Roman Chernyatchik
Roman Chernyatchik
It is PyCharm PyTypeChecker related inspection, doesn't work correctly in snakemake code  ``` rule npz_consensus_prepare_full_proportions_table: input: npz=lambda wildcards: { "merged_consensus": pu.collect_npz( rules.methylation_npz_merge_strands_cpg.output.npz, SAMPLES_DF, mmc_mincov=config["merge_cpg_mincov"] ), "stranded_consensus": pu.collect_npz( rules.methylation_npz_stranded_npz_from_bismark_cov.output.npz, SAMPLES_DF,...
Make `com.jetbrains.python.validatio.DocStringAnnotator.annotateDocStringStmt` public to be able to extend annotator for snakemake specific cases
Python code completion is broken in run/onstart/onerror/onsuccess blocks ``` rule boo: run: foo = 1 print(fo ```  ) Could be realted to #8
* Make PyCharm control flow builder do not visit `ScopeOwner` context child nodes * Add EP which allows to provide custom control flow builder for Unreachable code and other inspections....
Refactor rules names resolve/completion and use `PySyntheticType` API. At the moment this API isn't available the community edition. Subtask of #6.
Inspection: validate that rule defines all required input/output/params/etc keys for wrapper Wrappers contain `meta.yaml` and it has information about `input`, `output`, `params`, etc args. We could validate that our rule...
- [x] Basic parsing as valid SmkSl #214 - [ ] Syntax highlighting for format specifiers - [ ] Code completion for standard specifiers E.g. `echo {input:q}`, see https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html
Code insight support for case ``` # foo.smk rule foo: output: "foo.out" ``` ``` # boo.smk rule boo: input: rules.foo.output output: "out" ``` ``` # Snakefile include "foo.smk" include "boo.smk"...
``` from snakemake.utils import validate configfile: "config.yaml" validate(config, schema="schemas/config.schema.yaml") cells = pd.read_csv(config["cells"], sep="\t").set_index("id", drop=False) validate(cells, schema="schemas/cells.schema.yaml") rule foo: input: "boo" ``` Scheme is a *.yaml file relative to this file
Sometimes user expects that he is using already defined variable or rule section, but get error like: wildcard `threads` cannot be defined from input/output error. E.g. in: ``` rule: threads:...