Update remaining packages to use Stage.source_path (spack#11662)

spack#11528 updated Stage to always store a Package's source in a fixed
directory accessible via `Stage.source_path` This left behind a
number of packages which were expecting to access the source code
via `Stage.path`. This Updates those packages to use
`Stage.source_path` instead.

This also updates the name of the fixed directory: The original name
of the fixed directory was "src", so if an expanded archive created a
"src" directory, then users inspecting the directory structure could
see paths like "src/src" (which wasn't wrong but could be confusing).
Therefore this also updates the name of the fixed directory to
"spack-src".

lib/spack/spack/stage.py

@@ -28,7 +28,7 @@
 from spack.util.path import canonicalize_path
 from spack.util.crypto import prefix_bits, bit_length
 
-_source_path_subdir = 'src'
+_source_path_subdir = 'spack-src'
 _stage_prefix = 'spack-stage-'
 
 

lib/spack/spack/test/stage.py

@@ -48,15 +48,15 @@
 # to have the following structure:
 #
 # TMPDIR/                 temp stage dir
-#     src/                well-known stage source directory
+#     spack-src/          well-known stage source directory
 #         _readme_fn      Optional test_readme (contains _readme_contents)
 #     _hidden_fn          Optional hidden file (contains _hidden_contents)
 #     _archive_fn         archive_url = file:///path/to/_archive_fn
 #
 # while exploding tarball directories are expected to be structured as follows:
 #
 # TMPDIR/                 temp stage dir
-#     src/                well-known stage source directory
+#     spack-src/          well-known stage source directory
 #         archive_name/   archive dir
 #             _readme_fn  test_readme (contains _readme_contents)
 #         _extra_fn       test_extra file (contains _extra_contents)

var/spack/repos/builtin/packages/aspera-cli/package.py

@@ -21,7 +21,7 @@ def setup_environment(self, spack_env, run_env):
         run_env.prepend_path('PATH', self.prefix.cli.bin)
 
     def install(self, spec, prefix):
-        runfile = glob(join_path(self.stage.path, 'aspera-cli*.sh'))[0]
+        runfile = glob(join_path(self.stage.source_path, 'aspera-cli*.sh'))[0]
         # Update destination path
         filter_file('INSTALL_DIR=~/.aspera',
                     'INSTALL_DIR=%s' % prefix,

var/spack/repos/builtin/packages/bcl2fastq2/package.py

@@ -5,7 +5,6 @@
 
 from spack import *
 import os
-import shutil
 import glob
 import llnl.util.tty as tty
 
@@ -70,19 +69,34 @@ def do_stage(self, mirror_only=False):
     def unpack_it(self, f):
         def wrap():
             f()                 # call the original expand_archive()
+
+            # The tarfile should now reside in the well-known source
+            # directory (i.e., self.stage.source_path).
             with working_dir(self.stage.path):
-                if os.path.isdir('bcl2fastq'):
-                    tty.msg("The tarball has already been unpacked")
-                else:
+                source_subdir = os.path.relpath(self.stage.source_path,
+                                                self.stage.path)
+                files = glob.glob(os.path.join(source_subdir,
+                                               'bcl2fastq2*.tar.gz'))
+                if len(files) == 1:
+                    # Rename the tarball so it resides in self.stage.path
+                    # alongside the original zip file before unpacking it.
+                    tarball = files[0]
+                    basename = os.path.basename(tarball)
+                    os.rename(tarball, basename)
                     tty.msg("Unpacking bcl2fastq2 tarball")
-                    tarball = glob.glob(join_path('spack-expanded-archive',
-                                        'bcl2fastq2*.tar.gz'))[0]
-                    copy(tarball, '.')
-                    shutil.rmtree('spack-expanded-archive')
                     tar = which('tar')
-                    tarball = os.path.basename(tarball)
-                    tar('-xf', tarball)
+                    tar('-xf', basename)
+
+                    # Rename the unpacked directory to the well-known
+                    # source path self.stage.source_path.
+                    os.rename('bcl2fastq', source_subdir)
                     tty.msg("Finished unpacking bcl2fastq2 tarball")
+
+                elif self.stage.expanded:
+                    # The unpacked files already reside in the "well known"
+                    # source directory (i.e., self.stage.source_path).
+                    tty.msg("The tarball has already been unpacked.")
+
         return wrap
 
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/catalyst/package.py

@@ -119,7 +119,7 @@ def do_stage(self, mirror_only=False):
         super(Catalyst, self).do_stage(mirror_only)
 
