Add alpha_model option to modules and decouple model files from repo.

emle/_utils.py

@@ -0,0 +1,103 @@
+#######################################################################
+# EMLE-Engine: https://github.com/chemle/emle-engine
+#
+# Copyright: 2023-2024
+#
+# Authors: Lester Hedges   <[email protected]>
+#          Kirill Zinovjev <[email protected]>
+#
+# EMLE-Engine 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 2 of the License, or
+# (at your option) any later version.
+#
+# EMLE-Engine 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 EMLE-Engine. If not, see <http://www.gnu.org/licenses/>.
+#####################################################################
+
+"""EMLE utilities."""
+
+__author__ = "Lester Hedges"
+__email__ = "[email protected]"
+
+
+def _fetch_resources():
+    """Fetch resources required for EMLE."""
+
+    import os as _os
+    import pygit2 as _pygit2
+
+    # Create the name for the expected resources directory.
+    resource_dir = _os.path.dirname(_os.path.abspath(__file__)) + "/resources"
+
+    # Check if the resources directory exists.
+    if not _os.path.exists(resource_dir):
+        # If it doesn't, clone the resources repository.
+        print("Downloading EMLE resources...")
+        _pygit2.clone_repository(
+            "https://github.com/chemle/emle-models.git", resource_dir
+        )
+    else:
+        # If it does, open the repository and pull the latest changes.
+        repo = _pygit2.Repository(resource_dir)
+        _pull(repo)
+
+
+def _pull(repo, remote_name="origin", branch="main"):
+    """
+    Pull the latest changes from the remote repository.
+
+    Taken from:
+    https://github.com/MichaelBoselowitz/pygit2-examples/blob/master/examples.py
+    """
+
+    import pygit2 as _pygit2
+
+    for remote in repo.remotes:
+        if remote.name == remote_name:
+            remote.fetch()
+            remote_master_id = repo.lookup_reference(
+                "refs/remotes/origin/%s" % (branch)
+            ).target
+            merge_result, _ = repo.merge_analysis(remote_master_id)
+            # Up to date, do nothing
+            if merge_result & _pygit2.GIT_MERGE_ANALYSIS_UP_TO_DATE:
+                return
+            # We can just fastforward
+            elif merge_result & _pygit2.GIT_MERGE_ANALYSIS_FASTFORWARD:
+                print("Updating EMLE resources...")
+                repo.checkout_tree(repo.get(remote_master_id))
+                try:
+                    master_ref = repo.lookup_reference("refs/heads/%s" % (branch))
+                    master_ref.set_target(remote_master_id)
+                except KeyError:
+                    repo.create_branch(branch, repo.get(remote_master_id))
+                repo.head.set_target(remote_master_id)
+            elif merge_result & _pygit2.GIT_MERGE_ANALYSIS_NORMAL:
+                print("Updating EMLE resources...")
+                repo.merge(remote_master_id)
+
+                if repo.index.conflicts is not None:
+                    for conflict in repo.index.conflicts:
+                        print("Conflicts found in:", conflict[0].path)
+                    raise AssertionError("Conflicts!")
+
+                user = repo.default_signature
+                tree = repo.index.write_tree()
+                commit = repo.create_commit(
+                    "HEAD",
+                    user,
+                    user,
+                    "Merge!",
+                    tree,
+                    [repo.head.target, remote_master_id],
+                )
+                # We need to do this or git CLI will think we are still merging.
+                repo.state_cleanup()
+            else:
+                raise AssertionError("Unknown merge analysis result")

emle/calculator.py

@@ -221,13 +221,15 @@ class EMLECalculator:
 
     # Class attributes.
 
-    # Get the directory of this module file.
-    _module_dir = _os.path.dirname(_os.path.abspath(__file__))
+    # Store the expected path to the resources directory.
+    _resource_dir = _os.path.join(
+        _os.path.dirname(_os.path.abspath(__file__)), "resources"
+    )
 
     # Create the name of the default model file for each alpha mode.
     _default_models = {
-        "species": _os.path.join(_module_dir, "/resources/emle_qm7_aev.mat"),
-        "reference": _os.path.join(_module_dir, "/resources/emle_qm7_aev_alphagpr.mat"),
+        "species": _os.path.join(_resource_dir, "emle_qm7_aev.mat"),
+        "reference": _os.path.join(_resource_dir, "emle_qm7_aev_alphagpr.mat"),
     }
 
     # Store the list of supported species.
@@ -444,6 +446,11 @@ def __init__(
             the calculator.
         """
 
+        from ._utils import _fetch_resources
+
+        # Fetch or update the resources.
+        _fetch_resources()
+
         # Validate input.
 
         # First handle the logger.
@@ -489,10 +496,13 @@ def __init__(
 
         # Validate the alpha mode first so that we can choose an appropriate
         # default model.
-        if not isinstance(alpha_mode, str):
-            msg = "'alpha_mode' must be of type 'str'"
-            _logger.error(msg)
-            raise TypeError(msg)
+        if alpha_mode is not None:
+            if not isinstance(alpha_mode, str):
+                msg = "'alpha_mode' must be of type 'str'"
+                _logger.error(msg)
+                raise TypeError(msg)
+        else:
+            alpha_mode = "species"
 
         # Convert to lower case and strip whitespace.
         alpha_mode = alpha_mode.lower().replace(" ", "")