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Pull Request Pull Request #237: Raise warning on statically-linked Python binaries

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/pysr/julia_helpers.py

"""Functions for initializing the Julia environment and installing deps."""
import sys
import subprocess
import warnings
from pathlib import Path
import os
from julia.api import JuliaError

from .version import __version__, __symbolic_regression_jl_version__

juliainfo = None
julia_initialized = False
julia_kwargs_at_initialization = None
julia_activated_env = None


def _load_juliainfo():
    """Execute julia.core.JuliaInfo.load(), and store as juliainfo."""
    global juliainfo

    if juliainfo is None:
        from julia.core import JuliaInfo

        try:
            juliainfo = JuliaInfo.load(julia="julia")
        except FileNotFoundError:
            env_path = os.environ["PATH"]
            raise FileNotFoundError(
                f"Julia is not installed in your PATH. Please install Julia and add it to your PATH.\n\nCurrent PATH: {env_path}",
            )

    return juliainfo


def _get_julia_env_dir():
    # Have to manually get env dir:
    try:
        julia_env_dir_str = subprocess.run(
            ["julia", "-e using Pkg; print(Pkg.envdir())"],
            capture_output=True,
            env=os.environ,
        ).stdout.decode()
    except FileNotFoundError:
        env_path = os.environ["PATH"]
        raise FileNotFoundError(
            f"Julia is not installed in your PATH. Please install Julia and add it to your PATH.\n\nCurrent PATH: {env_path}",
        )
    return Path(julia_env_dir_str)


def _set_julia_project_env(julia_project, is_shared):
    if is_shared:
        if is_julia_version_greater_eq(version=(1, 7, 0)):
            os.environ["JULIA_PROJECT"] = "@" + str(julia_project)
        else:
            julia_env_dir = _get_julia_env_dir()
            os.environ["JULIA_PROJECT"] = str(julia_env_dir / julia_project)
    else:
        os.environ["JULIA_PROJECT"] = str(julia_project)


def _get_io_arg(quiet):
    io = "devnull" if quiet else "stderr"
    io_arg = f"io={io}" if is_julia_version_greater_eq(version=(1, 6, 0)) else ""
    return io_arg


def install(julia_project=None, quiet=False):  # pragma: no cover
    """
    Install PyCall.jl and all required dependencies for SymbolicRegression.jl.

    Also updates the local Julia registry.
    """
    import julia

    _julia_version_assertion()
    # Set JULIA_PROJECT so that we install in the pysr environment
    processed_julia_project, is_shared = _process_julia_project(julia_project)
    _set_julia_project_env(processed_julia_project, is_shared)

    julia.install(quiet=quiet)
    Main = init_julia(julia_project, quiet=quiet)
    io_arg = _get_io_arg(quiet)

    if is_shared:
        # Install SymbolicRegression.jl:
        _add_sr_to_julia_project(Main, io_arg)

    Main.eval("using Pkg")
    Main.eval(f"Pkg.instantiate({io_arg})")
    Main.eval(f"Pkg.precompile({io_arg})")
    if not quiet:
        warnings.warn(
            "It is recommended to restart Python after installing PySR's dependencies,"
            " so that the Julia environment is properly initialized."
        )


def _import_error():
    return """
    Required dependencies are not installed or built.  Run the following code in the Python REPL:

        >>> import pysr
        >>> pysr.install()
    """


def _process_julia_project(julia_project):
    if julia_project is None:
        is_shared = True
        processed_julia_project = f"pysr-{__version__}"
    elif julia_project[0] == "@":
        is_shared = True
        processed_julia_project = julia_project[1:]
    else:
        is_shared = False
        processed_julia_project = Path(julia_project)
    return processed_julia_project, is_shared


def is_julia_version_greater_eq(juliainfo=None, version=(1, 6, 0)):
    """Check if Julia version is greater than specified version."""
    if juliainfo is None:
        juliainfo = _load_juliainfo()
    current_version = (
        juliainfo.version_major,
        juliainfo.version_minor,
        juliainfo.version_patch,
    )
    return current_version >= version


def _check_for_conflicting_libraries():  # pragma: no cover
    """Check whether there are conflicting modules, and display warnings."""
    # See https://github.com/pytorch/pytorch/issues/78829: importing
    # pytorch before running `pysr.fit` causes a segfault.
    torch_is_loaded = "torch" in sys.modules
    if torch_is_loaded:
        warnings.warn(
            "`torch` was loaded before the Julia instance started. "
            "This may cause a segfault when running `PySRRegressor.fit`. "
            "To avoid this, please run `pysr.julia_helpers.init_julia()` *before* "
            "importing `torch`. "
            "For updates, see https://github.com/pytorch/pytorch/issues/78829"
        )


def init_julia(julia_project=None, quiet=False, julia_kwargs=None):
    """Initialize julia binary, turning off compiled modules if needed."""
    global julia_initialized
    global julia_kwargs_at_initialization
    global julia_activated_env

    if not julia_initialized:
        _check_for_conflicting_libraries()

    if julia_kwargs is None:
        julia_kwargs = {"optimize": 3}

    if "check_bounds" not in julia_kwargs and "JULIA_CHECK_BOUNDS" in os.environ:
        julia_kwargs["check_bounds"] = os.environ["JULIA_CHECK_BOUNDS"]

    from julia.core import JuliaInfo, UnsupportedPythonError

    _julia_version_assertion()
    processed_julia_project, is_shared = _process_julia_project(julia_project)
    _set_julia_project_env(processed_julia_project, is_shared)

    try:
        info = JuliaInfo.load(julia="julia")
    except FileNotFoundError:
        env_path = os.environ["PATH"]
        raise FileNotFoundError(
            f"Julia is not installed in your PATH. Please install Julia and add it to your PATH.\n\nCurrent PATH: {env_path}",
        )

    if not info.is_pycall_built():
        raise ImportError(_import_error())

    from julia.core import Julia

    try:
        Julia(**julia_kwargs)
    except UnsupportedPythonError:
        # Static python binary, so we turn off pre-compiled modules.
        warnings.warn(
            "You are using a statically-linked Python binary. "
            "The first run of PySR will be slower, as all dependencies need to be compiled. "
            "Switch to a dynamically-linked version of Python (like pyenv) to have a faster startup time."
        )
        julia_kwargs = {**julia_kwargs, "compiled_modules": False}
        Julia(**julia_kwargs)

    from julia import Main as _Main

    Main = _Main

    if julia_activated_env is None:
        julia_activated_env = processed_julia_project

    if julia_initialized and julia_kwargs_at_initialization is not None:
        # Check if the kwargs are the same as the previous initialization
        init_set = set(julia_kwargs_at_initialization.items())
        new_set = set(julia_kwargs.items())
        set_diff = new_set - init_set
        # Remove the `compiled_modules` key, since it is not a user-specified kwarg:
        set_diff = {k: v for k, v in set_diff if k != "compiled_modules"}
        if len(set_diff) > 0:
            warnings.warn(
                "Julia has already started. The new Julia options "
                + str(set_diff)
                + " will be ignored."
            )

    if julia_initialized and julia_activated_env != processed_julia_project:
        Main.eval("using Pkg")

        io_arg = _get_io_arg(quiet)
        # Can't pass IO to Julia call as it evaluates to PyObject, so just directly
        # use Main.eval:
        Main.eval(
            f'Pkg.activate("{_escape_filename(processed_julia_project)}",'
            f"shared = Bool({int(is_shared)}), "
            f"{io_arg})"
        )

