merge

.github/workflows/macos.yml

@@ -28,9 +28,15 @@ jobs:
         python -m pip install --upgrade pip
     - name: Install Mathics3 with full Python dependencies
       run: |
-        # We can comment out after next Mathics-Scanner release
+        # First install our patched version of stopit
+        git clone --depth 1 https://github.com/Mathics3/stopit.git
+        cd stopit/
+        pip install -e .
+        cd ..
         python -m pip install -e git+https://github.com/Mathics3/mathics-scanner#egg=Mathics-Scanner[full]
-        git clone https://github.com/Mathics3/mathics-scanner.git
+        # We can comment out after next Mathics-Scanner release
+        git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+        # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
         cd mathics-scanner/
         pip install -e .
         cd ..

.github/workflows/mypy.yml

@@ -22,9 +22,10 @@ jobs:
       run: |
         sudo apt update -qq && sudo apt install llvm-dev remake
         python -m pip install --upgrade pip
-        # 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]
-        git clone https://github.com/Mathics3/mathics-scanner.git
+        # We can comment out after next Mathics-Scanner release
+        git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+        # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
         cd mathics-scanner/
         pip install -e .
         cd ..

.github/workflows/packages.yml

@@ -0,0 +1,45 @@
+name: Mathics3 Packages (ubuntu)
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: '**'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install OS dependencies
+      run: |
+        sudo apt-get update -qq && sudo apt-get install -qq liblapack-dev llvm-dev tesseract-ocr remake
+    - name: Install Mathics3 with full dependencies
+      run: |
+        python -m pip install --upgrade pip
+        # 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]
+        git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+        # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
+        cd src/mathics-scanner/
+        pip install -e .
+        python -m mathics_scanner.generate.build_tables
+        cd ../..
+    - name: Run Mathics3 Combinatorica tests
+      run: |
+        git submodule init
+        git submodule update
+        remake -x develop
+        cd mathics/Packages/Combinatorica-repo
+        # If Combinatorica repo changes, we may need the below altered
+        # with a branch name, (not HEAD) for testing.
+        git pull origin HEAD
+        pip install -e .[dev]
+        remake -x check

.github/workflows/pyodide.yml

@@ -54,7 +54,9 @@ jobs:
 
           pip install "setuptools>=70.0.0" PyYAML click packaging pytest
 
-          git clone https://github.com/Mathics3/mathics-scanner.git
+          # We can comment out after next Mathics-Scanner release
+          git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+          # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
           cd mathics-scanner/
           pip install --no-build-isolation -e .
           cd ..

.github/workflows/ubuntu-cython.yml

@@ -24,9 +24,15 @@ jobs:
       run: |
         sudo apt-get update -qq && sudo apt-get install -qq liblapack-dev llvm-dev tesseract-ocr
         python -m pip install --upgrade pip
+        # First install our patched version of stopit
+        git clone --depth 1 https://github.com/Mathics3/stopit.git
+        cd stopit/
+        pip install -e .
+        cd ..
         # 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]
-        git clone https://github.com/Mathics3/mathics-scanner.git
+        git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+        # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
         cd mathics-scanner/
         pip install -e .
         cd ..

.github/workflows/ubuntu.yml

@@ -24,9 +24,15 @@ jobs:
     - name: Install Mathics3 with full dependencies
       run: |
         python -m pip install --upgrade pip
+        # First install our patched version of stopit
+        git clone --depth 1 https://github.com/Mathics3/stopit.git
+        cd stopit/
+        pip install -e .
+        cd ..
         # 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]
-        git clone https://github.com/Mathics3/mathics-scanner.git
+        git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+        # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
         cd mathics-scanner/
         pip install -e .
         python -m mathics_scanner.generate.build_tables

