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

Issue:
[2] Get mypy running on your codebase with clean output.
http://blog.zulip.org/2016/10/13/static-types-in-python-oh-mypy/

This usually requires just adding type annotations for empty global data structures. Back in January, this took a few hours of work (including reporting bugs with reproducers). It’s probably even less work now. By default, mypy will only check the interior of functions that are annotated, so with an unannotated codebase, this is just making sure mypy can analyze your entire codebase.


Discussion:

Resolving patch:
diff --git a/certbot/crypto_util.py b/certbot/crypto_util.py
--- a/certbot/crypto_util.py
+++ b/certbot/crypto_util.py
@@ -13,7 +13,7 @@
 import six
 import zope.component
 from cryptography.hazmat.backends import default_backend
-from cryptography import x509
+from cryptography import x509 # type: ignore
 
 from acme import crypto_util as acme_crypto_util
 
diff --git a/certbot/util.py b/certbot/util.py
--- a/certbot/util.py
+++ b/certbot/util.py
@@ -54,7 +54,7 @@
 # the dict are attempted to be cleaned up at program exit. If the
 # program exits before the lock is cleaned up, it is automatically
 # released, but the file isn't deleted.
-_LOCKS = OrderedDict()
+_LOCKS = OrderedDict() # type: OrderedDict[str, lock.LockFile]
 
 
 def run_script(params, log=logger.error):


Test patch:
diff --git a/certbot-dns-digitalocean/certbot_dns_digitalocean/dns_digitalocean_test.py b/certbot-dns-digitalocean/certbot_dns_digitalocean/dns_digitalocean_test.py
--- a/certbot-dns-digitalocean/certbot_dns_digitalocean/dns_digitalocean_test.py
+++ b/certbot-dns-digitalocean/certbot_dns_digitalocean/dns_digitalocean_test.py
@@ -50,7 +50,8 @@ def test_cleanup(self):
 
 
 class DigitalOceanClientTest(unittest.TestCase):
-    id = 1
+
+    id_num = 1
     record_prefix = "_acme-challenge"
     record_name = record_prefix + "." + DOMAIN
     record_content = "bar"
@@ -70,7 +71,7 @@ def test_add_txt_record(self):
 
         domain_mock = mock.MagicMock()
         domain_mock.name = DOMAIN
-        domain_mock.create_new_domain_record.return_value = {'domain_record': {'id': self.id}}
+        domain_mock.create_new_domain_record.return_value = {'domain_record': {'id': self.id_num}}
 
         self.manager.get_all_domains.return_value = [wrong_domain_mock, domain_mock]
 
diff --git a/certbot/tests/cert_manager_test.py b/certbot/tests/cert_manager_test.py
--- a/certbot/tests/cert_manager_test.py
+++ b/certbot/tests/cert_manager_test.py
@@ -216,11 +216,12 @@ def test_report_human_readable(self, mock_revoked):
         cert.is_test_cert = False
         parsed_certs = [cert]
 
+        mock_config = mock.MagicMock(certname=None, lineagename=None)
         # pylint: disable=protected-access
-        get_report = lambda: cert_manager._report_human_readable(mock_config, parsed_certs)
 
-        mock_config = mock.MagicMock(certname=None, lineagename=None)
         # pylint: disable=protected-access
+        get_report = lambda: cert_manager._report_human_readable(mock_config, parsed_certs)
+
         out = get_report()
         self.assertTrue("INVALID: EXPIRED" in out)
Repository: certbot/certbot

Issue:
line with bare plus sign after You are updating certificate when removing a domain is odd
## My operating system is (include version):
debian 9.3 stretch

## I installed Certbot with (certbot-auto, OS package manager, pip, etc):
certbot-auto

## I ran this command and it produced this output:

```sh
certbot-auto certonly --cert-name foo.example.com -d bar.example.com
Saving debug log to /var/log/letsencrypt/letsencrypt.log

How would you like to authenticate with the ACME CA?
-------------------------------------------------------------------------------
1: Apache Web Server plugin - Beta (apache)
2: Spin up a temporary webserver (standalone)
3: Place files in webroot directory (webroot)
-------------------------------------------------------------------------------
Select the appropriate number [1-3] then [enter] (press 'c' to cancel): 1
Plugins selected: Authenticator apache, Installer None

-------------------------------------------------------------------------------
You are updating certificate foo.example.com to include new domain(s):
+

You are also removing previously included domain(s):
- bar.example.com

Did you intend to make this change?
-------------------------------------------------------------------------------
(U)pdate cert/(C)ancel: u
```
## Certbot's behavior differed from what I expected because:
The line under "new domain(s)" is bizarre.

