Merge pull request #40 from molssi-seamm/dev

Update for new installer

Author: seamm

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2025.3.9 -- Update for new installer
+    * Changes in the installer required changes for codes that installed background
+      codes, like PACKMOL. This update allows PACKMOL to be automatically installed.
+      
 2025.1.29 -- Bugfixes: executable and SMILES
     * The configuration for the executable was not set up correctly.
     * There was a bug due to change in the SMILES interface for configurations.

devtools/conda-envs/test_env.yaml

@@ -9,6 +9,7 @@ dependencies:
   - pip
 
   # SEAMM
+  - libsqlite!=3.49.1
   - seamm
   - seamm-installer
   - pyyaml

packmol_step/installer.py

@@ -53,6 +53,7 @@ def __init__(self, logger=logger):
 
         logger.debug("Initializing the PACKMOL installer object.")
 
+        self.environment = "seamm-packmol"
         self.section = "packmol-step"
         self.executables = ["packmol"]
         self.resource_path = Path(pkg_resources.resource_filename(__name__, "data/"))
@@ -61,144 +62,6 @@ def __init__(self, logger=logger):
         logger.debug(f"data directory: {self.resource_path}")
         self.environment_file = self.resource_path / "seamm-packmol.yml"
 
-    def check(self):
-        """Check the status of the Packmol installation."""
-        print("Checking the Packmol installation.")
-
-        # What Conda environment is the default?
-        path = self.configuration.path.parent / "packmol.ini"
-        if not path.exists():
-            text = (self.resource_path / "packmol.ini").read_text()
-            path.write_text(text)
-            print(f"    The packmol.ini file did not exist. Created {path}")
-
-        self.exe_config.path = path
-
-        # Get the current values
-        data = self.exe_config.get_values("local")
-
-        if "conda-environment" in data and data["conda-environment"] != "":
-            self.environment = data["conda-environment"]
-        else:
-            self.environment = "seamm-packmol"
-
-        super().check()
-
-    def install(self):
-        """Install Packmol in a conda environment."""
-        print("Installing Packmol.")
-
-        # What Conda environment is the default?
-        path = self.configuration.path.parent / "packmol.ini"
-        if not path.exists():
-            text = (self.resource_path / "packmol.ini").read_text()
-            path.write_text(text)
-            print(f"    The packmol.ini file did not exist. Created {path}")
-
-        self.exe_config.path = path
-
-        # Get the current values
-        data = self.exe_config.get_values("local")
-
-        if "conda-environment" in data and data["conda-environment"] != "":
-            self.environment = data["conda-environment"]
-        else:
-            self.environment = "seamm-packmol"
-
-        super().install()
-
-    def show(self):
-        """Show the status of the Packmol installation."""
-        print("Showing the Packmol installation.")
-
-        # What Conda environment is the default?
-        path = self.configuration.path.parent / "packmol.ini"
-        if not path.exists():
-            text = (self.resource_path / "packmol.ini").read_text()
-            path.write_text(text)
-            print(f"    The packmol.ini file does not exist at {path}")
-            print("    The 'check' command will create it if Packmol is installed.")
-            print("    Otherwise 'install' will install Packmol.")
-            return
-
-        self.exe_config.path = path
-
-        if not self.exe_config.section_exists("local"):
-            print(
-                "    Packmol is not configured: there is no 'local' section in "
-                f"     {path}."
-            )
-            return
-
-        # Get the current values
-        data = self.exe_config.get_values("local")
-
-        if "conda-environment" in data and data["conda-environment"] != "":
-            self.environment = data["conda-environment"]
-        else:
-            self.environment = "seamm-packmol"
-
-        super().show()
-
-    def uninstall(self):
-        """Uninstall the Packmol installation."""
-        print("Uninstall the Packmol installation.")
-
-        # What Conda environment is the default?
-        path = self.configuration.path.parent / "packmol.ini"
-        if not path.exists():
-            text = (self.resource_path / "packmol.ini").read_text()
-            path.write_text(text)
-            print(
-                f""""    The packmol.ini file does not exist at {path}
-    Perhaps Packmol is not installed, but if it is the 'check' command may locate it
-    and create the ini file, after which 'uninstall' will remove it."""
-            )
-            return
-
-        self.exe_config.path = path
-
-        if not self.exe_config.section_exists("local"):
-            print(
-                f""""    The packmol.ini file at {path} does not have local section.
-    Perhaps Packmol is not installed, but if it is the 'check' command may locate it
-    and update the ini file, after which 'uninstall' will remove it."""
-            )
-            return
-
-        # Get the current values
-        data = self.exe_config.get_values("local")
-
-        if "conda-environment" in data and data["conda-environment"] != "":
-            self.environment = data["conda-environment"]
-        else:
-            self.environment = "seamm-packmol"
-
-        super().uninstall()
-
-    def update(self):
-        """Updates the Packmol installation."""
-        print("Updating the Packmol installation.")
-
-        # What Conda environment is the default?
-        path = self.configuration.path.parent / "packmol.ini"
-        if not path.exists():
-            text = (self.resource_path / "packmol.ini").read_text()
-            path.write_text(text)
-            print(f"    The packmol.ini file did not exist. Created {path}")
-
-        self.exe_config.path = path
-
-        # Get the current values
-        data = self.exe_config.get_values("local")
-
-        if "conda-environment" in data and data["conda-environment"] != "":
-            self.environment = data["conda-environment"]
-        else:
-            self.environment = "seamm-packmol"
-
-        super().update()
-
     def exe_version(self, config):
         """Get the version of the PACKMOL executable.
 

packmol_step/packmol_parameters.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
-"""Control parameters for Packmol, currently for packing fluids
-"""
+"""Control parameters for Packmol, currently for packing fluids"""
 
 import logging
 import seamm