scyjava 1.12.0__tar.gz → 1.12.2__tar.gz

{scyjava-1.12.0 → scyjava-1.12.2}/Makefile

@@ -1,32 +1,22 @@
 help:
 	@echo "Available targets:\n\
 		clean - remove build files and directories\n\
-		setup - create mamba developer environment\n\
 		lint  - run code formatters and linters\n\
 		test  - run automated test suite\n\
 		dist  - generate release archives\n\
-	\n\
-	Remember to 'mamba activate scyjava-dev' first!"
+	"
 
 clean:
 	bin/clean.sh
 
-setup:
-	bin/setup.sh
-
 check:
 	@bin/check.sh
 
 lint: check
 	bin/lint.sh
 
-fmt: check
-	bin/fmt.sh
-
 test: check
 	bin/test.sh
 
 dist: check clean
-	python -m build
-
-.PHONY: test
+	bin/dist.sh

{scyjava-1.12.0/src/scyjava.egg-info → scyjava-1.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scyjava
-Version: 1.12.0
+Version: 1.12.2
 Summary: Supercharged Java access from Python
 Author-email: SciJava developers <ctrueden@wisc.edu>
 License-Expression: Unlicense
@@ -32,17 +32,6 @@ Description-Content-Type: text/markdown
 Requires-Dist: jpype1>=1.3.0
 Requires-Dist: jgo
 Requires-Dist: cjdk
-Provides-Extra: dev
-Requires-Dist: assertpy; extra == "dev"
-Requires-Dist: build; extra == "dev"
-Requires-Dist: jep; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Requires-Dist: pytest-cov; extra == "dev"
-Requires-Dist: numpy; extra == "dev"
-Requires-Dist: pandas; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: toml; extra == "dev"
-Requires-Dist: validate-pyproject[all]; extra == "dev"
 
 [![build status](https://github.com/scijava/scyjava/actions/workflows/build.yml/badge.svg)](https://github.com/scijava/scyjava/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/scijava/scyjava/branch/main/graph/badge.svg?token=NLK3ADZUCU)](https://codecov.io/gh/scijava/scyjava)
@@ -131,6 +120,24 @@ u'1.8.0_152-release'
 
 See the [jgo documentation](https://github.com/scijava/jgo) for more about Maven endpoints.
 
+## Bootstrap a Java installation
+
+```python
+>>> from scyjava import config, jimport
+>>> config.set_java_constraints(fetch=True, vendor='zulu', version='17')
+>>> System = jimport('java.lang.System')
+cjdk: Installing JDK zulu:17.0.15 to /home/chuckles/.cache/cjdk
+Download 100% of 189.4 MiB |##########| Elapsed Time: 0:00:02 Time:  0:00:02
+Extract | |                 #                    | 714 Elapsed Time: 0:00:01
+cjdk: Installing Maven to /home/chuckles/.cache/cjdk
+Download 100% of   8.7 MiB |##########| Elapsed Time: 0:00:00 Time:  0:00:00
+Extract | |#                                     | 102 Elapsed Time: 0:00:00
+>>> System.getProperty('java.vendor')
+'Azul Systems, Inc.'
+>>> System.getProperty('java.version')
+'17.0.15'
+```
+
 ## Convert between Python and Java data structures
 
 ### Convert Java collections to Python
@@ -398,7 +405,7 @@ FUNCTIONS
     jvm_started() -> bool
         Return true iff a Java virtual machine (JVM) has been started.
 
-    jvm_version() -> str
+    jvm_version() -> tuple[int, ...]
         Gets the version of the JVM as a tuple, with each dot-separated digit
         as one element. Characters in the version string beyond only numbers
         and dots are ignored, in line with the java.version system property.

{scyjava-1.12.0 → scyjava-1.12.2}/README.md

@@ -85,6 +85,24 @@ u'1.8.0_152-release'
 
 See the [jgo documentation](https://github.com/scijava/jgo) for more about Maven endpoints.
 
+## Bootstrap a Java installation
+
+```python
+>>> from scyjava import config, jimport
+>>> config.set_java_constraints(fetch=True, vendor='zulu', version='17')
+>>> System = jimport('java.lang.System')
+cjdk: Installing JDK zulu:17.0.15 to /home/chuckles/.cache/cjdk
+Download 100% of 189.4 MiB |##########| Elapsed Time: 0:00:02 Time:  0:00:02
+Extract | |                 #                    | 714 Elapsed Time: 0:00:01
+cjdk: Installing Maven to /home/chuckles/.cache/cjdk
+Download 100% of   8.7 MiB |##########| Elapsed Time: 0:00:00 Time:  0:00:00
+Extract | |#                                     | 102 Elapsed Time: 0:00:00
+>>> System.getProperty('java.vendor')
+'Azul Systems, Inc.'
+>>> System.getProperty('java.version')
+'17.0.15'
+```
+
 ## Convert between Python and Java data structures
 
 ### Convert Java collections to Python
@@ -352,7 +370,7 @@ FUNCTIONS
     jvm_started() -> bool
         Return true iff a Java virtual machine (JVM) has been started.
 
-    jvm_version() -> str
+    jvm_version() -> tuple[int, ...]
         Gets the version of the JVM as a tuple, with each dot-separated digit
         as one element. Characters in the version string beyond only numbers
         and dots are ignored, in line with the java.version system property.

scyjava-1.12.2/bin/check.sh

@@ -0,0 +1,6 @@
+#!/bin/sh
+
+if ! command -v uv >/dev/null 2>&1; then
+  echo "Please install uv (https://docs.astral.sh/uv/getting-started/installation/)."
+  exit 1
+fi

{scyjava-1.12.0 → scyjava-1.12.2}/bin/clean.sh

@@ -6,4 +6,4 @@ cd "$dir/.."
 find . -name __pycache__ -type d | while read d
   do rm -rfv "$d"
 done
-rm -rfv .pytest_cache build dist src/*.egg-info
+rm -rfv .pytest_cache build dist src/*.egg-info tests/.pytest_cache

scyjava-1.12.0/bin/setup.sh → scyjava-1.12.2/bin/dist.sh

@@ -3,4 +3,4 @@
 dir=$(dirname "$0")
 cd "$dir/.."
 
-mamba env create -f dev-environment.yml
+uv run python -m build

scyjava-1.12.2/bin/lint.sh

@@ -0,0 +1,22 @@
+#!/bin/sh
+
+dir=$(dirname "$0")
+cd "$dir/.."
+
+exitCode=0
+
+# Check for errors and capture non-zero exit codes.
+uv run validate-pyproject pyproject.toml
+code=$?; test $code -eq 0 || exitCode=$code
+uv run ruff check >/dev/null 2>&1
+code=$?; test $code -eq 0 || exitCode=$code
+uv run ruff format --check >/dev/null 2>&1
+code=$?; test $code -eq 0 || exitCode=$code
+
+# Do actual code reformatting.
+uv run ruff check --fix
+code=$?; test $code -eq 0 || exitCode=$code
+uv run ruff format
+code=$?; test $code -eq 0 || exitCode=$code
+
+exit $exitCode

scyjava-1.12.2/bin/test.sh

@@ -0,0 +1,49 @@
+#!/bin/sh
+
+# Runs the unit tests.
+#
+# Usage examples:
+#   bin/test.sh
+#   bin/test.sh tests/test_basics.py
+#   bin/test.sh tests/test_convert.py::TestConvert::test2DStringArray
+
+set -e
+
+dir=$(dirname "$0")
+cd "$dir/.."
+
+echo
+echo "----------------------"
+echo "| Running unit tests |"
+echo "----------------------"
+
+if [ $# -gt 0 ]
+then
+  uv run python -m pytest -v -p no:faulthandler $@
+else
+  uv run python -m pytest -v -p no:faulthandler tests/
+fi
+jpypeCode=$?
+
+echo
+echo "-----------------------------"
+echo "| Running integration tests |"
+echo "-----------------------------"
+itCode=0
+for t in tests/it/*.py
+do
+  uv run python "$t"
+  code=$?
+  printf -- "--> %s " "$t"
+  if [ "$code" -eq 0 ]
+  then
+    echo "[OK]"
+  else
+    echo "[FAILED]"
+    itCode=$code
+  fi
+done
+
+test "$jpypeCode" -ne 0 && exit "$jpypeCode"
+test "$itCode" -ne 0 && exit "$itCode"
+exit 0

{scyjava-1.12.0 → scyjava-1.12.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "scyjava"
-version = "1.12.0"
+version = "1.12.2"
 description = "Supercharged Java access from Python"
 license = "Unlicense"
 authors = [{name = "SciJava developers", email = "ctrueden@wisc.edu"}]
@@ -30,7 +30,6 @@ classifiers = [
     "Topic :: Utilities",
 ]
 
-# NB: Keep this in sync with environment.yml AND dev-environment.yml!
 requires-python = ">=3.9"
 dependencies = [
     "jpype1 >= 1.3.0",
@@ -38,19 +37,17 @@ dependencies = [
     "cjdk",
 ]
 
