Implement PEP561 #4693

ethanhs · 2018-03-07T11:36:34Z

This is an implementation of PEP 561. I am picking up from #4403 because I'd rather not rebase over 100 commits (and some of the changes shouldn't go in!). Third times a charm I hope :)

Tasks:

Test PEP 561 implementation
Check PEP 561 conformance to resolution order
support running with alternate Python executable --python-executable
document PEP 561 features
document --python-executable flag
test --python-executable flag
test --no-site-packages flag
document --no-site-packages flag
--python-version flag sets --python-executable and visa-versa if possible

This branch likely works as intended and is feature complete, but it is possible that I've overlooked something/made a mistake.

Fixes #2625, #1190, #965.

eric-wieser · 2018-03-07T12:02:27Z

mypy/build.py

@@ -804,7 +806,7 @@ def remove_cwd_prefix_from_path(p: str) -> str:


 # Cache find_module: (id, lib_path) -> result.


This comment needs updating

eric-wieser · 2018-03-07T12:04:53Z

mypy/build.py

    """Return the path of the module source file, or None if not found."""
    lib_path = tuple(lib_path_arg)
-
-    def find() -> Optional[str]:


Can you make this refactor in a separate PR too?

ethanhs · 2018-03-07T22:10:03Z

I just reverted some of the more significant refactoring started in the last PR so that this is easier to review. Most of it will be refactored later anyway.

eric-wieser · 2018-03-10T19:11:30Z

mypy/main.py

+        options.python_version = _python_version_from_executable(
+            special_opts.python_executable)
+        options.python_executable = special_opts.python_executable
+    return options


Perhaps misleading that this modifies in place and returns the modified value

Are you suggesting that the comment at the beginning might be misleading? (That could be, I'm just not sure what you mean by this comment).

I'd expect either

options.python_version, options.python_executable = infer_python_version_and_executable(special_opts)

or

infer_python_version_and_executable(options, special_opts)

But not

options = infer_python_version_and_executable(options, special_opts)

(think how list.sort(), dict.update(), etc, all modify in place and do not return the new result)

eric-wieser · 2018-03-11T08:32:16Z

mypy/build.py

+                path = os.path.join(pkg_dir, dir_chain)
+                third_party_dirs.append(path)
+
+        candidate_base_dirs = tuple(third_party_dirs + find_module_dir_cache[dir_chain, lib_path])


Why the tuple conversion?

Ah, this is just due to it being in my previous commits. I will get rid of it when I probably end up rebasing this on #4623.

This looks pretty close to done to me - looks like your patch got a lot cleaner after adding the refactor and removing it again :). So maybe it will get in before #4623 after all?

Not sure. It is probably easier for me to rebase since my implementation is just one commit to rollback and apply, but I would prefer to get this PR in first. :)

eric-wieser · 2018-03-11T10:00:28Z

mypy/build.py

+
+        if python_executable is not None:
+            site_packages_dirs = get_site_packages_dirs(python_executable)
+            if not site_packages_dirs:


Should this be site_packages_dirs is not None?

In fact, is there any point in checking this?

No, I just realized it is dead code.

eric-wieser · 2018-03-11T10:29:53Z

mypy/test/testargs.py

+
+    def test_executable_inference(self) -> None:
+        """Test the --python-executable flag with --python-version"""
+        sys_ver_str = '.'.join(map(str, sys.version_info[:2]))


nit: possibly more readable as '{v.major}.{v.minor}'.format(sys.version_info)

eric-wieser · 2018-03-11T10:30:54Z

mypy/test/testargs.py

+        with pytest.raises(PythonExecutableInferenceError) as e:
+            options = infer_python_version_and_executable(options, special_opts)
+        assert str(e.value) == 'Python version (2, 10) did not match executable {}, got' \
+                               ' version {}.'.format(sys.executable, str(sys.version_info[:2]))


nit: No need for the str here

It is indeed needed. type(e.value) is mypy.main.PythonExecutableInferenceError.

I meant the second str on sys.version_info

eric-wieser · 2018-03-12T11:48:16Z

mypy/build.py

+            # the python executable is likely in a virtual environment, thus lacking
+            # needed site methods
+            output = call_python(python_executable, VIRTUALENV_SITE_PACKAGES)
+    return [line for line in output.splitlines() if os.path.isdir(line)]


Why do you check the directories exist in this path, but not in the python_executable == sys.executable path?

eric-wieser · 2018-03-12T11:49:27Z

mypy/build.py

    if key not in find_module_cache:
+        components = id.split('.')
+        dir_chain = os.sep.join(components[:-1])  # e.g., 'foo/bar'
+        site_packages_dirs = get_site_packages_dirs(python_executable)


Is there any reason not to put these three lines inside find, which makes the flow a little clearer?

Not really. They originally were broken out due to the refactor, but I agree putting them in find is ideal right now.

eric-wieser · 2018-03-12T11:52:13Z

mypy/build.py

-            dirs = []
+        # TODO (ethanhs): refactor to use lru_cache on each of these searches
+        dirs = find_module_dir_cache.get((dir_chain, lib_path), [])
+        if not dirs:


This is not equivalent to the previous code. Your new code ignores the cache if if says that dirs == [], which seems undesirable. I'd be inclined to leave it untouched

eric-wieser · 2018-03-12T11:53:03Z

mypy/build.py

        # If we're looking for a module like 'foo.bar.baz', then candidate_base_dirs now
        # contains just the subdirectories 'foo/bar' that actually exist under the
        # elements of lib_path.  This is probably much shorter than lib_path itself.
        # Now just look for 'baz.pyi', 'baz/__init__.py', etc., inside those directories.
-        seplast = os.sep + components[-1]  # so e.g. '/baz'
+        seplast = os.sep + components[-1]


Was this comment inaccurate?

It was at one revision but is no longer, so I should add it back.

eric-wieser · 2018-03-12T11:55:17Z

mypy/build.py

-def find_module(id: str, lib_path_arg: Iterable[str]) -> Optional[str]:
+USER_SITE_PACKAGES = \
+    'from __future__ import print_function; import site; print(site.getusersitepackages());' \
+    'print(*site.getsitepackages(), sep="\\n")'


This fails in the corner-case where the paths contain newlines(!)

Better would be to do

print(repr(site.getsitepackages() + [site.getusersitepackages()]))

and then read it with ast.literal_eval

I also worry that you might have a different between the stdout encoding and the default .decode() decoding, which using repr/ast.literal_eval or maybe even pickle would resolve.

Are site package paths unicode, bytes, or either?

Should be str, for each meaning in 2 and 3, so your recommendation is well taken.

gvanrossum · 2018-03-12T21:45:58Z

I am going to snooze this PR until the chatter dies down and it has been rebased on top of #4623 (which isn't quite ready to land yet, but will be later this week).

ethanhs · 2018-03-14T01:32:07Z

Okay now that #4623 is merged I will revert the last few commits I have made and hand-reapply them.

JukkaL

Here's another batch of review comments. I'll continue tomorrow.

JukkaL · 2018-04-04T15:42:04Z

docs/source/installed_packages.rst

+
+Generally, you do not need to do anything to use installed packages for the
+Python executable used to run mypy. They should be automatically picked up by
+mypy and used for type checking.


This only works if the packages ship with type information, and currently no (or hardly any) packages do it. So I'd like to add a qualifier and explicitly say that this does not work for most packages yet.

JukkaL · 2018-04-04T15:57:52Z

docs/source/installed_packages.rst

+Making PEP 561 compatible packages
+**********************************
+
+Packages that must be used at runtime and supply type information via type


I think that this can be a bit confusing still, since "used at runtime" is too vague. What about instead saying that this section is relevant if you are publishing your own packages on PyPI, or if you want mypy to type check installed packages? Typically user code is type checked by directly pointing to the source code in your repository instead of first installing the package. As written right now, some people may get the wrong impression that they are always supposed to install their package before running mypy.

Maybe give examples of some use cases where this could be useful? Examples:

You publish your package on PyPI (or a local package repository) and want users to be able to type check code that uses your package.

You want to type check a codebase spread over multiple repositories or directories, and you use setup.py script(s) to install your packages. Alternatively, you could also give mypy multiple files/directories to type check as command line arguments.

JukkaL · 2018-04-04T15:58:32Z

mypy/build.py

@@ -33,6 +36,7 @@
 if MYPY:
    from typing import Deque

+from . import sitepkgs


Style nit: We don't use relative imports in the mypy codebase.

JukkaL · 2018-04-04T16:00:00Z

mypy/build.py

@@ -809,6 +814,21 @@ def remove_cwd_prefix_from_path(fscache: FileSystemCache, p: str) -> str:
    return p


+@functools.lru_cache(maxsize=None)
+def _get_site_packages_dirs(python_executable: Optional[str]) -> List[str]:
+    """Find package directories for given python."""


Mention in the docstring that this involves running Python to determine where site packages live. Document why we are using lru_cache (starting up a Python interpreter is pretty slow).

JukkaL · 2018-04-04T16:07:41Z

mypy/build.py

@@ -822,20 +842,30 @@ class FindModuleCache:

    def __init__(self, fscache: Optional[FileSystemMetaCache] = None) -> None:
        self.fscache = fscache or FileSystemMetaCache()
-        # Cache find_module: (id, lib_path) -> result.
-        self.results = {}  # type: Dict[Tuple[str, Tuple[str, ...]], Optional[str]]
+        self.find_lib_path_dirs = functools.lru_cache(maxsize=None)(self._find_lib_path_dirs)


lru_cache uses a dictionary internally so I suspect that using lru_cache doesn't perform better. I'd prefer to not use it unless there is a clear benefit since it's not type safe (argument types can't be checked).

I'd argue that the cache-correctness of lru_cache is more valuable than the type-checking provided by mypy

I'd argue that we've spent more effort arguing about what to do that would have been the relative benefits of either approach :-)

We have an informal style guideline that we avoid idioms that can't be type checked unless there is particularly good reason, and here the benefit we gain at the cost of losing some typing precision is minor.

But I won't argue about this any more.

JukkaL · 2018-04-04T16:19:14Z

mypy/main.py

+    if sys.version_info[:2] == python_version:
+        return sys.executable
+    str_ver = '.'.join(map(str, python_version))
+    print(str_ver)


Is this a debug print?

JukkaL · 2018-04-04T16:42:50Z

mypy/main.py

+
+def _python_version_from_executable(python_executable: str) -> Tuple[int, int]:
+    try:
+        check = subprocess.check_output([python_executable, '-c',


Running multiple Python subprocess invocations can be pretty slow -- for example, I have a bunch of packages installed that seem to result in a simple python -c 'print(1)' run taking about 100ms. We seem to be running the interpreter multiple times: 1) for finding the executable 2) for finding the Python version and 3) for finding the search directories. It seems that all of these could be combined into a single call that prints all of that information, potentially saving hundreds of milliseconds per invocation. We could also cache the result of that call, just in case.

We only will at most run it twice. (3) is always run, but only one of (1) or (2) is needed to be run (to infer the other value). Though perhaps combining them is for the best.

Ah then this isn't as big of a problem as I first thought. Still, many of my incremental mypy runs only take under 1s, and a potential 20% performance impact is significant. I'll do some measurements -- maybe we can leave this optimization out for now.

~~I will leave a TODO.~~ (Done)

JukkaL · 2018-04-04T16:45:01Z

mypy/main.py

-                        help='use Python x.y')
+                        help='use Python x.y', dest='special-opts:python_version')
+    parser.add_argument('--python-executable', action='store', metavar='EXECUTABLE',
+                        help="Python executable which will be used in typechecking.",


The help text is a bit vague. What about something like "Python executable used for finding PEP 561 compliant installed packages and stubs"?

Remove dot from the end of the help text.

JukkaL · 2018-04-04T19:04:44Z

mypy/main.py

+                        dest='special-opts:python_executable')
+    parser.add_argument('--no-site-packages', action='store_true',
+                        dest='special-opts:no_executable',
+                        help="Do not search for installed PEP 561 compliant packages.")


Remove dot from the end of the help text.

JukkaL · 2018-04-04T19:05:40Z

mypy/main.py

    parser.add_argument('--platform', action='store', metavar='PLATFORM',
                        help="typecheck special-cased code for the given OS platform "
-                        "(defaults to sys.platform).")
+                             "(defaults to sys.platform).")


Remove dot from the end of the help text.

ethanhs · 2018-04-05T04:19:05Z

@JukkaL I've made all of the changes you requested save changing lru_caches to dicts, since there seems to be some disagreement over which to use. I also wanted to hear more of your thoughts on combining subprocess calls.

JukkaL

This is my final batch of comments. If you are short on time now, some of the suggestions can be left out and implemented in another PR so that we can merge this sooner. Let me know what you prefer. If you are able to update the PR by Monday we may just have enough time to include this in the next release, but even if that doesn't work out the next release after that won't be many weeks away.

Thanks for persevering with this -- this is going to make a big difference!

JukkaL · 2018-04-06T15:47:30Z

mypy/build.py

@@ -822,20 +842,30 @@ class FindModuleCache:

    def __init__(self, fscache: Optional[FileSystemMetaCache] = None) -> None:
        self.fscache = fscache or FileSystemMetaCache()
-        # Cache find_module: (id, lib_path) -> result.
-        self.results = {}  # type: Dict[Tuple[str, Tuple[str, ...]], Optional[str]]
+        self.find_lib_path_dirs = functools.lru_cache(maxsize=None)(self._find_lib_path_dirs)


I'd argue that we've spent more effort arguing about what to do that would have been the relative benefits of either approach :-)

We have an informal style guideline that we avoid idioms that can't be type checked unless there is particularly good reason, and here the benefit we gain at the cost of losing some typing precision is minor.

But I won't argue about this any more.

JukkaL · 2018-04-06T15:53:57Z

mypy/main.py

+
+def _python_version_from_executable(python_executable: str) -> Tuple[int, int]:
+    try:
+        check = subprocess.check_output([python_executable, '-c',


Ah then this isn't as big of a problem as I first thought. Still, many of my incremental mypy runs only take under 1s, and a potential 20% performance impact is significant. I'll do some measurements -- maybe we can leave this optimization out for now.

JukkaL · 2018-04-06T16:05:57Z

test-data/packages/typedpkg/typedpkg/sample.py

+
+def ex(a):
+    # type: (Iterable[str]) -> Tuple[str, ...]
+    """Example typed package. This intentionally has an error."""


It's not immediately obvious what the error is. Maybe describe it or make it more obvious?

Aha, this may in fact be an out of date docstring!

JukkaL · 2018-04-06T16:08:25Z

mypy/test/testpep561.py

+class TestPEP561(TestCase):
+    @contextmanager
+    def install_package(self, pkg: str,
+                        python_executable: str = sys.executable) -> Generator[None, None, None]:


Style nit: Iterator[None] would be sufficient for the return type and a little simpler.

JukkaL · 2018-04-06T16:14:47Z

mypy/test/testpep561.py

+        working_dir = os.path.join(package_path, pkg)
+        install_cmd = [python_executable, '-m', 'pip', 'install', '.']
+        # if we aren't in a virtualenv, install in the
+        # user package directory so we don't need sudo


It looks like sys.real_prefix is monkey patched by virtualenv. May be worth mentioning this in a comment, as it's doc mentioned in stdlib docs, I think.

JukkaL · 2018-04-06T16:57:08Z

mypy/build.py

+            stub_name = components[0] + '-stubs'
+            typed_file = os.path.join(pkg_dir, components[0], 'py.typed')
+            stub_dir = os.path.join(pkg_dir, stub_name)
+            if os.path.isdir(stub_dir):


Use fscache instead?

JukkaL · 2018-04-06T16:57:31Z

mypy/build.py

+            if os.path.isdir(stub_dir):
+                stub_components = [stub_name] + components[1:]
+                path = os.path.join(pkg_dir, *stub_components[:-1])
+                if os.path.isdir(path):


Use fscache?

JukkaL · 2018-04-06T16:58:17Z

mypy/build.py

+                path = os.path.join(pkg_dir, *stub_components[:-1])
+                if os.path.isdir(path):
+                    third_party_dirs.append(path)
+            elif os.path.isfile(typed_file):


Use fscache?

JukkaL · 2018-04-06T17:01:15Z

mypy/build.py

@@ -2129,8 +2167,6 @@ def dispatch(sources: List[BuildSource], manager: BuildManager) -> Graph:
                      stubs_found=sum(g.path is not None and g.path.endswith('.pyi')
                                      for g in graph.values()),
                      graph_load_time=(t1 - t0),
-                      fm_cache_size=len(manager.find_module_cache.results),
-                      fm_dir_cache_size=len(manager.find_module_cache.dirs),


If you refactor lru_cache uses away, these could be restored. Or maybe these stats could be retrieved from the lru caches?

Yes I should add these back based on the lru_cache.cache_info() currsize.

JukkaL · 2018-04-06T17:02:18Z

mypy/fscache.py

 from mypy.util import read_with_python_encoding


 class FileSystemMetaCache:
    def __init__(self) -> None:
-        self.flush()
+        self.stat = functools.lru_cache(maxsize=None)(self._stat)


What's the current status of the memory leak investigation? Do you believe it may still be happening?

ethanhs · 2018-04-06T23:57:11Z

If you are short on time now, some of the suggestions can be left out and implemented in another PR so that we can merge this sooner.

I left the lru_caches, as that is still somewhat a point of contention (also the memory usage issues disappeared when I put them in, so I'm a little hesitant to go back). I also left the current Python version/executable inference in as-is, which should be addressed at a later date once there is a better understanding of their performance impact.

If you are able to update the PR by Monday we may just have enough time to include this in the next release

Great! Now that I have updated it, and it will be merged by Monday, perhaps @dmoisset and or @carljm would be interested in testing this? (I realize it is a bad time, as it is already kinda late on a Friday...)

Thanks for persevering with this -- this is going to make a big difference!

Happy to do it, and I want to thank you, Eric, and Jelle for the reviews! They were quite helpful.

dmoisset · 2018-04-07T15:43:08Z

I'll try to take a look at this tomorrow... I don't have much time but I'm very eager to see this merged

…

On 7 April 2018 at 00:57, Ethan Smith ***@***.***> wrote: If you are short on time now, some of the suggestions can be left out and implemented in another PR so that we can merge this sooner. I left the lru_caches, as that is still somewhat a point of contention (also the memory usage issues disappeared when I put them in, so I'm a little hesitant to go back). I also left the current Python version/executable inference in as-is, which should be addressed at a later date once there is a better understanding of their performance impact. If you are able to update the PR by Monday we may just have enough time to include this in the next release Great! Now that I have updated it, and it will be merged by Monday, perhaps @dmoisset <https://github.com/dmoisset> and or @carljm <https://github.com/carljm> would be interested in testing this? (I realize its a bad time, as it is already kinda late on a Friday...) Thanks for persevering with this -- this is going to make a big difference! Happy to do it, and I want to thank you, Eric, and Jelle for the reviews! They were quite helpful. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#4693 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAMQHV_Z417Q4e-xVBFy_-CitGAhtfXwks5tmADcgaJpZM4SgTDj> .

-- Daniel F. Moisset - UK Country Manager - Machinalis Limited www.machinalis.co.uk <http://www.machinalis.com> Skype: @dmoisset T: + 44 7398 827139 1 Fore St, London, EC2Y 9DT Machinalis Limited is a company registered in England and Wales. Registered number: 10574987.

ethanhs · 2018-04-08T01:11:30Z

@dmoisset FWIW the release itself is Friday, so you do have some time.

JukkaL

This is good to merge now! A few follow-up issues remain:

Revert changes where existing caching was replaced with lru_cache, as discussed in earlier comments. If this causes memory leaks we should understand why the leaks are happening instead of (or in addition to) only finding a workaround.
Only invoke one Python subprocess per invocation.
Installed non-stubs can take precedence even if a stubs package exists (if they are installed in differnet places). I'll create an issue about this.
Restore caching for isfile_case.

JukkaL · 2018-04-09T15:24:40Z

mypy/fscache.py

@@ -88,8 +84,6 @@ def isfile_case(self, path: str) -> bool:
        TODO: We should maybe check the case for some directory components also,
        to avoid permitting wrongly-cased *packages*.
        """
-        if path in self.isfile_case_cache:


Tests may not be indicative of real-world performance. More importantly, the cache is not only used for improving performance -- the goal is to provide more transactional semantics for file operations, and omitting caching for some file operations breaks that.

ethanhs added 10 commits March 6, 2018 19:25

Add docs for python-executable

96041b1

Add --python-executable and --no-site-packages

4483b3e

Split inference out of process_options

53ff42c

Change --no-site-packages to --no-infer-executable

f523efa

Add --no-infer-executable to subprocessed tests

4d66827

Add test for python-executable and no-infer-executable

1582692

Change no-infer-executable back to no-site-packages

65ebca9

Add PEP 561 docs

4467356

Add PEP 561 tests

943e8e3

Add PEP 561 test packages

f28b901

ethanhs mentioned this pull request Mar 7, 2018

Implement PEP 561 searching #4403

Closed

8 tasks

eric-wieser reviewed Mar 7, 2018

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eric-wieser reviewed Mar 10, 2018

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gvanrossum mentioned this pull request Mar 11, 2018

Overhaul file-system operations to use FileSystemCache #4623

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eric-wieser reviewed Mar 11, 2018

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chadrik mentioned this pull request Mar 11, 2018

Add PEP484 stubs python-attrs/attrs#238

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ethanhs force-pushed the impl-pep561 branch from a74fbd8 to 0fd2bf0 Compare March 12, 2018 10:01

eric-wieser reviewed Mar 12, 2018

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asvetlov mentioned this pull request Mar 12, 2018

Type hinting in code aio-libs/aiohttp#1749

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JukkaL reviewed Apr 4, 2018

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ethanhs added 8 commits April 4, 2018 19:43

Make docs clearer

ddfa26a

Code cleanup, add details of _get_site_packages_dirs

a5e636c

Remove unneeded argument

262769c

Refactor python_executable_prefix

12920c9

Clarify python-executable flag

4177257

Merge branch 'master' into impl-pep561

ef44873

Remove unused argument

8948d6a

Change python_version -> python_executable

6916b09

JukkaL reviewed Apr 6, 2018

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ethanhs added 7 commits April 6, 2018 15:12

Add information about inference and add TODO

87cbdb2

Refactor testpep561

e44b1f5

Fix outdated docstring

88279fa

Add docstring describing sitepkgs.py

e590e66

Add note about python_executable option

df13f2a

Use fscache in a few more places

6525f13

Add back some cache info in dispatch

bc0141e

JukkaL approved these changes Apr 9, 2018

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JukkaL merged commit 80aee58 into python:master Apr 9, 2018

This was referenced Apr 9, 2018

Search procedure for inline annotations #1190

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Specifying which Python interpreter stubgen should use #965

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JelleZijlstra mentioned this pull request Apr 9, 2018

CI broken due to python/mypy#4693 python/typeshed#2035

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This was referenced Apr 9, 2018

Add a py.typed marker, per PEP 561 #4255

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Restore dict based typesafe caching #4898

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euresti mentioned this pull request Dec 27, 2018

Should we remove the stubs from typeshed? python-attrs/attrs#480

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shamrin mentioned this pull request Jul 8, 2020

Typeshedding issues with tornado and python typing microsoft/pyright#813

Closed

		@@ -804,7 +806,7 @@ def remove_cwd_prefix_from_path(p: str) -> str:


		# Cache find_module: (id, lib_path) -> result.

Implement PEP561 #4693

Implement PEP561 #4693

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ethanhs Apr 5, 2018 • edited Loading

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ethanhs commented Apr 5, 2018

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ethanhs commented Apr 6, 2018 • edited Loading

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ethanhs commented Mar 7, 2018 •

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ethanhs commented Apr 6, 2018 •

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