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

Issue:
Deprecate the old 'pyomo' command syntax
In earlier releases, we supported commands like
`  pyomo --solver=glpk foo.py bar.dat`
And we moved to a nested pyomo command, which uses the following syntax:
`  pyomo solve --solver=glpk foo.py bar.dat`

However, to enable graceful transition for users, we added a hack to transition to the old syntax if it looks like the user is not specifying a valid subcommand.  However, this leads to confusing error messages, and I think it's time to deprecate that hack and start throwing warnings that this hack will be removed in an upcoming release.


Discussion:
This has already been done, in that the warning is already there.
Reopening until I submit a PR to turn it into a true deprecation warning instead of just a "warning."

Resolving patch:
diff --git a/pyomo/scripting/pyomo_main.py b/pyomo/scripting/pyomo_main.py
--- a/pyomo/scripting/pyomo_main.py
+++ b/pyomo/scripting/pyomo_main.py
@@ -11,6 +11,7 @@
 
 import sys
 import copy
+from pyomo.common.deprecation import deprecation_warning
 
 try:
     import pkg_resources
@@ -59,13 +60,16 @@ def main(args=None):
     #
     if not args:
         args.append('-h')
-    # FIXME: This should use the logger and not print()
     if args[0][0] == '-':
         if args[0] not in ['-h', '--help', '--version']:
-            print("WARNING: converting to the 'pyomo solve' subcommand")
+            deprecation_warning("Running the 'pyomo' script with no subcommand is deprecated. "
+                                "Defaulting to 'pyomo solve'",
+                                version='TBD')
             args = ['solve'] + args[0:]
     elif args[0] not in pyomo_parser.subparsers:
-        print("WARNING: converting to the 'pyomo solve' subcommand")
+        deprecation_warning("Running the 'pyomo' script with no subcommand is deprecated. "
+                            "Defaulting to 'pyomo solve'",
+                            version='TBD')
         args = ['solve'] + args[0:]
     #
     # Process arguments


Test patch:
diff --git a/pyomo/scripting/tests/test_cmds.py b/pyomo/scripting/tests/test_cmds.py
--- a/pyomo/scripting/tests/test_cmds.py
+++ b/pyomo/scripting/tests/test_cmds.py
@@ -12,12 +12,21 @@
 import re
 import pyomo.common.unittest as unittest
 from pyomo.common.tee import capture_output
+from pyomo.common.log import LoggingIntercept
 
 from pyomo.environ import SolverFactory
 from pyomo.scripting.driver_help import help_solvers, help_transformations
+from pyomo.scripting.pyomo_main import main
 
 
 class Test(unittest.TestCase):
+
+    def test_pyomo_main_deprecation(self):
+        with LoggingIntercept() as LOG:
+            with unittest.pytest.raises(SystemExit) as e:
+                main(args=['--solvers=glpk', 'foo.py'])
+        self.assertIn("Running the 'pyomo' script with no subcommand", LOG.getvalue())
+
     def test_help_solvers(self):
         with capture_output() as OUT:
             help_solvers()
Repository: Pyomo/pyomo

Issue:
DataPortal bug
# bug found by: Maria Marcos Nuñez
```python
from pyomo.environ import *
model = AbstractModel()

# Definición de los diferentes parametros del modelo
model.qv = Param(within = NonNegativeReals)

# Definicion de las variables
model.D = Var(within = NonNegativeReals, bounds =(0.2, 6),initialize = 3, doc='Diametro del reactor')

# silly objective function supplied by DLW
def _e(m):
    return m.qv * m.D
model.silliness = Objective(rule=_e)

data = DataPortal()
data.load(filename="foobar.dat")
mc = model.create_instance(data)
```

# contents of foobar.dat:
```
param qv := 7.734;
```

# output (after stack trace):
```
ValueError: Parameter 'qv' defined with '1' dimensions, but data has '1' values: [7.734]. Are you missing a value for a 1-dimensional index?
```




Discussion:
This bug is still present in `pyomo 5.7.1`.
@alok-kinesso - I'm going through old bug reports. Is this bug still present in `pyomo 6.2`?
 @alok-kinesso, @mrmundt

I just tried this in pyomo 6.4 and got a similar error as is listed here.

A little more detail, attempting to initialize a scalar param. 

Resolving patch:
diff --git a/pyomo/dataportal/process_data.py b/pyomo/dataportal/process_data.py
--- a/pyomo/dataportal/process_data.py
+++ b/pyomo/dataportal/process_data.py
@@ -343,7 +343,8 @@ def _process_param(cmd, _model, _data, _default, index=None, param=None, ncolumn
                         _dim = _guess_set_dimen(_param.index_set())
                     finaldata = _process_data_list(pname, _dim, cmd)
                 else:
-                    finaldata = _process_data_list(pname, 1, cmd)
+                    _dim = 1 if len(cmd) > 1 else 0
+                    finaldata = _process_data_list(pname, _dim, cmd)
                 for key in finaldata:
                     _data[pname][key] = finaldata[key]
             else:


Test patch:
diff --git a/pyomo/dataportal/tests/data17.dat b/pyomo/dataportal/tests/data17.dat
new file mode 100644
--- /dev/null
+++ b/pyomo/dataportal/tests/data17.dat
@@ -0,0 +1,10 @@
+param A := 1;
+
+param B := a 1;
+
+param C := 
+a 1
+b 2
+c 3;
+
+table D := 1; 
\ No newline at end of file
diff --git a/pyomo/dataportal/tests/test_dataportal.py b/pyomo/dataportal/tests/test_dataportal.py
--- a/pyomo/dataportal/tests/test_dataportal.py
+++ b/pyomo/dataportal/tests/test_dataportal.py
@@ -669,6 +669,20 @@ def test_md17(self):
         except IOError:
             pass
 
+    def test_md18(self):
+        cwd = os.getcwd()
+        os.chdir(currdir)
+
+        md = DataPortal()
+        md.load(filename=currdir + "data17.dat")
+
+        self.assertEqual(md['A'], 1)
+        self.assertEqual(md['B'], {'a': 1})
+        self.assertEqual(md['C'], {'a': 1, 'b': 2, 'c': 3})
+        self.assertEqual(md['D'], 1)
+
+        os.chdir(cwd)
+
     def test_dat_type_conversion(self):
         model = AbstractModel()
         model.I = Set()
Repository: Pyomo/pyomo

Issue:
GDPOpt.LBB: name 'solve_data' is not defined
## Summary

<!-- Explain, in a clear and concise way, the command you ran and the result you were trying to achieve.
Example: "I ran `pyomo solve` to optimize a model and ..." -->

While working with `LBB` in `GDPOpt`, I encountered an error related to `solve_data`. It appears that `solve_data` was supposed to be eliminated in the last update, but it seems we overlooked a couple of instances.

### Error Message

<!-- If Pyomo reported an error, provide the error message. PLEASE INCLUDE THE ENTIRE STACK TRACE. -->

<!-- If it did not report an error but the output appears incorrect, provide the incorrect output. If there was no error message and no output but the result is incorrect, describe how it does not match what you expect. -->
```console
$ # Output message here, including entire stack trace, if available
  File "/local/scratch/a/peng372/github/LD-DSA-Dynamic/benchmark.py", line 148, in <module>
    results = solver.solve(
              ^^^^^^^^^^^^^
  File "/local/scratch/a/peng372/anaconda3/lib/python3.11/site-packages/pyomo/contrib/gdpopt/branch_and_bound.py", line 92, in solve
    return super().solve(model, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/local/scratch/a/peng372/anaconda3/lib/python3.11/site-packages/pyomo/contrib/gdpopt/algorithm_base_class.py", line 130, in solve
    self._solve_gdp(model, config)
  File "/local/scratch/a/peng372/anaconda3/lib/python3.11/site-packages/pyomo/contrib/gdpopt/branch_and_bound.py", line 233, in _solve_gdp
    if solve_data.objective_sense == minimize
       ^^^^^^^^^^
NameError: name 'solve_data' is not defined. Did you mean: 'node_data'?
```

