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

Issue:
authenticator/installer is set to "none"
This gets put into the renewal config file which will not be restored correctly. The correct value is "None".



Discussion:

Resolving patch:
diff --git a/letsencrypt/cli.py b/letsencrypt/cli.py
--- a/letsencrypt/cli.py
+++ b/letsencrypt/cli.py
@@ -236,8 +236,8 @@ def choose_configurator_plugins(config, plugins, verb):
 def record_chosen_plugins(config, plugins, auth, inst):
     "Update the config entries to reflect the plugins we actually selected."
     cn = config.namespace
-    cn.authenticator = plugins.find_init(auth).name if auth else "none"
-    cn.installer = plugins.find_init(inst).name if inst else "none"
+    cn.authenticator = plugins.find_init(auth).name if auth else "None"
+    cn.installer = plugins.find_init(inst).name if inst else "None"
 
 
 def set_by_cli(var):
diff --git a/letsencrypt/main.py b/letsencrypt/main.py
--- a/letsencrypt/main.py
+++ b/letsencrypt/main.py
@@ -462,7 +462,7 @@ def config_changes(config, unused_plugins):
 def revoke(config, unused_plugins):  # TODO: coop with renewal config
     """Revoke a previously obtained certificate."""
     # For user-agent construction
-    config.namespace.installer = config.namespace.authenticator = "none"
+    config.namespace.installer = config.namespace.authenticator = "None"
     if config.key_path is not None:  # revocation by cert key
         logger.debug("Revoking %s using cert key %s",
                      config.cert_path[0], config.key_path[0])


Test patch:
diff --git a/letsencrypt/tests/testdata/sample-renewal-ancient.conf b/letsencrypt/tests/testdata/sample-renewal-ancient.conf
--- a/letsencrypt/tests/testdata/sample-renewal-ancient.conf
+++ b/letsencrypt/tests/testdata/sample-renewal-ancient.conf
@@ -14,7 +14,7 @@ apache_dismod = a2dismod
 register_unsafely_without_email = False
 apache_handle_modules = True
 uir = None
-installer = none
+installer = None
 nginx_ctl = nginx
 config_dir = MAGICDIR
 text_mode = False
diff --git a/letsencrypt/tests/testdata/sample-renewal.conf b/letsencrypt/tests/testdata/sample-renewal.conf
--- a/letsencrypt/tests/testdata/sample-renewal.conf
+++ b/letsencrypt/tests/testdata/sample-renewal.conf
@@ -14,7 +14,7 @@ apache_dismod = a2dismod
 register_unsafely_without_email = False
 apache_handle_modules = True
 uir = None
-installer = none
+installer = None
 nginx_ctl = nginx
 config_dir = MAGICDIR
 text_mode = False
Repository: certbot/certbot

Issue:
Allude to renewal interval defaults in renewal config file
The renewal config file should somehow mention or explain the default renewal intervals even if none are explicitly set there (presumably in a comment created when the lineage was first created).



Discussion:
I think this is important. I was trying to explain to someone how to renew 60 days before expiration and had to tell them about undocumented options of the renewal config file.


Resolving patch:
diff --git a/certbot/storage.py b/certbot/storage.py
--- a/certbot/storage.py
+++ b/certbot/storage.py
@@ -78,6 +78,10 @@ def write_renewal_config(o_filename, n_filename, target, relevant_data):
         if k not in relevant_data:
             del config["renewalparams"][k]
 
+    if "renew_before_expiry" not in config:
+        default_interval = constants.RENEWER_DEFAULTS["renew_before_expiry"]
+        config.initial_comment = ["renew_before_expiry = " + default_interval]
+
     # TODO: add human-readable comments explaining other available
     #       parameters
     logger.debug("Writing new config %s.", n_filename)


Test patch:
Repository: certbot/certbot

Issue:
Don't fail when Detail field is empty
The Detail field of a [Problem Detail](https://tools.ietf.org/html/draft-ietf-appsawg-http-problem-03) is not required, and may in particular be absent when it is redundant with the status field. Right now the client throws a nasty exception when it receives a Problem Detail without a Detail field. Instead it should just print the type.



