def test_mv_dir2nonexdir():
assert os.system("sk run") == 0
assert os.system("sk mv code/subdf code/subdf2") == 0
# check the files
assert os.path.isfile("code/subdf2/pagesd.Rmd")
assert os.path.isfile("report/out_md/code/subdf2/pagesd.md")
# check the yaml
assert "code/subdf2/pagesd.Rmd" in yaml_in()["analysis"].keys()
assert "code/subdf2/non_rmd_dep.txt" in yaml_in(
)["analysis"]["code/subdf2/pagesd.Rmd"]
def test_mv_mul2dir():
assert os.system("sk run") == 0
assert os.system("sk mv code/*.Rmd code/subdir") == 0
# check the files
assert os.path.isfile("code/subdir/page1.Rmd")
assert os.path.isfile("code/subdir/page2.Rmd")
assert os.path.isfile("report/out_md/code/subdir/page1.md")
assert os.path.isfile("report/out_md/code/subdir/page2.md")
# check the yaml
assert "code/subdir/page1.Rmd" in yaml_in()["analysis"].keys()
assert "code/subdir/page2.Rmd" in yaml_in()["analysis"].keys()
def sk_mv(args):
"""Rename an Rmd in scikick.yml and associated files"""
config = yaml_in(need_pages=True)
# multiple args
src = [os.path.normpath(p) for p in args.src]
# only a single arg
dest = [os.path.normpath(p) for p in args.dest]
#check if src and dest are valid
sk_move_check(src, dest)
# save the (src, dest) pairs (to be used with moves in scikick.yml)
(new_src, new_dest) = sk_move_prepare_src_dest(src, dest)
new_src = list(map(os.path.normpath, new_src))
new_dest = list(map(os.path.normpath, new_dest))
# leave only unique pairs of (src, dest) files
mv_dict = ordereddict()
for k in new_src:
i = new_src.index(k)
mv_dict[new_src[i]] = new_dest[i]
# perform the move operation (using the initial args)
for s in src:
git_retcode = 0
if args.git:
print(f"sk: git mv {s} {dest[0]}")
git_res = subprocess.run(f"git mv {s} {dest[0]}", shell=True, \
stderr=subprocess.PIPE)
git_retcode = git_res.returncode
if git_retcode != 0:
warn("sk: Warning: Git returned an error:")
warn(git_res.stderr.decode().strip())
warn("sk: Warning: Falling back to mv")
if (git_retcode != 0) or (not args.git):
print(f"sk: mv {s} {dest[0]}")
shutil.move(s, dest[0])
sk_move_extras(mv_dict)
def test_mv_dir2exdir():
assert os.system("sk run") == 0
assert os.system("sk mv code/subdf code/subdir") == 0
# check the files
assert os.path.isfile("code/subdir/subdf/pagesd.Rmd")
assert os.path.isfile("report/out_md/code/subdir/subdf/pagesd.md")
# check the yaml
assert "code/subdir/subdf/pagesd.Rmd" in yaml_in()["analysis"].keys()
def test_mv_file2file():
assert os.system("sk run") == 0
assert os.system("sk mv code/page1.Rmd code/page3.Rmd") == 0
# check the files
assert os.path.isfile("code/page3.Rmd")
assert os.path.isfile("report/out_md/code/page3.md")
# check the yaml
assert "code/page3.Rmd" in yaml_in()["analysis"].keys()
def test_mv_file2subdirfile_runagain():
assert os.system("sk run") == 0
assert os.system("sk mv code/page1.Rmd code/subdf/page1.Rmd") == 0
# check the files
assert os.path.isfile("code/subdf/page1.Rmd")
assert os.path.isfile("report/out_md/code/subdf/page1.md")
# check the yaml
assert "code/subdf/page1.Rmd" in yaml_in()["analysis"].keys()
assert os.system("sk run > /dev/null") == 0
def write_snakefile_arg(arg, val):
"""Set the specified arg's value in scikick.yml
args -- name of the argument
val -- value of the argument
"""
yml = yaml_in()
if "snakefile_args" not in yml.keys():
yml["snakefile_args"] = dict()
yml["snakefile_args"][arg] = val
warn(f"sk: Argument {arg} set to {yml['snakefile_args'][arg]}")
yaml_dump(yml)
def main():
"""Parse the arguments and run the according function"""
args = parser.parse_args()
try:
func = args.func
except AttributeError:
parser.print_help()
return
if args.which in ["run", "config", "status"]:
# check for unsupported fields
ymli = yaml_in()
yaml_check(ymli)
func(args)
def sk_move_check(src, dest):
"""Perform checks on src and dest
and quit if bad arguments are given
src -- list of files to move
des -- list containing the file/dir to move to
"""
config = yaml_in()
for s in src:
if not os.path.exists(s):
reterr(f"sk: Error: file or directory {s} doesn't exist")
if len(src) > 1:
if not os.path.isdir(dest[0]):
reterr("sk: Error: moving multiple files to a single one")
elif len(src) == 1 and (not os.path.isdir(dest[0])):
old_ext = os.path.splitext(src[0])[1]
new_ext = os.path.splitext(dest[0])[1]
if old_ext.lower() != new_ext.lower():
warn("sk: Warning: changing file extension")
if (src[0] in config["analysis"].keys()) and \
(new_ext.lower() not in map(str.lower, supported_extensions)):
reterr(
f"sk: Error: only extensions {', '.join(supported_extensions)} are supported ({new_ext} given)"
)
def sk_move_extras(mv_dict):
"""Performs move operations specific to scikick
Moves md files, figures in output/ directories
and renames files in scikick.yml
mv_dict -- dict with keys as src and values as dest files
"""
# Moving mds, knitmetas and output figures in out_md/;
## No need to change _site.ymls, since
## they are recreated after each change in scikick.yml
yaml_dict = yaml_in()
analysis = yaml_dict["analysis"]
reportdir = yaml_dict["reportdir"]
for src, dest in mv_dict.items():
# if not in analysis.keys -> regular file
# in this case, rename and continue
if src not in analysis.keys():
if 1 == rename(src, dest):
warn("sk: %s renamed to %s in ./scikick.yml" % (src, dest))
else:
warn("sk: Warning: %s not found in ./scikick.yml" % src)
continue
md_rootdir = os.path.join(reportdir, "out_md")
md_destdir = os.path.join(md_rootdir, os.path.dirname(dest))
md_srcdir = os.path.join(md_rootdir, os.path.dirname(src))
if not os.path.isdir(md_destdir):
os.makedirs(md_destdir)
# Move .md
md_src = os.path.join(md_rootdir, os.path.splitext(src)[0] + ".md")
md_dest = os.path.join(
md_destdir,
os.path.splitext(os.path.basename(dest))[0] + ".md")
if os.path.isfile(md_src):
shutil.move(md_src, md_dest)
# Move knitmeta
k_src = sub(pattern="\.md$", repl=".knitmeta.RDS", string=md_src)
k_dest = sub(pattern="\.md$", repl=".knitmeta.RDS", string=md_dest)
if os.path.isfile(k_src):
shutil.move(k_src, k_dest)
# Move markdown outputs (figures)
tabname_src = sub(string=os.path.basename(md_src),
pattern="\.md$",
repl="")
tabname_dest = sub(string=os.path.basename(md_dest),
pattern="\.md$",
repl="")
# "figure" must match execute_code.R fig.path
md_srcfigdir = os.path.join(md_srcdir, "figure", tabname_src)
md_destfigdir = os.path.join(md_destdir, "figure", tabname_dest)
if os.path.isdir(md_srcfigdir):
dest_dirname = os.path.dirname(md_srcfigdir)
if not os.path.isdir(dest_dirname):
os.makedirs(dest_dirname, exist_oke=True)
print(f"sk: mv {md_srcfigdir} {md_destfigdir}")
shutil.move(md_srcfigdir, md_destfigdir)
# rename the figure/ directory name in the dest md
## get the initial timestamp
initial_timestamp = os.path.getmtime(md_dest)
md_file = open(md_dest, 'r+')
md_lines = [
sub(string=line,
pattern=f'src="figure/{tabname_src}',
repl=f'src="figure/{tabname_dest}') for line in md_file
]
md_file.seek(0)
for l in md_lines:
md_file.write(l)
md_file.close()
# set the initial timestamp back to avoid reexecution
os.utime(md_dest, (initial_timestamp, initial_timestamp))
# rename all entries in scikick.yml from from to f_dest
if 1 == rename(src, dest):
warn("sk: %s renamed to %s in ./scikick.yml" % (src, dest))
else:
warn("sk: Warning: %s not found in ./scikick.yml" % src)
def read(self, need_pages=False):
"""Read scikick.yml, eventually to replace yaml_in()"""
self.config = yaml_in(self.filename, need_pages)