Merge remote-tracking branch 'origin/main' into pr/MilesCranmerBot/746

Author: Christopher Rowley

.github/dependabot.yml

@@ -13,3 +13,7 @@ updates:
     directory: /
     schedule:
       interval: weekly
+  - package-ecosystem: julia
+    directory: /
+    schedule:
+      interval: weekly

CHANGELOG.md

@@ -3,6 +3,9 @@
 ## Unreleased
 * Added `juliacall.TypeValue.__numpy_dtype__` attribute to allow converting Julia types
   to the corresponding NumPy dtype, like `numpy.dtype(jl.Int)`.
+* JuliaCall now launches Julia with 1 thread by default.
+* Added options `trace_compile` and `trace_compile_timing` to JuliaCall.
+* Bug fixes.
 
 ## 0.9.31 (2025-12-17)
 * Restore support for Python 3.14+.

CondaPkg.toml

@@ -16,3 +16,4 @@ version = ">=3.10,!=3.14.0,!=3.14.1,<4"
 matplotlib = ""
 numpy = ""
 pyside6 = ""
+pandas = ""

README.md

@@ -14,7 +14,7 @@ Bringing [**Python®**](https://www.python.org/) and [**Julia**](https://juliala
 - Fast non-copying conversion of numeric arrays in either direction: modify Python arrays (e.g. `bytes`, `array.array`, `numpy.ndarray`) from Julia or Julia arrays from Python.
 - Helpful wrappers: interpret Python sequences, dictionaries, arrays, dataframes and IO streams as their Julia counterparts, and vice versa.
 - Beautiful stack-traces.
-- Supports modern systems: tested on Windows, MacOS and Linux, 64-bit, Julia 1.10 upwards and Python 3.10 upwards.
+- Supports modern systems: tested on Windows, MacOS and Linux; 64-bit; Julia 1.10 upwards and Python 3.10 upwards.
 
 ⭐ If you like this, a GitHub star would be lovely thank you. ⭐
 

docs/src/index.md

@@ -7,4 +7,4 @@ Bringing [**Python®**](https://www.python.org/) and [**Julia**](https://juliala
 - Fast non-copying conversion of numeric arrays in either direction: modify Python arrays (e.g. `bytes`, `array.array`, `numpy.ndarray`) from Julia or Julia arrays from Python.
 - Helpful wrappers: interpret Python sequences, dictionaries, arrays, dataframes and IO streams as their Julia counterparts, and vice versa.
 - Beautiful stack-traces.
-- Works anywhere: tested on Windows, MacOS and Linux, 32- and 64-bit, Julia Julia 1.10 upwards and Python 3.10 upwards.
+- Works anywhere: tested on Windows, MacOS and Linux; 64-bit; Julia 1.10 upwards and Python 3.10 upwards.

docs/src/juliacall.md

@@ -142,6 +142,8 @@ be configured in two ways:
 | `-X juliacall-heap-size-hint=<N>` | `PYTHON_JULIACALL_HEAP_SIZE_HINT=<N>` | Hint for initial heap size in bytes. |
 | `-X juliacall-exe=<file>` | `PYTHON_JULIACALL_EXE=<file>` | Path to Julia binary to use (overrides JuliaPkg). |
 | `-X juliacall-project=<dir>` | `PYTHON_JULIACALL_PROJECT=<dir>` | Path to the Julia project to use (overrides JuliaPkg). |
+| `-X juliacall-trace-compile=<stderr\|name>` | `PYTHON_JULIACALL_TRACE_COMPILE=<stderr\|name>` | Print precompile statements. |
+| `-X juliacall-trace-compile-timing` | `PYTHON_JULIACALL_TRACE_COMPILE_TIMING=<yes\|no>` | Include timings with precompile statements. |
 
 ## [Multi-threading](@id py-multi-threading)
 

pysrc/juliacall/__init__.py

@@ -64,7 +64,7 @@ def init():
             "For updates, see https://github.com/pytorch/pytorch/issues/78829."
         )
 
-    def option(name, default=None, xkey=None, envkey=None):
+    def option(name, default=None, xkey=None, envkey=None, allowflag=False):
         """Get an option.
 
         Options can be set as command line arguments '-X juliacall-{name}={value}' or as
@@ -73,13 +73,28 @@ def option(name, default=None, xkey=None, envkey=None):
         k = xkey or 'juliacall-'+name.lower().replace('_', '-')
         v = sys._xoptions.get(k)
         if v is not None:
+            if v is True:
+                if not allowflag:
+                    raise ValueError(f'-X{k}: expecting an argument')
+                return True, f'-X{k}'
             return v, f'-X{k}={v}'
         k = envkey or 'PYTHON_JULIACALL_'+name.upper()
         v = os.getenv(k)
         if v is not None:
             return v, f'{k}={v}'
         return default, f'<default>={default}'
 
