Sourcery refactored develop branch #1

sourcery-ai · 2023-12-04T23:04:50Z

Branch develop refactored by Sourcery.

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sourcery-ai

Sourcery timed out performing refactorings.

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sourcery-ai · 2023-12-04T23:04:52Z

doc/doctest2script.py

@@ -2,6 +2,7 @@
 """
 This takes doctest files and turns them into standalone scripts.
 """
+


Lines 25-33 refactored with the following changes:

Use with when opening file to ensure closure [×2] (ensure-file-closed)

Use f-string instead of string concatenation [×2] (use-fstring-for-concatenation)

sourcery-ai · 2023-12-04T23:04:52Z

doc/doctest_rsts.py

-            for sub_word in just:
-                if sub_word in fn:
-                    new.append(fn)
+            new.extend(fn for sub_word in just if sub_word in fn)
        file_paths = new
    elif exclude:
        exclude = exclude.split(",")
        new = []
        for fn in file_paths:
-            keep = True
-            for sub_word in exclude:
-                if sub_word in fn:
-                    keep = False
-                    break
+            keep = all(sub_word not in fn for sub_word in exclude)
            if keep:
                new.append(fn)
        file_paths = new

    if verbose:
-        print("File paths, after filtering: %s" % str(file_paths))
+        print(f"File paths, after filtering: {str(file_paths)}")


Function main refactored with the following changes:

Replace a for append loop with list extend (for-append-to-extend)

Use any() instead of for loop (use-any)

Replace interpolated string formatting with f-string (replace-interpolation-with-fstring)

Invert any/all to simplify comparisons (invert-any-all)

sourcery-ai · 2023-12-04T23:04:52Z

doc/examples/demo-mpi-parallel.py

-    for i in range(3, sqrt_n + 1, 2):
-        if n % i == 0:
-            return False
-
-    return True
+    return all(n % i != 0 for i in range(3, sqrt_n + 1, 2))


Function is_prime refactored with the following changes:

Use any() instead of for loop (use-any)

Invert any/all to simplify comparisons (invert-any-all)

sourcery-ai · 2023-12-04T23:04:52Z

doc/examples/demo-multiprocess-parallel.py

-    for i in range(3, sqrt_n + 1, 2):
-        if n % i == 0:
-            return False
-
-    return True
+    return all(n % i != 0 for i in range(3, sqrt_n + 1, 2))


Function is_prime refactored with the following changes:

Use any() instead of for loop (use-any)

Invert any/all to simplify comparisons (invert-any-all)

sourcery-ai · 2023-12-04T23:04:53Z

src/cogent3/__init__.py

@@ -2,6 +2,7 @@
 analysis experience within Jupyter notebooks plus supporting parallel
 execution on compute systems with 1000s of CPUs."""



Lines 94-94 refactored with the following changes:

Replace unneeded comprehension with generator (comprehension-to-generator)

sourcery-ai · 2023-12-04T23:04:54Z

src/cogent3/align/pairwise.py

-        mantissa = 0.0
-        if kw["use_scaling"]:
-            mantissa = numpy.log(0.0)
-
+        mantissa = numpy.log(0.0) if kw["use_scaling"] else 0.0


Function Pair.calc_rows refactored with the following changes:

Move setting of default value for variable into else branch (introduce-default-else)

Replace if statement with if expression (assign-if-exp)

sourcery-ai · 2023-12-04T23:04:54Z

src/cogent3/align/pairwise.py

-        # XXX the int case should be a different method?
        if isinstance(index, int):
            return self.pred[index]
-        else:
-            pog = self.pog[index]
-            leaf = self.leaf[index]
-            return AlignablePOG(leaf, pog)
+        pog = self.pog[index]
+        leaf = self.leaf[index]
+        return AlignablePOG(leaf, pog)


Function AlignablePOG.__getitem__ refactored with the following changes:

Remove unnecessary else after guard condition (remove-unnecessary-else)

This removes the following comments ( why? ):

# XXX the int case should be a different method?

sourcery-ai · 2023-12-04T23:04:54Z

src/cogent3/align/pairwise.py

-        # XXX the int case should be a different method?
-        if isinstance(index, int):
-            if index == 0:
-                return []
-            elif 0 < index < len(self.index):
-                return [index - 1]
-            else:
-                raise IndexError(index)
-        # elif index == slice(None, None, None):
-        #    return self
-        else:
+        if not isinstance(index, int):
            return AlignableSeq(self.leaf[index])
+        if index == 0:
+            return []
+        elif 0 < index < len(self.index):
+            return [index - 1]
+        else:
+            raise IndexError(index)


Function AlignableSeq.__getitem__ refactored with the following changes:

Swap if/else branches (swap-if-else-branches)

Remove unnecessary else after guard condition (remove-unnecessary-else)

This removes the following comments ( why? ):

# return self # XXX the int case should be a different method? # elif index == slice(None, None, None):

sourcery-ai · 2023-12-04T23:04:54Z

src/cogent3/align/pairwise.py

-        if kw["use_logs"]:
-            (impossible, inevitable) = (-numpy.inf, 0.0)
-        else:
-            (impossible, inevitable) = (0.0, 1.0)
+        (impossible, inevitable) = (-numpy.inf, 0.0) if kw["use_logs"] else (0.0, 1.0)


Function PairEmissionProbs._calc_global_probs refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

sourcery-ai · 2023-12-04T23:04:54Z

src/cogent3/align/pairwise.py

-        result = numpy.array([probs[p_rows.index(i)] for i in last_row])
-        return result
+        return numpy.array([probs[p_rows.index(i)] for i in last_row])


Function PairEmissionProbs.scores_at_rows refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2023-12-04T23:04:57Z

src/cogent3/align/pairwise.py

-                self.pair.size[0] - 2 >= 3
+                self.pair.size[0] >= 5


Function PairEmissionProbs.dp refactored with the following changes:

Simplify numeric comparison (simplify-numeric-comparison)

sourcery-ai · 2023-12-04T23:04:57Z

src/cogent3/align/pairwise.py

-        # Used during progressive sequence alignment.
-        # Because the alignment depends on the total length (so long as the
-        # model is reversable!) the same cached viterbi result can be re-used
-        # to calculate the partial likelihoods even if the root of the 2-seq
-        # tree is moved around.
-        alignable = self.pair_hmm.emission_probs.get_alignable(
+        return self.pair_hmm.emission_probs.get_alignable(
            self.aligned_positions, ratio=ratio
        )
-        return alignable


Function GlobalViterbiPath.get_alignable refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

This removes the following comments ( why? ):

# Because the alignment depends on the total length (so long as the # model is reversable!) the same cached viterbi result can be re-used # tree is moved around. # Used during progressive sequence alignment. # to calculate the partial likelihoods even if the root of the 2-seq

sourcery-ai · 2023-12-04T23:04:57Z

src/cogent3/align/progressive.py

-        ), "names don't match between seqs and tree: tree=%s; seqs=%s" % (
-            tip_names,
-            seq_names,
-        )
+        ), f"names don't match between seqs and tree: tree={tip_names}; seqs={seq_names}"


Function TreeAlign refactored with the following changes:

Replace interpolated string formatting with f-string (replace-interpolation-with-fstring)

sourcery-ai · 2023-12-04T23:04:57Z

src/cogent3/align/traceback.py

-            if pos is not None:
-                c = seqs[dimension][pos]
-            else:
-                c = gap_value
+            c = seqs[dimension][pos] if pos is not None else gap_value


Function seq_traceback refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

sourcery-ai · 2023-12-04T23:04:57Z

src/cogent3/app/__init__.py

-    for tys in _types.keys():
+    for tys in _types:
        types = getattr(obj, tys, None) or []
        types = [types] if type(types) == str else types
        _types[tys] = [{None: ""}.get(e, e) for e in types]

-    row = [
+    return [


Function _get_app_attr refactored with the following changes:

Remove unnecessary call to keys() (remove-dict-keys)

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2023-12-04T23:04:58Z

src/cogent3/app/data_store.py

-        if pattern:
-            result = [m for m in self if fnmatch(m, pattern)]
-        else:
-            result = [m for m in self if callback(m)]
-        return result
+        return (
+            [m for m in self if fnmatch(m, pattern)]
+            if pattern
+            else [m for m in self if callback(m)]
+        )


Function ReadOnlyDataStoreBase.filtered refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2023-12-04T23:04:58Z

src/cogent3/app/data_store.py

-            if not str(relativeid) in self:
+            if str(relativeid) not in self:


Function WritableDataStoreBase.add_file refactored with the following changes:

Simplify logical expression using De Morgan identities (de-morgan)

sourcery-ai · 2023-12-04T23:04:58Z

src/cogent3/app/data_store.py

-        for f in p.iterdir():
-            if get_format_suffixes(str(f))[0] not in allowed:
-                return True
-        return False
+        return any(get_format_suffixes(str(f))[0] not in allowed for f in p.iterdir())


Function WritableDirectoryDataStore._has_other_suffixes refactored with the following changes:

Use any() instead of for loop (use-any)

sourcery-ai · 2023-12-04T23:04:58Z

src/cogent3/app/data_store.py

-            relativeid = str(relativeid).replace(suffixes, f"-{num}{suffixes}")
+            relativeid = relativeid.replace(suffixes, f"-{num}{suffixes}")


Function WritableTinyDbDataStore.add_file refactored with the following changes:

Remove unnecessary casts to int, str, float or bool (remove-unnecessary-cast)

sourcery-ai · 2023-12-04T23:04:58Z

src/cogent3/app/io.py

-        data = dict(record for record in self._parser(data))
+        data = dict(iter(self._parser(data)))


Function _seq_loader.load refactored with the following changes:

Simplify generator expression (simplify-generator)

sourcery-ai · 2023-12-04T23:05:00Z

src/cogent3/app/io.py

-        if self.as_type == "pssm":
-            return make_pssm_from_tabular(data)
-
-        return None
+        return make_pssm_from_tabular(data) if self.as_type == "pssm" else None


Function load_tabular.load refactored with the following changes:

Lift code into else after jump in control flow (reintroduce-else)

Replace if statement with if expression (assign-if-exp)

sourcery-ai · 2023-12-04T23:05:00Z

src/cogent3/app/io.py

-        stored = self.data_store.write(identifier, output)
-        return stored
+        return self.data_store.write(identifier, output)


Function write_tabular.write refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2023-12-04T23:05:01Z

src/cogent3/app/result.py

-            aln = self.lf.simulate_alignment()
-            return aln
+            return self.lf.simulate_alignment()


Function model_result.simulate_alignment refactored with the following changes:

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2023-12-04T23:05:01Z

src/cogent3/app/result.py

-        if isinstance(model, DiscreteSubstitutionModel):
-            length_as = "paralinear"
-        else:
-            length_as = "ENS"
-
        if not hasattr(self, "_tree"):
+            length_as = (
+                "paralinear"
+                if isinstance(model, DiscreteSubstitutionModel)
+                else "ENS"
+            )


Function model_result.tree refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

Move assignments closer to their usage (move-assign)

sourcery-ai · 2023-12-04T23:05:01Z

src/cogent3/app/result.py

-            pvalue = 1
+            return 1
        elif self.LR > 0:
-            pvalue = chisqprob(self.LR, self.df)
+            return chisqprob(self.LR, self.df)
        else:
-            pvalue = None
-        return pvalue
+            return None


Function hypothesis_result.pvalue refactored with the following changes:

Lift return into if (lift-return-into-if)

sourcery-ai · 2023-12-04T23:05:02Z

src/cogent3/core/alignment.py

-        chars = set([chars])
+        chars = {chars}

    def just_chars(data):
-        if is_array:
-            data = set(data.flatten())
-        else:
-            data = set("".join(data))
+        data = set(data.flatten()) if is_array else set("".join(data))
        return data <= chars

    def not_chars(data):
-        if is_array:
-            data = set(data.flatten())
-        else:
-            data = set("".join(data))
+        data = set(data.flatten()) if is_array else set("".join(data))
        return not data & chars

-    if negate:
-        return not_chars
-
-    return just_chars
+    return not_chars if negate else just_chars


Function AllowedCharacters refactored with the following changes:

Unwrap a constant iterable constructor (unwrap-iterable-construction)

Replace if statement with if expression [×3] (assign-if-exp)

Lift code into else after jump in control flow (reintroduce-else)

sourcery-ai · 2023-12-04T23:05:02Z

src/cogent3/core/alignment.py

-            self.gap_chars = set([gap_chars])
+            self.gap_chars = {gap_chars}


Function GapsOk.__init__ refactored with the following changes:

Unwrap a constant iterable constructor (unwrap-iterable-construction)

sourcery-ai · 2023-12-04T23:05:02Z

src/cogent3/core/alignment.py

-        if self.is_array:
-            data = Counter(data.flatten())
-        else:
-            data = Counter("".join(data))
-
+        data = Counter(data.flatten()) if self.is_array else Counter("".join(data))
        num_gap = sum(data[g] for g in self.gap_chars)
-        gap_frac = num_gap / length
-        return gap_frac
+        return num_gap / length


Function GapsOk._get_gap_frac refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

Inline variable that is immediately returned (inline-immediately-returned-variable)

sourcery-ai · 2023-12-04T23:05:02Z

src/cogent3/core/alignment.py

-            if info:
-                info = InfoClass(info)
-            else:
-                info = InfoClass()
+            info = InfoClass(info) if info else InfoClass()
        self.info = info
        # if we're forcing the same data, skip the validation
        if force_same_data:
            self._force_same_data(data, names)
-            if isinstance(data, dict):
-                curr_seqs = list(data.values())
-            else:
-                curr_seqs = data
-        # otherwise, figure out what we got and coerce it into the right type
+            curr_seqs = list(data.values()) if isinstance(data, dict) else data


Function _SequenceCollectionBase.__init__ refactored with the following changes:

Replace if statement with if expression [×2] (assign-if-exp)

Convert for loop into list comprehension (list-comprehension)

This removes the following comments ( why? ):

# otherwise, figure out what we got and coerce it into the right type

sourcery-ai · 2023-12-04T23:05:02Z

src/cogent3/core/alignment.py

-            if (names is None) or (None in names):
-                per_seq_names = name_order
-            else:  # got names from seqs, so assume name_order is in Names
-                per_seq_names = names
-
+            per_seq_names = name_order if (names is None) or (None in names) else names
        # check for duplicate names
        duplicates, fixed_names, fixed_seqs = self._strip_duplicates(
            per_seq_names, curr_seqs
        )
        if duplicates:
-            if remove_duplicate_names:
-                per_seq_names, curr_seqs = fixed_names, fixed_seqs
-                # if name_order doesn't have the same names as per_seq_names,
-                # replace it with per_seq_names
-                if (set(name_order) != set(per_seq_names)) or (
-                    len(name_order) != len(per_seq_names)
-                ):
-                    name_order = per_seq_names
-            else:
+            if not remove_duplicate_names:
                raise ValueError(
                    "Some names were not unique. Duplicates are:\n"
                    + str(sorted(duplicates.keys()))
                )

+            per_seq_names, curr_seqs = fixed_names, fixed_seqs
+            # if name_order doesn't have the same names as per_seq_names,
+            # replace it with per_seq_names
+            if (set(name_order) != set(per_seq_names)) or (
+                len(name_order) != len(per_seq_names)
+            ):
+                name_order = per_seq_names


Function _SequenceCollectionBase._names_seqs_order refactored with the following changes:

Replace if statement with if expression (assign-if-exp)

Swap if/else branches (swap-if-else-branches)

Remove unnecessary else after guard condition (remove-unnecessary-else)

This removes the following comments ( why? ):

# got names from seqs, so assume name_order is in Names

sourcery-ai

PR Type: Refactoring

Summary of PR: This PR includes a series of refactoring changes aimed at improving the readability and efficiency of the codebase. It utilizes modern Python features such as list comprehensions, ternary operators, and f-strings to simplify the code. The changes also include logical simplifications, such as removing unnecessary conditionals and using set comprehensions.

General PR suggestions

Review the changes to ensure that the refactoring does not introduce any logical errors, especially where conditions have been simplified or ternary operators have been introduced.
Verify that the use of modern Python features such as f-strings and list comprehensions maintains the readability and does not compromise the maintainability of the code.
Consider encapsulating logic within object methods where appropriate, such as using an 'add' method for adding children to a tree node, to keep the code modular and maintainable.
Ensure that any changes to loop conditions or removal of checks do not affect the intended functionality, particularly in cases where input validation is crucial.
While the stylistic changes like reordering comparisons are generally positive, make sure they are consistent throughout the codebase to maintain a uniform coding style.

Your trial expires on December 18, 2023. Please email [email protected] to continue using Sourcery ✨

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/core/tree.py

@@ -107,7 +107,7 @@ def __init__(
        if children is not None:
            self.extend(children)
        self._parent = parent
-        if (parent is not None) and not (self in parent.children):
+        if parent is not None and self not in parent.children:


suggestion (llm): Consider using the 'add' method instead of 'append' for adding an element to the parent's children list. This would encapsulate the logic of adding a child within the parent object, which might include additional checks or operations.

Suggested change

if parent is not None and self not in parent.children:

parent.add(self)

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/core/tree.py

-            return True
-
-        return self.name == other.name
+        return True if self is other else self.name == other.name


nitpick (llm): The ternary operation is unnecessary here. You can directly return the result of the logical OR operation.

Suggested change

return True if self is other else self.name == other.name

return self is other or self.name == other.name

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/core/tree.py

-                return self.pre_and_postorder(include_self=include_self)
-            else:
-                return self.preorder(include_self=include_self)
+            return (


thought (llm): The refactoring to use a ternary operation for the return statement is a nice touch for readability. However, ensure that the readability is not compromised when the ternary operation becomes too complex or nested.

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/core/tree.py

@@ -676,7 +670,7 @@ def separation(self, other):
            if id(other) in my_ancestors:
                # need to figure out how many steps there were back from self
                curr = self
-                while not (curr is None or curr is other):
+                while curr is not None and curr is not other:


issue (llm): The condition 'curr is not other' will never be False if 'curr is not None' is True. This seems to be a logical error, as the intent is likely to check if 'curr' is 'other' or not.

Suggested change

while curr is not None and curr is not other:

while curr is not None and curr != other:

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/core/location.py

@@ -623,7 +613,7 @@ def __len__(self):
        return self.length

    def __repr__(self):
-        return repr(self.spans) + f"/{self.parent_length}"
+        return f"{repr(self.spans)}/{self.parent_length}"


suggestion (llm): Using f-string for the representation is more concise and readable. Good use of modern Python features.

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/evolve/coevolution.py

-    else:
-        pos2_dg = get_dg(pos2_probs, aln_probs)
-
+    pos2_dg = dgs[pos2] if dgs else get_dg(pos2_probs, aln_probs)


thought (llm): Using the inline if-else statement for conditional assignment is a neat way to reduce the number of lines and improve readability. However, ensure that the logic is clear and maintainable, especially for more complex conditions.

sourcery-ai · 2023-12-04T23:08:55Z

src/cogent3/core/alignment.py

@@ -1038,7 +997,7 @@ def to_rich_dict(self):
        data = {}
        moltype = self.moltype.label
        info = {} if self.info is None else self.info
-        if not info.get("Refs", None) is None and "Refs" in info:
+        if info.get("Refs", None) is not None and "Refs" in info:


nitpick (llm): The check for 'Refs' in info seems redundant since 'get' already ensures it exists. You could simplify the condition.

Suggested change

if info.get("Refs", None) is not None and "Refs" in info:

if info.get("Refs") is not None:

sourcery-ai · 2023-12-04T23:08:56Z

src/cogent3/align/pairwise.py

-            return AlignablePOG(leaf, pog)
+        pog = self.pog[index]
+        leaf = self.leaf[index]
+        return AlignablePOG(leaf, pog)


issue (llm): The removal of the check for 'index' being an integer might lead to unexpected behavior when 'index' is not an integer. It's important to ensure that the input is validated or handled appropriately.

Suggested change

return AlignablePOG(leaf, pog)

if isinstance(index, int): return self.pred[index] else: return AlignablePOG(self.leaf[index], self.pog[index])

sourcery-ai · 2023-12-04T23:08:56Z

src/cogent3/format/table.py

@@ -973,7 +959,7 @@ def formatted_array(
            base_format = "d"
        elif "float" in type_name:
            base_format = f".{precision}f"
-        elif "bool" == type_name:
+        elif type_name == "bool":


nitpick (llm): The change from 'elif "bool" == type_name:' to 'elif type_name == "bool":' is purely stylistic and does not affect functionality, but it does align with the more common practice of placing the variable on the left side of the comparison.

sourcery-ai · 2023-12-04T23:08:56Z

src/cogent3/evolve/coevolution.py

-        if count >= abs_cutoff:
-            result.append(char)
-    return result
+    return [char for char, count in zip(alphabet, counts) if count >= abs_cutoff]


praise (llm): Refactoring to use list comprehension for generating the result list is a good improvement for readability and conciseness.

'Refactored by Sourcery'

5d75cae

sourcery-ai bot requested a review from ben-silke December 4, 2023 23:04

sourcery-ai bot commented Dec 4, 2023

View reviewed changes

		@@ -2,6 +2,7 @@
		analysis experience within Jupyter notebooks plus supporting parallel
		execution on compute systems with 1000s of CPUs."""

		if not str(relativeid) in self:
		if str(relativeid) not in self:

		relativeid = str(relativeid).replace(suffixes, f"-{num}{suffixes}")
		relativeid = relativeid.replace(suffixes, f"-{num}{suffixes}")

		data = dict(record for record in self._parser(data))
		data = dict(iter(self._parser(data)))

		self.gap_chars = set([gap_chars])
		self.gap_chars = {gap_chars}

	if parent is not None and self not in parent.children:
	parent.add(self)

	return True if self is other else self.name == other.name
	return self is other or self.name == other.name

	while curr is not None and curr is not other:
	while curr is not None and curr != other:

	if info.get("Refs", None) is not None and "Refs" in info:
	if info.get("Refs") is not None:

	return AlignablePOG(leaf, pog)
	if isinstance(index, int): return self.pred[index] else: return AlignablePOG(self.leaf[index], self.pog[index])

Sourcery refactored develop branch #1

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Sourcery refactored develop branch #1

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