### Information on your system

Pyomo version: 6.7.1.dev0
Python version: Python 3.9.18 (pypy)
Operating system: Linux (CentOS)
How Pyomo was installed (PyPI, conda, source): source



Discussion:
@emma58 

Resolving patch:
diff --git a/pyomo/contrib/gdpopt/branch_and_bound.py b/pyomo/contrib/gdpopt/branch_and_bound.py
--- a/pyomo/contrib/gdpopt/branch_and_bound.py
+++ b/pyomo/contrib/gdpopt/branch_and_bound.py
@@ -230,12 +230,12 @@ def _solve_gdp(self, model, config):
                 no_feasible_soln = float('inf')
                 self.LB = (
                     node_data.obj_lb
-                    if solve_data.objective_sense == minimize
+                    if self.objective_sense == minimize
                     else -no_feasible_soln
                 )
                 self.UB = (
                     no_feasible_soln
-                    if solve_data.objective_sense == minimize
+                    if self.objective_sense == minimize
                     else -node_data.obj_lb
                 )
                 config.logger.info(


Test patch:
Repository: python-telegram-bot/python-telegram-bot

Issue:
Disable logging
Create a setting that allows you to disable logging output to the screen.
Even disabled debug, the program sends information messages to the screen.

2015-07-29 17:25:49,424 - telegram.bot - INFO - Starting bot @xxxxxxx_bot
2015-07-29 17:25:50,621 - telegram.bot - INFO - Getting updates: [434449746, 435444747, 444449748, 435444449, 4358444440, 4344444751, 4354444452]



Discussion:

Resolving patch:
diff --git a/examples/echobot.py b/examples/echobot.py
--- a/examples/echobot.py
+++ b/examples/echobot.py
@@ -2,21 +2,36 @@
 
 '''Simple Bot to reply Telegram messages'''
 
+import logging
 import telegram
 import time
 
-# Telegram Bot Authorization Token
-bot = telegram.Bot('TOKEN')
 
-# This will be our global variable to keep the latest update_id when requesting
-# for updates. It starts with the latest update_id if available.
-try:
-    LAST_UPDATE_ID = bot.getUpdates()[-1].update_id
-except IndexError:
-    LAST_UPDATE_ID = None
+LAST_UPDATE_ID = None
 
 
-def echo():
+def main():
+    global LAST_UPDATE_ID
+
+    logging.basicConfig(
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
+
+    # Telegram Bot Authorization Token
+    bot = telegram.Bot('TOKEN')
+
+    # This will be our global variable to keep the latest update_id when requesting
+    # for updates. It starts with the latest update_id if available.
+    try:
+        LAST_UPDATE_ID = bot.getUpdates()[-1].update_id
+    except IndexError:
+        LAST_UPDATE_ID = None
+
+    while True:
+        echo(bot)
+        time.sleep(3)
+
+
+def echo(bot):
     global LAST_UPDATE_ID
 
     # Request updates from last updated_id
@@ -36,6 +51,4 @@ def echo():
 
 
 if __name__ == '__main__':
-    while True:
-        echo()
-        time.sleep(3)
+    main()
diff --git a/examples/roboed.py b/examples/roboed.py
--- a/examples/roboed.py
+++ b/examples/roboed.py
@@ -5,14 +5,16 @@
 
 __author__ = 'leandrotoledodesouza@gmail.com'
 
+import logging
 import telegram
 import urllib
 
 
 def main():
+    logging.basicConfig(
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
     bot = telegram.Bot('TOKEN')  # Telegram Bot Authorization Token
 
-    global LAST_UPDATE_ID
     LAST_UPDATE_ID = bot.getUpdates()[-1].update_id  # Get lastest update
 
     while True:
diff --git a/telegram/bot.py b/telegram/bot.py
--- a/telegram/bot.py
+++ b/telegram/bot.py
@@ -18,9 +18,6 @@
 from telegram import (User, Message, Update, UserProfilePhotos, TelegramError,
                       ReplyMarkup, InputFile, TelegramObject)
 
