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

Issue:
Documentation doesn't list environment variables available for configuration
### Issue description

The [Configuration With Environment Variables section of the documentation page Advanced Usage of Pipenv](https://pipenv.pypa.io/en/latest/advanced/#configuration-with-environment-variables) doesn't appear to list all the available environment variables

### Expected result

I expect variables such as `PIPENV_SPINNER` to be documented.

### Actual result

Only `PIPENV_HIDE_EMOJIS` is documented, along with some functions.

### Steps to replicate

n/a

-------------------------------------------------------------------------------

Please run `$ pipenv --support`, and paste the results here. Don't put backticks (`` ` ``) around it! The output already contains Markdown formatting.

n/a


Discussion:
Yes, that is true. We currently could use help here.
I can definitely fix this issue, assign it to me 
> I can definitely fix this issue, assign it to me

Guys I have submitted the pull request, everything is crisp and clear all system environment are listed

Resolving patch:
diff --git a/pipenv/core.py b/pipenv/core.py
--- a/pipenv/core.py
+++ b/pipenv/core.py
@@ -146,7 +146,8 @@ def load_dot_env(project, as_dict=False, quiet=False):
                     err=True,
                 )
             dotenv.load_dotenv(dotenv_file, override=True)
-        project.s.initialize()
+
+            project.s = environments.Setting()
 
 
 def cleanup_virtualenv(project, bare=True):
diff --git a/pipenv/environments.py b/pipenv/environments.py
--- a/pipenv/environments.py
+++ b/pipenv/environments.py
@@ -107,19 +107,20 @@ def normalize_pipfile_path(p):
 
 
 class Setting:
+    """
+    Control various settings of pipenv via environment variables.
+    """
+
     def __init__(self) -> None:
-        self.USING_DEFAULT_PYTHON = True
-        self.initialize()
 
-    def initialize(self):
+        self.USING_DEFAULT_PYTHON = True
+        """Use the default Python"""
 
+        #: Location for Pipenv to store it's package cache.
+        #: Default is to use appdir's user cache directory.
         self.PIPENV_CACHE_DIR = os.environ.get(
             "PIPENV_CACHE_DIR", user_cache_dir("pipenv")
         )
-        """Location for Pipenv to store it's package cache.
-
-        Default is to use appdir's user cache directory.
-        """
 
         # Tells Pipenv which Python to default to, when none is provided.
         self.PIPENV_DEFAULT_PYTHON_VERSION = os.environ.get(


Test patch:
Repository: pypa/pipenv

Issue:
How can i pin some (or all) packages from --site-packages to not beeing overwritten in user env
use case:

+ install a specific hardware version of a python package from source, eg. 
   + https://aur.archlinux.org/packages/python-jax-rocm
   + this package has wheels for hardware support of amd rocm gpus.

+ make a new environment with pipenv, and parse requirements from other sources into it
+ other sources may depend on a different version of jax, but may work on the system compiled

question:

+ how can i assure that the --site-packages version of jax is used in dependency resolution ?

Currently i try to pin it in Pipfile by using jax="=3.6.1" by looking at the current system version, and hope pipenv does not overwrite it.

Is there another way to pin system packages in an pipenv environment ?



Discussion:

Resolving patch:
diff --git a/pipenv/core.py b/pipenv/core.py
--- a/pipenv/core.py
+++ b/pipenv/core.py
@@ -1529,7 +1529,6 @@ def pip_install(
         project_python(project, system=allow_global),
         _get_runnable_pip(),
         "install",
-        "--ignore-installed",
     ]
     pip_args = get_pip_args(
         project,
diff --git a/pipenv/patched/pip/__main__.py b/pipenv/patched/pip/__main__.py
--- a/pipenv/patched/pip/__main__.py
+++ b/pipenv/patched/pip/__main__.py
@@ -26,7 +26,13 @@
     warnings.filterwarnings(
         "ignore", category=DeprecationWarning, module=".*packaging\\.version"
     )
-    sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(__file__)))))
+    import importlib.util
+    import sys
+    spec = importlib.util.spec_from_file_location(
+        "pipenv", location=os.path.join(os.path.dirname(os.path.dirname(os.path.dirname(__file__))), "__init__.py"))
+    pipenv = importlib.util.module_from_spec(spec)
+    sys.modules["pipenv"] = pipenv
+    spec.loader.exec_module(pipenv)
     from pipenv.patched.pip._internal.cli.main import main as _main
 
     sys.exit(_main())


Test patch:
Repository: pypa/pipenv

Issue:
Include missing package data for Safety
### The issue

#5491 

### The fix

Include the missing package data for Safety.

