def clone_bundle(path, prefix):
"""
Clone the bundle (located at `path`) by creating a new environment at
`prefix`.
The directory `path` is located in should be some temp directory or
some other directory OUTSITE /opt/anaconda (this function handles
copying the of the file if necessary for you). After calling this
funtion, the original file (at `path`) may be removed.
"""
assert not abspath(path).startswith(abspath(config.root_dir))
assert not isdir(prefix)
fn = basename(path)
assert re.match(r'share-[0-9a-f]{40}-\d+\.tar\.bz2$', fn), fn
dist = fn[:-8]
if not install.is_extracted(config.pkgs_dir, dist):
shutil.copyfile(path, join(config.pkgs_dir, dist + '.tar.bz2'))
plan.execute_plan(['%s %s' % (plan.EXTRACT, dist)])
assert install.is_extracted(config.pkgs_dir, dist)
with open(join(config.pkgs_dir, dist, 'info', 'index.json')) as fi:
meta = json.load(fi)
# for backwards compatibility, use "requires" when "depends" is not there
dists = ['-'.join(r.split())
for r in meta.get('depends', meta.get('requires'))
if not r.startswith('conda ')]
dists.append(dist)
actions = plan.ensure_linked_actions(dists, prefix)
index = get_index()
plan.display_actions(actions, index)
plan.execute_actions(actions, index, verbose=True)
os.unlink(join(prefix, 'conda-meta', dist + '.json'))
def clone_bundle(path, prefix=None, bundle_name=None):
"""
Clone the bundle (located at `path`) by creating a new environment at
`prefix` (unless prefix is None or the prefix directory already exists)
"""
try:
t = tarfile.open(path, 'r:*')
meta = json.load(t.extractfile('info/index.json'))
except tarfile.ReadError:
raise RuntimeError('bad tar archive: %s' % path)
except KeyError:
raise RuntimeError("no archive 'info/index.json' in: %s" % (path))
if prefix and not isdir(prefix):
for m in t.getmembers():
if m.path.startswith((BDP, 'info/')):
continue
t.extract(m, path=prefix)
dists = discard_conda('-'.join(s.split())
for s in meta.get('depends', []))
actions = plan.ensure_linked_actions(dists, prefix)
index = get_index()
plan.display_actions(actions, index)
plan.execute_actions(actions, index, verbose=True)
bundle_dir = abspath(
expanduser('~/bundles/%s' % (bundle_name or meta.get('bundle_name'))))
for m in t.getmembers():
if m.path.startswith(BDP):
targetpath = join(bundle_dir, m.path[len(BDP):])
t._extract_member(m, targetpath)
t.close()
def old_clone_bundle(path, prefix):
"""
Clone the bundle (located at `path`) by creating a new environment at
`prefix`.
The directory `path` is located in should be some temp directory or
some other directory OUTSITE /opt/anaconda (this function handles
copying the of the file if necessary for you). After calling this
funtion, the original file (at `path`) may be removed.
"""
assert not abspath(path).startswith(abspath(config.root_dir))
assert not isdir(prefix)
fn = basename(path)
assert re.match(r'share-[0-9a-f]{40}-\d+\.tar\.bz2$', fn), fn
dist = fn[:-8]
pkgs_dir = config.pkgs_dirs[0]
if not install.is_extracted(pkgs_dir, dist):
shutil.copyfile(path, join(pkgs_dir, dist + '.tar.bz2'))
inst.execute_instructions([(inst.EXTRACT, (dist,))])
assert install.is_extracted(pkgs_dir, dist)
with open(join(pkgs_dir, dist, 'info', 'index.json')) as fi:
meta = json.load(fi)
# for backwards compatibility, use "requires" when "depends" is not there
dists = ['-'.join(r.split())
for r in meta.get('depends', meta.get('requires', []))
if not r.startswith('conda ')]
dists.append(dist)
actions = plan.ensure_linked_actions(dists, prefix)
index = get_index()
plan.execute_actions(actions, index, verbose=False)
os.unlink(join(prefix, 'conda-meta', dist + '.json'))
def clone_bundle(path, prefix=None, bundle_name=None):
"""
Clone the bundle (located at `path`) by creating a new environment at
`prefix` (unless prefix is None or the prefix directory already exists)
"""
try:
t = tarfile.open(path, 'r:*')
meta = json.load(t.extractfile('info/index.json'))
except tarfile.ReadError:
raise RuntimeError('bad tar archive: %s' % path)
except KeyError:
raise RuntimeError("no archive 'info/index.json' in: %s" % (path))
if prefix and not isdir(prefix):
for m in t.getmembers():
if m.path.startswith((BDP, 'info/')):
continue
t.extract(m, path=prefix)
dists = discard_conda('-'.join(s.split())
for s in meta.get('depends', []))
actions = plan.ensure_linked_actions(dists, prefix)
index = get_index()
plan.display_actions(actions, index)
plan.execute_actions(actions, index, verbose=True)
bundle_dir = abspath(expanduser('~/bundles/%s' %
(bundle_name or meta.get('bundle_name'))))
for m in t.getmembers():
if m.path.startswith(BDP):
targetpath = join(bundle_dir, m.path[len(BDP):])
t._extract_member(m, targetpath)
t.close()
def test_ensure_linked_actions_all_linked(self, load_meta):
dists = [Dist("test-88"), Dist("test-spec-42"), Dist("test-spec2-8.0.0.0.1-9")]
prefix = "some/prefix"
link_actions = plan.ensure_linked_actions(dists, prefix)
expected_output = defaultdict(list)
expected_output["PREFIX"] = prefix
expected_output["op_order"] = ('CHECK_FETCH', 'RM_FETCHED', 'FETCH', 'CHECK_EXTRACT',
'RM_EXTRACTED', 'EXTRACT', 'UNLINK', 'LINK',
'SYMLINK_CONDA')
self.assertEquals(link_actions, expected_output)
def test_ensure_linked_actions_all_linked(self, load_meta):
dists = [Dist("test-88"), Dist("test-spec-42"), Dist("test-spec2-8.0.0.0.1-9")]
prefix = "some/prefix"
link_actions = plan.ensure_linked_actions(dists, prefix)
expected_output = defaultdict(list)
expected_output["PREFIX"] = prefix
expected_output["op_order"] = ('CHECK_FETCH', 'RM_FETCHED', 'FETCH', 'CHECK_EXTRACT',
'RM_EXTRACTED', 'EXTRACT', 'UNLINK', 'LINK',
'SYMLINK_CONDA')
self.assertEquals(link_actions, expected_output)
def clone_env(prefix1, prefix2, verbose=True, quiet=False, index=None):
"""
clone existing prefix1 into new prefix2
"""
untracked_files = untracked(prefix1)
dists = discard_conda(install.linked(prefix1))
if verbose:
print('Packages: %d' % len(dists))
print('Files: %d' % len(untracked_files))
for f in untracked_files:
src = join(prefix1, f)
dst = join(prefix2, f)
dst_dir = dirname(dst)
if islink(dst_dir) or isfile(dst_dir):
os.unlink(dst_dir)
if not isdir(dst_dir):
os.makedirs(dst_dir)
if islink(src):
os.symlink(os.readlink(src), dst)
continue
try:
with open(src, 'rb') as fi:
data = fi.read()
except IOError:
continue
try:
s = data.decode('utf-8')
s = s.replace(prefix1, prefix2)
data = s.encode('utf-8')
except UnicodeDecodeError: # data is binary
pass
with open(dst, 'wb') as fo:
fo.write(data)
shutil.copystat(src, dst)
if index is None:
index = get_index()
r = Resolve(index)
sorted_dists = r.dependency_sort(dists)
actions = ensure_linked_actions(sorted_dists, prefix2)
execute_actions(actions, index=index, verbose=not quiet)
return actions, untracked_files
def clone_analysispackage(path,
prefix=None,
analysispackage_name=None,
data_path=None):
"""
Clone the analysispackage (located at `path`) by creating a new environment at
`prefix` (unless prefix is None or the prefix directory already exists)
"""
try:
t = tarfile.open(path, 'r:*')
meta = json.load(t.extractfile('info/index.json'))
except tarfile.ReadError:
raise RuntimeError('bad tar archive: %s' % path)
except KeyError:
raise RuntimeError("no archive 'info/index.json' in: %s" % (path))
if prefix and isdir(prefix):
print("erasing old environment at %s" % prefix)
shutil.rmtree(prefix)
if prefix and not isdir(prefix):
for m in t.getmembers():
if m.path.startswith((BDP, 'info/')):
continue
t.extract(m, path=prefix)
dists = discard_conda('-'.join(s.split())
for s in meta.get('depends', []))
actions = plan.ensure_linked_actions(dists, prefix)
index = get_index()
plan.display_actions(actions, index)
plan.execute_actions(actions, index, verbose=False)
if not data_path:
analysispackage_dir = abspath(
expanduser(
'~/analysispackages/%s' %
(analysispackage_name or meta.get('analysispackage_name'))))
else:
analysispackage_dir = data_path
for m in t.getmembers():
if m.path.startswith(BDP):
targetpath = join(analysispackage_dir, m.path[len(BDP):])
t._extract_member(m, targetpath)
with open(join(data_path, ".metadata.json"), "w+") as f:
json.dump({'env': prefix}, f)
t.close()
def clone_analysispackage(path, prefix=None, analysispackage_name=None, data_path=None):
"""
Clone the analysispackage (located at `path`) by creating a new environment at
`prefix` (unless prefix is None or the prefix directory already exists)
"""
try:
t = tarfile.open(path, 'r:*')
meta = json.load(t.extractfile('info/index.json'))
except tarfile.ReadError:
raise RuntimeError('bad tar archive: %s' % path)
except KeyError:
raise RuntimeError("no archive 'info/index.json' in: %s" % (path))
if prefix and isdir(prefix):
print ("erasing old environment at %s" % prefix)
shutil.rmtree(prefix)
if prefix and not isdir(prefix):
for m in t.getmembers():
if m.path.startswith((BDP, 'info/')):
continue
t.extract(m, path=prefix)
dists = discard_conda('-'.join(s.split())
for s in meta.get('depends', []))
actions = plan.ensure_linked_actions(dists, prefix)
index = get_index()
plan.display_actions(actions, index)
plan.execute_actions(actions, index, verbose=False)
if not data_path:
analysispackage_dir = abspath(expanduser('~/analysispackages/%s' %
(analysispackage_name or meta.get('analysispackage_name'))))
else:
analysispackage_dir = data_path
for m in t.getmembers():
if m.path.startswith(BDP):
targetpath = join(analysispackage_dir, m.path[len(BDP):])
t._extract_member(m, targetpath)
with open(join(data_path, ".metadata.json"), "w+") as f:
json.dump({'env' : prefix}, f)
t.close()
def clone_env(prefix1, prefix2, verbose=True):
"""
clone existing prefix1 into new prefix2
"""
untracked_files = untracked(prefix1)
dists = install.linked(prefix1)
print('Packages: %d' % len(dists))
print('Files: %d' % len(untracked_files))
for f in untracked_files:
src = join(prefix1, f)
dst = join(prefix2, f)
dst_dir = dirname(dst)
if islink(dst_dir) or isfile(dst_dir):
os.unlink(dst_dir)
if not isdir(dst_dir):
os.makedirs(dst_dir)
try:
with open(src, 'rb') as fi:
data = fi.read()
except IOError:
continue
try:
s = data.decode('utf-8')
s = s.replace(prefix1, prefix2)
data = s.encode('utf-8')
except UnicodeDecodeError: # data is binary
pass
with open(dst, 'wb') as fo:
fo.write(data)
shutil.copystat(src, dst)
actions = ensure_linked_actions(dists, prefix2)
execute_actions(actions, index=get_index(), verbose=verbose)