Pandas can take care of the conversion of a Counter to a DataFrameby itself but you need to add a column label:
pd.DataFrame({"YourColumnLabelGoesHere": counterObject})import pandas as pd
from collections import Counter
ctr = Counter()
ctr["a"] += 1
ctr["b"] += 1
ctr["a"] += 1
ctr["a"] += 1
ctr["b"] += 1
ctr["a"] += 1
ctr["c"] += 1
pd.DataFrame({"ctr": ctr})This will result in the following DataFrame:
import structlog
logger = structlog.get_logger()
# Usage example
logger.info("Test log")
While trying to enable the matplotlib xkcd style using
plt.style.use("xkcd")you see the following error message:
OSError: 'xkcd' not found in the style library and input is not a valid URL or path; see `style.available` for list of available styles
You can’t enable xkcd-style plots by running plt.style.use("xkcd"). Instead, use with plt.xkcd():
with plt.xkcd():
# TODO your plotting code goes here!
# plt.plot(x, y) # Example
I recommend using invoke instead of the built-in subprocess to handle executing any shell command in Python.
Not only does invoke‘s run() it provide a more user friendly syntax compared to e.g. subprocess.check_output():
run('make')but it also tends to act more like you’d expect especially regarding the output of the command and has easy-to-use parameters such as hide=True to hide the output of shell commands.
Furthermore, it provides a buch of really useful features such as automatically responding to prompts from the shell command.
Use this command to test if a given MongoDB database exists:
mongo --quiet --eval 'db.getMongo().getDBNames().indexOf("mydb")'This will return an index such as 0 or 241 if the database is found. On the other hand, it will return -1 if the database does not exist.
docker-compose version:
docker-compose exec mongodb mongo --quiet --eval 'db.getMongo().getDBNames().indexOf("mydb")'where mongodb is the name of your container.
Now we can put it together in a bash script to test if the database exists:
# Query if DB exists in MongoDB
mongo_indexof_db=$(mongo --quiet --eval 'db.getMongo().getDBNames().indexOf("mydb")')
if [ $mongo_indexof_db -ne "-1" ]; then
echo "MongoDB database exists"
else
echo "MongoDB database does not exist"
fi
docker-compose variant:
# Query if DB exists in MongoDB
mongo_indexof_db=$(docker-compose -f inspect.yml exec -T mongodb mongo --quiet --eval 'db.getMongo().getDBNames().indexOf("mydb")')
if [ $mongo_indexof_db -ne "-1" ]; then
echo "MongoDB database exists"
else
echo "MongoDB database does not exist"
fi
When trying to install pyarrow such as using
pip install pyarrow
you see an error log like
-- Found Python3Alt: /home/uli/.pypy3-virtualenv/bin/pypy3
CMake Warning (dev) at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:273 (message):
The package name passed to `find_package_handle_standard_args` (PkgConfig)
does not match the name of the calling package (Arrow). This can lead to
problems in calling code that expects `find_package` result variables
(e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
/usr/share/cmake-3.18/Modules/FindPkgConfig.cmake:59 (find_package_handle_standard_args)
cmake_modules/FindArrow.cmake:39 (include)
cmake_modules/FindArrowPython.cmake:46 (find_package)
CMakeLists.txt:229 (find_package)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
-- Could NOT find Arrow (missing: Arrow_DIR)
-- Checking for module 'arrow'
-- No package 'arrow' found
CMake Error at /usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:165 (message):
Could NOT find Arrow (missing: ARROW_INCLUDE_DIR ARROW_LIB_DIR
ARROW_FULL_SO_VERSION ARROW_SO_VERSION)
Call Stack (most recent call first):
/usr/share/cmake-3.18/Modules/FindPackageHandleStandardArgs.cmake:458 (_FPHSA_FAILURE_MESSAGE)
cmake_modules/FindArrow.cmake:450 (find_package_handle_standard_args)
cmake_modules/FindArrowPython.cmake:46 (find_package)
CMakeLists.txt:229 (find_package)
-- Configuring incomplete, errors occurred!
See also "/tmp/pip-install-409dctif/pyarrow_b70cde6894c3469483f7360493fc2e65/build/temp.linux-x86_64-pypy39/CMakeFiles/CMakeOutput.log".
error: command '/usr/bin/cmake' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for pyarrow
Failed to build pyarrow
ERROR: Could not build wheels for pyarrow, which is required to install pyproject.toml-based projects
You need to install the arrow library in order to be able to compile pyarrow from source. On Ubuntu, this can be done using
sudo apt install -y -V ca-certificates lsb-release wget wget https://apache.jfrog.io/artifactory/arrow/$(lsb_release --id --short | tr 'A-Z' 'a-z')/apache-arrow-apt-source-latest-$(lsb_release --codename --short).deb -O /tmp/apache-arrow.deb sudo apt -y install /tmp/apache-arrow.deb sudo apt -y update sudo apt -y install libarrow-dev libarrow-python-dev
When trying to install pillow such as using
pip install Pillow
you see an error log like
running build_ext
The headers or library files could not be found for jpeg,
a required dependency when compiling Pillow from source.
