update tutorial scripts

.gitignore

@@ -104,3 +104,6 @@ ENV/
 # profraw files from LLVM? Unclear exactly what triggers this
 # There are reports this comes from LLVM profiling, but also Xcode 9.
 *profraw
+
+
+*.test/

autosolvate/multicomponent.py

@@ -302,7 +302,7 @@ def startmulticomponent(argumentList):
     #print(values)
     for currentArgument, currentValue in arguments:
         if  currentArgument in ("-h", "--help"):
-            print('Usage: autosolvate boxgen [OPTIONS]')
+            print('Usage: autosolvate boxgen_multicomponent [OPTIONS]')
             print('  -m, --main                 solute xyz file')
             print('  -s, --solvent_lists        solvent xyz files, separated by slash. (ex. water.pdb/acetonitrile.pdb)')
             # print('  -o, --output               prefix of the output file names')                                     # not currently supporting this option

devtools/conda-envs/environment.yml

@@ -2,7 +2,7 @@
 # @Date:      May 9th 2024
 # @Author:    Patrick 
 # @Email:     [email protected] 
-# @Description: environment for merged autosolvate (multicomponent + continous integration) 
+# @Description: environment for tutorial
 ##################################################################################################
 name: autosolvate
 channels:

docs/tutorial_common_bug.rst

@@ -0,0 +1,68 @@
+NameError: name '_read_utf8_with_fallback' is not defined
+
+
+
+(test2) [pli@pascal run1]$ autosolvate boxgen_multicomponent
+Traceback (most recent call last):
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 589, in _build_master
+    ws.require(__requires__)
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 926, in require
+    needed = self.resolve(parse_requirements(requirements))
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 787, in resolve
+    dist = self._resolve_dist(
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 833, in _resolve_dist
+    raise VersionConflict(dist, req).with_context(dependent_req)
+pkg_resources.VersionConflict: (autosolvate 0.1.4+136.gda10105.dirty (/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/autosolvate-0.1.4+136.gda10105.dirty-py3.8.egg), Requirement.parse('autosolvate==0.1.4+154.gd24f652.dirty'))
+
+During handling of the above exception, another exception occurred:
+
+Traceback (most recent call last):
+  File "/home/pli/anaconda3/envs/test2/bin/autosolvate", line 33, in <module>
+    sys.exit(load_entry_point('autosolvate==0.1.4+154.gd24f652.dirty', 'console_scripts', 'autosolvate')())
+  File "/home/pli/anaconda3/envs/test2/bin/autosolvate", line 25, in importlib_load_entry_point
+    return next(matches).load()
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/importlib/metadata.py", line 77, in load
+    module = import_module(match.group('module'))
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/importlib/__init__.py", line 127, in import_module
+    return _bootstrap._gcd_import(name[level:], package, level)
+  File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
+  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
+  File "<frozen importlib._bootstrap>", line 961, in _find_and_load_unlocked
+  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
+  File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
+  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
+  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
+  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
+  File "<frozen importlib._bootstrap_external>", line 843, in exec_module
+  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/autosolvate-0.1.4+136.gda10105.dirty-py3.8.egg/autosolvate/__init__.py", line 7, in <module>
+    from .autosolvate import *
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/autosolvate-0.1.4+136.gda10105.dirty-py3.8.egg/autosolvate/autosolvate.py", line 1, in <module>
+    from .molecule import *
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/autosolvate-0.1.4+136.gda10105.dirty-py3.8.egg/autosolvate/molecule/__init__.py", line 1, in <module>
+    from .molecule import *
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/autosolvate-0.1.4+136.gda10105.dirty-py3.8.egg/autosolvate/molecule/molecule.py", line 6, in <module>
+    import pkg_resources
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3283, in <module>
+    def _initialize_master_working_set():
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3266, in _call_aside
+    f(*args, **kwargs)
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 3295, in _initialize_master_working_set
+    working_set = _declare_state('object', 'working_set', WorkingSet._build_master())
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 591, in _build_master
+    return cls._build_from_requirements(__requires__)
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 604, in _build_from_requirements
+    dists = ws.resolve(reqs, Environment())
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1014, in __init__
+    self.scan(search_path)
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1046, in scan
+    for dist in find_distributions(item):
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2091, in find_on_path
+    yield from factory(fullpath)
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2183, in resolve_egg_link
+    return next(dist_groups, ())
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2179, in <genexpr>
+    resolved_paths = (
+  File "/home/pli/anaconda3/envs/test2/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2167, in non_empty_lines
+    for line in _read_utf8_with_fallback(path).splitlines():
+NameError: name '_read_utf8_with_fallback' is not defined