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

* 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>

1 files changed, 65 insertions, 71 deletions

diff --git a/var/spack/repos/builtin/packages/perl-bioperl/package.py b/var/spack/repos/builtin/packages/perl-bioperl/package.py
index 790446ad91..1385bd5911 100644
--- a/var/spack/repos/builtin/packages/perl-bioperl/package.py
+++ b/var/spack/repos/builtin/packages/perl-bioperl/package.py
@@ -32,87 +32,81 @@ class PerlBioperl(PerlPackage):
     and contribute your own if possible."""
 
     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")
 
+    version("1.7.8", sha256="c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738")
     version(
         "1.7.6",
         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(
         "1.007002",
         sha256="17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1",
         url="https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz",
+        deprecated=True,
     )
 
-    depends_on("fortran", type="build")  # generated
-
-    # According to cpandeps.grinnz.com Module-Build is both a build and run
-    # time dependency for BioPerl
-    depends_on("perl-module-build", type=("build", "run"))
-    depends_on("perl-uri", type=("build", "run"))
-    depends_on("perl-io-string", type=("build", "run"))
-    depends_on("perl-data-stag", type=("build", "run"))
-    depends_on("perl-test-most", type=("build", "run"))
-    depends_on("perl-error", when="@1.7.6:", type=("build", "run"))
-    depends_on("perl-graph", when="@1.7.6:", type=("build", "run"))
-    depends_on("perl-http-message", when="@1.7.6:", type=("build", "run"))
-    depends_on("perl-io-stringy", when="@1.7.6:", type=("build", "run"))
-    depends_on("perl-ipc-run", when="@1.7.6:", type=("build", "run"))
-    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")
-    def configure(self, spec, prefix):
-        # Overriding default configure method in order to cater to interactive
-        # Build.pl
-        self.build_method = "Build.PL"
-        self.build_executable = Executable(join_path(self.stage.source_path, "Build"))
-
-        # Config questions consist of:
-        #    Do you want to run the Bio::DB::GFF or Bio::DB::SeqFeature::Store
-        #        live database tests? y/n [n]
-        #
-        #    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")
+    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")
+
+        with when("@:1.7.0"):
+            depends_on("perl-clone")
+            depends_on("perl-db-file")
+            depends_on("perl-dbd-mysql")
+            depends_on("perl-dbd-pg")
+            depends_on("perl-dbd-sqlite")
+            depends_on("perl-dbi")
+            depends_on("perl-gd")
+            depends_on("perl-graphviz")
+            depends_on("perl-scalar-list-utils")
+            depends_on("perl-set-scalar")
+            depends_on("perl-svg")
+
+        # TODO:
+        #     variant("optionaldeps", default=False, description="Add optional dependencies")
+        #        with when("@:1.7.0+optionaldeps"):
+        #            depends_on("perl-sort-naturally")
+        #            depends_on("perl-test-harness")
+        #            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")
+
+        def configure_args(self):
+            args = ["--accept=1"]
+            return args