### The checklist

* [ ] Build wheels and test if it is working fine.

<!--
### If this is a patch to the `vendor` directory...

Please try to refrain from submitting patches directly to `vendor` or `patched`, but raise your issue to the upstream project instead, and inform Pipenv to upgrade when the upstream project accepts the fix.

A pull request to upgrade vendor packages is strongly discouraged, unless there is a very good reason (e.g. you need to test Pipenv’s integration to a new vendor feature). Pipenv audits and performs vendor upgrades regularly, generally before a new release is about to drop.

If your patch is not or cannot be accepted by upstream, but is essential to Pipenv (make sure to discuss this with maintainers!), please remember to attach a patch file in `tasks/vendoring/patched`, so this divergence from upstream can be recorded and replayed afterwards.
-->



Discussion:

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -67,6 +67,7 @@
             "w32.exe",
             "w64.exe",
         ],
+        "pipenv.vendor.ruamel": ["yaml"],
     },
     python_requires=">=3.7",
     zip_safe=True,


Test patch:
Repository: pypa/pipenv

Issue:
Pipenv does not sync indexes to lockfile
### Issue description

When specifying an addtitional index as described [here](https://github.com/pypa/pipenv/blob/main/docs/advanced.rst), `pipenv install` does not synchronize the additional index to the lockfile, resulting in the following error:
```
...
Installing dependencies from Pipfile.lock (4204ea)...
Traceback (most recent call last):
  File "c:\python\lib\runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\python\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
...
    install_source = next(filter(lambda s: s["name"] == index_name, sources))
StopIteration
```

System:
OS: Windows Server 2019
Python: 3.9.1
Pipenv: 2022.11.25

When updating Pipfile.lock manually, everything works as expected.

### Expected result

Pipfile.lock:
```
...
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.org/simple",
                "verify_ssl": true
            },
            {
                "name": "pytorch",
                "url": "https://download.pytorch.org/whl/cu116",
                "verify_ssl": false
            }
        ]
...
```

### Actual result

Pipfile.lock:
```
...
        "sources": [
            {
                "name": "pypi",
                "url": "https://pypi.org/simple",
                "verify_ssl": true
            }
        ]
...
```

### Steps to replicate

Minimal Pipfile:
```
[[source]]
url = "https://pypi.org/simple"
verify_ssl = true
name = "pypi"

[[source]]
url = "https://download.pytorch.org/whl/cu116"
verify_ssl = false
name = "pytorch"

[packages]
torch = {version = "*", index = "pytorch"}

[dev-packages]

[requires]
python_version = "3.9"
python_full_version = "3.9.1"

```

-------------------------------------------------------------------------------

Unfortunately I cannot provide `pipenv --support` from my work PC.


Discussion:

Resolving patch:
diff --git a/pipenv/project.py b/pipenv/project.py
--- a/pipenv/project.py
+++ b/pipenv/project.py
@@ -759,13 +759,7 @@ def get_or_create_lockfile(self, categories, from_pipfile=False):
     def get_lockfile_meta(self):
         from .vendor.plette.lockfiles import PIPFILE_SPEC_CURRENT
 
-        if self.lockfile_exists:
-            sources = (
-                self.load_lockfile(expand_env_vars=False)
-                .get("_meta", {})
-                .get("sources", [])
-            )
-        elif "source" in self.parsed_pipfile:
+        if "source" in self.parsed_pipfile:
             sources = [dict(source) for source in self.parsed_pipfile["source"]]
         else:
             sources = self.pipfile_sources(expand_vars=False)


Test patch:
Repository: pypa/pipenv

Issue:
Private repo in pipfile not working
I'm trying to install a package from a private repo, using version [2020.11.15] it worked a long time, with the current version 2022.12.17 not anymore.

Example:

```
[packages] 
pack1 = {editable = true, git = "https://myToken@github.com/.../pack1"}
```
It looks forever:

`Locking [packages] dependencies...
`


Discussion:
I think this is related:  https://github.com/sarugaku/requirementslib/issues/353

Resolving patch:
diff --git a/pipenv/vendor/requirementslib/__init__.py b/pipenv/vendor/requirementslib/__init__.py
--- a/pipenv/vendor/requirementslib/__init__.py
+++ b/pipenv/vendor/requirementslib/__init__.py
@@ -5,7 +5,7 @@
 from .models.pipfile import Pipfile
 from .models.requirements import Requirement
 
