From 736530d7fd454e8686818c641a988f5ff7935208 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Mon, 1 Sep 2025 22:05:49 -0500
Subject: [PATCH 01/47] Start to migrate to `pyproject.toml`

---
 pyproject.toml |  41 ++++++
 setup.py       |  28 ----
 uv.lock        | 347 +++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 388 insertions(+), 28 deletions(-)
 create mode 100644 pyproject.toml
 create mode 100644 uv.lock

diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..361ee09
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,41 @@
+[build-system]
+requires = ["setuptools>=68.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "drudge"
+version = "0.11.0"
+description = "A CAS based on sympy focusing on tensor and noncommutative algebras"
+requires-python = "==3.10.*"
+dependencies = [
+  "sympy==1.13.2",
+  "jinja2",
+  "pyspark>=3.5,<3.6"
+]
+classifiers = [
+  'Development Status :: 1 - Planning',
+  'Intended Audience :: Developers',
+  'Intended Audience :: Science/Research',
+  'Programming Language :: Python :: 3 :: Only',
+  'Programming Language :: Python :: Implementation :: CPython',
+  'Topic :: Scientific/Engineering :: Mathematics'
+]
+readme = { file = "README.rst", content-type = "text/x-rst" }
+license = { file = "LICENSE" } 
+authors = [
+  { name = "Jinmo Zhao" },
+  { name = "Gustavo E. Scuseria" }
+]
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "ipython>=8.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/DrudgeCAS/drudge"
+
+[project.scripts]
+drudge = "drudge.drs:main"
+
diff --git a/setup.py b/setup.py
index 2dbdd0e..8a8cc9f 100644
--- a/setup.py
+++ b/setup.py
@@ -4,19 +4,6 @@
 
 from setuptools import setup, find_packages, Extension
 
-with open('README.rst', 'r') as readme:
-    DESCRIPTION = readme.read()
-
-CLASSIFIERS = [
-    'Development Status :: 1 - Planning',
-    'Intended Audience :: Developers',
-    'Intended Audience :: Science/Research',
-    'License :: OSI Approved :: MIT License',
-    'Programming Language :: Python :: 3 :: Only',
-    'Programming Language :: Python :: Implementation :: CPython',
-    'Topic :: Scientific/Engineering :: Mathematics'
-]
-
 PROJ_ROOT = os.path.dirname(os.path.abspath(__file__))
 INCLUDE_DIRS = [
     '/'.join([PROJ_ROOT, i])
@@ -39,22 +26,7 @@
 )
 
 setup(
-    name='drudge',
-    version='0.10.0dev0',
-    description=DESCRIPTION.splitlines()[0],
-    long_description=DESCRIPTION,
-    url='https://github.com/tschijnmo/drudge',
-    author='Jinmo Zhao and Gustavo E Scuseria',
-    author_email='tschijnmotschau@gmail.com',
-    license='MIT',
-    classifiers=CLASSIFIERS,
     packages=find_packages(),
     ext_modules=[canonpy, wickcore],
     package_data={'drudge': ['templates/*']},
-    install_requires=['sympy', 'ipython', 'Jinja2', 'pyspark'],
-    entry_points={
-        'console_scripts': [
-            'drudge = drudge.drs:main'
-        ]
-    }
 )
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..0101bbb
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,347 @@
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From f825bc43decbbadcec844c609bbc432a158b22d4 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Mon, 1 Sep 2025 22:10:12 -0500
Subject: [PATCH 02/47] Remove editor configuration files

---
 .gitignore                                     |  8 ++++++++
 .idea/dictionaries/tschijnmo.xml               | 17 -----------------
 .idea/drudge.iml                               | 15 ---------------
 .idea/encodings.xml                            |  6 ------
 .idea/inspectionProfiles/profiles_settings.xml |  7 -------
 .idea/misc.xml                                 |  4 ----
 .idea/modules.xml                              |  8 --------
 .idea/vcs.xml                                  |  6 ------
 .ycm_extra_conf.py                             | 16 ----------------
 9 files changed, 8 insertions(+), 79 deletions(-)
 delete mode 100644 .idea/dictionaries/tschijnmo.xml
 delete mode 100644 .idea/drudge.iml
 delete mode 100644 .idea/encodings.xml
 delete mode 100644 .idea/inspectionProfiles/profiles_settings.xml
 delete mode 100644 .idea/misc.xml
 delete mode 100644 .idea/modules.xml
 delete mode 100644 .idea/vcs.xml
 delete mode 100644 .ycm_extra_conf.py

diff --git a/.gitignore b/.gitignore
index 0dff672..aa24398 100644
--- a/.gitignore
+++ b/.gitignore
@@ -79,6 +79,7 @@ celerybeat-schedule
 .env
 
 # virtualenv
+.venv/
 venv/
 ENV/
 
@@ -102,3 +103,10 @@ ENV/
 
 # For usage in dockerignore.
 .git
+
+# Editors
+.idea/
+.ycm_extra_conf.py
+
+# macOS cruft
+.DS_Store
diff --git a/.idea/dictionaries/tschijnmo.xml b/.idea/dictionaries/tschijnmo.xml
deleted file mode 100644
index 19b8c75..0000000
--- a/.idea/dictionaries/tschijnmo.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<component name="ProjectDictionaryState">
-  <dictionary name="tschijnmo">
-    <words>
-      <w>adjoint</w>
-      <w>alegbras</w>
-      <w>bogoliubov</w>
-      <w>cartan</w>
-      <w>hermitian</w>
-      <w>indexable</w>
-      <w>noncommutative</w>
-      <w>noncommutativity</w>
-      <w>subalgebra</w>
-      <w>summand</w>
-      <w>summands</w>
-    </words>
-  </dictionary>
-</component>
\ No newline at end of file
diff --git a/.idea/drudge.iml b/.idea/drudge.iml
deleted file mode 100644
index 4e850c1..0000000
--- a/.idea/drudge.iml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$">
-      <sourceFolder url="file://$MODULE_DIR$/build/lib.macosx-10.12-x86_64-3.6" isTestSource="false" />
-      <excludeFolder url="file://$MODULE_DIR$/build" />
-    </content>
-    <orderEntry type="jdk" jdkName="Python 3.6.1 (/usr/local/bin/python3)" jdkType="Python SDK" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-  <component name="TestRunnerService">
-    <option name="projectConfiguration" value="Nosetests" />
-    <option name="PROJECT_TEST_RUNNER" value="Nosetests" />
-  </component>
-</module>
\ No newline at end of file
diff --git a/.idea/encodings.xml b/.idea/encodings.xml
deleted file mode 100644
index 97626ba..0000000
--- a/.idea/encodings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="Encoding">
-    <file url="PROJECT" charset="UTF-8" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index c23ecac..0000000
--- a/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,7 +0,0 @@
-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="useProjectProfile" value="false" />
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
deleted file mode 100644
index 2f9f52e..0000000
--- a/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6.1 (/usr/local/bin/python3)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
deleted file mode 100644
index dc7d84f..0000000
--- a/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/drudge.iml" filepath="$PROJECT_DIR$/.idea/drudge.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
deleted file mode 100644
index 94a25f7..0000000
--- a/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-  </component>
-</project>
\ No newline at end of file
diff --git a/.ycm_extra_conf.py b/.ycm_extra_conf.py
deleted file mode 100644
index efbbc03..0000000
--- a/.ycm_extra_conf.py
+++ /dev/null
@@ -1,16 +0,0 @@
-import os
-import subprocess
-
-def FlagsForFile(filename, **kwargs):
-
-    flags = ['-std=c++14', '-I/usr/local/include']
-
-    proj_root = os.path.dirname(os.path.abspath(__file__))
-    libcanon_include = ''.join(['-I', proj_root, '/deps/libcanon/include'])
-    python_include = subprocess.run(
-        ["pkg-config", '--cflags', 'python3'], stdout=subprocess.PIPE
-    ).stdout.decode("utf-8")
-    proj_include = ''.join(['-I', proj_root, '/drudge'])
-    flags.extend([libcanon_include, proj_include])
-
-    return {'flags': flags}

From b369f7683e849e155075fe772165d8fd55837416 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Mon, 1 Sep 2025 22:41:42 -0500
Subject: [PATCH 03/47] Install `pytest` and `ipython` by default

---
 pyproject.toml |  10 +---
 uv.lock        | 146 ++++++++++++++++++++++++-------------------------
 2 files changed, 73 insertions(+), 83 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 361ee09..e6e56c1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,7 +10,9 @@ requires-python = "==3.10.*"
 dependencies = [
   "sympy==1.13.2",
   "jinja2",
-  "pyspark>=3.5,<3.6"
+  "pyspark>=3.5,<3.6",
+  "pytest",
+  "ipython>=8.0"
 ]
 classifiers = [
   'Development Status :: 1 - Planning',
@@ -27,12 +29,6 @@ authors = [
   { name = "Gustavo E. Scuseria" }
 ]
 
-[project.optional-dependencies]
-dev = [
-  "pytest",
-  "ipython>=8.0",
-]
-
 [project.urls]
 Homepage = "https://github.com/DrudgeCAS/drudge"
 
diff --git a/uv.lock b/uv.lock
index 0101bbb..ef57c4c 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,32 +1,31 @@
 version = 1
-revision = 3
 requires-python = "==3.10.*"
 
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 [[package]]
@@ -34,26 +33,21 @@ name = "drudge"
 version = "0.11.0"
 source = { editable = "." }
 dependencies = [
+    { name = "ipython" },
     { name = "jinja2" },
     { name = "pyspark" },
-    { name = "sympy" },
-]
-
-[package.optional-dependencies]
-dev = [
-    { name = "ipython" },
     { name = "pytest" },
+    { name = "sympy" },
 ]
 
 [package.metadata]
 requires-dist = [
-    { name = "ipython", marker = "extra == 'dev'", specifier = ">=8.0" },
+    { name = "ipython", specifier = ">=8.0" },
     { name = "jinja2" },
     { name = "pyspark", specifier = ">=3.5,<3.6" },
-    { name = "pytest", marker = "extra == 'dev'" },
+    { name = "pytest" },
     { name = "sympy", specifier = "==1.13.2" },
 ]
-provides-extras = ["dev"]
 
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 name = "exceptiongroup"
@@ -62,27 +56,27 @@ source = { registry = "https://pypi.org/simple" }
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     { name = "typing-extensions" },
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From f47d5bcc66e6516369d4b5d76a604bd301fe29a0 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 09:47:09 -0500
Subject: [PATCH 04/47] Rewind to Python 3.9 and build with `dummy_spark`

---
 MANIFEST.in    |   4 +
 pyproject.toml |  20 +++-
 uv.lock        | 260 +++++++++++++++++++++++++++++++++++++++++++++----
 3 files changed, 262 insertions(+), 22 deletions(-)
 create mode 100644 MANIFEST.in

diff --git a/MANIFEST.in b/MANIFEST.in
new file mode 100644
index 0000000..5887818
--- /dev/null
+++ b/MANIFEST.in
@@ -0,0 +1,4 @@
+recursive-include drudge *.h
+
+recursive-include deps/libcanon/include *.h
+
diff --git a/pyproject.toml b/pyproject.toml
index e6e56c1..a7286e1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,18 +1,18 @@
 [build-system]
-requires = ["setuptools>=68.0", "wheel"]
+requires = ["setuptools>=68", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "drudge"
 version = "0.11.0"
 description = "A CAS based on sympy focusing on tensor and noncommutative algebras"
-requires-python = "==3.10.*"
+requires-python = "==3.9.*"
 dependencies = [
   "sympy==1.13.2",
   "jinja2",
   "pyspark>=3.5,<3.6",
-  "pytest",
-  "ipython>=8.0"
+  "ipython>=8.0",
+  "dummyrdd @ git+https://github.com/tschijnmo/DummyRDD.git@master"
 ]
 classifiers = [
   'Development Status :: 1 - Planning',
@@ -23,15 +23,25 @@ classifiers = [
   'Topic :: Scientific/Engineering :: Mathematics'
 ]
 readme = { file = "README.rst", content-type = "text/x-rst" }
-license = { file = "LICENSE" } 
+license = "MIT"
 authors = [
   { name = "Jinmo Zhao" },
   { name = "Gustavo E. Scuseria" }
 ]
 
+[project.optional-dependencies]
+docs = ["sphinx"]
+dev = ["pytest"]
+
 [project.urls]
 Homepage = "https://github.com/DrudgeCAS/drudge"
 
 [project.scripts]
 drudge = "drudge.drs:main"
 
+[tool.setuptools]
+license-files = ["LICENSE"]
+include-package-data = true
+
+[tool.setuptools.package-data]
+drudge = ["templates/*", "*.h"]
diff --git a/uv.lock b/uv.lock
index ef57c4c..a5a8c37 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,14 @@
 version = 1
-requires-python = "==3.10.*"
+requires-python = "==3.9.*"
+
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+version = "0.7.16"
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@@ -10,6 +19,44 @@ wheels = [
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+]
+docs = [
+    { name = "sphinx" },
+]
+
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     { name = "jinja2" },
     { name = "pyspark", specifier = ">=3.5,<3.6" },
-    { name = "pytest" },
+    { name = "pytest", marker = "extra == 'dev'" },
+    { name = "sphinx", marker = "extra == 'docs'" },
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+version = "2.0.0"
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 name = "stack-data"
 version = "0.6.3"
@@ -331,6 +539,15 @@ wheels = [
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 ]
 
+[[package]]
+name = "urllib3"
+version = "2.5.0"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/15/22/9ee70a2574a4f4599c47dd506532914ce044817c7752a79b6a51286319bc/urllib3-2.5.0.tar.gz", hash = "sha256:3fc47733c7e419d4bc3f6b3dc2b4f890bb743906a30d56ba4a5bfa4bbff92760", size = 393185 }
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+
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 name = "wcwidth"
 version = "0.2.13"
@@ -339,3 +556,12 @@ sdist = { url = "https://files.pythonhosted.org/packages/6c/63/53559446a878410fc
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 ]
+
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+name = "zipp"
+version = "3.23.0"
+source = { registry = "https://pypi.org/simple" }
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From 5eb2d59ddfc96b1738832d722e9d1769e03b3132 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 09:52:20 -0500
Subject: [PATCH 05/47] Update GitHub action

---
 .github/workflows/pythonapp.yml | 44 +++++++++++++++------------------
 1 file changed, 20 insertions(+), 24 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 586741b..ab3dcfc 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -3,37 +3,33 @@ name: Python application
 on: [push, pull_request]
 
 jobs:
-  build:
-
+  build-and-test:
+    name: Drudge
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v5
+
     - name: Download submodules
       shell: bash
       run: |
-          git submodule update --init --recursive 
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+        git submodule update --init --recursive
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        python-version: 3.7
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        # pip install -r requirements.txt
-        git clone https://github.com/tschijnmo/DummyRDD.git
-        cd DummyRDD; python3 setup.py install; cd ..
-    - name: Install
+        python-version-file: "pyproject.toml"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: Install the project
       run: |
-        python3 setup.py install
-    - name: Test with pytest
+        uv sync --locked --extra --dev
+        uv build
+
+    - name: Run tests
       env:
         DUMMY_SPARK: 1
-      run: |
-        cd tests 
-        pip install pytest
-        pip install coveralls
-        coverage run --source=drudge -m pytest -sv
-        cd ..
-        coveralls
-        
+      run: uv run pytest tests
+ 

From 4c549e57df85d0bbd14c46c2a45c7b5240b3e310 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 09:53:48 -0500
Subject: [PATCH 06/47] Fix typo in `uv sync`

---
 .github/workflows/pythonapp.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index ab3dcfc..2d851aa 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -25,7 +25,7 @@ jobs:
 
     - name: Install the project
       run: |
-        uv sync --locked --extra --dev
+        uv sync --locked --extra dev
         uv build
 
     - name: Run tests

From 487b37c3b862d75d40d6287e6d3f24dc1bc65e51 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 15:08:27 -0500
Subject: [PATCH 07/47] Fix deprecated APIs according to PEP 623 and bump
 Python to 3.12

---
 drudge/canonpy.cpp |   2 +-
 pyproject.toml     |   2 +-
 uv.lock            | 146 +++++++++++++++++----------------------------
 3 files changed, 58 insertions(+), 92 deletions(-)

diff --git a/drudge/canonpy.cpp b/drudge/canonpy.cpp
index f6489f3..418a7b9 100644
--- a/drudge/canonpy.cpp
+++ b/drudge/canonpy.cpp
@@ -317,7 +317,7 @@ static PyObject* perm_repr(Perm_object* self)
     // This is used for empty or non-empty permutation.
     repr += L')';
 
-    return PyUnicode_FromUnicode(repr.data(), repr.size());
+    return PyUnicode_FromWideChar(repr.data(), (Py_ssize_t)repr.size());
 }
 
 /** Creates a new Perm object.
diff --git a/pyproject.toml b/pyproject.toml
index a7286e1..618e191 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "drudge"
 version = "0.11.0"
 description = "A CAS based on sympy focusing on tensor and noncommutative algebras"
-requires-python = "==3.9.*"
+requires-python = "==3.12.*"
 dependencies = [
   "sympy==1.13.2",
   "jinja2",
diff --git a/uv.lock b/uv.lock
index a5a8c37..2b64c9d 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,13 +1,13 @@
 version = 1
-requires-python = "==3.9.*"
+requires-python = "==3.12.*"
 
 [[package]]
 name = "alabaster"
-version = "0.7.16"
+version = "1.0.0"
 source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/c9/3e/13dd8e5ed9094e734ac430b5d0eb4f2bb001708a8b7856cbf8e084e001ba/alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65", size = 23776 }
+sdist = { url = "https://files.pythonhosted.org/packages/a6/f8/d9c74d0daf3f742840fd818d69cfae176fa332022fd44e3469487d5a9420/alabaster-1.0.0.tar.gz", hash = "sha256:c00dca57bca26fa62a6d7d0a9fcce65f3e026e9bfe33e9c538fd3fbb2144fd9e", size = 24210 }
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+    { url = "https://files.pythonhosted.org/packages/7e/b3/6b4067be973ae96ba0d615946e314c5ae35f9f993eca561b356540bb0c2b/alabaster-1.0.0-py3-none-any.whl", hash = "sha256:fc6786402dc3fcb2de3cabd5fe455a2db534b371124f1f21de8731783dec828b", size = 13929 },
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 [[package]]
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 source = { registry = "https://pypi.org/simple" }
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+    { url = "https://files.pythonhosted.org/packages/53/97/d2cbbaa10c9b826af0e10fdf836e1bf344d9f0abb873ebc34d1f49642d3f/roman_numerals_py-3.1.0-py3-none-any.whl", hash = "sha256:9da2ad2fb670bcf24e81070ceb3be72f6c11c440d73bd579fbeca1e9f330954c", size = 7742 },
+]
+
 [[package]]
 name = "snowballstemmer"
 version = "3.0.1"
@@ -405,7 +399,7 @@ wheels = [
 
 [[package]]
 name = "sphinx"
-version = "7.4.7"
+version = "8.2.3"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "alabaster" },
@@ -413,11 +407,11 @@ dependencies = [
     { name = "colorama", marker = "sys_platform == 'win32'" },
     { name = "docutils" },
     { name = "imagesize" },
-    { name = "importlib-metadata" },
     { name = "jinja2" },
     { name = "packaging" },
     { name = "pygments" },
     { name = "requests" },
+    { name = "roman-numerals-py" },
     { name = "snowballstemmer" },
     { name = "sphinxcontrib-applehelp" },
     { name = "sphinxcontrib-devhelp" },
@@ -425,11 +419,10 @@ dependencies = [
     { name = "sphinxcontrib-jsmath" },
     { name = "sphinxcontrib-qthelp" },
     { name = "sphinxcontrib-serializinghtml" },
-    { name = "tomli" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/5b/be/50e50cb4f2eff47df05673d361095cafd95521d2a22521b920c67a372dcb/sphinx-7.4.7.tar.gz", hash = "sha256:242f92a7ea7e6c5b406fdc2615413890ba9f699114a9c09192d7dfead2ee9cfe", size = 8067911 }
+sdist = { url = "https://files.pythonhosted.org/packages/38/ad/4360e50ed56cb483667b8e6dadf2d3fda62359593faabbe749a27c4eaca6/sphinx-8.2.3.tar.gz", hash = "sha256:398ad29dee7f63a75888314e9424d40f52ce5a6a87ae88e7071e80af296ec348", size = 8321876 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/0d/ef/153f6803c5d5f8917dbb7f7fcf6d34a871ede3296fa89c2c703f5f8a6c8e/sphinx-7.4.7-py3-none-any.whl", hash = "sha256:c2419e2135d11f1951cd994d6eb18a1835bd8fdd8429f9ca375dc1f3281bd239", size = 3401624 },
+    { url = "https://files.pythonhosted.org/packages/31/53/136e9eca6e0b9dc0e1962e2c908fbea2e5ac000c2a2fbd9a35797958c48b/sphinx-8.2.3-py3-none-any.whl", hash = "sha256:4405915165f13521d875a8c29c8970800a0141c14cc5416a38feca4ea5d9b9c3", size = 3589741 },
 ]
 
 [[package]]
@@ -512,15 +505,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/c1/f9/6845bf8fca0eaf847da21c5d5bc6cd92797364662824a11d3f836423a1a5/sympy-1.13.2-py3-none-any.whl", hash = "sha256:c51d75517712f1aed280d4ce58506a4a88d635d6b5dd48b39102a7ae1f3fcfe9", size = 6189289 },
 ]
 
-[[package]]
-name = "tomli"
-version = "2.2.1"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/18/87/302344fed471e44a87289cf4967697d07e532f2421fdaf868a303cbae4ff/tomli-2.2.1.tar.gz", hash = "sha256:cd45e1dc79c835ce60f7404ec8119f2eb06d38b1deba146f07ced3bbc44505ff", size = 17175 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/6e/c2/61d3e0f47e2b74ef40a68b9e6ad5984f6241a942f7cd3bbfbdbd03861ea9/tomli-2.2.1-py3-none-any.whl", hash = "sha256:cb55c73c5f4408779d0cf3eef9f762b9c9f147a77de7b258bef0a5628adc85cc", size = 14257 },
-]
-
 [[package]]
 name = "traitlets"
 version = "5.14.3"
@@ -530,15 +514,6 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/00/c0/8f5d070730d7836adc9c9b6408dec68c6ced86b304a9b26a14df072a6e8c/traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f", size = 85359 },
 ]
 
-[[package]]
-name = "typing-extensions"
-version = "4.15.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/72/94/1a15dd82efb362ac84269196e94cf00f187f7ed21c242792a923cdb1c61f/typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466", size = 109391 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/18/67/36e9267722cc04a6b9f15c7f3441c2363321a3ea07da7ae0c0707beb2a9c/typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548", size = 44614 },
-]
-
 [[package]]
 name = "urllib3"
 version = "2.5.0"
@@ -556,12 +531,3 @@ sdist = { url = "https://files.pythonhosted.org/packages/6c/63/53559446a878410fc
 wheels = [
     { url = "https://files.pythonhosted.org/packages/fd/84/fd2ba7aafacbad3c4201d395674fc6348826569da3c0937e75505ead3528/wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859", size = 34166 },
 ]
-
-[[package]]
-name = "zipp"
-version = "3.23.0"
-source = { registry = "https://pypi.org/simple" }
-sdist = { url = "https://files.pythonhosted.org/packages/e3/02/0f2892c661036d50ede074e376733dca2ae7c6eb617489437771209d4180/zipp-3.23.0.tar.gz", hash = "sha256:a07157588a12518c9d4034df3fbbee09c814741a33ff63c05fa29d26a2404166", size = 25547 }
-wheels = [
-    { url = "https://files.pythonhosted.org/packages/2e/54/647ade08bf0db230bfea292f893923872fd20be6ac6f53b2b936ba839d75/zipp-3.23.0-py3-none-any.whl", hash = "sha256:071652d6115ed432f5ce1d34c336c0adfd6a884660d1e9712a256d3d3bd4b14e", size = 10276 },
-]

From 6763d8ca5d306fce88ed1d5e9926cfaf4caee2e9 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 15:36:37 -0500
Subject: [PATCH 08/47] Fix more deprecations

---
 drudge/drs.py  | 2 +-
 pyproject.toml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/drudge/drs.py b/drudge/drs.py
index d9c465b..dedaa02 100644
--- a/drudge/drs.py
+++ b/drudge/drs.py
@@ -82,7 +82,7 @@ def __getitem__(self, indices):
         In drudge scripts, all symbols are by itself indexed bases.
         """
         base = IndexedBase(self._orig)
-        if isinstance(indices, collections.Sequence):
+        if isinstance(indices, collections.abc.Sequence):
             return DrsIndexed(self._drudge, base, *indices)
         else:
             return DrsIndexed(self._drudge, base, indices)
diff --git a/pyproject.toml b/pyproject.toml
index 618e191..e024285 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,6 +24,7 @@ classifiers = [
 ]
 readme = { file = "README.rst", content-type = "text/x-rst" }
 license = "MIT"
+license-files = ["LICENSE"]
 authors = [
   { name = "Jinmo Zhao" },
   { name = "Gustavo E. Scuseria" }
@@ -40,7 +41,6 @@ Homepage = "https://github.com/DrudgeCAS/drudge"
 drudge = "drudge.drs:main"
 
 [tool.setuptools]
-license-files = ["LICENSE"]
 include-package-data = true
 
 [tool.setuptools.package-data]

From 05aadaa814b4e6203942fb2b12c257ef5f556ab4 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 17:52:02 -0500
Subject: [PATCH 09/47] Convert README to markdown

---
 MANIFEST.in |  2 ++
 README.md   | 33 ++++++++++++++++++++++++
 README.rst  | 73 -----------------------------------------------------
 3 files changed, 35 insertions(+), 73 deletions(-)
 create mode 100644 README.md
 delete mode 100644 README.rst

diff --git a/MANIFEST.in b/MANIFEST.in
index 5887818..82488ca 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -2,3 +2,5 @@ recursive-include drudge *.h
 
 recursive-include deps/libcanon/include *.h
 
+recursive-include drudge/templates *
+
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..3a2debe
--- /dev/null
+++ b/README.md
@@ -0,0 +1,33 @@
+![CircleCI](https://circleci.com/gh/DrudgeCAS/drudge.svg?style=shield)
+[![Coveralls](https://coveralls.io/repos/github/DrudgeCAS/drudge/badge.svg?branch=master)](https://coveralls.io/github/DrudgeCAS/drudge?branch=master)
+
+# Drudge
+
+Drudge is a symbolic algebra system built on top of the [SymPy](http://www.sympy.org) library with its primary focus on tensorial and non-commutative algebras. It is motivated by complex symbolic problems in quantum chemistry and many-body theory, but it could be useful for any tedious and error-prone symbolic manipulation and simplification in any problem with indexed quantities, symbolic summations, and non-commutative algebra.
+
+Built on the generic algorithm for the canonicalization of combinatorial objects, like strings and graphs, in [libcanon](https://github.com/DrudgeCAS/libcanon), drudge is able to find a canonical form for mathematical expressions with tensors with symmetries and symbolic summations. For instance, for a 4th-order tensor *u* with symmetry
+
+$$
+u_{abcd} = -u_{bacd} = -u_{abdc} = u_{badc}
+$$
+
+expression like
+
+$$
+\sum_{cd} u_{acbd} \rho_{dc} - \sum_{cd} u_{cabd} \rho_{dc}
++ \sum_{cd} u_{cdbc} \rho_{cd}
+$$
+
+can be automatically simplified into a single term like,
+
+$$
+3 \sum_{cd} u_{acbd} \rho_{dc}
+$$
+
+despite the initial different placement of the indices to the symmetric *u* tensor and different naming of the dummy indices for summations.
+
+In addition to the full consideration of the combinatorial properties of symmetric tensors and summations during the simplification, drudge also offers a general system for handling non-commutative algebraic systems. Currently, drudge directly supports the [CCR and CAR algebra](https://en.wikipedia.org/wiki/CCR_and_CAR_algebras) for treating fermions and bosons in many-body theory, general [Clifford algebras](https://en.wikipedia.org/wiki/Clifford_algebra), and [su(2) algebra](https://en.m.wikipedia.org/wiki/Special_unitary_group#Lie_Algebra) in its Cartan-Killing basis. Other non-commutative algebraic systems should be able to be added with ease.
+
+Based on the symbolic results from drudge, a companion package [gristmill](https://github.com/DrudgeCAS/gristmill) is able to automatically optimize and generate numerical code. For computations with heavy dependence on tensor contraction and sums of tensor contractions, substantial optimization could be given.
+
+Drudge is developed by Jinmo Zhao and Prof Gustavo E Scuseria at Rice University, and was supported as part of the Center for the Computational Design of Functional Layered Materials, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award DE-SC0012575.
diff --git a/README.rst b/README.rst
deleted file mode 100644
index 13d0de4..0000000
--- a/README.rst
+++ /dev/null
@@ -1,73 +0,0 @@
-.. image:: https://circleci.com/gh/tschijnmo/drudge.svg?style=shield
-    :target: https://circleci.com/gh/tschijnmo/drudge
-
-.. image:: https://travis-ci.org/tschijnmo/drudge.svg?branch=master
-    :target: https://travis-ci.org/tschijnmo/drudge
-
-.. image:: https://coveralls.io/repos/github/tschijnmo/drudge/badge.svg?branch=master
-    :target: https://coveralls.io/github/tschijnmo/drudge?branch=master
-
-
-Drudge
-------
-
-Drudge is a symbolic algebra system built on top of the `SymPy`_ library with
-its primary focus on tensorial and non-commutative algebras.  It is motivated by
-complex symbolic problems in quantum chemistry and many-body theory, but it
-could be useful for any tedious and error-prone symbolic manipulation and
-simplification in any problem with indexed quantities, symbolic summations, and
-non-commutative algebra.
-
-Built on the generic algorithm for the canonicalization of combinatorial
-objects, like strings and graphs, in `libcanon`_, drudge is able to find a
-canonical form for mathematical expressions with tensors with symmetries and
-symbolic summations.  For instance, for a 4th-order tensor *u* with symmetry
-
-.. math::
-
-    u_{abcd} = -u_{bacd} = -u_{abdc} = u_{badc}
-
-expression like
-
-.. math::
-
-    \sum_{cd} u_{acbd} \rho_{dc} - \sum_{cd} u_{cabd} \rho_{dc}
-    + \sum_{cd} u_{cdbc} \rho_{cd}
-
-can be automatically simplified into a single term like,
-
-.. math::
-
-    3 \sum_{cd} u_{acbd} \rho_{dc}
-
-despite the initial different placement of the indices to the symmetric *u*
-tensor and different naming of the dummy indices for summations.
-
-In addition to the full consideration of the combinatorial properties of
-symmetric tensors and summations during the simplification, drudge also offers a
-general system for handling non-commutative algebraic systems.  Currently,
-drudge directly supports the `CCR and CAR algebra`_ for treating fermions and
-bosons in many-body theory, general `Clifford algebras`_, and `su(2) algebra`_
-in its Cartan-Killing basis.  Other non-commutative algebraic systems should be
-able to be added with ease.
-
-
-Based on the symbolic results from drudge, a companion package `gristmill`_ is
-able to automatically optimize and generate numerical code.  For computations
-with heavy dependence on tensor contraction and sums of tensor contractions,
-substantial optimization could be given.
-
-
-Drudge is developed by Jinmo Zhao and Prof Gustavo E Scuseria at Rice
-University, and was supported as part of the Center for the Computational Design
-of Functional Layered Materials, an Energy Frontier Research Center funded by
-the U.S. Department of Energy, Office of Science, Basic Energy Sciences under
-Award DE-SC0012575.
-
-
-.. _SymPy: http://www.sympy.org
-.. _libcanon: https://github.com/tschijnmo/libcanon
-.. _CCR and CAR algebra: https://en.wikipedia.org/wiki/CCR_and_CAR_algebras
-.. _Clifford algebras: https://en.wikipedia.org/wiki/Clifford_algebra
-.. _su(2) algebra: https://en.m.wikipedia.org/wiki/Special_unitary_group#Lie_Algebra
-.. _gristmill: https://github.com/tschijnmo/gristmill

From aedc37bc29aa71a423f14b1ec4fcce39b024c2eb Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 18:45:20 -0500
Subject: [PATCH 10/47] Polish the README

---
 README.md      | 63 ++++++++++++++++++++++++++++++++------------------
 pyproject.toml |  2 +-
 2 files changed, 42 insertions(+), 23 deletions(-)

diff --git a/README.md b/README.md
index 3a2debe..d3fd51e 100644
--- a/README.md
+++ b/README.md
@@ -3,31 +3,50 @@
 
 # Drudge
 
-Drudge is a symbolic algebra system built on top of the [SymPy](http://www.sympy.org) library with its primary focus on tensorial and non-commutative algebras. It is motivated by complex symbolic problems in quantum chemistry and many-body theory, but it could be useful for any tedious and error-prone symbolic manipulation and simplification in any problem with indexed quantities, symbolic summations, and non-commutative algebra.
-
-Built on the generic algorithm for the canonicalization of combinatorial objects, like strings and graphs, in [libcanon](https://github.com/DrudgeCAS/libcanon), drudge is able to find a canonical form for mathematical expressions with tensors with symmetries and symbolic summations. For instance, for a 4th-order tensor *u* with symmetry
-
+Drudge is a symbolic algebra system built on top of
+[SymPy](http://www.sympy.org), focusing primarily on tensorial and
+non-commutative algebras. It is motivated by complex symbolic problems in
+quantum chemistry and many-body theory but is also useful for any symbolic
+manipulation and simplification involving indexed quantities, symbolic
+summations, and non-commutative algebras.
+
+Leveraging the generic algorithms implemented in
+[libcanon](https://github.com/DrudgeCAS/libcanon) for canonicalization of
+combinatorial objects, such as strings and graphs, Drudge can find canonical
+forms for mathematical expressions involving tensors with symmetries and
+symbolic summations. For example, considering a fourth-order tensor $u$
+satisfying
 $$
-u_{abcd} = -u_{bacd} = -u_{abdc} = u_{badc}
+u_{abcd} = -u_{bacd} = -u_{abdc} = u_{badc},
 $$
-
-expression like
-
+an expression like
 $$
-\sum_{cd} u_{acbd} \rho_{dc} - \sum_{cd} u_{cabd} \rho_{dc}
-+ \sum_{cd} u_{cdbc} \rho_{cd}
+\sum_{cd} u_{acbd} \rho_{dc} - \sum_{cd} u_{cabd} \rho_{dc} + \sum_{cd} u_{cdbc} \rho_{cd}
 $$
-
-can be automatically simplified into a single term like,
-
+can be automatically simplified to a single term,
 $$
-3 \sum_{cd} u_{acbd} \rho_{dc}
+3 \sum_{cd} u_{acbd} \rho_{dc},
 $$
-
-despite the initial different placement of the indices to the symmetric *u* tensor and different naming of the dummy indices for summations.
-
-In addition to the full consideration of the combinatorial properties of symmetric tensors and summations during the simplification, drudge also offers a general system for handling non-commutative algebraic systems. Currently, drudge directly supports the [CCR and CAR algebra](https://en.wikipedia.org/wiki/CCR_and_CAR_algebras) for treating fermions and bosons in many-body theory, general [Clifford algebras](https://en.wikipedia.org/wiki/Clifford_algebra), and [su(2) algebra](https://en.m.wikipedia.org/wiki/Special_unitary_group#Lie_Algebra) in its Cartan-Killing basis. Other non-commutative algebraic systems should be able to be added with ease.
-
-Based on the symbolic results from drudge, a companion package [gristmill](https://github.com/DrudgeCAS/gristmill) is able to automatically optimize and generate numerical code. For computations with heavy dependence on tensor contraction and sums of tensor contractions, substantial optimization could be given.
-
-Drudge is developed by Jinmo Zhao and Prof Gustavo E Scuseria at Rice University, and was supported as part of the Center for the Computational Design of Functional Layered Materials, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award DE-SC0012575.
+irrespective of the names and ordering of the summation indices.
+
+In addition to fully considering the permutational symmetries of tensors and
+summations, Drudge provides a general framework for handling non-commutative
+algebraic systems. Currently, Drudge directly supports the [CCR and CAR
+algebras](https://en.wikipedia.org/wiki/CCR_and_CAR_algebras) for fermions and
+bosons, respectively, in many-body theory, general [Clifford
+algebras](https://en.wikipedia.org/wiki/Clifford_algebra), and the [su(2)
+algebra](https://en.m.wikipedia.org/wiki/Special_unitary_group#Lie_Algebra) in
+its Cartan-Killing basis. Other non-commutative algebraic systems can be added
+with ease.
+
+Using symbolic expressions from Drudge, the companion package
+[gristmill](https://github.com/DrudgeCAS/gristmill) can automatically optimize
+and generate numerical code. Optimal computational complexity can be achieved
+for various methods in quantum chemistry, which heavily rely on tensor
+contractions and their sums.
+
+Drudge is developed by Jinmo Zhao and Prof Gustavo E Scuseria at Rice
+University, and was supported as part of the Center for the Computational
+Design of Functional Layered Materials, an Energy Frontier Research Center
+funded by the U.S. Department of Energy, Office of Science, Basic Energy
+Sciences under Award DE-SC0012575.
diff --git a/pyproject.toml b/pyproject.toml
index e024285..fd839aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,7 +22,7 @@ classifiers = [
   'Programming Language :: Python :: Implementation :: CPython',
   'Topic :: Scientific/Engineering :: Mathematics'
 ]
-readme = { file = "README.rst", content-type = "text/x-rst" }
+readme = "README.md"
 license = "MIT"
 license-files = ["LICENSE"]
 authors = [

From bcde6ff27229150863a425faee57878f2979dbee Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 18:46:26 -0500
Subject: [PATCH 11/47] Fix formatting

---
 README.md | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/README.md b/README.md
index d3fd51e..308a0bc 100644
--- a/README.md
+++ b/README.md
@@ -16,17 +16,23 @@ combinatorial objects, such as strings and graphs, Drudge can find canonical
 forms for mathematical expressions involving tensors with symmetries and
 symbolic summations. For example, considering a fourth-order tensor $u$
 satisfying
+
 $$
 u_{abcd} = -u_{bacd} = -u_{abdc} = u_{badc},
 $$
+
 an expression like
+
 $$
 \sum_{cd} u_{acbd} \rho_{dc} - \sum_{cd} u_{cabd} \rho_{dc} + \sum_{cd} u_{cdbc} \rho_{cd}
 $$
+
 can be automatically simplified to a single term,
+
 $$
 3 \sum_{cd} u_{acbd} \rho_{dc},
 $$
+
 irrespective of the names and ordering of the summation indices.
 
 In addition to fully considering the permutational symmetries of tensors and

From 2b4443ad920d03ff964e66a263748e1005075b0d Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 19:16:23 -0500
Subject: [PATCH 12/47] Add installation guide

---
 README.md | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 308a0bc..4fd9dfe 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 ![CircleCI](https://circleci.com/gh/DrudgeCAS/drudge.svg?style=shield)
 [![Coveralls](https://coveralls.io/repos/github/DrudgeCAS/drudge/badge.svg?branch=master)](https://coveralls.io/github/DrudgeCAS/drudge?branch=master)
 
-# Drudge
+<h1 align="center">Drudge</h1>
 
 Drudge is a symbolic algebra system built on top of
 [SymPy](http://www.sympy.org), focusing primarily on tensorial and
@@ -56,3 +56,16 @@ University, and was supported as part of the Center for the Computational
 Design of Functional Layered Materials, an Energy Frontier Research Center
 funded by the U.S. Department of Energy, Office of Science, Basic Energy
 Sciences under Award DE-SC0012575.
+
+## Installation
+
+Drudge can be installed directly from the GitHub repository using
+[uv](https://github.com/astral-sh/uv) (preferred)
+```bash
+uv pip install git+https://github.com/DrudgeCAS/drudge.git
+```
+or [pip](https://pypi.org/project/pip/)
+```bash
+pip install git+https://github.com/DrudgeCAS/drudge.git
+```
+

From 6dc79a0998d6cf518eb3ae9e28271345ceeb3305 Mon Sep 17 00:00:00 2001
From: Matthew Wholey <15wholeym@gmail.com>
Date: Thu, 8 May 2025 16:10:32 -0500
Subject: [PATCH 13/47] typo fixed

---
 drudge/drudge.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/drudge/drudge.py b/drudge/drudge.py
index 8f9f6a0..f28bd7a 100644
--- a/drudge/drudge.py
+++ b/drudge/drudge.py
@@ -3490,7 +3490,7 @@ def _union(orig, new):
 
 
 def _inters(orig, new):
-    """Make the interaction of two sets.
+    """Make the intersection of two sets.
 
     If the original is a None value, a new set will be created with elements
     from the new set.  When both operands are None, the result is None.

From 22bf6f140e5f23aad379cd4004816560d223a329 Mon Sep 17 00:00:00 2001
From: Copilot <198982749+Copilot@users.noreply.github.com>
Date: Tue, 2 Sep 2025 21:53:24 -0500
Subject: [PATCH 14/47] Restore coveralls integration to GitHub Actions
 workflow (#19)

---
 .github/workflows/pythonapp.yml | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/pythonapp.yml
index 2d851aa..58a7488 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/pythonapp.yml
@@ -28,8 +28,17 @@ jobs:
         uv sync --locked --extra dev
         uv build
 
-    - name: Run tests
+    - name: Install coverage tools
+      run: |
+        uv pip install coverage coveralls
+
+    - name: Run tests with coverage
       env:
         DUMMY_SPARK: 1
-      run: uv run pytest tests
+      run: uv run coverage run --source=drudge -m pytest tests
+
+    - name: Upload coverage to Coveralls
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      run: uv run coveralls --service=github
  

From 259d8ef7f6999cc264406ede581551b091c0b691 Mon Sep 17 00:00:00 2001
From: Matthew Wholey <15wholeym@gmail.com>
Date: Fri, 25 Oct 2024 15:11:41 -0500
Subject: [PATCH 15/47] 1) ManagedProperties metaclass is no longer used by
 Basic in sympy and has been deprecated, functionality tested and no changes
 on tests 2) Slight wording change on comment of EnumSymbs class 3) Added
 __getstate__() and __setstate__() functions to EnumSymbs class as pickling
 was using default __getstate__() provided by basic which just returns null.
 This allows pickling to account for and store slotted variables and fixes
 basic_wick_test.py::test_ancr_character_has_basic_properties

---
 drudge/utils.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/drudge/utils.py b/drudge/utils.py
index ac489e3..d97e349 100644
--- a/drudge/utils.py
+++ b/drudge/utils.py
@@ -89,7 +89,7 @@ def __call__(self, *args, **kwargs):
         return self._func(*args, **kwargs)
 
 
-class _EnumSymbsMeta(ManagedProperties):
+class _EnumSymbsMeta(type):
     """The meta class for enumeration symbols.
 
     The primary purpose of this metaclass is to set the concrete singleton
@@ -140,7 +140,7 @@ class EnumSymbs(AtomicExpr, metaclass=_EnumSymbsMeta):
 
     Subclasses can set `_symbs_` inside the class body to be a sequence of
     string pairs.  Then attributes named after the first field of the pairs will
-    be created, with the LaTeX form controlled by the second pair.
+    be created, with the LaTeX form controlled by the second field of the pair.
 
     The resulted values are valid SymPy expressions.  They are ordered according
     to their order in the given enumeration sequence.
@@ -222,6 +222,15 @@ def __rsub__(self, other):
         """
         return self.__sub__(other)
 
+    def __getstate__(self):
+        """Retrieve state of object for pickling/serialization"""
+        return {slot: getattr(self, slot) for slot in self.__slots__}
+
+    def __setstate__(self, state):
+        """Create state of object for deserialization"""
+        for key, value in state.items():
+            setattr(self, key, value)
+
     def sort_key(self, order=None):
         return (
             self.class_key(),

From 30507cae54f4740dff0cbda217aa08d948f5c0a4 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 2 Sep 2025 23:34:34 -0500
Subject: [PATCH 16/47] Fix warnings

---
 drudge/drs.py    | 4 ++--
 drudge/drudge.py | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/drudge/drs.py b/drudge/drs.py
index dedaa02..3fc5471 100644
--- a/drudge/drs.py
+++ b/drudge/drs.py
@@ -235,9 +235,9 @@ class _NumFixer(ast.NodeTransformer):
     Integer literals will be changed into creation of symbolic integers.
     """
 
-    def visit_Num(self, node: ast.Num):
+    def visit_Constant(self, node: ast.Constant):
         """Update the number nodes."""
-        val = node.n
+        val = node.value
         if isinstance(val, int):
             constr = ast.Name(id='Integer', ctx=ast.Load())
             ast.copy_location(constr, node)
diff --git a/drudge/drudge.py b/drudge/drudge.py
index f28bd7a..069c125 100644
--- a/drudge/drudge.py
+++ b/drudge/drudge.py
@@ -1657,7 +1657,7 @@ class TensorDef(Tensor):
 
     .. math::
 
-        \sum_j o_{i, j} f_j
+        \\sum_j o_{i, j} f_j
 
     can be construed as a tensor.  By storing it as a :py:class:`Tensor`
     object, we can mathematically manipulate it.  With an explicit left-hand
@@ -1665,7 +1665,7 @@ class TensorDef(Tensor):
 
     .. math::
 
-        t_j = \sum_j o_{i, j} f_j
+        t_j = \\sum_j o_{i, j} f_j
 
     is now a tensor definition, which can be handled by the current class.
 
@@ -1673,7 +1673,7 @@ class TensorDef(Tensor):
     left-hand side, it can be convenient to be used for :py:meth:`Tensor.subst`
     or :py:meth:`Tensor.subst_all` method, or it can be directly indexed.  For
     example, with the above definition stored in ``t_def``, for tensor ``v``
-    holding :math:`\sum_j u_{i, j} t_j`,
+    holding :math:`\\sum_j u_{i, j} t_j`,
 
     ::
 
@@ -1691,7 +1691,7 @@ class TensorDef(Tensor):
 
     .. math::
 
-        \sum_{j, k} u_{i, j} o_{j, k} f_k
+        \\sum_{j, k} u_{i, j} o_{j, k} f_k
 
     Tensor definition can also be directly subscripts, like ``t_def[1]``
     gives :math:`sum_i o_{1, i} f_i`.

From e4428db21440322e05950cd998e4381aca144024 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Wed, 3 Sep 2025 01:12:21 -0500
Subject: [PATCH 17/47] Revert renaming method

---
 drudge/drs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/drudge/drs.py b/drudge/drs.py
index 3fc5471..ac92b37 100644
--- a/drudge/drs.py
+++ b/drudge/drs.py
@@ -235,7 +235,7 @@ class _NumFixer(ast.NodeTransformer):
     Integer literals will be changed into creation of symbolic integers.
     """
 
-    def visit_Constant(self, node: ast.Constant):
+    def visit_Num(self, node: ast.Constant):
         """Update the number nodes."""
         val = node.value
         if isinstance(val, int):

From 9f6e1857a932b30cedd930d3728d20e2ef61a99f Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Wed, 3 Sep 2025 01:19:27 -0500
Subject: [PATCH 18/47] Remove travis build

---
 .travis.yml | 29 -----------------------------
 1 file changed, 29 deletions(-)
 delete mode 100644 .travis.yml

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 3c0a645..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,29 +0,0 @@
-language: python
-python:
-    - 3.6
-
-addons:
-  apt:
-    sources:
-    - ubuntu-toolchain-r-test
-    packages:
-    - gcc-7
-    - g++-7
-
-before_install:
-    - pip3 install coveralls
-    - git clone https://github.com/tschijnmo/DummyRDD.git
-    - cd DummyRDD; python3 setup.py install; cd ..
-install:
-    - export CC=gcc-7
-    - export CXX=g++-7
-    - python3 setup.py install
-
-script:
-    - export DUMMY_SPARK=1
-    - cd tests
-    - coverage run --source=drudge -m pytest -sv
-
-after_success:
-  - coveralls
-

From e989b633b6ba25d8e09d2eff52f9af11c14f1df4 Mon Sep 17 00:00:00 2001
From: Copilot <198982749+Copilot@users.noreply.github.com>
Date: Wed, 3 Sep 2025 01:25:31 -0500
Subject: [PATCH 19/47] Add GitHub Actions workflows for Ubuntu, macOS, and
 Windows with updated README badges (#21)

