Merge branch 'master' into fix_unevaluated

.github/workflows/autoblack.yml → .github/workflows/isort-and-black-checks.yml

@@ -3,7 +3,7 @@
 # Othewrwise, Black is run and its changes are committed back to the incoming pull request.
 # https://github.com/cclauss/autoblack
 
-name: autoblack
+name: isort and black check
 on: [pull_request]
 jobs:
   build:
@@ -14,11 +14,11 @@ jobs:
         uses: actions/setup-python@v2
         with:
           python-version: 3.9
-      - name: Install click
-        run: pip install 'click==8.0.4'
-      - name: Install Black
-        run: pip install 'black==22.3.0'
-      - name: Run black --check .
+      - name: Install click, black and isort
+        run: pip install 'click==8.0.4' 'black==22.3.0' 'isort==5.10.1'
+      - name: Run isort --check .
+        run: isort --check .
+      - name: Run isort --check .
         run: black --check .
       - name: If needed, commit black changes to the pull request
         if: failure()

.github/workflows/windows.yml

@@ -27,7 +27,7 @@ jobs:
         set LLVM_DIR="C:\Program Files\LLVM"
         # We can comment out after next Mathics-Scanner release
         python -m pip install -e git+https://github.com/Mathics3/mathics-scanner#egg=Mathics-Scanner[full]
-        make develop
+        make develop-full
     - name: Install Mathics
       run: |
         python setup.py install

.isort.cfg

@@ -0,0 +1,10 @@
+[settings]
+multi_line_output = 3
+include_trailing_comma = True
+force_grid_wrap = 0
+use_parentheses = True
+line_length = 88
+sections = FUTURE,STDLIB,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
+default_section = THIRDPARTY
+combine_as_imports = 1
+profile = black

.pre-commit-config.yaml

@@ -9,6 +9,11 @@ repos:
       stages: [commit]
     - id: end-of-file-fixer
       stages: [commit]
+-   repo: https://github.com/pycqa/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        stages: [commit]
 -   repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:

CHANGES.rst

@@ -6,16 +6,34 @@ CHANGES
 5.0.3dev0
 ---------
 
+API
++++
+
+#. New function ``mathics.system_info.python_implementation()`` shows the Python Implementation, e.g. CPython, PyPy, Pyston that is running Python. This is included in the information ``mathics.system_info.mathics_system__system_info()`` returns and is used in ``$PythonImplementation``
+#. A list of optional software can be found in ``mathics.optional_software``. Versions of that software are included in ``mathics.version_info``.
+
+
+Package update
+..............
+
+#. SymPy 1.11.1 accepted
+#. Numpy 1.24.0 accepted
+
+
 New Builtins
 +++++++++++
 
 #. ``$BoxForms``
 #. ``$OutputForms``
 #. ``$PrintForms``
+#. ``$PythonImplementation``
 #. ``Accuracy``
 #. ``ClebschGordan``
 #. ``Curl`` (2-D and 3-D vector forms only)
+#. ``DiscretePlot``
 #. ``Kurtosis``
+#. ``ListLogPlot``
+#. ``LogPlot``
 #. ``PauliMatrix``
 #. ``Remove``
 #. ``SetOptions``
@@ -31,25 +49,31 @@ Documentation
 #. "Exponential Functional" split out from "Trigonometry Functions"
 #. A new section on "Accuracy and Precision" was included in the manual.
 #. "Forms of Input and Output" is its own section
+#. All Builtins have links to WMA pages.
+#. More url links to Wiki pages added; more internal cross links added.
+#. Image has been split off from Graphics and Drawing. There are now subsections for Image
 
 Internals
 +++++++++
 
 #. ``boxes_to_`` methods are now optional for ``BoxElement`` subclasses. Most of the code is now moved to the ``mathics.format`` submodule, and implemented in a more scalable way.
 #. ``mathics.builtin.inout`` was splitted in several modules (``inout``, ``messages``, ``layout``, ``makeboxes``) in order to improve the documentation.
-#. `from_mpmath` conversion supports a new parameter ``acc`` to set the accuracy of the number.
+#. ``from_mpmath`` conversion supports a new parameter ``acc`` to set the accuracy of the number.
 #. Operator name to unicode or ASCII comes from Mathics scanner character tables.
-#. ``eval*`` methods in `Builtin` classes are considerer as synonyms of ``apply*`` methods.
-#. Modularize and improve the way in which `Builtin` classes are selected to have an associated `Definition`.
-#. `_SetOperator.assign_elementary` was renamed as `_SetOperator.assign`. All the special cases are not handled by the `_SetOperator.special_cases` dict.
-
+#. Builtin instance methods that start ``apply`` are considered rule matching and function application; the use of the name ``apply``is deprecated, when ``eval`` is intended.
+#. Modularize and improve the way in which ``Builtin`` classes are selected to have an associated ``Definition``.
+#. ``_SetOperator.assign_elementary`` was renamed as ``_SetOperator.assign``. All the special cases are not handled by the ``_SetOperator.special_cases`` dict.
+#. ``isort`` run over all Python files. More type annotations and docstrings on functions added.
+#. caching on immutable atoms like, ``String``, ``Integer``, ``Real``, etc. was improved; the ``__hash__()`` function was sped up. There is a small speedup overall from this at the expense of increased memory.
 
 
 Bugs
 ++++
 
 # ``0`` with a given precision (like in ```0`3```) is now parsed as ``0``, an integer number.
 #. ``RandomSample`` with one list argument now returns a random ordering of the list items. Previously it would return just one item.
+#. Origin placement corrected on ``ListPlot`` and ``LinePlot``.
+#. Fix long-standing bugs in Image handling
 
 
 Enhancements

SYMBOLS_MANIFEST.txt

@@ -56,6 +56,7 @@ System`$PreRead
 System`$PrintForms
 System`$ProcessID
 System`$ProcessorType
+System`$PythonImplementation
 System`$RandomState
 System`$RecursionLimit
 System`$RootDirectory
@@ -244,7 +245,6 @@ System`Continue
 System`ContinuedFraction
 System`Convert`B64Dump`B64Decode
 System`Convert`B64Dump`B64Encode
-System`Convert`CommonDump`RemoveLinearSyntax
 System`ConvertersDump`$extensionMappings
 System`ConvertersDump`$formatMappings
 System`CoprimeQ
@@ -311,6 +311,7 @@ System`DirectoryName
 System`DirectoryQ
 System`DirectoryStack
 System`DiscreteLimit
+System`DiscretePlot
 System`DisjointQ
 System`Disk
 System`DiskBox
@@ -462,7 +463,7 @@ System`Hash
 System`Haversine
 System`Head
 System`HermiteH
-System`HexidecimalCharacter
+System`HexadecimalCharacter
 System`Histogram
 System`Hold
 System`HoldAll
@@ -592,6 +593,7 @@ System`LinearModelFit
 System`LinearSolve
 System`List
 System`ListLinePlot
+System`ListLogPlot
 System`ListPlot
 System`ListQ
 System`Listable
@@ -601,6 +603,7 @@ System`Log
 System`Log10
 System`Log2
 System`LogGamma
+System`LogPlot
 System`LogisticSigmoid
 System`Longest
 System`Lookup

admin-tools/build_and_check_manifest.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python
 
-from mathics.builtin import name_is_builtin_symbol, modules, Builtin
 import sys
 
+from mathics.builtin import Builtin, modules, name_is_builtin_symbol
 
-def generate_avaliable_builtins_names():
+
+def generate_available_builtins_names():
     msg = ""
     builtins_by_name = {}
     for module in modules:
@@ -37,15 +38,15 @@ def generate_avaliable_builtins_names():
 
 
 def build_builtin_manifest():
-    builtins_by_name = generate_avaliable_builtins_names()
+    builtins_by_name = generate_available_builtins_names()
     with open("SYMBOLS_MANIFEST.txt", "w") as f_out:
         for key in sorted(key for key in builtins_by_name):
             f_out.write(key + "\n")
 
 
 def check_manifest():
     status_OK = True
-    builtins_by_name = generate_avaliable_builtins_names()
+    builtins_by_name = generate_available_builtins_names()
     with open("SYMBOLS_MANIFEST.txt", "r") as f_in:
         manifest_symbols = {name[:-1]: "OK" for name in f_in.readlines()}
     # Check that all the Symbols in the manifest are available

admin-tools/time-mathmp-sympy-fns.py

@@ -3,9 +3,10 @@
 Program to time mpmath pi vs sympy pi
 """
 
+import math
 from timeit import timeit
+
 import mpmath
-import math
 import sympy
 
 PRECISION = 100

mathics/__init__.py

@@ -1,28 +1,50 @@
 # -*- coding: utf-8 -*-
 
-import sys
 import platform
-import sympy
+import sys
+from importlib import import_module
+from typing import Dict
+
 import mpmath
 import numpy
+import sympy
 
 from mathics.version import __version__
 
-version_info = {
+# version_info contains a list of Python packages
+# and the versions infsalled or "Not installed"
+# if the package is not installed and "No version information"
+# if we can't get version infomation.
+version_info: Dict[str, str] = {
     "mathics": __version__,
-    "sympy": sympy.__version__,
     "mpmath": mpmath.__version__,
     "numpy": numpy.__version__,
     "python": platform.python_implementation() + " " + sys.version.split("\n")[0],
+    "sympy": sympy.__version__,
 }
 
-try:
-    import cython
-except ImportError:
-    pass
-else:
-    version_info["cython"] = cython.__version__
 
+# optional_software contains a list of Python packages
+# that add functionality but are optional
+optional_software: Dict[str, str] = (
+    "cython",
+    "lxml",
+    "networkx",
+    "nltk",
+    "psutil",
+    "scikit-image",
+    "scipy",
+    "wordcloud",
+)
+
+for package in optional_software:
+    try:
+        mod = import_module(package)
+        package_version = mod.__dict__.get("__version__", "No version information")
+    except ImportError:
+        package_version = "Not installed"
+
+    version_info[package] = package_version
 
 version_string = """Mathics {mathics}
 on {python}

mathics/algorithm/clusters.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 
 
-import random
-from itertools import chain, islice
 import bisect
 import math
+import random
+from itertools import chain, islice
 
 from mpmath import fsum
 

mathics/algorithm/integrators.py

@@ -2,18 +2,11 @@
 
 import numpy as np
 
-from mathics.core.number import machine_epsilon
+from mathics.core.atoms import Integer, Integer0, Number
 from mathics.core.expression import Expression
-from mathics.core.atoms import (
-    Integer,
-    Integer0,
-    Number,
-)
-
 from mathics.core.list import ListExpression
+from mathics.core.number import machine_epsilon
 from mathics.core.symbols import Symbol, SymbolPlus, SymbolSequence, SymbolTimes
-
-
 from mathics.core.systemsymbols import (
     SymbolBlank,
     SymbolComplex,

mathics/algorithm/introselect.py

@@ -164,8 +164,8 @@ def introselect(a, k):  # changes a
 
 
 if __name__ == "__main__":
-    import random
     import itertools
+    import random
 
     def test_algorithm(l, r_max, name, f):
         a = [random.randint(-r_max, r_max) for _ in range(l)]

mathics/algorithm/optimizers.py

@@ -3,31 +3,22 @@
 from typing import Optional
 
 from mathics.builtin.scoping import dynamic_scoping
-
-
 from mathics.core.atoms import (
-    String,
     Integer,
     Integer0,
-    IntegerM1,
     Integer1,
     Integer2,
     Integer3,
     Integer10,
+    IntegerM1,
     Number,
     Real,
+    String,
 )
 from mathics.core.convert.python import from_python
 from mathics.core.evaluation import Evaluation
-from mathics.eval.nevaluator import eval_N
 from mathics.core.expression import Expression
-from mathics.core.symbols import (
-    BaseElement,
-    SymbolPlus,
-    SymbolTimes,
-    SymbolTrue,
-)
-
+from mathics.core.symbols import BaseElement, SymbolPlus, SymbolTimes, SymbolTrue
 from mathics.core.systemsymbols import (
     SymbolAutomatic,
     SymbolD,
@@ -37,6 +28,7 @@
     SymbolLog,
     SymbolNone,
 )
+from mathics.eval.nevaluator import eval_N
 
 
 def find_minimum_newton1d(f, x0, x, opts, evaluation) -> (Number, bool):

mathics/algorithm/parts.py

@@ -17,10 +17,9 @@
 )
 from mathics.core.expression import Expression
 from mathics.core.list import ListExpression
+from mathics.core.subexpression import SubExpression
 from mathics.core.symbols import Atom, Symbol, SymbolList
 from mathics.core.systemsymbols import SymbolDirectedInfinity, SymbolInfinity
-from mathics.core.subexpression import SubExpression
-
 
 SymbolNothing = Symbol("Nothing")