constrain {chart} wildcard in format_altair (#94)

* constrain `{chart}` wildcard in `format_altair`

This fixes a Periodic WildCard Error that could sometimes arise from wildcards
that recursively contained _nolegend, see #171

* fix linting of notebooks in test

* format w latest version of `snakefmt`

.github/workflows/test.yaml

@@ -28,16 +28,12 @@ jobs:
           auto-update-conda: true
           channel-priority: strict
 
-      - name: lint code with ruff
+      - name: lint with ruff
         # NOTE: must specify the shell so that conda init updates bashrc see:
         #      https://github.com/conda-incubator/setup-miniconda#IMPORTANT
         shell: bash -el {0}
         run: ruff check .
 
-      - name: lint Jupyter notebooks with ruff
-        shell: bash -el {0}
-        run: nbqa ruff .
-
       - name: check code format with black
         shell: bash -el {0}
         run: black --check .
@@ -65,7 +61,6 @@ jobs:
 
       - name: run pipeline with prebuilt variants
         shell: bash -el {0}
-#        run: rm -rf docs && cd test_example && rm -rf results && snakemake --use-conda -j 2 --config prebuilt_variants=https://raw.githubusercontent.com/dms-vep/dms-vep-pipeline/main/test_example/results/variants/codon_variants.csv prebuilt_geneseq=https://raw.githubusercontent.com/dms-vep/dms-vep-pipeline/main/test_example/results/gene_sequence/codon.fasta prebuilt_muteffects=https://raw.githubusercontent.com/dms-vep/dms-vep-pipeline/main/test_example/results/muteffects_functional/muteffects_observed.csv && cd ..
         run: >
           rm -rf docs
           && cd test_example

CHANGELOG.md

@@ -1,5 +1,9 @@
 # CHANGELOG
 
+#### version 3.5.5
+- Fix `PeriodicWildCardError` that was raised by `snakemake` for the `_nolegend` output HTML plots for certain wildcards.
+- Fix how notebook linting done with `ruff` in tests.
+
 #### version 3.5.4
 - Fix bug in reporting pre-selection counts cutoff in `func_scores`. See [this issue](https://github.com/dms-vep/dms-vep-pipeline-3/issues/87). The cutoff was applied correctly before and that has not changed, this just fixes reporting of it in plots in `analyze_func_scores`.
 

common.smk

@@ -6,6 +6,8 @@ include: "common_funcs.smk"
 
 rule format_altair_html:
     """Format ``altair`` charts by adding title, legend, etc."""
+    wildcard_constraints:
+        chart="((?!nolegend).)*",  # do not match, https://stackoverflow.com/a/6259570
     input:
         html="results/{chart}_nolegend.html",
         pyscript=os.path.join(config["pipeline_path"], "scripts/format_altair_html.py"),

environment.yml

@@ -20,7 +20,6 @@ dependencies:
   - matplotlib=3.8
   - minimap2=2.26
   - nbstripout
-  - nbqa
   - openpyxl
   - pandas=2.0
   - papermill=2.4

func_effects.smk

@@ -105,7 +105,7 @@ rule func_effects_global_epistasis:
         global_epistasis_params_yaml=lambda wc: yaml.round_trip_dump(
             {
                 "global_epistasis_params": func_scores[wc.selection][
-                "global_epistasis_params"
+                    "global_epistasis_params"
                 ],
             }
         ),