-__version__ = "2.2.1"
+__version__ = "2.2.2"
 
 
 logger = logging.getLogger(__name__)
diff --git a/pipenv/vendor/requirementslib/models/setup_info.py b/pipenv/vendor/requirementslib/models/setup_info.py
--- a/pipenv/vendor/requirementslib/models/setup_info.py
+++ b/pipenv/vendor/requirementslib/models/setup_info.py
@@ -94,8 +94,7 @@ def pep517_subprocess_runner(cmd, cwd=None, extra_environ=None):
     if extra_environ:
         env.update(extra_environ)
 
-    cmd_as_str = " ".join(cmd)
-    sp.run(cmd_as_str, cwd=cwd, env=env, stdout=sp.PIPE, stderr=sp.STDOUT, shell=True)
+    sp.run(cmd, cwd=cwd, env=env, stdout=sp.PIPE, stderr=sp.STDOUT)
 
 
 class BuildEnv(envbuild.BuildEnvironment):
@@ -110,7 +109,7 @@ def pip_install(self, reqs):
             self.path,
         ] + list(reqs)
 
-        sp.run(cmd, shell=True, stderr=sp.PIPE, stdout=sp.PIPE)
+        sp.run(cmd, stderr=sp.PIPE, stdout=sp.PIPE)
 
 
 class HookCaller(wrappers.Pep517HookCaller):


Test patch:
Repository: pypa/pipenv

Issue:
`--keep-outdated` deprecation text is missing spaces
Be sure to check the existing issues (both open and closed!), and make sure you are running the latest version of Pipenv.

Check the [diagnose documentation](https://pipenv.pypa.io/en/latest/diagnose/) for common issues before posting! We may close your issue if it is very similar to one of them. Please be considerate, or be on your way.

Make sure to mention your debugging experience if the documented solution failed.


### Issue description

The text displayed when using the `--keep-outdated` flag is missing a space.

This was observed while reviewing [a failed workflow in the `actions/setup-python` repo](https://github.com/actions/setup-python/actions/runs/4165220806/jobs/7221316524#step:5:17):

```text
The flag --keep-outdated has been deprecated for removal.The flag [...]
                                                 ^^^^^^^^^^^
```

This occurs due to missing spaces in `pipenv/cli/options.py`:

https://github.com/pypa/pipenv/blob/ebdf1ff8de76a2884d4698d81193630602c3cdca/pipenv/cli/options.py#L159-L161

I'll submit a patch shortly.


Discussion:
@kurtmckee I think I may have covered this in this PR:  https://github.com/pypa/pipenv/pull/5617/files#diff-f303741aa3a324b79c0fca4837cc712dc7379fd76479ceb3b71caacc92a8f562L162

Resolving patch:
diff --git a/pipenv/cli/options.py b/pipenv/cli/options.py
--- a/pipenv/cli/options.py
+++ b/pipenv/cli/options.py
@@ -157,7 +157,7 @@ def callback(ctx, param, value):
         state.installstate.keep_outdated = value
         if value:
             click.secho(
-                "The flag --keep-outdated has been deprecated for removal."
+                "The flag --keep-outdated has been deprecated for removal.  "
                 "The flag does not respect package resolver results and leads to inconsistent lock files.  "
                 "Please pin relevant requirements in your Pipfile and discontinue use of this flag.",
                 fg="yellow",


Test patch:
Repository: pypa/pipenv

Issue:
pipenv update --outdated became noisy
### Issue description

`pipenv update --outdated` writes extensive INFO logs to console.
Flags `--bare` and `--quiet` do not change this.
The new behaviour began in release 2023.8.19 and persists at least through release 2023.8.22.

### Expected result

Console output _without added flags_; possibly less with `--bare` or `--quiet`:

```
Running $ pipenv lock then $ pipenv sync.
Building requirements...
Resolving dependencies...
✔ Success!
Building requirements...
Resolving dependencies...
✔ Success!
Building requirements...
Resolving dependencies...
✔ Success!
Building requirements...
Resolving dependencies...
✔ Success!
All packages are up to date!

```

### Actual result

More than 120k of log output to the console:
[pipenv.log.txt](https://github.com/pypa/pipenv/files/12408204/pipenv.log.txt)

### Steps to replicate

Any one of

`pipenv update --outdated`
`pipenv --bare update --outdated`
`pipenv --quiet update --outdated`

-------------------------------------------------------------------------------

[pipenv.support.txt](https://github.com/pypa/pipenv/files/12408219/pipenv.support.txt)



Discussion:
To add to this, even with `PIPENV_QUIET=true` or `--quiet` the command is still noisy, filled with `INFO:pipenv.patched.pip...` messages.
We'll want to figure out how to make those flags reduce the output, without breaking verbose again.   The line I removed that caused this was just globally silencing the pip logging which was leading to a lot of reports where folks could not debug why their lock phases were failing.

Resolving patch:
diff --git a/pipenv/resolver.py b/pipenv/resolver.py
--- a/pipenv/resolver.py
+++ b/pipenv/resolver.py
@@ -1,5 +1,6 @@
 import importlib.util
 import json
+import logging
 import os
 import sys
 
@@ -654,6 +655,9 @@ def main(argv=None):
     os.environ["PYTHONIOENCODING"] = "utf-8"
     os.environ["PYTHONUNBUFFERED"] = "1"
     parsed = handle_parsed_args(parsed)
+    if not parsed.verbose:
+        print(parsed.verbose)
+        logging.getLogger("pipenv").setLevel(logging.WARN)
     _main(
         parsed.pre,
         parsed.clear,


Test patch:
Repository: pypa/pipenv

Issue:
documentation is a mix of markdown and restructuredtext
### Issue description

documentation is a mix of markdown and restructuredtext, but the [documentation says the documentation is restructuredtext](https://pipenv.pypa.io/en/latest/dev/contributing/#documentation-contributions). I found out commit 761a03d seemingly did a conversion to markdown which did not go all the way to the end.
I would like to know what is the pursued direction (markdown + restructuredtext or full markdown), and if the direction is full markdown, try to help.

### Expected result

* either the documentation says the documentation is both markdown and restructuredtext
* either we clean out one of them (restructuredtext, I guess)

### Actual result

mix of both

### Steps to replicate

N/A


Discussion:
@deronnax Full markdown would be preferred I think; I ran out of time when I was working on that before.   Any help is appreciated.
Hey @deronnax, @matteius , I am new in open source community, if possible, could I be assigned to this task? Just to be clear, if I be assigned, once I start making the contribution, I convert to fully *md* or fully *rst*?
@thiagogquinto I believe @deronnax is offering to help with this, but either way -- the plan is to go fully markdown.  (so .md)
Ok @matteius, thanks for the reply! I will let him work on it then. Will just ask @deronnax that in case he changes of mind, let me know, please.
@thiagogquinto I have not started the work, so you can take it :)
Thanks, I will work on it then.
Hey @matteius, could you help me with the following question: do you know what this reference points to?

```console
No, it does not, intentionally. Pipfile and setup.py serve different purposes,
and should not consider each other by default. See :ref:`pipfile-vs-setuppy`
for more information.
```
The file is [here](https://github.com/thiagogquinto/pipenv/blob/main/docs/diagnose.rst), the line in question is on the line 102 of the file.

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -72,8 +72,8 @@
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
-# source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+source_suffix = [".rst", ".md"]
+# source_suffix = ".rst"
 
 # The master toctree document.
 master_doc = "index"


Test patch:
diff --git a/tests/fixtures/fake-package/README.md b/tests/fixtures/fake-package/README.md
new file mode 100644
--- /dev/null
+++ b/tests/fixtures/fake-package/README.md
@@ -0,0 +1 @@
+# fake_package: A fake python package.
diff --git a/tests/fixtures/fake-package/README.rst b/tests/fixtures/fake-package/README.rst
deleted file mode 100644
--- a/tests/fixtures/fake-package/README.rst
+++ /dev/null
@@ -1,3 +0,0 @@
-===============================================================================
-fake_package: A fake python package.
-===============================================================================
Repository: pypa/pipenv

Issue:
[bug] virtualenv creation pollute script outputs
### Issue description

I have a shell command that gets me a token, defined in my scripts as `get-token`.  I rely on the output of this command to populate an env var `export MY_TOKEN=$(pipenv run get-token)` in automated workflows. If the virtualenv is not created, I will get new print statements as of Release v2023.12.0 that match the python version in my pipfile. This is breaking my workflows.

Here is a toy example
```
# in Pipfile
[scripts]
get-token="echo 'some_token_value'"

[requires]
python_version = "3.11"
```

When the virtualenv is created
```bash
> export MY_TOKEN=$(pipenv run get-token)
> echo $MY_TOKEN
some_token_value
```

When the virtualenv is not created, it outputs "3.11" twice before outputting the token value.
```bash
> pipenv --rm
> export MY_TOKEN=$(pipenv run get-token)
> echo $MY_TOKEN
3.11
3.11
some_token_value
```



Discussion:
Browsing the diff for the latest version, I see two culprints
https://github.com/pypa/pipenv/blob/v2023.12.0/pipenv/utils/shell.py#L240
https://github.com/pypa/pipenv/blob/v2023.12.0/pipenv/utils/virtualenv.py#L356


Resolving patch:
diff --git a/pipenv/utils/shell.py b/pipenv/utils/shell.py
--- a/pipenv/utils/shell.py
+++ b/pipenv/utils/shell.py
@@ -237,7 +237,6 @@ def find_python(finder, line=None):
     :return: A path to python
     :rtype: str
     """
-    print(line)
     if line and not isinstance(line, str):
         raise TypeError(f"Invalid python search type: expected string, received {line!r}")
     if line:
diff --git a/pipenv/utils/virtualenv.py b/pipenv/utils/virtualenv.py
--- a/pipenv/utils/virtualenv.py
+++ b/pipenv/utils/virtualenv.py
@@ -353,7 +353,6 @@ def find_a_system_python(line):
     # Use the windows finder executable
     if (line.startswith(("py ", "py.exe "))) and os.name == "nt":
         line = line.split(" ", 1)[1].lstrip("-")
-    print(line)
     python_entry = find_python(finder, line)
     return python_entry
 


Test patch:
Repository: django-crispy-forms/django-crispy-forms

Issue:
Update PyPI uploads
Releasing v.1.5.0 I ran the customary `python setup.py sdist upload` — no problem. 

I then went for `python setup.py bdist_wheel upload` and got errors: 

```
Submitting dist/django-crispy-forms-1.5.0.tar.gz to http://pypi.python.org/pypi
Server response (200): OK
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
   or: setup.py --help [cmd1 cmd2 ...]
   or: setup.py --help-commands
   or: setup.py cmd --help

error: invalid command 'bdist_wheel'
```
1. This normally works. Why not here? 
2. OK... but we may as well review the best practices here whilst we've got the lid off. 

Following input from @kevin-brown:
- [ ] Add development requirements. 



Discussion:
> error: invalid command 'bdist_wheel'

Do you have the `wheel` package installed locally?

It might be useful to have a requirements file that includes it (along with any other development packages).

@kevin-brown — Thanks for the input here! (I've had this going fine for Django Filter and was a little bemused by the error)

> Do you have the wheel package installed locally?

Not in the virtualenv. And looking at my DF setup, of course, there it is: 

```
~ $ workon django-filter
(django-filter)~/Documents/Django-Stack/django-filter (master)$ pip freeze | grep wheel
wheel==0.24.0
```

> It might be useful to have a requirements file that includes it (along with any other development packages).

Absolutely. :-)

I guess I just install and retry that now. 

Right. And that worked. Thanks @kevin-brown! 

Looking at [DRF's setup.py](https://github.com/tomchristie/django-rest-framework/blob/master/setup.py#L54), do you happened to know what the `twine` bit is all about? (Ta!)


Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,5 @@
+import os
+import sys
 import crispy_forms
 
 from setuptools import setup, find_packages
@@ -7,6 +9,20 @@
     'Django',
 ]
 
+if sys.argv[-1] == 'publish':
+    if os.system("pip freeze | grep wheel"):
+        print("wheel not installed.\nUse `pip install wheel`.\nExiting.")
+        sys.exit()
+    if os.system("pip freeze | grep twine"):
+        print("twine not installed.\nUse `pip install twine`.\nExiting.")
+        sys.exit()
+    os.system("python setup.py sdist bdist_wheel")
+    os.system("twine upload dist/*")
+    print("You probably want to also tag the version now:")
+    print("  git tag -a %s -m 'version %s'" % (crispy_forms.__version__, crispy_forms.__version__))
+    print("  git push --tags")
+    sys.exit()
+
 setup(
     name='django-crispy-forms',
     version=crispy_forms.__version__,
@@ -22,6 +38,7 @@
         "Programming Language :: Python :: 2.6",
         "Programming Language :: Python :: 2.7",
         "Programming Language :: Python :: 3.3",
+        "Programming Language :: Python :: 3.4",
         "Topic :: Internet :: WWW/HTTP",
         "Topic :: Internet :: WWW/HTTP :: Dynamic Content",
         "Topic :: Software Development :: Libraries :: Python Modules",


Test patch:
Repository: django-crispy-forms/django-crispy-forms

Issue:
Remove `crispy_forms.base.from_iterable`
We no longer support Python 2.5



Discussion:

Resolving patch:
diff --git a/crispy_forms/base.py b/crispy_forms/base.py
--- a/crispy_forms/base.py
+++ b/crispy_forms/base.py
@@ -1,14 +1,3 @@
-def from_iterable(iterables):
-    """
-    Backport of `itertools.chain.from_iterable` compatible with Python 2.5
-    """
-    for it in iterables:
-        for element in it:
-            if isinstance(element, dict):
-                for key in element:
-                    yield key
-            else:
-                yield element
 
 
 class KeepContext(object):


Test patch: