From 7064bf5ea9939244bc020bf11cf5c2fbf1bad8c5 Mon Sep 17 00:00:00 2001
From: Harmen Stoppels <harmenstoppels@gmail.com>
Date: Sat, 14 Feb 2026 22:24:05 +0100
Subject: [PATCH] repo: inline filter_file(..., **kwargs)

Type checkers have issue with `kwargs = {...}`, `f(**kwargs)` due to
type erasure, but the pattern is often not needed and probably just
copied over from existing packages.

* Inline `**kwargs`
* Remove kwargs that repeat defaults

Signed-off-by: Harmen Stoppels <harmenstoppels@gmail.com>
---
 .../builtin/packages/astral/package.py        |  5 +-
 .../builtin/packages/beagle/package.py        |  5 +-
 .../builtin/packages/bowtie2/package.py       |  8 ++--
 .../builtin/packages/bref3/package.py         |  5 +-
 .../builtin/packages/bzip2/package.py         | 10 ++--
 .../builtin/packages/cantera/package.py       | 26 +++++++---
 .../builtin/packages/cctools/package.py       |  3 +-
 .../builtin/packages/chexmix/package.py       |  5 +-
 .../builtin/packages/corenlp/package.py       |  3 +-
 .../builtin/packages/cromwell/package.py      |  5 +-
 .../packages/cromwell_womtool/package.py      |  5 +-
 .../builtin/packages/daligner/package.py      |  3 +-
 .../builtin/packages/eccodes/package.py       | 12 ++---
 .../builtin/packages/gatk/package.py          |  8 +---
 .../packages/genomefinisher/package.py        |  5 +-
 .../builtin/packages/haploview/package.py     |  5 +-
 .../builtin/packages/igvtools/package.py      |  5 +-
 .../builtin/packages/libxstream/package.py    |  8 ++--
 .../builtin/packages/mono/package.py          |  3 +-
 .../builtin/packages/multitail/package.py     |  5 +-
 .../builtin/packages/mummer/package.py        |  3 +-
 .../builtin/packages/parallel/package.py      |  3 +-
 .../builtin/packages/perl/package.py          |  9 ++--
 .../builtin/packages/pgdspider/package.py     |  5 +-
 .../builtin/packages/picard/package.py        |  5 +-
 .../builtin/packages/pilon/package.py         |  5 +-
 .../builtin/packages/psi4/package.py          | 25 +++++++---
 .../builtin/packages/python/package.py        |  5 +-
 .../builtin/packages/qorts/package.py         |  5 +-
 .../builtin/packages/rna_seqc/package.py      |  5 +-
 .../builtin/packages/scalpel/package.py       |  4 +-
 .../builtin/packages/sessreg/package.py       |  3 +-
 .../builtin/packages/snpeff/package.py        |  7 +--
 .../builtin/packages/sundials/package.py      | 47 +++++++++++++++----
 .../builtin/packages/trimmomatic/package.py   |  5 +-
 .../builtin/packages/varscan/package.py       |  5 +-
 .../builtin/packages/vcftools/package.py      |  3 +-
 37 files changed, 147 insertions(+), 131 deletions(-)

diff --git a/repos/spack_repo/builtin/packages/astral/package.py b/repos/spack_repo/builtin/packages/astral/package.py
index be82073c401..7e4a7075d4b 100644
--- a/repos/spack_repo/builtin/packages/astral/package.py
+++ b/repos/spack_repo/builtin/packages/astral/package.py
@@ -44,9 +44,8 @@ def install(self, spec, prefix):
         set_executable(script)
 
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("astral.jar", join_path(prefix.tools, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("astral.jar", join_path(prefix.tools, jar_file), script)
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:
         env.set("ASTRAL_HOME", self.prefix.tools)
diff --git a/repos/spack_repo/builtin/packages/beagle/package.py b/repos/spack_repo/builtin/packages/beagle/package.py
index 9fd2da21763..84767032879 100644
--- a/repos/spack_repo/builtin/packages/beagle/package.py
+++ b/repos/spack_repo/builtin/packages/beagle/package.py
@@ -58,6 +58,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("beagle.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("beagle.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/bowtie2/package.py b/repos/spack_repo/builtin/packages/bowtie2/package.py
index 31755be4096..c9a12b57fa0 100644
--- a/repos/spack_repo/builtin/packages/bowtie2/package.py
+++ b/repos/spack_repo/builtin/packages/bowtie2/package.py
@@ -51,19 +51,17 @@ class Bowtie2(MakefilePackage):
     conflicts("@2.4.1", when="target=aarch64:")
 
