internlm/SWE-Fixer-Train-110K huggingface dataset:
Repository: spack/spack

Issue:
Use spack debug output in concretizer errors
### Summary

I noticed after I updated one of my projects to the latest spack I was getting these errors:
```
==> Starting concretization pool with 4 processes
==> Error: errors occurred during concretization of the environment:
cannot emit requirements for the solver
cannot emit requirements for the solver
cannot emit requirements for the solver
cannot emit requirements for the solver
```
Since I know `spack -d` exists, I tried `spack -d concretize` and it gave me information that certain variants in a package didn't exist, so I fixed them and then it concretized. Seems like those errors would be good to have in the regular output if possible.

### Rationale

_No response_

### Description

_No response_

### Additional information

_No response_

### General information

- [X] I have searched the issues of this repo and believe this is not a duplicate


Discussion:

Resolving patch:
diff --git a/lib/spack/spack/solver/asp.py b/lib/spack/spack/solver/asp.py
--- a/lib/spack/spack/solver/asp.py
+++ b/lib/spack/spack/solver/asp.py
@@ -1569,7 +1569,9 @@ def emit_facts_from_requirement_rules(self, rules: List[RequirementRule]):
                     )
                 except Exception as e:
                     if rule.kind != RequirementKind.DEFAULT:
-                        raise RuntimeError("cannot emit requirements for the solver") from e
+                        raise RuntimeError(
+                            "cannot emit requirements for the solver: " + str(e)
+                        ) from e
                     continue
 
                 self.gen.fact(
@@ -1601,7 +1603,9 @@ def emit_facts_from_requirement_rules(self, rules: List[RequirementRule]):
                     # would be impaired. If a rule does not apply for a specific package, just
                     # discard it.
                     if rule.kind != RequirementKind.DEFAULT:
-                        raise RuntimeError("cannot emit requirements for the solver") from e
+                        raise RuntimeError(
+                            "cannot emit requirements for the solver: " + str(e)
+                        ) from e
                     continue
 
                 self.gen.fact(fn.requirement_group_member(member_id, pkg_name, requirement_grp_id))


Test patch:
Repository: spack/spack

Issue:
Overwrite install doesn't install missing build deps
### Steps to reproduce

When you install something with overwrite, the build deps are not installed when they're missing.

### Error message

_No response_

### Information on your system

.

### General information

- [X] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [X] I have searched the issues of this repo and believe this is not a duplicate
- [X] I have run the failing commands in debug mode and reported the output


Discussion:

Resolving patch:
diff --git a/lib/spack/spack/installer.py b/lib/spack/spack/installer.py
--- a/lib/spack/spack/installer.py
+++ b/lib/spack/spack/installer.py
@@ -847,10 +847,11 @@ def get_depflags(self, pkg: "spack.package_base.PackageBase") -> int:
         else:
             cache_only = self.install_args.get("dependencies_cache_only")
 
-        # Include build dependencies if pkg is not installed and cache_only
-        # is False, or if build depdencies are explicitly called for
-        # by include_build_deps.
-        if include_build_deps or not (cache_only or pkg.spec.installed):
+        # Include build dependencies if pkg is going to be built from sources, or
+        # if build deps are explicitly requested.
+        if include_build_deps or not (
+            cache_only or pkg.spec.installed and not pkg.spec.dag_hash() in self.overwrite
+        ):
             depflag |= dt.BUILD
         if self.run_tests(pkg):
             depflag |= dt.TEST


Test patch:
diff --git a/lib/spack/spack/test/installer.py b/lib/spack/spack/test/installer.py
--- a/lib/spack/spack/test/installer.py
+++ b/lib/spack/spack/test/installer.py
@@ -20,6 +20,7 @@
 import spack.concretize
 import spack.config
 import spack.database
+import spack.deptypes as dt
 import spack.installer as inst
 import spack.package_base
 import spack.package_prefs as prefs
@@ -1388,6 +1389,26 @@ def test_single_external_implicit_install(install_mockery, explicit_args, is_exp
     assert spack.store.STORE.db.get_record(pkg).explicit == is_explicit
 
