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

Issue:
Unregister command not listed in help
## I ran this command and it produced this output:
The command `certbot --help` only lists the `register` and `update_account`
commands.

```
manage your account with Let's Encrypt:
    register        Create a Let's Encrypt ACME account
    update_account  Update a Let's Encrypt ACME account
  --agree-tos       Agree to the ACME server's Subscriber Agreement
   -m EMAIL         Email address for important account notifications
```

## Certbot's behavior differed from what I expected because:
The help command should list the `unregister` under manage account.

Additionally it is not completely clear from the `--help` output that a more complete help is available with `--help all`, which does list the `unregister`.


Discussion:
@bmw, do you think this omission in the help output was intentional or deliberate?
No I think this was a simple oversight. Thanks for noticing this @martijnjanssen.

Fixing this is as simple as adding a line to the string at https://github.com/certbot/certbot/blob/50607eb0ff4279f3395231f3c6f35586d21557f3/certbot/cli.py#L78.
I am taking this up if thats not a problem :) 
(I see no open pull regarding this)
(Also this is my first issue on certbot)

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -101,6 +101,7 @@
 
 manage your account with Let's Encrypt:
     register        Create a Let's Encrypt ACME account
+    unregister      Deactivate a Let's Encrypt ACME account
     update_account  Update a Let's Encrypt ACME account
   --agree-tos       Agree to the ACME server's Subscriber Agreement
    -m EMAIL         Email address for important account notifications
@@ -117,7 +118,7 @@
    all, automation, commands, paths, security, testing, or any of the
    subcommands or plugins (certonly, renew, install, register, nginx,
    apache, standalone, webroot, etc.)
-
+  -h all                print a detailed help page including all topics 
   --version             print the version number
 """
 


Test patch:
Repository: certbot/certbot

Issue:
Fix test_sdists.sh
https://github.com/certbot/certbot/blob/master/tests/letstest/scripts/test_sdists.sh is now broken on `master` on every system we test on in our test farm tests. Before #6932 landed, it worked, but afterwards it does not.

A snippet of the output from running the tests is:
```
certbot/tests/util_test.py .........................................................
certbot/tests/display/completer_test.py .....
certbot/tests/display/enhancements_test.py .....
certbot/tests/display/ops_test.py .........................................
certbot/tests/display/util_test.py ............................................

========================= 871 passed in 23.56 seconds ==========================
NameError: global name 'sys' is not defined
Please see the logfile '/tmp/tmpYaIPn2' for more details.
```

The last line about the logfile is from Certbot, but unfortunately the logfile doesn't exist after the process exits.

@adferrand, are you able to look into this? You can run the tests by cloning this repo into a directory named letsencrypt and then running the tests from just outside that directory (e.g. run `letsencrypt/tests/letstest/scripts/test_sdists.sh`).

Because this certainly needs be fixed before the next release, I'm not sure if we should land any more Windows security PRs until this is fixed. On the off chance we don't get this fixed in time, we'll need to revert #6932 and any PRs depending on it which will be every PR about Windows security. This includes some pretty massive changes and will generate a lot of conflicts with git so I'd personally rather see this resolved before trying to make more progress there.


Discussion:
Actually, I think I figured it out.

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -1,6 +1,7 @@
 import codecs
 import os
 import re
+import sys
 
 from setuptools import find_packages, setup
 from setuptools.command.test import test as TestCommand


Test patch:
Repository: certbot/certbot

Issue:
client.query_registration uses POST instead of POST as GET
[Here](https://github.com/certbot/certbot/blob/d7610c1ae73699cbac7d3433d8ff286d201ea018/acme/acme/client.py#L134) acme module uses empty UpdateRegistration message (POST with payload `{}`), instead of using standard POST as GET (POST with `null` content), resulting in some servers (`pebble` in strict mode) rejecting these requests.



Discussion:
Is it something you started to see with recent versions of Pebble? If so, do you know which one? 
It should be reproduce-able with Pebble 2.0.x and up.  https://github.com/letsencrypt/pebble/commit/fea30198d2ca1f74f558824c76510ae7ff70e439 is when Pebble's `wfe.UpdateAccount` function would have started to return an error for an empty account update.

