phytop #51926
phytop #51926
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant updates to the Suggested labels
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Actionable comments posted: 27
🧹 Outside diff range and nitpick comments (30)
recipes/phytop/example_data/setcladefile (1)
2-2: LGTM: Appropriate outgroup selection.Using Carya illinoinensis (Pecan) as an outgroup is taxonomically sound, as it's from a different genus within the same family (Juglandaceae), providing a suitable evolutionary distance for phylogenetic analysis.
Consider adding a comment or documentation about:
- The expected file format
- The rationale for outgroup selection
- The taxonomic context of these species
This would help users create their own clade definitions correctly.
recipes/phytop/meta.yaml (2)
147-155: Consider adding version constraints to run requirementsWhile the run requirements list the correct dependencies, adding version constraints would help ensure reproducibility.
Consider adding minimum version constraints:
run: - python >=3.8 - - biopython - - matplotlib - - networkx - - lazy-property - - ete3 - - numpy - - scipy + - biopython >=1.81 + - matplotlib >=3.7 + - networkx >=3.1 + - lazy-property >=0.0.1 + - ete3 >=3.1 + - numpy >=1.24 + - scipy >=1.10
4-4: Fix YAML formatting issuesThe YAML file has some minor formatting issues:
- Remove trailing spaces on lines 4 and 156
- Add a newline at the end of file
Also applies to: 156-156, 159-159
🧰 Tools
🪛 yamllint
[error] 4-4: trailing spaces
(trailing-spaces)
recipes/phytop/src/plot.py (5)
1-16: Clean up unused imports to improve maintainability.Several imported modules appear to be unused in the current implementation. Consider removing or documenting the necessity of these imports:
-import copy -import shutil -import json -import math -import multiprocessing -from collections import OrderedDict, Counter🧰 Tools
🪛 Ruff
2-2:
copyimported but unusedRemove unused import:
copy(F401)
4-4:
shutilimported but unusedRemove unused import:
shutil(F401)
5-5:
jsonimported but unusedRemove unused import:
json(F401)
6-6:
mathimported but unusedRemove unused import:
math(F401)
7-7:
multiprocessingimported but unusedRemove unused import:
multiprocessing(F401)
8-8:
collections.OrderedDictimported but unusedRemove unused import
(F401)
8-8:
collections.Counterimported but unusedRemove unused import
(F401)
60-66: Remove or document commented-out code.The commented-out code for pie chart options should either be removed if no longer needed or documented if intended for future use.
83-83: Fix typo in argument group title.- group_clade = parser.add_argument_group('Clade operateion', '') + group_clade = parser.add_argument_group('Clade operation', '')
107-109: Add error handling to the plot function.Consider adding try-except blocks to handle potential errors during directory creation and AstralTree execution. This would provide better error messages to users.
Example:
def plot(**kargs): - mkdirs(kargs['tmpdir']) - AstralTree(**kargs).run() + try: + mkdirs(kargs['tmpdir']) + AstralTree(**kargs).run() + except Exception as e: + logger.error(f"Error during plotting: {str(e)}") + raise
115-115: Remove unused pipeline variable.- pipeline = plot(**args.__dict__) + plot(**args.__dict__)🧰 Tools
🪛 Ruff
115-115: Local variable
pipelineis assigned to but never usedRemove assignment to unused variable
pipeline(F841)
recipes/phytop/README.md (5)
2-6: Improve documentation formatting and readabilityPlease make the following improvements to the introduction section:
- Convert the bare URL to a proper markdown link
- Fix sentence structure and punctuation
-We defined the ILS/IH index to represent the degree of Incomplete lineage sorting (ILS) and introgression (IH) among lineages. This tool can quickly detect and visualize ILS/IH index between lineages of tree results run by ASTRAL option -u 2 or -t -2, with short running time, helping users to preliminatively determine ILS and IH and screen lineages for further analysis.For more details of ILS/IH index, please see https://www.biorxiv.org/content/10.1101/2024.09.02.610893v1. +We defined the ILS/IH index to represent the degree of Incomplete Lineage Sorting (ILS) and Introgression (IH) among lineages. This tool can quickly detect and visualize the ILS/IH index between lineages of tree results run by ASTRAL option -u 2 or -t -2, helping users to preliminarily determine ILS and IH and screen lineages for further analysis. For more details of the ILS/IH index, please see [our preprint](https://www.biorxiv.org/content/10.1101/2024.09.02.610893v1).🧰 Tools
🪛 Markdownlint
3-3: null
Bare URL used(MD034, no-bare-urls)
8-18: Enhance installation instructions
- Add language specifiers to code blocks for proper syntax highlighting
- Include information about prerequisites
### Quick install and start ### Download and install Phytop: -``` +```bash git clone https://github.com/zhangrengang/phytop cd phytop # install conda env create -f phytop.yaml conda activate phytop python setup.py install
+Prerequisites:
+- Conda package manager
+- Git<details> <summary>🧰 Tools</summary> <details> <summary>🪛 Markdownlint</summary> 10-10: null Fenced code blocks should have a language specified (MD040, fenced-code-language) </details> </details> --- `32-41`: **Fix grammar and improve output documentation** 1. Fix the grammatical error in the figure description 2. Improve the directory structure formatting ```diff ### Outputs ### -``` +```text ├── /tmp # Transition File (unused) ├── *.pdf # Visualization of the tree file generated by astral ├── *.info.tsv # The specific value of each node-The block diagram in PDF shows the ratio of q1, q2 and q3 of nodes. q2 and q3 are topologies that conflict with q1. Higher ILS-i or IH-i represent stronger ILS or IH respectively. In this example, there are strong ILS and IH among Juglans nigra, Juglans mandshurica, and (Juglans regia, Juglans sigillata). Since q2 is much larger than q3, we can roughly infer that there is strong IH from Juglans nigra and Juglans mandshurica to (Juglans regia, Juglans sigillata). There are almost no ILS and IH among Juglans regia, Juglans sigillata and outgroup, and this node can be considered as a well-resolved node. The below is an output figures of Phytop with default parameters:
+The block diagram in PDF shows the ratio of q1, q2 and q3 of nodes. q2 and q3 are topologies that conflict with q1. Higher ILS-i or IH-i represent stronger ILS or IH respectively. In this example, there are strong ILS and IH among Juglans nigra, Juglans mandshurica, and (Juglans regia, Juglans sigillata). Since q2 is much larger than q3, we can roughly infer that there is strong IH from Juglans nigra and Juglans mandshurica to (Juglans regia, Juglans sigillata). There are almost no ILS and IH among Juglans regia, Juglans sigillata and outgroup, and this node can be considered as a well-resolved node. Below is an output figure of Phytop with default parameters:<details> <summary>🧰 Tools</summary> <details> <summary>🪛 LanguageTool</summary> [grammar] ~39-~39: The plural noun “figures” cannot be used with the article “an”. Did you mean “an output figure”? Context: ...d as a well-resolved node. The below is an output figures of Phytop with default parameters: ![ba... (A_NNS) </details> <details> <summary>🪛 Markdownlint</summary> 33-33: null Fenced code blocks should have a language specified (MD040, fenced-code-language) </details> </details> --- `44-119`: **Add language specification to usage section** Add language specifier to the help output code block for proper syntax highlighting. ```diff ### Usage ### -``` +```text usage: phytop [-h] [-alter NEWICK] [-g NEWICK] [-align] [-cp] [-branch_size BRANCH_SIZE] ...🧰 Tools
🪛 Markdownlint
45-45: null
Fenced code blocks should have a language specified(MD040, fenced-code-language)
121-190: Fix formatting issues in examples section
- Add language specifiers to all command examples
- Fix word repetition in the final description
- Replace hard tabs with spaces
-``` +```bash phytop astral.tree -clades setcladefile -collapse-This parameter can be used to adjust font size of of piecharts.