.github/workflows/windows.yml

@@ -33,10 +33,15 @@ jobs:
         set LLVM_DIR="C:\Program Files\LLVM"
     - name: Install Mathics3 with Python dependencies
       run: |
+        # First install our patched version of stopit
+        git clone --depth 1 https://github.com/Mathics3/stopit.git
+        cd stopit/
+        pip install -e .
+        cd ..
         # 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]
-
-        git clone https://github.com/Mathics3/mathics-scanner.git
+        git clone --depth 1 https://github.com/Mathics3/mathics-scanner.git
+        # git clone --single-branch --branch operator-refactor-part1.5 https://github.com/Mathics3/mathics-scanner.git
         cd mathics-scanner
         pip install -e .
         python -m mathics_scanner.generate.build_tables

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "mathics/Packages/Combinatorica-repo"]
+	path = mathics/Packages/Combinatorica-repo
+	url = https://github.com/Mathics3/Mathics3-Combinatorica.git
+[submodule "mathics/Packages/Rubi"]
+	path = mathics/Packages/Rubi
+	url = https://github.com/Mathics3/Mathics3-Rubi.git

.pre-commit-config.yaml

@@ -6,17 +6,17 @@ repos:
     hooks:
     - id: check-merge-conflict
     - id: debug-statements
-      stages: [commit]
+      stages: [pre-commit]
     - id: end-of-file-fixer
-      stages: [commit]
+      stages: [pre-commit]
 -   repo: https://github.com/pycqa/isort
     rev: 5.13.2
     hooks:
       - id: isort
-        stages: [commit]
+        stages: [pre-commit]
 -   repo: https://github.com/psf/black
     rev: 23.12.1
     hooks:
     - id: black
       language_version: python3
-      stages: [commit]
+      stages: [pre-commit]

CHANGES.rst

@@ -1,13 +1,52 @@
 CHANGES
 =======
 
+This release is to get out some of the major changes that have gone on
+already in advance of redoing Boxing and Formatting.
+
+Operators are now controlled from a new operators YAML table from the
+``mathics-scanner`` repository. A pass was made over the Mathics parser
+to handle box operators more properly. More work is needed here.
+
+We started adding more debugging capabilites:
+
+* ``Breakpoint[]``
+* ``Stack[]``, and
+* ``Trace[]``
+
+And in the ``Mathics3-Trepan`` repository:
+
+* ``DebugActivate[]``
+* ``Debugger[]``, and
+* ``TraceActivate[]``
+
+This code is very much alpha quality, but it greatly improves the
+ability to debug problems in loading existing packages written from
+Mathematica. So packages ``BoolEval`` and ``CleanSlate`` were added to
+the repostiory.
+
+Also as a result of the improved ability to debug Mathics3, we now
+provide a version of Rubi 4.17 using git submodules . To use this you
+will need a patched version of ``stopit``.  Aravindh Krishnamoorthy
+led the initial port of Rubi.
+
+David A. Roberts worked on ensuring Mathics3 runs on pyodide and
+contributed a number of new Built-in Functions that are found in `The
+On-Line Encyclopedia of Integer Sequences (OEIS) <https://oeis.org/>`_
+
 
 New Builtins
 ++++++++++++
 
+* ``Between``
+* ``Breakpoint`` - forces a Python ``breakpoint()``
 * ``CheckAbort``
 * ``FileNameDrop``
+* ``FormatValues``
 * ``SetEnvironment``
+* ``SequenceForm``
+* ``Stack``
+* ``Trace``
 
 By `@davidar <https://github.com/davidar>`_:
 
@@ -40,16 +79,18 @@ By `@davidar <https://github.com/davidar>`_:
 
 * ``--post-mortem`` option added which will go into the `trepan3k debugger <https https://pypi.org/project/trepan3k/>`_ on an unrecoverable error.
 
-Compatibility
--------------
+WMA Compatibility
+-----------------
 
 * ``GetEnvironment`` expanded to handle ``[]`` and ``{var1, var2,...}`` forms
+* The system ``packages`` directory has been renamed ``Packages`` to conformance with WMA.
+* ``$Path`` now includes a ``Packages`` directory under ``$HOME``.
 