-logging.basicConfig(
-    format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
-
 
 class Bot(TelegramObject):
 


Test patch:
diff --git a/telegram_test.py b/telegram_test.py
--- a/telegram_test.py
+++ b/telegram_test.py
@@ -1,6 +1,9 @@
+import logging
 import unittest
 from tests.test_bot import BotTest
 
 if __name__ == '__main__':
+    logging.basicConfig(
+        format='%(asctime)s - %(name)s - %(levelname)s - %(message)s')
     testsuite = unittest.TestLoader().loadTestsFromTestCase(BotTest)
     unittest.TextTestRunner(verbosity=1).run(testsuite)
Repository: python-telegram-bot/python-telegram-bot

Issue:
@ character
If I type @ in a chat I got this. (using https://github.com/leandrotoledo/python-telegram-bot/blob/master/examples/echobot.py)

TypeError: b'hola @honguitobot' is not JSON serializable



Discussion:
The error isn't about the `@`, it's about the byte array not being serializable. Hmmm... interesting

I can reproduce on py3:

```
Traceback (most recent call last):
  File "echobot.py", line 66, in <module>
    main()
  File "echobot.py", line 44, in main
    echo(bot)
  File "echobot.py", line 59, in echo
    text=message)
  File "/home/fd/src/tgbots/venv/lib/python3.5/site-packages/telegram/bot.py", line 126, in decorator
    result = func(self, *args, **kwargs)
  File "/home/fd/src/tgbots/venv/lib/python3.5/site-packages/telegram/bot.py", line 158, in decorator
    result = request.post(url, data)
  File "/home/fd/src/tgbots/venv/lib/python3.5/site-packages/telegram/utils/request.py", line 88, in post
    data = json.dumps(data)
  File "/usr/lib64/python3.5/json/__init__.py", line 230, in dumps
    return _default_encoder.encode(obj)
  File "/usr/lib64/python3.5/json/encoder.py", line 199, in encode
    chunks = self.iterencode(o, _one_shot=True)
  File "/usr/lib64/python3.5/json/encoder.py", line 257, in iterencode
    return _iterencode(o, 0)
  File "/usr/lib64/python3.5/json/encoder.py", line 180, in default
    raise TypeError(repr(o) + " is not JSON serializable")
TypeError: b'this is an echo test' is not JSON serializable
```

Dropping the `.encode('utf-8')` part fixes it, and it works on 2.7.10 and 3.5.0


Resolving patch:
diff --git a/examples/echobot.py b/examples/echobot.py
--- a/examples/echobot.py
+++ b/examples/echobot.py
@@ -51,12 +51,12 @@ def echo(bot):
     for update in bot.getUpdates(offset=LAST_UPDATE_ID, timeout=10):
         # chat_id is required to reply any message
         chat_id = update.message.chat_id
-        message = update.message.text.encode('utf-8')
+        reply_text = update.message.text
 
-        if (message):
+        if (reply_text):
             # Reply the message
             bot.sendMessage(chat_id=chat_id,
-                            text=message)
+                            text=reply_text)
 
             # Updates global offset to get the new updates
             LAST_UPDATE_ID = update.update_id + 1


Test patch:
Repository: python-telegram-bot/python-telegram-bot

Issue:
Execfile does not exist in py3k
<!--
Thanks for reporting issues of python-telegram-bot!
To make it easier for us to help you please enter detailed information below.

Please note, we only support the latest version of python-telegram-bot and
master branch. Please make sure to upgrade & recreate the issue on the latest
version prior to opening an issue.
-->
### Steps to reproduce
1. Use python 3
2. Try to install from git:
   `$ pip install -e git+https://github.com/python-telegram-bot/python-telegram-bot.git@555e36ee8036a179f157f60dcb0c3fcf958146f4#egg=telegram`
### Expected behaviour

The library should be installed.
### Actual behaviour

NameError due to `execfile` not being a thing in python 3.
See here for alternatives: https://stackoverflow.com/a/437857
I would fix it myself, but I am unable to actually find the execfile call anywhere .-.
### Configuration