-[project.optional-dependencies]
-# NB: Keep this in sync with dev-environment.yml!
+[dependency-groups]
 dev = [
     "assertpy",
     "build",
-    "jep",
     "pytest",
     "pytest-cov",
     "numpy",
     "pandas",
     "ruff",
     "toml",
-    "validate-pyproject[all]"
+    "validate-pyproject[all]",
 ]
 
 [project.urls]
@@ -68,7 +65,6 @@ include-package-data = false
 where = ["src"]
 namespaces = false
 
-# ruff configuration
 [tool.ruff]
 line-length = 88
 src = ["src", "tests"]

{scyjava-1.12.0 → scyjava-1.12.2}/src/scyjava/_cjdk_fetch.py

@@ -47,7 +47,7 @@ def is_jvm_available() -> bool:
     try:
         with patch.object(subprocess, "check_output", new=_silent_check_output):
             jpype.getDefaultJVMPath()
-    # on Darwin, may raise a CalledProcessError when invoking `/user/libexec/java_home`
+    # on Darwin, may raise a CalledProcessError when invoking `/usr/libexec/java_home`
     except (jpype.JVMNotFoundException, subprocess.CalledProcessError):
         return False
     return True

{scyjava-1.12.0 → scyjava-1.12.2}/src/scyjava/_convert.py

@@ -7,6 +7,7 @@ import inspect
 import logging
 import math
 from bisect import insort
+from importlib.util import find_spec
 from pathlib import Path
 from typing import Any, Callable, Dict, List, NamedTuple
 
@@ -236,72 +237,90 @@ def _stock_java_converters() -> List[Converter]:
         ),
         Converter(
             name="int -> java.lang.Byte",
-            predicate=lambda obj, **hints: isinstance(obj, int)
-            and ("type" in hints and hints["type"] in ("b", "byte", "Byte"))
-            and _jc.Byte.MIN_VALUE <= obj <= _jc.Byte.MAX_VALUE,
+            predicate=lambda obj, **hints: (
+                isinstance(obj, int)
+                and ("type" in hints and hints["type"] in ("b", "byte", "Byte"))
+                and _jc.Byte.MIN_VALUE <= obj <= _jc.Byte.MAX_VALUE
+            ),
             converter=_jc.Byte,
             priority=Priority.HIGH,
         ),
         Converter(
             name="int -> java.lang.Short",
-            predicate=lambda obj, **hints: isinstance(obj, int)
-            and ("type" in hints and hints["type"] in ("s", "short", "Short"))
-            and _jc.Short.MIN_VALUE <= obj <= _jc.Short.MAX_VALUE,
+            predicate=lambda obj, **hints: (
+                isinstance(obj, int)
+                and ("type" in hints and hints["type"] in ("s", "short", "Short"))
+                and _jc.Short.MIN_VALUE <= obj <= _jc.Short.MAX_VALUE
+            ),
             converter=_jc.Short,
             priority=Priority.HIGH,
         ),
         Converter(
             name="int -> java.lang.Integer",
-            predicate=lambda obj, **hints: isinstance(obj, int)
-            and ("type" not in hints or hints["type"] in ("i", "int", "Integer"))
-            and _jc.Integer.MIN_VALUE <= obj <= _jc.Integer.MAX_VALUE,
+            predicate=lambda obj, **hints: (
+                isinstance(obj, int)
+                and ("type" not in hints or hints["type"] in ("i", "int", "Integer"))
+                and _jc.Integer.MIN_VALUE <= obj <= _jc.Integer.MAX_VALUE
+            ),
             converter=_jc.Integer,
         ),
         Converter(
             name="int -> java.lang.Long",
-            predicate=lambda obj, **hints: isinstance(obj, int)
-            and ("type" not in hints or hints["type"] in ("j", "l", "long", "Long"))
-            and _jc.Long.MIN_VALUE <= obj <= _jc.Long.MAX_VALUE,
+            predicate=lambda obj, **hints: (
+                isinstance(obj, int)
+                and ("type" not in hints or hints["type"] in ("j", "l", "long", "Long"))
+                and _jc.Long.MIN_VALUE <= obj <= _jc.Long.MAX_VALUE
+            ),
             converter=_jc.Long,
             priority=Priority.NORMAL - 1,
         ),
         Converter(
             name="int -> java.math.BigInteger",
-            predicate=lambda obj, **hints: isinstance(obj, int)
-            and (
-                "type" not in hints or hints["type"] in ("bi", "bigint", "BigInteger")
+            predicate=lambda obj, **hints: (
+                isinstance(obj, int)
+                and (
+                    "type" not in hints
+                    or hints["type"] in ("bi", "bigint", "BigInteger")
+                )
             ),
             converter=lambda obj: _jc.BigInteger(str(obj)),
             priority=Priority.NORMAL - 2,
         ),
         Converter(
             name="float -> java.lang.Float",
-            predicate=lambda obj, **hints: isinstance(obj, float)
-            and ("type" not in hints or hints["type"] in ("f", "float", "Float"))
-            and (
-                math.isinf(obj)
-                or math.isnan(obj)
-                or -_jc.Float.MAX_VALUE <= obj <= _jc.Float.MAX_VALUE
+            predicate=lambda obj, **hints: (
+                isinstance(obj, float)
+                and ("type" not in hints or hints["type"] in ("f", "float", "Float"))
+                and (
+                    math.isinf(obj)
+                    or math.isnan(obj)
+                    or -_jc.Float.MAX_VALUE <= obj <= _jc.Float.MAX_VALUE
+                )
             ),
             converter=_jc.Float,
         ),
         Converter(
             name="float -> java.lang.Double",
-            predicate=lambda obj, **hints: isinstance(obj, float)
-            and ("type" not in hints or hints["type"] in ("d", "double", "Double"))
-            and (
-                math.isinf(obj)
-                or math.isnan(obj)
-                or -_jc.Double.MAX_VALUE <= obj <= _jc.Double.MAX_VALUE
+            predicate=lambda obj, **hints: (
+                isinstance(obj, float)
+                and ("type" not in hints or hints["type"] in ("d", "double", "Double"))
+                and (
+                    math.isinf(obj)
+                    or math.isnan(obj)
+                    or -_jc.Double.MAX_VALUE <= obj <= _jc.Double.MAX_VALUE
+                )
             ),
             converter=_jc.Double,
             priority=Priority.NORMAL - 1,
         ),
         Converter(
             name="float -> java.math.BigDecimal",
-            predicate=lambda obj, **hints: isinstance(obj, float)
-            and (
-                "type" not in hints or hints["type"] in ("bd", "bigdec", "BigDecimal")
+            predicate=lambda obj, **hints: (
+                isinstance(obj, float)
+                and (
+                    "type" not in hints
+                    or hints["type"] in ("bd", "bigdec", "BigDecimal")
+                )
             ),
             converter=lambda obj: _jc.BigDecimal(str(obj)),
             priority=Priority.NORMAL - 2,
@@ -677,7 +696,7 @@ def _stock_py_converters() -> List:
             priority=Priority.VERY_LOW,
         ),
     ]
-    if _import_pandas(required=False):
+    if find_spec("pandas"):
         converters.append(
             Converter(
                 name="org.scijava.table.Table -> pandas.DataFrame",
@@ -716,7 +735,7 @@ def _stock_py_converters() -> List:
                 ),
             ]
         )
-        if _import_numpy(required=False):
+        if find_spec("numpy"):
             converters.append(
                 Converter(
                     name="primitive array -> numpy.ndarray",
@@ -803,16 +822,15 @@ def _jarray_shape(jarr):
     return shape
 
 
-def _import_numpy(required=True):
+def _import_numpy():
     try:
         import numpy as np
 
         return np
     except ImportError as e:
-        if required:
-            msg = "The NumPy library is missing (https://numpy.org/). "
-            msg += "Please install it before using this function."
-            raise RuntimeError(msg) from e
+        msg = "The NumPy library is missing (https://numpy.org/). "
+        msg += "Please install it before using this function."
+        raise RuntimeError(msg) from e
 
 
 ######################################
@@ -838,16 +856,15 @@ def _convert_table(obj: Any):
         return None
 
 
-def _import_pandas(required=True):
+def _import_pandas():
     try:
         import pandas as pd
 
         return pd
     except ImportError as e:
-        if required:
-            msg = "The Pandas library is missing (http://pandas.pydata.org/). "
-            msg += "Please install it before using this function."
-            raise RuntimeError(msg) from e
+        msg = "The Pandas library is missing (http://pandas.pydata.org/). "
+        msg += "Please install it before using this function."
+        raise RuntimeError(msg) from e
 
 
 def _table_to_pandas(table):

{scyjava-1.12.0 → scyjava-1.12.2}/src/scyjava/_introspect.py

@@ -100,7 +100,7 @@ def jsource(data) -> str:
 
         # Discern the Java version.
         jv_digits = jvm_version()
-        assert jv_digits is not None and len(jv_digits) > 1
+        assert jv_digits is not None and len(jv_digits) > 0
         java_version = jv_digits[1] if jv_digits[0] == 1 else jv_digits[0]
 