I would not expect it to show the `+` sign, I think it would be better to show `(None)` instead of `+`.

## Here is a Certbot log showing the issue (if available):
###### Logs are stored in `/var/log/letsencrypt` by default. Feel free to redact domains, e-mail and IP addresses as you see fit.
There is nothing in the log file that seems to relate to this part of the process (it's before the actual discussion w/ boulder).

## Here is the relevant nginx server block or Apache virtualhost for the domain I am configuring:



Discussion:
I'm working on this.

Resolving patch:
diff --git a/certbot/main.py b/certbot/main.py
--- a/certbot/main.py
+++ b/certbot/main.py
@@ -340,7 +340,10 @@ def _get_added_removed(after, before):
 def _format_list(character, strings):
     """Format list with given character
     """
-    formatted = "{br}{ch} " + "{br}{ch} ".join(strings)
+    if len(strings) == 0:
+        formatted = "{br}(None)"
+    else:
+        formatted = "{br}{ch} " + "{br}{ch} ".join(strings)
     return formatted.format(
         ch=character,
         br=os.linesep


Test patch:
Repository: certbot/certbot

Issue:
Certbot docs don't build in Sphinx 1.6.1+
In their 1.6.1 release, Sphinx started requiring the package `latexmk` when trying to make PDFs of docs using the Makefile target `latexpdf`. This would be fine, but it also came with a change in behavior for us.

Apparently, Sphinx does not support SVGs when building PDFs (see sphinx-doc/sphinx#1907). Previously, this would be silent error and our documentation would just build without the SVG images. Now it's a hard error and causes the build to fail.

While it's nice that we're now aware of the problem, it has broken our tests on the https://github.com/certbot/website repo. I'm going to pin `Sphinx<=1.5.6` until this issue has either been resolved by us or upstream. This problem only affects the Certbot package and the problem is the badges in the Certbot README.
Certbot docs don't build in Sphinx 1.6.1+
In their 1.6.1 release, Sphinx started requiring the package `latexmk` when trying to make PDFs of docs using the Makefile target `latexpdf`. This would be fine, but it also came with a change in behavior for us.

Apparently, Sphinx does not support SVGs when building PDFs (see sphinx-doc/sphinx#1907). Previously, this would be silent error and our documentation would just build without the SVG images. Now it's a hard error and causes the build to fail.

While it's nice that we're now aware of the problem, it has broken our tests on the https://github.com/certbot/website repo. I'm going to pin `Sphinx<=1.5.6` until this issue has either been resolved by us or upstream. This problem only affects the Certbot package and the problem is the badges in the Certbot README.


Discussion:
Looks like the sphinx issue has been resolved so we can look into removing the pinning here.
Looks like the sphinx issue has been resolved so we can look into removing the pinning here.

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -40,6 +40,7 @@
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
+    'sphinx.ext.imgconverter',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -71,8 +71,8 @@ def read_file(filename, encoding='utf8'):
 
 docs_extras = [
     'repoze.sphinx.autointerface',
-    # autodoc_member_order = 'bysource', autodoc_default_flags, and #4686
-    'Sphinx >=1.0,<=1.5.6',
+    # sphinx.ext.imgconverter
+    'Sphinx >=1.6',
     'sphinx_rtd_theme',
 ]
 


Test patch:
Repository: certbot/certbot

Issue:
certbot-nginx requires acme >= 0.25
Because of the import of symbols `from acme.magic_typing`, the nginx plugin released in 0.25 depends on acme 0.25 or better.  However, setup.py only lists `acme>0.21.1`, leading to a failure to build from source (and potential run-time failures).


Discussion:
Actually, it looks like `certbot-nginx` isn't the only thing that needs to require `acme>=0.25.0` but doesn't. It looks like `certbot`, `certbot-apache`, and `certbot-dns-route53` all also use `acme.magic_typing` but only list `acme>0.24.0` in `setup.py`.

**Edit**: Never mind. Since the only version that satisfies `acme>0.24.0` is `0.25.0`, it doesn't really matter in this case.

