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perl-bioperl: add v1.6.924, v1.7.8, deprecate v1.007002, refactor dependeicies, update url (#46213)

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* perl-bioperl: add v1.6.924

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* fix style

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* perl-bioperl: add v1.6.924, v1.7.2, deprecate v1.007002, refactor dependencies

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* perl-bioperl: add v1.7.8

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* perl-bioperl: update url

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* perl-bioperl: cleanup version urls

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>

* remove v1.7.2

---------

Signed-off-by: Teague Sterling <teaguesterling@gmail.com>
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Teague Sterling 2024-09-10 03:36:43 -07:00 committed by GitHub
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commit 6f5ba44431
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1 changed files with 62 additions and 68 deletions
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var/spack/repos/builtin/packages/perl-bioperl/package.py
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@ -32,87 +32,81 @@ class PerlBioperl(PerlPackage):
and contribute your own if possible.""" and contribute your own if possible."""
homepage = "https://metacpan.org/pod/BioPerl" homepage = "https://metacpan.org/pod/BioPerl"
url = "https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz" url = "https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.7.8.tar.gz"
license("Artistic-1.0") license("Artistic-1.0")
version("1.7.8", sha256="c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738")
version( version(
"1.7.6", "1.7.6",
sha256="df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d", sha256="df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d",
preferred=True, url="https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz",
) )
version("1.6.924", sha256="616a7546bb3c58504de27304a0f6cb904e18b6bbcdb6a4ec8454f2bd37bb76d0")
# This is technically the same as 1.7.2, but with a more conventional version number.
version( version(
"1.007002", "1.007002",
sha256="17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1", sha256="17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1",
url="https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz", url="https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz",
deprecated=True,
) )
depends_on("fortran", type="build") # generated with default_args(type=("build", "run")):
depends_on("perl-data-stag")
depends_on("perl-error")
depends_on("perl-graph")
depends_on("perl-http-message")
depends_on("perl-io-string")
depends_on("perl-io-stringy")
depends_on("perl-ipc-run")
depends_on("perl-libwww-perl")
depends_on("perl-libxml-perl")
depends_on("perl-list-moreutils")
depends_on("perl-module-build")
depends_on("perl-set-scalar")
depends_on("perl-test-most")
depends_on("perl-test-requiresinternet")
depends_on("perl-uri")
depends_on("perl-xml-dom")
depends_on("perl-xml-dom-xpath")
depends_on("perl-xml-libxml")
depends_on("perl-xml-parser")
depends_on("perl-xml-sax")
depends_on("perl-xml-sax-base")
depends_on("perl-xml-sax-writer")
depends_on("perl-xml-simple")
depends_on("perl-xml-twig")
depends_on("perl-yaml")
# According to cpandeps.grinnz.com Module-Build is both a build and run with when("@:1.7.0"):
# time dependency for BioPerl depends_on("perl-clone")
depends_on("perl-module-build", type=("build", "run")) depends_on("perl-db-file")
depends_on("perl-uri", type=("build", "run")) depends_on("perl-dbd-mysql")
depends_on("perl-io-string", type=("build", "run")) depends_on("perl-dbd-pg")
depends_on("perl-data-stag", type=("build", "run")) depends_on("perl-dbd-sqlite")
depends_on("perl-test-most", type=("build", "run")) depends_on("perl-dbi")
depends_on("perl-error", when="@1.7.6:", type=("build", "run")) depends_on("perl-gd")
depends_on("perl-graph", when="@1.7.6:", type=("build", "run")) depends_on("perl-graphviz")
depends_on("perl-http-message", when="@1.7.6:", type=("build", "run")) depends_on("perl-scalar-list-utils")
depends_on("perl-io-stringy", when="@1.7.6:", type=("build", "run")) depends_on("perl-set-scalar")
depends_on("perl-ipc-run", when="@1.7.6:", type=("build", "run")) depends_on("perl-svg")
depends_on("perl-list-moreutils", when="@1.7.6:", type=("build", "run"))
depends_on("perl-set-scalar", when="@1.7.6:", type=("build", "run"))
depends_on("perl-test-requiresinternet", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-dom", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-dom-xpath", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-libxml", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-sax", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-sax-base", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-sax-writer", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-twig", when="@1.7.6:", type=("build", "run"))
depends_on("perl-xml-writer", when="@1.7.6:", type=("build", "run"))
depends_on("perl-yaml", when="@1.7.6:", type=("build", "run"))
depends_on("perl-libwww-perl", when="@1.7.6:", type=("build", "run"))
depends_on("perl-libxml-perl", when="@1.7.6:", type=("build", "run"))
@when("@1.007002") # TODO:
def configure(self, spec, prefix): # variant("optionaldeps", default=False, description="Add optional dependencies")
# Overriding default configure method in order to cater to interactive # with when("@:1.7.0+optionaldeps"):
# Build.pl # depends_on("perl-sort-naturally")
self.build_method = "Build.PL" # depends_on("perl-test-harness")
self.build_executable = Executable(join_path(self.stage.source_path, "Build")) # depends_on("perl-text-parsewords")
# depends_on("perl-algorithm-munkres")
# depends_on("perl-array-compare")
# depends_on("perl-bio-phylo")
# depends_on("perl-convert-binary-c")
# depends_on("perl-html-entities")
# depends_on("perl-html-headparser")
# depends_on("perl-html-tableextract")
# depends_on("perl-svg-graph")
# Config questions consist of: def configure_args(self):
# Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store args = ["--accept=1"]
# live database tests? y/n [n] return args
#
# Install [a]ll BioPerl scripts, [n]one, or choose groups
# [i]nteractively? [a]
#
# Do you want to run tests that require connection to servers across
# the internet (likely to cause some failures)? y/n [n]
#
# Eventually, someone can add capability for the other options, but
# the current answers are the most practical for a spack install.
config_answers = ["n\n", "a\n", "n\n"]
config_answers_filename = "spack-config.in"
with open(config_answers_filename, "w") as f:
f.writelines(config_answers)
with open(config_answers_filename, "r") as f:
perl("Build.PL", "--install_base=%s" % self.prefix, input=f)
# Need to also override the build and install methods to make sure that the
# Build script is run through perl and not use the shebang, as it might be
# too long. This is needed because this does not pick up the
# `@run_after(configure)` step defined in `PerlPackage`.
@when("@1.007002")
def build(self, spec, prefix):
perl("Build")
@when("@1.007002")
def install(self, spec, prefix):
perl("Build", "install")