        julia_activated_env = processed_julia_project

    if not julia_initialized:
        julia_kwargs_at_initialization = julia_kwargs

    julia_initialized = True
    return Main


def _add_sr_to_julia_project(Main, io_arg):
    Main.eval("using Pkg")
    Main.sr_spec = Main.PackageSpec(
        name="SymbolicRegression",
        url="https://github.com/MilesCranmer/SymbolicRegression.jl",
        rev="v" + __symbolic_regression_jl_version__,
    )
    Main.clustermanagers_spec = Main.PackageSpec(
        name="ClusterManagers",
        url="https://github.com/JuliaParallel/ClusterManagers.jl",
        rev="14e7302f068794099344d5d93f71979aaf4fbeb3",
    )
    Main.eval(f"Pkg.add([sr_spec, clustermanagers_spec], {io_arg})")


def _escape_filename(filename):
    """Turn a path into a string with correctly escaped backslashes."""
    str_repr = str(filename)
    str_repr = str_repr.replace("\\", "\\\\")
    return str_repr


def _julia_version_assertion():
    if not is_julia_version_greater_eq(version=(1, 6, 0)):
        raise NotImplementedError(
            "PySR requires Julia 1.6.0 or greater. "
            "Please update your Julia installation."
        )


def _backend_version_assertion(Main):
    try:
        backend_version = Main.eval("string(SymbolicRegression.PACKAGE_VERSION)")
        expected_backend_version = __symbolic_regression_jl_version__
        if backend_version != expected_backend_version:  # pragma: no cover
            warnings.warn(
                f"PySR backend (SymbolicRegression.jl) version {backend_version} "
                f"does not match expected version {expected_backend_version}. "
                "Things may break. "
                "Please update your PySR installation with "
                "`python -c 'import pysr; pysr.install()'`."
            )
    except JuliaError:  # pragma: no cover
        warnings.warn(
            "You seem to have an outdated version of SymbolicRegression.jl. "
            "Things may break. "
            "Please update your PySR installation with "
            "`python -c 'import pysr; pysr.install()'`."
        )


def _load_cluster_manager(Main, cluster_manager):
    Main.eval(f"import ClusterManagers: addprocs_{cluster_manager}")
    return Main.eval(f"addprocs_{cluster_manager}")


def _update_julia_project(Main, is_shared, io_arg):
    try:
        if is_shared:
            _add_sr_to_julia_project(Main, io_arg)
        Main.eval("using Pkg")
        Main.eval(f"Pkg.resolve({io_arg})")
    except (JuliaError, RuntimeError) as e:
        raise ImportError(_import_error()) from e


def _load_backend(Main):
    try:
        # Load namespace, so that various internal operators work:
        Main.eval("using SymbolicRegression")
    except (JuliaError, RuntimeError) as e:
        raise ImportError(_import_error()) from e

    _backend_version_assertion(Main)

    # Load Julia package SymbolicRegression.jl
    from julia import SymbolicRegression

    return SymbolicRegression

1	"""Functions for initializing the Julia environment and installing deps."""
2	import sys	1✔
3	import subprocess	1✔
4	import warnings	1✔
5	from pathlib import Path	1✔
6	import os	1✔
7	from julia.api import JuliaError	1✔
8
9	from .version import __version__, __symbolic_regression_jl_version__	1✔
10
11	juliainfo = None	1✔
12	julia_initialized = False	1✔
13	julia_kwargs_at_initialization = None	1✔
14	julia_activated_env = None	1✔
15
16
17	def _load_juliainfo():	1✔
18	"""Execute julia.core.JuliaInfo.load(), and store as juliainfo."""
19	global juliainfo
20
21	if juliainfo is None:	1✔
22	from julia.core import JuliaInfo	1✔
23
24	try:	1✔
25	juliainfo = JuliaInfo.load(julia="julia")	1✔
26	except FileNotFoundError:	×
27	env_path = os.environ["PATH"]	×
28	raise FileNotFoundError(	×
29	f"Julia is not installed in your PATH. Please install Julia and add it to your PATH.\n\nCurrent PATH: {env_path}",
30	)
31
32	return juliainfo	1✔
33
34
35	def _get_julia_env_dir():	1✔
36	# Have to manually get env dir:
37	try:	×
38	julia_env_dir_str = subprocess.run(	×
39	["julia", "-e using Pkg; print(Pkg.envdir())"],
40	capture_output=True,
41	env=os.environ,
42	).stdout.decode()
43	except FileNotFoundError:	×
44	env_path = os.environ["PATH"]	×
45	raise FileNotFoundError(	×
46	f"Julia is not installed in your PATH. Please install Julia and add it to your PATH.\n\nCurrent PATH: {env_path}",
47	)
48	return Path(julia_env_dir_str)	×
49
50
51	def _set_julia_project_env(julia_project, is_shared):	1✔
52	if is_shared:	1✔
53	if is_julia_version_greater_eq(version=(1, 7, 0)):	1✔
54	os.environ["JULIA_PROJECT"] = "@" + str(julia_project)	1✔
55	else:
56	julia_env_dir = _get_julia_env_dir()	×
57	os.environ["JULIA_PROJECT"] = str(julia_env_dir / julia_project)	×
58	else:
59	os.environ["JULIA_PROJECT"] = str(julia_project)	×
60
61
62	def _get_io_arg(quiet):	1✔
63	io = "devnull" if quiet else "stderr"	1✔
64	io_arg = f"io={io}" if is_julia_version_greater_eq(version=(1, 6, 0)) else ""	1✔
65	return io_arg	1✔
66
67
68	def install(julia_project=None, quiet=False): # pragma: no cover
69	"""
70	Install PyCall.jl and all required dependencies for SymbolicRegression.jl.
71
72	Also updates the local Julia registry.
73	"""
74	import julia
75
76	_julia_version_assertion()
77	# Set JULIA_PROJECT so that we install in the pysr environment
78	processed_julia_project, is_shared = _process_julia_project(julia_project)
79	_set_julia_project_env(processed_julia_project, is_shared)
80
81	julia.install(quiet=quiet)
82	Main = init_julia(julia_project, quiet=quiet)
83	io_arg = _get_io_arg(quiet)
84
85	if is_shared:
86	# Install SymbolicRegression.jl:
87	_add_sr_to_julia_project(Main, io_arg)
88
89	Main.eval("using Pkg")
90	Main.eval(f"Pkg.instantiate({io_arg})")
91	Main.eval(f"Pkg.precompile({io_arg})")
92	if not quiet:
93	warnings.warn(
94	"It is recommended to restart Python after installing PySR's dependencies,"
95	" so that the Julia environment is properly initialized."
96	)
97
98
99	def _import_error():	1✔
100	return """	×
101	Required dependencies are not installed or built. Run the following code in the Python REPL:
102
103	>>> import pysr
104	>>> pysr.install()
105	"""
106
107
108	def _process_julia_project(julia_project):	1✔
109	if julia_project is None:	1✔
110	is_shared = True	1✔
111	processed_julia_project = f"pysr-{__version__}"	1✔
112	elif julia_project[0] == "@":	1✔
113	is_shared = True	1✔
114	processed_julia_project = julia_project[1:]	1✔
115	else:
116	is_shared = False	×
117	processed_julia_project = Path(julia_project)	×
118	return processed_julia_project, is_shared	1✔
119
120
121	def is_julia_version_greater_eq(juliainfo=None, version=(1, 6, 0)):	1✔
122	"""Check if Julia version is greater than specified version."""
123	if juliainfo is None:	1✔
124	juliainfo = _load_juliainfo()	1✔
125	current_version = (	1✔
126	juliainfo.version_major,
127	juliainfo.version_minor,
128	juliainfo.version_patch,
129	)
130	return current_version >= version	1✔
131
132
133	def _check_for_conflicting_libraries(): # pragma: no cover
134	"""Check whether there are conflicting modules, and display warnings."""
135	# See https://github.com/pytorch/pytorch/issues/78829: importing
136	# pytorch before running `pysr.fit` causes a segfault.
137	torch_is_loaded = "torch" in sys.modules
138	if torch_is_loaded:
139	warnings.warn(
140	"`torch` was loaded before the Julia instance started. "
141	"This may cause a segfault when running `PySRRegressor.fit`. "
142	"To avoid this, please run `pysr.julia_helpers.init_julia()` before "
143	"importing `torch`. "
144	"For updates, see https://github.com/pytorch/pytorch/issues/78829"
145	)
146
147
148	def init_julia(julia_project=None, quiet=False, julia_kwargs=None):	1✔
149	"""Initialize julia binary, turning off compiled modules if needed."""
150	global julia_initialized
151	global julia_kwargs_at_initialization
152	global julia_activated_env
153
154	if not julia_initialized:	1✔
155	_check_for_conflicting_libraries()	1✔
156
157	if julia_kwargs is None:	1✔
158	julia_kwargs = {"optimize": 3}	1✔
159
160	if "check_bounds" not in julia_kwargs and "JULIA_CHECK_BOUNDS" in os.environ:	1✔
NEW 161	julia_kwargs["check_bounds"] = os.environ["JULIA_CHECK_BOUNDS"]	×
162
163	from julia.core import JuliaInfo, UnsupportedPythonError	1✔
164
165	_julia_version_assertion()	1✔
166	processed_julia_project, is_shared = _process_julia_project(julia_project)	1✔
167	_set_julia_project_env(processed_julia_project, is_shared)	1✔
168
169	try:	1✔
170	info = JuliaInfo.load(julia="julia")	1✔
171	except FileNotFoundError:	×
172	env_path = os.environ["PATH"]	×
173	raise FileNotFoundError(	×
174	f"Julia is not installed in your PATH. Please install Julia and add it to your PATH.\n\nCurrent PATH: {env_path}",
175	)
176
177	if not info.is_pycall_built():	1✔
178	raise ImportError(_import_error())	×
179
180	from julia.core import Julia	1✔
181
182	try:	1✔
183	Julia(**julia_kwargs)	1✔
184	except UnsupportedPythonError:	×
185	# Static python binary, so we turn off pre-compiled modules.
NEW 186	warnings.warn(	×
187	"You are using a statically-linked Python binary. "
188	"The first run of PySR will be slower, as all dependencies need to be compiled. "
189	"Switch to a dynamically-linked version of Python (like pyenv) to have a faster startup time."
190	)
191	julia_kwargs = {**julia_kwargs, "compiled_modules": False}	×
192	Julia(**julia_kwargs)	×
193
194	from julia import Main as _Main	1✔
195
196	Main = _Main	1✔
197
198	if julia_activated_env is None:	1✔
199	julia_activated_env = processed_julia_project	1✔
200
201	if julia_initialized and julia_kwargs_at_initialization is not None:	1✔
202	# Check if the kwargs are the same as the previous initialization
203	init_set = set(julia_kwargs_at_initialization.items())	1✔
204	new_set = set(julia_kwargs.items())	1✔
205	set_diff = new_set - init_set	1✔
206	# Remove the `compiled_modules` key, since it is not a user-specified kwarg:
207	set_diff = {k: v for k, v in set_diff if k != "compiled_modules"}	1✔
208	if len(set_diff) > 0:	1✔
209	warnings.warn(	1✔
210	"Julia has already started. The new Julia options "
211	+ str(set_diff)
212	+ " will be ignored."
213	)
214
215	if julia_initialized and julia_activated_env != processed_julia_project:	1✔
216	Main.eval("using Pkg")	1✔
217
218	io_arg = _get_io_arg(quiet)	1✔
219	# Can't pass IO to Julia call as it evaluates to PyObject, so just directly
220	# use Main.eval:
221	Main.eval(	1✔
222	f'Pkg.activate("{_escape_filename(processed_julia_project)}",'
223	f"shared = Bool({int(is_shared)}), "
224	f"{io_arg})"
225	)
226
227	julia_activated_env = processed_julia_project	1✔
228
229	if not julia_initialized:	1✔
230	julia_kwargs_at_initialization = julia_kwargs	1✔
231
232	julia_initialized = True	1✔
233	return Main	1✔
234
235
236	def _add_sr_to_julia_project(Main, io_arg):	1✔
237	Main.eval("using Pkg")	1✔
238	Main.sr_spec = Main.PackageSpec(	1✔
239	name="SymbolicRegression",
240	url="https://github.com/MilesCranmer/SymbolicRegression.jl",
241	rev="v" + __symbolic_regression_jl_version__,
242	)
243	Main.clustermanagers_spec = Main.PackageSpec(	1✔
244	name="ClusterManagers",
245	url="https://github.com/JuliaParallel/ClusterManagers.jl",
246	rev="14e7302f068794099344d5d93f71979aaf4fbeb3",
247	)
248	Main.eval(f"Pkg.add([sr_spec, clustermanagers_spec], {io_arg})")	1✔
249
250
251	def _escape_filename(filename):	1✔
252	"""Turn a path into a string with correctly escaped backslashes."""
253	str_repr = str(filename)	1✔
254	str_repr = str_repr.replace("\\", "\\\\")	1✔
255	return str_repr	1✔
256
257
258	def _julia_version_assertion():	1✔
259	if not is_julia_version_greater_eq(version=(1, 6, 0)):	1✔
260	raise NotImplementedError(	×
261	"PySR requires Julia 1.6.0 or greater. "
262	"Please update your Julia installation."
263	)
264
265
266	def _backend_version_assertion(Main):	1✔
267	try:	1✔
268	backend_version = Main.eval("string(SymbolicRegression.PACKAGE_VERSION)")	1✔
269	expected_backend_version = __symbolic_regression_jl_version__	1✔
270	if backend_version != expected_backend_version: # pragma: no cover
271	warnings.warn(
272	f"PySR backend (SymbolicRegression.jl) version {backend_version} "
273	f"does not match expected version {expected_backend_version}. "
274	"Things may break. "
275	"Please update your PySR installation with "
276	"`python -c 'import pysr; pysr.install()'`."
277	)
278	except JuliaError: # pragma: no cover
279	warnings.warn(
280	"You seem to have an outdated version of SymbolicRegression.jl. "
281	"Things may break. "
282	"Please update your PySR installation with "
283	"`python -c 'import pysr; pysr.install()'`."
284	)
285
286
287	def _load_cluster_manager(Main, cluster_manager):	1✔
288	Main.eval(f"import ClusterManagers: addprocs_{cluster_manager}")	×
289	return Main.eval(f"addprocs_{cluster_manager}")	×
290
291
292	def _update_julia_project(Main, is_shared, io_arg):	1✔
293	try:	×
294	if is_shared:	×
295	_add_sr_to_julia_project(Main, io_arg)	×
296	Main.eval("using Pkg")	×
297	Main.eval(f"Pkg.resolve({io_arg})")	×
298	except (JuliaError, RuntimeError) as e:	×
299	raise ImportError(_import_error()) from e	×
300
301
302	def _load_backend(Main):	1✔
303	try:	1✔
304	# Load namespace, so that various internal operators work:
305	Main.eval("using SymbolicRegression")	1✔
306	except (JuliaError, RuntimeError) as e:	×
307	raise ImportError(_import_error()) from e	×
308
309	_backend_version_assertion(Main)	1✔
310
311	# Load Julia package SymbolicRegression.jl
312	from julia import SymbolicRegression	1✔
313
314	return SymbolicRegression	1✔

MilesCranmer / PySR / 3665741319

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