         # extract the catalyst part
-        paraview_dir = os.path.join(self.stage.path,
+        paraview_dir = os.path.join(self.stage.source_path,
                                     'ParaView-v' + str(self.version))
         catalyst_script = os.path.join(paraview_dir, 'Catalyst', 'catalyze.py')
         editions_dir = os.path.join(paraview_dir, 'Catalyst', 'Editions')
@@ -135,10 +135,10 @@ def do_stage(self, mirror_only=False):
         if not os.path.isdir(catalyst_source_dir):
             os.mkdir(catalyst_source_dir)
             subprocess.check_call(command)
-            tty.msg("Generated catalyst source in %s" % self.stage.path)
+            tty.msg("Generated catalyst source in %s" % self.stage.source_path)
         else:
             tty.msg("Already generated %s in %s" % (self.name,
-                                                    self.stage.path))
+                                                    self.stage.source_path))
 
     def setup_environment(self, spack_env, run_env):
         # paraview 5.5 and later
@@ -174,7 +174,8 @@ def root_cmakelists_dir(self):
 
         :return: directory containing CMakeLists.txt
         """
-        return os.path.join(self.stage.path, 'Catalyst-v' + str(self.version))
+        return os.path.join(self.stage.source_path,
+                            'Catalyst-v' + str(self.version))
 
     @property
     def build_directory(self):

var/spack/repos/builtin/packages/charmpp/package.py

@@ -241,5 +241,5 @@ def install(self, spec, prefix):
     @run_after('install')
     @on_package_attributes(run_tests=True)
     def check_build(self):
-        make('-C', join_path(self.stage.path, 'charm/tests'),
+        make('-C', join_path(self.stage.source_path, 'charm/tests'),
              'test', parallel=False)

var/spack/repos/builtin/packages/clhep/package.py

@@ -51,8 +51,7 @@ class Clhep(CMakePackage):
     def patch(self):
         filter_file('SET CMP0042 OLD',
                     'SET CMP0042 NEW',
-                    '%s/%s/CLHEP/CMakeLists.txt'
-                    % (self.stage.path, self.spec.version))
+                    '%s/CLHEP/CMakeLists.txt' % self.stage.source_path)
 
     def cmake_args(self):
         cmake_args = ['-DCLHEP_BUILD_CXXSTD=-std=c++{0}'.format(

var/spack/repos/builtin/packages/cuda/package.py

@@ -41,7 +41,7 @@ def setup_environment(self, spack_env, run_env):
         run_env.set('CUDA_HOME', self.prefix)
 
     def install(self, spec, prefix):
-        runfile = glob(join_path(self.stage.path, 'cuda*_linux*'))[0]
+        runfile = glob(join_path(self.stage.source_path, 'cuda*_linux*'))[0]
         chmod = which('chmod')
         chmod('+x', runfile)
         runfile = which(runfile)

var/spack/repos/builtin/packages/lmod/package.py

@@ -51,7 +51,7 @@ class Lmod(AutotoolsPackage):
 
     def setup_environment(self, spack_env, run_env):
         stage_lua_path = join_path(
-            self.stage.path, 'Lmod-{version}', 'src', '?.lua')
+            self.stage.source_path, 'src', '?.lua')
         spack_env.append_path('LUA_PATH', stage_lua_path.format(
             version=self.version), separator=';')
 

var/spack/repos/builtin/packages/nseg/package.py

@@ -71,7 +71,7 @@ def prepare_source(self):
         for key in self.resources:
             for res in self.resources[key]:
                 res_name = res.name
-                res_path = join_path(res.fetcher.stage.path, res.name)
+                res_path = join_path(res.fetcher.stage.source_path, res.name)
                 copy(res_path, join_path(self.build_directory, res_name))
 
     def install(self, spec, prefix):

var/spack/repos/builtin/packages/singularity/package.py

@@ -38,7 +38,7 @@ class Singularity(MakefilePackage):
     # tree into the proper subdir in our overridden do_stage below.
     @property
     def gopath(self):
-        return join_path(self.stage.path)
+        return self.stage.path
 
     @property
     def sylabs_gopath_dir(self):
@@ -52,13 +52,15 @@ def singularity_gopath_dir(self):
     # its home within GOPATH.
     def do_stage(self, mirror_only=False):
         super(Singularity, self).do_stage(mirror_only)
-        source_path = self.stage.source_path
         if not os.path.exists(self.singularity_gopath_dir):
+            # Move the expanded source to its destination
             tty.debug("Moving {0} to {1}".format(
-                source_path, self.singularity_gopath_dir))
-            mkdirp(self.sylabs_gopath_dir)
-            shutil.move(source_path,
-                        self.singularity_gopath_dir)
+                self.stage.source_path, self.singularity_gopath_dir))
+            shutil.move(self.stage.source_path, self.singularity_gopath_dir)
+
+            # The build process still needs access to the source path,
+            # so create a symlink.
+            force_symlink(self.singularity_gopath_dir, self.stage.source_path)
 
     # MakefilePackage's stages use this via working_dir()
     @property