Remove outdated fimo wrapper and galaxy-sequence-utils dependency

The fimo tool was removed from `tool_conf.xml.sample` in 2014
(commit fa11d10) and migrated to the
tools-iuc repository since 2015
( galaxyproject/tools-iuc#499 ).
This bundled version doesn't probably work any more and is not
available on the UseGalaxy.* servers.

This allows us to remove `galaxy-sequence-utils` from the project
dependencies, since the other 2 tools
(`lib/galaxy/datatypes/converters/vcf_to_interval_index_converter.xml`
and `tools/maf/vcf_to_maf_customtrack.xml`) correctly specify it as a
requirement.

lib/galaxy/dependencies/pinned-requirements.txt

@@ -72,7 +72,6 @@ frozenlist==1.4.1 ; python_version >= "3.8" and python_version < "3.13"
 fs==2.4.16 ; python_version >= "3.8" and python_version < "3.13"
 fsspec==2024.9.0 ; python_version >= "3.8" and python_version < "3.13"
 future==1.0.0 ; python_version >= "3.8" and python_version < "3.13"
-galaxy-sequence-utils==1.1.5 ; python_version >= "3.8" and python_version < "3.13"
 galaxy2cwl==0.1.4 ; python_version >= "3.8" and python_version < "3.13"
 graphene-sqlalchemy==3.0.0rc1 ; python_version >= "3.8" and python_version < "3.13"
 graphene==3.3 ; python_version >= "3.8" and python_version < "3.13"

mypy.ini

@@ -115,8 +115,6 @@ check_untyped_defs = False
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.phenotype_association.pagetag]
 check_untyped_defs = False
-[mypy-galaxy.tools.bundled.meme.fimo_wrapper]
-check_untyped_defs = False
 [mypy-galaxy.tools.bundled.maf.maf_to_bed]
 check_untyped_defs = False
 [mypy-galaxy.tools.bundled.filters.trimmer]

pyproject.toml

@@ -60,7 +60,6 @@ edam-ontology = "*"
 fastapi-slim = ">=0.111.0"
 fs = "*"
 future = ">=1.0.0"  # Python 3.12 support
-galaxy_sequence_utils = "*"
 graphene = "*"
 graphene-sqlalchemy = ">=3.0.0rc1"  # need a beta release to be compat. with starlette plugin
 graphql-core = "*"

run_tests.sh

@@ -492,14 +492,15 @@ do
       -u|-unit|--unit)
           report_file="run_unit_tests.html"
           unit_extra='--doctest-modules
-			--ignore lib/galaxy/jobs/runners/chronos.py
-			--ignore lib/galaxy/model/migrations/alembic
-			--ignore lib/galaxy/tools/bundled
-			--ignore lib/galaxy/web/proxy/js/node_modules/
-			--ignore lib/galaxy_test
-			--ignore lib/tool_shed/test
-			--ignore lib/tool_shed/webapp/controllers
-			--ignore=lib/tool_shed/webapp/model/migrations/alembic/'
+            --ignore lib/galaxy/datatypes/converters/
+            --ignore lib/galaxy/jobs/runners/chronos.py
+            --ignore lib/galaxy/model/migrations/alembic
+            --ignore lib/galaxy/tools/bundled
+            --ignore lib/galaxy/web/proxy/js/node_modules/
+            --ignore lib/galaxy_test
+            --ignore lib/tool_shed/test
+            --ignore lib/tool_shed/webapp/controllers
+            --ignore=lib/tool_shed/webapp/model/migrations/alembic/'
           generate_cwl_conformance_tests=1
           if [ $# -gt 1 ]; then
               unit_extra="$unit_extra $2"