Also attempt to fix the Windows build, without success.
---
 .github/workflows/macos.yml                   | 63 ++++++++++++++
 .../workflows/{pythonapp.yml => ubuntu.yml}   | 34 +++++++-
 .github/workflows/windows.yml                 | 84 +++++++++++++++++++
 README.md                                     |  4 +-
 drudge/canonpy.cpp                            | 16 ++--
 drudge/wickcore.cpp                           |  4 +-
 pyproject.toml                                |  3 +-
 setup.py                                      | 12 ++-
 8 files changed, 201 insertions(+), 19 deletions(-)
 create mode 100644 .github/workflows/macos.yml
 rename .github/workflows/{pythonapp.yml => ubuntu.yml} (59%)
 create mode 100644 .github/workflows/windows.yml

diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
new file mode 100644
index 0000000..5517088
--- /dev/null
+++ b/.github/workflows/macos.yml
@@ -0,0 +1,63 @@
+name: macOS
+
+on: [push]
+
+jobs:
+  build:
+    name: macOS Build
+    runs-on: macos-latest
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Download submodules
+      shell: bash
+      run: |
+        git submodule update --init --recursive
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: "pyproject.toml"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: Install the project
+      run: |
+        uv sync --locked --extra dev
+        uv build
+
+  test:
+    name: macOS Tests
+    runs-on: macos-latest
+    needs: build
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Download submodules
+      shell: bash
+      run: |
+        git submodule update --init --recursive
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: "pyproject.toml"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: Install the project
+      run: |
+        uv sync --locked --extra dev
+
+    - name: Install coverage tools
+      run: |
+        uv pip install coverage coveralls
+
+    - name: Run tests with coverage
+      env:
+        DUMMY_SPARK: 1
+      run: uv run coverage run --source=drudge -m pytest tests
diff --git a/.github/workflows/pythonapp.yml b/.github/workflows/ubuntu.yml
similarity index 59%
rename from .github/workflows/pythonapp.yml
rename to .github/workflows/ubuntu.yml
index 58a7488..bf01b7a 100644
--- a/.github/workflows/pythonapp.yml
+++ b/.github/workflows/ubuntu.yml
@@ -1,10 +1,10 @@
-name: Python application
+name: Ubuntu
 
-on: [push, pull_request]
+on: [push]
 
 jobs:
-  build-and-test:
-    name: Drudge
+  build:
+    name: Ubuntu Build
     runs-on: ubuntu-latest
 
     steps:
@@ -28,6 +28,31 @@ jobs:
         uv sync --locked --extra dev
         uv build
 
+  test:
+    name: Ubuntu Tests
+    runs-on: ubuntu-latest
+    needs: build
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Download submodules
+      shell: bash
+      run: |
+        git submodule update --init --recursive
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: "pyproject.toml"
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: Install the project
+      run: |
+        uv sync --locked --extra dev
+
     - name: Install coverage tools
       run: |
         uv pip install coverage coveralls
@@ -38,6 +63,7 @@ jobs:
       run: uv run coverage run --source=drudge -m pytest tests
 
     - name: Upload coverage to Coveralls
+      if: always()
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       run: uv run coveralls --service=github
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
new file mode 100644
index 0000000..bb4c900
--- /dev/null
+++ b/.github/workflows/windows.yml
@@ -0,0 +1,84 @@
+name: Windows
+
+on: [push]
+
+jobs:
+  build:
+    name: Windows Build
+    runs-on: windows-latest
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Download submodules
+      shell: bash
+      run: |
+        git submodule update --init --recursive
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: "pyproject.toml"
+
+    - name: Setup MSVC
+      uses: ilammy/msvc-dev-cmd@v1
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: Check Python and environment
+      run: |
+        python --version
+        python -c "import sys; print('Platform:', sys.platform)"
+        echo "MSVC environment variables:"
+        echo "INCLUDE: $env:INCLUDE"
+        echo "LIB: $env:LIB"
+
+    - name: Install the project
+      run: |
+        uv sync --locked --extra dev
+        echo "Dependencies installed successfully"
+        uv build
+        echo "Package build completed successfully"
+
+  test:
+    name: Windows Tests
+    runs-on: windows-latest
+    needs: build
+
+    steps:
+    - uses: actions/checkout@v5
+
+    - name: Download submodules
+      shell: bash
+      run: |
+        git submodule update --init --recursive
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version-file: "pyproject.toml"
+
+    - name: Setup MSVC
+      uses: ilammy/msvc-dev-cmd@v1
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v6
+
+    - name: Check Python and environment
+      run: |
+        python --version
+        python -c "import sys; print('Platform:', sys.platform)"
+
+    - name: Install the project
+      run: |
+        uv sync --locked --extra dev
+
+    - name: Install coverage tools
+      run: |
+        uv pip install coverage coveralls
+
+    - name: Run tests with coverage
+      env:
+        DUMMY_SPARK: 1
+      run: uv run coverage run --source=drudge -m pytest tests
diff --git a/README.md b/README.md
index 4fd9dfe..6e8f029 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,6 @@
-![CircleCI](https://circleci.com/gh/DrudgeCAS/drudge.svg?style=shield)
+[![Ubuntu](https://github.com/DrudgeCAS/drudge/workflows/Ubuntu/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/ubuntu.yml)
+[![macOS](https://github.com/DrudgeCAS/drudge/workflows/macOS/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/macos.yml)
+[![Windows](https://github.com/DrudgeCAS/drudge/workflows/Windows/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/windows.yml)
 [![Coveralls](https://coveralls.io/repos/github/DrudgeCAS/drudge/badge.svg?branch=master)](https://coveralls.io/github/DrudgeCAS/drudge?branch=master)
 
 <h1 align="center">Drudge</h1>
diff --git a/drudge/canonpy.cpp b/drudge/canonpy.cpp
index 418a7b9..2561a59 100644
--- a/drudge/canonpy.cpp
+++ b/drudge/canonpy.cpp
@@ -131,10 +131,10 @@ static Simple_perm make_perm_from_args(PyObject* args, PyObject* kwargs)
     PyObject* pre_images;
     char acc = 0;
 
-    static char* kwlist[] = { "pre_images", "acc", NULL };
+    static const char* kwlist[] = { "pre_images", "acc", nullptr };
 
     auto args_stat = PyArg_ParseTupleAndKeywords(
-        args, kwargs, "O|b", kwlist, &pre_images, &acc);
+        args, kwargs, "O|b", const_cast<char**>(kwlist), &pre_images, &acc);
 
     if (!args_stat)
         throw err;
@@ -222,7 +222,7 @@ static Simple_perm make_perm_from_args(PyObject* args, PyObject* kwargs)
 // -------------------
 //
 
-const static char* perm_getnewargs_doc
+static const char* perm_getnewargs_doc
     = "Get the arguments for new to construct the Perm.";
 
 static PyObject* perm_getnewargs(Perm_object* self)
@@ -744,10 +744,10 @@ static Transv_ptr build_sims_transv_from_args(PyObject* args, PyObject* kwargs)
 {
     PyObject* input;
 
-    static char* kwlist[] = { "gens", NULL };
+    static const char* kwlist[] = { "gens", NULL };
 
     auto args_stat
-        = PyArg_ParseTupleAndKeywords(args, kwargs, "O", kwlist, &input);
+        = PyArg_ParseTupleAndKeywords(args, kwargs, "O", const_cast<char**>(kwlist), &input);
     if (!args_stat) {
         return nullptr;
     }
@@ -813,7 +813,7 @@ static Transv_ptr build_sims_transv_from_args(PyObject* args, PyObject* kwargs)
 // -------------------
 //
 
-const static char* group_getnewargs_doc
+static const char* group_getnewargs_doc
     = "Get the arguments for new to construct the Group.";
 
 static PyObject* group_getnewargs(Group_object* self)
@@ -1188,9 +1188,9 @@ static PyObject* canon_eldag_func(
 
     constexpr int err_code = 1;
 
-    static char* kwlist[] = { "edges", "ia", "symms", "colours", NULL };
+    static const char* kwlist[] = { "edges", "ia", "symms", "colours", NULL };
 
-    auto arg_stat = PyArg_ParseTupleAndKeywords(args, keywds, "OOOO", kwlist,
+    auto arg_stat = PyArg_ParseTupleAndKeywords(args, keywds, "OOOO", const_cast<char**>(kwlist),
         &edges_arg, &ia_arg, &symms_arg, &colours_arg);
     if (!arg_stat) {
         return NULL;
diff --git a/drudge/wickcore.cpp b/drudge/wickcore.cpp
index cea7411..44a10b7 100644
--- a/drudge/wickcore.cpp
+++ b/drudge/wickcore.cpp
@@ -169,10 +169,10 @@ static PyObject* compose_wick_func(
     PyObject* vec_order_arg;
     PyObject* contrs_arg;
 
-    static char* kwlist[] = { "vec_order", "contrs", NULL };
+    static const char* kwlist[] = { "vec_order", "contrs", NULL };
 
     auto arg_stat = PyArg_ParseTupleAndKeywords(
-        args, keywds, "OO", kwlist, &vec_order_arg, &contrs_arg);
+        args, keywds, "OO", const_cast<char**>(kwlist), &vec_order_arg, &contrs_arg);
     if (!arg_stat) {
         return NULL;
     }
diff --git a/pyproject.toml b/pyproject.toml
index fd839aa..1d78b71 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,8 +23,7 @@ classifiers = [
   'Topic :: Scientific/Engineering :: Mathematics'
 ]
 readme = "README.md"
-license = "MIT"
-license-files = ["LICENSE"]
+license = {text = "MIT"}
 authors = [
   { name = "Jinmo Zhao" },
   { name = "Gustavo E. Scuseria" }
diff --git a/setup.py b/setup.py
index 8a8cc9f..57b7eb2 100644
--- a/setup.py
+++ b/setup.py
@@ -1,15 +1,23 @@
 """Setup script for drudge."""
 
 import os.path
+import sys
 
 from setuptools import setup, find_packages, Extension
 
 PROJ_ROOT = os.path.dirname(os.path.abspath(__file__))
 INCLUDE_DIRS = [
-    '/'.join([PROJ_ROOT, i])
+    os.path.join(PROJ_ROOT, i)
     for i in ['deps/libcanon/include', 'drudge']
 ]
-COMPILE_FLAGS = ['-std=c++14']
+
+# Platform-specific compiler flags
+if sys.platform == "win32":
+    # MSVC compiler flags
+    COMPILE_FLAGS = ['/std:c++14', '/EHsc', '/bigobj', '/wd4996', '/wd4267', '/Zc:twoPhase-']
+else:
+    # GCC/Clang compiler flags  
+    COMPILE_FLAGS = ['-std=c++14']
 
 canonpy = Extension(
     'drudge.canonpy',

From e685d7cd1c60c62a83ab1803bab4323d94efe64c Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Wed, 3 Sep 2025 10:51:30 -0500
Subject: [PATCH 20/47] Set up development environment for GitHub Copilot
 coding agent

---
 copilot-setup-steps.yml | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 copilot-setup-steps.yml

diff --git a/copilot-setup-steps.yml b/copilot-setup-steps.yml
new file mode 100644
index 0000000..89b7816
--- /dev/null
+++ b/copilot-setup-steps.yml
@@ -0,0 +1,37 @@
+name: Copilot Setup Steps
+
+on:
+  workflow_dispatch:
+  push:
+    paths: [".github/workflows/copilot-setup-steps.yml"]
+  pull_request:
+    paths: [".github/workflows/copilot-setup-steps.yml"]
+
+jobs:
+  copilot-setup-steps:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+
+      - name: Download submodules
+        shell: bash
+        run: |
+          git submodule update --init --recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install the project
+        run: |
+          uv sync --locked --extra dev
+          uv build
+

From ce50f3a2ab2377938ffb159c707f9a1f7adad9f4 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Wed, 3 Sep 2025 10:53:35 -0500
Subject: [PATCH 21/47] Fix file location

---
 .../workflows/copilot-setup-steps.yml                             | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename copilot-setup-steps.yml => .github/workflows/copilot-setup-steps.yml (100%)

diff --git a/copilot-setup-steps.yml b/.github/workflows/copilot-setup-steps.yml
similarity index 100%
rename from copilot-setup-steps.yml
rename to .github/workflows/copilot-setup-steps.yml

From dd8bf9ad59323fdebb00bf94dd686dbfbcc82032 Mon Sep 17 00:00:00 2001
From: Matthew Wholey <15wholeym@gmail.com>
Date: Wed, 15 Jan 2025 15:25:19 -0600
Subject: [PATCH 22/47] changed simplify to simplify_am, simplify was
 attempting to numerically resolve a clebsch-gordan coefficient but the test
 was made to check a symbolic simplification, the clebsch-gordan function
 failed attempting to resolve a number to these symbols. Altering
 simplify->simplify_am passes test

---
 tests/nuclear_test.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/nuclear_test.py b/tests/nuclear_test.py
index 45093fc..fd9610f 100644
--- a/tests/nuclear_test.py
+++ b/tests/nuclear_test.py
@@ -113,6 +113,7 @@ def test_varsh_872_5(nuclear: NuclearBogoliubovDrudge):
 
     TODO: Investigate its failure in Apache Spark environment.
     """
+
     dr = nuclear
     a, alpha, b, beta, b_prm, beta_prm = symbols(
         'a alpha b beta bprm betaprm', integer=True
@@ -132,7 +133,7 @@ def test_varsh_872_5(nuclear: NuclearBogoliubovDrudge):
     )
     for sums_i in [sums, reversed(sums)]:
         tensor = dr.sum(*sums_i, amp)
-        res = tensor.deep_simplify().merge()
+        res = tensor.simplify_am().merge() #previously used deep_simplify
         assert res.n_terms == 1
         term = res.local_terms[0]
         assert len(term.sums) == 0

From d6a1e4519795b6fe77c408115748fbc138d380ea Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Thu, 4 Sep 2025 00:05:36 -0500
Subject: [PATCH 23/47] Start to fix the nuclear `doit` issue

---
 drudge/drudge.py      | 24 ++++++++++++++----------
 drudge/nuclear.py     |  6 +++---
 tests/nuclear_test.py |  6 +++---
 3 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/drudge/drudge.py b/drudge/drudge.py
index 069c125..b782b86 100644
--- a/drudge/drudge.py
+++ b/drudge/drudge.py
@@ -435,7 +435,7 @@ def _reset_dumms(self, terms: RDD, excl) -> RDD:
         )
         return res_terms
 
-    def simplify_amps(self):
+    def simplify_amps(self, **kwargs):
         """Simplify the amplitudes in the tensor.
 
         This method simplifies the amplitude in the terms of the tensor by using
@@ -445,15 +445,19 @@ def simplify_amps(self):
 
         # Some free variables might be canceled.
         return self.apply(
-            self._simplify_amps, free_vars=None, repartitioned=False
+            functools.partial(
+                self._simplify_amps, **kwargs
+            ),
+            free_vars=None, repartitioned=False
         )
 
     @staticmethod
-    def _simplify_amps(terms):
+    def _simplify_amps(terms, **kwargs):
         """Get the terms with amplitude simplified by SymPy."""
 
         simplified_terms = terms.map(
-            lambda term: term.map(lambda x: x.simplify(), skip_vecs=True)
+            lambda term: term.map(lambda x: x.simplify(**kwargs),
+                                  skip_vecs=True)
         ).filter(_is_nonzero)
 
         return simplified_terms
@@ -694,7 +698,7 @@ def normal_order(self):
     # The driver simplification.
     #
 
-    def simplify(self):
+    def simplify(self, **kwargs):
         """Simplify the tensor.
 
         This is the master driver function for tensor simplification.  Inside
@@ -705,7 +709,7 @@ def simplify(self):
         """
 
         result = Tensor(
-            self._drudge, self._simplify(self._terms), expanded=True
+            self._drudge, self._simplify(self._terms, **kwargs), expanded=True
         )
 
         if self._drudge.inside_drs:
@@ -714,7 +718,7 @@ def simplify(self):
 
         return result
 
-    def _simplify(self, terms):
+    def _simplify(self, terms, **kwargs):
         """Get the terms in the simplified form."""
 
         num_partitions = self._drudge.num_partitions
@@ -733,9 +737,9 @@ def _simplify(self, terms):
             terms = terms.repartition(num_partitions)
 
         # Simplify the amplitude part.
-        terms = self._simplify_amps(terms)
+        terms = self._simplify_amps(terms, **kwargs)
         terms = self._simplify_sums(terms)
-        terms = self._simplify_amps(terms)
+        terms = self._simplify_amps(terms, **kwargs)
         terms = self._simplify_deltas(terms, False)
 
         # Canonicalize the terms and see if they can be merged.
@@ -750,7 +754,7 @@ def _simplify(self, terms):
 
         # Finally simplify the merged amplitude again.
         if self._drudge.full_simplify:
-            terms = self._simplify_amps(terms)
+            terms = self._simplify_amps(terms, **kwargs)
 
         # Make the final expansion.
         terms = self._expand(terms)
diff --git a/drudge/nuclear.py b/drudge/nuclear.py
index 4eb2049..e701311 100644
--- a/drudge/nuclear.py
+++ b/drudge/nuclear.py
@@ -423,7 +423,7 @@ def simplify_pono(self, tensor: Tensor):
         )
 
     @staticmethod
-    def deep_simplify(tensor: Tensor):
+    def deep_simplify(tensor: Tensor, **kwargs):
         """Simplify the given tensor deeply.
 
         This driver function attempts to perform simplifications relevant to
@@ -434,13 +434,13 @@ def deep_simplify(tensor: Tensor):
         """
 
         # Initial simplification.
-        res = tensor.simplify()
+        res = tensor.simplify(**kwargs)
         # This can possibly reduce the number of terms.
         res = res.merge_j()
         res = res.simplify_am()
 
         # Final trial.
-        res = res.simplify().merge_j()
+        res = res.simplify(**kwargs).merge_j()
 
         return res
 
diff --git a/tests/nuclear_test.py b/tests/nuclear_test.py
index fd9610f..0c0b4f7 100644
--- a/tests/nuclear_test.py
+++ b/tests/nuclear_test.py
@@ -209,17 +209,17 @@ def test_wigner3j_sum_to_wigner6j(nuclear: NuclearBogoliubovDrudge):
             ((-1) ** (j3 - m3) / (2 * j3 + 1))
             * KroneckerDelta(j3, jprm3) * KroneckerDelta(m3, mprm3)
             * Wigner6j(j1, j2, j3, j4, j5, j6)
-    ).expand().simplify()
+    ).expand().simplify(doit=False)
 
     # For performance reason, just test a random arrangement of the summations.
     random.shuffle(sums)
     tensor = dr.sum(*sums, phase * amp)
-    res = tensor.deep_simplify().merge()
+    res = tensor.deep_simplify(doit=False).merge()
     assert res.n_terms == 1
     term = res.local_terms[0]
     assert len(term.sums) == 0
     assert len(term.vecs) == 0
-    difference = (res - dr.sum(expected)).deep_simplify()
+    difference = (res - dr.sum(expected)).deep_simplify(doit=False)
     assert len(difference.local_terms) == 0
 
 

From a82d78e87255820b997cfe21a5bb5cf236fc93f2 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Thu, 4 Sep 2025 01:18:48 -0500
Subject: [PATCH 24/47] Set `doit=False` for sum simplifications

---
 drudge/nuclear.py | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/drudge/nuclear.py b/drudge/nuclear.py
index e701311..b0bfa01 100644
--- a/drudge/nuclear.py
+++ b/drudge/nuclear.py
@@ -11,6 +11,7 @@
     sqrt, factor, Mul, Expr, Matrix, Pow
 )
 from sympy.physics.quantum.cg import CG, Wigner3j, Wigner6j, Wigner9j
+from sympy.concrete.summations import eval_sum_symbolic
 
 from .drudge import Tensor
 from .fock import BogoliubovDrudge
@@ -184,6 +185,9 @@ def __init__(
             CG=CG, Wigner3j=Wigner3j, Wigner6j=Wigner6j, Wigner9j=Wigner9j
         )
 
+        self.sum_simplifiers = BCastVar(self._ctx, {
+            1: [_simplify_symbolic_sum_nodoit]
+        })
         self._am_sum_simplifiers = BCastVar(self.ctx, {
             # TODO: Add more simplifications here.
             2: [_sum_2_3j_to_delta],
@@ -1644,3 +1648,14 @@ def _simpl_varsh_911_8(expr: Sum):
     ) * KroneckerDelta(match[m], match[m_prm]) * Wigner6j(
         match[j1], match[j2], match[j12], match[j3], match[j], match[j23]
     )
+
+
+def _simplify_symbolic_sum_nodoit(expr, **_):
+    """Try to simplify a symbolic summation of one dummy with `doit=False`.
+    """
+
+    assert len(expr.args) == 2
+
+    return eval_sum_symbolic(
+        expr.args[0].simplify(doit=False), expr.args[1]
+    )

From 58f81341c56edab27cfa9680f547ba6967f866e7 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Thu, 4 Sep 2025 01:31:13 -0500
Subject: [PATCH 25/47] `deep_simplify` in `NuclearBogoliubovDrudge` should now
 work

---
 tests/nuclear_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/nuclear_test.py b/tests/nuclear_test.py
index 0c0b4f7..4a5a8cb 100644
--- a/tests/nuclear_test.py
+++ b/tests/nuclear_test.py
@@ -133,7 +133,7 @@ def test_varsh_872_5(nuclear: NuclearBogoliubovDrudge):
     )
     for sums_i in [sums, reversed(sums)]:
         tensor = dr.sum(*sums_i, amp)
-        res = tensor.simplify_am().merge() #previously used deep_simplify
+        res = tensor.deep_simplify().merge()
         assert res.n_terms == 1
         term = res.local_terms[0]
         assert len(term.sums) == 0

From fe59399cb4caef5b297582eb26bcc01e19f7092e Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Thu, 4 Sep 2025 01:42:21 -0500
Subject: [PATCH 26/47] Make `doit=False` the default for
 `NuclearBogoliubovDrudge.deep_simplify`

---
 drudge/nuclear.py     | 6 +++---
 tests/nuclear_test.py | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/drudge/nuclear.py b/drudge/nuclear.py
index b0bfa01..07d940f 100644
--- a/drudge/nuclear.py
+++ b/drudge/nuclear.py
@@ -427,7 +427,7 @@ def simplify_pono(self, tensor: Tensor):
         )
 
     @staticmethod
-    def deep_simplify(tensor: Tensor, **kwargs):
+    def deep_simplify(tensor: Tensor):
         """Simplify the given tensor deeply.
 
         This driver function attempts to perform simplifications relevant to
@@ -438,13 +438,13 @@ def deep_simplify(tensor: Tensor, **kwargs):
         """
 
         # Initial simplification.
-        res = tensor.simplify(**kwargs)
+        res = tensor.simplify(doit=False)
         # This can possibly reduce the number of terms.
         res = res.merge_j()
         res = res.simplify_am()
 
         # Final trial.
-        res = res.simplify(**kwargs).merge_j()
+        res = res.simplify(doit=False).merge_j()
 
         return res
 
diff --git a/tests/nuclear_test.py b/tests/nuclear_test.py
index 4a5a8cb..6c88734 100644
--- a/tests/nuclear_test.py
+++ b/tests/nuclear_test.py
@@ -214,12 +214,12 @@ def test_wigner3j_sum_to_wigner6j(nuclear: NuclearBogoliubovDrudge):
     # For performance reason, just test a random arrangement of the summations.
     random.shuffle(sums)
     tensor = dr.sum(*sums, phase * amp)
-    res = tensor.deep_simplify(doit=False).merge()
+    res = tensor.deep_simplify().merge()
     assert res.n_terms == 1
     term = res.local_terms[0]
     assert len(term.sums) == 0
     assert len(term.vecs) == 0
-    difference = (res - dr.sum(expected)).deep_simplify(doit=False)
+    difference = (res - dr.sum(expected)).deep_simplify()
     assert len(difference.local_terms) == 0
 
 

From b1bcb4bcc5bd9886642506c1f9a244f114b1f0eb Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Thu, 4 Sep 2025 10:44:05 -0500
Subject: [PATCH 27/47] Bump SymPy version to 1.14

---
 pyproject.toml | 2 +-
 uv.lock        | 8 ++++----
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 1d78b71..03a8652 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -8,7 +8,7 @@ version = "0.11.0"
 description = "A CAS based on sympy focusing on tensor and noncommutative algebras"
 requires-python = "==3.12.*"
 dependencies = [
-  "sympy==1.13.2",
+  "sympy>=1.14",
   "jinja2",
   "pyspark>=3.5,<3.6",
   "ipython>=8.0",
diff --git a/uv.lock b/uv.lock
index 2b64c9d..8e03b0b 100644
--- a/uv.lock
+++ b/uv.lock
@@ -112,7 +112,7 @@ requires-dist = [
     { name = "pyspark", specifier = ">=3.5,<3.6" },
     { name = "pytest", marker = "extra == 'dev'" },
     { name = "sphinx", marker = "extra == 'docs'" },
-    { name = "sympy", specifier = "==1.13.2" },
+    { name = "sympy", specifier = ">=1.14" },
 ]
 