 Internals
 ---------
 
-Operator precedence has been gone over and is picked up in tables from the Mathics Scanner project.
-
+* Operator information has been gone over and is picked up from JSON
+tables produced from the Mathics Scanner project.
 
 Performance
 -----------
@@ -60,17 +101,41 @@ API incompatibility
 -------------------
 
 * ``Matcher`` now requires an additional ``evaluation`` parameter
-* ``Romberg`` removed as an ``NIntegrate[]`` method. It is depcrecated in SciPy and is to be removed by SciPy 1.15.
+* ``Romberg`` removed as an ``NIntegrate[]`` method. It is deprecated in SciPy and is to be removed by SciPy 1.15.
+* The signature of the ``Definition.__init__`` now receives a single dict parameter instead of the several `*values` parameters.
+* Rule positions in ``Definition.{get|set}_values`` now includes the word ``values``. For example ``pos="up"`` now is ``pos="upvalues"``.
+* ``Definitions.get_ownvalue`` now returns a ``BaseElement`` instead of a ``BaseRule`` object.
+* Patterns in ``eval_`` and ``format_`` methods of builtin classes
+  parses patterns in docstrings of the form
+  ``Symbol: Expr`` as ``Pattern[Symbol, Expr]``.
+  To specify associated format in ``format_`` methods the
+  docstring, the list of format must be wrapped in parenthesis, like
+  ``(InputForm,): Definitions[...]`` instead of just ``InputForm: Definitions[...]``.
+
 
 
 Bugs
 ----
 
 * Fix infinite recursion when formatting ``Sequence[...]``
 
+Mathics3 Packages
++++++++++++++++++
+
+* Added ``BoolEval``
+* Added ``CleanSlate``
+* ``Combinatorica`` moved to a separate repository and v.9 renamed to 0.9.1.
+    More code v0.9.1 works. v2.0 renamed v2.0.1 and some code now works.
+* ``Rubi`` version 4.17 (work in progress; algebraic integrations work)
 
-Package updates
-+++++++++++++++
+
+Mathics3 Modules
+++++++++++++++++
+
+* Added preliminary Mathics3 debugger ("pymathics.trepan")
+
+Python Package Updates
++++++++++++++++++++++++
 
 #. Python 3.12 is now supported
 #. SymPy 1.13 is now supported
@@ -785,13 +850,13 @@ New variables and builtins
 Enhancements
 ++++++++++++
 
-#. a function `evaluate_predicate` allows for a basic predicate evaluation using `$Assumptions`.
+#. a function ``evaluate_predicate`` allows for a basic predicate evaluation using ``$Assumptions``.
 #. ``Attributes`` accepts a string parameter.
 #. ``Cases`` accepts Heads option. Issue #1302.
 #. ``ColorNegate`` for colors is supported.
 #. ``D`` and ``Derivative`` improvements.
 #. ``Expand`` and ``ExpandAll`` now support a second parameter ``patt`` Issue #1301.
-#. ``Expand`` and ``ExpandAll`` works with hyperbolic functions (`Sinh`, `Cosh`, `Tanh`, `Coth`).
+#. ``Expand`` and ``ExpandAll`` works with hyperbolic functions (``Sinh``, ``Cosh``, ``Tanh``, ``Coth``).
 #. ``FileNames`` returns a sorted list. Issue #1250.
 #. ``FindRoot`` now accepts several optional parameters like ``Method`` and ``MaxIterations``. See Issue #1235.
 #. ``FixedPoint`` now supports the ``SameTest`` option.
@@ -876,10 +941,10 @@ Bug fixes
 ``TeXForm[]`` for integrals are now properly formatted.
 
 
-Pymathics Modules
-+++++++++++++++++
+Mathics3 Modules
+++++++++++++++++
 
-#. Pymathics modules now can run initialization code when are loaded.
+#. Mathics3 modules now can run initialization code when are loaded.
 #. The ``builtins`` list is not hard-linked to the library anymore. This simplifies the loading and reloading of pymathics modules.
 #. Decoupling of BoxConstructors from the library. Now are defined at the level of the definition objects. This is useful for customizing the Graphics output if it is available.
 

Makefile

@@ -143,7 +143,7 @@ latexdoc texdoc doc:
 
 #: Build JSON ASCII to unicode opcode table and operator table
 mathics/data/operator-tables.json mathics/data/op-tables.json mathics/data/operators.json:
-	$(BASH) ./admin-tools/make-op-tables.sh
+	$(BASH) ./admin-tools/make-JSON-tables.sh
 
 #: Remove ChangeLog
 rmChangeLog:

README.rst

@@ -1,16 +1,20 @@
 Welcome to Mathics Core!
 ========================
 
-|Pypi Installs| |Latest Version| |Supported Python Versions|
+|PyPI Installs| |Latest Version| |Supported Python Versions|
 
 |Packaging status|
 
 
 Mathics3 is a general-purpose computer algebra system (CAS).
 
-However this repository contains just the Python modules for WL Built-in functions, variables, core primitives, e.g. Symbol, a parser to create Expressions, and an evaluator to execute them.
+However this repository contains just the Mathics3 Kernel: Python
+modules for WL Built-in functions, variables, core primitives,
+e.g. Symbol, a parser to create Expressions, and an evaluator to
+execute them.
 
-The home page for Mathics is https://mathics.org where you will find a list of screenshots and components making up the system.
+The home page for Mathics is https://mathics.org where you will find a
+list of screenshots and components making up the system.
 
 Installing
 ----------
@@ -22,15 +26,15 @@ See the `Installing Mathics3 <https://mathics-development-guide.readthedocs.io/e
 Running:
 --------
 
-Mathics3, the core library comes with a very simple command-line program called ``mathics``::
+Mathics3 Kernel comes with a very simple command-line program called ``mathics``::
 
   $ mathics
 
-  Mathics 5.0.3dev0
-  on CPython 3.8.12 (heads/v2.3.4.1_release:4a6b4d3504, Jun  3 2022, 15:46:12)
-  using SymPy 1.10.1, mpmath 1.2.1, numpy 1.23.1, cython 0.29.30
+  Mathics 8.0.0
+  on CPython 3.12.8 (main, Dec  9 2024, 11:38:23) [GCC 13.2.0]
+  using SymPy 1.13.3, mpmath 1.3.0, numpy 1.26.4, cython Not installed
 
-  Copyright (C) 2011-2022 The Mathics Team.
+ Copyright (C) 2011-2025 The Mathics3 Team.
   This program comes with ABSOLUTELY NO WARRANTY.
   This is free software, and you are welcome to redistribute it
   under certain conditions.
@@ -60,14 +64,12 @@ License
 
 Mathics is released under the GNU General Public License Version 3 (GPL3).
 
-.. |Travis| image:: https://secure.travis-ci.org/Mathics3/mathics-core.svg?branch=master
-.. _Travis: https://travis-ci.org/Mathics3/mathics-core
 .. _PyPI: https://pypi.org/project/Mathics/
 .. |mathicsscript| image:: https://github.com/Mathics3/mathicsscript/blob/master/screenshots/mathicsscript1.gif
 .. |mathicssserver| image:: https://mathics.org/images/mathicsserver.png
 .. |Latest Version| image:: https://badge.fury.io/py/Mathics3.svg
 		 :target: https://badge.fury.io/py/Mathics3
-.. |Pypi Installs| image:: https://pepy.tech/badge/Mathics3
+.. |PyPI Installs| image:: https://pepy.tech/badge/Mathics3
 .. |Supported Python Versions| image:: https://img.shields.io/pypi/pyversions/Mathics3.svg
 .. |Packaging status| image:: https://repology.org/badge/vertical-allrepos/mathics.svg
 			    :target: https://repology.org/project/mathics/versions