**Operating System:**
Windows 10 Education

**Version of Python, python-telegram-bot & dependencies:**
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 5 2016, 11:41:13) [MSC v.1900 64 bit (AMD64)]
### Logs

``````
$ pip install -e git+https://github.com/python-telegram-bot/python-telegram-bot.git@555e36ee8036a179f157f60dcb0c3fcf958146f4#egg=telegram
Obtaining telegram from git+https://github.com/python-telegram-bot/python-telegram-bot.git@555e36ee8036a179f157f60dcb0c3fcf958146f4#egg=telegram
  Skipping because already up-to-date.
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Development\telegram\VocaBot2\src\telegram\setup.py", line 20, in <module>
        execfile(os.path.join('telegram', 'version.py'))
    NameError: name 'execfile' is not defined
Command "python setup.py egg_info" failed with error code 1```
``````



Discussion:
Actually nevermind, turns out I was looking for the execfile on a very old version of the library... I'll go make a pull-request.


Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -16,6 +16,13 @@ def requirements():
 
     return requirements_list
 
+
+def execfile(fn):
+    with open(fn) as f:
+        code = compile(f.read(), fn, 'exec')
+        exec(code)
+
+
 with codecs.open('README.rst', 'r', 'utf-8') as fd:
     execfile(os.path.join('telegram', 'version.py'))
 


Test patch:
Repository: python-telegram-bot/python-telegram-bot

Issue:
Execfile does not exist in py3k
<!--
Thanks for reporting issues of python-telegram-bot!
To make it easier for us to help you please enter detailed information below.

Please note, we only support the latest version of python-telegram-bot and
master branch. Please make sure to upgrade & recreate the issue on the latest
version prior to opening an issue.
-->
### Steps to reproduce
1. Use python 3
2. Try to install from git:
   `$ pip install -e git+https://github.com/python-telegram-bot/python-telegram-bot.git@555e36ee8036a179f157f60dcb0c3fcf958146f4#egg=telegram`
### Expected behaviour

The library should be installed.
### Actual behaviour

NameError due to `execfile` not being a thing in python 3.
See here for alternatives: https://stackoverflow.com/a/437857
I would fix it myself, but I am unable to actually find the execfile call anywhere .-.
### Configuration

**Operating System:**
Windows 10 Education

**Version of Python, python-telegram-bot & dependencies:**
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 5 2016, 11:41:13) [MSC v.1900 64 bit (AMD64)]
### Logs

``````
$ pip install -e git+https://github.com/python-telegram-bot/python-telegram-bot.git@555e36ee8036a179f157f60dcb0c3fcf958146f4#egg=telegram
Obtaining telegram from git+https://github.com/python-telegram-bot/python-telegram-bot.git@555e36ee8036a179f157f60dcb0c3fcf958146f4#egg=telegram
  Skipping because already up-to-date.
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "C:\Development\telegram\VocaBot2\src\telegram\setup.py", line 20, in <module>
        execfile(os.path.join('telegram', 'version.py'))
    NameError: name 'execfile' is not defined
Command "python setup.py egg_info" failed with error code 1```
``````



Discussion:
Actually nevermind, turns out I was looking for the execfile on a very old version of the library... I'll go make a pull-request.


Resolving patch:
diff --git a/setup.py b/setup.py
--- a/setup.py
+++ b/setup.py
@@ -16,8 +16,12 @@ def requirements():
 
     return requirements_list
 
+
 with codecs.open('README.rst', 'r', 'utf-8') as fd:
-    execfile(os.path.join('telegram', 'version.py'))
+    fn = os.path.join('telegram', 'version.py')
+    with open(fn) as fh:
+        code = compile(fh.read(), fn, 'exec')
+        exec(code)
 
     setup(name='python-telegram-bot',
           version=__version__,


Test patch:
Repository: python-telegram-bot/python-telegram-bot

Issue:
edit_reply_markup is calling edit_message_caption
```
    def edit_reply_markup(self, *args, **kwargs):
        """
        Shortcut for

            >>> bot.editReplyMarkup(chat_id=message.chat_id,
            ...                     message_id=message.message_id,
            ...                     *args, **kwargs)

        Note:
            You can only edit messages that the bot sent itself,
            therefore this method can only be used on the
            return value of the ``bot.send_*`` family of methods.
        """
        return self.bot.edit_message_caption(
            chat_id=self.chat_id, message_id=self.message_id, *args, **kwargs)
```


Discussion:

Resolving patch:
diff --git a/telegram/message.py b/telegram/message.py
--- a/telegram/message.py
+++ b/telegram/message.py
@@ -494,7 +494,7 @@ def edit_reply_markup(self, *args, **kwargs):
             therefore this method can only be used on the
             return value of the ``bot.send_*`` family of methods.
         """
-        return self.bot.edit_message_caption(
+        return self.bot.edit_message_reply_markup(
             chat_id=self.chat_id, message_id=self.message_id, *args, **kwargs)
 
     def parse_entity(self, entity):


Test patch:
Repository: python-telegram-bot/python-telegram-bot

Issue:
BadRequest message has wrong format (u"Bad Request: ...")
### Steps to reproduce
1. Create an `Updater` with a valid bot token.

2. Call `bot.sendMessage` which will raise a BadRequest, such as with `parse_mode="HTML"` and `text="<b>"` (unclosed tag)

3. Catch the exception and read it. `except BadRequest as e: look_at(e.message)`

### Expected behaviour
BadRequest message should say: `Can't parse message text: Can't found end tag corresponding to start tag at byte offset 0`

### Actual behaviour
BadReqeust message actually says: `u"Bad Request: Can't parse message text: Can't found end tag corresponding to start tag at byte offset 0"` (notice it's literally surrounded with u" ")

### Configuration
**Operating System:**
Debian

**Version of Python, python-telegram-bot & dependencies:**


``$ python -m telegram``
python-telegram-bot 5.2.0
urllib3 1.19.1
certifi 2016.09.26
future 0.16.0
Python 2.7.6 (default, Jun 22 2015, 17:58:13)  [GCC 4.8.2]


### Notes

Notice the repr(message):

https://github.com/python-telegram-bot/python-telegram-bot/blob/master/telegram/utils/request.py#L152

Should the repr call be removed, or should message have another format?



Discussion:
Alright, after discussing with @tsnoam it seems that it's just a bug, which we will fix in the next major release. 

Resolving patch:
diff --git a/telegram/bot.py b/telegram/bot.py
--- a/telegram/bot.py
+++ b/telegram/bot.py
@@ -415,7 +415,7 @@ def sendDocument(self,
             chat_id: Unique identifier for the message recipient - Chat id.
             document: File to send. You can either pass a file_id as String to resend a file that
                 is already on the Telegram servers, or upload a new file using multipart/form-data.
-            filename (Optional[str]): File name that shows in telegram message (it is usefull when
+            filename (Optional[str]): File name that shows in telegram message (it is useful when
                 you send file generated by temp module, for example).
             caption (Optional[str]): Document caption (may also be used when resending documents by
                 file_id), 0-200 characters.
diff --git a/telegram/utils/request.py b/telegram/utils/request.py
--- a/telegram/utils/request.py
+++ b/telegram/utils/request.py
@@ -173,7 +173,7 @@ def _request_wrapper(self, *args, **kwargs):
         if resp.status in (401, 403):
             raise Unauthorized()
         elif resp.status == 400:
-            raise BadRequest(repr(message))
+            raise BadRequest(message)
         elif resp.status == 404:
             raise InvalidToken()
         elif resp.status == 502:


Test patch:
diff --git a/tests/test_bot.py b/tests/test_bot.py
--- a/tests/test_bot.py
+++ b/tests/test_bot.py
@@ -365,7 +365,7 @@ def test_set_game_score3(self):
                 chat_id=game.chat_id,
                 message_id=game.message_id)
 
-        self.assertTrue('BOT_SCORE_NOT_MODIFIED' in cm.exception.message)
+        self.assertTrue('BOT_SCORE_NOT_MODIFIED' in str(cm.exception.message).upper())
 
     @flaky(3, 1)
     @timeout(10)