feat: create nanosim wrapper for all three modes of simulator.py #3165
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WalkthroughThe changes introduce multiple new configuration files and scripts for the NanoSim simulator, including environment setup files, a metadata file, a Snakefile for testing, and a wrapper script for integration with Snakemake. These additions enable the simulation of genomic and transcriptomic data while enhancing usability and configuration options for researchers utilizing nanopore sequencing data. Changes
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Outside diff range, codebase verification and nitpick comments (3)
bio/nanosim/simulator/meta.yaml (1)
31-31: Fix minor formatting issues.yamllint reports the following formatting issues:
- Trailing spaces at line 31.
- Missing new line character at the end of file.
Please apply the following diff to fix the formatting issues:
- `NanoSim documentation for model training <https://github.com/bcgsc/NanoSim?tab=readme-ov-file#1-characterization-stage>`_. + `NanoSim documentation for model training <https://github.com/bcgsc/NanoSim?tab=readme-ov-file#1-characterization-stage>`_. * If the ``input:`` for a ``transcriptome`` mode simulator run does not @@ -47,0 +48 @@ notes: | +Also applies to: 47-47
Tools
yamllint
[error] 31-31: trailing spaces
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bio/nanosim/simulator/test/Snakefile (2)
38-71: LGTM with a minor suggestion!The
nanosim_transcriptomerule is well-defined and follows the Snakemake syntax. The input and output files are clearly specified, and the extra parameters provide flexibility to customize the simulation.Consider expanding the comment about the optional
reference_genomeinput to provide more details about the potential issue of infinitely running simulations. This will help users make an informed decision when enabling or disabling this input.
74-124: LGTM with a minor suggestion!The
nanosim_metagenomerule is well-defined and follows the Snakemake syntax. The input and output files are clearly specified, and thespeciesparameter provides a way to specify details for each species in the metagenome simulation.Consider adding a comment to explain that commenting out the
unaligned_readsoutput sets the--perfectflag for the simulation. This will help users understand the behavior of the rule when the unaligned reads are not requested.
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Files ignored due to path filters (2)
bio/nanosim/simulator/test/brca2.expression_abundance.tsvis excluded by!**/*.tsvbio/nanosim/simulator/test/config/sample_x.abundances.tsvis excluded by!**/*.tsv
Files selected for processing (9)
- bio/nanosim/simulator/environment.linux-64.pin.txt (1 hunks)
- bio/nanosim/simulator/environment.yaml (1 hunks)
- bio/nanosim/simulator/meta.yaml (1 hunks)
- bio/nanosim/simulator/test/Snakefile (1 hunks)
- bio/nanosim/simulator/test/download_models.smk (1 hunks)
- bio/nanosim/simulator/test/resources/brca2.genome2.fa (1 hunks)
- bio/nanosim/simulator/test/resources/brca2.transcriptome.fa (1 hunks)
- bio/nanosim/simulator/wrapper.py (1 hunks)
- test.py (1 hunks)
Files skipped from review due to trivial changes (2)
- bio/nanosim/simulator/environment.linux-64.pin.txt
- bio/nanosim/simulator/environment.yaml
Additional context used
Path-based instructions (2)
bio/nanosim/simulator/wrapper.py (2)
Pattern
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
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Do not suggest return type annotation if a function or method does not contain areturnstatement.
Pattern
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.test.py (1)
Pattern
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
yamllint
bio/nanosim/simulator/meta.yaml
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Gitleaks
bio/nanosim/simulator/test/resources/brca2.transcriptome.fa
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(aws-access-token)
577-577: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
590-590: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
593-593: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
594-594: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
613-613: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
614-614: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
619-619: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
621-621: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
633-633: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
645-645: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
648-648: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
650-650: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
651-651: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
685-685: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
697-697: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
701-701: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
711-711: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
714-714: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
732-732: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
733-733: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
741-741: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
743-743: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
753-753: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
759-759: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
766-766: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
767-767: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
768-768: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
775-775: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
777-777: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
785-785: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
786-786: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
788-788: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
790-790: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
796-796: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
800-800: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
802-802: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
802-802: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
803-803: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
804-804: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
807-807: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
811-811: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
821-821: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
Additional comments not posted (15)
bio/nanosim/simulator/test/download_models.smk (3)
1-24: LGTM!The code changes are approved.
26-49: LGTM!The code changes are approved.
52-74: LGTM!The code changes are approved.
bio/nanosim/simulator/meta.yaml (1)
1-47: LGTM!The metadata file is well-structured and provides comprehensive information about the nanosim simulator wrapper. The notes section is particularly helpful in guiding users on how to use the wrapper effectively.
Tools
yamllint
[error] 31-31: trailing spaces
(trailing-spaces)
[error] 47-47: no new line character at the end of file
(new-line-at-end-of-file)
bio/nanosim/simulator/test/Snakefile (1)
5-35: LGTM!The
nanosim_genomerule is well-defined and follows the Snakemake syntax. The input and output files are clearly specified, and the extra parameters provide flexibility to customize the simulation.bio/nanosim/simulator/wrapper.py (5)
1-7: LGTM!The module-level docstring, author, copyright, email and license information look good.
8-13: LGTM!The imports and logging setup look good.
The undefined name warning for
snakemakecan be safely ignored as this is expected in a Snakemake wrapper script.Tools
Ruff
12-12: Undefined name
snakemake(F821)
15-23: LGTM!The placeholder variable for optional parameters and the helper function to generate error messages look good.
The undefined name warning for
snakemakecan be safely ignored as this is expected in a Snakemake wrapper script.Tools
Ruff
16-16: Undefined name
snakemake(F821)
25-143: The overall logic to determine the subcommand and set up the input arguments looks good!Simplify the code by using
key in dictinstead ofkey in dict.keys().Ruff correctly suggests using
key in dictinstead ofkey in dict.keys()for simplicity. Please apply this change at lines 27, 84, 86, 90, 95, 111, 137.-if "reference_genomes" in snakemake.input.keys(): +if "reference_genomes" in snakemake.input:The undefined name warnings for
snakemakecan be safely ignored as this is expected in a Snakemake wrapper script.Tools
Ruff
27-27: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
27-27: Undefined name
snakemake(F821)
33-33: Undefined name
snakemake(F821)
33-33: Undefined name
snakemake(F821)
45-45: Undefined name
snakemake(F821)
46-46: Undefined name
snakemake(F821)
49-49: Undefined name
snakemake(F821)
50-50: Undefined name
snakemake(F821)
53-53: Undefined name
snakemake(F821)
54-54: Undefined name
snakemake(F821)
56-56: Undefined name
snakemake(F821)
57-57: Undefined name
snakemake(F821)
66-66: Undefined name
snakemake(F821)
68-68: Undefined name
snakemake(F821)
72-72: Undefined name
snakemake(F821)
74-74: Undefined name
snakemake(F821)
80-80: Undefined name
snakemake(F821)
81-81: Undefined name
snakemake(F821)
82-82: Undefined name
snakemake(F821)
84-84: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
84-84: Undefined name
snakemake(F821)
86-86: Use
key not in dictinstead ofkey not in dict.keys()Remove
.keys()(SIM118)
86-86: Undefined name
snakemake(F821)
90-90: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
90-90: Undefined name
snakemake(F821)
91-91: Undefined name
snakemake(F821)
94-94: Undefined name
snakemake(F821)
94-94: Undefined name
snakemake(F821)
95-95: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
95-95: Undefined name
snakemake(F821)
97-97: Undefined name
snakemake(F821)
107-107: Undefined name
snakemake(F821)
111-111: Use
key not in dictinstead ofkey not in dict.keys()Remove
.keys()(SIM118)
111-111: Undefined name
snakemake(F821)
117-117: Undefined name
snakemake(F821)
120-120: Undefined name
snakemake(F821)
127-127: Undefined name
snakemake(F821)
137-137: Use
key in dictinstead ofkey in dict.keys()Remove
.keys()(SIM118)
137-137: Undefined name
snakemake(F821)
139-139: Undefined name
snakemake(F821)
144-158: LGTM!The shell command construction and execution using a temporary directory for intermediate files looks good.
The undefined name warnings for
snakemakecan be safely ignored as this is expected in a Snakemake wrapper script.bio/nanosim/simulator/test/resources/brca2.transcriptome.fa (1)
1-132: LGTM!The file is a FASTA file containing transcriptome sequences related to the BRCA2 gene and its transcripts. It is a test resource and does not contain any code.
The static analysis hints from Gitleaks are false positives as the file does not contain any AWS credentials.
The file is good to go.
Tools
Gitleaks
5-5: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
8-8: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
22-22: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
24-24: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
28-28: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
39-39: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
43-43: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
44-44: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
44-44: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
61-61: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
63-63: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
67-67: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
75-75: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
79-79: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
88-88: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
91-91: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
104-104: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
106-106: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
110-110: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
113-113: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
122-122: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
123-123: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
bio/nanosim/simulator/test/resources/brca2.genome2.fa (1)
1-822: The file looks good, no issues found.This is a standard FASTA file containing a genomic DNA sequence. The hints from the static analysis tools about potential AWS access tokens are false positives and can be safely ignored. The file does not contain any secrets, just nucleotide sequence data.
Tools
Gitleaks
22-22: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
23-23: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
24-24: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
26-26: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
31-31: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
36-36: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
41-41: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
43-43: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
50-50: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
52-52: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
58-58: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
59-59: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
62-62: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
63-63: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
80-80: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
82-82: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
99-99: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
104-104: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
107-107: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
108-108: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
114-114: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
115-115: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
119-119: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
124-124: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
125-125: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
127-127: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
129-129: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
136-136: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
138-138: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
147-147: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
149-149: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
152-152: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
157-157: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
160-160: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
165-165: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
165-165: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
174-174: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
175-175: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
178-178: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
191-191: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
196-196: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
202-202: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
203-203: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
210-210: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
213-213: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
214-214: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
221-221: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
222-222: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
225-225: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
227-227: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
236-236: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
241-241: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
252-252: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
253-253: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
254-254: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
258-258: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
259-259: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
267-267: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
277-277: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
279-279: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
282-282: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
288-288: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
292-292: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
296-296: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
302-302: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
304-304: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
305-305: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
306-306: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
307-307: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
313-313: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
317-317: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
319-319: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
321-321: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
325-325: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
328-328: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
330-330: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
330-330: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
337-337: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
340-340: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
340-340: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
341-341: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
350-350: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
352-352: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
356-356: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
358-358: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
358-358: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
366-366: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
389-389: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
398-398: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
398-398: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
405-405: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
412-412: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
413-413: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
419-419: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
429-429: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
432-432: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
433-433: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
437-437: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
447-447: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
448-448: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
455-455: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
457-457: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
460-460: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
465-465: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
468-468: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
469-469: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
474-474: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
475-475: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
476-476: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
477-477: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
482-482: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
490-490: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
493-493: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
495-495: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
506-506: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
513-513: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
515-515: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
519-519: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
523-523: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
527-527: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
531-531: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
547-547: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
569-569: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
569-569: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
571-571: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
572-572: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
576-576: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
577-577: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
577-577: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
590-590: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
593-593: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
594-594: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
613-613: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
614-614: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
619-619: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
621-621: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
633-633: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
645-645: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
648-648: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
650-650: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
651-651: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
685-685: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
697-697: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
701-701: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
711-711: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
714-714: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
732-732: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
733-733: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
741-741: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
743-743: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
753-753: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
759-759: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
766-766: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
767-767: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
768-768: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
775-775: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
777-777: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
785-785: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
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790-790: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
796-796: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
800-800: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
802-802: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
802-802: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
803-803: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
804-804: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
807-807: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
811-811: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
821-821: Identified a pattern that may indicate AWS credentials, risking unauthorized cloud resource access and data breaches on AWS platforms.
(aws-access-token)
test.py (3)
3730-3743: Looks good!The new
test_nanosim_genomefunction follows the established pattern and tests the nanosim genome simulator appropriately.
3747-3760: Looks good!The new
test_nanosim_transcriptomefunction follows the established pattern and tests the nanosim transcriptome simulator appropriately.
3763-3779: Looks good!The new
test_nanosim_metagenomefunction follows the established pattern and tests the nanosim metagenome simulator appropriately.
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Instead of the extra snakefile to download the envs for testing, would it make sense for the wrapper to also allow a gzipped model? |
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I think I would prefer actually listing the required files with And yes, I agree that the download via the extra snakefile is a bit of a hacky workaround, but I think for testing purposes this is good enough / OK. |
…hanging) masterbranch
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- bio/nanosim/simulator/wrapper.py (1 hunks)
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Path-based instructions (1)
bio/nanosim/simulator/wrapper.py (2)
Pattern
**/*.py: Do not try to improve formatting.
Do not suggest type annotations for functions that are defined inside of functions or methods.
Do not suggest type annotation of theselfargument of methods.
Do not suggest type annotation of theclsargument of classmethods.
Do not suggest return type annotation if a function or method does not contain areturnstatement.
Pattern
**/wrapper.py: Do not complain about use of undefined variable calledsnakemake.
Ruff
bio/nanosim/simulator/wrapper.py
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Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
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…anosim` wrapper (#3165) (#3143) <!-- Ensure that the PR title follows conventional commit style (<type>: <description>)--> <!-- Possible types are here: https://github.com/commitizen/conventional-commit-types/blob/master/index.json --> <!-- Add a description of your PR here--> ### QC <!-- Make sure that you can tick the boxes below. --> * [x] I confirm that I have followed the [documentation for contributing to `snakemake-wrappers`](https://snakemake-wrappers.readthedocs.io/en/stable/contributing.html). While the contributions guidelines are more extensive, please particularly ensure that: * [x] `test.py` was updated to call any added or updated example rules in a `Snakefile` * [x] `input:` and `output:` file paths in the rules can be chosen arbitrarily * [x] wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in `input:` or `output:`) * [x] temporary files are either written to a unique hidden folder in the working directory, or (better) stored where the Python function `tempfile.gettempdir()` points to * [x] the `meta.yaml` contains a link to the documentation of the respective tool or command under `url:` * [x] conda environments use a minimal amount of channels and packages, in recommended ordering <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced the simulator's configuration with a new URL linking to the project's GitHub repository. - Expanded the parameters section with detailed descriptions for command line arguments, improving clarity for users. - Added a `max_read_len` parameter to the `nanosimh` rule, allowing for longer simulated reads. - **Improvements** - Reformatted the description in the configuration file for better readability. - Improved input handling in the simulation function for enhanced flexibility. - **Bug Fixes** - Updated parameter handling to ensure correct execution of commands with new inputs. - Removed outdated test function to streamline testing strategy. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
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@fgvieira any more time for a review, or should I ask around? |
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Learnings (1)
Common learnings
Learnt from: dlaehnemann PR: snakemake/snakemake-wrappers#3165 File: bio/nanosim/simulator/wrapper.py:1-163 Timestamp: 2024-09-04T18:46:15.788Z Learning: In the `wrapper.py` script for the NanoSim Snakemake wrapper, the subcommand is inferred from the pattern of named input files, rather than being explicitly specified.
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@dlaehnemann sorry for the delay, but I was looking a bit into it and, from bcgsc/NanoSim#162, it seems that the |
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Thanks for looking into this further. A thorough review is always appreciated. And any ideas for making this more useful are welcome. We do need those pre-trained models, if we want to do the CI tests here. And I have only seen the dorado model for the Or do you have any good ideas how to got about this? |
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Well, I guess no perfect solution here. 😄 I can see three options:
You know the program better, so I'll leave it up to you. |
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I cross-referenced this once more over in the NanoSim repo, and will merge it as is, for now. They have recently provided a newly trained model for genomic DNA, but not yet for transcriptomic or metagenomic data. So I would merge this as is for now, and we can then hopefully remove the TODO in the |
🤖 I have created a release \*beep\* \*boop\* --- ## [4.8.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v4.7.8...v4.8.0) (2024-10-31) ### Features * create nanosim wrapper for all three modes of simulator.py ([#3165](https://www.github.com/snakemake/snakemake-wrappers/issues/3165)) ([d533df5](https://www.github.com/snakemake/snakemake-wrappers/commit/d533df57ddace846cb0e224193a04c32b45d66dd)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
respective tests already passed locally
QC
snakemake-wrappers.While the contributions guidelines are more extensive, please particularly ensure that:
test.pywas updated to call any added or updated example rules in aSnakefileinput:andoutput:file paths in the rules can be chosen arbitrarilyinput:oroutput:)tempfile.gettempdir()points tometa.yamlcontains a link to the documentation of the respective tool or command underurl:Summary by CodeRabbit
New Features
Snakefilefor structured rules to simulate genomic, transcriptomic, and metagenomic data.wrapper.pyto enhance usability within a Snakemake pipeline.meta.yamlfile providing essential metadata and configuration parameters for the NanoSim simulator.Bug Fixes
Tests