def nbconvert():
"""helper function to convert all .ipynb files in the current directory to
html files.
The output html files are in a directory named `html` under the current
directory. Existing html files with the same name are overwritten.
If no directory named `html` is present, it will be created (jupyter nbconvert
does that automatically)
"""
# Get the current directory
#cdir = path.dirname(path.realpath(__file__))
cdir = _getcwd()
# Get a list of .ipynb files
files2convert = [f for f in _listdir(cdir) if f.endswith('.ipynb')]
# Convert the files within a try-except block
count_files_successfully_converted = 0
failedFiles = []
for i, f in enumerate(files2convert):
_getMD5(f)
print(">>> [{}] Converting file ... ".format(i+1))
if _convert(f):
count_files_successfully_converted += 1
else:
failedFiles.append(f)
# Print some human readable feedback
print("\n")
print("*******************************************")
print(" REPORT ")
print("*******************************************")
print("\nCurrent Directory: ", cdir)
print("Number of IPython notebooks found: ", len(files2convert))
print("Number of files successfully converted to html:",
count_files_successfully_converted)
print("Number of files failed to convert to html:", len(failedFiles))
if failedFiles:
print("Files that failed to convert:")
for f in failedFiles:
print(f)
print("\nDONE!")
raw_input("Press ENTER to close the appliation ...")
from os import getcwd as _getcwd
from os import getenv as _getenv
from os.path import normpath as _normpath
SUBREDDIT: str = _getenv("SUBREDDIT", "")
WEBHOOK_URL: str = _getenv("WEBHOOK_URL", "")
DB_URI: str = _getenv("DB_URI",
"sqlite:///" + (_normpath(_getcwd() + "/app.db")))
FEED_LIMIT: int = int(_getenv("FEED_LIMIT", 100))
REFRESH_TIME: int = int(_getenv("REFRESH_TIME", 60))
POST: bool = _getenv("POST", "true").lower() == "true"
FEED: bool = _getenv("FEED_ONLY", "true").lower() == "true"
DIRTY: int = int(_getenv("DIRTY", "86400"))
NAME = 'tosdb'
VERSION = '0.8'
DESCRIPTION = "Python Front-End / Wrapper for TOSDataBridge"
AUTHOR = "Jonathon Ogden"
AUTHOR_EMAIL = "*****@*****.**"
PACKAGES = ['tosdb', 'tosdb/cli_scripts', 'tosdb/intervalize']
_AUTO_EXT = '_tosdb'
# everything should be relative to the python/setup.py
_OUR_PATH = _dirname(_realpath(__file__))
_HEADER_NAME = 'tos_databridge.h'
_HEADER_PATH = _path_join(_OUR_PATH, '..', 'include', _HEADER_NAME)
_OUTPUT_PATH = _path_join(_OUR_PATH, NAME, _AUTO_EXT + '.py')
if _OUR_PATH != _getcwd():
_sys.stderr.write(
"fatal: setup.py must be run from its own directory(python/)\n")
exit(1)
#string that should bookmark the topics in Topic_Enum_Wrapper::TOPICS<T>
_MAGIC_TOPIC_STR = 'ksxaw9834hr84hf;esij?><'
#regex for finding our header #define consts
#TODO: adjust so we can pull non-ints
_REGEX_HEADER_CONST = "#define[\s]+([\w]+)[\s]+.*?(-?[\d][\w]*)"
#adjust for topics we had to permute to form valid enum vars
TOPIC_VAL_REPLACE = {'HIGH52': '52HIGH', 'LOW52': '52LOW'}
#exclude certain header consts
NAME = 'tosdb'
VERSION = '0.9'
DESCRIPTION = "Python Front-End / Wrapper for TOSDataBridge"
AUTHOR = "Jonathon Ogden"
AUTHOR_EMAIL = "*****@*****.**"
PACKAGES = ['tosdb','tosdb/cli_scripts','tosdb/intervalize', 'tosdb/streaming']
_AUTO_EXT = '_tosdb'
# everything should be relative to the python/setup.py
_OUR_PATH = _dirname(_realpath(__file__))
_HEADER_NAME = 'tos_databridge.h'
_HEADER_PATH = _path_join(_OUR_PATH, '..', 'include', _HEADER_NAME)
_OUTPUT_PATH = _path_join(_OUR_PATH, NAME, _AUTO_EXT + '.py')
if _OUR_PATH != _getcwd():
_sys.stderr.write("fatal: setup.py must be run from its own directory(python/)\n")
exit(1)
#string that should bookmark the topics in Topic_Enum_Wrapper::TOPICS<T>
_MAGIC_TOPIC_STR = 'ksxaw9834hr84hf;esij?><'
#regex for finding our header #define consts
#TODO: adjust so we can pull non-ints
_REGEX_HEADER_CONST = "#define[\s]+([\w]+)[\s]+.*?(-?[\d][\w]*)"
#adjust for topics we had to permute to form valid enum vars
TOPIC_VAL_REPLACE = {'HIGH52':'52HIGH','LOW52':'52LOW'}
#exclude certain header consts
# coding: utf-8 from os import getcwd as _getcwd file_glob = _getcwd() + '/devel-docs/*/*-decl.txt' maintainer = 'David Nečas (Yeti) <*****@*****.**>' syntax_name = 'gwyddion' url = 'http://trific.ath.cx/Ftp/vim/syntax/gwyddion.vim'
# coding: utf-8 from os import getcwd as _getcwd file_glob = _getcwd() + '/devel-docs/*/*-decl.txt' maintainer = 'David Nečas (Yeti) <*****@*****.**>' syntax_name = 'gwyddion' url = 'http://gwyddion.net/download/test/gwyddion.vim'
def remember_cwd():
curdir = _getcwd()
try:
yield
finally:
_chdir(curdir)
#
# mdciao is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with mdciao. If not, see <https://www.gnu.org/licenses/>.
##############################################################################
from os import path as _path, getcwd as _getcwd, chdir as _chdir, link as _link
from mdciao import __path__ as mdc_path
from subprocess import run as _run
mdc_path = _path.split(mdc_path[0])[0]
cwd = _getcwd()
long2short = {
"--residues": "-r",
"--n_smooth_hw": "-ns",
"--table_ext": "-tx",
"--BW_uniprot": "--BW",
"--CGN_PDB": "--CGN"
}
long2long = {key: key for key in long2short.keys()}
from mdciao.filenames import filenames
filenames = filenames()