 
+def test_overwrite_install_does_install_build_deps(install_mockery, mock_fetch):
+    """When overwrite installing something from sources, build deps should be installed."""
+    s = spack.spec.Spec("dtrun3").concretized()
+    create_installer([(s, {})]).install()
+
+    # Verify there is a pure build dep
+    edge = s.edges_to_dependencies(name="dtbuild3").pop()
+    assert edge.depflag == dt.BUILD
+    build_dep = edge.spec
+
+    # Uninstall the build dep
+    build_dep.package.do_uninstall()
+
+    # Overwrite install the root dtrun3
+    create_installer([(s, {"overwrite": [s.dag_hash()]})]).install()
+
+    # Verify that the build dep was also installed.
+    assert build_dep.installed
+
+
 @pytest.mark.parametrize("run_tests", [True, False])
 def test_print_install_test_log_skipped(install_mockery, mock_packages, capfd, run_tests):
     """Confirm printing of install log skipped if not run/no failures."""
Repository: spack/spack

Issue:
_matching_specs() is called with 2 arguments
### Steps to reproduce

```console
$ spack -d buildcache check -s /<somehash>
==> [2023-10-10-17:55:15.829587] Imported buildcache from built-in commands
==> [2023-10-10-17:55:15.832476] Imported buildcache from built-in commands
==> [2023-10-10-17:55:15.833612] Reading config from file /home/stesachs/spack/etc/spack/defaults/config.yaml
Traceback (most recent call last):
  File "/home/stesachs/spack/bin/spack", line 52, in <module>
    sys.exit(main())
  File "/home/stesachs/spack/lib/spack/spack_installable/main.py", line 37, in main
    sys.exit(spack.main.main(argv))
  File "/home/stesachs/spack/lib/spack/spack/main.py", line 1022, in main
    return _main(argv)
  File "/home/stesachs/spack/lib/spack/spack/main.py", line 977, in _main
    return finish_parse_and_run(parser, cmd_name, env_format_error)
  File "/home/stesachs/spack/lib/spack/spack/main.py", line 1005, in finish_parse_and_run
    return _invoke_command(command, parser, args, unknown)
  File "/home/stesachs/spack/lib/spack/spack/main.py", line 646, in _invoke_command
    return_val = command(parser, args)
  File "/home/stesachs/spack/lib/spack/spack/cmd/buildcache.py", line 638, in buildcache
    args.func(args)
  File "/home/stesachs/spack/lib/spack/spack/cmd/buildcache.py", line 432, in check_fn
    specs = _matching_specs(specs, specs)
TypeError: _matching_specs() takes 1 positional argument but 2 were given
```

### Error message

_No response_

### Information on your system

$ spack debug report
* **Spack:** 0.21.0.dev0 (6c7b2e1056bbd158544da9b6a79fd4099c18cd7a)
* **Python:** 3.7.16
* **Platform:** linux-amzn2-icelake
* **Concretizer:** clingo


### General information

- [X] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [X] I have searched the issues of this repo and believe this is not a duplicate
- [X] I have run the failing commands in debug mode and reported the output


Discussion:

Resolving patch:
diff --git a/lib/spack/spack/cmd/buildcache.py b/lib/spack/spack/cmd/buildcache.py
--- a/lib/spack/spack/cmd/buildcache.py
+++ b/lib/spack/spack/cmd/buildcache.py
@@ -268,7 +268,7 @@ def _matching_specs(specs: List[Spec]) -> List[Spec]:
     return [spack.cmd.disambiguate_spec(s, ev.active_environment(), installed=any) for s in specs]
 
 
-def push_fn(args):
+def push_fn(args: argparse.Namespace):
     """create a binary package and push it to a mirror"""
     if args.spec_file:
         tty.warn(
@@ -414,7 +414,7 @@ def preview_fn(args):
     )
 
 
-def check_fn(args):
+def check_fn(args: argparse.Namespace):
     """check specs against remote binary mirror(s) to see if any need to be rebuilt
 
     this command uses the process exit code to indicate its result, specifically, if the
@@ -429,7 +429,7 @@ def check_fn(args):
     specs = spack.cmd.parse_specs(args.spec or args.spec_file)
 
     if specs:
-        specs = _matching_specs(specs, specs)
+        specs = _matching_specs(specs)
     else:
         specs = spack.cmd.require_active_env("buildcache check").all_specs()
 