+This parameter can be used to adjust the size of piecharts.<details> <summary>🧰 Tools</summary> <details> <summary>🪛 LanguageTool</summary> [duplication] ~190-~190: Possible typo: you repeated a word Context: ...rameter can be used to adjust font size of of piecharts. (ENGLISH_WORD_REPEAT_RULE) </details> <details> <summary>🪛 Markdownlint</summary> 126-126: Column: 86 Hard tabs (MD010, no-hard-tabs) --- 126-126: Column: 104 Hard tabs (MD010, no-hard-tabs) --- 122-122: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 129-129: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 136-136: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 143-143: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 150-150: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 156-156: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 162-162: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 168-168: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 174-174: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 180-180: null Fenced code blocks should have a language specified (MD040, fenced-code-language) --- 186-186: null Fenced code blocks should have a language specified (MD040, fenced-code-language) </details> </details> </blockquote></details> <details> <summary>recipes/phytop/src/small_tools.py (7)</summary><blockquote> `17-17`: **Remove unused import `sys`** The `sys` module is imported but not used in the code. Removing it will help clean up the imports. <details> <summary>🧰 Tools</summary> <details> <summary>🪛 Ruff</summary> 17-17: `sys` imported but unused Remove unused import: `sys` (F401) </details> </details> --- `19-19`: **Remove unused import `gzip`** The `gzip` module is imported but not used in the code. Consider removing it to tidy up the imports. <details> <summary>🧰 Tools</summary> <details> <summary>🪛 Ruff</summary> 19-19: `gzip` imported but unused Remove unused import: `gzip` (F401) </details> </details> --- `32-33`: **Simplify exception handling in `lazy_decode`** Instead of using a `try`-`except` block with a `pass`, you can use `contextlib.suppress(AttributeError)` for cleaner code. Also, ensure that each statement is on its own line for better readability. Apply this change: ```diff +from contextlib import suppress def lazy_decode(line): - try: line = line.decode() - except AttributeError: pass + with suppress(AttributeError): + line = line.decode() return line🧰 Tools
🪛 Ruff
32-33: Use
contextlib.suppress(AttributeError)instead oftry-except-passReplace with
contextlib.suppress(AttributeError)(SIM105)
32-32: Multiple statements on one line (colon)
(E701)
33-33: Multiple statements on one line (colon)
(E701)
182-182: Remove unused variablepro_seqThe variable
pro_seqis assigned but not used. Since we only need to check if the translation succeeds, the variable isn't necessary.Apply this change:
def is_complete_cds(Seq, translate_table=1): '''Check if a Bio.Seq object (CDS) is complete (both start and end codons present).''' try: - pro_seq = Seq.translate(table=translate_table, to_stop=True, cds=True) + Seq.translate(table=translate_table, to_stop=True, cds=True) return True except CodonTable.TranslationError: return False🧰 Tools
🪛 Ruff
182-182: Local variable
pro_seqis assigned to but never usedRemove assignment to unused variable
pro_seq(F841)
289-289: Remove unused variabletitleThe variable
titleis assigned but not used in thereadmethod of thepypslclass. Consider removing it to clean up the code.Apply this change:
class pypsl: def __init__(self, inPsl): self.input = inPsl def read(self): - title = '' for line in open(self.input, 'r'): if re.compile(r'\d+').match(line): # Process the line🧰 Tools
🪛 Ruff
289-289: Local variable
titleis assigned to but never usedRemove assignment to unused variable
title(F841)
290-290: Use a context manager when opening filesUsing a context manager ensures that the file is properly closed after its usage, even if an error occurs.
Apply this change:
def read(self): # Remove unused variable 'title' with open(self.input, 'r') as file: - for line in open(self.input, 'r'): + for line in file: if re.compile(r'\d+').match(line): # Process the line🧰 Tools
🪛 Ruff
290-290: Use a context manager for opening files
(SIM115)
343-344: Separate multiple statements onto individual linesLines 343 and 344 have multiple statements on one line, which can reduce readability. Each statement should be on its own line.
Apply this change:
output = job.communicate() - try: return int(output[0]) - except ValueError: print(output) + try: + return int(output[0]) + except ValueError: + print(output)🧰 Tools
🪛 Ruff
343-343: Multiple statements on one line (colon)
(E701)
344-344: Multiple statements on one line (colon)
(E701)
recipes/phytop/src/RunCmdsMP.py (7)
6-6: Remove unused importshutilThe module
shutilis imported but not used anywhere in the code.Apply this diff to remove the unused import:
-import shutil🧰 Tools
🪛 Ruff
6-6:
shutilimported but unusedRemove unused import:
shutil(F401)
18-21: Simplify exception handling usingcontextlib.suppress(ImportError)You can simplify the
try-exceptblock by usingcontextlib.suppress(ImportError)to make the code cleaner.Apply this diff to refactor the code:
+import contextlib -try: - import pp -except ImportError as e: - pass +with contextlib.suppress(ImportError): + import pp🧰 Tools
🪛 Ruff
18-21: Use
contextlib.suppress(ImportError)instead oftry-except-passReplace with
contextlib.suppress(ImportError)(SIM105)
20-20: Local variable
eis assigned to but never usedRemove assignment to unused variable
e(F841)
49-49: Replace deprecatedlogger.warnwithlogger.warningThe
logger.warnmethod is deprecated in Python 3 and should be replaced withlogger.warningto ensure compatibility.Apply these diffs to update the logging calls:
-logger.warn(e) +logger.warning(e) -logger.warn('Job {}: {}'.format(curjob, e)) +logger.warning('Job {}: {}'.format(curjob, e)) -logger.warn('Please provide your grid system `{}` to auther'.format(name)) +logger.warning('Please provide your grid system `{}` to author'.format(name)) -logger.warn("exit code {} for CMD `{}`: ".format(status, cmd)) +logger.warning("exit code {} for CMD `{}`: ".format(status, cmd)) -logger.warn('\n###STDOUT:<< {0} >>\n###STDERR:<< {1} >>'.format(*map(lambda x:x.decode(), output))) +logger.warning('\n###STDOUT:<< {0} >>\n###STDERR:<< {1} >>'.format(*map(lambda x:x.decode(), output)))Also applies to: 125-125, 153-153, 297-298
61-66: Use context managers when opening filesConsider using
withstatements to ensure files are properly closed, even if an exception occurs.Apply this diff to refactor the code:
if self.script is None: - fp = NamedTemporaryFile('w+t', delete=False) - self.script = fp.name - else: - fp = open(self.script, 'w') - self.make_script(fp) - fp.close() + with NamedTemporaryFile('w+t', delete=False) as fp: + self.script = fp.name + self.make_script(fp) + else: + with open(self.script, 'w') as fp: + self.make_script(fp)🧰 Tools
🪛 Ruff
61-61: Use a context manager for opening files
(SIM115)
64-64: Use a context manager for opening files
(SIM115)
137-137: Use context manager when opening filesUsing a
withstatement ensures that files are properly closed after use.Apply this diff:
- for line in open(outfile): + with open(outfile) as f: + for line in f:🧰 Tools
🪛 Ruff
137-137: Use a context manager for opening files
(SIM115)
246-247: Separate multiple statements onto individual linesFor better readability and adherence to PEP 8 guidelines, avoid multiple statements on one line.
Apply this diff:
- try: mem = float(mem) - except ValueError: return mem + try: + mem = float(mem) + except ValueError: + return mem🧰 Tools
🪛 Ruff
246-246: Multiple statements on one line (colon)
(E701)
247-247: Multiple statements on one line (colon)
(E701)
540-540: Fix typo in exception messageCorrect the typo in the error message for clarity.
Apply this diff:
- raise ValueError('faild to run {}, see detail in {}'.format(cmd_file, out_path)) + raise ValueError('failed to run {}, see details in {}'.format(cmd_file, out_path))recipes/phytop/src/Astral.py (3)
457-458: Simplify exception handling usingcontextlib.suppress.Instead of a
try-exceptblock that does nothing in theexceptclause, you can usecontextlib.suppressfor cleaner code.Apply this diff:
- try: ancestor = tree&leaf_name - except TreeError as e: pass + with contextlib.suppress(TreeError): + ancestor = tree & leaf_name🧰 Tools
🪛 Ruff
457-458: Use
contextlib.suppress(TreeError)instead oftry-except-passReplace with
contextlib.suppress(TreeError)(SIM105)
457-457: Multiple statements on one line (colon)
(E701)
458-458: Local variable
eis assigned to but never usedRemove assignment to unused variable
e(F841)
458-458: Multiple statements on one line (colon)
(E701)
496-499: Simplify conditional assignment with a ternary operator.You can condense the
if-elseblock into a single line using a ternary expression for clarity.Apply this diff:
- if node.is_leaf(): - taxon = [taxon] - else: - taxon = node.get_leaf_names() + taxon = [taxon] if node.is_leaf() else node.get_leaf_names()🧰 Tools
🪛 Ruff
496-499: Use ternary operator
taxon = [taxon] if node.is_leaf() else node.get_leaf_names()instead ofif-else-blockReplace
if-else-block withtaxon = [taxon] if node.is_leaf() else node.get_leaf_names()(SIM108)
589-590: Add a main guard to prevent unintended execution.It's good practice to add a
mainguard (if __name__ == "__main__":) to prevent code from running when modules are imported.Apply this diff:
-if __name__ == '__main__': +if __name__ == "__main__": main()
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⛔ Files ignored due to path filters (20)
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📒 Files selected for processing (21)
recipes/phytop/LICENSE(1 hunks)recipes/phytop/PhyTop.egg-info/PKG-INFO(1 hunks)recipes/phytop/PhyTop.egg-info/SOURCES.txt(1 hunks)recipes/phytop/PhyTop.egg-info/dependency_links.txt(1 hunks)recipes/phytop/PhyTop.egg-info/entry_points.txt(1 hunks)recipes/phytop/PhyTop.egg-info/top_level.txt(1 hunks)recipes/phytop/README.md(1 hunks)recipes/phytop/build.sh(1 hunks)recipes/phytop/example_data/astral.tree(1 hunks)recipes/phytop/example_data/setcladefile(1 hunks)recipes/phytop/meta.yaml(1 hunks)recipes/phytop/phytop.py(1 hunks)recipes/phytop/phytop.spec(1 hunks)recipes/phytop/phytop.yaml(1 hunks)recipes/phytop/setup.py(1 hunks)recipes/phytop/src/Astral.py(1 hunks)recipes/phytop/src/RunCmdsMP.py(1 hunks)recipes/phytop/src/__init__.py(1 hunks)recipes/phytop/src/__version__.py(1 hunks)recipes/phytop/src/plot.py(1 hunks)recipes/phytop/src/small_tools.py(1 hunks)
✅ Files skipped from review due to trivial changes (10)
- recipes/phytop/LICENSE
- recipes/phytop/PhyTop.egg-info/PKG-INFO
- recipes/phytop/PhyTop.egg-info/SOURCES.txt
- recipes/phytop/PhyTop.egg-info/dependency_links.txt
- recipes/phytop/PhyTop.egg-info/top_level.txt
- recipes/phytop/build.sh
- recipes/phytop/example_data/astral.tree
- recipes/phytop/phytop.py
- recipes/phytop/phytop.spec
- recipes/phytop/src/version.py
🧰 Additional context used
🪛 LanguageTool
recipes/phytop/README.md
[grammar] ~39-~39: The plural noun “figures” cannot be used with the article “an”. Did you mean “an output figure”?
Context: ...d as a well-resolved node. The below is an output figures of Phytop with default parameters: ![ba...
(A_NNS)
[duplication] ~190-~190: Possible typo: you repeated a word
Context: ...rameter can be used to adjust font size of of piecharts.
(ENGLISH_WORD_REPEAT_RULE)
🪛 Markdownlint
recipes/phytop/README.md
126-126: Column: 86
Hard tabs
(MD010, no-hard-tabs)
126-126: Column: 104
Hard tabs
(MD010, no-hard-tabs)
3-3: null
Bare URL used
(MD034, no-bare-urls)
10-10: null
Fenced code blocks should have a language specified
(MD040, fenced-code-language)
21-21: null
Fenced code blocks should have a language specified
(MD040, fenced-code-language)
25-25: null
Fenced code blocks should have a language specified
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Fenced code blocks should have a language specified
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Fenced code blocks should have a language specified
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Fenced code blocks should have a language specified
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Fenced code blocks should have a language specified
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Fenced code blocks should have a language specified
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Fenced code blocks should have a language specified
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🪛 yamllint
recipes/phytop/meta.yaml
[error] 4-4: trailing spaces
(trailing-spaces)
[error] 156-156: trailing spaces
(trailing-spaces)
[error] 159-159: no new line character at the end of file
(new-line-at-end-of-file)
🪛 Ruff
recipes/phytop/setup.py
5-5: distutils.extension.Extension imported but unused
Remove unused import: distutils.extension.Extension
(F401)
recipes/phytop/src/Astral.py
3-3: math imported but unused
Remove unused import: math
(F401)
57-57: Use a context manager for opening files
(SIM115)
68-68: Multiple statements on one line (colon)
(E701)
69-69: Multiple statements on one line (colon)
(E701)
104-104: Use a context manager for opening files
(SIM115)
177-177: Use a context manager for opening files
(SIM115)
188-188: Multiple statements on one line (colon)
(E701)
195-195: Use a context manager for opening files
(SIM115)
212-212: Use not ... instead of False if ... else True
Replace with not ...
(SIM211)
226-226: Multiple statements on one line (colon)
(E701)
227-227: Multiple statements on one line (colon)
(E701)
227-227: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
(B904)
295-295: Use a context manager for opening files
(SIM115)
312-312: Multiple statements on one line (colon)
(E701)
319-319: Local variable coalescent_unit is assigned to but never used
Remove assignment to unused variable coalescent_unit
(F841)
326-326: Multiple statements on one line (colon)
(E701)
327-327: Multiple statements on one line (colon)
(E701)
347-347: Multiple statements on one line (colon)
(E701)
348-348: Multiple statements on one line (colon)
(E701)
439-439: Use a context manager for opening files
(SIM115)
450-450: Multiple statements on one line (colon)
(E701)
451-451: Multiple statements on one line (colon)
(E701)
457-458: Use contextlib.suppress(TreeError) instead of try-except-pass
Replace with contextlib.suppress(TreeError)
(SIM105)
457-457: Multiple statements on one line (colon)
(E701)
458-458: Local variable e is assigned to but never used
Remove assignment to unused variable e
(F841)
458-458: Multiple statements on one line (colon)
(E701)
461-462: Use contextlib.suppress(ValueError) instead of try-except-pass
Replace with contextlib.suppress(ValueError)
(SIM105)
461-461: Multiple statements on one line (colon)
(E701)
462-462: Local variable e is assigned to but never used
Remove assignment to unused variable e
(F841)
462-462: Multiple statements on one line (colon)
(E701)
471-471: Multiple statements on one line (colon)
(E701)
472-472: Local variable e is assigned to but never used
Remove assignment to unused variable e
(F841)
496-499: Use ternary operator taxon = [taxon] if node.is_leaf() else node.get_leaf_names() instead of if-else-block
Replace if-else-block with taxon = [taxon] if node.is_leaf() else node.get_leaf_names()
(SIM108)
503-503: Undefined name d_collapse
(F821)
527-527: Do not use mutable data structures for argument defaults
Replace with None; initialize within function
(B006)
recipes/phytop/src/RunCmdsMP.py
6-6: shutil imported but unused
Remove unused import: shutil
(F401)
18-21: Use contextlib.suppress(ImportError) instead of try-except-pass
Replace with contextlib.suppress(ImportError)
(SIM105)
20-20: Local variable e is assigned to but never used
Remove assignment to unused variable e
(F841)
47-47: Multiple statements on one line (colon)
(E701)
61-61: Use a context manager for opening files
(SIM115)
64-64: Use a context manager for opening files
(SIM115)
137-137: Use a context manager for opening files
(SIM115)
169-169: Use a context manager for opening files
(SIM115)
172-172: Local variable out_path0 is assigned to but never used
Remove assignment to unused variable out_path0
(F841)
194-194: Use a context manager for opening files
(SIM115)
246-246: Multiple statements on one line (colon)
(E701)
247-247: Multiple statements on one line (colon)
(E701)
261-261: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
(B904)
273-273: Test for membership should be not in
Convert to not in
(E713)
282-282: Use a context manager for opening files
(SIM115)
319-319: Multiple statements on one line (colon)
(E701)
320-320: Do not use bare except
(E722)
320-320: Multiple statements on one line (colon)
(E701)
357-357: Multiple statements on one line (colon)
(E701)
369-369: Test for membership should be not in
Convert to not in
(E713)
388-388: Test for membership should be not in
Convert to not in
(E713)
427-427: Local variable cmd_out_file is assigned to but never used
Remove assignment to unused variable cmd_out_file
(F841)
435-435: Use a context manager for opening files
(SIM115)
437-437: Use a context manager for opening files
(SIM115)
438-438: Use a context manager for opening files
(SIM115)
445-445: Use status != 0 instead of not status == 0
Replace with != operator
(SIM201)
542-543: Use contextlib.suppress(FileExistsError) instead of try-except-pass
Replace with contextlib.suppress(FileExistsError)
(SIM105)
542-542: Multiple statements on one line (colon)
(E701)
543-543: Multiple statements on one line (colon)
(E701)
recipes/phytop/src/__init__.py
1-1: .small_tools imported but unused; consider removing, adding to __all__, or using a redundant alias
(F401)
recipes/phytop/src/plot.py
2-2: copy imported but unused
Remove unused import: copy
(F401)
4-4: shutil imported but unused
Remove unused import: shutil
(F401)
5-5: json imported but unused
Remove unused import: json
(F401)
6-6: math imported but unused
Remove unused import: math
(F401)
7-7: multiprocessing imported but unused
Remove unused import: multiprocessing
(F401)
8-8: collections.OrderedDict imported but unused
Remove unused import
(F401)
8-8: collections.Counter imported but unused
Remove unused import
(F401)
115-115: Local variable pipeline is assigned to but never used
Remove assignment to unused variable pipeline
(F841)
recipes/phytop/src/small_tools.py
17-17: sys imported but unused
Remove unused import: sys
(F401)
19-19: gzip imported but unused
Remove unused import: gzip
(F401)
32-33: Use contextlib.suppress(AttributeError) instead of try-except-pass
Replace with contextlib.suppress(AttributeError)
(SIM105)
32-32: Multiple statements on one line (colon)
(E701)
33-33: Multiple statements on one line (colon)
(E701)
56-56: Multiple statements on one line (colon)
(E701)
57-57: Multiple statements on one line (colon)
(E701)
62-62: Multiple statements on one line (colon)
(E701)
63-63: Do not use bare except
(E722)
64-64: Multiple statements on one line (colon)
(E701)
65-65: Do not use bare except
(E722)
65-65: Multiple statements on one line (colon)
(E701)
90-90: Local variable v is assigned to but never used
Remove assignment to unused variable v
(F841)
99-99: Local variable cm is assigned to but never used
Remove assignment to unused variable cm
(F841)
126-126: Do not use bare except
(E722)
133-133: Use a context manager for opening files
(SIM115)
155-156: Use contextlib.suppress(OSError) instead of try-except-pass
Replace with contextlib.suppress(OSError)
(SIM105)
155-155: Multiple statements on one line (colon)
(E701)
156-156: Multiple statements on one line (colon)
(E701)
160-160: Multiple statements on one line (colon)
(E701)
161-161: Multiple statements on one line (colon)
(E701)
174-174: Use a context manager for opening files
(SIM115)
177-177: Do not use bare except
(E722)
182-182: Local variable pro_seq is assigned to but never used
Remove assignment to unused variable pro_seq
(F841)
184-184: Undefined name CodonTable
(F821)
202-205: Return the condition os.path.splitext(input_file)[-1] == '.gz' directly
Replace with return os.path.splitext(input_file)[-1] == '.gz'
(SIM103)
217-217: Use a context manager for opening files
(SIM115)
224-224: Use enumerate() for index variable j in for loop
(SIM113)
225-225: Use enumerate() for index variable i in for loop
(SIM113)
231-231: Undefined name table_file
(F821)
233-233: Undefined name table_file
(F821)
235-235: Undefined name xlwt
(F821)
239-239: Use a context manager for opening files
(SIM115)
244-244: Use enumerate() for index variable j in for loop
(SIM113)
245-245: Use enumerate() for index variable i in for loop
(SIM113)
253-253: Use a context manager for opening files
(SIM115)
258-258: Use a context manager for opening files
(SIM115)
273-273: Use a context manager for opening files
(SIM115)
289-289: Local variable title is assigned to but never used
Remove assignment to unused variable title
(F841)
290-290: Use a context manager for opening files
(SIM115)
292-292: Undefined name temp
(F821)
293-293: Undefined name temp
(F821)
294-294: Undefined name temp
(F821)
295-295: Undefined name temp
(F821)
296-296: Undefined name temp
(F821)
297-297: Undefined name temp
(F821)
298-298: Undefined name temp
(F821)
299-299: Undefined name temp
(F821)
300-300: Undefined name temp
(F821)
301-301: Undefined name temp
(F821)
302-302: Undefined name temp
(F821)
303-303: Undefined name temp
(F821)
304-304: Undefined name temp
(F821)
305-305: Undefined name temp
(F821)
306-306: Undefined name temp
(F821)
307-307: Undefined name temp
(F821)
308-308: Undefined name temp
(F821)
309-309: Undefined name temp
(F821)
310-310: Undefined name temp
(F821)
311-311: Undefined name temp
(F821)
312-312: Undefined name temp
(F821)
330-333: Use ternary operator cat = 'zcat' if is_gz(inFile) else 'cat' instead of if-else-block
Replace if-else-block with cat = 'zcat' if is_gz(inFile) else 'cat'
(SIM108)
343-343: Multiple statements on one line (colon)
(E701)
344-344: Multiple statements on one line (colon)
(E701)
🔇 Additional comments (5)
recipes/phytop/example_data/setcladefile (1)
1-1: LGTM: Biologically valid clade definition.
The clade definition groups two closely related Juglans species (J. regia and J. sigillata), which is taxonomically appropriate as they belong to the same genus.
recipes/phytop/setup.py (2)
8-10: LGTM: README loading is implemented correctly.
The README.md content is properly loaded for the long description.
12-28:
Fix typo in description and verify version import.
- There's a typo in the description: "visualing" should be "visualizing"
- The version import from
src.__version__needs verification to ensure it's properly packaged
Apply this fix for the typo:
name='PhyTop',
version=version,
- description='PhyTop: visualing species tree from ASTRAL',
+ description='PhyTop: visualizing species tree from ASTRAL',
url='https://github.com/zhangrengang/phytop/',✅ Verification successful
Fix typo in description and update version import
- Fix typo "visualing" -> "visualizing" in setup.py description
- Version import is properly defined in src/version.py and correctly imported in setup.py
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify the version file exists and is properly structured
echo "Checking for version file..."
fd "__version__.py" src/
# Check the content of version.py if found
echo "Checking version file content..."
if [ -f "src/__version__.py" ]; then
cat "src/__version__.py"
fi
Length of output: 290
Script:
#!/bin/bash
# Let's first check the directory structure to locate the version
echo "Checking directory structure..."
fd -t d
# Let's also check where version is imported from in setup.py
echo "Checking setup.py content..."
cat recipes/phytop/setup.py
# Let's also check if version might be defined in __init__.py
echo "Checking for __init__.py files..."
fd "__init__.py"
Length of output: 253361
Script:
#!/bin/bash
# Let's check if version is properly imported in setup.py and defined in __init__.py
echo "Checking version import in setup.py..."
head -n 5 recipes/phytop/setup.py
echo "Checking src/__init__.py content..."
cat recipes/phytop/src/__init__.py
echo "Checking if __version__.py exists and its content..."
find recipes/phytop/src -name "__version__.py" -type f -exec cat {} \;
Length of output: 614
recipes/phytop/src/plot.py (1)
1-118: Overall implementation looks good!
The command-line interface is well-structured with comprehensive argument handling and clear organization. The suggested improvements are minor and focused on code cleanup rather than functional issues.
🧰 Tools
🪛 Ruff
2-2: copy imported but unused
Remove unused import: copy
(F401)
4-4: shutil imported but unused
Remove unused import: shutil
(F401)
5-5: json imported but unused
Remove unused import: json
(F401)
6-6: math imported but unused
Remove unused import: math
(F401)
7-7: multiprocessing imported but unused
Remove unused import: multiprocessing
(F401)
8-8: collections.OrderedDict imported but unused
Remove unused import
(F401)
8-8: collections.Counter imported but unused
Remove unused import
(F401)
115-115: Local variable pipeline is assigned to but never used
Remove assignment to unused variable pipeline
(F841)
recipes/phytop/src/small_tools.py (1)
184-184:
Correct the exception handling in is_complete_cds
The exception CodonTable.TranslationError should be Bio.Data.CodonTable.TranslationError. Make sure to import the correct exception or adjust the exception handling.
If you imported CodonTable as suggested earlier, adjust the exception handling:
except CodonTable.TranslationError:
return FalseAlternatively, if using Bio.Data.CodonTable, the exception might be Bio.Data.CodonTable.TranslationError, ensure that the exception name is correct.
🧰 Tools
🪛 Ruff
184-184: Undefined name CodonTable
(F821)
| [console_scripts] | ||
| phytop = src.plot:main |
There was a problem hiding this comment.
💡 Codebase verification
Remove the PhyTop.egg-info directory and add entry_points to meta.yaml
The .egg-info directory is confirmed to be a build artifact that should not be committed. The meta.yaml file needs to be updated to include the entry point configuration.
Please make these changes:
- Remove the
recipes/phytop/PhyTop.egg-infodirectory - Add the following under the
buildsection in meta.yaml:
build:
noarch: python
number: 1
entry_points:
- phytop = src.plot:main🔗 Analysis chain
Remove this generated file and define entry points in meta.yaml instead.
The .egg-info directory contains build artifacts that should not be committed to the repository. Instead, the console script entry point should be defined in the meta.yaml file under the build section.
Here's how to properly define the entry point in meta.yaml:
build:
entry_points:
- phytop = src.plot:mainPlease:
- Remove the entire
PhyTop.egg-infodirectory - Add the entry point definition to
meta.yaml
Let me check the meta.yaml file content to provide accurate guidance.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify if meta.yaml already has entry points defined
rg -A 5 "entry_points:" recipes/phytop/meta.yaml
# Check for other egg-info files that should be removed
fd -g "*.egg-info" recipes/phytop
Length of output: 116
Script:
#!/bin/bash
# Check meta.yaml content
cat recipes/phytop/meta.yaml
Length of output: 5099
| #!/usr/bin/env python | ||
| from src.__version__ import version | ||
|
|
||
| from setuptools import setup, find_packages | ||
| from distutils.extension import Extension | ||
| #from Cython.Build import cythonize | ||
|
|
There was a problem hiding this comment.
🛠️ Refactor suggestion
Clean up imports and clarify Cython usage.
- The
Extensionimport fromdistutils.extensionis unused and should be removed. - The commented Cython import suggests potential future compilation needs. If Cython compilation is not planned, remove this comment.
#!/usr/bin/env python
from src.__version__ import version
from setuptools import setup, find_packages
-from distutils.extension import Extension
-#from Cython.Build import cythonize📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| #!/usr/bin/env python | |
| from src.__version__ import version | |
| from setuptools import setup, find_packages | |
| from distutils.extension import Extension | |
| #from Cython.Build import cythonize | |
| #!/usr/bin/env python | |
| from src.__version__ import version | |
| from setuptools import setup, find_packages |
🧰 Tools
🪛 Ruff
5-5: distutils.extension.Extension imported but unused
Remove unused import: distutils.extension.Extension
(F401)
| python_requires='>=3.6', | ||
| packages=find_packages(), | ||
| include_package_data=True, | ||
| scripts=[], | ||
| entry_points={ | ||
| 'console_scripts': ['phytop = src.plot:main', | ||
| ], | ||
| }, |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Consider adding package dependencies.
The setup configuration is missing package dependencies. For a bioconda recipe, it's important to explicitly declare all required packages.
Add dependencies using install_requires:
python_requires='>=3.6',
packages=find_packages(),
include_package_data=True,
+ install_requires=[
+ # Add required packages here
+ # Example: 'numpy>=1.15.0',
+ ],
scripts=[],
entry_points={Would you like me to help identify the required dependencies by analyzing the codebase?
Committable suggestion skipped: line range outside the PR's diff.
| channels: | ||
| - conda-forge | ||
| - bioconda |
There was a problem hiding this comment.
Incorrect channel ordering for Bioconda recipes.
According to Bioconda guidelines, the channel order should be:
- bioconda
- conda-forge
This ensures proper package resolution and adherence to Bioconda's dependency hierarchy.
Apply this diff to fix the channel ordering:
channels:
- - conda-forge
- bioconda
+ - conda-forge📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| channels: | |
| - conda-forge | |
| - bioconda | |
| channels: | |
| - bioconda | |
| - conda-forge |
| - krb5=1.19.3=h3790be6_0 | ||
| - lazy-property=0.0.1=pyh9f0ad1d_0 | ||
| - lcms2=2.12=hddcbb42_0 | ||
| - ld_impl_linux-64=2.40=h41732ed_0 | ||
| - lerc=3.0=h9c3ff4c_0 | ||
| - libblas=3.9.0=17_linux64_openblas | ||
| - libbrotlicommon=1.0.9=h166bdaf_8 | ||
| - libbrotlidec=1.0.9=h166bdaf_8 | ||
| - libbrotlienc=1.0.9=h166bdaf_8 | ||
| - libcblas=3.9.0=17_linux64_openblas | ||
| - libclang=11.1.0=default_ha53f305_1 | ||
| - libdeflate=1.10=h7f98852_0 | ||
| - libedit=3.1.20191231=he28a2e2_2 | ||
| - libevent=2.1.10=h9b69904_4 | ||
| - libexpat=2.5.0=hcb278e6_1 | ||
| - libffi=3.3=h58526e2_2 | ||
| - libgcc-ng=13.1.0=he5830b7_0 | ||
| - libgfortran-ng=13.1.0=h69a702a_0 | ||
| - libgfortran5=13.1.0=h15d22d2_0 | ||
| - libglib=2.68.4=h3e27bee_0 | ||
| - libgomp=13.1.0=he5830b7_0 | ||
| - libiconv=1.17=h166bdaf_0 | ||
| - liblapack=3.9.0=17_linux64_openblas | ||
| - libllvm11=11.1.0=he0ac6c6_5 | ||
| - libogg=1.3.4=h7f98852_1 | ||
| - libopenblas=0.3.23=pthreads_h80387f5_0 | ||
| - libopus=1.3.1=h7f98852_1 | ||
| - libpng=1.6.39=h753d276_0 | ||
| - libpq=13.8=hd77ab85_0 | ||
| - libsqlite=3.42.0=h2797004_0 | ||
| - libstdcxx-ng=13.1.0=hfd8a6a1_0 | ||
| - libtiff=4.3.0=h0fcbabc_4 | ||
| - libuuid=2.38.1=h0b41bf4_0 | ||
| - libvorbis=1.3.7=h9c3ff4c_0 | ||
| - libwebp-base=1.3.0=h0b41bf4_0 | ||
| - libxcb=1.15=h0b41bf4_0 | ||
| - libxkbcommon=1.0.3=he3ba5ed_0 | ||
| - libxml2=2.9.10=h72842e0_4 | ||
| - libxslt=1.1.33=h15afd5d_2 | ||
| - libzlib=1.2.13=h166bdaf_4 | ||
| - lxml=4.8.0=py38h0a891b7_3 | ||
| - matplotlib=3.7.1=py38h578d9bd_0 | ||
| - matplotlib-base=3.7.1=py38hd6c3c57_0 | ||
| - munkres=1.1.4=pyh9f0ad1d_0 | ||
| - mysql-common=8.0.32=h14678bc_0 | ||
| - mysql-libs=8.0.32=h54cf53e_0 | ||
| - ncurses=6.4=hcb278e6_0 | ||
| - networkx=3.1=pyhd8ed1ab_0 | ||
| - nspr=4.35=h27087fc_0 | ||
| - nss=3.89=he45b914_0 | ||
| - numpy=1.24.3=py38h59b608b_0 | ||
| - olefile=0.46=pyh9f0ad1d_1 | ||
| - openjpeg=2.5.0=h7d73246_0 | ||
| - openssl=1.1.1u=hd590300_0 | ||
| - packaging=23.1=pyhd8ed1ab_0 | ||
| - pcre=8.45=h9c3ff4c_0 | ||
| - pillow=8.4.0=py38h8e6f84c_0 | ||
| - pip=23.1.2=pyhd8ed1ab_0 | ||
| - platformdirs=3.5.3=pyhd8ed1ab_0 | ||
| - pooch=1.7.0=pyha770c72_3 | ||
| - pthread-stubs=0.4=h36c2ea0_1001 | ||
| - pyparsing=3.0.9=pyhd8ed1ab_0 | ||
| - pyqt=5.12.3=py38h578d9bd_8 | ||
| - pyqt-impl=5.12.3=py38h0ffb2e6_8 | ||
| - pyqt5-sip=4.19.18=py38h709712a_8 | ||
| - pyqtchart=5.12=py38h7400c14_8 | ||
| - pyqtwebengine=5.12.1=py38h7400c14_8 | ||
| - pysocks=1.7.1=py38h578d9bd_5 | ||
| - python=3.8.8=hffdb5ce_0_cpython | ||
| - python-dateutil=2.8.2=pyhd8ed1ab_0 | ||
| - python_abi=3.8=3_cp38 | ||
| - qt=5.12.9=hda022c4_4 | ||
| - readline=8.2=h8228510_1 | ||
| - requests=2.31.0=pyhd8ed1ab_0 | ||
| - scipy=1.10.1=py38h59b608b_3 | ||
| - setuptools=67.7.2=pyhd8ed1ab_0 | ||
| - six=1.16.0=pyh6c4a22f_0 | ||
| - sqlite=3.42.0=h2c6b66d_0 | ||
| - tk=8.6.12=h27826a3_0 | ||
| - tornado=6.3.2=py38h01eb140_0 | ||
| - typing-extensions=4.6.3=hd8ed1ab_0 | ||
| - typing_extensions=4.6.3=pyha770c72_0 | ||
| - unicodedata2=15.0.0=py38h0a891b7_0 | ||
| - urllib3=2.0.3=pyhd8ed1ab_0 | ||
| - wheel=0.40.0=pyhd8ed1ab_0 | ||
| - xorg-kbproto=1.0.7=h7f98852_1002 | ||
| - xorg-libice=1.1.1=hd590300_0 | ||
| - xorg-libsm=1.2.4=h7391055_0 | ||
| - xorg-libx11=1.8.5=h8ee46fc_0 | ||
| - xorg-libxau=1.0.11=hd590300_0 | ||
| - xorg-libxdmcp=1.1.3=h7f98852_0 | ||
| - xorg-libxext=1.3.4=h0b41bf4_2 | ||
| - xorg-libxrender=0.9.10=h7f98852_1003 | ||
| - xorg-renderproto=0.11.1=h7f98852_1002 | ||
| - xorg-xextproto=7.3.0=h0b41bf4_1003 | ||
| - xorg-xproto=7.0.31=h7f98852_1007 | ||
| - xz=5.2.6=h166bdaf_0 | ||
| - zipp=3.15.0=pyhd8ed1ab_0 | ||
| - zlib=1.2.13=h166bdaf_4 | ||
| - zstd=1.5.2=h3eb15da_6 |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Simplify dependencies and update Python version.