Resolving patch:
diff --git a/certbot-nginx/setup.py b/certbot-nginx/setup.py
--- a/certbot-nginx/setup.py
+++ b/certbot-nginx/setup.py
@@ -7,10 +7,7 @@
 # Remember to update local-oldest-requirements.txt when changing the minimum
 # acme/certbot version.
 install_requires = [
-    # This plugin works with an older version of acme, but Certbot does not.
-    # 0.22.0 is specified here to work around
-    # https://github.com/pypa/pip/issues/988.
-    'acme>0.21.1',
+    'acme>=0.25.0',
     'certbot>0.21.1',
     'mock',
     'PyOpenSSL',


Test patch:
Repository: certbot/certbot

Issue:
Reuse ACMEv1 accounts for ACMEv2 production
The lines removed following the discussion at https://github.com/certbot/certbot/pull/5902#discussion_r192532446 need to be added back.


Discussion:
We should test to make sure everything works, but I believe we can do this now.

Resolving patch:
diff --git a/certbot/constants.py b/certbot/constants.py
--- a/certbot/constants.py
+++ b/certbot/constants.py
@@ -160,6 +160,7 @@
 """Directory where all accounts are saved."""
 
 LE_REUSE_SERVERS = {
+    'acme-v02.api.letsencrypt.org/directory': 'acme-v01.api.letsencrypt.org/directory',
     'acme-staging-v02.api.letsencrypt.org/directory':
         'acme-staging.api.letsencrypt.org/directory'
 }


Test patch:
diff --git a/certbot/tests/account_test.py b/certbot/tests/account_test.py
--- a/certbot/tests/account_test.py
+++ b/certbot/tests/account_test.py
@@ -218,12 +218,18 @@ def test_find_all_server_downgrade(self):
         self._set_server('https://acme-staging.api.letsencrypt.org/directory')
         self.assertEqual([], self.storage.find_all())
 
-    def test_upgrade_version(self):
+    def test_upgrade_version_staging(self):
         self._set_server('https://acme-staging.api.letsencrypt.org/directory')
         self.storage.save(self.acc, self.mock_client)
         self._set_server('https://acme-staging-v02.api.letsencrypt.org/directory')
         self.assertEqual([self.acc], self.storage.find_all())
 
+    def test_upgrade_version_production(self):
+        self._set_server('https://acme-v01.api.letsencrypt.org/directory')
+        self.storage.save(self.acc, self.mock_client)
+        self._set_server('https://acme-v02.api.letsencrypt.org/directory')
+        self.assertEqual([self.acc], self.storage.find_all())
+
     @mock.patch('os.rmdir')
     def test_corrupted_account(self, mock_rmdir):
         # pylint: disable=protected-access
Repository: certbot/certbot

Issue:
Change the default ACME server to the v2 endpoint
Step 4 of #5365 
- [ ] tools/deactivate.py
- [ ] acme/examples/example_client.py
The backend data structures are the same for the different endpoints, but we might want to either determine the client to use based on the server like we do in certbot, or at least use acmev2 styles.


Discussion:
We won't be doing this in our 0.22.0 release which will be coming out before the endpoint goes live, so I'm kicking this to 0.23.0.
@bmw It's live, but I can't figure out how to change the endpoint? 
```
Obtaining a new certificate
The currently selected ACME CA endpoint does not support issuing wildcard certificates.
```
Oh you need server flag  --preferred-challenges dns-01 --server https://acme-v02.api.letsencrypt.org/directory

With command
`certbot certonly --rsa-key-size 2048  --preferred-challenges dns-01 --server https://acme-v02.api.letsencrypt.org/directory`

I have this answer:
`Obtaining a new certificate
Performing the following challenges:
None of the preferred challenges are supported by the selected plugin`

nginx 1.13.9
certbot 0.22.0
Centos 7.4
@kysil I used the instructions in this post https://github.com/certbot/certbot/issues/5719
Unfortunately we had to revert this change because things like `certbot revoke --cert-path /path/to/cert` would suddenly stop working due to a different account being used. #5820 should be resolved before releasing this change.
@ohemorange, are you able to get to this this week? If not, I can take it.
I've got it.

Resolving patch:
diff --git a/certbot/constants.py b/certbot/constants.py
--- a/certbot/constants.py
+++ b/certbot/constants.py
@@ -88,7 +88,7 @@
     config_dir="/etc/letsencrypt",
     work_dir="/var/lib/letsencrypt",
     logs_dir="/var/log/letsencrypt",
-    server="https://acme-v01.api.letsencrypt.org/directory",
+    server="https://acme-v02.api.letsencrypt.org/directory",
 
     # Plugins parsers
     configurator=None,


Test patch:
Repository: certbot/certbot

Issue:
socket-related parameters to the listen directive should not be copied over for an already used address:port pair
CentOS 7.5, certbot 0.24.0 from epel, NGINX plugin.

http-01 challenge (for a renew) failed, the modified nginx.conf resulted in a `nginx: [emerg] duplicate listen options for` error.

