Coverage for python/lsst/utils/packages.py: 25%
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1# This file is part of utils.
2#
3# Developed for the LSST Data Management System.
4# This product includes software developed by the LSST Project
5# (https://www.lsst.org).
6# See the COPYRIGHT file at the top-level directory of this distribution
7# for details of code ownership.
8#
9# Use of this source code is governed by a 3-clause BSD-style
10# license that can be found in the LICENSE file.
11#
12from __future__ import annotations
14"""
15Determine which packages are being used in the system and their versions
16"""
17import hashlib
18import importlib
19import io
20import json
21import logging
22import os
23import pickle
24import re
25import subprocess
26import sys
27import types
28from collections.abc import Mapping
29from functools import lru_cache
30from typing import Any, Dict, Tuple, Type
32import yaml
34log = logging.getLogger(__name__)
36__all__ = [
37 "getVersionFromPythonModule",
38 "getPythonPackages",
39 "getEnvironmentPackages",
40 "getCondaPackages",
41 "Packages",
42]
45# Packages used at build-time (e.g., header-only)
46BUILDTIME = set(["boost", "eigen", "tmv"])
48# Python modules to attempt to load so we can try to get the version
49# We do this because the version only appears to be available from python,
50# but we use the library
51PYTHON = set(["galsim"])
53# Packages that don't seem to have a mechanism for reporting the runtime
54# version. We need to guess the version from the environment
55ENVIRONMENT = set(["astrometry_net", "astrometry_net_data", "minuit2", "xpa"])
58def getVersionFromPythonModule(module: types.ModuleType) -> str:
59 """Determine the version of a python module.
61 Parameters
62 ----------
63 module : `module`
64 Module for which to get version.
66 Returns
67 -------
68 version : `str`
70 Raises
71 ------
72 AttributeError
73 Raised if __version__ attribute is not set.
75 Notes
76 -----
77 We supplement the version with information from the
78 ``__dependency_versions__`` (a specific variable set by LSST's
79 `~lsst.sconsUtils` at build time) only for packages that are typically
80 used only at build-time.
81 """
82 version = module.__version__
83 if hasattr(module, "__dependency_versions__"):
84 # Add build-time dependencies
85 deps = module.__dependency_versions__
86 buildtime = BUILDTIME & set(deps.keys())
87 if buildtime:
88 version += " with " + " ".join("%s=%s" % (pkg, deps[pkg]) for pkg in sorted(buildtime))
89 return str(version)
92def getPythonPackages() -> Dict[str, str]:
93 """Get imported python packages and their versions.
95 Returns
96 -------
97 packages : `dict`
98 Keys (type `str`) are package names; values (type `str`) are their
99 versions.
101 Notes
102 -----
103 We wade through `sys.modules` and attempt to determine the version for each
104 module. Note, therefore, that we can only report on modules that have
105 *already* been imported.
107 We don't include any module for which we cannot determine a version.
108 """
109 # Attempt to import libraries that only report their version in python
110 for module_name in PYTHON:
111 try:
112 importlib.import_module(module_name)
113 except Exception:
114 pass # It's not available, so don't care
116 packages = {"python": sys.version}
117 # Not iterating with sys.modules.iteritems() because it's not atomic and
118 # subject to race conditions
119 moduleNames = list(sys.modules.keys())
120 for name in moduleNames:
121 module = sys.modules[name]
122 try:
123 ver = getVersionFromPythonModule(module)
124 except Exception:
125 continue # Can't get a version from it, don't care
127 # Remove "foo.bar.version" in favor of "foo.bar"
128 # This prevents duplication when the __init__.py includes
129 # "from .version import *"
130 for ending in (".version", "._version"):
131 if name.endswith(ending):
132 name = name[: -len(ending)]
133 if name in packages:
134 assert ver == packages[name]
135 elif name in packages:
136 assert ver == packages[name]
138 # Use LSST package names instead of python module names
139 # This matches the names we get from the environment (i.e., EUPS)
140 # so we can clobber these build-time versions if the environment
141 # reveals that we're not using the packages as-built.
142 if "lsst" in name:
143 name = name.replace("lsst.", "").replace(".", "_")
145 packages[name] = ver
147 return packages
150_eups = None # Singleton Eups object
153@lru_cache(maxsize=1)
154def getEnvironmentPackages() -> Dict[str, str]:
155 """Get products and their versions from the environment.