Discussion:
This is not a bug in the implementation, but in the spec (at most). https://ietf-wg-acme.github.io/acme/#rfc.section.5.4: "The “type” and “detail” fields MUST be populated.". I can fix this, but please send a PR against spec first.

https://github.com/ietf-wg-acme/acme/pull/84


Resolving patch:
diff --git a/acme/acme/messages.py b/acme/acme/messages.py
--- a/acme/acme/messages.py
+++ b/acme/acme/messages.py
@@ -37,9 +37,9 @@ class Error(jose.JSONObjectWithFields, errors.Error):
         )
     )
 
-    typ = jose.Field('type')
+    typ = jose.Field('type', omitempty=True, default='about:blank')
     title = jose.Field('title', omitempty=True)
-    detail = jose.Field('detail')
+    detail = jose.Field('detail', omitempty=True)
 
     @property
     def description(self):


Test patch:
diff --git a/acme/acme/client_test.py b/acme/acme/client_test.py
--- a/acme/acme/client_test.py
+++ b/acme/acme/client_test.py
@@ -484,9 +484,11 @@ def from_json(cls, value):
     def test_check_response_not_ok_jobj_no_error(self):
         self.response.ok = False
         self.response.json.return_value = {}
-        # pylint: disable=protected-access
-        self.assertRaises(
-            errors.ClientError, self.net._check_response, self.response)
+        with mock.patch('acme.client.messages.Error.from_json') as from_json:
+            from_json.side_effect = jose.DeserializationError
+            # pylint: disable=protected-access
+            self.assertRaises(
+                errors.ClientError, self.net._check_response, self.response)
 
     def test_check_response_not_ok_jobj_error(self):
         self.response.ok = False
diff --git a/acme/acme/messages_test.py b/acme/acme/messages_test.py
--- a/acme/acme/messages_test.py
+++ b/acme/acme/messages_test.py
@@ -28,6 +28,14 @@ def setUp(self):
         self.error_custom = Error(typ='custom', detail='bar')
         self.jobj_cusom = {'type': 'custom', 'detail': 'bar'}
 
+    def test_default_typ(self):
+        from acme.messages import Error
+        self.assertEqual(Error().typ, 'about:blank')
+
+    def test_from_json_empty(self):
+        from acme.messages import Error
+        self.assertEqual(Error(), Error.from_json('{}'))
+
     def test_from_json_hashable(self):
         from acme.messages import Error
         hash(Error.from_json(self.error.to_json()))
Repository: certbot/certbot

Issue:
Domain order not preserved in generated CSR
4d6a1ee7ff23b29d4416ee91610a7d8a58173292 introduced a change which causes the domain order passed to the client not to be preserved.

The previous implementation in `get_authorizations` would iterate over the original domain list, preserving the original order, whereas the new implementation uses `authzr.values()`, which does not follow the same sorting order.

As a side-effect, the Common Name field is not guaranteed to be the first domain passed via `-d`, causing issues for users who are relying on this after upgrading to 0.5.0.



Discussion:

Resolving patch:
diff --git a/certbot/client.py b/certbot/client.py
--- a/certbot/client.py
+++ b/certbot/client.py
@@ -245,8 +245,9 @@ def obtain_certificate(self, domains):
                 domains,
                 self.config.allow_subset_of_names)
 
-        domains = [a.body.identifier.value.encode('ascii')
-                                          for a in authzr]
+        auth_domains = set(a.body.identifier.value.encode('ascii')
+                           for a in authzr)
+        domains = [d for d in domains if d in auth_domains]
 
         # Create CSR from names
         key = crypto_util.init_save_key(


Test patch:
diff --git a/certbot/tests/client_test.py b/certbot/tests/client_test.py
--- a/certbot/tests/client_test.py
+++ b/certbot/tests/client_test.py
@@ -201,7 +201,8 @@ def test_obtain_certificate(self, mock_crypto_util):
 
         authzr = []
 
