neurodamus: move core modifications into packages (#1615)

bluebrain/repo-bluebrain/packages/model-neocortex/package.py

@@ -5,7 +5,7 @@
 
 from spack import *
 
-from .sim_model import SimModel
+from .sim_model import SimModel, copy_all, make_link
 
 
 class ModelNeocortex(SimModel):

bluebrain/repo-bluebrain/packages/neurodamus-core/package.py

@@ -10,7 +10,7 @@
 
 from spack import *
 
-from .sim_model import SimModel
+from .sim_model import SimModel, copy_all
 
 # Definitions
 _CORENRN_MODLIST_FNAME = "coreneuron_modlist.txt"

bluebrain/repo-bluebrain/packages/neurodamus-model/package.py

@@ -11,7 +11,7 @@
 from spack import *
 
 from .py_neurodamus import PyNeurodamus
-from .sim_model import SimModel
+from .sim_model import SimModel, copy_all, make_link
 
 # Definitions
 _CORENRN_MODLIST_FNAME = "coreneuron_modlist.txt"

bluebrain/repo-bluebrain/packages/neurodamus-neocortex/package.py

@@ -7,6 +7,8 @@
 
 from .neurodamus_model import (
  NeurodamusModel,
+ copy_all,
+ make_link,
  version_from_model_core_dep,
  version_from_model_ndpy_dep,
 )

bluebrain/repo-bluebrain/packages/sim-model/package.py

@@ -249,3 +249,39 @@ def profiling_wrapper_on():
  os.environ['USE_PROFILER_WRAPPER'] = '1'
  yield
  del os.environ['USE_PROFILER_WRAPPER']
+
+
+def copy_all(src, dst, copyfunc=shutil.copy):
+ """Copy/process all files in a src dir into a destination dir.
+ """
+ isdir = os.path.isdir
+ for name in os.listdir(src):
+ pth = join_path(src, name)
+ isdir(pth) or copyfunc(pth, dst)
+
+
+def make_link(src, dst):
+ """Create a symlink in a given destination.
+ make_link is copy compatible i.e. will take the same args and behave
+ similarly to shutil.copy except that it will create a soft link instead.
+ If destination is a directory then a new symlink is created inside with
+ the same name as the original file.
+ Relative src paths create a relative symlink (properly relocated) while
+ absolute paths crete an abolute-path symlink.
+ If another link already exists in the destination with the same it is
+ deleted before link creation.
+ Args:
+ src (str): The path of the file to create a link to
+ dst (str): The link destination path (may be a directory)
+ """
+ if os.path.isdir(dst):
+ dst_dir = dst
+ dst = join_path(dst, os.path.basename(src))
+ else:
+ dst_dir = os.path.dirname(dst)
+ if not os.path.isabs(src):
+ src = os.path.relpath(src, dst_dir) # update path relation
+ # Silently replace links, just like copy replaces files
+ if os.path.islink(dst):
+ os.remove(dst)
+ os.symlink(src, dst)

lib/spack/llnl/util/filesystem.py

@@ -57,8 +57,6 @@
  'is_exe',
  'join_path',
  'last_modification_time_recursive',
- 'copy_all',
- 'make_link',
  'mkdirp',
  'partition_path',
  'prefixes',
@@ -645,42 +643,6 @@ def force_remove(*paths):
  pass
 
 
-def copy_all(src, dst, copyfunc=shutil.copy):
- """Copy/process all files in a src dir into a destination dir.
- """
- isdir = os.path.isdir
- for name in os.listdir(src):
- pth = join_path(src, name)
- isdir(pth) or copyfunc(pth, dst)
-
-
-def make_link(src, dst):
- """Create a symlink in a given destination.
- make_link is copy compatible i.e. will take the same args and behave
- similarly to shutil.copy except that it will create a soft link instead.
- If destination is a directory then a new symlink is created inside with
- the same name as the original file.
- Relative src paths create a relative symlink (properly relocated) while
- absolute paths crete an abolute-path symlink.
- If another link already exists in the destination with the same it is
- deleted before link creation.
- Args:
- src (str): The path of the file to create a link to
- dst (str): The link destination path (may be a directory)
- """
- if os.path.isdir(dst):
- dst_dir = dst
- dst = join_path(dst, os.path.basename(src))
- else:
- dst_dir = os.path.dirname(dst)
- if not os.path.isabs(src):
- src = os.path.relpath(src, dst_dir) # update path relation
- # Silently replace links, just like copy replaces files
- if os.path.islink(dst):
- os.remove(dst)
- os.symlink(src, dst)
-
-
 @contextmanager
 def working_dir(dirname, **kwargs):
  if kwargs.get('create', False):