Please see the install instructions at:
https://pillow.readthedocs.io/en/latest/installation.html
Traceback (most recent call last):
File "/tmp/pip-install-_g5fa7ox/pillow_7cb18c0d6bec468e8844184b98c8bf45/setup.py", line 989, in <module>
setup(
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/core.py", line 148, in setup
return run_commands(dist)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/core.py", line 163, in run_commands
dist.run_commands()
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands
self.run_command(cmd)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/dist.py", line 1214, in run_command
super().run_command(command)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/command/install.py", line 68, in run
return orig.install.run(self)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/command/install.py", line 670, in run
self.run_command('build')
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/dist.py", line 1214, in run_command
super().run_command(command)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/command/build.py", line 136, in run
self.run_command(cmd_name)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/dist.py", line 1214, in run_command
super().run_command(command)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/dist.py", line 986, in run_command
cmd_obj.run()
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/command/build_ext.py", line 79, in run
_build_ext.run(self)
File "/home/uli/.pypy3-virtualenv/lib/pypy3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 339, in run
self.build_extensions()
File "/tmp/pip-install-_g5fa7ox/pillow_7cb18c0d6bec468e8844184b98c8bf45/setup.py", line 804, in build_extensions
raise RequiredDependencyException(f)
RequiredDependencyException: jpeg
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-_g5fa7ox/pillow_7cb18c0d6bec468e8844184b98c8bf45/setup.py", line 1009, in <module>
raise RequiredDependencyException(msg)
RequiredDependencyException:
The headers or library files could not be found for jpeg,
a required dependency when compiling Pillow from source.
Please see the install instructions at:
https://pillow.readthedocs.io/en/latest/installation.html
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> PillowPillow needs a buch of libraries to be installed in order to work properly. Use the following command from the official Pillow website on Ubuntu:
sudo apt-get install cmake libtiff5-dev libjpeg8-dev libopenjp2-7-dev zlib1g-dev libfreetype6-dev liblcms2-dev libwebp-dev tcl8.6-dev tk8.6-dev python3-tk libharfbuzz-dev libfribidi-dev libxcb1-dev
or check out the installation guide for commands for other operating systems.
When trying to export data as JSON that has originally been queried from MongoDB using code like
with open("alle.json", "w") as outfile:
json.dump(alle, outfile)you see the following error message:
File /usr/lib/python3.9/json/__init__.py:179, in dump(obj, fp, skipkeys, ensure_ascii, check_circular, allow_nan, cls, indent, separators, default, sort_keys, **kw)
173 iterable = cls(skipkeys=skipkeys, ensure_ascii=ensure_ascii,
174 check_circular=check_circular, allow_nan=allow_nan, indent=indent,
175 separators=separators,
176 default=default, sort_keys=sort_keys, **kw).iterencode(obj)
177 # could accelerate with writelines in some versions of Python, at
178 # a debuggability cost
--> 179 for chunk in iterable:
180 fp.write(chunk)
File /usr/lib/python3.9/json/encoder.py:429, in _make_iterencode.<locals>._iterencode(o, _current_indent_level)
427 yield _floatstr(o)
428 elif isinstance(o, (list, tuple)):
--> 429 yield from _iterencode_list(o, _current_indent_level)
430 elif isinstance(o, dict):
431 yield from _iterencode_dict(o, _current_indent_level)
File /usr/lib/python3.9/json/encoder.py:325, in _make_iterencode.<locals>._iterencode_list(lst, _current_indent_level)
323 else:
324 chunks = _iterencode(value, _current_indent_level)
--> 325 yield from chunks
326 if newline_indent is not None:
327 _current_indent_level -= 1
File /usr/lib/python3.9/json/encoder.py:405, in _make_iterencode.<locals>._iterencode_dict(dct, _current_indent_level)
403 else:
404 chunks = _iterencode(value, _current_indent_level)
--> 405 yield from chunks
406 if newline_indent is not None:
407 _current_indent_level -= 1
File /usr/lib/python3.9/json/encoder.py:438, in _make_iterencode.<locals>._iterencode(o, _current_indent_level)
436 raise ValueError("Circular reference detected")
437 markers[markerid] = o
--> 438 o = _default(o)
439 yield from _iterencode(o, _current_indent_level)
440 if markers is not None:
File /usr/lib/python3.9/json/encoder.py:179, in JSONEncoder.default(self, o)
160 def default(self, o):
161 """Implement this method in a subclass such that it returns
162 a serializable object for ``o``, or calls the base implementation
163 (to raise a ``TypeError``).
(...)
177
178 """
--> 179 raise TypeError(f'Object of type {o.__class__.__name__} '
180 f'is not JSON serializable')
TypeError: Object of type ObjectId is not JSON serializableThis error occurs because objects queried from PyMongo always contain _id which is of type ObjectId and the normal JSON library (or drop-in replacements like simplejson do not know how to create JSON representations of Objects of type ObjectId).
In order to fix this, use pymongo‘s json_util instead of json. Note that the bson.json_util package contains dumps but does not contain dump, so use the following snippet to write to a file:
import bson.json_util as json_util
with open("alle.json", "w") as outfile:
outfile.write(json_util.dumps(alle))
While trying to install RcppGSL using
BiocManager::install("RcppGSL")
you see the following error message:
checking for gcc option to accept ISO C89... none needed
checking for gsl-config... no
configure: error: gsl-config not found, is GSL installed?
ERROR: configuration failed for package ‘RcppGSL’
* removing ‘/usr/local/lib/R/site-library/RcppGSL’
The downloaded source packages are in
‘/tmp/RtmpqSzFab/downloaded_packages’
Warning message:
In .inet_warning(msg) :
installation of package ‘RcppGSL’ had non-zero exit status
You need to install the libgsl2 development headers which include the gsl-config executable.
On Ubuntu, you can install it using
sudo apt -y install libgsl2-dev
This short example shows how to iterate all databases or list all database names for a MongoDB in Python using pymongo:
from pymongo import MongoClient
client = MongoClient("mongodb://localhost")
for database in client.list_databases():
print(database['name'])s
This will start Jupyter listening on all network interfaces / bind to all IP addresses in order to make direct browser access possible not only from localhost but any remote host that has network access to the host where you’re running Jupyter:
jupyter lab --ip=0.0.0.0
While installing some R package, you see an error message like
cram/cram_io.c:61:10: fatal error: lzma.h: No such file or directory
61 | #include
| ^~~~~~~~
compilation terminated.
You need to install the liblzma development headers. On Ubuntu, you can do that using
sudo apt -y install liblzma-dev
While installing some R package, you see an error message like
cram/cram_io.c:57:10: fatal error: bzlib.h: No such file or directory
57 | #include
| ^~~~~~~~~
compilation terminated.
You need to install the libbz2 development headers. On Ubuntu, you can do that using
sudo apt -y install libbz2-dev
When running
jupyter lab
you see the following error message:
Traceback (most recent call last):
File "/usr/local/bin/jupyter-lab", line 5, in <module>
from jupyterlab.labapp import main
File "/usr/local/lib/python3.8/dist-packages/jupyterlab/labapp.py", line 13, in <module>
from jupyter_server.serverapp import flags
File "/usr/local/lib/python3.8/dist-packages/jupyter_server/serverapp.py", line 39, in <module>
from jinja2 import Environment, FileSystemLoader
File "/usr/lib/python3/dist-packages/jinja2/__init__.py", line 33, in <module>
from jinja2.environment import Environment, Template
File "/usr/lib/python3/dist-packages/jinja2/environment.py", line 15, in <module>
from jinja2 import nodes
File "/usr/lib/python3/dist-packages/jinja2/nodes.py", line 23, in <module>
from jinja2.utils import Markup
File "/usr/lib/python3/dist-packages/jinja2/utils.py", line 656, in <module>
from markupsafe import Markup, escape, soft_unicode
ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/usr/local/lib/python3.8/dist-packages/markupsafe/__init__.py)
You need to install an older version of markupsafe using
sudo pip3 install markupsafe==2.0.1
until other packages have been updated.
While installing some R package, you see an error message like
/bin/bash: gfortran: command not found
You need to install the gfortran compiler. On Ubuntu, you can do that using
sudo apt -y install gfortran
While installing some R package, you see an error message like
/usr/bin/ld: cannot find -lblas
You need to install the libblas development headers. On Ubuntu, you can do that using
sudo apt -y install libblas-dev
While installing some R package, you see an error message like
/usr/bin/ld: cannot find -llapack
You need to install the liblapack development headers. On Ubuntu, you can do that using
sudo apt -y install liblapack-dev
While installing some R package, you see an error message like
/bin/bash: libpng-config: command not found
read.c:3:10: fatal error: png.h: No such file or directory
3 | #include
| ^~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: read.o] Error 1You need to install the libpng development headers. On Ubuntu, you can do that using
sudo apt -y install libpng-dev
While installing some R package, you see an error message like
io_utils.c:16:10: fatal error: zlib.h: No such file or directory
16 | #include <zlib.h>
| ^~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: io_utils.o] Error 1You need to install the zlib development headers. On Ubuntu, you can do that using
sudo apt -y install zlib1g-dev
When installing the R openssl package using
BiocManager::install("openssl")
or any package depending on the openssl package, you see an error message like
-------------------------- [ERROR MESSAGE] ---------------------------
tools/version.c:1:10: fatal error: openssl/opensslv.h: File or directory not found
1 | #include <openssl/opensslv.h>
| ^~~~~~~~~~~~~~~~~~~~
compilation terminated.
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/uli/R/x86_64-pc-linux-gnu-library/4.0/openssl’
You need to install OpenSSL. On Ubuntu, install it using
sudo apt -y install libssl-dev
For other systems, see the description just above the error message by the authors of the package:
--------------------------- [ANTICONF] -------------------------------- Configuration failed because openssl was not found. Try installing: * deb: libssl-dev (Debian, Ubuntu, etc) * rpm: openssl-devel (Fedora, CentOS, RHEL) * csw: libssl_dev (Solaris) * brew: [email protected] (Mac OSX) If openssl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'