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Generate code Python source cross-reference facts in Kythe format

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Python indexer (for Kythe)

The pykythe package provides code for preprocessing Python source code into a representation for easy entity cross-referencing, using entities in the style of the Kythe indexing schema.

License

Apache 2.0

Warning, Avis, Achtung,ご注意

This code is pre-alpha and is intended for collaboration with other people, to create an industrial-strength indexer for Python. The author intends to make significant changes and improvements to the code, so if you want to work on it, please contact peter.ludemann@gmail.com first.

Debugging note

Sometimes pykythe.qlf can output an "unexpectedly failed" error message without enough context to figure out where the failure happened. To track this down, run the command again, but with the /tmp/pykythe_test/pykythe.qlf replaced by swipl -l pykythe/pykythe.pl (including the additional command line parameters); then run two commands:

debug.
pykythe:pykythe_main2.

Browsing

Experimental source browser

The browser directory contains code for browsing the source with hyperlinks. (See below under "Run the Kythe browser")

The code in ast_color.py creates "color" facts that have colorization information for the source (e.g., token, string, whitespace, comment). The Kythe schema is augmented by /pykythe/color/... facts.

A simple server loads the Kythe facts and makes them available to the front-end using Javascript fetch.

You can process the test files and run the browser by make SRC_BROWSER_PORT=9999 test make-json run-src-browser

Browsing with underhood

Pykythe works with underhood to allow source code browsing. A rough outline of how to set up the servers in the Makefile rule run-underhood-all (after running add-index-pykythe or make-tables to set up the serving tables).

Browsing with the Kythe browser

The Kythe browser is obsolete and unsupported by the Kythe team. The "underhood" browser uses the Kythe server (which is still supported) with a new front-end. Alternatively, an experimental source browser is included in pykythe (see above: "Experimental source browser").

Competition

Pytype has an experimental indexer, which runs at least 10x slower and crashes on some inputs. (Pykythe does about 100-200 files per minute on a 4 CPU workstation and can process the entire Python3 library without crashing.) Pytype also requires a system such as Bazel with associated BUILD files, or ninja, to run in parallel.

Run demo

Installation

There is no installation script, because this code is pre-alpha. If you run scripts/demo.sh, then most of the prerequisites are loaded (with the exception of the Kythe code).

The following probably has some wrong information about git and submodules. Finding accurate up-to-date documentation is nearly impossible and I really don't feel like becoming a git guru.

  • cd to your top-level source directory (pykythe assumes that all sources are in this, including those from other projects such as kythe and typeshed).

  • git clone --recursive https://github.com/google/kythe.git

    • This requires git 2.23 or newer (sudo add-apt-repository ppa:git-core/ppa). Otherwise: git pull --recursive, and if you have something older, you also need git submodule update --init --recursive --depth 1 (you will also need to do this each time you do git pull on the pykythe respository).

  • git submodule update --remote --merge

    • You should do this each time you do git pull on the pykythe respository.
    • For older versions of git, this might do what you want: git submodule update --init --recursive --depth 1
    • You may wish to do these commands, but the might also cause problems with git push (I tried them at one point but reverted):
    • git submodule -q foreach 'echo $name' | xargs -L1 -I{} git config -f .gitmodules submodule.{}.shallow true
    • git submodule -q foreach 'echo $name' | xargs -L1 -I{} git config -f .gitmodules submodule.{}.fetchRecurseSubmodules true

  • From time to time:

    • git submodule foreach git pull --recurse

  • Follow the instructions at Kythe - getting started to download the latest tarball from the Kythe repository and follow the instructions to copy the binaries into /opt/kythe.

    • The build-kythe rule in the pykythe Makefile will build Kythe from scratch, but the rule often breaks with new releases.

  • Install python3.11

    This needs the latest version of Python 3.11. On Ubuntu, you might need to first run sudo add-apt-repository ppa:deadsnakes/ppa, then sudo apt install python3.11. More choices are given in this tutorial.

    If you get an error in DISPATCH[node.type], then it probably means that there's a conflict with Ubuntu package python3-lib2to3. The easiest way to fix this is to clone cprolog from github and then sudo cp -r --preserve=mode,timestamps cpython/Lib/lib2to3/* /usr/lib/python3.11/lib2to3/. Alternatively, sudo apt install 2to3 python3-lib2to3 python3-toolz.

  • Install lib2to3 for Python.

