tidies | A Grammar of Data Manipulation for Omics Data | Data Manipulation library
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A Grammar of Data Manipulation for Omics Data
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QUESTION
If I want to open one file I can do
...ANSWER
Answered 2021-Apr-25 at 13:08The standard library offers a nice way of doing this using contextlib.ExitStack
.
QUESTION
Consider the follow code:
...ANSWER
Answered 2020-Sep-18 at 09:15If the std::future
is created via std::async
, the destructor waits for end of the task. This does not mean that the task does not run in parallel - it just waits for the end of the task at the end of scope of variable. Yet it makes usage of std::async
without storing a std::future
a bit tricky and I would generally recommend storing the future somewhere to avoid nasty surprises. Take a look at page about std::future
destructor (emphasis mine):
these actions will not block for the shared state to become ready, except that it may block if all of the following are true: the shared state was created by a call to std::async, the shared state is not yet ready, and this was the last reference to the shared state.
QUESTION
I have a bunch of survey data, something like: I have some survey data, let's say it's about how often respondents tackle various daily routines:
...ANSWER
Answered 2020-Aug-21 at 23:45If we need to do this for each row, an option is c_across
after doing rowwise
QUESTION
I'm currently in the process of refactoring a java project and I have come across a number of classes (8) which all of them have a shared functionality. So, using the Extract Super Class refactoring, I created a super class with that functionality and passed it to all the sub-classes. Now, 2 of the classes have also a second shared functionality. Should I create another super class which inherits from the first super class and, in turn, is extended by the sub-classes or simply extend multiple classes on the 2 sub-classes?
ThoughtsEven though both options would work, I feel that going for multiple extensions is preferable since it describes and clarifies the responsibilities of the class. Also, we would avoid making continuous super() calls in order to reach the top super class.
On the other hand, maybe having an inheritance chain kinda tidies up the place.
Edit: I understand I stated my problem completely wrong. The 8 classes that are mentioned above are made to abide by the command pattern and as such each one has a different purpose and functionality. I have extracted a super class to avoid code duplication inside their constructors. Two of those classes have also have a little bit more duplicate code (not duplicate functionality, in the sense that they do the same thing). Unfortunately, due to the nature of the project, the fact that I did not write the original code and the tight time schedule do not allow me to completely reconstruct the whole project. It's, let's say, beyond repair for now. But what I can do is patchwork to try to remove duplicate code and tidy the place up a bit.
...ANSWER
Answered 2019-Dec-18 at 20:21Both methods seems to be a bad practice in most cases (favorize composition over inheritance). If you can avoid it by using design patterns (facade, composite, adapter,decorator...). If it can't be done in your case the principle of encapsulation and inheritance is what I would apply. So, when necessary chain inheritance.
QUESTION
I am trying to write a macro that tidies up and interrogates raw data exported from some analytical instrumentation. I would like it to look through one column (sample names) down all rows and look for indicators of specific sample types e.g. duplicates. Finding these indicators I want to insert a row, and in the new inserted row do some simple calculations based on the two rows above. For now I will just be happy getting the row insertion to work.
I can get it to find the key word and insert 1 row, but it finds the first one and stops. There are multiple instances of these keywords in my data, and i want to insert a row below each
...ANSWER
Answered 2019-Oct-30 at 13:36Assuming you do want to insert a row under every instance of a cell in column B containing "_dup" this should work.
The problem with your code was that it wasn't looping and so only ever found one instance.
It's advisable not to specify a fixed range as you are inserting rows and the range will expand; however, you could do this and set the search direction as "previous".
QUESTION
I have recently discovered the Objects.hash()
method.
My first thought was, that this tidies up your hashCode()
implementation a lot. See the following example:
ANSWER
Answered 2017-Aug-23 at 06:56Note that the parameter of Objects.hash
is Object...
. This has two main consequences:
- Primitive values used in the hash code calculation have to be boxed, e.g.
this.id
is converted fromlong
toLong
. - An
Object[]
has to be created to invoke the method.
The cost of creating of these "unnecessary" objects may add up if hashCode
is called frequently.
QUESTION
I'm wondering how I can make this "tidy model" code "cleaner".
Generally I fit a model and provide predictions in one wrapper function, but sometimes I want to pass back other pieces of data from the fitting or predicting (the model itself, metadata, or fitted values, etc). It's a list that is returned. What's the tidiest way to pass this result back as additionally columns, one per element in the list (here it is yhat_fit
and yhat
), with piping
ANSWER
Answered 2018-Dec-31 at 05:34This seems to be one way: convert the output (a list of stuff) to a tibble of list columns and then unnest.
QUESTION
A question about semicolon ; in language C
in shell script, if write multiple lines into one single line, semicolons are utilized.
date; cal; time
else, write multiple lines into a file:
...ANSWER
Answered 2018-Oct-25 at 12:02C came from B which in turn came from a language called BCPL.
A superior statement separator was required for B as the grammar became more complex, and the semicolon was a good candidate. The colon was already in use by then and the period used as a decimal separator.
After that, with the introduction of C, the semicolon became the standard.
QUESTION
I don't always write make files but when I do I like to try and write them well. Trying to make the interface consistent with what other developers might expect is always a struggle. What I am looking for is a summary of all the common make something cleaner (GNU) make targets.
What are the commonly found cleaning make targets?
When is each target normally used?
How does each target compare to others?
I have worked with a system using make clean
, make clobber
and make mrproper
before. Those got steadily more extream with; make clean
only tidying up temporaries, make clobber
getting read of most configuration and make mrproper
almost going back to a just checked out state. Is that the normal order of things? Should make mrproper
always remove the generated binaries and shared libraries for deployment?
Reading around suggests that make distclean
tidies things up to the point of being ready to make a distribution package. I would image that leaves behind some automatically generated version tagging files, file manifests and shared libraries but possibly strips out temporary files that you would not want archived?
make realclean
was completely new to me when I spied it on the GNU Make Goals manual page. As it is listed with distclean
and clobber
I would guess it had similar effects. Have I never come across it as it is a historical artifact or just quite specific to a set of projects I have to worked on?
Sorry, that is is a bit rambling. I have found various questions and answers that compare one target to the other but none that seemed to give a good overview.
...ANSWER
Answered 2018-Aug-14 at 10:35Trying to form my own answer based on some research. I think the approximate order of severity is; mostlyclean
, clean
, maintainer-clean
, mrproper
, distclean
and finally clobber
(which is combined distclean
and uninstall
).
make clean
make clean
is the most basic level. It cleans up most generated files but not anything that records configuration. GNU Make Manual's Goals page states:
Delete all files that are normally created by running make.
Further, the GNU Make Manual's Standard Targets page stages:
Delete all files in the current directory that are normally created by building the program. Also delete files in other directories if they are created by this makefile. However, don’t delete the files that record the configuration. Also preserve files that could be made by building, but normally aren’t because the distribution comes with them. There is no need to delete parent directories that were created with ‘mkdir -p’, since they could have existed anyway.
Delete .dvi files here if they are not part of the distribution.
make mostlyclean
make mostlyclean
is the only gentler form of clean I have found, it behaves like clean but leaves behind files that would take a long time to compile and do not often need to be regenerated.
The GNU Make Manual's Standard Targets page stages:
Like ‘clean’, but may refrain from deleting a few files that people normally don’t want to recompile. For example, the ‘mostlyclean’ target for GCC does not delete libgcc.a, because recompiling it is rarely necessary and takes a lot of time.
make distclean
make distclean
is the first step up from the basic make clean
on many GNU Make systems. It seems to be pseudonymous or at least very similar to with make realclean
and make clobber
in many, but not all cases. It will delete everything that make clean
does and remove the configuration.
In the Linux system this is one step beyond make mrpropper
, see the section below for details.
I am not sure if the name implies that things are being made clean enough for distribution (the forming of a tar archive) or that the process is returning them to the state equal to what was distributed (just as things were immediately after unpacking a tar archive).
GNU Make Manual's Goals page states:
Any of these targets might be defined to delete more files than ‘clean’ does. For example, this would delete configuration files or links that you would normally create as preparation for compilation, even if the makefile itself cannot create these files.
Further, the GNU Make Manual's Standard Targets page stages:
Delete all files in the current directory (or created by this makefile) that are created by configuring or building the program. If you have unpacked the source and built the program without creating any other files, ‘make distclean’ should leave only the files that were in the distribution. However, there is no need to delete parent directories that were created with ‘mkdir -p’, since they could have existed anyway.
make uninstall
make uninstall
will uninstall software installed via make install
or one of the install-*
variants. This is similar to part of the behaviour to make clobber
on some systems but make uninstall
should not touch the build area as make clobber
will.
The GNU Make Manual's Standard Targets page stages:
Delete all the installed files—the copies that the ‘install’ and ‘install-*’ targets create.
This rule should not modify the directories where compilation is done, only the directories where files are installed.
make maintainer-clean
make maintainer-clean
seems to be one step back from the more common make distclean
. It deletes almost everything apart from the configuration. This makes it very similar to make clean
.
The GNU Make Manual's Standard Targets page stages:
Delete almost everything that can be reconstructed with this Makefile. This typically includes everything deleted by distclean, plus more: C source files produced by Bison, tags tables, Info files, and so on.
It is also highlighted that this is not a commonly used target as it is for a specific set of users:
The ‘maintainer-clean’ target is intended to be used by a maintainer of the package, not by ordinary users.
make mrproper
make mrproper
seems to be a Linux Kernel version of make distclean
or make clobber
.
that stops short of removing backup and patch files. It does everything that the make clean
target does and strips out configuration.
I believe the name comes from a cleaning product known in the USA as Mr. Clean and the UK as Flash (which is why I had not heard of the product as named). Linus Torvalds being Finnish-American was presumably familiar with the Mr. Propper brand name.
The Linux Kernel Makefile states:
QUESTION
I am using the ipython shell a lot, and decided to make some tidies wrapper function more easy to type. Goal is to be able to type AnObject | dump
, instead of dump(AnObject)
. This is only inside an ipython shell, and in dev. To make it easier to type.
I have come up with this so far:
...ANSWER
Answered 2018-Jun-20 at 19:15If you are willing to use a metaclass then yes, it is possible:
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