     def edit(self, spec, prefix):
-        kwargs = {"ignore_absent": True, "backup": False, "string": False}
-
         match = "^#!/usr/bin/env perl"
         perl = spec["perl"].command
         substitute = "#!{perl}".format(perl=perl)
         files = ["bowtie2"]
-        filter_file(match, substitute, *files, **kwargs)
+        filter_file(match, substitute, *files, ignore_absent=True)
 
         match = "^#!/usr/bin/env python.*"
         python = spec["python"].command
         substitute = "#!{python}".format(python=python)
         files = ["bowtie2-build", "bowtie2-inspect"]
-        filter_file(match, substitute, *files, **kwargs)
+        filter_file(match, substitute, *files, ignore_absent=True)
 
         if self.spec.satisfies("@2.4.0:2.4.2 target=aarch64:") or self.spec.satisfies(
             "@2.4.0:2.4.2 target=ppc64le:"
@@ -72,7 +70,7 @@ def edit(self, spec, prefix):
             simdepath = spec["simde"].prefix.include
             substitute = "-I{simdepath}".format(simdepath=simdepath)
             files = ["Makefile"]
-            filter_file(match, substitute, *files, **kwargs)
+            filter_file(match, substitute, *files, ignore_absent=True)
 
     @property
     def build_targets(self):
diff --git a/repos/spack_repo/builtin/packages/bref3/package.py b/repos/spack_repo/builtin/packages/bref3/package.py
index e8112e07273..23454a15cd8 100644
--- a/repos/spack_repo/builtin/packages/bref3/package.py
+++ b/repos/spack_repo/builtin/packages/bref3/package.py
@@ -54,6 +54,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("bref.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("bref.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/bzip2/package.py b/repos/spack_repo/builtin/packages/bzip2/package.py
index ff5695ffa16..43f52cb2fee 100644
--- a/repos/spack_repo/builtin/packages/bzip2/package.py
+++ b/repos/spack_repo/builtin/packages/bzip2/package.py
@@ -98,8 +98,6 @@ def patch(self):
             v = self.spec.version
             v1, v2, v3 = (v.up_to(i) for i in (1, 2, 3))
 
-            kwargs = {"ignore_absent": False, "backup": False, "string": True}
-
             mf = FileFilter("Makefile-libbz2_so")
             mf.filter(
                 "$(CC) -shared -Wl,-soname -Wl,libbz2.so.{0} -o libbz2.so.{1} $(OBJS)".format(
@@ -109,21 +107,21 @@ def patch(self):
                     "$(CC) -dynamiclib -Wl,-install_name -Wl,@rpath/libbz2.{0}.dylib "
                     "-current_version {1} -compatibility_version {2} -o libbz2.{3}.dylib $(OBJS)"
                 ).format(v1, v2, v3, v3),
-                **kwargs,
+                string=True,
             )
 
             mf.filter(
                 "$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.so.{0}".format(v3),
                 "$(CC) $(CFLAGS) -o bzip2-shared bzip2.c libbz2.{0}.dylib".format(v3),
-                **kwargs,
+                string=True,
             )
             mf.filter(
-                "rm -f libbz2.so.{0}".format(v2), "rm -f libbz2.{0}.dylib".format(v2), **kwargs
+                "rm -f libbz2.so.{0}".format(v2), "rm -f libbz2.{0}.dylib".format(v2), string=True
             )
             mf.filter(
                 "ln -s libbz2.so.{0} libbz2.so.{1}".format(v3, v2),
                 "ln -s libbz2.{0}.dylib libbz2.{1}.dylib".format(v3, v2),
-                **kwargs,
+                string=True,
             )
 
     def install(self, spec, prefix):
diff --git a/repos/spack_repo/builtin/packages/cantera/package.py b/repos/spack_repo/builtin/packages/cantera/package.py
index b7339c493b9..4c227faffa3 100644
--- a/repos/spack_repo/builtin/packages/cantera/package.py
+++ b/repos/spack_repo/builtin/packages/cantera/package.py
@@ -357,8 +357,6 @@ def filter_compilers(self):
         If this isn't done, they'll have CC, CXX, F77, and FC set to Spack's
         generic cc, c++, f77, and f90. We want them to be bound to whatever
         compiler they were built with."""
-
-        kwargs = {"ignore_absent": True, "backup": False, "string": True}
         dirname = os.path.join(self.prefix, "share/cantera/samples")
 
         cc_files = [
@@ -384,20 +382,36 @@ def filter_compilers(self):
 
         for filename in cc_files:
             filter_file(
-                os.environ["CC"], self.compiler.cc, os.path.join(dirname, filename), **kwargs
+                os.environ["CC"],
+                self.compiler.cc,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         for filename in cxx_files:
             filter_file(
-                os.environ["CXX"], self.compiler.cxx, os.path.join(dirname, filename), **kwargs
+                os.environ["CXX"],
+                self.compiler.cxx,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         for filename in f77_files:
             filter_file(
-                os.environ["F77"], self.compiler.f77, os.path.join(dirname, filename), **kwargs
+                os.environ["F77"],
+                self.compiler.f77,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         for filename in fc_files:
             filter_file(
-                os.environ["FC"], self.compiler.fc, os.path.join(dirname, filename), **kwargs
+                os.environ["FC"],
+                self.compiler.fc,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
             )
diff --git a/repos/spack_repo/builtin/packages/cctools/package.py b/repos/spack_repo/builtin/packages/cctools/package.py
index b6e7225380c..df1b490bc2d 100644
--- a/repos/spack_repo/builtin/packages/cctools/package.py
+++ b/repos/spack_repo/builtin/packages/cctools/package.py
@@ -57,8 +57,7 @@ def patch(self):
         before = "#if defined(__linux__) && defined(SYS_memfd_create)"
         after = "#if defined(__linux__) && defined(SYS_memfd_create) && defined(__NR_memfd_create)"
         f = "dttools/src/memfdexe.c"
-        kwargs = {"ignore_absent": False, "backup": True, "string": True}
-        filter_file(before, after, f, **kwargs)
+        filter_file(before, after, f, backup=True, string=True)
         if self.spec.satisfies("%fj"):
             makefiles = ["chirp/src/Makefile", "grow/src/Makefile"]
             for m in makefiles:
diff --git a/repos/spack_repo/builtin/packages/chexmix/package.py b/repos/spack_repo/builtin/packages/chexmix/package.py
index 479b9f977a8..c0c6e85fc6c 100644
--- a/repos/spack_repo/builtin/packages/chexmix/package.py
+++ b/repos/spack_repo/builtin/packages/chexmix/package.py
@@ -45,6 +45,5 @@ def install(self, spec, prefix):
         set_executable(script)
         # set the helper script to explicitly point to java and the .jar file
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("chexmix.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("chexmix.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/corenlp/package.py b/repos/spack_repo/builtin/packages/corenlp/package.py
index 254ed493f5c..d850aef6d7f 100644
--- a/repos/spack_repo/builtin/packages/corenlp/package.py
+++ b/repos/spack_repo/builtin/packages/corenlp/package.py
@@ -60,8 +60,7 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
+        filter_file("^java", java, script)
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:
         class_paths = []
diff --git a/repos/spack_repo/builtin/packages/cromwell/package.py b/repos/spack_repo/builtin/packages/cromwell/package.py
index 8f86250fc99..418cf32f921 100644
--- a/repos/spack_repo/builtin/packages/cromwell/package.py
+++ b/repos/spack_repo/builtin/packages/cromwell/package.py
@@ -45,6 +45,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("cromwell.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("cromwell.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/cromwell_womtool/package.py b/repos/spack_repo/builtin/packages/cromwell_womtool/package.py
index b975ff45a54..d06f718655d 100644
--- a/repos/spack_repo/builtin/packages/cromwell_womtool/package.py
+++ b/repos/spack_repo/builtin/packages/cromwell_womtool/package.py
@@ -40,6 +40,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("womtool.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("womtool.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/daligner/package.py b/repos/spack_repo/builtin/packages/daligner/package.py
index cc681a7ca36..4237ee7a6e1 100644
--- a/repos/spack_repo/builtin/packages/daligner/package.py
+++ b/repos/spack_repo/builtin/packages/daligner/package.py
@@ -19,8 +19,7 @@ class Daligner(MakefilePackage):
 
     def edit(self, spec, prefix):
         makefile = FileFilter("Makefile")
-        kwargs = {"ignore_absent": False, "backup": False, "string": True}
-        makefile.filter("cp $(ALL) ~/bin", "cp $(ALL) {0}".format(prefix.bin), **kwargs)
+        makefile.filter("cp $(ALL) ~/bin", "cp $(ALL) {0}".format(prefix.bin), string=True)
         # He changed the Makefile in commit dae119.
         # You'll need this instead if/when he cuts a new release
         # or if you try to build from the tip of master.
diff --git a/repos/spack_repo/builtin/packages/eccodes/package.py b/repos/spack_repo/builtin/packages/eccodes/package.py
index 8d68e523936..87dae44b437 100644
--- a/repos/spack_repo/builtin/packages/eccodes/package.py
+++ b/repos/spack_repo/builtin/packages/eccodes/package.py
@@ -227,20 +227,18 @@ def patch(self):
                 ]
             )
 