+    def flag(name, default=None, **kw):
+        v, s = option(name, allowflag=True, **kw)
+        if v is None:
+            return default, s
+        elif v is True or v == 'yes':
+            return True, s
+        elif v == 'no':
+            return False, s
+        else:
+            raise ValueError(f'{s}: expecting yes or no')
+
     def choice(name, choices, default=None, **kw):
         v, s = option(name, **kw)
         if v is None:
@@ -128,7 +143,11 @@ def args_from_config(config):
                         val = 'no'
                     else:
                         continue
-                argv.append('--' + opt[4:].replace('_', '-') + '=' + val)
+                arg = '--' + opt[4:].replace('_', '-')
+                if val is True:
+                    argv.append(arg)
+                elif val is not None:
+                    argv.append(f"{arg}={val}")
         argv = [s.encode("utf-8") for s in argv]
 
         argc = len(argv)
@@ -145,14 +164,16 @@ def args_from_config(config):
     CONFIG['opt_home'] = bindir = path_option('home', check_exists=True, envkey='PYTHON_JULIACALL_BINDIR')[0]
     CONFIG['opt_check_bounds'] = choice('check_bounds', ['yes', 'no', 'auto'])[0]
     CONFIG['opt_compile'] = choice('compile', ['yes', 'no', 'all', 'min'])[0]
+    CONFIG["opt_trace_compile"] = option('trace_compile')[0]
+    CONFIG["opt_trace_compile_timing"] = flag('trace_compile_timing')[0]
     CONFIG['opt_compiled_modules'] = choice('compiled_modules', ['yes', 'no'])[0]
     CONFIG['opt_depwarn'] = choice('depwarn', ['yes', 'no', 'error'])[0]
     CONFIG['opt_inline'] = choice('inline', ['yes', 'no'])[0]
     CONFIG['opt_min_optlevel'] = choice('min_optlevel', ['0', '1', '2', '3'])[0]
     CONFIG['opt_optimize'] = choice('optimize', ['0', '1', '2', '3'])[0]
     CONFIG['opt_procs'] = int_option('procs', accept_auto=True)[0]
     CONFIG['opt_sysimage'] = sysimg = path_option('sysimage', check_exists=True)[0]
-    CONFIG['opt_threads'] = int_option('threads', accept_auto=True)[0]
+    CONFIG['opt_threads'] = option('threads', default='1')[0]
     CONFIG['opt_warn_overwrite'] = choice('warn_overwrite', ['yes', 'no'])[0]
     CONFIG['opt_handle_signals'] = choice('handle_signals', ['yes', 'no'])[0]
     CONFIG['opt_startup_file'] = choice('startup_file', ['yes', 'no'])[0]

src/Wrap/Wrap.jl

@@ -55,18 +55,22 @@ function __init__()
     pyconvert_add_rule("collections.abc:Mapping", PyDict, pyconvert_rule_mapping, priority)
     pyconvert_add_rule("io:IOBase", PyIO, pyconvert_rule_io, priority)
     pyconvert_add_rule("_io:_IOBase", PyIO, pyconvert_rule_io, priority)
-    pyconvert_add_rule(
-        "pandas.core.frame:DataFrame",
-        PyPandasDataFrame,
-        pyconvert_rule_pandasdataframe,
-        priority,
-    )
-    pyconvert_add_rule(
-        "pandas.core.arrays.base:ExtensionArray",
-        PyList,
-        pyconvert_rule_sequence,
-        priority,
-    )
+    for typename in ["pandas.core.frame:DataFrame", "pandas:DataFrame"]
+        pyconvert_add_rule(
+            typename,
+            PyPandasDataFrame,
+            pyconvert_rule_pandasdataframe,
+            priority,
+        )
+    end
+    for typename in ["pandas.core.arrays.base:ExtensionArray", "pandas.api.extensions:ExtensionArray"]
+        pyconvert_add_rule(
+            typename,
+            PyList,
+            pyconvert_rule_sequence,
+            priority,
+        )
+    end
 
     priority = PYCONVERT_PRIORITY_NORMAL
     pyconvert_add_rule("<arraystruct>", Array, pyconvert_rule_array, priority)

test/Compat.jl

@@ -105,12 +105,14 @@ end
     end
 end
 
-@testitem "Tables.jl" begin
+@testitem "Tables.jl" setup=[Setup] begin
     @testset "pytable" begin
         x = (x = [1, 2, 3], y = ["a", "b", "c"])
         # pandas
-        # TODO: install pandas and test properly
-        @test_throws PyException pytable(x, :pandas)
+        if Setup.devdeps
+            y = pytable(x, :pandas)
+            @test pyeq(Bool, pytype(y), pyimport("pandas").DataFrame)
+        end
         # columns
         y = pytable(x, :columns)
         @test pyeq(Bool, y, pydict(x = [1, 2, 3], y = ["a", "b", "c"]))

test/Convert.jl

@@ -305,6 +305,19 @@ end
     @test_throws Exception pyconvert(Second, td(microseconds = 1000))
 end
 
+@testitem "pandas.DataFrame → PyPandasDataFrame" setup=[Setup] begin
+    if Setup.devdeps
+        pd = pyimport("pandas")
+        df = pd.DataFrame()
+        df2 = pyconvert(PyPandasDataFrame, df)
+        @test df2 isa PyPandasDataFrame
+        @test pyis(df2, df)
+        df3 = pyconvert(PyTable, df)
+        @test df3 isa PyPandasDataFrame
+        @test pyis(df3, df)
+    end
+end
+
 @testitem "pyconvert_add_rule (#364)" begin
     id = string(rand(UInt128), base = 16)
     pyexec(