 [[package]]
@@ -495,14 +495,14 @@ wheels = [
 
 [[package]]
 name = "sympy"
-version = "1.13.2"
+version = "1.14.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "mpmath" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/94/15/4a041424c7187f41cce678f5a02189b244e9aac61a18b45cd415a3a470f3/sympy-1.13.2.tar.gz", hash = "sha256:401449d84d07be9d0c7a46a64bd54fe097667d5e7181bfe67ec777be9e01cb13", size = 7532926 }
+sdist = { url = "https://files.pythonhosted.org/packages/83/d3/803453b36afefb7c2bb238361cd4ae6125a569b4db67cd9e79846ba2d68c/sympy-1.14.0.tar.gz", hash = "sha256:d3d3fe8df1e5a0b42f0e7bdf50541697dbe7d23746e894990c030e2b05e72517", size = 7793921 }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/c1/f9/6845bf8fca0eaf847da21c5d5bc6cd92797364662824a11d3f836423a1a5/sympy-1.13.2-py3-none-any.whl", hash = "sha256:c51d75517712f1aed280d4ce58506a4a88d635d6b5dd48b39102a7ae1f3fcfe9", size = 6189289 },
+    { url = "https://files.pythonhosted.org/packages/a2/09/77d55d46fd61b4a135c444fc97158ef34a095e5681d0a6c10b75bf356191/sympy-1.14.0-py3-none-any.whl", hash = "sha256:e091cc3e99d2141a0ba2847328f5479b05d94a6635cb96148ccb3f34671bd8f5", size = 6299353 },
 ]
 
 [[package]]

From d9f2cb72af8e672e3d2fe929aba7657107135bb6 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Fri, 5 Sep 2025 10:55:03 -0500
Subject: [PATCH 28/47] Fix a issue of simplifying Kronecker deltas involving
 spins

The failed test in
`tests/spin_one_half_test.py::test_restricted_parthole_drudge_simplification`
is due to this issue. Specifically, when we have
`KroneckerDelta(SpinOneHalf(0), sigma0)` and `sigma0` is summed over
`Range('\\uparrow\\downarrow', 0, 2)`, it should simplify to 1, but it
didn't. The problem was, `Eq(SpinOneHalf(0), sigma0).simplify()`
lead to `Eq(0, sigma0)`, which messed up the following implementation in
`drudge/term.py::proc_delta`.
---
 drudge/term.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/drudge/term.py b/drudge/term.py
index fceb82a..01d9cfd 100644
--- a/drudge/term.py
+++ b/drudge/term.py
@@ -1839,21 +1839,21 @@ def proc_delta(arg1, arg2, sums_dict, resolvers):
         else:
             return _NAUGHT, None
 
-    eqn = Eq(arg1, arg2).simplify()
+    eqn = Eq(arg1.simplify(), arg2.simplify())
 
     # We try to solve for each of the dummies.  Most likely this will only be
     # executed for one loop.
 
     for dumm in dumms:
         range_ = sums_dict[dumm]
-        # Here we assume the same integral domain, since dummies are summed over
-        # and we can mostly assume that they are integral.
+        # Here we assume the integer domain, since dummies are summed over
+        # and we can mostly assume that they are integers.
         #
         # TODO: infer actual domain from the range.
         domain = S.Integers
         sol = solveset(eqn, dumm, domain)
 
-        # Strip off trivial intersecting with the domain.
+        # Strip off trivial intersecting with the domain (intergers).
         if isinstance(sol, Intersection) and len(sol.args) == 2:
             if sol.args[0] == domain:
                 sol = sol.args[1]

From 8ea2ae64e783593ac836291be139270d0d9b72c3 Mon Sep 17 00:00:00 2001
From: Matthew Wholey <15wholeym@gmail.com>
Date: Fri, 25 Oct 2024 17:01:37 -0500
Subject: [PATCH 29/47] Sharing state between tests was failing them. Running
 pytest in terminal did not run in parallel and so did not show the issue,
 running tests in vscode runs in parallel and thus more than half the tests
 failed when batch run (which some vscode users would do) but passed perfectly
 fine when run individually. Removing the scope='module' from the free algebra
 fixture disallows sharing state between tests and thus prevents collisions. I
 also did not notice any slowdown from forcing individual environment
 creations for each test.

---
 tests/free_algebra_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/free_algebra_test.py b/tests/free_algebra_test.py
index a45075e..45448b0 100644
--- a/tests/free_algebra_test.py
+++ b/tests/free_algebra_test.py
@@ -19,7 +19,7 @@
 from conftest import skip_in_spark
 
 
-@pytest.fixture(scope='module')
+@pytest.fixture
 def free_alg(spark_ctx):
     """Initialize the environment for a free algebra."""
 

From a28d112ea33654264f5fc66bd5fbe507d49a8ae7 Mon Sep 17 00:00:00 2001
From: Copilot <198982749+Copilot@users.noreply.github.com>
Date: Sat, 6 Sep 2025 15:45:21 -0500
Subject: [PATCH 30/47] Fix DrsSymbol and DrsIndexed pickle compatibility with
 SymPy v1.9+ (#25)

---
 drudge/drs.py | 26 +++++++++++++++++++++++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/drudge/drs.py b/drudge/drs.py
index ac92b37..c807eff 100644
--- a/drudge/drs.py
+++ b/drudge/drs.py
@@ -135,9 +135,19 @@ def __getnewargs__(self):
         """Get the arguments for __new__."""
         return None, self.name
 
+    def __getnewargs_ex__(self):
+        """Get the arguments and keyword arguments for __new__.
+        
+        This method takes precedence over __getnewargs__ in Python 3.6+
+        and is used by SymPy v1.9+. We need to override it to ensure
+        proper pickling/unpickling of DrsSymbol objects.
+        """
+        return (None, self.name), {}
+
     def __getstate__(self):
         """Get the state for pickling."""
-        return None
+        # Return a non-None state to ensure __setstate__ is called
+        return {}
 
     def __setstate__(self, state):
         """Set the state according to pickled content."""
@@ -205,10 +215,20 @@ def __getnewargs__(self):
         """Get the arguments for __new__."""
         return (None, self.base) + self.indices
 
+    def __getnewargs_ex__(self):
+        """Get the arguments and keyword arguments for __new__.
+        
+        This method takes precedence over __getnewargs__ in Python 3.6+
+        and is used by SymPy v1.9+. We need to override it to ensure
+        proper pickling/unpickling of DrsIndexed objects.
+        """
+        return ((None, self.base) + self.indices), {}
+
     def __getstate__(self):
         """Get the state for pickling."""
-        return None
-
+        # Return a non-None state to ensure __setstate__ is called
+        return {}
+        
     def __setstate__(self, state):
         """Set the state according to pickled content."""
         from .drudge import current_drudge

From 9306391b994ed9473226d75b57ed8e220da0007c Mon Sep 17 00:00:00 2001
From: "Guo P. Chen" <peizhi.chen@gmail.com>
Date: Sat, 6 Sep 2025 15:51:36 -0500
Subject: [PATCH 31/47] Fix a typo in the comment

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
---
 drudge/term.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/drudge/term.py b/drudge/term.py
index 01d9cfd..3c776da 100644
--- a/drudge/term.py
+++ b/drudge/term.py
@@ -1853,7 +1853,7 @@ def proc_delta(arg1, arg2, sums_dict, resolvers):
         domain = S.Integers
         sol = solveset(eqn, dumm, domain)
 
-        # Strip off trivial intersecting with the domain (intergers).
+        # Strip off trivial intersecting with the domain (integers).
         if isinstance(sol, Intersection) and len(sol.args) == 2:
             if sol.args[0] == domain:
                 sol = sol.args[1]

From 3c454ae5de46511ea63f4a3e679939f7c159fc2f Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 7 Sep 2025 10:42:45 -0500
Subject: [PATCH 32/47] Set Python version to >=3.12

---
 pyproject.toml |  6 +++---
 uv.lock        | 46 ++++++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 47 insertions(+), 5 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 03a8652..4b39995 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,17 +1,17 @@
 [build-system]
-requires = ["setuptools>=68", "wheel"]
+requires = ["setuptools>=77", "wheel"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "drudge"
 version = "0.11.0"
 description = "A CAS based on sympy focusing on tensor and noncommutative algebras"
-requires-python = "==3.12.*"
+requires-python = ">=3.12"
 dependencies = [
   "sympy>=1.14",
   "jinja2",
   "pyspark>=3.5,<3.6",
-  "ipython>=8.0",
+  "ipython>=9.0",
   "dummyrdd @ git+https://github.com/tschijnmo/DummyRDD.git@master"
 ]
 classifiers = [
diff --git a/uv.lock b/uv.lock
index 8e03b0b..1766c26 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,5 +1,5 @@
 version = 1
-requires-python = "==3.12.*"
+requires-python = ">=3.12"
 
 [[package]]
 name = "alabaster"
@@ -54,6 +54,28 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/c1/35/6525b21aa0db614cf8b5792d232021dca3df7f90a1944db934efa5d20bb1/charset_normalizer-3.4.3-cp312-cp312-musllinux_1_2_x86_64.whl", hash = "sha256:320e8e66157cc4e247d9ddca8e21f427efc7a04bbd0ac8a9faf56583fa543f9f", size = 153173 },
     { url = "https://files.pythonhosted.org/packages/50/ee/f4704bad8201de513fdc8aac1cabc87e38c5818c93857140e06e772b5892/charset_normalizer-3.4.3-cp312-cp312-win32.whl", hash = "sha256:fb6fecfd65564f208cbf0fba07f107fb661bcd1a7c389edbced3f7a493f70e37", size = 99822 },
     { url = "https://files.pythonhosted.org/packages/39/f5/3b3836ca6064d0992c58c7561c6b6eee1b3892e9665d650c803bd5614522/charset_normalizer-3.4.3-cp312-cp312-win_amd64.whl", hash = "sha256:86df271bf921c2ee3818f0522e9a5b8092ca2ad8b065ece5d7d9d0e9f4849bcc", size = 107543 },
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@@ -107,7 +129,7 @@ docs = [
 [package.metadata]
 requires-dist = [
     { name = "dummyrdd", git = "https://github.com/tschijnmo/DummyRDD.git?rev=master" },
-    { name = "ipython", specifier = ">=8.0" },
+    { name = "ipython", specifier = ">=9.0" },
     { name = "jinja2" },
     { name = "pyspark", specifier = ">=3.5,<3.6" },
     { name = "pytest", marker = "extra == 'dev'" },
@@ -229,6 +251,26 @@ wheels = [
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 [[package]]

From 0c88b269d6ce18acfe055bfe80c860ac82047078 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 7 Sep 2025 11:38:35 -0500
Subject: [PATCH 33/47] Replace the deprecated `visit_Num` with
 `visit_Constant` in Python 3.8+

---
 drudge/drs.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/drudge/drs.py b/drudge/drs.py
index c807eff..a41a17e 100644
--- a/drudge/drs.py
+++ b/drudge/drs.py
@@ -255,7 +255,7 @@ class _NumFixer(ast.NodeTransformer):
     Integer literals will be changed into creation of symbolic integers.
     """
 
-    def visit_Num(self, node: ast.Constant):
+    def visit_Constant(self, node: ast.Constant):
         """Update the number nodes."""
         val = node.value
         if isinstance(val, int):
@@ -265,7 +265,7 @@ def visit_Num(self, node: ast.Constant):
             ast.copy_location(fixed, node)
             return fixed
         else:
-            return val
+            return node
 
 
 _DEF_METH_NAME = 'def_as'

From 075aa0add244cf42c2036ef438774301c94dd29f Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 20:08:13 -0500
Subject: [PATCH 34/47] Address Gaurav's comments on `pyproject.toml`

---
 pyproject.toml | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4b39995..b75477d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,7 @@ dependencies = [
   "dummyrdd @ git+https://github.com/tschijnmo/DummyRDD.git@master"
 ]
 classifiers = [
-  'Development Status :: 1 - Planning',
+  'Development Status :: 4 - Beta',
   'Intended Audience :: Developers',
   'Intended Audience :: Science/Research',
   'Programming Language :: Python :: 3 :: Only',
@@ -28,6 +28,11 @@ authors = [
   { name = "Jinmo Zhao" },
   { name = "Gustavo E. Scuseria" }
 ]
+maintainers = [
+  { name = "Guo P. Chen" },
+  { name = "Gaurav Harsha" },
+  { name = "Matthew Wholey" }
+]
 
 [project.optional-dependencies]
 docs = ["sphinx"]

From 58cad562895e310d830286114ed62cec097f37fc Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 20:42:59 -0500
Subject: [PATCH 35/47] Address Gaurav's comments on the README file

---
 README.md | 15 +++++++++------
 1 file changed, 9 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 6e8f029..ae3a11e 100644
--- a/README.md
+++ b/README.md
@@ -39,7 +39,8 @@ irrespective of the names and ordering of the summation indices.
 