         # Note: some classes (e.g. corba and jaxp) will not be located correctly before

{scyjava-1.12.0 → scyjava-1.12.2}/src/scyjava/_jvm.py

@@ -70,8 +70,14 @@ def jvm_version() -> tuple[int, ...]:
     default_jvm_path = jpype.getDefaultJVMPath()
     if not default_jvm_path:
         raise RuntimeError("Cannot glean the default JVM path")
+    _logger.debug(f"Default JVM path from JPype: {default_jvm_path}")
 
-    p = Path(default_jvm_path)
+    # Good ol' macOS! Nothing beats macOS.
+    jvm_path = default_jvm_path.replace(
+        "/Contents/MacOS/libjli.dylib", "/Contents/Home/lib/libjli.dylib"
+    )
+
+    p = Path(jvm_path)
     if not p.exists():
         raise RuntimeError(f"Invalid default JVM path: {p}")
 
@@ -93,6 +99,7 @@ def jvm_version() -> tuple[int, ...]:
     if java is None:
         raise RuntimeError(f"No java executable found inside: {p}")
 
+    _logger.debug(f"Invoking `{java} -version`...")
     try:
         output = subprocess.check_output(
             [str(java), "-version"], stderr=subprocess.STDOUT
@@ -101,11 +108,19 @@ def jvm_version() -> tuple[int, ...]:
         raise RuntimeError("System call to java failed") from e
 
     output = output.replace("\n", " ").replace("\r", "")
-    m = re.match('.*version "(([0-9]+\\.)+[0-9]+)', output)
+    m = re.match('.* version "([^"]*)"', output)
     if not m:
-        raise RuntimeError(f"Inscrutable java command output:\n{output}")
+        raise RuntimeError(
+            f"Inscrutable java command output:\n$ {java} -version\n{output}"
+        )
 
-    return tuple(map(int, m.group(1).split(".")))
+    v = m.group(1)
+    _logger.debug(f"Got Java version: {v}")
+
+    try:
+        return tuple(map(int, v.split(".")))
+    except ValueError:
+        raise RuntimeError(f"Inscrutable java version: {v}")
 
 
 def start_jvm(options: Sequence[str] = None) -> None:

{scyjava-1.12.0 → scyjava-1.12.2}/src/scyjava/config.py

@@ -13,10 +13,10 @@ from jgo import maven_scijava_repository as _scijava_public
 _logger = _logging.getLogger(__name__)
 
 # Constraints on the Java installation to be used.
-_fetch_java: str = "auto"
+_fetch_java: str = "always"
 _java_vendor: str = "zulu-jre"
 _java_version: str = "11"
-_maven_url: str = "tgz+https://dlcdn.apache.org/maven/maven-3/3.9.9/binaries/apache-maven-3.9.9-bin.tar.gz"  # noqa: E501
+_maven_url: str = "tgz+https://archive.apache.org/dist/maven/maven-3/3.9.9/binaries/apache-maven-3.9.9-bin.tar.gz"  # noqa: E501
 _maven_sha: str = "a555254d6b53d267965a3404ecb14e53c3827c09c3b94b5678835887ab404556bfaf78dcfe03ba76fa2508649dca8531c74bca4d5846513522404d48e8c4ac8b"  # noqa: E501
 
 endpoints: list[str] = []
@@ -55,10 +55,10 @@ def set_java_constraints(
     Set constraints on the version of Java to be used.
 
     :param fetch:
-        If "auto" (default), when a JVM/or maven cannot be located on the system,
-        [`cjdk`](https://github.com/cachedjdk/cjdk) will be used to download
-        a JDK/JRE distribution and set up the JVM.
-        If "always", cjdk will always be used; if "never", cjdk will never be used.
+        If "always" (default), cjdk will always be used; if "never", cjdk will
+        never be used. If "auto", when a JVM/or maven cannot be located on the system,
+        [`cjdk`](https://github.com/cachedjdk/cjdk) will be used to download a
+        JDK/JRE distribution and set up the JVM.
     :param vendor:
         The vendor of the JDK/JRE distribution for cjdk to download and cache.
         Defaults to "zulu-jre". See the cjdk documentation for details.

