Merge branch 'main' of gitlab.pasteur.fr:gem/macsylib

Author: bneron

pyproject.toml

@@ -61,7 +61,7 @@ model = [
 
 [project.scripts]
 msl_data = "macsylib.scripts.macsydata:main"
-msl_profile = "macslib.scripts.macsyprofile:main"
+msl_profile = "macsylib.scripts.macsyprofile:main"
 
 [project.urls]
 Homepage = "https://github.com/gem-pasteur/macsylib/"

src/macsylib/scripts/macsydata.py

@@ -662,7 +662,7 @@ def prefix(indent:int, char:str, prev_indent:int, pipe:bool = True) -> str:
 
         def explore_def(def_loc: DefinitionLocation, indent:int = 0, prev_indent:int = 0, char:str = '', pipe:bool = True) -> None:
             """
-            explore recursively the tree structure of DefintionLocation with subdefinition. and compute what to dispaly for each line
+            explore recursively the tree structure of DefintionLocation with subdefinition. and compute what to display for each line
 
             :param def_loc: The definition location to explore
             :param indent: the indentation of the label
@@ -1112,7 +1112,7 @@ def create_repo(model_package_name: str, models_dir: str | None = None) -> str:
     pre_push_path = impresources.files('macsylib') / 'data' / 'pre-push'
     dest = os.path.join(repo.git_dir, 'hooks', 'pre-push')
     if os.path.exists(dest):
-        _log.warning(f"A git hook '{pre_push_path}' already exists cannot install macsydata prepush hook.")
+        _log.warning(f"A git hook '{pre_push_path}' already exists cannot install msl_data prepush hook.")
         _log.warning("Do it manually, check documentation: ")
     else:
         shutil.copy(pre_push_path, dest)
@@ -1127,7 +1127,7 @@ def create_repo(model_package_name: str, models_dir: str | None = None) -> str:
 - A configuration file has been added (model_conf.xml) with default value tweak this file if needed.
   (https://macsylib.readthedocs.io/en/latest/modeler_guide/package.html#model-configuration)
 
-Before to publish your package you can use `macsydata check` to verify it's integrity.
+Before to publish your package you can use `msl_data check` to verify it's integrity.
 """
               )
     _log.warning("To share your models with the MacSyModels community.")
@@ -1166,7 +1166,7 @@ def build_arg_parser(header:str, version:str,
     """
     Build argument parser.
 
-    :param header: the header of console scriot
+    :param header: the header of console script
     :param args: The arguments provided on the command line
     :param package_name: the name of the higher package that embed the macsylib (eg 'macsyfinder')
     :param tool_name: the name of this tool as it appear in pyproject.toml
@@ -1233,7 +1233,7 @@ def build_arg_parser(header:str, version:str,
                                    help='Reinstall Model package even if it is already up-to-date.')
     install_subparser.add_argument('--org',
                                    default="macsy-models",
-                                   help="The name of Model orgagnization"
+                                   help="The name of Model organization"
                                         "(default 'macsy-models'))"
                                    )
     install_dest = install_subparser.add_mutually_exclusive_group()

tests/test_functional.py

@@ -0,0 +1,74 @@
+#########################################################################
+# MacSyLib - Python library to detect macromolecular systems            #
+#            in prokaryotes protein dataset using systems modelling     #
+#            and similarity search.                                     #
+#                                                                       #
+# Authors: Sophie Abby, Bertrand Neron                                  #
+# Copyright (c) 2014-2025  Institut Pasteur (Paris) and CNRS.           #
+# See the COPYRIGHT file for details                                    #
+#                                                                       #
+# This file is part of MacSyLib package.                                #
+#                                                                       #
+# MacSyLib 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.                                   #
+#                                                                       #
+# MacSyLib 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 MacSyLib (COPYING).                                        #
+# If not, see <https://www.gnu.org/licenses/>.                          #
+#########################################################################
+
+import subprocess
+from tests import MacsyTest
+
+
+class Test_msl_data(MacsyTest):
+
+    def test_help(self):
+
+        expected_output = r"""usage: msl_data [-h] [-v] [--version]
+                {available,download,install,uninstall,search,info,list,freeze,cite,help,check,show,definition,init}"""
+
+        p = subprocess.run("msl_data --help", shell=True, check=True, capture_output=True, text=True, encoding='utf8')
+        self.assertEqual(p.returncode, 0)
+        # for an unknow reason the output is not exactly formated in same manner on all plateform/execution
+        # on some execution some lines ar wrapped
+        # on some other no
+        # so I test only the beginning of the help message
+        self.assertTrue(p.stdout.startswith(expected_output))
+
+
+class Test_msl_profile(MacsyTest):
+
+    def test_help(self):
+
+        expected_output = r"""usage: msl_profile [-h] [--coverage-profile COVERAGE_PROFILE]
+                   [--i-evalue-sel I_EVALUE_SEL]
+                   [--best-hits {score,i_eval,profile_coverage}] [-p PATTERN]
+                   [-o OUT] [--index-dir INDEX_DIR] [-f] [-V] [-v] [--mute]
+                   previous_run
+
+     *            *               *                   * *
+            *               *   *   *  *    **           
+  **     *    *   *  *     *                    *        
+            *       _   *             **    __ _ _     *         
+      _ __ ___  ___| |     _ __  _ __ ___  / _(_) | ___          
+     | '_ ` _ \/ __| |    | '_ \| '__/ _ \| |_| | |/ _ \       
+     | | | | | \__ \ |    | |_) | | | (_) |  _| | |  __/
+     |_| |_| |_|___/_|____| .__/|_|  \___/|_| |_|_|\___|
+           *         |_____|_|        *                  *
+        *   * *     *   **         *   *  *           *
+  *      *         *        *    *              *        
+             *                           *  *           * 
+
+msl_profile - MacSyLib profile helper tool
+"""
+        p = subprocess.run("msl_profile --help", shell=True, check=True, capture_output=True, text=True, encoding='utf8')
+        self.assertEqual(p.returncode, 0)
+        self.assertTrue(p.stdout.startswith(expected_output))

tests/test_io.py

@@ -44,7 +44,7 @@
 from macsylib.system import System, HitSystemTracker, RejectedCandidate, AbstractUnordered, LikelySystem, UnlikelySystem
 from macsylib.solution import Solution
 
-from src.macsylib.io import loner_warning
+from macsylib.io import loner_warning
 from tests import MacsyTest