tzok/eltetrado

A Python application to find and classify tetrads and quadruplexes in DNA/RNA 3D structures

eltetrado's Issues

Add a licence?

👋 Hi! I came across this package in your paper in BMC Bioinformatics and was wondering - would you consider adding a licence file to allow others to potentially re-use the code?

More info:

• why no licence means code can't be reused: https://choosealicense.com/no-permission/
• choosing an appropriate licence: https://choosealicense.com

Can not install eltetrado using "pip install eltetrado" in Ubuntu 18.

The installation command returns the following error on Ubuntu 18

`
Keyring is skipped due to an exception: module 'collections' has no attribute 'MutableMapping'
Defaulting to user installation because normal site-packages is not writeable
Collecting eltetrado
Using cached eltetrado-1.5.7-py3-none-any.whl (28 kB)
Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from eltetrado) (1.13.3)
Collecting orjson
Using cached orjson-3.8.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (270 kB)
Collecting rnapolis
Using cached RNApolis-0.0.12-py3-none-any.whl (20 kB)
Collecting mmcif
Using cached mmcif-0.80.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (613 kB)
Collecting msgpack
Downloading msgpack-1.0.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (316 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 317.0/317.0 kB 1.8 MB/s eta 0:00:00
Collecting requests>=2.25
Downloading requests-2.28.2-py3-none-any.whl (62 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 62.8/62.8 kB 9.9 MB/s eta 0:00:00
Collecting future
Using cached future-0.18.3.tar.gz (840 kB)
Preparing metadata (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [20 lines of output]
Traceback (most recent call last):
File "", line 2, in
File "", line 14, in
File "/usr/lib/python3/dist-packages/setuptools/init.py", line 12, in
import setuptools.version
File "/usr/lib/python3/dist-packages/setuptools/version.py", line 1, in
import pkg_resources
File "/usr/lib/python3/dist-packages/pkg_resources/init.py", line 77, in
import('pkg_resources.extern.packaging.requirements')
File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/requirements.py", line 9, in
from pkg_resources.extern.pyparsing import stringStart, stringEnd, originalTextFor, ParseException
File "", line 1027, in _find_and_load
File "", line 1006, in _find_and_load_unlocked
File "", line 672, in _load_unlocked
File "", line 632, in _load_backward_compatible
File "/usr/lib/python3/dist-packages/pkg_resources/extern/init.py", line 43, in load_module
import(extant)
File "/usr/lib/python3/dist-packages/pkg_resources/_vendor/pyparsing.py", line 943, in
collections.MutableMapping.register(ParseResults)
AttributeError: module 'collections' has no attribute 'MutableMapping'
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
--- Logging error ---
Traceback (most recent call last):
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/utils/logging.py", line 177, in emit
self.console.print(renderable, overflow="ignore", crop=False, style=style)
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/rich/console.py", line 1673, in print
extend(render(renderable, render_options))
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/rich/console.py", line 1305, in render
for render_output in iter_render:
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/utils/logging.py", line 134, in rich_console
for line in lines:
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/rich/segment.py", line 249, in split_lines
for segment in segments:
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/rich/console.py", line 1283, in render
renderable = rich_cast(renderable)
File "/usr/local/lib/python3.10/dist-packages/pip/_vendor/rich/protocol.py", line 36, in rich_cast
renderable = cast_method()
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/self_outdated_check.py", line 130, in rich
pip_cmd = get_best_invocation_for_this_pip()
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/utils/entrypoints.py", line 58, in get_best_invocation_for_this_pip
if found_executable and os.path.samefile(
File "/usr/lib/python3.10/genericpath.py", line 101, in samefile
s2 = os.stat(f2)
FileNotFoundError: [Errno 2] No such file or directory: '/usr/bin/pip'
Call stack:
File "/usr/local/bin/pip", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/cli/main.py", line 70, in main
return command.main(cmd_args)
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/cli/base_command.py", line 101, in main
return self._main(args)
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/cli/base_command.py", line 223, in _main
self.handle_pip_version_check(options)
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/cli/req_command.py", line 190, in handle_pip_version_check
pip_self_version_check(session, options)
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/self_outdated_check.py", line 236, in pip_self_version_check
logger.warning("[present-rich] %s", upgrade_prompt)
File "/usr/lib/python3.10/logging/init.py", line 1489, in warning
self._log(WARNING, msg, args, **kwargs)
File "/usr/lib/python3.10/logging/init.py", line 1624, in _log
self.handle(record)
File "/usr/lib/python3.10/logging/init.py", line 1634, in handle
self.callHandlers(record)
File "/usr/lib/python3.10/logging/init.py", line 1696, in callHandlers
hdlr.handle(record)
File "/usr/lib/python3.10/logging/init.py", line 968, in handle
self.emit(record)
File "/usr/local/lib/python3.10/dist-packages/pip/_internal/utils/logging.py", line 179, in emit
self.handleError(record)
Message: '[present-rich] %s'
Arguments: (UpgradePrompt(old='22.2.1', new='22.3.1'),)
`