157 Returns
158 -------
159 packages : `dict`
160 Keys (type `str`) are product names; values (type `str`) are their
161 versions.
163 Notes
164 -----
165 We use EUPS to determine the version of certain products (those that don't
166 provide a means to determine the version any other way) and to check if
167 uninstalled packages are being used. We only report the product/version
168 for these packages.
169 """
170 try:
171 from eups import Eups
172 from eups.Product import Product
173 except ImportError:
174 log.warning("Unable to import eups, so cannot determine package versions from environment")
175 return {}
177 # Cache eups object since creating it can take a while
178 global _eups
179 if not _eups:
180 _eups = Eups()
181 products = _eups.findProducts(tags=["setup"])
183 # Get versions for things we can't determine via runtime mechanisms
184 # XXX Should we just grab everything we can, rather than just a
185 # predetermined set?
186 packages = {prod.name: prod.version for prod in products if prod in ENVIRONMENT}
188 # The string 'LOCAL:' (the value of Product.LocalVersionPrefix) in the
189 # version name indicates uninstalled code, so the version could be
190 # different than what's being reported by the runtime environment (because
191 # we don't tend to run "scons" every time we update some python file,
192 # and even if we did sconsUtils probably doesn't check to see if the repo
193 # is clean).
194 for prod in products:
195 if not prod.version.startswith(Product.LocalVersionPrefix):
196 continue
197 ver = prod.version
199 gitDir = os.path.join(prod.dir, ".git")
200 if os.path.exists(gitDir):
201 # get the git revision and an indication if the working copy is
202 # clean
203 revCmd = ["git", "--git-dir=" + gitDir, "--work-tree=" + prod.dir, "rev-parse", "HEAD"]
204 diffCmd = [
205 "git",
206 "--no-pager",
207 "--git-dir=" + gitDir,
208 "--work-tree=" + prod.dir,
209 "diff",
210 "--patch",
211 ]
212 try:
213 rev = subprocess.check_output(revCmd).decode().strip()
214 diff = subprocess.check_output(diffCmd)
215 except Exception:
216 ver += "@GIT_ERROR"
217 else:
218 ver += "@" + rev
219 if diff:
220 ver += "+" + hashlib.md5(diff).hexdigest()
221 else:
222 ver += "@NO_GIT"
224 packages[prod.name] = ver
225 return packages
228@lru_cache(maxsize=1)
229def getCondaPackages() -> Dict[str, str]:
230 """Get products and their versions from the conda environment.
232 Returns
233 -------
234 packages : `dict`
235 Keys (type `str`) are product names; values (type `str`) are their
236 versions.
238 Notes
239 -----
240 Returns empty result if a conda environment is not in use or can not
241 be queried.
242 """
243 try:
244 from conda.cli.python_api import Commands, run_command
245 except ImportError:
246 return {}
248 # Get the installed package list
249 versions_json = run_command(Commands.LIST, "--json")
250 packages = {pkg["name"]: pkg["version"] for pkg in json.loads(versions_json[0])}
252 # Try to work out the conda environment name and include it as a fake
253 # package. The "obvious" way of running "conda info --json" does give
254 # access to the active_prefix but takes about 2 seconds to run.
255 # The equivalent to the code above would be:
256 # info_json = run_command(Commands.INFO, "--json")
257 # As a comporomise look for the env name in the path to the python
258 # executable
259 match = re.search(r"/envs/(.*?)/bin/", sys.executable)
260 if match:
261 packages["conda_env"] = match.group(1)
263 return packages
266class Packages(dict):
267 """A table of packages and their versions.
269 There are a few different types of packages, and their versions are
270 collected in different ways:
272 1. Installed Conda packages are obtained via the Conda API. Conda is
273 not required.
274 2. Python modules (e.g., afw, numpy; galsim is also in this group even
275 though we only use it through the library, because no version
276 information is currently provided through the library): we get their
277 version from the ``__version__`` module variable. Note that this means
278 that we're only aware of modules that have already been imported.
279 3. Other packages provide no run-time accessible version information (e.g.,
280 astrometry_net): we get their version from interrogating the
281 environment. Currently, that means EUPS; if EUPS is replaced or dropped
282 then we'll need to consider an alternative means of getting this version
283 information.
284 4. Local versions of packages (a non-installed EUPS package, selected with
285 ``setup -r /path/to/package``): we identify these through the
286 environment (EUPS again) and use as a version the path supplemented with
287 the ``git`` SHA and, if the git repo isn't clean, an MD5 of the diff.
289 These package versions are collected and stored in a Packages object, which
290 provides useful comparison and persistence features.
292 Example usage:
294 .. code-block:: python
296 from lsst.utils.packages import Packages
297 pkgs = Packages.fromSystem()
298 print("Current packages:", pkgs)
299 old = Packages.read("/path/to/packages.pickle")
300 print("Old packages:", old)
301 print("Missing packages compared to before:", pkgs.missing(old))
302 print("Extra packages compared to before:", pkgs.extra(old))
303 print("Different packages: ", pkgs.difference(old))
304 old.update(pkgs) # Include any new packages in the old
305 old.write("/path/to/packages.pickle")
307 Parameters
308 ----------
309 packages : `dict`
310 A mapping {package: version} where both keys and values are type `str`.
312 Notes
313 -----
314 This is a wrapper around a dict with some convenience methods.
315 """
317 formats = {".pkl": "pickle", ".pickle": "pickle", ".yaml": "yaml", ".json": "json"}
319 def __setstate__(self, state: Dict[str, Any]) -> None:
320 # This only seems to be called for old pickle files where
321 # the data was stored in _packages.
322 self.update(state["_packages"])
324 @classmethod
325 def fromSystem(cls) -> Packages:
326 """Construct a `Packages` by examining the system.
328 Determine packages by examining python's `sys.modules`, conda
329 libraries and EUPS. EUPS packages take precedence over conda and
330 general python packages.
332 Returns
333 -------
334 packages : `Packages`
335 All version package information that could be obtained.
336 """
337 packages = {}
338 packages.update(getPythonPackages())
339 packages.update(getCondaPackages())
340 packages.update(getEnvironmentPackages()) # Should be last, to override products with LOCAL versions
341 return cls(packages)
343 @classmethod
344 def fromBytes(cls, data: bytes, format: str) -> Packages:
345 """Construct the object from a byte representation.
347 Parameters
348 ----------
349 data : `bytes`
350 The serialized form of this object in bytes.
351 format : `str`
352 The format of those bytes. Can be ``yaml``, ``json``, or
353 ``pickle``.
355 Returns
356 -------
357 packages : `Packages`
358 The package information read from the input data.
359 """
360 if format == "pickle":
361 file = io.BytesIO(data)
362 new = _BackwardsCompatibilityUnpickler(file).load()
363 elif format == "yaml":
364 new = yaml.load(data, Loader=yaml.SafeLoader)
365 elif format == "json":
366 new = cls(json.loads(data))
367 else:
368 raise ValueError(f"Unexpected serialization format given: {format}")
369 if not isinstance(new, cls):
370 raise TypeError(f"Extracted object of class '{type(new)}' but expected '{cls}'")
371 return new
373 @classmethod
374 def read(cls, filename: str) -> Packages:
375 """Read packages from filename.
377 Parameters
378 ----------
379 filename : `str`
380 Filename from which to read. The format is determined from the
381 file extension. Currently support ``.pickle``, ``.pkl``,
382 ``.json``, and ``.yaml``.
384 Returns
385 -------
386 packages : `Packages`
387 The packages information read from the file.
388 """
389 _, ext = os.path.splitext(filename)
390 if ext not in cls.formats:
391 raise ValueError(f"Format from {ext} extension in file {filename} not recognized")
392 with open(filename, "rb") as ff:
393 # We assume that these classes are tiny so there is no
394 # substantive memory impact by reading the entire file up front
395 data = ff.read()
396 return cls.fromBytes(data, cls.formats[ext])
398 def toBytes(self, format: str) -> bytes:
399 """Convert the object to a serialized bytes form using the
400 specified format.
402 Parameters
403 ----------
404 format : `str`
405 Format to use when serializing. Can be ``yaml``, ``json``,
406 or ``pickle``.
408 Returns
409 -------
410 data : `bytes`
411 Byte string representing the serialized object.
412 """
413 if format == "pickle":
414 return pickle.dumps(self)
415 elif format == "yaml":
416 return yaml.dump(self).encode("utf-8")
417 elif format == "json":
418 return json.dumps(self).encode("utf-8")
419 else:
420 raise ValueError(f"Unexpected serialization format requested: {format}")
422 def write(self, filename: str) -> None:
423 """Write to file.
425 Parameters
426 ----------
427 filename : `str`
428 Filename to which to write. The format of the data file
429 is determined from the file extension. Currently supports
430 ``.pickle``, ``.json``, and ``.yaml``
431 """
432 _, ext = os.path.splitext(filename)
433 if ext not in self.formats:
434 raise ValueError(f"Format from {ext} extension in file {filename} not recognized")
435 with open(filename, "wb") as ff:
436 # Assumes that the bytes serialization of this object is
437 # relatively small.
438 ff.write(self.toBytes(self.formats[ext]))
440 def __str__(self) -> str:
441 ss = "%s({\n" % self.__class__.__name__
442 # Sort alphabetically by module name, for convenience in reading
443 ss += ",\n".join(f"{prod!r}:{self[prod]!r}" for prod in sorted(self))
444 ss += ",\n})"
445 return ss
447 def __repr__(self) -> str:
448 # Default repr() does not report the class name.
449 return f"{self.__class__.__name__}({super().__repr__()})"
451 def extra(self, other: Mapping) -> Dict[str, str]:
452 """Get packages in self but not in another `Packages` object.
454 Parameters
455 ----------
456 other : `Packages` or `Mapping`
457 Other packages to compare against.
459 Returns
460 -------
461 extra : `dict`
462 Extra packages. Keys (type `str`) are package names; values
463 (type `str`) are their versions.
464 """
465 return {pkg: self[pkg] for pkg in self.keys() - other.keys()}
467 def missing(self, other: Mapping) -> Dict[str, str]:
468 """Get packages in another `Packages` object but missing from self.
470 Parameters
471 ----------
472 other : `Packages`
473 Other packages to compare against.
475 Returns
476 -------
477 missing : `dict` [`str`, `str`]
478 Missing packages. Keys (type `str`) are package names; values
479 (type `str`) are their versions.
480 """
481 return {pkg: other[pkg] for pkg in other.keys() - self.keys()}
483 def difference(self, other: Mapping) -> Dict[str, Tuple[str, str]]:
484 """Get packages in symmetric difference of self and another `Packages`
485 object.
487 Parameters
488 ----------
489 other : `Packages`
490 Other packages to compare against.
492 Returns
493 -------
494 difference : `dict` [`str`, `tuple` [`str`, `str`]]
495 Packages in symmetric difference. Keys (type `str`) are package
496 names; values (type `tuple`[`str`, `str`]) are their versions.
497 """
498 return {pkg: (self[pkg], other[pkg]) for pkg in self.keys() & other.keys() if self[pkg] != other[pkg]}
501class _BackwardsCompatibilityUnpickler(pickle.Unpickler):
502 """Replacement for the default unpickler.
504 It is required so that users of this API can read pickle files
505 created when the `~lsst.utils.packages.Packages` class was in a different
506 package and known as ``lsst.base.Packages``. If this unpickler is being
507 used then we know for sure that we must return a
508 `~lsst.utils.packages.Packages` instance.
509 """
511 def find_class(self, module: str, name: str) -> Type:
512 """Return the class that should be used for unpickling.
514 This is always known to be the class in this package.
515 """
516 return Packages
519# Register YAML representers
522def pkg_representer(dumper: yaml.Dumper, data: Any) -> yaml.MappingNode:
523 """Represent Packages as a simple dict"""
524 return dumper.represent_mapping("lsst.utils.packages.Packages", data, flow_style=None)
527yaml.add_representer(Packages, pkg_representer)
530def pkg_constructor(loader: yaml.constructor.SafeConstructor, node: yaml.Node) -> Any:
531 yield Packages(loader.construct_mapping(node, deep=True))
534for loader in (yaml.Loader, yaml.CLoader, yaml.UnsafeLoader, yaml.SafeLoader, yaml.FullLoader):
535 yaml.add_constructor("lsst.utils.packages.Packages", pkg_constructor, Loader=loader)
537 # Register the old name with YAML.
538 yaml.add_constructor("lsst.base.Packages", pkg_constructor, Loader=loader)