:
+            caller = metadata[standalone].get("caller", standalone)
+            check_cmd = shlex.split(caller)[0]
+        else:
+            check_cmd = standalone
+        if shutil.which(check_cmd) is None:
+            if verbose:
+                logger.error(f"{check_cmd} command not found in your environment")
+            sys.exit(1)
 
     # is it registered ?
     if standalone in metadata.keys():
@@ -174,7 +182,7 @@ def search_registered(standalone, container_runner=None):
         raise ValueError(f"parsers for {standalone} is incorrect. Must be a list of valid parsers")
 
     try:
-        cmd = f"{caller} {options}"
+        cmd = f"{caller} {options}".strip()
         if container_runner:
             cmd = f"{container_runner} {cmd}"
         p = subprocess.run(cmd, capture_output=True, universal_newlines=True, shell=True)

versionix/registry.py

@@ -18,7 +18,7 @@
     "circlator": {"options": "version", "parsers": [lambda x: x.stdout.strip()]},
     "DESeq2": {
         "caller": "Rscript -e \"library(DESeq2);packageVersion('DESeq2')\"",
-        "parsers": [lambda x: x.stdout.split()[1].strip("’‘")],
+        "parsers": [lambda x: x.stdout.split()[1].strip("'")],
     },
     # dot -v hangs so we need to register this command.
     "dot": {"options": "-V", "parsers": [lambda x: x.stderr.split()[4].strip()]},
@@ -45,8 +45,4 @@
     #    # "parser": parser_split_2
     # },
     # "vt": {"options": "--version", "parser": parser_split_2_strip_v},
-    "for_testing_empty_parsers": {"options": "", "parsers": []},
-    "for_testing_no_parsers": {
-        "options": "",
-    },
 }

versionix/scripts.py

@@ -1,25 +1,15 @@
-###########################################################################
-# Versionix is a project to manage reproducible containers                #
-#                                                                         #
-# Authors: see CONTRIBUTORS.rst                                           #
-# Copyright © 2023 Sequana dev team                                       #
-# See the COPYRIGHT file for details                                      #
-#                                                                         #
-# Versionix is free software: you can redistribute it and/or modify       #
-# it under the terms of the GNU General Public License as published by    #
-# the Free Software Foundation, either version 3 of the License, or       #
-# (at your option) any later version.                                     #
-#                                                                         #
-# Versionix  is distributed in the hope that it will be useful,           #
-# but WITHOUT ANY WARRANTY; without even the implied warranty of          #
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           #
-# GNU General Public License for more details.                            #
-#                                                                         #
-# You should have received a copy of the GNU General Public License       #
-# along with this program (COPYING file).                                 #
-# If not, see <http://www.gnu.org/licenses/>.                             #
-###########################################################################
-""".. rubric:: Standalone application dedicated to Damona"""
+#
+#  This file is part of Versionix software
+#
+#  Copyright (c) 2023 - Sequana Dev Team (https://sequana.readthedocs.io)
+#
+#  Distributed under the terms of the 3-clause BSD license.
+#  The full license is in the LICENSE file, distributed with this software.
+#
+#  Website:       https://github.com/sequana/versionix
+#  Contributors:  https://github.com/sequana/versionix/graphs/contributors
+##############################################################################
+""".. rubric:: Standalone application (CLI entry point) for Versionix"""
 import sys
 
 import colorlog
@@ -32,9 +22,7 @@
 
 CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
 
-click.rich_click.USE_MARKDOWN = True
-click.rich_click.SHOW_METAVARS_COLUMN = True
-click.rich_click.APPEND_METAVARS_HELP = True
+click.rich_click.TEXT_MARKUP = "markdown"
 click.rich_click.STYLE_ERRORS_SUGGESTION = "magenta italic"
 click.rich_click.SHOW_ARGUMENTS = True