-        for domain in domains:
+        # domain ordering should not be affected by authorization order
+        for domain in reversed(domains):
             authzr.append(
                 mock.MagicMock(
                     body=mock.MagicMock(
Repository: certbot/certbot

Issue:
Print a deprecation warning for users running the old letsencrypt-auto
Parts:
- wrangle sudo to pass a variable in to the client
- if the client detects leauto but neithert that variable nor `--no-self-upgrade`, its the old non-self-updating version, so print a warning



Discussion:

Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -37,8 +37,14 @@
 # should only be used for purposes where inability to detect letsencrypt-auto
 # fails safely
 
+LEAUTO = "letsencrypt-auto"
+if "CERTBOT_AUTO" in os.environ:
+    # if we're here, this is probably going to be certbot-auto, unless the
+    # user saved the script under a different name
+    LEAUTO = os.path.basename(os.environ["CERTBOT_AUTO"])
+
 fragment = os.path.join(".local", "share", "letsencrypt")
-cli_command = "letsencrypt-auto" if fragment in sys.argv[0] else "certbot"
+cli_command = LEAUTO if fragment in sys.argv[0] else "certbot"
 
 # Argparse's help formatting has a lot of unhelpful peculiarities, so we want
 # to replace as much of it as we can...
@@ -141,6 +147,22 @@ def usage_strings(plugins):
     return USAGE % (apache_doc, nginx_doc), SHORT_USAGE
 
 
+def possible_deprecation_warning(config):
+    "A deprecation warning for users with the old, not-self-upgrading letsencrypt-auto."
+    if cli_command != LEAUTO:
+        return
+    if config.no_self_upgrade:
+        # users setting --no-self-upgrade might be hanging on a clent version like 0.3.0
+        # or 0.5.0 which is the new script, but doesn't set CERTBOT_AUTO; they don't
+        # need warnings
+        return
+    if "CERTBOT_AUTO" not in os.environ:
+        logger.warn("You are running with an old copy of letsencrypt-auto that does "
+            "not receive updates, and is less reliable than more recent versions. "
+            "We recommend upgrading to the latest certbot-auto script, or using native "
+            "OS packages.")
+
+
 class _Default(object):
     """A class to use as a default to detect if a value is set by a user"""
 
diff --git a/certbot/main.py b/certbot/main.py
--- a/certbot/main.py
+++ b/certbot/main.py
@@ -661,6 +661,7 @@ def main(cli_args=sys.argv[1:]):
     le_util.make_or_verify_dir(
         config.logs_dir, 0o700, os.geteuid(), "--strict-permissions" in cli_args)
     setup_logging(config, _cli_log_handler, logfile='letsencrypt.log')
+    cli.possible_deprecation_warning(config)
 
     logger.debug("certbot version: %s", certbot.__version__)
     # do not log `config`, as it contains sensitive data (e.g. revoke --key)!


Test patch:
Repository: certbot/certbot

Issue:
Auto venv details
In #2885 I did not change the name of the venv created by `*-auto`. The reason for this is I believe we expressed some concern about people reaching into the venv to run `letsencrypt` directly, e.g. `~/.local/share/letsencrypt/bin/letsencrypt`.

Do we want to rename the venv? If not, we need to revert the change made on this [line](https://github.com/letsencrypt/letsencrypt/blob/master/certbot/cli.py#L40).



Discussion:
Making this issue more general, do we want `*-auto` to continue to install the `letsencrypt` package? If we do not do this, people reaching into the venv (if they exist) will get the same breakage I described above.

We decided to keep `~/.local/share/letsencrypt/bin/letsencrypt`. I'll revert the change I mentioned above.


