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rename "geneset" to "gene set" in CLI (#2088)

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* remove dead code

* rename geneset to gene_set
This commit is contained in:
Bruce Martin
2021-03-02 15:36:01 -08:00
committed by GitHub
parent b00496198d
commit c037f4eaa6
14 changed files with 101 additions and 102 deletions
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local_server/cli/launch.py
+9 -9
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@@ -42,7 +42,7 @@ def annotation_args(func):
multiple=False,
metavar="<directory path>",
help="Directory of where to save output annotations; filename will be specified in the application. "
"Incompatible with --annotations-file and --genesets-file.",
"Incompatible with --annotations-file and --gene-sets-file.",
)
@click.option(
"--experimental-annotations-ontology",
@@ -59,16 +59,16 @@ def annotation_args(func):
help="Location of OBO file defining cell annotation autosuggest terms.",
)
@click.option(
"--disable-genesets-save",
"--disable-gene-sets-save",
is_flag=True,
default=DEFAULT_CONFIG.dataset_config.user_annotations__genesets__readonly,
default=DEFAULT_CONFIG.dataset_config.user_annotations__gene_sets__readonly,
show_default=False,
help="Disable saving gene sets. If disabled, users will be able to make changes to gene sets but all "
"changes will be lost on browser refresh.",
)
@click.option(
"--genesets-file",
default=DEFAULT_CONFIG.dataset_config.user_annotations__local_file_csv__genesets_file,
"--gene-sets-file",
default=DEFAULT_CONFIG.dataset_config.user_annotations__local_file_csv__gene_sets_file,
show_default=True,
multiple=False,
metavar="<path>",
@@ -334,8 +334,8 @@ def launch(
disable_annotations,
annotations_file,
user_generated_data_dir,
genesets_file,
disable_genesets_save,
gene_sets_file,
disable_gene_sets_save,
backed,
disable_diffexp,
experimental_annotations_ontology,
@@ -394,8 +394,8 @@ def launch(
user_annotations__enable=not disable_annotations,
user_annotations__local_file_csv__file=annotations_file,
user_annotations__local_file_csv__directory=user_generated_data_dir,
user_annotations__local_file_csv__genesets_file=genesets_file,
user_annotations__genesets__readonly=disable_genesets_save,
user_annotations__local_file_csv__gene_sets_file=gene_sets_file,
user_annotations__gene_sets__readonly=disable_gene_sets_save,
user_annotations__ontology__enable=experimental_annotations_ontology,
user_annotations__ontology__obo_location=experimental_annotations_ontology_obo,
presentation__max_categories=max_category_items,