The original `listen` directive for port 80 had the `deferred` parameter set and this was copied over to the `listen` directive inserted by `certbot-nginx`. The `deferred` parameter can be, similarly to the `ipv6only` parameter, only specified once for a given address:port pair.

There's a whole bunch of `listen` directive parameters like this, see https://nginx.org/en/docs/http/ngx_http_core_module.html#listen. I see there's a "blacklist" in `certbot_nginx/parser.py` that (optionally) takes care of the `default_server` and `ipv6_only` parameters. I'm not aware of all the contexts in which a new server block for an already used address:port pair needs to be created by certbot-nginx, but for temporary server blocks for challenge response serving, perhaps ignoring all the listen parameters altogether, apart from the address:port pair, could be an option? (Just a speculation on my part, perhaps shortsighted...)



Discussion:
Thanks for opening this issue! Extending the current blacklisting behavior of `ipv6_only` for the other directives with similar behavior looks like the way ahead here.

Resolving patch:
diff --git a/certbot-nginx/certbot_nginx/parser.py b/certbot-nginx/certbot_nginx/parser.py
--- a/certbot-nginx/certbot_nginx/parser.py
+++ b/certbot-nginx/certbot_nginx/parser.py
@@ -395,12 +395,17 @@ def duplicate_vhost(self, vhost_template, remove_singleton_listen_params=False,
                 addr.ipv6only = False
             for directive in enclosing_block[new_vhost.path[-1]][1]:
                 if len(directive) > 0 and directive[0] == 'listen':
-                    if 'default_server' in directive:
-                        del directive[directive.index('default_server')]
-                    if 'default' in directive:
-                        del directive[directive.index('default')]
-                    if 'ipv6only=on' in directive:
-                        del directive[directive.index('ipv6only=on')]
+                    # Exclude one-time use parameters which will cause an error if repeated.
+                    # https://nginx.org/en/docs/http/ngx_http_core_module.html#listen
+                    exclude = set(('default_server', 'default', 'setfib', 'fastopen', 'backlog',
+                                   'rcvbuf', 'sndbuf', 'accept_filter', 'deferred', 'bind',
+                                   'ipv6only', 'reuseport', 'so_keepalive'))
+
+                    for param in exclude:
+                        # See: github.com/certbot/certbot/pull/6223#pullrequestreview-143019225
+                        keys = [x.split('=')[0] for x in directive]
+                        if param in keys:
+                            del directive[keys.index(param)]
         return new_vhost
 
 


Test patch:
Repository: certbot/certbot

Issue:
Conditionally depend on sphinx imgconverter?
This is needed in Sphinx>=1.6, but Sphinx this new may not be available in older distros. Can we configure Sphinx to work with both versions by conditionally depending on imgconverter? Is there another approach we can take entirely?

The relevant PR here is https://github.com/certbot/certbot/pull/6070/files.


Discussion:

Resolving patch:
diff --git a/docs/conf.py b/docs/conf.py
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -17,6 +17,8 @@
 import re
 import sys
 
+import sphinx
+
 
 here = os.path.abspath(os.path.dirname(__file__))
 
@@ -33,14 +35,13 @@
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = '1.0'
+needs_sphinx = '1.2'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
     'sphinx.ext.autodoc',
-    'sphinx.ext.imgconverter',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
     'sphinx.ext.coverage',
@@ -48,6 +49,9 @@
     'repoze.sphinx.autointerface',
 ]
 
+if sphinx.version_info >= (1, 6):
+    extensions.append('sphinx.ext.imgconverter')
+
 autodoc_member_order = 'bysource'
 autodoc_default_flags = ['show-inheritance', 'private-members']
 
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -68,9 +68,10 @@ def read_file(filename, encoding='utf8'):
 ]
 
 docs_extras = [
+    # If you have Sphinx<1.5.1, you need docutils<0.13.1
+    # https://github.com/sphinx-doc/sphinx/issues/3212
     'repoze.sphinx.autointerface',
-    # sphinx.ext.imgconverter
-    'Sphinx >=1.6',
+    'Sphinx>=1.2', # Annotation support
     'sphinx_rtd_theme',
 ]
 


Test patch:
Repository: certbot/certbot

Issue:
certbot delete list must be sorted
Subj.


Discussion:
Would you like to propose a sorting scheme and PR for this, @bes-internal ? The relevant code is in this function: https://github.com/certbot/certbot/blob/master/certbot/storage.py#L44 which is called by `certbot/cert_manager.py` to grab the certificate names.
Hi @bes-internal! I noticed that in this issue and in #6625 you used "must," which people may interpret as demanding and rude. I'm sure that's not what you intended. You might have better results in the future replacing "must" with "should," which is less likely to be understood as demanding.

Also, in this particular case, can you explain more about the task you are trying to achieve and why sorting the list would help with that task?


> why sorting the list would help with that task

Because `certbot delete` provides an interactive interface for the user in order to find the one he needs cert name. Maybe it works for 5-10 domains, but not for 1500 in my case.
And no matter what other functions this subcommand has (--cert-name). We are talking about the interactive select.

P.S. My "must" is not rude, but indicate requirement level. Thank you, I will take your comments for normal speech, because apparently there will be a discussion.


Resolving patch:
diff --git a/certbot/storage.py b/certbot/storage.py
--- a/certbot/storage.py
+++ b/certbot/storage.py
@@ -41,7 +41,9 @@ def renewal_conf_files(config):
     :rtype: `list` of `str`
 
     """
-    return glob.glob(os.path.join(config.renewal_configs_dir, "*.conf"))
+    result = glob.glob(os.path.join(config.renewal_configs_dir, "*.conf"))
+    result.sort()
+    return result
 
 def renewal_file_for_certname(config, certname):
     """Return /path/to/certname.conf in the renewal conf directory"""


Test patch:
Repository: certbot/certbot

Issue:
Nightly tests are failing on the new CERTBOT_NO_PIN tests
See https://travis-ci.com/certbot/certbot/jobs/171340638. I think the solution may be to remove `--ignore-installed`.

@adferrand, are you able to look into this today?


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
@@ -90,7 +90,7 @@ def main(args):
 
         if os.environ.get('CERTBOT_NO_PIN') == '1':
             # With unpinned dependencies, there is no constraint
-            call_with_print('"{0}" -m pip install --ignore-installed {1}'
+            call_with_print('"{0}" -m pip install {1}'
                             .format(sys.executable, ' '.join(args)))
         else:
             # Otherwise, we merge requirements to build the constraints and pin dependencies


Test patch:
Repository: certbot/certbot

Issue:
Depend on josepy>=1.1.0 in setup.py files
Where we depend on `josepy`, I think we should depend on `josepy>=1.1.0`.

The reason for this is when older versions of `josepy` are used with `cryptography>=2.0`, users hit https://github.com/certbot/josepy/issues/13. Really, we'd like logic like "if cryptography>=2.0 is the version being used, depend on josepy>=1.1.0", but I'm not even sure logic like this is possible and if it is, it complicates things significantly.

A small bump to the version requirements in new versions of acme, certbot, etc. for another package of ours shouldn't be a problem at all and avoids this complexity.
Depend on josepy>=1.1.0 in setup.py files
Where we depend on `josepy`, I think we should depend on `josepy>=1.1.0`.

The reason for this is when older versions of `josepy` are used with `cryptography>=2.0`, users hit https://github.com/certbot/josepy/issues/13. Really, we'd like logic like "if cryptography>=2.0 is the version being used, depend on josepy>=1.1.0", but I'm not even sure logic like this is possible and if it is, it complicates things significantly.

A small bump to the version requirements in new versions of acme, certbot, etc. for another package of ours shouldn't be a problem at all and avoids this complexity.


Discussion:

Resolving patch:
diff --git a/acme/setup.py b/acme/setup.py
--- a/acme/setup.py
+++ b/acme/setup.py
@@ -11,7 +11,9 @@
     # rsa_recover_prime_factors (>=0.8)
     'cryptography>=1.2.3',
     # formerly known as acme.jose:
-    'josepy>=1.0.0',
+    # 1.1.0+ is required to avoid the warnings described at
+    # https://github.com/certbot/josepy/issues/13.
+    'josepy>=1.1.0',
     # Connection.set_tlsext_host_name (>=0.13)
     'mock',
     'PyOpenSSL>=0.13.1',
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -38,7 +38,9 @@ def read_file(filename, encoding='utf8'):
     'ConfigArgParse>=0.9.3',
     'configobj',
     'cryptography>=1.2.3',  # load_pem_x509_certificate
-    'josepy',
+    # 1.1.0+ is required to avoid the warnings described at
+    # https://github.com/certbot/josepy/issues/13.
+    'josepy>=1.1.0',
     'mock',
     'parsedatetime>=1.3',  # Calendar.parseDT
     'pyrfc3339',


Test patch: