>>> import pdb, test3
>>> pdb.run("reload(test3)")
> <string>(1)<module>()
(Pdb) s
--Call--
> c:\documents and settings\perry\desktop\coding_projects\python\test3.py(1)<module>()
-> foo = 7789
(Pdb) b 2
Breakpoint 1 at c:\documents and settings\perry\desktop\coding_projects\python\test3.py:2
(Pdb) c
> c:\documents and settings\perry\desktop\coding_projects\python\test3.py(2)<module>()
-> bar = 7788
(Pdb) c
>>> pdb.run("reload(test3)")
> <string>(1)<module>()
(Pdb) s
--Call--
> c:\documents and settings\perry\desktop\coding_projects\python\test3.py(1)<module>()
-> foo = 7789
(Pdb) b 1
Breakpoint 2 at c:\documents and settings\perry\desktop\coding_projects\python\test3.py:1
(Pdb) cl 1

Traceback (most recent call last):
  File "<pyshell#592>", line 1, in <module>
    pdb.run("reload(test3)")
  File "C:\Python27\lib\pdb.py", line 1238, in run
    Pdb().run(statement, globals, locals)
  File "C:\Python27\lib\bdb.py", line 400, in run
    exec cmd in globals, locals
  File "<string>", line 1, in <module>
  File "test3.py", line 1, in <module>
    foo = 7789
  File "C:\Python27\lib\bdb.py", line 51, in trace_dispatch
    return self.dispatch_call(frame, arg)
  File "C:\Python27\lib\bdb.py", line 80, in dispatch_call
    self.user_call(frame, arg)
  File "C:\Python27\lib\pdb.py", line 148, in user_call
    self.interaction(frame, None)
  File "C:\Python27\lib\pdb.py", line 210, in interaction
    self.cmdloop()
  File "C:\Python27\lib\cmd.py", line 142, in cmdloop
    stop = self.onecmd(line)
  File "C:\Python27\lib\pdb.py", line 279, in onecmd
    return cmd.Cmd.onecmd(self, line)
  File "C:\Python27\lib\cmd.py", line 221, in onecmd
    return func(arg)
  File "C:\Python27\lib\pdb.py", line 622, in do_clear
    err = self.clear_bpbynumber(i)
  File "C:\Python27\lib\bdb.py", line 297, in clear_bpbynumber
    self._prune_breaks(bp.file, bp.line)
  File "C:\Python27\lib\bdb.py", line 268, in _prune_breaks
    self.breaks[filename].remove(lineno)
ValueError: list.remove(x): x not in list
Running the same code without first defining a breakpoint (in the second debugger instance) raises KeyError: [path to test3.py] on the same lien
The contents of test3.py are irrelevant, as long as it is at least two lines long and syntactically correct.

I can reproduce the problem on python 3.5 with test3.py as:
def foo():
    foo = 7789
    bar = 7788

$ python
Python 3.5.0a4+ (default:8bac00eadfda, May  6 2015, 17:40:12) 
[GCC 4.9.2 20150304 (prerelease)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pdb, test3
>>> pdb.run('test3.foo()')
> <string>(1)<module>()
(Pdb) step
--Call--
> /home/xavier/tmp/test3.py(1)foo()
-> def foo():
(Pdb) break 3
Breakpoint 1 at /home/xavier/tmp/test3.py:3
(Pdb) continue
> /home/xavier/tmp/test3.py(3)foo()
-> bar = 7788
(Pdb) continue
>>> pdb.run('test3.foo()')
> <string>(1)<module>()
(Pdb) step
--Call--
> /home/xavier/tmp/test3.py(1)foo()
-> def foo():
(Pdb) break                                   # 'break' lists no breakpoints.
(Pdb) break 2
Breakpoint 2 at /home/xavier/tmp/test3.py:2
(Pdb) break                                   # 'break' lists two breakpoints.
Num Type         Disp Enb   Where
1   breakpoint   keep yes   at /home/xavier/tmp/test3.py:3
        breakpoint already hit 1 time
2   breakpoint   keep yes   at /home/xavier/tmp/test3.py:2
(Pdb) 


On the second debugging session, the first 'break' command lists no
breakpoints, while the second 'break' command lists two breakpoints including
the one set in the first debugging session.

The problem is that the 'breaks' attribute of the Pdb instance is inconsistent
with the 'bplist' and 'bpbynumber' class attributes of the bdb.Breakpoint
class when the second debugging session is started.

I've submitted a patch that I believe fixes this problem. It adds in Bdb's __init__ a call to a function that reads the Breakpoint's 'bplist' and 'bpbynumber' class attributes and populates the new instances' 'breaks' dict.

Irit, I like the approach of your PR for an immediate fix, that we could consider backporting.

In the long term, ISTM that we should refactor to store the breakpoints with only a single source of truth, and avoid the duplication between Breakpoint.bplist, Breakpoint.bpbynumber and Bdb.breaks.

New changeset ad442a674ca443feec43a88a2d3671784712e550 by Irit Katriel in branch 'master':
bpo-24160: Fix breakpoints persistence across multiple pdb sessions (GH-21989)
https://github.com/python/cpython/commit/ad442a674ca443feec43a88a2d3671784712e550

Thanks!

Unfortunately PR21989 has breaking the refleaks buildbots. Example:

https://buildbot.python.org/all/#/builders/320/builds/226/steps/5/logs/stdio

To reproduce:

❯ ./python -m test test_pdb -R 3:3
0:00:00 load avg: 1.40 Run tests sequentially
0:00:00 load avg: 1.40 [1/1] test_pdb
beginning 6 repetitions
123456
.test test_pdb failed -- Traceback (most recent call last):
  File "/home/pablogsal/github/cpython/Lib/doctest.py", line 2205, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for test.test_pdb.test_pdb_breakpoints_preserved_across_interactive_sessions
  File "/home/pablogsal/github/cpython/Lib/test/test_pdb.py", line 326, in test_pdb_breakpoints_preserved_across_interactive_sessions

----------------------------------------------------------------------
File "/home/pablogsal/github/cpython/Lib/test/test_pdb.py", line 330, in test.test_pdb.test_pdb_breakpoints_preserved_across_interactive_sessions
Failed example:
    with PdbTestInput([  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
       'import test.test_pdb',
       'break test.test_pdb.do_something',
       'break test.test_pdb.do_nothing',
       'break',
       'continue',
    ]):
       pdb.run('print()')
Expected:
    > <string>(1)<module>()
    (Pdb) import test.test_pdb
    (Pdb) break test.test_pdb.do_something
    Breakpoint 1 at ...test_pdb.py:...
    (Pdb) break test.test_pdb.do_nothing
    Breakpoint 2 at ...test_pdb.py:...
    (Pdb) break
    Num Type         Disp Enb   Where
    1   breakpoint   keep yes   at ...test_pdb.py:...
    2   breakpoint   keep yes   at ...test_pdb.py:...
    (Pdb) continue
Got:
    > <string>(1)<module>()->None
    (Pdb) import test.test_pdb
    (Pdb) break test.test_pdb.do_something
    Breakpoint 1 at /home/pablogsal/github/cpython/Lib/test/test_pdb.py:396
    (Pdb) break test.test_pdb.do_nothing
    Breakpoint 2 at /home/pablogsal/github/cpython/Lib/test/test_pdb.py:393
    (Pdb) break
    Num Type         Disp Enb   Where
    1   breakpoint   keep yes   at /home/pablogsal/github/cpython/Lib/test/test_pdb.py:396
    2   breakpoint   keep yes   at /home/pablogsal/github/cpython/Lib/test/test_pdb.py:393
    (Pdb) continue
    <BLANKLINE>
----------------------------------------------------------------------
File "/home/pablogsal/github/cpython/Lib/test/test_pdb.py", line 350, in test.test_pdb.test_pdb_breakpoints_preserved_across_interactive_sessions
Failed example:
    with PdbTestInput([  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
       'break',
       'break pdb.find_function',
       'break',
       'clear 1',
       'continue',
    ]):
       pdb.run('print()')
Expected:
    > <string>(1)<module>()
    (Pdb) break
    Num Type         Disp Enb   Where
    2   breakpoint   keep yes   at ...test_pdb.py:...
    3   breakpoint   keep yes   at ...pdb.py:...
    (Pdb) clear 2
    Deleted breakpoint 2 at ...test_pdb.py:...
    (Pdb) clear 3
    Deleted breakpoint 3 at ...pdb.py:...
    (Pdb) continue
Got:
    > <string>(1)<module>()->None
    (Pdb) break
    Num Type         Disp Enb   Where
    2   breakpoint   keep yes   at /home/pablogsal/github/cpython/Lib/test/test_pdb.py:393
    3   breakpoint   keep yes   at /home/pablogsal/github/cpython/Lib/pdb.py:94
    (Pdb) clear 2
    Deleted breakpoint 2 at /home/pablogsal/github/cpython/Lib/test/test_pdb.py:393
    (Pdb) clear 3
    Deleted breakpoint 3 at /home/pablogsal/github/cpython/Lib/pdb.py:94
    (Pdb) continue
    <BLANKLINE>


test_pdb failed

== Tests result: FAILURE ==

1 test failed:
    test_pdb

Total duration: 2.8 sec
Tests result: FAILURE

Per our buildbot policy (https://discuss.python.org/t/policy-to-revert-commits-on-buildbot-failure/404) we will need to revert this in 24 hours if is not fixed to avoid masking future errors.

Thanks, I'm looking.

With the patch:

PS C:\Users\User\src\cpython-dev> ./python -m test test_pdb -R 3:3
Running Debug|x64 interpreter...
0:00:00 Run tests sequentially
0:00:00 [1/1] test_pdb
beginning 6 repetitions
123456
......

== Tests result: SUCCESS ==

1 test OK.

Total duration: 34.2 sec
Tests result: SUCCESS

New changeset aadd4e10fda87b64ea527667238503da326a06e7 by Irit Katriel in branch 'master':
bpo-24160: Fix test_pdb refleaks failure (GH-25182)
https://github.com/python/cpython/commit/aadd4e10fda87b64ea527667238503da326a06e7

PR 25182 fixes the issue, so I am closing this again.

Thanks for the quick fix, Irit!