Resolving patch:
diff --git a/certbot/cli.py b/certbot/cli.py
--- a/certbot/cli.py
+++ b/certbot/cli.py
@@ -37,7 +37,7 @@
 # should only be used for purposes where inability to detect letsencrypt-auto
 # fails safely
 
-fragment = os.path.join(".local", "share", "certbot")
+fragment = os.path.join(".local", "share", "letsencrypt")
 cli_command = "letsencrypt-auto" if fragment in sys.argv[0] else "certbot"
 
 # Argparse's help formatting has a lot of unhelpful peculiarities, so we want


Test patch:
Repository: certbot/certbot

Issue:
setup.py: datetime dep needs versioning
letsencrypt actually requires datetime >= 1.2, however the dependency in setup.py is unversioned, meaning it can be satisfied by old distro packages. Versioning it forces an install from a newer upstream version, which resolves the breakage.



Discussion:
Please correct me if I'm wrong, but I believe you're referring to `parsedatetime` and I think the version needs to be pinned at `parsedatetime>=1.3`. Tests fail on my system when using `parsedatetime==1.2`.


Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -39,7 +39,7 @@ def read_file(filename, encoding='utf8'):
     'ConfigArgParse>=0.9.3',
     'configobj',
     'cryptography>=0.7',  # load_pem_x509_certificate
-    'parsedatetime',
+    'parsedatetime>=1.3',  # Calendar.parseDT
     'psutil>=2.1.0',  # net_connections introduced in 2.1.0
     'PyOpenSSL',
     'pyrfc3339',


Test patch:
Repository: certbot/certbot

Issue:
Allow unrecognized fields in Directory
This is necessary for forward API compatibility, for instance implementing the authorizations and certificates fields on the Boulder side.



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
@@ -143,12 +143,6 @@ def register(cls, resource_body_cls):
 
     def __init__(self, jobj):
         canon_jobj = util.map_keys(jobj, self._canon_key)
-        if not set(canon_jobj).issubset(
-                set(self._REGISTERED_TYPES).union(['meta'])):
-            # TODO: acme-spec is not clear about this: 'It is a JSON
-            # dictionary, whose keys are the "resource" values listed
-            # in {{https-requests}}'
-            raise ValueError('Wrong directory fields')
         # TODO: check that everything is an absolute URL; acme-spec is
         # not clear on that
         self._jobj = canon_jobj
@@ -171,10 +165,7 @@ def to_partial_json(self):
     @classmethod
     def from_json(cls, jobj):
         jobj['meta'] = cls.Meta.from_json(jobj.pop('meta', {}))
-        try:
-            return cls(jobj)
-        except ValueError as error:
-            raise jose.DeserializationError(str(error))
+        return cls(jobj)
 
 
 class Resource(jose.JSONObjectWithFields):


Test patch:
diff --git a/acme/acme/messages_test.py b/acme/acme/messages_test.py
--- a/acme/acme/messages_test.py
+++ b/acme/acme/messages_test.py
@@ -97,9 +97,9 @@ def setUp(self):
             ),
         })
 
-    def test_init_wrong_key_value_error(self):
+    def test_init_wrong_key_value_success(self):  # pylint: disable=no-self-use
         from acme.messages import Directory
-        self.assertRaises(ValueError, Directory, {'foo': 'bar'})
+        Directory({'foo': 'bar'})
 
     def test_getitem(self):
         self.assertEqual('reg', self.dir['new-reg'])
@@ -127,10 +127,9 @@ def test_to_json(self):
             },
         })
 
-    def test_from_json_deserialization_error_on_wrong_key(self):
+    def test_from_json_deserialization_unknown_key_success(self):  # pylint: disable=no-self-use
         from acme.messages import Directory
-        self.assertRaises(
-            jose.DeserializationError, Directory.from_json, {'foo': 'bar'})
+        Directory.from_json({'foo': 'bar'})
 
 
 class RegistrationTest(unittest.TestCase):
Repository: certbot/certbot

Issue:
AttributeError: 'Namespace' object has no attribute 'changes_since_path'
This error comes up when I try to use certbot-auto with apache, so it is unable to set up enhancement redirect.



Discussion:
This looks like a bug that was introduced in #2794. It'll be fixed in the next release which should come out in the next week or so.


Resolving patch:
diff --git a/certbot/reverter.py b/certbot/reverter.py
--- a/certbot/reverter.py
+++ b/certbot/reverter.py
@@ -7,6 +7,7 @@
 import time
 import traceback
 
+
 import zope.component
 
 from certbot import constants
@@ -489,7 +490,7 @@ def finalize_checkpoint(self, title):
 
         if not os.path.exists(changes_since_path):
             logger.info("Rollback checkpoint is empty (no changes made?)")
-            with open(self.config.changes_since_path) as f:
+            with open(changes_since_path, 'w') as f:
                 f.write("No changes\n")
 
         # Add title to self.config.in_progress_dir CHANGES_SINCE


Test patch:
diff --git a/certbot/tests/reverter_test.py b/certbot/tests/reverter_test.py
--- a/certbot/tests/reverter_test.py
+++ b/certbot/tests/reverter_test.py
@@ -34,6 +34,20 @@ def tearDown(self):
 
         logging.disable(logging.NOTSET)
 
+    @mock.patch("certbot.reverter.Reverter._read_and_append")
+    def test_no_change(self, mock_read):
+        mock_read.side_effect = OSError("cannot even")
+        try:
+            self.reverter.add_to_checkpoint(self.sets[0], "save1")
+        except OSError:
+            pass
+        self.reverter.finalize_checkpoint("blah")
+        path = os.listdir(self.reverter.config.backup_dir)[0]
+        no_change = os.path.join(self.reverter.config.backup_dir, path, "CHANGES_SINCE")
+        with open(no_change, "r") as f:
+            x = f.read()
+        self.assertTrue("No changes" in x)
+
     def test_basic_add_to_temp_checkpoint(self):
         # These shouldn't conflict even though they are both named config.txt
         self.reverter.add_to_temp_checkpoint(self.sets[0], "save1")
Repository: certbot/certbot

Issue:
Error that results when run without root is unclear
When running `letsencrypt` without root, I get

```
An unexpected error occurred:
OSError: [Errno 13] Permission denied: '/etc/letsencrypt'
Please see the logfile 'letsencrypt.log' for more details.
```

The underlying reason is that, to run without root, I need to specify `--config-dir`, `--work-dir`, and `--logs-dir`. However, the client doesn't give me any suggestion about this or about the possibility of doing anything (even reading help) without root access.

While a sysadmin would probably conclude that the reason for the `OSError` is simply that the client needs root to run, it would be great to have a clearer and more useful error message in this case.



Discussion:
`certbot.eff.org` shows the instructions as regular user (starting with `$`), which adds to the confusion.


Resolving patch:
diff --git a/certbot/main.py b/certbot/main.py
--- a/certbot/main.py
+++ b/certbot/main.py
@@ -1,6 +1,7 @@
 """Certbot main entry point."""
 from __future__ import print_function
 import atexit
+import errno
 import functools
 import logging.handlers
 import os
@@ -588,8 +589,16 @@ def renew(config, unused_plugins):
 def setup_log_file_handler(config, logfile, fmt):
     """Setup file debug logging."""
     log_file_path = os.path.join(config.logs_dir, logfile)
-    handler = logging.handlers.RotatingFileHandler(
-        log_file_path, maxBytes=2 ** 20, backupCount=10)
+    try:
+        handler = logging.handlers.RotatingFileHandler(
+            log_file_path, maxBytes=2 ** 20, backupCount=10)
+    except IOError as e:
+        if e.errno == errno.EACCES:
+            msg = ("Access denied writing to {0}. To run as non-root, set " +
+                "--logs-dir, --config-dir, --work-dir to writable paths.")
+            raise errors.Error(msg.format(log_file_path))
+        else:
+            raise
     # rotate on each invocation, rollover only possible when maxBytes
     # is nonzero and backupCount is nonzero, so we set maxBytes as big
     # as possible not to overrun in single CLI invocation (1MB).


Test patch:
Repository: certbot/certbot

Issue:
Log whether renewing or obtaining a new certificate
It appears we don't log whether we're renewing an existing certificate or obtaining a new one. We should do this as it makes our logs more useful for debugging.



Discussion:
@bmw  I'm going to start taking a crack at this one as a volunteer.

Is there a single place in the code where cert obtainment/renewal occurs, or are there a variety of places that this can happen?

Great! If you have any questions don't hesitate to stop by #letsencrypt-dev on Freenode or #certbot-dev on OFTC.

The common function here is `_auth_from_domains` in `certbot/main.py`. The purpose of this function is to determine whether we should get a new cert, renew an existing one, or simply reinstall the current certificate. We should log the choice here as I was trying to help as user debug a problem they were having with the client and couldn't tell exactly what the client was doing.


Resolving patch:
diff --git a/certbot/main.py b/certbot/main.py
--- a/certbot/main.py
+++ b/certbot/main.py
@@ -83,14 +83,17 @@ def _auth_from_domains(le_client, config, domains, lineage=None):
     if action == "reinstall":
         # The lineage already exists; allow the caller to try installing
         # it without getting a new certificate at all.
+        logger.info("Keeping the existing certificate")
         return lineage, "reinstall"
 
     hooks.pre_hook(config)
     try:
         if action == "renew":
+            logger.info("Renewing an existing certificate")
             renewal.renew_cert(config, domains, le_client, lineage)
         elif action == "newcert":
             # TREAT AS NEW REQUEST
+            logger.info("Obtaining a new certificate")
             lineage = le_client.obtain_and_enroll_certificate(domains)
             if lineage is False:
                 raise errors.Error("Certificate could not be obtained")


Test patch:
Repository: certbot/certbot

Issue:
prevent Github commits from modifying certbot-auto and letsencrypt-auto
`certbot-auto` and `letsencrypt-auto` in the root of our repo should only be modified during our releases, however, this is not enforced by any of our tests. It should be enforced by something running in Travis.

Probably the easiest way to do that is to use `letsencrypt-auto-source/pieces/fetch.py` to download the latest stable copy of the script and diff that against `certbot-auto` and `letsencrypt-auto` in the root. If they differ, the test should fail.



Discussion:

Resolving patch:
diff --git a/letsencrypt-auto-source/pieces/fetch.py b/letsencrypt-auto-source/pieces/fetch.py
--- a/letsencrypt-auto-source/pieces/fetch.py
+++ b/letsencrypt-auto-source/pieces/fetch.py
@@ -2,7 +2,7 @@
 
     # Print latest released version of LE to stdout:
     python fetch.py --latest-version
-    
+
     # Download letsencrypt-auto script from git tag v1.2.3 into the folder I'm
     # in, and make sure its signature verifies:
     python fetch.py --le-auto-script v1.2.3


Test patch:
diff --git a/tests/modification-check.sh b/tests/modification-check.sh
new file mode 100755
--- /dev/null
+++ b/tests/modification-check.sh
@@ -0,0 +1,35 @@
+#!/bin/bash
+
+temp_dir=`mktemp -d`
+
+# Script should be run from Certbot's root directory
+cp letsencrypt-auto ${temp_dir}/letsencrypt-to-be-checked
+cp certbot-auto ${temp_dir}/certbot-to-be-checked
+
+cp letsencrypt-auto-source/pieces/fetch.py ${temp_dir}/fetch.py
+cd ${temp_dir}
+
+LATEST_VERSION=`python fetch.py --latest-version`
+python fetch.py --le-auto-script v${LATEST_VERSION}
+
+cmp -s letsencrypt-auto letsencrypt-to-be-checked
+
+if [ $? != 0 ]; then
+	echo "Root letsencrypt-auto has changed."
+	rm -rf temp_dir
+	exit 1
+else
+	echo "Root letsencrypt-auto is unchanged."
+fi
+
+cmp -s letsencrypt-auto certbot-to-be-checked
+
+if [ $? != 0 ]; then
+	echo "Root certbot-auto has changed."
+	rm -rf temp_dir
+	exit 1
+else
+	echo "Root certbot-auto is unchanged."
+fi
+
+rm -rf temp_dir