- Many low-level system dependencies are automatically resolved by conda and shouldn't be explicitly listed. Consider keeping only the direct dependencies:
dependencies:
- - _libgcc_mutex=0.1=conda_forge
- - _openmp_mutex=4.5=2_gnu
- - alsa-lib=1.2.3.2=h166bdaf_0
+ - python>=3.8
- biopython=1.81
- - brotli=1.0.9=h166bdaf_8
- - brotli-bin=1.0.9=h166bdaf_8
- matplotlib=3.7.1
- networkx=3.1
- numpy=1.24.3
- scipy=1.10.1
- ete3=3.1.2-
Python 3.8.8 is quite old. Consider supporting newer Python versions (3.9+) for better features and security updates.
-
Remove duplicate dependencies:
- Both
typing-extensionsandtyping_extensionsare listed - Multiple X11-related packages that are auto-resolved
- Both
Committable suggestion skipped: line range outside the PR's diff.
💡 Codebase verification
Security vulnerabilities found in dependencies
Several critical dependencies have known security vulnerabilities:
-
Pillow 8.4.0 is vulnerable to:
- High severity DoS via textlength in ImageDraw (CVE-2023-4863)
- High severity buffer overflow in libwebp (CVE-2023-5129)
- Multiple other high and critical severity issues
-
requests 2.31.0 has a moderate severity issue with Proxy-Authorization header leakage
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urllib3 2.0.3 is vulnerable to:
- Moderate severity issues with Proxy-Authorization and Cookie headers
- Moderate severity issue with request body handling in 303 redirects
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lxml 4.8.0 has no known vulnerabilities in this version
Recommend upgrading to:
- Pillow >= 10.0.1
- requests >= 2.32.0
- urllib3 >= 2.2.2
🔗 Analysis chain
Verify dependencies for security vulnerabilities.
Let's check if any of the specified package versions have known security vulnerabilities.
Security vulnerabilities found in numpy version 1.24.3
The specified numpy version (1.24.3) is secure as it's higher than all vulnerable versions reported in the advisories. However, let's verify other critical dependencies that weren't covered in the first check.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for known vulnerabilities in dependencies using GitHub Advisory Database
# Test: Search for security advisories affecting the core dependencies
gh api graphql -f query='
{
securityVulnerabilities(first: 100, ecosystem: PIP, package: "numpy") {
nodes {
package { name }
vulnerableVersionRange
advisory {
description
severity
}
}
}
}' 2>/dev/null
# Repeat for other core packages: scipy, biopython, matplotlib, networkx
for pkg in scipy biopython matplotlib networkx; do
gh api graphql -f query="$(echo '{
securityVulnerabilities(first: 100, ecosystem: PIP, package: "'$pkg'") {
nodes {
package { name }
vulnerableVersionRange
advisory {
description
severity
}
}
}
}')" 2>/dev/null
done
Length of output: 7064
Script:
#!/bin/bash
# Check for vulnerabilities in other critical dependencies
for pkg in pillow requests urllib3 lxml; do
gh api graphql -f query="$(echo '{
securityVulnerabilities(first: 100, ecosystem: PIP, package: "'$pkg'") {
nodes {
package { name }
vulnerableVersionRange
advisory {
description
severity
}
}
}
}')" 2>/dev/null
done
Length of output: 45937
| names += taxon | ||
| return names | ||
| def collapsed_leaf(node): | ||
| return node not in d_collapse |
There was a problem hiding this comment.
Fix undefined variable d_collapse in collapsed_leaf function.
The variable d_collapse is not defined within the function scope, which will result in a NameError.
Apply this diff to pass d_collapse as a parameter:
-def collapsed_leaf(node):
+def collapsed_leaf(node, d_collapse):
return node not in d_collapseEnsure that d_collapse is provided when calling collapsed_leaf.
📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| return node not in d_collapse | |
| def collapsed_leaf(node, d_collapse): | |
| return node not in d_collapse |
🧰 Tools
🪛 Ruff
503-503: Undefined name d_collapse
(F821)
| try: ancestor = tree&name | ||
| except TreeError as e: raise TreeError('{} {}'.format(name, e)) |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Refactor try-except block and improve exception handling.
- Separate
tryandexceptstatements onto different lines with proper indentation. - When re-raising an exception, use
raise ... from eto preserve the traceback.
Apply this diff:
- try: ancestor = tree&name
- except TreeError as e: raise TreeError('{} {}'.format(name, e))
+ try:
+ ancestor = tree & name
+ except TreeError as e:
+ raise TreeError('{} {}'.format(name, e)) from e📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| try: ancestor = tree&name | |
| except TreeError as e: raise TreeError('{} {}'.format(name, e)) | |
| try: | |
| ancestor = tree & name | |
| except TreeError as e: | |
| raise TreeError('{} {}'.format(name, e)) from e |
🧰 Tools
🪛 Ruff
226-226: Multiple statements on one line (colon)
(E701)
227-227: Multiple statements on one line (colon)
(E701)
227-227: Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
(B904)
| patterns.append( line[last_end:] ) | ||
| return ''.join(patterns) | ||
| nwk = [] | ||
| for line in open(inNwk): |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Use a context manager when opening files.
Ensure files are properly closed by using a context manager when opening them.
Apply this diff:
- for line in open(inNwk):
+ with open(inNwk) as f:
+ for line in f:📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| for line in open(inNwk): | |
| with open(inNwk) as f: | |
| for line in f: |
🧰 Tools
🪛 Ruff
104-104: Use a context manager for opening files
(SIM115)
| def number_nodes(self, tree): | ||
| i = 0 | ||
| clades_file = '{}/{}.nodes.tsv'.format(self.tmpdir, self.prefix) | ||
| f_nodes = open(clades_file, 'w') |
There was a problem hiding this comment.
🛠️ Refactor suggestion
Use a context manager when opening files for writing.
Using a context manager ensures that the file is properly closed after writing.
Apply this diff:
- f_nodes = open(clades_file, 'w')
+ with open(clades_file, 'w') as f_nodes:Committable suggestion skipped: line range outside the PR's diff.
🧰 Tools
🪛 Ruff
195-195: Use a context manager for opening files
(SIM115)
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