Resolving patch:
diff --git a/acme/acme/client.py b/acme/acme/client.py
--- a/acme/acme/client.py
+++ b/acme/acme/client.py
@@ -123,15 +123,6 @@ def deactivate_registration(self, regr):
         """
         return self.update_registration(regr, update={'status': 'deactivated'})
 
-    def query_registration(self, regr):
-        """Query server about registration.
-
-        :param messages.RegistrationResource: Existing Registration
-            Resource.
-
-        """
-        return self._send_recv_regr(regr, messages.UpdateRegistration())
-
     def _authzr_from_response(self, response, identifier=None, uri=None):
         authzr = messages.AuthorizationResource(
             body=messages.Authorization.from_json(response.json()),
@@ -276,6 +267,15 @@ def register(self, new_reg=None):
         # pylint: disable=no-member
         return self._regr_from_response(response)
 
+    def query_registration(self, regr):
+        """Query server about registration.
+
+        :param messages.RegistrationResource: Existing Registration
+            Resource.
+
+        """
+        return self._send_recv_regr(regr, messages.UpdateRegistration())
+
     def agree_to_tos(self, regr):
         """Agree to the terms-of-service.
 
@@ -603,10 +603,13 @@ def query_registration(self, regr):
             Resource.
 
         """
-        self.net.account = regr
-        updated_regr = super(ClientV2, self).query_registration(regr)
-        self.net.account = updated_regr
-        return updated_regr
+        self.net.account = regr  # See certbot/certbot#6258
+        # ACME v2 requires to use a POST-as-GET request (POST an empty JWS) here.
+        # This is done by passing None instead of an empty UpdateRegistration to _post().
+        response = self._post(regr.uri, None)
+        self.net.account = self._regr_from_response(response, uri=regr.uri,
+                                                    terms_of_service=regr.terms_of_service)
+        return self.net.account
 
     def update_registration(self, regr, update=None):
         """Update registration.


Test patch:
Repository: certbot/certbot

Issue:
Fix "oldest" tests on point release branches
In https://github.com/certbot/certbot/pull/6921, we made a change to properly update `local-oldest-requirements.txt` for point release branches, but it broke the tests. See https://travis-ci.com/certbot/certbot/jobs/197027330.

Until now, we've never had the case in the "oldest" tests where the pinned version like `certbot==0.34.0` matches the local files. Before either an older, non-local version was pinned or it was something like `-e acme` which instructs pip to install the local package into the virtual environment.

When we go to install the package in the oldest tests in the 0.34.x branch, we ask for `certbot==0.34.0`, which is found to be already available in the current working directory so pip does nothing.

Then when we change directories to run tests to prevent local files from impacting tests (which has been a problem in the past), the local package that was found before is no longer there, can't be imported, and the tests fail.


Discussion:

Resolving patch:
diff --git a/tools/pip_install.py b/tools/pip_install.py
--- a/tools/pip_install.py
+++ b/tools/pip_install.py
@@ -99,8 +99,15 @@ def main(args):
         else:
             # Otherwise, we merge requirements to build the constraints and pin dependencies
             requirements = None
+            reinstall = False
             if os.environ.get('CERTBOT_OLDEST') == '1':
                 requirements = certbot_oldest_processing(tools_path, args, test_constraints)
+                # We need to --force-reinstall the tested distribution when using oldest
+                # requirements because of an error in these tests in particular situations
+                # described in https://github.com/certbot/certbot/issues/7014.
+                # However this slows down considerably the oldest tests (5 min -> 10 min),
+                # so we need to find a better mitigation in the future.
+                reinstall = True
             else:
                 certbot_normal_processing(tools_path, test_constraints)
 
@@ -109,8 +116,8 @@ def main(args):
                 pip_install_with_print('--constraint "{0}" --requirement "{1}"'
                                        .format(all_constraints, requirements))
 
-            pip_install_with_print('--constraint "{0}" {1}'
-                                   .format(all_constraints, ' '.join(args)))
+            pip_install_with_print('--constraint "{0}" {1} {2}'.format(
+                all_constraints, '--force-reinstall' if reinstall else '', ' '.join(args)))
     finally:
         if os.environ.get('TRAVIS'):
             print('travis_fold:end:install_certbot_deps')


Test patch:
Repository: certbot/certbot

Issue:
Remove the version cap of urllib3 on certbot-route53-dns when urllib 1.25+ is supported
PR #7081 added a cap on `urllib3` version to avoid 1.25 to be installed, as it is incompatible with latest version of `boto3` at the time of writting.

Once https://github.com/boto/botocore/issues/1733 is fixed, changes in #7081 can be reverted.


Discussion:

Resolving patch:
diff --git a/certbot-dns-route53/setup.py b/certbot-dns-route53/setup.py
--- a/certbot-dns-route53/setup.py
+++ b/certbot-dns-route53/setup.py
@@ -6,11 +6,6 @@
 # Remember to update local-oldest-requirements.txt when changing the minimum
 # acme/certbot version.
 install_requires = [
-    # boto3 requires urllib<1.25 while requests 2.22+ requires urllib<1.26
-    # Since pip lacks a real dependency graph resolver, it will peak the constraint only from
-    # requests, and install urllib==1.25.2. Setting an explicit dependency here solves the issue.
-    # Check https://github.com/boto/botocore/issues/1733 for resolution in botocore.
-    'urllib3<1.25',
     'acme>=0.29.0',
     'certbot>=0.34.0',
     'boto3',


Test patch:
Repository: certbot/certbot

Issue:
Add dependency on docker-compose to certbot-ci
It's written in Python and it not being installed regularly bites me. I often install it in my venv so I have a newer version available than that provided by the OS without making global changes to my system, but when I recreate the venv, I often forget.

I'm not sure what other devs setups look like, but making this change would make mine easier.

What do you think @adferrand?


Discussion:

Resolving patch:
diff --git a/certbot-ci/setup.py b/certbot-ci/setup.py
--- a/certbot-ci/setup.py
+++ b/certbot-ci/setup.py
@@ -10,6 +10,7 @@
 install_requires = [
     'coverage',
     'cryptography',
+    'docker-compose',
     'pyopenssl',
     'pytest',
     'pytest-cov',


Test patch:
diff --git a/certbot-ci/certbot_integration_tests/conftest.py b/certbot-ci/certbot_integration_tests/conftest.py
--- a/certbot-ci/certbot_integration_tests/conftest.py
+++ b/certbot-ci/certbot_integration_tests/conftest.py
@@ -6,6 +6,7 @@
 
 See https://docs.pytest.org/en/latest/reference.html#hook-reference
 """
+from __future__ import print_function
 import contextlib
 import subprocess
 import sys
Repository: certbot/certbot

Issue:
"manage your account" help is unnecessarily specific to Let's Encrypt
From the output of "certbot -h":

```
manage your account with Let's Encrypt:
    register        Create a Let's Encrypt ACME account
    unregister      Deactivate a Let's Encrypt ACME account
    update_account  Update a Let's Encrypt ACME account
  --agree-tos       Agree to the ACME server's Subscriber Agreement
   -m EMAIL         Email address for important account notifications
```

Since these subcommands translate to generic ACME protocol messages (rather than anything that's specific to Let's Encrypt's ACME server), please could this be changed to...

```
manage your account:
    register        Create an ACME account
    unregister      Deactivate an ACME account
    update_account  Update an ACME account
  --agree-tos       Agree to the ACME server's Subscriber Agreement
   -m EMAIL         Email address for important account notifications
```

?


Discussion:
Indeed, we should make the help more generic. Do not hesitate to submit a PR if you want !

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -96,10 +96,10 @@
     revoke          Revoke a certificate (supply --cert-path or --cert-name)
     delete          Delete a certificate
 
-manage your account with Let's Encrypt:
-    register        Create a Let's Encrypt ACME account
-    unregister      Deactivate a Let's Encrypt ACME account
-    update_account  Update a Let's Encrypt ACME account
+manage your account:
+    register        Create an ACME account
+    unregister      Deactivate an ACME account
+    update_account  Update an ACME account
   --agree-tos       Agree to the ACME server's Subscriber Agreement
    -m EMAIL         Email address for important account notifications
 """


Test patch:
Repository: certbot/certbot

Issue:
Verify permissions of conf root in Apache
There's a todo for this in `certbot-apache/certbot_apache/configurator.py` and some work was done in https://github.com/certbot/certbot/pull/5785 whose code was moved to https://github.com/certbot/certbot/tree/eicksl-verify-permissions.


Discussion:
To help us better see what issues are still affecting our users, this issue has been automatically marked as stale. If you still have this issue with an up-to-date version of Certbot and are interested in seeing it resolved, please add a comment letting us know. If there is no further activity, this issue will be automatically closed.


Resolving patch:
diff --git a/certbot-apache/certbot_apache/configurator.py b/certbot-apache/certbot_apache/configurator.py
--- a/certbot-apache/certbot_apache/configurator.py
+++ b/certbot-apache/certbot_apache/configurator.py
@@ -276,7 +276,10 @@ def prepare(self):
             util.lock_dir_until_exit(self.option("server_root"))
         except (OSError, errors.LockError):
             logger.debug("Encountered error:", exc_info=True)
-            raise errors.PluginError("Unable to lock {0}".format(self.option("server_root")))
+            raise errors.PluginError(
+                "Unable to create a lock file in {0}. Are you running"
+                " Certbot with sufficient privileges to modify your"
+                " Apache configuration?".format(self.option("server_root")))
         self._prepared = True
 
     def _verify_exe_availability(self, exe):


Test patch:
Repository: certbot/certbot

Issue:
topicless flags
Currently, the `add` method of the `HelpfulArgumentParser` includes the following phrase about the parameter `topic`: `can be None for "always documented"`. Despite this, flags with a topic of `None` are ONLY documented in `--help all` output. If the behavior is incorrect, it should be fixed. If the comment is incorrect, it should be updated to reflect the actual behavior of the client.



Discussion:
We've made a lot of changes to Certbot since this issue was opened. If you still have this issue with an up-to-date version of Certbot, can you please add a comment letting us know? This helps us to better see what issues are still affecting our users. If there is no further activity, this issue will be automatically closed.


Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -751,9 +751,10 @@ def add(self, topics, *args, **kwargs):
         """Add a new command line argument.
 
         :param topics: str or [str] help topic(s) this should be listed under,
-                       or None for "always documented". The first entry
-                       determines where the flag lives in the "--help all"
-                       output (None -> "optional arguments").
+                       or None for options that don't fit under a specific
+                       topic which will only be shown in "--help all" output.
+                       The first entry determines where the flag lives in the
+                       "--help all" output (None -> "optional arguments").
         :param list *args: the names of this argument flag
         :param dict **kwargs: various argparse settings for this argument
 


Test patch:
Repository: certbot/certbot

Issue:
Clarify that dns-cloudflare requires the global API key
Since the Cloudflare plugin was written, Cloudflare has added support for API tokens with permissions a (slightly) smaller scope. For more information about this see https://github.com/certbot/certbot/issues/7252.

As pointed out in that thread at https://github.com/certbot/certbot/issues/7252#issuecomment-515739140, our Cloudflare plugin isn't very clear which kind of credentials it requires. While #7252 remains unresolved, we require the global API key so we should update the docs and CLI output to clarify this.


Discussion:

Resolving patch:
diff --git a/certbot-dns-cloudflare/certbot_dns_cloudflare/__init__.py b/certbot-dns-cloudflare/certbot_dns_cloudflare/__init__.py
--- a/certbot-dns-cloudflare/certbot_dns_cloudflare/__init__.py
+++ b/certbot-dns-cloudflare/certbot_dns_cloudflare/__init__.py
@@ -22,7 +22,9 @@
 
 Use of this plugin requires a configuration file containing Cloudflare API
 credentials, obtained from your Cloudflare
-`account page <https://www.cloudflare.com/a/account/my-account>`_.
+`account page <https://www.cloudflare.com/a/account/my-account>`_. This plugin
+does not currently support Cloudflare's "API Tokens", so please ensure you use
+the "Global API Key" for authentication.
 
 .. code-block:: ini
    :name: credentials.ini


Test patch:
Repository: certbot/certbot

Issue:
Certbot's Apache plugin doesn't work on Scientific Linux
See https://community.letsencrypt.org/t/noinstallationerror-cannot-find-apache-executable-apache2ctl/97980.

This should be fixable by adding an override in https://github.com/certbot/certbot/blob/master/certbot-apache/certbot_apache/entrypoint.py#L17.


Discussion:

Resolving patch:
diff --git a/certbot-apache/certbot_apache/entrypoint.py b/certbot-apache/certbot_apache/entrypoint.py
--- a/certbot-apache/certbot_apache/entrypoint.py
+++ b/certbot-apache/certbot_apache/entrypoint.py
@@ -31,6 +31,8 @@
     "gentoo base system": override_gentoo.GentooConfigurator,
     "opensuse": override_suse.OpenSUSEConfigurator,
     "suse": override_suse.OpenSUSEConfigurator,
+    "scientific": override_centos.CentOSConfigurator,
+    "scientific linux": override_centos.CentOSConfigurator,
 }
 
 


Test patch:
Repository: certbot/certbot

Issue:
Warn about Python 3.4 deprecation
Once https://github.com/certbot/certbot/pull/7268 lands, we should warn about Certbot and its components deprecating Python 3.4 support. To do this we should:

1. Have `acme` use Python's warning system to register deprecation warnings.
2. Log warnings using the logging module in Certbot.

You can see how we did this for previous versions of Python in our git history.


Discussion:

Resolving patch:
diff --git a/acme/acme/__init__.py b/acme/acme/__init__.py
--- a/acme/acme/__init__.py
+++ b/acme/acme/__init__.py
@@ -48,3 +48,10 @@ def __delattr__(self, attr):  # pragma: no cover
 
     def __dir__(self):  # pragma: no cover
         return ['_module'] + dir(self._module)
+
+if sys.version_info[:2] == (3, 4):
+    warnings.warn(
+            "Python 3.4 support will be dropped in the next release of "
+            "acme. Please upgrade your Python version.",
+            PendingDeprecationWarning,
+    ) # pragma: no cover
diff --git a/certbot/main.py b/certbot/main.py
--- a/certbot/main.py
+++ b/certbot/main.py
@@ -1368,6 +1368,10 @@ def main(cli_args=None):
         if config.func != plugins_cmd:
             raise
 
+    if sys.version_info[:2] == (3, 4):
+        logger.warning("Python 3.4 support will be dropped in the next release "
+                    "of Certbot - please upgrade your Python version.")
+
     set_displayer(config)
 
     # Reporter


Test patch:
Repository: certbot/certbot

Issue:
Include missing directory field in error message
At https://community.letsencrypt.org/t/ubuntu-certbot-migration-for/110684/5, Osiris suggested that if we fail to find a field in a directory object, we should include the field we were looking for in the error message. I agree.

The value that should be included in the error message is the result of `self._canon_key(name)` as sometimes `name` is an ACME object rather than a string.


Discussion:

Resolving patch:
diff --git a/acme/acme/messages.py b/acme/acme/messages.py
--- a/acme/acme/messages.py
+++ b/acme/acme/messages.py
@@ -251,7 +251,7 @@ def __getitem__(self, name):
         try:
             return self._jobj[self._canon_key(name)]
         except KeyError:
-            raise KeyError('Directory field not found')
+            raise KeyError('Directory field "' + self._canon_key(name) + '" not found')
 
     def to_partial_json(self):
         return self._jobj


Test patch:
Repository: certbot/certbot

Issue:
Properly use collections.abc
Python 3.9 is planning on enforcing that abstract base classes in the collections module are imported from `collections.abc`. See https://docs.python.org/3/library/collections.html#module-collections.

We currently are not always doing this in Certbot and are ignoring the deprecation warning about it at https://github.com/certbot/certbot/blob/6e07e8b5c0f3c6da2ae03a2a63adc7ce8e15a202/pytest.ini#L16

Properly testing and finding all occurrences of this problem is a little tricky (see https://github.com/certbot/certbot/issues/7691), but we should fix this and remove the `pytest.ini` entry well before Python 3.9 is released.


Discussion:
Report in Fedora : https://bugzilla.redhat.com/show_bug.cgi?id=1793478

Resolving patch:
diff --git a/certbot/certbot/_internal/plugins/disco.py b/certbot/certbot/_internal/plugins/disco.py
--- a/certbot/certbot/_internal/plugins/disco.py
+++ b/certbot/certbot/_internal/plugins/disco.py
@@ -13,6 +13,12 @@
 from certbot import interfaces
 from certbot._internal import constants
 
+try:
+    # Python 3.3+
+    from collections.abc import Mapping
+except ImportError:  # pragma: no cover
+    from collections import Mapping
+
 logger = logging.getLogger(__name__)
 
 
@@ -178,7 +184,7 @@ def __str__(self):
         return "\n".join(lines)
 
 
-class PluginsRegistry(collections.Mapping):
+class PluginsRegistry(Mapping):
     """Plugins registry."""
 
     def __init__(self, plugins):


Test patch: