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

Issue:
GofmtBear: Add advanced asciinema
The coala bear GofmtBear does not have a proper asciinema.

`gofmt` is a command line tool that automatically solves formatting / styling issues to the absolute coding style that Go has.

I'm planning to use a working code as the sample where it's filled with mixed indentation (spaces and tabs), semicolons and demonstrate how gofmt formats the code automatically and correctly to the absolute Go coding style.



Discussion:
Also, I request myself to be assigned to this task. Thanks.

Resolving patch:
diff --git a/bears/go/GofmtBear.py b/bears/go/GofmtBear.py
--- a/bears/go/GofmtBear.py
+++ b/bears/go/GofmtBear.py
@@ -20,6 +20,7 @@ class GofmtBear:
     AUTHORS_EMAILS = {'coala-devel@googlegroups.com'}
     LICENSE = 'AGPL-3.0'
     CAN_FIX = {'Formatting'}
+    ASCIINEMA_URL = 'https://asciinema.org/a/94812'
 
     @staticmethod
     def create_arguments(filename, file, config_file):


Test patch:
Repository: coala/coala-bears

Issue:
JuliaLintBear: Use JuliaRequirement
`REQUIREMENTS` should be a `JuliaRequirement` instead of a `DistributionRequirement`.


Discussion:
[this](https://github.com/coala/coala-bears/blob/master/bears/julia/JuliaLintBear.py#L28) needs to be changed, right?
@prakashdanish , correct.

Resolving patch:
diff --git a/bears/julia/JuliaLintBear.py b/bears/julia/JuliaLintBear.py
--- a/bears/julia/JuliaLintBear.py
+++ b/bears/julia/JuliaLintBear.py
@@ -1,7 +1,7 @@
 from coala_utils.string_processing.Core import escape
 from coalib.bearlib.abstractions.Linter import linter
-from dependency_management.requirements.DistributionRequirement import (
-    DistributionRequirement)
+from dependency_management.requirements.JuliaRequirement import (
+    JuliaRequirement)
 from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
 
 
@@ -25,7 +25,7 @@ class JuliaLintBear:
     on the analysis provided.
     """
     LANGUAGES = {'Julia'}
-    REQUIREMENTS = {DistributionRequirement(apt_get='julia')}
+    REQUIREMENTS = {JuliaRequirement('Lint')}
     AUTHORS = {'The coala developers'}
     AUTHORS_EMAILS = {'coala-devel@googlegroups.com'}
     LICENSE = 'AGPL-3.0'


Test patch:
Repository: coala/coala-bears

Issue:
Upgrade memento_client to 0.6.1
Currently `memento_client` in our repo is still at version 0.5.3 which still contains bugs. Upgrading to `0.6.1` would fix many bugs that are found in `0.5.3`


Discussion:

Resolving patch:
diff --git a/bears/general/MementoBear.py b/bears/general/MementoBear.py
--- a/bears/general/MementoBear.py
+++ b/bears/general/MementoBear.py
@@ -14,7 +14,7 @@
 class MementoBear(LocalBear):
     DEFAULT_TIMEOUT = 15
     LANGUAGES = {'All'}
-    REQUIREMENTS = {PipRequirement('memento_client', '0.5.3')}
+    REQUIREMENTS = {PipRequirement('memento_client', '0.6.1')}
     AUTHORS = {'The coala developers'}
     AUTHORS_EMAILS = {'coala-devel@googlegroups.com'}
     LICENSE = 'AGPL-3.0'


Test patch:
Repository: coala/coala-bears

Issue:
Set setup.py url = http://coala.io/
difficulty/newcomer
Opened by @jayvdb at [Gitter](https://gitter.im/coala/coala?at=5a1181aff257ad9109b396a0)


Discussion:
[GitMate.io](https://gitmate.io) thinks the contributor most likely able to help you is @coala-bot.

Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -72,7 +72,7 @@ def run(self):
           maintainer_email=('lasse.schuirmann@gmail.com, '
                             'fabian@neuschmidt.de, '
                             'makman@alice.de'),
-          url='http://coala.rtfd.org/',
+          url='http://coala.io/',
           platforms='any',
           packages=find_packages(exclude=('build.*', 'tests', 'tests.*')),
           install_requires=required,


Test patch:
Repository: coala/coala-bears

Issue:
HgCommitBear: Make asciinema



Discussion:
please @sangamcse assign this to me and please can you describe issue a little bit more .

@XLAR-8, this issue is reserved for GCI participants.
@sangamcse yes i know.
@jayvdb assingned me to this.

It isnt reserved for GCI until it has the label. ;P

Yes, I did say @XLAR-8 should do this one.
@XLAR-8 Have a look at asciinema of [GitCommitBear](https://github.com/coala/coala-bears/blob/master/bears/vcs/git/GitCommitBear.py). This asciinema will also look same; the only thing that will change is you need to work on `mercurial` in place `git`.
IMO, create one dummy repo using `mercurial` and add `.coafile` to that. Then, add one bad commit there and run `coala`.
@sangamcse working on it

@XLAR-8 I see that you are assigned. Are you still working on this?

Resolving patch:
diff --git a/bears/vcs/mercurial/HgCommitBear.py b/bears/vcs/mercurial/HgCommitBear.py
--- a/bears/vcs/mercurial/HgCommitBear.py
+++ b/bears/vcs/mercurial/HgCommitBear.py
@@ -9,6 +9,7 @@
 class HgCommitBear(_CommitBear):
     LANGUAGES = {'Hg'}
     CAN_DETECT = {'Formatting'}
+    ASCIINEMA_URL = 'https://asciinema.org/a/3Kfn2EDjYLmsbPoL7lRuLyhlN'
 
     @classmethod
     def check_prerequisites(cls):


Test patch:
Repository: coala/coala-bears

Issue:
PySafetyBear: Add asciinema 
Content of file on Bear will perform it's action also have to shown in asciinema.

difficulty/newcomer


Discussion:
[GitMate.io](https://gitmate.io) thinks possibly related issues are https://github.com/coala/coala-bears/issues/875 (PyDocStyleBear: Make asciinema), https://github.com/coala/coala-bears/issues/1081 (GofmtBear: Add advanced asciinema), https://github.com/coala/coala-bears/issues/1075 (JSONFormatBear: Add advanced asciinema), https://github.com/coala/coala-bears/issues/895 (YapfBear: Make asciinema ), and https://github.com/coala/coala-bears/issues/876 (PyImportSortBear: Make asciinema.).
Hello, could I get assigned please ?
@RaiVaibhav and iam new to this and excited to work on the issue. could you please assign me? iam also requesting for further description to get me started.
hello. tried to give this a go while waiting on an assignment, but in the process of trying to build my asciinemer, it reveals that asciicinema doesn't work out of the box on Windows. On my Win10 machine It fails with ImportError: No module named termios. iam going to install linux and try again. or is there another way?
Seems like, `termios` is Unix-only. But should work also pretty well from a Linux VM.
Reassigned to @rlemasquerier , as the PR wasnt creating the asciinema for PySafetyBear at all.
This issue reserved for Google Code-in task [5109379524198400](https://codein.withgoogle.com/dashboard/tasks/5109379524198400).
Can I take this issue?@jayvdb  @Makman2 @RaiVaibhav
It would be great if I get some insight on how to fix this issue.  

Resolving patch:
diff --git a/bears/python/requirements/PySafetyBear.py b/bears/python/requirements/PySafetyBear.py
--- a/bears/python/requirements/PySafetyBear.py
+++ b/bears/python/requirements/PySafetyBear.py
@@ -64,6 +64,7 @@ class PySafetyBear(LocalBear):
     AUTHORS_EMAILS = {'bence@underyx.me'}
     LICENSE = 'AGPL'
     CAN_DETECT = {'Security'}
+    ASCIINEMA_URL = 'https://asciinema.org/a/221386'
 
     def setup_dependencies(self):
         file = self.download_cached_file(_insecure_full_json_url,


Test patch:
Repository: coala/coala-bears

Issue:
Replace dep munkres3 with munkres
https://github.com/bmc/munkres now has Python 3 support, so we dont need to use https://github.com/datapublica/munkres

openSUSE already has the former, doesnt have the latter (c.f. https://github.com/coala/coala-bears/issues/2849)

https://packages.ubuntu.com/cosmic/python3-munkres appears to also be the former.


Discussion:
@jayvdb @li-boxuan I would like to work on this issue. Can anyone of you assign this to me ?

Resolving patch:
diff --git a/bears/c_languages/codeclone_detection/ClangFunctionDifferenceBear.py b/bears/c_languages/codeclone_detection/ClangFunctionDifferenceBear.py
--- a/bears/c_languages/codeclone_detection/ClangFunctionDifferenceBear.py
+++ b/bears/c_languages/codeclone_detection/ClangFunctionDifferenceBear.py
@@ -107,7 +107,7 @@ def get_difference(function_pair,
 class ClangFunctionDifferenceBear(GlobalBear):
     check_prerequisites = classmethod(clang_available)
     LANGUAGES = ClangBear.LANGUAGES
-    REQUIREMENTS = ClangBear.REQUIREMENTS | {PipRequirement('munkres3', '1.0')}
+    REQUIREMENTS = ClangBear.REQUIREMENTS | {PipRequirement('munkres', '1.1.2')}
 
     def run(self,
             counting_conditions: counting_condition_dict = default_cc_dict,


Test patch:
Repository: microsoft/MLOS

Issue:
Sphinx Python API docs generation broken in recent nightly CI runs
For example: <https://github.com/microsoft/MLOS/runs/1635132574?check_suite_focus=true>


Discussion:

Resolving patch:
diff --git a/source/Mlos.Python/mlos/Spaces/Point.py b/source/Mlos.Python/mlos/Spaces/Point.py
--- a/source/Mlos.Python/mlos/Spaces/Point.py
+++ b/source/Mlos.Python/mlos/Spaces/Point.py
@@ -55,7 +55,10 @@ def __getattr__(self, dimension_name):
         if dimension_name == "__isabstractmethod__":
             # A sad but necessary way to deal with ABC.
             return False
-        return self[dimension_name]
+        try:
+            return self[dimension_name]
+        except KeyError:
+            raise AttributeError(f"This Point does not have a {dimension_name} attribute.")
 
     def __setattr__(self, name, value):
         if name == "dimension_value_dict":


Test patch:
Repository: microsoft/MLOS

Issue:
flake8 and/or prettier setup for devcontainer
Per comments in #354 and #340 
We should "just" add flake8 and some type of auto prettier to the devcontainer setup so that those types of things are caught during dev cycle instead of review nits as much as possible.


Discussion:
#340 has two improvements for this:
- https://github.com/microsoft/MLOS/pull/340/commits/50b5cad3771f6f6d35c209ef2b53c4b0f0cff2b6
- https://github.com/microsoft/MLOS/pull/340/commits/cadc5f5faa4086d60d03fabe834afe52fc4201d6

Resolving patch:
diff --git a/mlos_bench/setup.py b/mlos_bench/setup.py
--- a/mlos_bench/setup.py
+++ b/mlos_bench/setup.py
@@ -18,14 +18,14 @@
     from setuptools_scm import get_version
     version = get_version(root='..', relative_to=__file__)
     if version is not None:
-        _VERSION = version
+        _VERSION = version  # noqa: F811
 except ImportError:
     warning("setuptools_scm not found, using version from _version.py")
 except LookupError as e:
     warning(f"setuptools_scm failed to find git version, using version from _version.py: {e}")
 
 
-extra_requires: Dict[str, List[str]] = {
+extra_requires: Dict[str, List[str]] = {    # pylint: disable=consider-using-namedtuple-or-dataclass
     # Additional tools for extra functionality.
     'azure': ['azure-storage-file-share'],
     'storage-sql-duckdb': ['sqlalchemy', 'duckdb_engine'],
diff --git a/mlos_core/setup.py b/mlos_core/setup.py
--- a/mlos_core/setup.py
+++ b/mlos_core/setup.py
@@ -18,14 +18,14 @@
     from setuptools_scm import get_version
     version = get_version(root='..', relative_to=__file__)
     if version is not None:
-        _VERSION = version
+        _VERSION = version  # noqa: F811
 except ImportError:
     warning("setuptools_scm not found, using version from _version.py")
 except LookupError as e:
     warning(f"setuptools_scm failed to find git version, using version from _version.py: {e}")
 
 
-extra_requires: Dict[str, List[str]] = {
+extra_requires: Dict[str, List[str]] = {  # pylint: disable=consider-using-namedtuple-or-dataclass
     'emukit': ['emukit'],
     'skopt': ['scikit-optimize<=0.9.0'],  # FIXME: temporarily work around some version mismatch issues (PR 850)
 }
@@ -52,10 +52,10 @@
         '': ['py.typed', '**/*.pyi'],
     },
     install_requires=[
-        'scikit-learn<1.2', # FIXME: temporarily work around some version mismatch issues (PR 850)
-        'joblib>=1.1.1',    # CVE-2022-21797: scikit-learn dependency, addressed in 1.2.0dev0, which isn't currently released
+        'scikit-learn<1.2',     # FIXME: temporarily work around some version mismatch issues (PR 850)
+        'joblib>=1.1.1',        # CVE-2022-21797: scikit-learn dependency, addressed in 1.2.0dev0, which isn't currently released
         'scipy>=1.3.2',
-        'numpy<1.24',       # FIXME: temporarily work around some version mismatch issues (PR 850)
+        'numpy<1.24',           # FIXME: temporarily work around some version mismatch issues (PR 850)
         'pandas>=1.0.3',
         'ConfigSpace>=0.6.1',
     ],


Test patch:
Repository: microsoft/MLOS

Issue:
Don't require `trial_id` to be specified in the globals config.
The value is generally not used anyways since it's pulled from the storage layer.

So, we should impute a sane default when not present in order to avoid unnecessary error messages.


Discussion:

Resolving patch:
diff --git a/mlos_bench/mlos_bench/launcher.py b/mlos_bench/mlos_bench/launcher.py
--- a/mlos_bench/mlos_bench/launcher.py
+++ b/mlos_bench/mlos_bench/launcher.py
@@ -88,6 +88,10 @@ def __init__(self, description: str, long_text: str = "", argv: Optional[List[st
             {key: val for (key, val) in config.items() if key not in vars(args)},
         )
         self.global_config = self._expand_vars(self.global_config)
+        assert isinstance(self.global_config, dict)
+        # Ensure that the trial_id is present since it gets used by some other
+        # configs but is typically controlled by the run optimize loop.
+        self.global_config.setdefault('trial_id', 1)
 
         env_path = args.environment or config.get("environment")
         if not env_path:
diff --git a/mlos_bench/mlos_bench/run.py b/mlos_bench/mlos_bench/run.py
--- a/mlos_bench/mlos_bench/run.py
+++ b/mlos_bench/mlos_bench/run.py
@@ -72,7 +72,7 @@ def _optimize(*,
         _LOG.info("Root Environment:\n%s", env.pprint())
 
     experiment_id = global_config["experiment_id"].strip()
-    trial_id = int(global_config.get("trial_id", 1))
+    trial_id = int(global_config["trial_id"])
     config_id = int(global_config.get("config_id", -1))
 
     # Start new or resume the existing experiment. Verify that the


Test patch:
diff --git a/mlos_bench/mlos_bench/tests/config/environments/test_load_environment_config_examples.py b/mlos_bench/mlos_bench/tests/config/environments/test_load_environment_config_examples.py
--- a/mlos_bench/mlos_bench/tests/config/environments/test_load_environment_config_examples.py
+++ b/mlos_bench/mlos_bench/tests/config/environments/test_load_environment_config_examples.py
@@ -50,6 +50,7 @@ def load_environment_config_examples(config_loader_service: ConfigPersistenceSer
     """Loads an environment config example."""
     # Make sure that any "required_args" are provided.
     global_config = config_loader_service.load_config("experiments/experiment_test_config.jsonc", ConfigSchema.GLOBALS)
+    global_config.setdefault('trial_id', 1)     # normally populated by Launcher
 
     # Make sure we have the required services for the envs being used.
     mock_service_configs = [
diff --git a/mlos_bench/mlos_bench/tests/config/experiments/experiment_test_config.jsonc b/mlos_bench/mlos_bench/tests/config/experiments/experiment_test_config.jsonc
--- a/mlos_bench/mlos_bench/tests/config/experiments/experiment_test_config.jsonc
+++ b/mlos_bench/mlos_bench/tests/config/experiments/experiment_test_config.jsonc
@@ -2,7 +2,6 @@
 // Specifically the azure-redis-bench and azure-redis-opt tests.
 {
     "experiment_id": "test",
-    "trial_id": 1,
 
     "mountPoint": "/mnt/tmp",
Repository: microsoft/MLOS

Issue:
Don't expose all params as shell environment variables by default
_Originally posted by @bpkroth in https://github.com/microsoft/MLOS/pull/557#discussion_r1374921396_
            


Discussion:

Resolving patch:
diff --git a/mlos_bench/mlos_bench/environments/script_env.py b/mlos_bench/mlos_bench/environments/script_env.py
--- a/mlos_bench/mlos_bench/environments/script_env.py
+++ b/mlos_bench/mlos_bench/environments/script_env.py
@@ -54,7 +54,7 @@ def __init__(self,
                   of the script parameters. If not specified, replace all
                   non-alphanumeric characters with underscores.
             If neither `shell_env_params` nor `shell_env_params_rename` are specified,
-            pass *all* parameters to the script.
+            *no* additional shell parameters will be passed to the script.
         global_config : dict
             Free-format dictionary of global parameters (e.g., security credentials)
             to be mixed in into the "const_args" section of the local config.
@@ -71,7 +71,7 @@ def __init__(self,
         self._script_run = self.config.get("run")
         self._script_teardown = self.config.get("teardown")
 
-        self._shell_env_params: Optional[Iterable[str]] = self.config.get("shell_env_params")
+        self._shell_env_params: Iterable[str] = self.config.get("shell_env_params", [])
         self._shell_env_params_rename: Dict[str, str] = self.config.get("shell_env_params_rename", {})
 
         results_stdout_pattern = self.config.get("results_stdout_pattern")
@@ -88,20 +88,8 @@ def _get_env_params(self) -> Dict[str, str]:
             Parameters to pass as *shell* environment variables into the script.
             This is usually a subset of `_params` with some possible conversions.
         """
-        rename: Dict[str, str]  # {to: from} mapping of the script parameters.
-        if self._shell_env_params is None:
-            if self._shell_env_params_rename:
-                # Only rename specified - use it.
-                rename = self._shell_env_params_rename.copy()
-            else:
-                # FIXME: We should not be exposing all params by default.
-                # Neither `shell_env_params` nor rename are specified - use all params.
-                rename = {self._RE_INVALID.sub("_", key): key for key in self._params}
-        else:
-            # Use `shell_env_params` and rename if specified.
-            rename = {self._RE_INVALID.sub("_", key): key for key in self._shell_env_params}
-            rename.update(self._shell_env_params_rename)
-
+        rename = {self._RE_INVALID.sub("_", key): key for key in self._shell_env_params}
+        rename.update(self._shell_env_params_rename)
         return {key_sub: str(self._params[key]) for (key_sub, key) in rename.items()}
 
     def _extract_stdout_results(self, stdout: str) -> Dict[str, TunableValue]:


Test patch:
Repository: platformsh/platformsh-docs

Issue:
Document the file location for build hooks
It turns out that when you run a build hook, the files are stored in `/app/out`.

Example hook to manually move a `settings.php` for a profile:

```
    build: |
        PROFILE=my_profile;
        ROOT=/app/out/public;
        rm $ROOT/sites/default/settings.php;
        mv $ROOT/profiles/$PROFILE/settings.php $ROOT/sites/default/;
```



Discussion:

Resolving patch:
diff --git a/_ext/github.py b/_ext/github.py
new file mode 100644
--- /dev/null
+++ b/_ext/github.py
@@ -0,0 +1,31 @@
+import os
+import warnings
+ 
+# Loosely based on https://gist.github.com/mgedmin/6052926 (BSD)
+ 
+def get_github_url(app, view, path):
+    return 'https://github.com/{project}/{view}/{branch}/{path}'.format(
+        project=app.config.github_project,
+        view=view,
+        branch=app.config.github_branch,
+        path=path,
+        )
+
+def html_page_context(app, pagename, templatename, context, doctree):
+    if templatename != 'page.html':
+        return
+ 
+    if not app.config.github_project:
+        return
+ 
+    path = os.path.relpath(doctree.get('source'), app.builder.srcdir)
+    show_url = get_github_url(app, 'blob', path)
+    edit_url = get_github_url(app, 'edit', path)
+ 
+    context['github_show_url'] = show_url
+    context['github_edit_url'] = edit_url
+  
+def setup(app):
+    app.add_config_value('github_project', '', True)
+    app.add_config_value('github_branch', 'master', True)
+    app.connect('html-page-context', html_page_context)
diff --git a/conf.py b/conf.py
--- a/conf.py
+++ b/conf.py
@@ -2,6 +2,7 @@
 
 import sys, os
 
+sys.path.insert(0, os.path.join(os.path.dirname(__file__), '_ext'))
 
 # -- General configuration -----------------------------------------------------
 
@@ -10,7 +11,7 @@
 
 # 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.viewcode', 'sphinx.ext.todo']
+extensions = ['sphinx.ext.viewcode', 'sphinx.ext.todo', 'github']
 
 # Set this to False if you don't want to display the todo.
 todo_include_todos = False
@@ -31,6 +32,9 @@
 project = u'Documentation'
 copyright = u'2014, Commerce Guys'
 
+github_project = 'platformsh/platformsh-docs'
+github_branch = 'dev'
+
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
@@ -128,7 +132,7 @@
 
 # Custom sidebar templates, maps document names to template names.
 html_sidebars = {
-  '**': ['searchbox.html', 'localtoc.html', 'support.html'],
+  '**': ['searchbox.html', 'localtoc.html', 'support.html', 'sourcelink.html'],
 }
 
 # Additional templates that should be rendered to pages, maps page names to
@@ -145,7 +149,7 @@
 #html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
-html_show_sourcelink = False
+html_show_sourcelink = True
 
 # If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
 html_show_sphinx = False


Test patch:
Repository: platformsh/platformsh-docs

Issue:
Poor search results
If I search on https://docs.platform.sh for "routes", I get the following results:

* https://docs.platform.sh/administration/web/configure-environment.html#routes
* https://docs.platform.sh/gettingstarted/introduction/own-code/routes-configuration.html
* https://docs.platform.sh/configuration/app/upgrading.html#platformroutesyaml
* https://docs.platform.sh/guides/gatsby/headless/drupal.html#platformroutesyaml
* https://docs.platform.sh/guides/gatsby/headless/strapi.html#platformroutesyaml
* https://docs.platform.sh/guides/gatsby/headless/wordpress.html#platformroutesyaml
* https://docs.platform.sh/guides/drupal9/deploy/configure.html#requests-configuration-routesyaml

Note the absence of the main resource on this topic: https://docs.platform.sh/configuration/routes.html

I've also tried "routes.yaml" and "configure routes" neither of which return the main routing configuration page.

The same issue appears to afflict these pages as well which seem near-impossible to locate by search:
* https://docs.platform.sh/configuration/services.html
* https://docs.platform.sh/configuration/app.html

Doing a bit of digging if I make the same search query with 1000 results limit the routes URL does not show up in the results, so perhaps it's not being indexed.


Discussion:

Resolving patch:
diff --git a/search/main.py b/search/main.py
--- a/search/main.py
+++ b/search/main.py
@@ -23,7 +23,7 @@ def __init__(self):
         # Data available to the dropdown React app in docs, used to fill out autocomplete results.
         self.displayed_attributes = ['title', 'text', 'url', 'site', 'section']
         # Data actually searchable by our queries.
-        self.searchable_attributes = ['title', 'text', 'section']
+        self.searchable_attributes = ['title', 'text', 'url', 'section']
 
         # Show results for one query with the listed pages, when they by default would not show up as best results. Note: these
         # are not automatically two-way, so that's why they all appear to be defined twice.


Test patch: