Using IPython notebooks under version control

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What is a good strategy for keeping IPython notebooks under version control?

The notebook format is quite amenable for version control: if one wants to version control the notebook and the outputs then this works quite well. The annoyance comes when one wants only to version control the input, excluding the cell outputs (aka. "build products") which can be large binary blobs, especially for movies and plots. In particular, I am trying to find a good workflow that:

  • allows me to choose between including or excluding output,
  • prevents me from accidentally committing output if I do not want it,
  • allows me to keep output in my local version,
  • allows me to see when I have changes in the inputs using my version control system (i.e. if I only version control the inputs but my local file has outputs, then I would like to be able to see if the inputs have changed (requiring a commit). Using the version control status command will always register a difference since the local file has outputs.)
  • allows me to update my working notebook (which contains the output) from an updated clean notebook. (update)

As mentioned, if I chose to include the outputs (which is desirable when using nbviewer for example), then everything is fine. The problem is when I do not want to version control the output. There are some tools and scripts for stripping the output of the notebook, but frequently I encounter the following issues:

  1. I accidentally commit a version with the the output, thereby polluting my repository.
  2. I clear output to use version control, but would really rather keep the output in my local copy (sometimes it takes a while to reproduce for example).
  3. Some of the scripts that strip output change the format slightly compared to the Cell/All Output/Clear menu option, thereby creating unwanted noise in the diffs. This is resolved by some of the answers.
  4. When pulling changes to a clean version of the file, I need to find some way of incorporating those changes in my working notebook without having to rerun everything. (update)

I have considered several options that I shall discuss below, but have yet to find a good comprehensive solution. A full solution might require some changes to IPython, or may rely on some simple external scripts. I currently use mercurial, but would like a solution that also works with git: an ideal solution would be version-control agnostic.

This issue has been discussed many times, but there is no definitive or clear solution from the user"s perspective. The answer to this question should provide the definitive strategy. It is fine if it requires a recent (even development) version of IPython or an easily installed extension.

Update: I have been playing with my modified notebook version which optionally saves a .clean version with every save using Gregory Crosswhite"s suggestions. This satisfies most of my constraints but leaves the following unresolved:

  1. This is not yet a standard solution (requires a modification of the ipython source. Is there a way of achieving this behaviour with a simple extension? Needs some sort of on-save hook.
  2. A problem I have with the current workflow is pulling changes. These will come in to the .clean file, and then need to be integrated somehow into my working version. (Of course, I can always re-execute the notebook, but this can be a pain, especially if some of the results depend on long calculations, parallel computations, etc.) I do not have a good idea about how to resolve this yet. Perhaps a workflow involving an extension like ipycache might work, but that seems a little too complicated.

Notes

Removing (stripping) Output

  • When the notebook is running, one can use the Cell/All Output/Clear menu option for removing the output.
  • There are some scripts for removing output, such as the script nbstripout.py which remove the output, but does not produce the same output as using the notebook interface. This was eventually included in the ipython/nbconvert repo, but this has been closed stating that the changes are now included in ipython/ipython,but the corresponding functionality seems not to have been included yet. (update) That being said, Gregory Crosswhite"s solution shows that this is pretty easy to do, even without invoking ipython/nbconvert, so this approach is probably workable if it can be properly hooked in. (Attaching it to each version control system, however, does not seem like a good idea ‚Äî this should somehow hook in to the notebook mechanism.)

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Using IPython notebooks under version control exp: Questions

exp

How do I merge two dictionaries in a single expression (taking union of dictionaries)?

5 answers

Carl Meyer By Carl Meyer

I have two Python dictionaries, and I want to write a single expression that returns these two dictionaries, merged (i.e. taking the union). The update() method would be what I need, if it returned its result instead of modifying a dictionary in-place.

>>> x = {"a": 1, "b": 2}
>>> y = {"b": 10, "c": 11}
>>> z = x.update(y)
>>> print(z)
None
>>> x
{"a": 1, "b": 10, "c": 11}

How can I get that final merged dictionary in z, not x?

(To be extra-clear, the last-one-wins conflict-handling of dict.update() is what I"m looking for as well.)

5839

Answer #1

How can I merge two Python dictionaries in a single expression?

For dictionaries x and y, z becomes a shallowly-merged dictionary with values from y replacing those from x.

  • In Python 3.9.0 or greater (released 17 October 2020): PEP-584, discussed here, was implemented and provides the simplest method:

    z = x | y          # NOTE: 3.9+ ONLY
    
  • In Python 3.5 or greater:

    z = {**x, **y}
    
  • In Python 2, (or 3.4 or lower) write a function:

    def merge_two_dicts(x, y):
        z = x.copy()   # start with keys and values of x
        z.update(y)    # modifies z with keys and values of y
        return z
    

    and now:

    z = merge_two_dicts(x, y)
    

Explanation

Say you have two dictionaries and you want to merge them into a new dictionary without altering the original dictionaries:

x = {"a": 1, "b": 2}
y = {"b": 3, "c": 4}

The desired result is to get a new dictionary (z) with the values merged, and the second dictionary"s values overwriting those from the first.

>>> z
{"a": 1, "b": 3, "c": 4}

A new syntax for this, proposed in PEP 448 and available as of Python 3.5, is

z = {**x, **y}

And it is indeed a single expression.

Note that we can merge in with literal notation as well:

z = {**x, "foo": 1, "bar": 2, **y}

and now:

>>> z
{"a": 1, "b": 3, "foo": 1, "bar": 2, "c": 4}

It is now showing as implemented in the release schedule for 3.5, PEP 478, and it has now made its way into the What"s New in Python 3.5 document.

However, since many organizations are still on Python 2, you may wish to do this in a backward-compatible way. The classically Pythonic way, available in Python 2 and Python 3.0-3.4, is to do this as a two-step process:

z = x.copy()
z.update(y) # which returns None since it mutates z

In both approaches, y will come second and its values will replace x"s values, thus b will point to 3 in our final result.

Not yet on Python 3.5, but want a single expression

If you are not yet on Python 3.5 or need to write backward-compatible code, and you want this in a single expression, the most performant while the correct approach is to put it in a function:

def merge_two_dicts(x, y):
    """Given two dictionaries, merge them into a new dict as a shallow copy."""
    z = x.copy()
    z.update(y)
    return z

and then you have a single expression:

z = merge_two_dicts(x, y)

You can also make a function to merge an arbitrary number of dictionaries, from zero to a very large number:

def merge_dicts(*dict_args):
    """
    Given any number of dictionaries, shallow copy and merge into a new dict,
    precedence goes to key-value pairs in latter dictionaries.
    """
    result = {}
    for dictionary in dict_args:
        result.update(dictionary)
    return result

This function will work in Python 2 and 3 for all dictionaries. e.g. given dictionaries a to g:

z = merge_dicts(a, b, c, d, e, f, g) 

and key-value pairs in g will take precedence over dictionaries a to f, and so on.

Critiques of Other Answers

Don"t use what you see in the formerly accepted answer:

z = dict(x.items() + y.items())

In Python 2, you create two lists in memory for each dict, create a third list in memory with length equal to the length of the first two put together, and then discard all three lists to create the dict. In Python 3, this will fail because you"re adding two dict_items objects together, not two lists -

>>> c = dict(a.items() + b.items())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: unsupported operand type(s) for +: "dict_items" and "dict_items"

and you would have to explicitly create them as lists, e.g. z = dict(list(x.items()) + list(y.items())). This is a waste of resources and computation power.

Similarly, taking the union of items() in Python 3 (viewitems() in Python 2.7) will also fail when values are unhashable objects (like lists, for example). Even if your values are hashable, since sets are semantically unordered, the behavior is undefined in regards to precedence. So don"t do this:

>>> c = dict(a.items() | b.items())

This example demonstrates what happens when values are unhashable:

>>> x = {"a": []}
>>> y = {"b": []}
>>> dict(x.items() | y.items())
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: unhashable type: "list"

Here"s an example where y should have precedence, but instead the value from x is retained due to the arbitrary order of sets:

>>> x = {"a": 2}
>>> y = {"a": 1}
>>> dict(x.items() | y.items())
{"a": 2}

Another hack you should not use:

z = dict(x, **y)

This uses the dict constructor and is very fast and memory-efficient (even slightly more so than our two-step process) but unless you know precisely what is happening here (that is, the second dict is being passed as keyword arguments to the dict constructor), it"s difficult to read, it"s not the intended usage, and so it is not Pythonic.

Here"s an example of the usage being remediated in django.

Dictionaries are intended to take hashable keys (e.g. frozensets or tuples), but this method fails in Python 3 when keys are not strings.

>>> c = dict(a, **b)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: keyword arguments must be strings

From the mailing list, Guido van Rossum, the creator of the language, wrote:

I am fine with declaring dict({}, **{1:3}) illegal, since after all it is abuse of the ** mechanism.

and

Apparently dict(x, **y) is going around as "cool hack" for "call x.update(y) and return x". Personally, I find it more despicable than cool.

It is my understanding (as well as the understanding of the creator of the language) that the intended usage for dict(**y) is for creating dictionaries for readability purposes, e.g.:

dict(a=1, b=10, c=11)

instead of

{"a": 1, "b": 10, "c": 11}

Response to comments

Despite what Guido says, dict(x, **y) is in line with the dict specification, which btw. works for both Python 2 and 3. The fact that this only works for string keys is a direct consequence of how keyword parameters work and not a short-coming of dict. Nor is using the ** operator in this place an abuse of the mechanism, in fact, ** was designed precisely to pass dictionaries as keywords.

Again, it doesn"t work for 3 when keys are not strings. The implicit calling contract is that namespaces take ordinary dictionaries, while users must only pass keyword arguments that are strings. All other callables enforced it. dict broke this consistency in Python 2:

>>> foo(**{("a", "b"): None})
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: foo() keywords must be strings
>>> dict(**{("a", "b"): None})
{("a", "b"): None}

This inconsistency was bad given other implementations of Python (PyPy, Jython, IronPython). Thus it was fixed in Python 3, as this usage could be a breaking change.

I submit to you that it is malicious incompetence to intentionally write code that only works in one version of a language or that only works given certain arbitrary constraints.

More comments:

dict(x.items() + y.items()) is still the most readable solution for Python 2. Readability counts.

My response: merge_two_dicts(x, y) actually seems much clearer to me, if we"re actually concerned about readability. And it is not forward compatible, as Python 2 is increasingly deprecated.

{**x, **y} does not seem to handle nested dictionaries. the contents of nested keys are simply overwritten, not merged [...] I ended up being burnt by these answers that do not merge recursively and I was surprised no one mentioned it. In my interpretation of the word "merging" these answers describe "updating one dict with another", and not merging.

Yes. I must refer you back to the question, which is asking for a shallow merge of two dictionaries, with the first"s values being overwritten by the second"s - in a single expression.

Assuming two dictionaries of dictionaries, one might recursively merge them in a single function, but you should be careful not to modify the dictionaries from either source, and the surest way to avoid that is to make a copy when assigning values. As keys must be hashable and are usually therefore immutable, it is pointless to copy them:

from copy import deepcopy

def dict_of_dicts_merge(x, y):
    z = {}
    overlapping_keys = x.keys() & y.keys()
    for key in overlapping_keys:
        z[key] = dict_of_dicts_merge(x[key], y[key])
    for key in x.keys() - overlapping_keys:
        z[key] = deepcopy(x[key])
    for key in y.keys() - overlapping_keys:
        z[key] = deepcopy(y[key])
    return z

Usage:

>>> x = {"a":{1:{}}, "b": {2:{}}}
>>> y = {"b":{10:{}}, "c": {11:{}}}
>>> dict_of_dicts_merge(x, y)
{"b": {2: {}, 10: {}}, "a": {1: {}}, "c": {11: {}}}

Coming up with contingencies for other value types is far beyond the scope of this question, so I will point you at my answer to the canonical question on a "Dictionaries of dictionaries merge".

Less Performant But Correct Ad-hocs

These approaches are less performant, but they will provide correct behavior. They will be much less performant than copy and update or the new unpacking because they iterate through each key-value pair at a higher level of abstraction, but they do respect the order of precedence (latter dictionaries have precedence)

You can also chain the dictionaries manually inside a dict comprehension:

{k: v for d in dicts for k, v in d.items()} # iteritems in Python 2.7

or in Python 2.6 (and perhaps as early as 2.4 when generator expressions were introduced):

dict((k, v) for d in dicts for k, v in d.items()) # iteritems in Python 2

itertools.chain will chain the iterators over the key-value pairs in the correct order:

from itertools import chain
z = dict(chain(x.items(), y.items())) # iteritems in Python 2

Performance Analysis

I"m only going to do the performance analysis of the usages known to behave correctly. (Self-contained so you can copy and paste yourself.)

from timeit import repeat
from itertools import chain

x = dict.fromkeys("abcdefg")
y = dict.fromkeys("efghijk")

def merge_two_dicts(x, y):
    z = x.copy()
    z.update(y)
    return z

min(repeat(lambda: {**x, **y}))
min(repeat(lambda: merge_two_dicts(x, y)))
min(repeat(lambda: {k: v for d in (x, y) for k, v in d.items()}))
min(repeat(lambda: dict(chain(x.items(), y.items()))))
min(repeat(lambda: dict(item for d in (x, y) for item in d.items())))

In Python 3.8.1, NixOS:

>>> min(repeat(lambda: {**x, **y}))
1.0804965235292912
>>> min(repeat(lambda: merge_two_dicts(x, y)))
1.636518670246005
>>> min(repeat(lambda: {k: v for d in (x, y) for k, v in d.items()}))
3.1779992282390594
>>> min(repeat(lambda: dict(chain(x.items(), y.items()))))
2.740647904574871
>>> min(repeat(lambda: dict(item for d in (x, y) for item in d.items())))
4.266070580109954
$ uname -a
Linux nixos 4.19.113 #1-NixOS SMP Wed Mar 25 07:06:15 UTC 2020 x86_64 GNU/Linux

Resources on Dictionaries

5839

Answer #2

In your case, what you can do is:

z = dict(list(x.items()) + list(y.items()))

This will, as you want it, put the final dict in z, and make the value for key b be properly overridden by the second (y) dict"s value:

>>> x = {"a":1, "b": 2}
>>> y = {"b":10, "c": 11}
>>> z = dict(list(x.items()) + list(y.items()))
>>> z
{"a": 1, "c": 11, "b": 10}

If you use Python 2, you can even remove the list() calls. To create z:

>>> z = dict(x.items() + y.items())
>>> z
{"a": 1, "c": 11, "b": 10}

If you use Python version 3.9.0a4 or greater, then you can directly use:

x = {"a":1, "b": 2}
y = {"b":10, "c": 11}
z = x | y
print(z)
{"a": 1, "c": 11, "b": 10}

5839

Answer #3

An alternative:

z = x.copy()
z.update(y)

List comprehension vs. lambda + filter

5 answers

I happened to find myself having a basic filtering need: I have a list and I have to filter it by an attribute of the items.

My code looked like this:

my_list = [x for x in my_list if x.attribute == value]

But then I thought, wouldn"t it be better to write it like this?

my_list = filter(lambda x: x.attribute == value, my_list)

It"s more readable, and if needed for performance the lambda could be taken out to gain something.

Question is: are there any caveats in using the second way? Any performance difference? Am I missing the Pythonic Way‚Ñ¢ entirely and should do it in yet another way (such as using itemgetter instead of the lambda)?

957

Answer #1

It is strange how much beauty varies for different people. I find the list comprehension much clearer than filter+lambda, but use whichever you find easier.

There are two things that may slow down your use of filter.

The first is the function call overhead: as soon as you use a Python function (whether created by def or lambda) it is likely that filter will be slower than the list comprehension. It almost certainly is not enough to matter, and you shouldn"t think much about performance until you"ve timed your code and found it to be a bottleneck, but the difference will be there.

The other overhead that might apply is that the lambda is being forced to access a scoped variable (value). That is slower than accessing a local variable and in Python 2.x the list comprehension only accesses local variables. If you are using Python 3.x the list comprehension runs in a separate function so it will also be accessing value through a closure and this difference won"t apply.

The other option to consider is to use a generator instead of a list comprehension:

def filterbyvalue(seq, value):
   for el in seq:
       if el.attribute==value: yield el

Then in your main code (which is where readability really matters) you"ve replaced both list comprehension and filter with a hopefully meaningful function name.

957

Answer #2

This is a somewhat religious issue in Python. Even though Guido considered removing map, filter and reduce from Python 3, there was enough of a backlash that in the end only reduce was moved from built-ins to functools.reduce.

Personally I find list comprehensions easier to read. It is more explicit what is happening from the expression [i for i in list if i.attribute == value] as all the behaviour is on the surface not inside the filter function.

I would not worry too much about the performance difference between the two approaches as it is marginal. I would really only optimise this if it proved to be the bottleneck in your application which is unlikely.

Also since the BDFL wanted filter gone from the language then surely that automatically makes list comprehensions more Pythonic ;-)

How do I do a not equal in Django queryset filtering?

5 answers

MikeN By MikeN

In Django model QuerySets, I see that there is a __gt and __lt for comparative values, but is there a __ne or != (not equals)? I want to filter out using a not equals. For example, for

Model:
    bool a;
    int x;

I want to do

results = Model.objects.exclude(a=True, x!=5)

The != is not correct syntax. I also tried __ne.

I ended up using:

results = Model.objects.exclude(a=True, x__lt=5).exclude(a=True, x__gt=5)
784

Answer #1

You can use Q objects for this. They can be negated with the ~ operator and combined much like normal Python expressions:

from myapp.models import Entry
from django.db.models import Q

Entry.objects.filter(~Q(id=3))

will return all entries except the one(s) with 3 as their ID:

[<Entry: Entry object>, <Entry: Entry object>, <Entry: Entry object>, ...]

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