Merge branch 'refactor/remove_system_option_settings'

.gitignore

@@ -105,6 +105,7 @@ mdout.mdp
 traj_comp.xtc
 
 # Jupyter notebook
+.ipynb
 .ipynb_checkpoints/
 
 # Pycharm

biobb_common/tools/test_fixtures.py

@@ -1,8 +1,9 @@
 """Boiler plate functions for testsys
 """
 import os
+import pickle
 import typing
-from typing import Optional
+from typing import Optional, Union, List, Dict
 from pathlib import Path
 import sys
 import shutil
@@ -34,7 +35,7 @@ def test_setup(test_object, dict_key: Optional[str] = None, config: Optional[str
         test_object.conf_file_path = str(Path(test_object.test_dir).joinpath('conf.yml'))
 
     test_object.system = os.getenv('testsys')
-    conf = settings.ConfReader(test_object.conf_file_path, test_object.system)
+    conf = settings.ConfReader(test_object.conf_file_path)
 
     if dict_key:
         test_object.properties = conf.get_prop_dic()[dict_key]
@@ -291,3 +292,67 @@ def compare_images(file_a: str, file_b: str, percent_tolerance: float = 1.0) ->
     if difference > tolerance:
         return False
     return True
+
+
+def compare_object_pickle(python_object: typing.Any, pickle_file_path: Union[str, Path], **kwargs) -> bool:
+    """ Compare a python object with a pickle file """
+    print(f"Loading pickle file: {pickle_file_path}")
+    with open(pickle_file_path, 'rb') as f:
+        pickle_object = pickle.load(f)
+
+    # Special case for dictionaries
+    if isinstance(python_object, dict) and isinstance(pickle_object, dict):
+        differences = compare_dictionaries(python_object, pickle_object, ignore_keys=kwargs.get('ignore_keys', []), compare_values=kwargs.get('compare_values', True), ignore_substring=kwargs.get('ignore_substring', ""))
+        if differences:
+            print(50*'*')
+            print("OBJECT:")
+            print(python_object)
+            print(50*'*')
+            print()
+            print(50*'*')
+            print("EXPECTED OBJECT:")
+            print(pickle_object)
+            print(50*'*')
+
+            print("Differences found:")
+            for difference in differences:
+                print(f"     {difference}")
+            return False
+        return True
+
+    return python_object == pickle_object
+
+
+def compare_dictionaries(dict1: Dict, dict2: Dict, path: str = "", ignore_keys: Optional[List[str]] = None, compare_values: bool = True, ignore_substring: str = "") -> List[str]:
+    """Compare two dictionaries and print only the differences, ignoring specified keys."""
+    if ignore_keys is None:
+        ignore_keys = []
+
+    differences = []
+
+    # Get all keys from both dictionaries
+    all_keys = set(dict1.keys()).union(set(dict2.keys()))
+
+    for key in all_keys:
+        if key in ignore_keys:
+            continue
+        if key not in dict1:
+            differences.append(f"Key '{path + key}' found in dict2 but not in dict1")
+        elif key not in dict2:
+            differences.append(f"Key '{path + key}' found in dict1 but not in dict2")
+        else:
+            value1 = dict1[key]
+            value2 = dict2[key]
+            if isinstance(value1, dict) and isinstance(value2, dict):
+                # Recursively compare nested dictionaries
+                nested_differences = compare_dictionaries(value1, value2, path + key + ".", ignore_keys, compare_values, ignore_substring)
+                differences.extend(nested_differences)
+            elif (value1 != value2) and compare_values:
+                if ignore_substring:
+                    if (not str(value1).endswith(str(value2).replace(ignore_substring, ""))) and (not str(value2).endswith(str(value1).replace(ignore_substring, ""))):
+                        differences.append(f"Difference at '{path + key}': dict1 has {value1}, dict2 has {value2}")
+
+                else:
+                    differences.append(f"Difference at '{path + key}': dict1 has {value1}, dict2 has {value2}")
+
+    return differences

test/conf.yml

@@ -0,0 +1,25 @@
+global_properties:
+  can_write_console_log: False
+  remove_tmp: False
+  working_dir_path: /tmp/biobb/unitests
+
+confreader:
+  paths:
+    config_complete: file:test_data_dir/configuration/config_complete.yml
+    config_empty: file:test_data_dir/configuration/config_empty.yml
+    config_nostep_globals: file:test_data_dir/configuration/config_nostep_globals.yml
+    config_nostep: file:test_data_dir/configuration/config_nostep.yml
+
+    ref_config_complete_pkl: file:test_reference_dir/configuration/config_complete.pkl
+    ref_config_empty_pkl: file:test_reference_dir/configuration/config_empty.pkl
+    ref_config_nostep_globals_pkl: file:test_reference_dir/configuration/config_nostep_globals.pkl
+    ref_config_nostep_pkl: file:test_reference_dir/configuration/config_nostep.pkl
+
+    ref_config_complete_paths_pkl: file:test_reference_dir/configuration/config_complete_paths.pkl
+    ref_config_empty_paths_pkl: file:test_reference_dir/configuration/config_empty_paths.pkl
+    ref_config_nostep_globals_paths_pkl: file:test_reference_dir/configuration/config_nostep_globals_paths.pkl
+    ref_config_nostep_paths_pkl: file:test_reference_dir/configuration/config_nostep_paths.pkl
+
+  properties:
+    remove_tmp: False
+

test/data/configuration/config_complete.yml

@@ -0,0 +1,40 @@
+global_properties:
+  working_dir_path: biobb_wf_protein-complex_md_setup
+  can_write_console_log: False
+  run_md: false
+
+step00_cat_pdb:
+  tool: cat_pdb
+  paths:
+    input_structure1: superinput.pdb
+    input_structure2: /path/to/inputs/ions.pdb
+    output_structure_path: protein.ions.pdb
+
+step4_fix_side_chain:
+  tool: fix_side_chain
+  paths:
+    input_pdb_path: dependency/step00_cat_pdb/output_structure_path
+    output_pdb_path: fixsidechain.pdb
+
+step5_pdb2gmx:
+  tool: pdb2gmx
+  paths:
+    input_pdb_path:  dependency/step4_fix_side_chain/output_pdb_path
+    output_gro_path: pdb2gmx.gro
+    output_top_zip_path: pdb2gmx_top.zip
+  properties:
+    force_field: amber99sb
+    water_type: tip3p
+
+step9_make_ndx:
+  paths:
+    input_structure_path: file:/path/to/inputs/ligand.gro
+    output_ndx_path: ligand.index.ndx
+  properties:
+    selection: 0 & ! a H*
+
+step9_bis_make_ndx:
+  paths:
+    input_structure_path: /path/to/inputs/ligand.gro
+    output_ndx_path: ligand.index.ndx
+  properties:

test/data/configuration/config_nostep.yml

@@ -0,0 +1,8 @@
+tool: pdb2gmx
+paths:
+  input_pdb_path:  path/to/output_pdb_path
+  output_gro_path: pdb2gmx.gro
+  output_top_zip_path: pdb2gmx_top.zip
+properties:
+  force_field: amber99sb
+  water_type: tip3p

test/data/configuration/config_nostep_globals.yml

@@ -0,0 +1,13 @@
+global_properties:
+  working_dir_path: biobb_wf_protein-complex_md_setup
+  can_write_console_log: False
+  run_md: false
+
+tool: pdb2gmx
+paths:
+  input_pdb_path:  path/to/output_pdb_path
+  output_gro_path: pdb2gmx.gro
+  output_top_zip_path: pdb2gmx_top.zip
+properties:
+  force_field: amber99sb
+  water_type: tip3p

test/reference/configuration/config_empty_paths.pkl

@@ -0,0 +1 @@
+�}�.

test/unitests/test_configuration/test_confreader.py

@@ -0,0 +1,24 @@
+# type: ignore
+from biobb_common.tools import test_fixtures as fx
+from biobb_common.configuration.settings import ConfReader
+
+
+class TestConfReader():
+    def setup_class(self):
+        fx.test_setup(self, 'confreader')
+
+    def teardown_class(self):
+        # pass
+        fx.test_teardown(self)
+
+    def test_confreader_properties(self):
+        print()  # Add a new line for better readability in the console
+        for file_name in ['config_complete', 'config_empty', 'config_nostep', 'config_nostep_globals']:
+            conf = ConfReader(self.paths[file_name])
+            assert fx.compare_object_pickle(conf.get_prop_dic(), self.paths[f'ref_{file_name}_pkl'], ignore_keys=['path', 'working_dir_path', 'sandbox_path'])
+
+    def test_confreader_paths(self):
+        print()  # Add a new line for better readability in the console
+        for file_name in ['config_complete', 'config_empty', 'config_nostep', 'config_nostep_globals']:
+            conf = ConfReader(self.paths[file_name])
+            assert fx.compare_object_pickle(conf.get_paths_dic(), self.paths[f'ref_{file_name}_paths_pkl'], ignore_keys=['working_dir_path', 'sandbox_path'], ignore_substring='/Users/pau/projects/biobb_common/')