feat: use primer3-py for primer3 instead of the executable #101
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| @@ -208,7 +208,7 @@ def __str__(self) -> str: | |||
| """ | |||
| # If the bases field is None, replace with MISSING_BASES_STRING | |||
| bases: str = self.bases if self.bases is not None else MISSING_BASES_STRING | |||
| return f"{bases}\t{self.tm}\t{self.penalty}\t{self.span}" | |||
| return f"{bases}\t{self.tm:.2f}\t{self.penalty:.2f}\t{self.span}" | |||
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## dev #101 +/- ##
==========================================
+ Coverage 96.81% 97.30% +0.48%
==========================================
Files 26 26
Lines 1789 1778 -11
Branches 215 208 -7
==========================================
- Hits 1732 1730 -2
+ Misses 31 27 -4
+ Partials 26 21 -5 ☔ View full report in Codecov by Sentry. |
prymer/primer3/primer3.py
Outdated
| for tag, value in assembled_primer3_tags.items(): | ||
| tag_str = f"{tag}" | ||
| if tag_str.startswith("SEQUENCE"): | ||
| seq_args[tag_str] = value | ||
| else: | ||
| global_args[tag] = value |
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This works ... but I think we could probably also add a is_global_arg() to Primer3InputTag that does this more efficiently (e.g. based on ordinal) or split Primer3InputTag into two classes - one for globals and one for sequence tags?
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Since PrimerInputTag's value is a string, I don't think it's inefficient, so I am going to centralize this as properties in the enum, and get rid of the f-string call (since I don't think that is needed).
prymer/primer3/primer3.py
Outdated
| for key, value in design_primers_retval.items(): | ||
| # Because Primer3 will emit both the input given and the output generated, we | ||
| # discard the input that is echo'ed back by looking for tags (keys) | ||
| # that do not match any Primer3InputTag | ||
| if not any(key == item.value for item in Primer3InputTag): | ||
| primer3_results[key] = value |
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Is this actually needed? I don't think there's any harm in allow the inputs to be present in the dict() used below.
If you feel strongly about this .. perhaps we have a more efficient way than looping through all the values in Primer3InputTag - e.g. create a _ALL_INPUT_TAG_STRINGS set and at the class level and check for membership?
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I'll keep removing them, we can open a PR later if you want to see them. I made it not inefficient via set membership.
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WalkthroughThe pull request introduces several modifications across the Prymer library. In Finishing Touches
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Actionable comments posted: 0
🧹 Nitpick comments (3)
prymer/primer3/primer3.py (2)
248-256: Remove unnecessary call tosuper().__exit__().Since
AbstractContextManagerdoes not have an operational__exit__method, callingsuper().__exit__()is redundant and can be omitted.Apply this diff to remove the call:
def __exit__( self, exc_type: Optional[type[BaseException]], exc_value: Optional[BaseException], traceback: Optional[TracebackType], ) -> None: """Gracefully terminates any running subprocesses.""" - super().__exit__(exc_type, exc_value, traceback) self.close()
383-393: Simplify tag separation with dictionary comprehensions.You can streamline the splitting of
assembled_primer3_tagsintoseq_argsandglobal_argsusing dictionary comprehensions.Apply this refactor:
- seq_args = {} - global_args = {} - for tag, value in assembled_primer3_tags.items(): - if tag.is_sequence_arg: - seq_args[tag] = value - else: - global_args[tag] = value + seq_args = {tag: value for tag, value in assembled_primer3_tags.items() if tag.is_sequence_arg} + global_args = {tag: value for tag, value in assembled_primer3_tags.items() if not tag.is_sequence_arg}prymer/primer3/primer3_input_tag.py (1)
34-43: Enhance docstrings for clarity.Provide more detailed docstrings for
is_sequence_argandis_global_argto explain their roles and usage.
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⛔ Files ignored due to path filters (1)
poetry.lockis excluded by!**/*.lock
📒 Files selected for processing (7)
prymer/api/oligo.py(1 hunks)prymer/primer3/primer3.py(9 hunks)prymer/primer3/primer3_input_tag.py(1 hunks)pyproject.toml(2 hunks)tests/api/test_oligo.py(9 hunks)tests/primer3/test_primer3.py(2 hunks)tests/primer3/test_primer3_input_tag.py(1 hunks)
✅ Files skipped from review due to trivial changes (2)
- prymer/api/oligo.py
- tests/api/test_oligo.py
🧰 Additional context used
🪛 GitHub Check: codecov/patch
prymer/primer3/primer3.py
[warning] 406-406: prymer/primer3/primer3.py#L406
Added line #L406 was not covered by tests
[warning] 408-408: prymer/primer3/primer3.py#L408
Added line #L408 was not covered by tests
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Tests (3.12)
🔇 Additional comments (6)
prymer/primer3/primer3.py (1)
404-410: 🛠️ Refactor suggestionAdd tests for error handling paths.
Lines 406 and 409 raise exceptions but are not covered by tests. Enhance your test suite to include scenarios that trigger these exceptions.
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🪛 GitHub Check: codecov/patch
[warning] 406-406: prymer/primer3/primer3.py#L406
Added line #L406 was not covered by tests
[warning] 408-408: prymer/primer3/primer3.py#L408
Added line #L408 was not covered by teststests/primer3/test_primer3_input_tag.py (1)
4-9: Tests effectively validate new properties.The test function accurately verifies the
is_sequence_argandis_global_argproperties for all tags.tests/primer3/test_primer3.py (2)
162-162: LGTM: Error message is more specific.New error message better reflects the actual validation failure.
364-364: LGTM: Error message matches new implementation.Error message correctly reflects file I/O error instead of subprocess termination.
pyproject.toml (2)
43-43: LGTM: Added primer3-py dependency.Version constraint ^2.0.3 is appropriate.
122-122: LGTM: Updated mypy configuration.Added primer3 to ignore_missing_imports list.
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Actionable comments posted: 0
🧹 Nitpick comments (2)
prymer/primer3/primer3.py (2)
442-442: Consider using a more specific type thanAny.While
Anyworks, a more specific type likeUnion[str, int, float]would provide better type safety.Also applies to: 547-547, 610-610
404-405: Remove outdated comment about error_lines.Comment references removed error handling logic.
- # Check for any errors. Typically, these are in error_lines, but also the results can - # contain the PRIMER_ERROR key. + # Check for any errors in the results
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prymer/primer3/primer3.py(9 hunks)
🔇 Additional comments (2)
prymer/primer3/primer3.py (2)
213-213: LGTM: Clean context manager implementation.Proper resource management with context manager protocol.
Also applies to: 245-256, 258-259
384-392: LGTM: Clean refactoring to use primer3 module.Efficient separation of sequence and global arguments.
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Actionable comments posted: 0
🧹 Nitpick comments (1)
prymer/primer3/primer3.py (1)
404-405: Update comment to match implementation.Comment mentions error_lines but code only checks PRIMER_ERROR.
- # Check for any errors. Typically, these are in error_lines, but also the results can - # contain the PRIMER_ERROR key. + # Check for any errors in the PRIMER_ERROR key.
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⛔ Files ignored due to path filters (1)
poetry.lockis excluded by!**/*.lock
📒 Files selected for processing (7)
prymer/api/oligo.py(1 hunks)prymer/primer3/primer3.py(9 hunks)prymer/primer3/primer3_input_tag.py(1 hunks)pyproject.toml(3 hunks)tests/api/test_oligo.py(9 hunks)tests/primer3/test_primer3.py(2 hunks)tests/primer3/test_primer3_input_tag.py(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (5)
- tests/api/test_oligo.py
- prymer/api/oligo.py
- prymer/primer3/primer3_input_tag.py
- tests/primer3/test_primer3.py
- tests/primer3/test_primer3_input_tag.py
⏰ Context from checks skipped due to timeout of 90000ms (1)
- GitHub Check: Tests (3.12)
🔇 Additional comments (7)
pyproject.toml (3)
3-3: LGTM: Major version bump is appropriate.Breaking change from executable to library justifies the bump to 3.0.0.
122-122: LGTM: Mypy override added for primer3.Consistent with existing pattern for external dependencies.
43-43: Verify primer3-py version.Check if 2.0.3 is the latest stable version.
✅ Verification successful
Version 2.0.3 is current. No security issues.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash # Check PyPI for latest version and potential security advisories curl -s https://pypi.org/pypi/primer3-py/json | jq '.info.version' # Check for security advisories gh api graphql -f query=' { securityVulnerabilities(first: 5, ecosystem: PIP, package: "primer3-py") { nodes { advisory { summary severity publishedAt } vulnerableVersionRange firstPatchedVersion { identifier } } } }'Length of output: 418
prymer/primer3/primer3.py (4)
213-213: LGTM: Context manager implementation is correct.Clean transition from ExecutableRunner to AbstractContextManager.
Also applies to: 245-256
384-392: LGTM: Clean primer3 library integration.Efficient separation of sequence and global args.
442-442: LGTM: Type changes accommodate primer3-py return types.Consistent use of dict[str, Any] across methods.
Also applies to: 547-547, 610-610
89-93: LGTM: Consistent string formatting.Clear and readable output format for oligo properties.
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