3cdf4e7ccf
Python lets you do things like
```python
"these are " "one string"
'so are' "these"
```
This can be useful for breaking strings over multiple lines. It also often happens
unintentionally and indicates that there are subtle errors in the code.
There are a lot of variant descriptions that have implicit concatenation harmlessly
due to refactors, e.g.:
```python
variant("myvariant", default=True, description="this used to be" "on two lines")
```
But there are also real bugs, like this, where the author probably omitted a comma and
didn't notice that `black` reformatted the implicit concatenation onto one line:
```python
args = [
"--with-thing",
"--with-second-thing" "--with-third-thing",
]
```
And other bugs like this, where the author probably intended to add a space, but didn't:
```python
options = "${CFLAGS}" "${SPECIAL_PIC_OPTION}"
```
Some things are harmless but confusing:
```python
"first part of string {0} " "second part {1}".format("zero", "one")
```
It's not broken. String concatenation happens *before* the `format()` call, and the
whole string is formatted. But it sure is hard to read.
Unfortunately, you can't detect this stuff with an AST pass, as implicit concatenation
is done at the parsing phase. I had to detect this with grep:
```console
> grep -l '^[^"]*"[^"]*" "' */package.py
> grep -l "^[^']*'[^']*' '" */package.py
```
- [x] Get rid of nearly all implicit string concatenation in packages
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
133 lines
5.0 KiB
Python
133 lines
5.0 KiB
Python
# Copyright Spack Project Developers. See COPYRIGHT file for details.
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#
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# SPDX-License-Identifier: (Apache-2.0 OR MIT)
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from spack.package import *
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class Bcftools(AutotoolsPackage):
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"""BCFtools is a set of utilities that manipulate variant calls in the
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Variant Call Format (VCF) and its binary counterpart BCF. All
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commands work transparently with both VCFs and BCFs, both
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uncompressed and BGZF-compressed."""
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maintainers("jbeal-work")
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homepage = "https://samtools.github.io/bcftools/"
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url = "https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2"
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license("GPL-3.0-or-later")
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version("1.19", sha256="782b5f1bc690415192231e82213b3493b047f45e630dc8ef6f154d6126ab3e68")
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version("1.18", sha256="d9b9d36293e4cc62ab7473aa2539389d4e1de79b1a927d483f6e91f3c3ceac7e")
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version("1.17", sha256="01f75d8e701d85b2c759172412009cc04f29b61616ace2fa75116123de4596cc")
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version("1.16", sha256="293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982")
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version("1.15.1", sha256="f21f9564873eb27ccf22d13b91a64acb8fbbfe4f9e4c37933a54b9a95857f2d7")
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version("1.14", sha256="b7ef88ae89fcb55658c5bea2e8cb8e756b055e13860036d6be13756782aa19cb")
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version("1.13", sha256="13bfa1da2a5edda8fa51196a47a0b4afb3fef17516451e4f0e78477f3dd30b90")
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version("1.12", sha256="7a0e6532b1495b9254e38c6698d955e5176c1ee08b760dfea2235ee161a024f5")
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version("1.10.2", sha256="f57301869d0055ce3b8e26d8ad880c0c1989bf25eaec8ea5db99b60e31354e2c")
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version("1.9", sha256="6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8")
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version("1.8", sha256="4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced")
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version("1.7", sha256="dd4f63d91b0dffb0f0ce88ac75c2387251930c8063f7799611265083f8d302d1")
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version("1.6", sha256="293010736b076cf684d2873928924fcc3d2c231a091084c2ac23a8045c7df982")
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version("1.4", sha256="8fb1b0a47ed4e1f9d7c70129d7993aa650da1688fd931b10646d1c4707ae234d")
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version("1.3.1", sha256="12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924")
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version("1.2", sha256="53c628339020dd45334a007c9cefdaf1cba3f1032492ec813b116379fa684fd6")
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depends_on("c", type="build") # generated
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depends_on("cxx", type="build") # generated
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variant(
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"libgsl",
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default=False,
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description="build options that require the GNU scientific library",
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)
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variant(
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"perl-filters",
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default=False,
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description="build in support for PERL scripts in -i/-e "
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"filtering expressions, for versions >= 1.8.",
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)
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depends_on("gsl", when="+libgsl")
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depends_on("py-matplotlib", when="@1.6:", type="run")
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depends_on("py-gffutils", when="@1.9:", type="run")
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depends_on("perl", when="@1.8:~perl-filters", type="run")
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depends_on("perl", when="@1.8:+perl-filters", type=("build", "run"))
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depends_on("htslib@1.19", when="@1.19")
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depends_on("htslib@1.18", when="@1.18")
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depends_on("htslib@1.17", when="@1.17")
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depends_on("htslib@1.16", when="@1.16")
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depends_on("htslib@1.15", when="@1.15")
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depends_on("htslib@1.14", when="@1.14")
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depends_on("htslib@1.13", when="@1.13")
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depends_on("htslib@1.12", when="@1.12")
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depends_on("htslib@1.10.2", when="@1.10.2")
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depends_on("htslib@1.9", when="@1.9")
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depends_on("htslib@1.8", when="@1.8")
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depends_on("htslib@1.7", when="@1.7")
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depends_on("htslib@1.6", when="@1.6")
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depends_on("htslib@1.4", when="@1.4")
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depends_on("htslib@1.3.1", when="@1.3.1")
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depends_on("htslib@1.2", when="@1.2")
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patch("makefile_12.patch", when="@1.2")
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patch("fix_mk.patch", when="@1.2")
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patch("makefile_13.patch", when="@1.3")
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patch("makefile_14.patch", when="@1.4")
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patch("guess-ploidy.py_2to3.patch", when="@1.6:1.9")
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@when("@1.5:")
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def configure_args(self):
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args = []
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args.append("--with-htslib={0}".format(self.spec["htslib"].prefix))
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args.extend(self.enable_or_disable("libgsl"))
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if self.spec.satisfies("@1.8:"):
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args.extend(self.enable_or_disable("perl-filters"))
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return args
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@when("@1.2:1.4")
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def set_make_options(self):
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options = []
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options.append("prefix={0}".format(self.prefix))
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options.append("HTSDIR={0}".format(self.spec["htslib"].prefix))
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if self.spec.satisfies("+libgsl"):
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options.append("USE_GPL=1")
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return options
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@when("@1.2:1.4")
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def autoreconf(self, spec, prefix):
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touch("configure")
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@when("@1.2:1.4")
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def configure(self, spec, prefix):
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pass
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@when("@1.2:1.4")
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def build(self, spec, prefix):
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make_options = self.set_make_options()
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make(*make_options)
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@when("@1.2:1.4")
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def install(self, spec, prefix):
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make_options = self.set_make_options()
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make("install", *make_options)
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if spec.satisfies("@1.2"):
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mkdirp(self.prefix.libexec.bcftools)
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install("plugins/*.so", self.prefix.libexec.bcftools)
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@when("@1.2")
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def setup_run_environment(self, env):
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env.set("BCFTOOLS_PLUGINS", self.prefix.libexec.bcftools)
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