{scyjava-1.12.0 → scyjava-1.12.2/src/scyjava.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scyjava
-Version: 1.12.0
+Version: 1.12.2
 Summary: Supercharged Java access from Python
 Author-email: SciJava developers <ctrueden@wisc.edu>
 License-Expression: Unlicense
@@ -32,17 +32,6 @@ Description-Content-Type: text/markdown
 Requires-Dist: jpype1>=1.3.0
 Requires-Dist: jgo
 Requires-Dist: cjdk
-Provides-Extra: dev
-Requires-Dist: assertpy; extra == "dev"
-Requires-Dist: build; extra == "dev"
-Requires-Dist: jep; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Requires-Dist: pytest-cov; extra == "dev"
-Requires-Dist: numpy; extra == "dev"
-Requires-Dist: pandas; extra == "dev"
-Requires-Dist: ruff; extra == "dev"
-Requires-Dist: toml; extra == "dev"
-Requires-Dist: validate-pyproject[all]; extra == "dev"
 
 [![build status](https://github.com/scijava/scyjava/actions/workflows/build.yml/badge.svg)](https://github.com/scijava/scyjava/actions/workflows/build.yml)
 [![codecov](https://codecov.io/gh/scijava/scyjava/branch/main/graph/badge.svg?token=NLK3ADZUCU)](https://codecov.io/gh/scijava/scyjava)
@@ -131,6 +120,24 @@ u'1.8.0_152-release'
 
 See the [jgo documentation](https://github.com/scijava/jgo) for more about Maven endpoints.
 
+## Bootstrap a Java installation
+
+```python
+>>> from scyjava import config, jimport
+>>> config.set_java_constraints(fetch=True, vendor='zulu', version='17')
+>>> System = jimport('java.lang.System')
+cjdk: Installing JDK zulu:17.0.15 to /home/chuckles/.cache/cjdk
+Download 100% of 189.4 MiB |##########| Elapsed Time: 0:00:02 Time:  0:00:02
+Extract | |                 #                    | 714 Elapsed Time: 0:00:01
+cjdk: Installing Maven to /home/chuckles/.cache/cjdk
+Download 100% of   8.7 MiB |##########| Elapsed Time: 0:00:00 Time:  0:00:00
+Extract | |#                                     | 102 Elapsed Time: 0:00:00
+>>> System.getProperty('java.vendor')
+'Azul Systems, Inc.'
+>>> System.getProperty('java.version')
+'17.0.15'
+```
+
 ## Convert between Python and Java data structures
 
 ### Convert Java collections to Python
@@ -398,7 +405,7 @@ FUNCTIONS
     jvm_started() -> bool
         Return true iff a Java virtual machine (JVM) has been started.
 
-    jvm_version() -> str
+    jvm_version() -> tuple[int, ...]
         Gets the version of the JVM as a tuple, with each dot-separated digit
         as one element. Characters in the version string beyond only numbers
         and dots are ignored, in line with the java.version system property.

{scyjava-1.12.0 → scyjava-1.12.2}/src/scyjava.egg-info/SOURCES.txt

@@ -2,14 +2,11 @@ MANIFEST.in
 Makefile
 README.md
 UNLICENSE
-dev-environment.yml
-environment.yml
 pyproject.toml
 bin/check.sh
 bin/clean.sh
-bin/fmt.sh
+bin/dist.sh
 bin/lint.sh
-bin/setup.sh
 bin/test.sh
 src/scyjava/__init__.py
 src/scyjava/_arrays.py

scyjava-1.12.2/src/scyjava.egg-info/requires.txt

@@ -0,0 +1,3 @@
+jpype1>=1.3.0
+jgo
+cjdk

{scyjava-1.12.0 → scyjava-1.12.2}/tests/it/jvm_version.py

@@ -10,15 +10,16 @@ assert_that(scyjava.jvm_started()).is_false()
 
 before_version = scyjava.jvm_version()
 assert_that(before_version).is_not_none()
-assert_that(len(before_version)).is_greater_than_or_equal_to(3)
+assert_that(len(before_version)).is_greater_than_or_equal_to(1)
 assert_that(before_version[0]).is_greater_than(0)
 
+scyjava.config.set_java_constraints(fetch="never")
 scyjava.config.enable_headless_mode()
 scyjava.start_jvm()
 
 after_version = scyjava.jvm_version()
 assert_that(after_version).is_not_none()
-assert_that(len(after_version)).is_greater_than_or_equal_to(3)
+assert_that(len(after_version)).is_greater_than_or_equal_to(1)
 assert_that(after_version[0]).is_greater_than(0)
 
 assert_that(before_version).is_equal_to(after_version)

{scyjava-1.12.0 → scyjava-1.12.2}/tests/test_introspect.py

@@ -53,7 +53,9 @@ class TestIntrospection(object):
         arraylist_Obj = scyjava.jreflect(ArrayList, "constructors")
         assert len(str_Obj) == len(arraylist_Obj) == 3
         arraylist_Obj.sort(
-            key=lambda row: f"{row['type']}:{row['name']}:{','.join(str(row['arguments']))}"
+            key=lambda row: (
+                f"{row['type']}:{row['name']}:{','.join(str(row['arguments']))}"
+            )
         )
         assert arraylist_Obj == [
             {

{scyjava-1.12.0 → scyjava-1.12.2}/tests/test_pandas.py

@@ -60,11 +60,11 @@ class TestPandas(object):
         df = pd.DataFrame(array, columns=columns)
 
         # Convert column 0 to integer
-        df.iloc[:, 0] = (df.iloc[:, 0] * 100).astype("int")
+        df[columns[0]] = (df[columns[0]] * 100).astype("int")
         # Convert column 1 to bool
-        df.iloc[:, 1] = df.iloc[:, 1] > 0.5
+        df[columns[1]] = df[columns[1]] > 0.5
         # Convert column 2 to string
-        df.iloc[:, 2] = df.iloc[:, 2].to_string(index=False).split("\n")
+        df[columns[2]] = df[columns[2]].to_string(index=False).split("\n")
 
         table = to_java(df)
 
@@ -137,11 +137,11 @@ class TestPandas(object):
 
         # fill mixed table
         for i in range(table.getRowCount()):
-            table.set(0, i, Float(float(array_float[i])))
+            table.set(0, i, Float(float(array_float[i].item())))
             table.set(1, i, Integer(int(array_int[i].item())))
-            table.set(2, i, Boolean(bool(array_bool[i])))
+            table.set(2, i, Boolean(bool(array_bool[i].item())))
             table.set(3, i, String(array_str[i]))
-            table.set(4, i, Double(float(array_double[i])))
+            table.set(4, i, Double(float(array_double[i].item())))
 
         df = to_python(table)
         # Table types cannot be the same here, unless we want to cast.

scyjava-1.12.0/bin/check.sh

@@ -1,10 +0,0 @@
-#!/bin/sh
-
-case "$CONDA_PREFIX" in
-  */scyjava-dev)
-    ;;
-  *)
-    echo "Please run 'make setup' and then 'mamba activate scyjava-dev' first."
-    exit 1
-    ;;
-esac

scyjava-1.12.0/bin/fmt.sh

@@ -1,11 +0,0 @@
-#!/bin/sh
-
-dir=$(dirname "$0")
-cd "$dir/.."
-
-exitCode=0
-ruff check --fix
-code=$?; test $code -eq 0 || exitCode=$code
-ruff format
-code=$?; test $code -eq 0 || exitCode=$code
-exit $exitCode

scyjava-1.12.0/bin/lint.sh

@@ -1,13 +0,0 @@
-#!/bin/sh
-
-dir=$(dirname "$0")
-cd "$dir/.."
-
-exitCode=0
-ruff check
-code=$?; test $code -eq 0 || exitCode=$code
-ruff format --check
-code=$?; test $code -eq 0 || exitCode=$code
-validate-pyproject pyproject.toml
-code=$?; test $code -eq 0 || exitCode=$code
-exit $exitCode

scyjava-1.12.0/bin/test.sh

@@ -1,107 +0,0 @@
-#!/bin/sh
-
-# Executes the pytest framework in both JPype and Jep modes.
-#
-# Usage examples:
-#   bin/test.sh
-#   bin/test.sh tests/test_basics.py
-#   bin/test.sh tests/test_convert.py::TestConvert::test2DStringArray
-
-set -e
-
-dir=$(dirname "$0")
-cd "$dir/.."
-
-echo
-echo "-------------------------------------------"
-echo "| Testing JPype mode (Java inside Python) |"
-echo "-------------------------------------------"
-
-if [ $# -gt 0 ]
-then
-  python -m pytest -p no:faulthandler $@
-else
-  python -m pytest -p no:faulthandler tests/
-fi
-jpypeCode=$?
-
-echo
-echo "-------------------------------------------"
-echo "| Running integration tests (JPype only)  |"
-echo "-------------------------------------------"
-itCode=0
-for t in tests/it/*.py
-do
-  python "$t"
-  code=$?
-  printf -- "--> %s " "$t"
-  if [ "$code" -eq 0 ]
-  then
-    echo "[OK]"
-  else
-    echo "[FAILED]"
-    itCode=$code
-  fi
-done
-
-echo
-echo "-------------------------------------------"
-echo "|  Testing Jep mode (Python inside Java)  |"
-echo "-------------------------------------------"
-
-# Discern the Jep installation.
-site_packages=$(python -c 'import sys; print(next(p for p in sys.path if p.endswith("site-packages")))')
-test -d "$site_packages/jep" || {
-  echo "[ERROR] Failed to detect Jep installation in current environment!" 1>&2
-  exit 1
-}
-
-# We execute the pytest framework through Jep via jgo, so that
-# the surrounding JVM includes scijava-table on the classpath.
-#
-# Arguments to the shell script are translated into an argument
-# list to the pytest.main function. A weak attempt at handling
-# special characters, e.g. single quotation marks and backslashes,
-# is made, but there are surely other non-working cases.
-
-if [ $# -gt 0 ]
-then
-  a=$(echo "$@" | sed 's/\\/\\\\/g')     # escape backslashes
-  a=$(echo "$a" | sed 's/'\''/\\'\''/g') # escape single quotes
-  a=$(echo "$a" | sed 's/ /'\'','\''/g') # replace space with ','
-  argString="['-v', '$a']"
-else
-  argString=""
-fi
-if ! java -version 2>&1 | grep -q '^openjdk version "\(1\.8\|9\|10\|11\|12\|13\|14\|15\|16\)\.'
-then
-  echo "Skipping jep tests due to unsupported Java version:"
-  java -version || true
-  jepCode=0
-elif [ "$(uname -s)" = "Darwin" ]
-then
-  echo "Skipping jep tests on macOS due to flakiness"
-  jepCode=0
-else
-  echo "# AUTOGENERATED test file for jep; safe to delete.
-import logging, sys, pytest, scyjava
-scyjava._logger.addHandler(logging.StreamHandler(sys.stderr))
-scyjava._logger.setLevel(logging.INFO)
-scyjava.config.set_verbose(2)
-result = pytest.main($argString)
-if result:
-  sys.exit(result)
-" > jep_test.py
-  jgo -vv \
-    -r scijava.public=https://maven.scijava.org/content/groups/public \
-    -Djava.library.path="$site_packages/jep" \
-    black.ninia:jep:jep.Run+org.scijava:scijava-table \
-    jep_test.py
-  jepCode=$?
-  rm -f jep_test.py
-fi
-
-test "$jpypeCode" -ne 0 && exit "$jpypeCode"
-test "$itCode" -ne 0 && exit "$itCode"
-test "$jepCode" -ne 0 && exit "$jepCode"
-exit 0

scyjava-1.12.0/dev-environment.yml

@@ -1,41 +0,0 @@
-# Use this file to construct an environment
-# for developing scyjava from source.
-#
-# First, install mambaforge:
-#
-#   https://github.com/conda-forge/miniforge#mambaforge
-#
-# Then run:
-#
-#   mamba env create -f dev-environment.yml
-#   conda activate scyjava-dev
-#
-# In addition to the dependencies needed for using scyjava, it
-# includes tools for developer-related actions like running
-# automated tests (pytest) and linting the code (ruff). If you
-# want an environment without these tools, use environment.yml.
-name: scyjava-dev
-channels:
-  - conda-forge
-dependencies:
-  - python = 3.9
-  # Project dependencies
-  - jpype1 >= 1.3.0
-  - jgo
-  - cjdk
-  # Test dependencies
-  - numpy
-  - pandas
-  # Developer tools
-  - assertpy
-  - pytest
-  - pytest-cov
-  - python-build
-  - ruff
-  - toml
-  - validate-pyproject
-  # Project from source
-  - pip
-  - pip:
-    - git+https://github.com/ninia/jep.git@cfca63f8b3398daa6d2685428660dc4b2bfab67d
-    - -e .

scyjava-1.12.0/environment.yml

@@ -1,30 +0,0 @@
-# Use this file to construct an environment for
-# working with scyjava in a runtime setting.
-#
-# First, install mambaforge:
-#
-#   https://github.com/conda-forge/miniforge#mambaforge
-#
-# Then run:
-#
-#   mamba env create
-#   mamba activate scyjava
-#
-# It includes the dependencies needed for using scyjava, but not tools
-# for developer-related actions like running automated tests (pytest),
-# linting the code (ruff), and generating the API documentation (sphinx).
-# If you want an environment including these tools, use dev-environment.yml.
-
-name: scyjava
-channels:
-  - conda-forge
-dependencies:
-  - python >= 3.9
-  # Project dependencies
-  - jpype1 >= 1.3.0
-  - jgo
-  - cjdk
-  # Project from source
-  - pip
-  - pip:
-    - -e .

scyjava-1.12.0/src/scyjava.egg-info/requires.txt

@@ -1,15 +0,0 @@
-jpype1>=1.3.0
-jgo
-cjdk
-
-[dev]
-assertpy
-build
-jep
-pytest
-pytest-cov
-numpy
-pandas
-ruff
-toml
-validate-pyproject[all]