    This might not be needed, depending on the exact state of Python3.x tools

    sudo apt install python3.11-lib2to3 or sudo apt install 2to3 python3-lib2to3 python3-toolz

  • Install SWI-Prolog. You need at least version 9.3.5, so as of 2024-04-30, this means using the "devel" download or PPA. For Ubuntu, Debian, and similar (following the instructions at https://www.swi-prolog.org/build/PPA.html):

    • sudo apt install software-properties-common
    • sudo apt-add-repository ppa:swi-prolog/devel
    • sudo apt update
    • sudo apt install swi-prolog

    After installing, add the packages edcg and

    by these commands:

    echo 'pack_install(edcg, [interactive(false), upgrade(true)]).' | swipl

    Check that you have the correct versions (echo 'forall(pack_property(N, version(V)), writeln(N:V)).' | swipl):

    • edcg 0.9.1.7

  • Install mypy_extensions: sudo apt install python3-mypy-extensions or python3.11 -m pip install mypy mypy_extensions

  • Optional (htis is now a submodule of pytype): git clone https://github.com/python/typeshed.git

  • Optional:

    • Install mypy and pytype (using pip, or by cloning the git repository, cd-ing into it, then running sudo -H pip3 install --upgrade .) (pytype is special -- see its installation instructions).
      • You might need to symlink mypy_extensions into /usr/local/lib/python3.11/dist-packages.

  • Optional:

    • git clone https://github.com/google/pytype
    • git clone https://github.com/python/mypy.git
    • git clone https://github.com/google/yapf.git

  • make -C <pkgdir> clean_lite test

  • You can see the generated facts in /tmp/pykythe_test/KYTHE/pykythe/test_data/*.json-decoded (requres running scripts/decode_json.py -- see Makefile rule json-decoded-all).

  • Run the source browser by:

    • make -C <pkgdir> make-json
    • make -C <pkgdir> SRC_BROWSER_PORT=9999 run-src-browser
    • http://localhost:9999 to browse the Kythe facts created by the test rule and which were processed into a database for the browser by make-json.

    The test files are in /tmp/pykythe_test/SUBST/home/peter/src/pykythe/test_data.

  • Run the Kythe browser by:

  • make -C <pkgdir> make-tables This creates /tmp/pykythe_test/tables, which can be used by the Kythe browser. Alternatively, make -C <pkgdir> add-index-pykythe.

    make -C <pkgdir> run-kythe-server

    You can look run the browser: http://localhost:8080

  • Run the underhood browser by cloning https://github.com/TreeTide/underhood.git and running the commands in run-underhood-all (

  • You can run scripts/test3.sh to see how the system works both with processing from source or by reusing the cache (or a combination). Note that this has some extra pre-processing steps that aren't needed for ordinary use.

Coding conventions

Code formatting

All the Python code is formatted using yapf configured with .style.yapf. You can either install it from github or using pip. The Makefile has a rule pyformat that formats everything.

Prolog code is formatted according to the recommendations in plcoding.pdf with an extension for EDCGs that shows the accumulators.

If you use Emacs, I recommend using prolog.el from https://bruda.ca/emacs/prolog_mode_for_emacs (https://bruda.ca/_media/emacs/prolog.el), customized with prolog-align-small-comments-flag set to nil (a copy of this is in directory emacs). See also https://www.swi-prolog.org/FAQ/GnuEmacs.html

Type declarations

The code is processed with mypy (using the Makefile rule mypy) and pylint. It is intended to also be processed by pytype.

Implementation notes

Python Grammar

Pykythe depends on the deprecated lib2to3 parser, and the details of the Grammar.txt file.

This requires Python version 3.11.2.

If you can't install it, you can create it in $HOME/.local/bin/python3.11 by the following:

git clone --depth=1 git@github.com:python/cpython.git
git checkout v3.11.2
./configure --prefix=$HOME/.local --enable-optimizations
make -j8
make -j8 test
make install

How a single file is processed

A source file is processed in the following steps:

  • pykythe.pl invokes a Python program to create an AST with fully qualified names:

    • ast_raw.parse generates an AST in lib2to3.pytree's form. (Actually, this is more like a concrete syntax tree, which is why the next step is done.)

    • ast_raw.cvt_parse_tree converts the "raw" AST to a more convenient "cooked" form.

    • ast_cooked.Base.add_fqns traverses the "cooked" AST to fill in as many fully qualified names (FQNs) as possible (most names can be resolved, but those from builtins or from … import * cannot be known at this point (builtins are in effect from builtins import *).

    • The resulting AST (with FQNs) is serialized and passed back to pykythe.pl.

  • A pass is made over the AST, generating Kythe anchors and a list of "expressions" in the AST.

  • Each "import" is recursively processed (if there is a circular import, this is detected and the recursive import is treated as a no-op).

    • This includes outputting the .kythe.json, .kythe.entries, and .pykythe.symtab files.
    • The .pykythe.symtab files are reused as a "cache" to avoid reprocessing a source file.
      • There is no "lock" on these files (except for outputting the completed .pykythe.symtab file); this means that an imported file may be processed multiple times but once it is available, it won't be reprocessed.

  • The expressions are symbolically evaluated to fill in the symtab. This is, in effect, a simple type inferencer / abstract interpretation (for example, resolving a function call to a class constructor, then applying the "dot" operator to determine the attribute's type).

    • When a symtab entry is updated with additional information, it is recorded in the "changed" list (symchg).
    • If the "changed" list is non-empty after symbolically evaluating the expressions, the process is repeated. Generally, no more than 3 passes are needed to incorporate all the information.
    • While symbolically evaluating the expressions, additional Kythe facts can be generated; for example, attributes (after a . operator) can be resolved to the appropriate class attribute/method or module variable/function.

  • The symtab and Kythe facts are output to pykythe.symtab, .kythe.json file, and .kythe.entries files. The test cases can be checked with kythe/cxx/verifier/verifier.

Symbol table (symtab) of fully qualifed names (FQNs)

A fully qualified name (FQN) is the absolute path to an abstract entity, using '.'s to separate the path items.

The symbol table ("symtab") is a mapping of fully qualified names (FQNs) to their "types". (The word "type" is used a bit loosely; essentially it is a term such as class_type(FQN, Bases) or module_type(module_and_token(Module,Path,Token)) This is different from the usual definition of symtab, which maps a single ID to to a type and where there is a "stack" of IDs of the various scopes (the FQN resolution is done in two passes in the Python program that parses the source and outputs an AST).

For example, in file foo/bar.py:

import os
sep = os.sep

the symtab would contain entries like the following (note that os results in both a definition in the namespace of module foo.bar and a reference to the imported module in typeshed).

'foo.bar.os': module_type(module_alone(
    '${FQN_TYPESHED}.os',
    '${FQN_TYPESHED}/stdlib/3/os/__init__.pyi'))
'.foo.bar.sep': class_type('${FQN_TYPESHED}.stdlib.builtins.str', [])
'${FQN_TYPESHED}.os': module_type(module_alone(
    '${FQN_TYPESHED}.os',
    '${FQN_TYPESHED}/stdlib/os/__init__.pyi'))
'${FQN_TYPESHED}.os.sep': class_type('${FQN_TYPESHED}.stdlib.builtins.str', [])

A symtab is self-contained: there is no need to import the symtabs of modules that it imports. However, the imports' symtabs need to be checked (recursively) to ensure that they are up-to-date; if any of the imports's symtabs is out of date, the entire chain of symtabs need to be recomputed.

When an "import *" is processed, the symtab entries that start with the module name are added to the importing module's symtab (e.g., if foo.py has from bar import *, then all symtab entries that start with path.to.bar are added to the symtab, with the path.to.bar replaced by path.to.foo).

Builtins are added to the "scope" of each program, as if there were a from builtins import * added to each program. This is not how Python actually resolves builtin name lookup, but the effect is essentially the same (with a few corner cass that probably don't matter for real programs; after all pykythe can't figure out everything anyway, because of Python's dynamic nature). In this way, we avoid having a stack of symtabs.

Imports, cache, and batches

When a source file is processed, all the imports must be processed first. Pykythe doesn't depend on information about dependencies from a build system (which typically aren't available for Python, in comparison to C++ or similar, which have dependency information in a build system or compiler (e.g., gcc-M), although importlab could be used. Additionally, there can be circular imports, which prevent a strict ordering of dependencies. (Python doesn't directly allow circular imports; but they can be simulated by putting import statements inside functions, so that they are evaluated at run time rather than when the module is first compiled.)

Pykythe processes each import statement as it is encountered. Circular imports are handled by keeping track of all imports that are "in process" and skipping them when they are encountered a second time (more details on this are in the Symtab section).

When processing a codebase, reprocessing the imports can easily get O(N3) behavior (where N is the number of lines of code), so a cache is used to avoid this. For each .py or .pyi file, a corresponding .kythe.json file (and .kythe.entries) is created, containing all the Kythe facts; the the pykythe symtab and a hash of the source file go into a .pykythe.symtab file. When an import is encountered, the cache file is used if possible:

  • The cache file must have been created using the same source file.

  • All imports (recursively) must have useable cache files.

If any of the imported cache files is not useable, all source files that depend on it must be reprocssed to generate new cache files (that is, if a.py imports b.py, b.py imports c.py, and c.py imports d.py; and d.pykythe.symtab is useable but c.pykythe.symtab is not (because c.py has changed since c.pykythe.symtab was created), then c.py, b.py, and a.py must be reprocessed (d.py can be reused as-is).

This kind of caching reduces the algorithm to O(M2) (where M is the number of files), which is still a problem. A further refinement reduces the cost to O(N). Assuming that we can snapshot the code base (which is identified by a "batch id", given with the --batch_suffix command-line option, typically a nano-second time stamp plus a random number), then a single pass over all the source files suffices.

To sum up, pykythe uses two kinds of caches:

  • .pykythe.symtab requires checking that the source and all the dependencies haven't changed.

  • .pykythe.batch-$BATCH_ID can be used without checking dependencies (The --batch_suffix command-line option is used to set the batch ID).

Multiple pykythe processes can run at the same time; all output is "atomic", as long as it's all on the same file system. (That is, if the same file is being processed by two processes at the same time, their outputs won't interfere with each other, because they should both have the same content and they are written atomically; that is if the same thing is done multiple times, it doesn't matter because the actions are "idempotent".)

(A detail: to allow for read-only source trees, the cache files are in a separate directory, as specified by --kytheout. This could in future be generalized by specifying patterns for transforming an input file to an output file, e.g. kytheout_pattern='s!/stuff/to/remove/(.*/)([^/]*)\..*}!/path/to/dir/\\1\\2.kythe.json!' ... this probably should allow multiple patterns, to accomodate files in multiple repositories.)

To give an idea of performance improvements, when processing the 7071 files in the Python library (this is total CPU time; wall time was roughly 1/3 on a 4 CPU machine (with SSD, so the affects of cache are less than with HDD) running up to 8 pykythe processes in parallel):

  • Initial run: 69 minutes (using "batch" caching for newly created files -- without this caching, performance would have been much worse).

  • With regular caching and without batch files from the first run: 33 minutes.

  • With batch files from the first run: 5 minutes.

Base64

For the JSON version of Kythe facts, base64 encoding is used, to handle the some data being pure binary and not UTF8 (e.g., if the /kythe/text fact is in Latin-1 encoding, which is not legal UTF-8). Unfortunately, Prolog's base64 support isn't super fast, nor is its UTF-8 encoding/decoding (the latter is needed because base64 works on ASCII only, so encoding/decoding from Unicode is needed).

For performance reasons, the Kythe facts are all created as regular strings (or atoms), and converted to base64 only on output. This is because each pass over the AST creates Kythe facts, and there's a significant saving by only doing the base64 translation once. (Some micro-optimizations are possible by distinguishing between strings that can only be ASCII and those that can be any Unicode; these probably aren't worth doing and things are simpler by just assuming UTF8 everywhere).

Known issues

  • You might get a mysterious error message about "builtins_version(...) should be ..."; this typically indicates that the Prolog or Python interpreter has changed since the last processing. The simplest solution is to delete all the output (e.g., rm -rf /tmp/pykythe) and re-run.

  • See also https://github.com/kamahen/pykythe/issues

  • Needs more documentation.

  • Needs many more test cases.

  • Needs proper code review.

  • Only works with UTF-8 files (actually, only ASCII), with Unix newline conventions.

    • 8859-1 (Latin1) may cause bogus error messages.

  • Performance: symtab, color data: search for comments in pykythe.pl about using fast_read/2 etc.

  • Only tested with Python 3 source (probably works with Python 2, with a bit of fiddling for things like print statements and (when implemented) some details of name scope, such as for list comprehensions).

    • Doesn't yet handle Python 3.8 "walrus" operator.

  • Requires Python 3.11

    • On Ubuntu: sudo apt install python3.11
    • You also might have to do something like this: cd /usr/lib/python3/dist-packages && sudo ln -s apt_pkg.cpython-36m-x86_64-linux-gnu.so apt_pkg.cpython-37m-x86_64-linux-gnu.so

  • Requires Python 3.11 2to3, mypy, mypy_extensions

    • (See above with "Install lib2to3 for Python", although that might not be needed any more.)

  • Outputs JSON and uses entrystream --read_format=json to convert to the form that write_tables expects (it would be more efficient to output protobufs directly).

  • Packaging of pykythe is incomplete and possibly wrong.

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Generate code Python source cross-reference facts in Kythe format

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