Test patch:
Repository: spack/spack

Issue:
Deprecated features slated for removal in v0.21
A brief list of features that are already deprecated and will be removed in v0.21:

- [x] #37246
- [x] #38199
- [x] #40600 
~- [ ] Old format for the stand-alone tests in packages~


Discussion:
@tldahlgren I see that the last item was barred. What are we going to do with:

https://github.com/spack/spack/blob/da0813b049b016b2bcd021abcf2e520ac8bb41ea/lib/spack/spack/package_base.py#L1152-L1162

and 

https://github.com/spack/spack/blob/da0813b049b016b2bcd021abcf2e520ac8bb41ea/lib/spack/spack/package_base.py#L1820-L1843

?

Thanks for the reminder. 

Resolving patch:
diff --git a/lib/spack/spack/package_base.py b/lib/spack/spack/package_base.py
--- a/lib/spack/spack/package_base.py
+++ b/lib/spack/spack/package_base.py
@@ -1157,7 +1157,7 @@ def install_test_root(self):
         """Return the install test root directory."""
         tty.warn(
             "The 'pkg.install_test_root' property is deprecated with removal "
-            "expected v0.21. Use 'install_test_root(pkg)' instead."
+            "expected v0.22. Use 'install_test_root(pkg)' instead."
         )
         return install_test_root(self)
 
@@ -1829,7 +1829,7 @@ def cache_extra_test_sources(self, srcs):
         """
         msg = (
             "'pkg.cache_extra_test_sources(srcs) is deprecated with removal "
-            "expected in v0.21. Use 'cache_extra_test_sources(pkg, srcs)' "
+            "expected in v0.22. Use 'cache_extra_test_sources(pkg, srcs)' "
             "instead."
         )
         warnings.warn(msg)


Test patch:
Repository: spack/spack

Issue:
clingo: fix i out of n
The old concretizer just drops py-setuptools. Add it unconditionally then.

Might get us back to the issue with Python 3.6 :) :tada:  



Discussion:
Sigh. @alalazo suggestions? Either python 3.6 fails cause the old concretizer doesn't know how to deal with conflicts on setuptools, or it just entirely ignores the conditional depends on for 3.12.


Wondering if we can use a variant, and construct the specs in a way that depends on the interpreter version when bootstrapping.
Also, it seems GA is in the middle of a migration, so we're getting Python versions randomly on macOS. This one https://github.com/spack/spack/actions/runs/6745185158/job/18336769272?pr=40861 (from the PR) is Python 3.11
You can try concretization locally I guess
Bit frustrating that Spack can barely self-bootstrap :)
> Bit frustrating that Spack can barely self-bootstrap :)

Yes, it's frustrating to support Python 3.6 and Python 3.12 together. But bootstrapping started failing on a single case over eleven tested, so "can barely self-bootstrap" seems a bit too much :wink: 

Resolving patch:
diff --git a/lib/spack/spack/bootstrap/core.py b/lib/spack/spack/bootstrap/core.py
--- a/lib/spack/spack/bootstrap/core.py
+++ b/lib/spack/spack/bootstrap/core.py
@@ -291,6 +291,10 @@ def try_import(self, module: str, abstract_spec_str: str) -> bool:
         with spack_python_interpreter():
             # Add hint to use frontend operating system on Cray
             concrete_spec = spack.spec.Spec(abstract_spec_str + " ^" + spec_for_current_python())
+            # This is needed to help the old concretizer taking the `setuptools` dependency
+            # only when bootstrapping from sources on Python 3.12
+            if spec_for_current_python() == "python@3.12":
+                concrete_spec.constrain("+force_setuptools")
 
             if module == "clingo":
                 # TODO: remove when the old concretizer is deprecated  # pylint: disable=fixme
diff --git a/var/spack/repos/builtin/packages/clingo-bootstrap/package.py b/var/spack/repos/builtin/packages/clingo-bootstrap/package.py
--- a/var/spack/repos/builtin/packages/clingo-bootstrap/package.py
+++ b/var/spack/repos/builtin/packages/clingo-bootstrap/package.py
@@ -32,6 +32,13 @@ class ClingoBootstrap(Clingo):
         description="Enable a series of Spack-specific optimizations (PGO, LTO, mimalloc)",
     )
 
+    variant(
+        "force_setuptools",
+        default=False,
+        description="Force a dependency on setuptools to help the old concretizer",
+    )
+    depends_on("py-setuptools", type="build", when="+force_setuptools")
+
     # Enable LTO
     conflicts("~ipo", when="+optimized")
 


Test patch:
Repository: spack/spack

Issue:
Installation issue: py-torch
### Steps to reproduce the issue

Hello, I have a build error with `py-torch` since [this commit](https://github.com/spack/spack/commit/bb64b22066d359ace40c944cc42ab5ff34bf8c7e). `py-torch:2.1.0` was building fine on my laptop before that commit.

```console
$ spack spec -I py-torch@2.1 ~gloo ~fbgemm ~kineto +distributed
```
@adamjstewart 

### Error message

```
/home/tbouvier/Dev/spack-envs/local/.spack-env/view/bin/ld: /home/tbouvier/Dev/spack/opt/spack/linux-fedora38-skylake/gcc-13.1.1/sleef-3.5.1_2020-12-22-jm5alvqtwrfed6lcx7ct4ekzw4ewptjs/lib64/libsleef.a(dispavx.c.o): relocation R_X86_64_32 against symbol `Sleef_fmad4_fma4' can not be used when making a shared object; recompile with -fPIC
```

<details><summary>Error message</summary>

<pre>
  [5366/5504] Linking CXX shared library lib/libtorch_cpu.so
  FAILED: lib/libtorch_cpu.so

  /home/tbouvier/Dev/spack-envs/local/.spack-env/view/bin/ld: /home/tbouvier/Dev/spack/opt/spack/linux-fedora38-skylake/gcc-13.1.1/sleef-3.5.1_2020-12-22-jm5alvqtwrfed6lcx7ct4ekzw4ewptjs/lib64/libsleef.a(dispavx.c.o): relocation R_X86_64_32 against symbol `Sleef_fmad4_fma4' can not be used when making a shared object; recompile with -fPIC
  /home/tbouvier/Dev/spack-envs/local/.spack-env/view/bin/ld: failed to set dynamic section sizes: bad value
  collect2: error: ld returned 1 exit status
</pre></details>


### Information on your system

* **Spack:** 0.21.0.dev0 (668a5b45e5ca5b5c16ea042d0121c5a958564089)
* **Python:** 3.11.6
* **Platform:** linux-fedora38-skylake
* **Concretizer:** clingo


### Additional information

[spack-build-env.txt](https://github.com/spack/spack/files/13256493/spack-build-env.txt)
[spack-build-out.txt](https://github.com/spack/spack/files/13256494/spack-build-out.txt)


### General information

- [X] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [X] I have run `spack maintainers <name-of-the-package>` and **@mentioned** any maintainers
- [X] I have uploaded the build log and environment files
- [X] I have searched the issues of this repo and believe this is not a duplicate


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/sleef/package.py b/var/spack/repos/builtin/packages/sleef/package.py
--- a/var/spack/repos/builtin/packages/sleef/package.py
+++ b/var/spack/repos/builtin/packages/sleef/package.py
@@ -53,10 +53,9 @@ class Sleef(CMakePackage):
     # conflicts("^mpfr@4.2:")
 
     def cmake_args(self):
-        # Taken from PyTorch's aten/src/ATen/CMakeLists.txt
+        # https://salsa.debian.org/science-team/sleef/-/blob/master/debian/rules
         return [
-            self.define("BUILD_SHARED_LIBS", False),
             self.define("BUILD_DFT", False),
-            self.define("BUILD_GNUABI_LIBS", False),
+            self.define("SLEEF_TEST_ALL_IUT", True),
             self.define("BUILD_TESTS", False),
         ]


Test patch:
Repository: spack/spack

Issue:
checksum mismatch for py-metomi-isodatetime@3.1.0
### Steps to reproduce

When I added py-metomi-isodatetime@3.1.0, I originally had `git` configured and not `pypi` and I got the checksum this way. When I merged my updates into spack develop, I found that @LydDeb already added the packages (and used `pypi`). I found today that the `pypi` version parser is unable to replace the version in
```
    pypi = "metomi-isodatetime/metomi-isodatetime-1!3.0.0.tar.gz"
```
and therefore installation of `3.1.0` fails with:
```
==> Error: Terminating after first install failure: ChecksumError: sha256 checksum failed for /Users/heinzell/work/spack-stack/spack-stack-cylc8/cache/build_stage/spack-stage-py-metomi-isodatetime-3.1.0-cia6vnosk5f62gxiih6sanmdtsjwpoj6/metomi-isodatetime-1!3.0.0.tar.gz
```
One can verify this by running:
```
> spack checksum py-metomi-isodatetime@3.1.0
==> Error: Couldn't detect version in: https://files.pythonhosted.org/packages/source/m/metomi-isodatetime/metomi-isodatetime-1!3.0.0.tar.gz
```

@adamjstewart Do you know how to fix this? Can the url_for_version logic be applied to the pypi? I tried `url_for_version` but that of course didn't work. Thanks!

### Error message

See above

### Information on your system

```
* **Spack:** 0.21.0 (87e53319cfb7940c8687583b304bee1cf035e6a8)
* **Python:** 3.8.9
* **Platform:** darwin-monterey-m1
* **Concretizer:** clingo
```

### General information

- [X] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [X] I have searched the issues of this repo and believe this is not a duplicate
- [X] I have run the failing commands in debug mode and reported the output


Discussion:

Resolving patch:
diff --git a/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py b/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
--- a/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
+++ b/var/spack/repos/builtin/packages/py-metomi-isodatetime/package.py
@@ -10,6 +10,7 @@ class PyMetomiIsodatetime(PythonPackage):
     """Python ISO 8601 date time parser and data model/manipulation utilities."""
 
     homepage = "https://github.com/metomi/isodatetime"
+    # NOTE: spack checksum does not yet work for epoch versions
     pypi = "metomi-isodatetime/metomi-isodatetime-1!3.0.0.tar.gz"
 
     maintainers("LydDeb")
@@ -18,3 +19,6 @@ class PyMetomiIsodatetime(PythonPackage):
     version("3.0.0", sha256="2141e8aaa526ea7f7f1cb883e6c8ed83ffdab73269658d84d0624f63a6e1357e")
 
     depends_on("py-setuptools", type="build")
+
+    def url_for_version(self, version):
+        return f"https://files.pythonhosted.org/packages/source/m/metomi-isodatetime/metomi-isodatetime-1!{version}.tar.gz"


Test patch:
Repository: spack/spack

Issue:
Installation issue: tcl with <= gcc@11
### Steps to reproduce

I started the most up to date version of spack, 05-12-2023, and had a glitch when trying to compile `tcl`:

    spack install -v tcl@8.6.11
    
it appears to be as a result of the addition of this edit [40946](https://github.com/spack/spack/pull/40946)

    filter_compiler_wrappers("tclConfig.sh", relative_root="lib")
    
I think the error is related to the `filter_compile_wrappers function` trying to replace a line containing `gcc` and `g++`, however the file in question, `tclConfig.sh` only has one line containing `gcc`, no `g++`:

    # C compiler to use for compilation.
    TCL_CC='/mnt/sda/cadtools/spack_git/lib/spack/env/gcc/gcc'


My base system, ubuntu22.04, has `gcc@11.4.0` as its default. I have stripped this back to a clean checkout of spack and go straight into a compile of `tcl`.

If I compile and instead use `gcc@12.3.` it do not get the error, the installation is successful. Also if I comment out that one line from the `tcl/package.py` file, the installation is successful using `gcc@11.4.0`.

### Error message

```
==> [2023-12-05-10:43:44.657378] Find complete: /mnt/sda/cadtools/spack_install/opt/linux-ubuntu22.04-skylake/gcc-11.4.0/tcl/8.6.11-yvwju3kstvxvughqov6ommkuxr7mzrpm/lib ('tclConfig.sh',)
==> [2023-12-05-10:43:44.658905] FILTER FILE: /mnt/sda/cadtools/spack_install/opt/linux-ubuntu22.04-skylake/gcc-11.4.0/tcl/8.6.11-yvwju3kstvxvughqov6ommkuxr7mzrpm/lib/tclConfig.sh [replacing "/mnt/sda/cadtools/spack_git/lib/spack/env/gcc/gcc"]
==> [2023-12-05-10:43:44.659794] FILTER FILE: /mnt/sda/cadtools/spack_install/opt/linux-ubuntu22.04-skylake/gcc-11.4.0/tcl/8.6.11-yvwju3kstvxvughqov6ommkuxr7mzrpm/lib/tclConfig.sh [replacing "/mnt/sda/cadtools/spack_git/lib/spack/env/gcc/g\+\+"]
==> Error: AttributeError: 'NoneType' object has no attribute 'replace'
```

### Information on your system

* **Spack:** 0.22.0.dev0 (798770f9e54bfd3cb1a52af4a9bd2937f826018e)
* **Python:** 3.11.6
* **Platform:** linux-ubuntu22.04-skylake
* **Concretizer:** clingo


### General information

- [X] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [X] I have searched the issues of this repo and believe this is not a duplicate
- [X] I have run the failing commands in debug mode and reported the output


Discussion:

Resolving patch:
diff --git a/lib/spack/spack/mixins.py b/lib/spack/spack/mixins.py
--- a/lib/spack/spack/mixins.py
+++ b/lib/spack/spack/mixins.py
@@ -93,7 +93,7 @@ def _filter_compiler_wrappers_impl(pkg_or_builder):
         replacements = []
 
         for idx, (env_var, compiler_path) in enumerate(compiler_vars):
-            if env_var in os.environ:
+            if env_var in os.environ and compiler_path is not None:
                 # filter spack wrapper and links to spack wrapper in case
                 # build system runs realpath
                 wrapper = os.environ[env_var]


Test patch:
Repository: spack/spack

Issue:
spack -h does not show extension commands
### Steps to reproduce


add an extension with commands to `spack:extensions` and run

```console
spack -h
```

the extensions commands will not show, even if they have `level = "short"` defined.

They will display if you run `spack help --all`.

### Error message

No error message,  extension commands do not display in help message.

### Information on your system

* **Spack:** 0.20.1 (2df338660c37158945c8c94c9fe7e42ed3d68e58)
* **Python:** 3.10.8
* **Platform:** darwin-monterey-m1
* **Concretizer:** clingo


### General information

- [X] I have run `spack debug report` and reported the version of Spack/Python/Platform
- [X] I have searched the issues of this repo and believe this is not a duplicate
- [X] I have run the failing commands in debug mode and reported the output


Discussion:

Resolving patch:
diff --git a/lib/spack/spack/main.py b/lib/spack/spack/main.py
--- a/lib/spack/spack/main.py
+++ b/lib/spack/spack/main.py
@@ -950,14 +950,10 @@ def _main(argv=None):
         parser.print_help()
         return 1
 
-    # -h, -H, and -V are special as they do not require a command, but
-    # all the other options do nothing without a command.
+    # version is special as it does not require a command or loading and additional infrastructure
     if args.version:
         print(get_version())
         return 0
-    elif args.help:
-        sys.stdout.write(parser.format_help(level=args.help))
-        return 0
 
     # ------------------------------------------------------------------------
     # This part of the `main()` sets up Spack's configuration.
@@ -996,6 +992,12 @@ def _main(argv=None):
         print_setup_info(*args.print_shell_vars.split(","))
         return 0
 
+    # -h and -H are special as they do not require a command, but
+    # all the other options do nothing without a command.
+    if args.help:
+        sys.stdout.write(parser.format_help(level=args.help))
+        return 0
+
     # At this point we've considered all the options to spack itself, so we
     # need a command or we're done.
     if not args.command:


Test patch: