Merge pull request #30 from paulsaxe/main

Updated for new installation scheme

.github/workflows/CI.yaml

@@ -7,11 +7,6 @@ on:
   pull_request:
     branches:
       - "main"
-  schedule:
-    # Run on master by default Sunday morning at 3:30:
-    #   Scheduled workflows run on the latest commit on the default or base branch.
-    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
-    - cron: "30 3 * * 0"
 
 jobs:
   ci:

.github/workflows/Release.yaml

@@ -13,3 +13,12 @@ jobs:
     with:
       src : packmol_step
     secrets: inherit
+
+  docker:
+    name: Docker
+    needs: release
+    uses: molssi-seamm/devops/.github/workflows/Docker.yaml@main
+    with:
+      image : molssi-seamm/seamm-packmol
+      description: A Packmol executable packaged for use with SEAMM or standalone
+    secrets: inherit

HISTORY.rst

@@ -1,6 +1,11 @@
 =======
 History
 =======
+2024.3.19 -- Updated installer for new scheme
+    * packmol-step-installer now uses the new scheme, which supports both Conda and
+      Docker installation.
+    * Added seamm-packmol Docker image
+
 2024.1.16 -- Adding support for containers
     * Added the ability to work in Docker containers.
 

devtools/docker/Dockerfile

@@ -0,0 +1,8 @@
+FROM molssi/mamba141
+
+COPY ./environment.yml /root/environment.yml
+
+RUN mamba env update -f /root/environment.yml
+
+WORKDIR /home
+ENTRYPOINT ["packmol"]

devtools/docker/environment.yml

@@ -0,0 +1,8 @@
+name: base
+channels:
+  - conda-forge
+dependencies:
+  - python
+    # Executables, etc.
+  - packmol==20.2.2
+

packmol_step/data/configuration.txt

@@ -1,19 +1,6 @@
 [packmol-step]
-# Information about where/how the executables are installed
-# installation may be 'user', 'conda' or 'module'. If a module is
-# specified it will be loaded and those executables used.  In this
-# case, any path specified using -path will be ignored.
 
-installation = 
-conda-environment = 
-modules = 
+# The level of logging for the Packmol Step
 
-# The path to the executable. Can be empty or not present, in which
-# case the default PATH is used.  If a path is given, packmol
-# from this location will be used.
-#
-# Ignored if a module is used. The default is to use the PATH
-# environment variable.
-
-packmol-path = 
+# log-level WARNING
 

packmol_step/data/packmol.ini

@@ -0,0 +1,71 @@
+# Configuration options for how to run Packmol
+
+[docker]
+# The code to use. This may maybe more than just the name of the code, and variables in
+# braces {} will be expanded. For example:
+#   code = mpiexec -np {NTASKS} lmp_mpi
+# would expand {NTASKS} to the number of tasks and run the command
+
+code = packmol
+
+# The name and location of the Docker container to use, optionally with the version
+
+container = ghcr.io/molssi-seamm/seamm-packmol:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# app silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+# platform = linux/amd64
+
+[local]
+# The type of local installation to use. Options are:
+#     conda: Use a conda environment
+#   modules: Use the modules system
+#     local: Use a local installation
+#    docker: Use a Docker container
+# By default SEAMM installs Packmol using conda.
+
+installation = conda
+
+# The command line to use, which should start with the executable followed by any options.
+# Variables in braces {} will be expanded. For example:
+#
+#   code = mpiexec -np {NTASKS} lmp_mpi
+#
+# would expand {NTASKS} to the number of tasks and run the command.
+# For a 'local' installation, the command line should include the full path to the
+# executable or it should be in the path. 
+
+code = packmol
+
+######################### conda section ############################
+# The full path to the conda executable:
+
+# conda = 
+
+# The Conda environment to use. This is either the name or full path.
+
+# conda-environment = seamm-packmol
+
+######################### modules section ############################
+# The modules to load to run Packmol, as a list of strings.
+# For example, to load the modules packmol and openmpi, you would use:
+#   modules = packmol openmpi
+
+# modules = 
+
+######################### local section ############################
+# The full path to the Packmol executable should be in the 'code' option.
+
+######################### docker section ############################
+# The name and location of the Docker container to use, optionally with the version.
+# {version} will be expanded to the version of the plug-in.
+
+# container = ghcr.io/molssi-seamm/seamm-packmol:{version}
+
+# In addition, you can specify the platform to use. This is useful on e.g. Macs with
+# app silicon (M1, M3...) where the default platform is linux/arm64 but some containers
+# are only available for linux/amd64.
+
+# platform = linux/amd64

packmol_step/installer.py

@@ -54,40 +54,183 @@ def __init__(self, logger=logger):
         logger.debug("Initializing the PACKMOL installer object.")
 
         self.section = "packmol-step"
-        self.path_name = "packmol-path"
         self.executables = ["packmol"]
         self.resource_path = Path(pkg_resources.resource_filename(__name__, "data/"))
+
+        # The environment.yaml file for Conda installations.
+        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?
-        data = self.configuration.get_values(self.section)
+        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"
 
-        # The environment.yaml file for Conda installations.
-        path = Path(pkg_resources.resource_filename(__name__, "data/"))
-        logger.debug(f"data directory: {path}")
-        self.environment_file = path / "seamm-packmol.yml"
+        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"
 
-    def exe_version(self, path):
+        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.
 
         Parameters
         ----------
-        path : pathlib.Path
-            Path to the executable.
+        config : dict
+            Dictionary of options for running Packmol
 
         Returns
         -------
-        str
+        "Packmol", str
             The version reported by the executable, or 'unknown'.
         """
+        environment = config["conda-environment"]
+        conda = config["conda"]
+        if environment[0] == "~":
+            environment = str(Path(environment).expanduser())
+            command = f"'{conda}' run --live-stream -p '{environment}'"
+        elif Path(environment).is_absolute():
+            command = f"'{conda}' run --live-stream -p '{environment}'"
+        else:
+            command = f"'{conda}' run --live-stream -n '{environment}'"
+        command += " packmol -log none"
+
+        logger.debug(f"    Running {command}")
         try:
             result = subprocess.run(
-                [str(path), "-log", "none"],
+                command,
                 stdin=subprocess.DEVNULL,
                 capture_output=True,
                 text=True,
+                shell=True,
             )
         except Exception:
             version = "unknown"
@@ -103,4 +246,4 @@ def exe_version(self, path):
                         version = value
                         break
 
-        return version
+        return "Packmol", version