-        kwargs = {"string": False, "backup": False, "ignore_absent": True}
-
         # Return the kind and not the size:
         filter_file(
             r"(^\s*kind_of_double\s*=\s*)(\d{1,2})(\s*$)",
             "\\1kind(real\\2)\\3",
             "fortran/grib_types.f90",
-            **kwargs,
+            ignore_absent=True,
         )
         filter_file(
             r"(^\s*kind_of_\w+\s*=\s*)(\d{1,2})(\s*$)",
             "\\1kind(x\\2)\\3",
             "fortran/grib_types.f90",
-            **kwargs,
+            ignore_absent=True,
         )
 
         # Replace integer kinds:
@@ -249,7 +247,7 @@ def patch(self):
                 r"(^\s*integer\((?:kind=)?){0}(\).*)".format(size),
                 "\\1selected_int_kind({0})\\2".format(r),
                 *patch_kind_files,
-                **kwargs,
+                ignore_absent=True,
             )
 
         # Replace real kinds:
@@ -258,7 +256,7 @@ def patch(self):
                 r"(^\s*real\((?:kind=)?){0}(\).*)".format(size),
                 "\\1selected_real_kind({0}, {1})\\2".format(p, r),
                 *patch_kind_files,
-                **kwargs,
+                ignore_absent=True,
             )
 
         # Enable getarg and exit subroutines:
@@ -266,7 +264,7 @@ def patch(self):
             r"(^\s*program\s+\w+)(\s*$)",
             "\\1; use f90_unix_env; use f90_unix_proc\\2",
             *patch_unix_ext_files,
-            **kwargs,
+            ignore_absent=True,
         )
 
     @property
diff --git a/repos/spack_repo/builtin/packages/gatk/package.py b/repos/spack_repo/builtin/packages/gatk/package.py
index 4c8d33db822..55e7200d05e 100644
--- a/repos/spack_repo/builtin/packages/gatk/package.py
+++ b/repos/spack_repo/builtin/packages/gatk/package.py
@@ -94,13 +94,9 @@ def install(self, spec, prefix):
             # Munge the helper script to explicitly point to java and the
             # jar file.
             java = join_path(self.spec["java"].prefix, "bin", "java")
-            kwargs = {"ignore_absent": False, "backup": False, "string": False}
-            filter_file("^java", java, script, **kwargs)
+            filter_file("^java", java, script)
             filter_file(
-                "GenomeAnalysisTK.jar",
-                join_path(prefix.bin, "GenomeAnalysisTK.jar"),
-                script,
-                **kwargs,
+                "GenomeAnalysisTK.jar", join_path(prefix.bin, "GenomeAnalysisTK.jar"), script
             )
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:
diff --git a/repos/spack_repo/builtin/packages/genomefinisher/package.py b/repos/spack_repo/builtin/packages/genomefinisher/package.py
index be88d3ef6e4..c3b077da58d 100644
--- a/repos/spack_repo/builtin/packages/genomefinisher/package.py
+++ b/repos/spack_repo/builtin/packages/genomefinisher/package.py
@@ -38,6 +38,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the jar file
         # jar file.
         java = spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file(jar_file, join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file(jar_file, join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/haploview/package.py b/repos/spack_repo/builtin/packages/haploview/package.py
index 42d749732f8..515699ee056 100644
--- a/repos/spack_repo/builtin/packages/haploview/package.py
+++ b/repos/spack_repo/builtin/packages/haploview/package.py
@@ -35,6 +35,5 @@ def install(self, spec, prefix):
         set_executable(script)
 
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("haploview.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("haploview.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/igvtools/package.py b/repos/spack_repo/builtin/packages/igvtools/package.py
index 9f79e8eb4d4..1609bc06de9 100644
--- a/repos/spack_repo/builtin/packages/igvtools/package.py
+++ b/repos/spack_repo/builtin/packages/igvtools/package.py
@@ -36,6 +36,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file(jar_file, join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file(jar_file, join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/libxstream/package.py b/repos/spack_repo/builtin/packages/libxstream/package.py
index d58f90e0efd..0141dc127fc 100644
--- a/repos/spack_repo/builtin/packages/libxstream/package.py
+++ b/repos/spack_repo/builtin/packages/libxstream/package.py
@@ -24,12 +24,10 @@ class Libxstream(Package):
     depends_on("gmake", type="build")
 
     def patch(self):
-        kwargs = {"ignore_absent": False, "backup": True, "string": True}
         makefile = FileFilter("Makefile.inc")
-
-        makefile.filter("CC =", "CC ?=", **kwargs)
-        makefile.filter("CXX =", "CXX ?=", **kwargs)
-        makefile.filter("FC =", "FC ?=", **kwargs)
+        makefile.filter("CC =", "CC ?=", backup=True, string=True)
+        makefile.filter("CXX =", "CXX ?=", backup=True, string=True)
+        makefile.filter("FC =", "FC ?=", backup=True, string=True)
 
     def install(self, spec, prefix):
         make()
diff --git a/repos/spack_repo/builtin/packages/mono/package.py b/repos/spack_repo/builtin/packages/mono/package.py
index a3c86e9566b..02878f23042 100644
--- a/repos/spack_repo/builtin/packages/mono/package.py
+++ b/repos/spack_repo/builtin/packages/mono/package.py
@@ -76,8 +76,7 @@ def patch(self):
             before = 'return "/usr/share";'
             after = 'return "{0}";'.format(self.prefix.share)
             f = "mcs/class/corlib/System/Environment.cs"
-            kwargs = {"ignore_absent": False, "backup": True, "string": True}
-            filter_file(before, after, f, **kwargs)
+            filter_file(before, after, f, backup=True, string=True)
 
     def configure_args(self):
         args = []
diff --git a/repos/spack_repo/builtin/packages/multitail/package.py b/repos/spack_repo/builtin/packages/multitail/package.py
index 8f1086c08b4..0488d6e2825 100644
--- a/repos/spack_repo/builtin/packages/multitail/package.py
+++ b/repos/spack_repo/builtin/packages/multitail/package.py
@@ -41,7 +41,8 @@ def edit(self, spec, prefix):
 
         # Copy the conf file directly into place (don't worry about
         # overwriting an existing file...)
-        kwargs = {"ignore_absent": False, "backup": False, "string": True}
         makefile.filter(
-            r"cp multitail.conf $(CONFIG_FILE).new", "cp multitail.conf $(CONFIG_FILE)", **kwargs
+            r"cp multitail.conf $(CONFIG_FILE).new",
+            "cp multitail.conf $(CONFIG_FILE)",
+            string=True,
         )
diff --git a/repos/spack_repo/builtin/packages/mummer/package.py b/repos/spack_repo/builtin/packages/mummer/package.py
index 4b5063c8625..0ae1357a02b 100644
--- a/repos/spack_repo/builtin/packages/mummer/package.py
+++ b/repos/spack_repo/builtin/packages/mummer/package.py
@@ -31,8 +31,7 @@ def patch(self):
         """Fix mummerplot's use of defined on hashes (deprecated
         since perl@5.10, made illegal in perl@5.20."""
 
-        kwargs = {"string": True}
-        filter_file("defined (%", "(%", "scripts/mummerplot.pl", **kwargs)
+        filter_file("defined (%", "(%", "scripts/mummerplot.pl", string=True)
 
     def install(self, spec, prefix):
         if self.run_tests:
diff --git a/repos/spack_repo/builtin/packages/parallel/package.py b/repos/spack_repo/builtin/packages/parallel/package.py
index 82e9bd4cb47..ea5049c9138 100644
--- a/repos/spack_repo/builtin/packages/parallel/package.py
+++ b/repos/spack_repo/builtin/packages/parallel/package.py
@@ -45,13 +45,12 @@ def filter_sbang(self):
         can fix up the path to the perl binary.
         """
         perl = self.spec["perl"].command
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
 
         with working_dir("src"):
             match = "^#!/usr/bin/env perl|^#!/usr/bin/perl.*"
             substitute = f"#!{perl}"
             files = ["parallel", "niceload", "parcat", "sql"]
-            filter_file(match, substitute, *files, **kwargs)
+            filter_file(match, substitute, *files)
             # Since scripts are run during installation, we need to add sbang
             for file in files:
                 filter_shebang(file)
diff --git a/repos/spack_repo/builtin/packages/perl/package.py b/repos/spack_repo/builtin/packages/perl/package.py
index eb6f4e4f87c..ddb65e69c7c 100644
--- a/repos/spack_repo/builtin/packages/perl/package.py
+++ b/repos/spack_repo/builtin/packages/perl/package.py
@@ -358,7 +358,6 @@ def filter_config_dot_pm(self):
         """
         if sys.platform == "win32":
             return
-        kwargs = {"ignore_absent": True, "backup": False, "string": False}
 
         # Find the actual path to the installed Config.pm file.
         config_dot_pm = self.command(
@@ -369,7 +368,7 @@ def filter_config_dot_pm(self):
         with self.make_briefly_writable(config_dot_pm):
             match = "cc *=>.*"
             substitute = "cc => '{cc}',".format(cc=c_compiler)
-            filter_file(match, substitute, config_dot_pm, **kwargs)
+            filter_file(match, substitute, config_dot_pm, ignore_absent=True)
 
         # And the path Config_heavy.pl
         d = os.path.dirname(config_dot_pm)
@@ -378,15 +377,15 @@ def filter_config_dot_pm(self):
         with self.make_briefly_writable(config_heavy):
             match = "^cc=.*"
             substitute = "cc='{cc}'".format(cc=c_compiler)
-            filter_file(match, substitute, config_heavy, **kwargs)
+            filter_file(match, substitute, config_heavy, ignore_absent=True)
 
             match = "^ld=.*"
             substitute = "ld='{ld}'".format(ld=c_compiler)
-            filter_file(match, substitute, config_heavy, **kwargs)
+            filter_file(match, substitute, config_heavy, ignore_absent=True)
 
             match = "^ccflags='"
             substitute = "ccflags='%s " % " ".join(self.spec.compiler_flags["cflags"])
-            filter_file(match, substitute, config_heavy, **kwargs)
+            filter_file(match, substitute, config_heavy, ignore_absent=True)
 
     @contextmanager
     def make_briefly_writable(self, path):
diff --git a/repos/spack_repo/builtin/packages/pgdspider/package.py b/repos/spack_repo/builtin/packages/pgdspider/package.py
index 5b102341d55..763df29d686 100644
--- a/repos/spack_repo/builtin/packages/pgdspider/package.py
+++ b/repos/spack_repo/builtin/packages/pgdspider/package.py
@@ -37,6 +37,5 @@ def install(self, spec, prefix):
         set_executable(script)
 
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("pgdspider.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("pgdspider.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/picard/package.py b/repos/spack_repo/builtin/packages/picard/package.py
index 4e1fc1ec698..cffde8a4fa2 100644
--- a/repos/spack_repo/builtin/packages/picard/package.py
+++ b/repos/spack_repo/builtin/packages/picard/package.py
@@ -197,9 +197,8 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("picard.jar", join_path(prefix.bin, "picard.jar"), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("picard.jar", join_path(prefix.bin, "picard.jar"), script)
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:
         """The Picard docs suggest setting this as a convenience."""
diff --git a/repos/spack_repo/builtin/packages/pilon/package.py b/repos/spack_repo/builtin/packages/pilon/package.py
index f626fe8b555..1c78554ba5a 100644
--- a/repos/spack_repo/builtin/packages/pilon/package.py
+++ b/repos/spack_repo/builtin/packages/pilon/package.py
@@ -44,6 +44,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("pilon-{0}.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("pilon-{0}.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/psi4/package.py b/repos/spack_repo/builtin/packages/psi4/package.py
index 1149e7f9d95..39dc9a40484 100644
--- a/repos/spack_repo/builtin/packages/psi4/package.py
+++ b/repos/spack_repo/builtin/packages/psi4/package.py
@@ -71,25 +71,37 @@ def filter_compilers(self):
         spec = self.spec
         prefix = spec.prefix
 
-        kwargs = {"ignore_absent": True, "backup": False, "string": True}
-
         cc_files = ["bin/psi4-config"]
         cxx_files = ["bin/psi4-config", "include/psi4/psiconfig.h"]
         template = "share/psi4/plugin/Makefile.template"
 
         for filename in cc_files:
             filter_file(
-                os.environ["CC"], self.compiler.cc, os.path.join(prefix, filename), **kwargs
+                os.environ["CC"],
+                self.compiler.cc,
+                os.path.join(prefix, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         for filename in cxx_files:
             filter_file(
-                os.environ["CXX"], self.compiler.cxx, os.path.join(prefix, filename), **kwargs
+                os.environ["CXX"],
+                self.compiler.cxx,
+                os.path.join(prefix, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         # The binary still keeps track of the compiler used to install Psi4
         # and uses it when creating a plugin template
-        filter_file("@PLUGIN_CXX@", self.compiler.cxx, os.path.join(prefix, template), **kwargs)
+        filter_file(
+            "@PLUGIN_CXX@",
+            self.compiler.cxx,
+            os.path.join(prefix, template),
+            ignore_absent=True,
+            string=True,
+        )
 
         # The binary links to the build include directory instead of the
         # installation include directory:
@@ -109,5 +121,6 @@ def filter_compilers(self):
                 )
             ),
             os.path.join(prefix, template),
-            **kwargs,
+            ignore_absent=True,
+            string=True,
         )
diff --git a/repos/spack_repo/builtin/packages/python/package.py b/repos/spack_repo/builtin/packages/python/package.py
index d1b30111d0e..c0bd0277574 100644
--- a/repos/spack_repo/builtin/packages/python/package.py
+++ b/repos/spack_repo/builtin/packages/python/package.py
@@ -763,13 +763,12 @@ def filter_compilers(self):
         they were built with."""
         if sys.platform == "win32":
             return
-        kwargs = {"ignore_absent": True, "backup": False, "string": True}
 
         filenames = [self.get_sysconfigdata_name(), self.config_vars["makefile_filename"]]
 
-        filter_file(spack_cc, self["c"].cc, *filenames, **kwargs)
+        filter_file(spack_cc, self["c"].cc, *filenames, ignore_absent=True, string=True)
         if spack_cxx:
-            filter_file(spack_cxx, self["cxx"].cxx, *filenames, **kwargs)
+            filter_file(spack_cxx, self["cxx"].cxx, *filenames, ignore_absent=True, string=True)
 
     @run_after("install")
     def symlink(self):
diff --git a/repos/spack_repo/builtin/packages/qorts/package.py b/repos/spack_repo/builtin/packages/qorts/package.py
index 0af4163e0a5..4de67322e8e 100644
--- a/repos/spack_repo/builtin/packages/qorts/package.py
+++ b/repos/spack_repo/builtin/packages/qorts/package.py
@@ -46,6 +46,5 @@ def install_jar(self):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"backup": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("QoRTs.jar", join_path(self.prefix.bin, "QoRTs.jar"), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("QoRTs.jar", join_path(self.prefix.bin, "QoRTs.jar"), script)
diff --git a/repos/spack_repo/builtin/packages/rna_seqc/package.py b/repos/spack_repo/builtin/packages/rna_seqc/package.py
index 94d893a12b6..9d1ad57557c 100644
--- a/repos/spack_repo/builtin/packages/rna_seqc/package.py
+++ b/repos/spack_repo/builtin/packages/rna_seqc/package.py
@@ -59,6 +59,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("RNA-SeQC_v{0}.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("RNA-SeQC_v{0}.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/scalpel/package.py b/repos/spack_repo/builtin/packages/scalpel/package.py
index f87a07cd693..dab77d4725b 100644
--- a/repos/spack_repo/builtin/packages/scalpel/package.py
+++ b/repos/spack_repo/builtin/packages/scalpel/package.py
@@ -37,8 +37,6 @@ def filter_sbang(self):
         """
 
         with working_dir(self.stage.source_path):
-            kwargs = {"ignore_absent": True, "backup": False, "string": False}
-
             match = "^#!/usr/bin/env perl"
             perl = self.spec["perl"].command
             substitute = "#!{perl}".format(perl=perl)
@@ -49,7 +47,7 @@ def filter_sbang(self):
                 "FindVariants.pl",
                 "FindSomatic.pl",
             ]
-            filter_file(match, substitute, *files, **kwargs)
+            filter_file(match, substitute, *files, ignore_absent=True)
 
     # Scalpel doesn't actually *have* an install step.  The authors
     # expect you to unpack the tarball, build it in the resulting
diff --git a/repos/spack_repo/builtin/packages/sessreg/package.py b/repos/spack_repo/builtin/packages/sessreg/package.py
index dc1d84fa7aa..97fcd1e4261 100644
--- a/repos/spack_repo/builtin/packages/sessreg/package.py
+++ b/repos/spack_repo/builtin/packages/sessreg/package.py
@@ -30,5 +30,4 @@ class Sessreg(AutotoolsPackage, XorgPackage):
     depends_on("util-macros", type="build")
 
     def patch(self):
-        kwargs = {"string": True}
-        filter_file("$(CPP) $(DEFS)", "$(CPP) -P $(DEFS)", "man/Makefile.in", **kwargs)
+        filter_file("$(CPP) $(DEFS)", "$(CPP) -P $(DEFS)", "man/Makefile.in", string=True)
diff --git a/repos/spack_repo/builtin/packages/snpeff/package.py b/repos/spack_repo/builtin/packages/snpeff/package.py
index 20fa5fd829f..4eada92f38d 100644
--- a/repos/spack_repo/builtin/packages/snpeff/package.py
+++ b/repos/spack_repo/builtin/packages/snpeff/package.py
@@ -40,8 +40,5 @@ def install(self, spec, prefix):
             # Munge the helper script to explicitly point to java and the
             # jar file.
             java = self.spec["java"].prefix.bin.java
-            kwargs = {"backup": False}
-            filter_file("^java", java, script_path, **kwargs)
-            filter_file(
-                script + ".jar", join_path(prefix.bin, script + ".jar"), script_path, **kwargs
-            )
+            filter_file("^java", java, script_path)
+            filter_file(script + ".jar", join_path(prefix.bin, script + ".jar"), script_path)
diff --git a/repos/spack_repo/builtin/packages/sundials/package.py b/repos/spack_repo/builtin/packages/sundials/package.py
index 8831cf0385b..f8c51a0b908 100644
--- a/repos/spack_repo/builtin/packages/sundials/package.py
+++ b/repos/spack_repo/builtin/packages/sundials/package.py
@@ -553,7 +553,6 @@ def filter_compilers(self):
 
         spec = self.spec
 
-        kwargs = {"ignore_absent": True, "backup": False, "string": True}
         dirname = os.path.join(self.prefix, "examples")
 
         cc_files = [
@@ -643,36 +642,68 @@ def filter_compilers(self):
 
         for filename in cc_files:
             filter_file(
-                os.environ["CC"], self.compiler.cc, os.path.join(dirname, filename), **kwargs
+                os.environ["CC"],
+                self.compiler.cc,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         for filename in cc_files:
-            filter_file(r"^CPP\s*=.*", self.compiler.cc, os.path.join(dirname, filename), **kwargs)
+            filter_file(
+                r"^CPP\s*=.*",
+                self.compiler.cc,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
+            )
 
         for filename in cxx_files:
             filter_file(
-                os.environ["CXX"], self.compiler.cxx, os.path.join(dirname, filename), **kwargs
+                os.environ["CXX"],
+                self.compiler.cxx,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
             )
 
         for filename in cxx_files:
-            filter_file(r"^CPP\s*=.*", self.compiler.cc, os.path.join(dirname, filename), **kwargs)
+            filter_file(
+                r"^CPP\s*=.*",
+                self.compiler.cc,
+                os.path.join(dirname, filename),
+                ignore_absent=True,
+                string=True,
+            )
 
         if ("+fcmix" in spec) and ("+examples" in spec):
             for filename in f77_files:
                 filter_file(
-                    os.environ["F77"], self.compiler.f77, os.path.join(dirname, filename), **kwargs
+                    os.environ["F77"],
+                    self.compiler.f77,
+                    os.path.join(dirname, filename),
+                    ignore_absent=True,
+                    string=True,
                 )
 
         if ("+fcmix" in spec) and ("+examples" in spec):
             for filename in f90_files:
                 filter_file(
-                    os.environ["FC"], self.compiler.fc, os.path.join(dirname, filename), **kwargs
+                    os.environ["FC"],
+                    self.compiler.fc,
+                    os.path.join(dirname, filename),
+                    ignore_absent=True,
+                    string=True,
                 )
 
         if ("+f2003" in spec) and ("+examples" in spec):
             for filename in f2003_files:
                 filter_file(
-                    os.environ["FC"], self.compiler.fc, os.path.join(dirname, filename), **kwargs
+                    os.environ["FC"],
+                    self.compiler.fc,
+                    os.path.join(dirname, filename),
+                    ignore_absent=True,
+                    string=True,
                 )
 
     @property
diff --git a/repos/spack_repo/builtin/packages/trimmomatic/package.py b/repos/spack_repo/builtin/packages/trimmomatic/package.py
index 089c5566d7f..f6dff2b10d1 100644
--- a/repos/spack_repo/builtin/packages/trimmomatic/package.py
+++ b/repos/spack_repo/builtin/packages/trimmomatic/package.py
@@ -45,6 +45,5 @@ def install(self, spec, prefix):
         # Munge the helper script to explicitly point to java and the
         # jar file.
         java = self.spec["java"].prefix.bin.java
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("trimmomatic.jar", join_path(prefix.bin, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("trimmomatic.jar", join_path(prefix.bin, jar_file), script)
diff --git a/repos/spack_repo/builtin/packages/varscan/package.py b/repos/spack_repo/builtin/packages/varscan/package.py
index 8633783ab55..5c11d6cef53 100644
--- a/repos/spack_repo/builtin/packages/varscan/package.py
+++ b/repos/spack_repo/builtin/packages/varscan/package.py
@@ -36,9 +36,8 @@ def install(self, spec, prefix):
         set_executable(script)
 
         java = join_path(self.spec["java"].prefix, "bin", "java")
-        kwargs = {"ignore_absent": False, "backup": False, "string": False}
-        filter_file("^java", java, script, **kwargs)
-        filter_file("varscan.jar", join_path(prefix.jar, jar_file), script, **kwargs)
+        filter_file("^java", java, script)
+        filter_file("varscan.jar", join_path(prefix.jar, jar_file), script)
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:
         env.set("VARSCAN_HOME", self.prefix.jar)
diff --git a/repos/spack_repo/builtin/packages/vcftools/package.py b/repos/spack_repo/builtin/packages/vcftools/package.py
index cc8e6ea2929..a20f46214d9 100644
--- a/repos/spack_repo/builtin/packages/vcftools/package.py
+++ b/repos/spack_repo/builtin/packages/vcftools/package.py
@@ -81,8 +81,7 @@ def filter_sbang(self):
                 "vcf-tstv",
                 "vcf-validator",
             ]
-            kwargs = {"ignore_absent": True, "backup": False, "string": False}
-            filter_file(match, substitute, *files, **kwargs)
+            filter_file(match, substitute, *files, ignore_absent=True)
 
     def setup_run_environment(self, env: EnvironmentModifications) -> None:
         env.prepend_path("PERL5LIB", self.prefix.lib)