Fix/bug container install (#459)

* fixing bug with adding singularity container
* also fixing circle ci tests!

the container and environment file should be added to the container base, and
the module file alongside modules. Without this fix all are installed to
containers


Signed-off-by: vsoch <[email protected]>
Co-authored-by: vsoch <[email protected]>

Author: vsoch

.circleci/config.yml

@@ -61,8 +61,8 @@ install_podman: &install_podman
   name: Install Podman
   command: |-
     . /etc/os-release
-    echo "deb https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/testing/xUbuntu_${VERSION_ID}/ /" | sudo tee /etc/apt/sources.list.d/devel:kubic:libcontainers:testing.list
-    curl -L https://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/testing/xUbuntu_${VERSION_ID}/Release.key | sudo apt-key add -
+    sudo sh -c "echo 'deb http://download.opensuse.org/repositories/devel:/kubic:/libcontainers:/stable/xUbuntu_${VERSION_ID}/ /' > /etc/apt/sources.list.d/devel:kubic:libcontainers:stable.list"
+    wget -nv https://download.opensuse.org/repositories/devel:kubic:libcontainers:stable/xUbuntu_${VERSION_ID}/Release.key -O- | sudo apt-key add -
     sudo apt-get update -qq
     sudo apt-get -qq -y install podman
  

CHANGELOG.md

@@ -14,6 +14,7 @@ and **Merged pull requests**. Critical items to know are:
 The versions coincide with releases on pip. Only major versions will be released as tags on Github.
 
 ## [0.0.x](https://github.scom/singularityhub/singularity-hpc/tree/master) (0.0.x)
+ - fixing bug with container install (does not honor module directory) (0.0.36)
  - `.version` file should be written in top level of module folders [#450](https://github.com/singularityhub/singularity-hpc/issues/450) (0.0.35)
   - tcl module functions need `$@` to handle additional arguments
  - Tcl modules use shell functions for bash, to export to child shells (0.0.34)

shpc/main/container/singularity.py

@@ -75,6 +75,8 @@ def add(self, sif, module_name, modulefile, template, **kwargs):
         """
         Manually add a registry container.
         """
+        module_dir = os.path.dirname(modulefile)
+
         # Ensure the container exists
         sif = os.path.abspath(sif)
         if not os.path.exists(sif):
@@ -92,8 +94,7 @@ def add(self, sif, module_name, modulefile, template, **kwargs):
 
         # The user can have a different container directory defined
         container_dir = self.container_dir(module_name)
-        module_path = os.path.join(container_dir, modulefile)
-        shpc.utils.mkdirp([container_dir])
+        shpc.utils.mkdirp([container_dir, module_dir])
 
         # Name the container appropriately
         name = module_name.replace("/", "-")
@@ -105,14 +106,14 @@ def add(self, sif, module_name, modulefile, template, **kwargs):
         parsed_name = ContainerName(module_name)
 
         self.install(
-            module_path,
+            modulefile,
             dest,
             module_name,
             template,
             parsed_name=parsed_name,
             features=kwargs.get("features"),
         )
-        self.add_environment(container_dir, {}, self.settings.environment_file)
+        self.add_environment(module_dir, {}, self.settings.environment_file)
         logger.info("Module %s was created." % (module_name))
 
     def install(
@@ -144,7 +145,8 @@ def install(
         )
 
         # Remove any previous containers
-        for older in glob("%s%s*.sif" % (module_path, os.sep)):
+        container_dir = os.path.dirname(container_path)
+        for older in glob("%s%s*.sif" % (container_dir, os.sep)):
             if older == container_path:
                 continue
             os.remove(older)

shpc/main/modules/__init__.py

@@ -146,7 +146,8 @@ def add(self, sif, module_name, **kwargs):
         """
         module_name = self.add_namespace(module_name)
         template = self._load_template(self.templatefile)
-        self.container.add(sif, module_name, self.modulefile, template, **kwargs)
+        modulefile = os.path.join(self.settings.module_base, module_name.replace(":", os.sep), self.modulefile)
+        self.container.add(sif, module_name, modulefile, template, **kwargs)
 
     def get(self, module_name, env_file=False):
         """

shpc/version.py

@@ -2,7 +2,7 @@
 __copyright__ = "Copyright 2021, Vanessa Sochat"
 __license__ = "MPL 2.0"
 
-__version__ = "0.0.35"
+__version__ = "0.0.36"
 AUTHOR = "Vanessa Sochat"
 NAME = "singularity-hpc"
 PACKAGE_URL = "https://github.com/singularityhub/singularity-hpc"