 In addition to fully considering the permutational symmetries of tensors and
 summations, Drudge provides a general framework for handling non-commutative
-algebraic systems. Currently, Drudge directly supports the [CCR and CAR
+algebraic systems. Currently, Drudge directly supports the [canonical
+commutation relations (CCR) and canonical anticommutation relations (CAR)
 algebras](https://en.wikipedia.org/wiki/CCR_and_CAR_algebras) for fermions and
 bosons, respectively, in many-body theory, general [Clifford
 algebras](https://en.wikipedia.org/wiki/Clifford_algebra), and the [su(2)
@@ -53,11 +54,6 @@ and generate numerical code. Optimal computational complexity can be achieved
 for various methods in quantum chemistry, which heavily rely on tensor
 contractions and their sums.
 
-Drudge is developed by Jinmo Zhao and Prof Gustavo E Scuseria at Rice
-University, and was supported as part of the Center for the Computational
-Design of Functional Layered Materials, an Energy Frontier Research Center
-funded by the U.S. Department of Energy, Office of Science, Basic Energy
-Sciences under Award DE-SC0012575.
 
 ## Installation
 
@@ -71,3 +67,10 @@ or [pip](https://pypi.org/project/pip/)
 pip install git+https://github.com/DrudgeCAS/drudge.git
 ```
 
+## Acknowledgments
+
+Drudge is developed by Jinmo Zhao and Prof Gustavo E. Scuseria at Rice
+University, and was supported as part of the Center for the Computational
+Design of Functional Layered Materials, an Energy Frontier Research Center
+funded by the U.S. Department of Energy, Office of Science, Basic Energy
+Sciences under Award DE-SC0012575.

From acfac990b77b94e6c68e8debbbcec4206b2dcc73 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 21:09:53 -0500
Subject: [PATCH 36/47] Polish the README

---
 README.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index ae3a11e..3306403 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
 
 Drudge is a symbolic algebra system built on top of
 [SymPy](http://www.sympy.org), focusing primarily on tensorial and
-non-commutative algebras. It is motivated by complex symbolic problems in
+non-commutative algebras. It is motivated by tedious symbolic derivations in
 quantum chemistry and many-body theory but is also useful for any symbolic
 manipulation and simplification involving indexed quantities, symbolic
 summations, and non-commutative algebras.
@@ -39,7 +39,7 @@ irrespective of the names and ordering of the summation indices.
 
 In addition to fully considering the permutational symmetries of tensors and
 summations, Drudge provides a general framework for handling non-commutative
-algebraic systems. Currently, Drudge directly supports the [canonical
+algebraic systems. Currently, Drudge natively supports the [canonical
 commutation relations (CCR) and canonical anticommutation relations (CAR)
 algebras](https://en.wikipedia.org/wiki/CCR_and_CAR_algebras) for fermions and
 bosons, respectively, in many-body theory, general [Clifford
@@ -58,7 +58,7 @@ contractions and their sums.
 ## Installation
 
 Drudge can be installed directly from the GitHub repository using
-[uv](https://github.com/astral-sh/uv) (preferred)
+[uv](https://github.com/astral-sh/uv) (recommended)
 ```bash
 uv pip install git+https://github.com/DrudgeCAS/drudge.git
 ```

From f7f87fa4120439b2af524b38796447774079355b Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 22:27:58 -0500
Subject: [PATCH 37/47] Add proper citations

---
 CITATION.cff | 39 +++++++++++++++++++++++++++++++++
 README.md    | 61 ++++++++++++++++++++++++++++++++++++++++++++--------
 2 files changed, 91 insertions(+), 9 deletions(-)
 create mode 100644 CITATION.cff

diff --git a/CITATION.cff b/CITATION.cff
new file mode 100644
index 0000000..64c51af
--- /dev/null
+++ b/CITATION.cff
@@ -0,0 +1,39 @@
+# CITATION.cff
+cff-version: 1.2.0
+message: "If you use Drudge, please cite the following works."
+authors:
+  - family-names: Zhao
+    given-names: Jinmo
+  - family-names: Chen
+    given-names: Guo P.
+  - family-names: Gaurav
+    given-names: Harsha
+  - family-names: Matthew
+    given-names: Wholey
+  - family-names: Henderson
+    given-names: Thomas M.
+  - family-names: Scuseria
+    given-names: Gustavo E.
+title: "Drudge: A symbolic algebra system for tensorial and noncommutative algebras"
+type: software
+repository-code: "https://github.com/DrudgeCAS/drudge"
+abstract: "Drudge is a symbolic algebra system built on top of SymPy, focusing primarily on tensorial and noncommutative algebras. It is motivated by tedious symbolic derivations in quantum chemistry and many-body theory but is also useful for any symbolic manipulation and simplification involving indexed quantities, symbolic summations, and noncommutative algebras."
+keywords:
+  - symbolic algebra
+  - tensor algebra
+  - quantum chemistry
+  - many-body theory
+license: MIT
+version: 0.11.0
+date-released: 2025-09-15
+
+references:
+  - type: thesis
+    authors:
+      - family-names: Zhao
+        given-names: Jinmo
+    title: "Symbolic Solution for Computational Quantum Many-Body Theory Development"
+    year: 2018
+    publisher: Rice University
+    url: "https://www.proquest.com/openview/61a9a86c07dbb6e5270bdeb1c84384db/1?pq-origsite=gscholar&cbl=18750&diss=y"
+
diff --git a/README.md b/README.md
index 3306403..3ec1eee 100644
--- a/README.md
+++ b/README.md
@@ -7,10 +7,10 @@
 
 Drudge is a symbolic algebra system built on top of
 [SymPy](http://www.sympy.org), focusing primarily on tensorial and
-non-commutative algebras. It is motivated by tedious symbolic derivations in
+noncommutative algebras. It is motivated by tedious symbolic derivations in
 quantum chemistry and many-body theory but is also useful for any symbolic
 manipulation and simplification involving indexed quantities, symbolic
-summations, and non-commutative algebras.
+summations, and noncommutative algebras.
 
 Leveraging the generic algorithms implemented in
 [libcanon](https://github.com/DrudgeCAS/libcanon) for canonicalization of
@@ -38,14 +38,14 @@ $$
 irrespective of the names and ordering of the summation indices.
 
 In addition to fully considering the permutational symmetries of tensors and
-summations, Drudge provides a general framework for handling non-commutative
+summations, Drudge provides a general framework for handling noncommutative
 algebraic systems. Currently, Drudge natively supports the [canonical
 commutation relations (CCR) and canonical anticommutation relations (CAR)
 algebras](https://en.wikipedia.org/wiki/CCR_and_CAR_algebras) for fermions and
 bosons, respectively, in many-body theory, general [Clifford
 algebras](https://en.wikipedia.org/wiki/Clifford_algebra), and the [su(2)
 algebra](https://en.m.wikipedia.org/wiki/Special_unitary_group#Lie_Algebra) in
-its Cartan-Killing basis. Other non-commutative algebraic systems can be added
+its Cartan-Killing basis. Other noncommutative algebraic systems can be added
 with ease.
 
 Using symbolic expressions from Drudge, the companion package
@@ -67,10 +67,53 @@ or [pip](https://pypi.org/project/pip/)
 pip install git+https://github.com/DrudgeCAS/drudge.git
 ```
 
+
+## Citations
+
+If you use Drudge in your work, please cite this repository and Jinmo Zhao's
+Ph.D. thesis:
+
+**1. The Drudge GitHub repository**  
+```bibtex
+@misc{DrudgeCAS,
+  author       = {Jinmo Zhao and Guo P. Chen and Gaurav Harsha and Matthew Wholey and Thomas M. Henderson and Gustavo E. Scuseria},
+  title        = {Drudge: A symbolic algebra system for tensorial and noncommutative algebras},
+  publisher    = {GitHub},
+  year         = {2016--2025},
+  url          = {https://github.com/DrudgeCAS/drudge},
+  note         = {GitHub repository}
+}
+```
+Link: [Drudge on GitHub](https://github.com/DrudgeCAS/drudge)
+
+**2. Jinmo Zhao’s Ph.D. thesis**  
+```bibtex
+@phdthesis{Zhao2018Drudge,
+  author       = {Jinmo Zhao},
+  title        = {Symbolic Solution for Computational Quantum Many-Body Theory Development},
+  school       = {Rice University},
+  year         = {2018},
+  month        = {April},
+  address      = {Houston, Texas, USA},
+  type         = {PhD thesis},
+  url          = {https://www.proquest.com/openview/61a9a86c07dbb6e5270bdeb1c84384db/1?pq-origsite=gscholar&cbl=18750&diss=y}
+}
+```
+Link: [Symbolic Solution for Computational Quantum Many-Body Theory Development — Jinmo Zhao (2018)](https://www.proquest.com/openview/61a9a86c07dbb6e5270bdeb1c84384db/1?pq-origsite=gscholar&cbl=18750&diss=y)
+
+---
+
+You may also use the [`CITATION.cff`](./CITATION.cff) file provided in this
+repository, which is compatible with citation managers such as Zotero and
+Mendeley.
+
 ## Acknowledgments
 
-Drudge is developed by Jinmo Zhao and Prof Gustavo E. Scuseria at Rice
-University, and was supported as part of the Center for the Computational
-Design of Functional Layered Materials, an Energy Frontier Research Center
-funded by the U.S. Department of Energy, Office of Science, Basic Energy
-Sciences under Award DE-SC0012575.
+Drudge was originally developed by Jinmo Zhao during his Ph.D. at Rice
+University, under the supervision of Prof. Gustavo E. Scuseria. The project was
+supported as part of the Center for the Computational Design of Functional
+Layered Materials, an Energy Frontier Research Center funded by the U.S.
+Department of Energy, Office of Science, Basic Energy Sciences under Award
+DE-SC0012575. The package is currently maintained by Guo P. Chen, Gaurav
+Harsha, Matthew Wholey, and members of the Scueria group.
+

From b9a675e3bb3b02f1d7837ca806428411263aae59 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 22:32:38 -0500
Subject: [PATCH 38/47] Add citation badge and correct typos

---
 CITATION.cff | 8 ++++----
 README.md    | 3 ++-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 64c51af..9411309 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -6,10 +6,10 @@ authors:
     given-names: Jinmo
   - family-names: Chen
     given-names: Guo P.
-  - family-names: Gaurav
-    given-names: Harsha
-  - family-names: Matthew
-    given-names: Wholey
+  - family-names: Harsha
+    given-names: Gaurav
+  - family-names: Wholey
+    given-names: Matthew
   - family-names: Henderson
     given-names: Thomas M.
   - family-names: Scuseria
diff --git a/README.md b/README.md
index 3ec1eee..2ea73bd 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,7 @@
 [![macOS](https://github.com/DrudgeCAS/drudge/workflows/macOS/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/macos.yml)
 [![Windows](https://github.com/DrudgeCAS/drudge/workflows/Windows/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/windows.yml)
 [![Coveralls](https://coveralls.io/repos/github/DrudgeCAS/drudge/badge.svg?branch=master)](https://coveralls.io/github/DrudgeCAS/drudge?branch=master)
+[![Cite this repo](https://img.shields.io/badge/Cite-this_repo-blue.svg)](./CITATION.cff)
 
 <h1 align="center">Drudge</h1>
 
@@ -68,7 +69,7 @@ pip install git+https://github.com/DrudgeCAS/drudge.git
 ```
 
 
-## Citations
+## Citation
 
 If you use Drudge in your work, please cite this repository and Jinmo Zhao's
 Ph.D. thesis:

From f8e079f7324279c8ae139a2da8adc7d852db67f8 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 22:36:11 -0500
Subject: [PATCH 39/47] No need to provide the link to the Drudge repo

---
 README.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/README.md b/README.md
index 2ea73bd..c39bedb 100644
--- a/README.md
+++ b/README.md
@@ -85,7 +85,6 @@ Ph.D. thesis:
   note         = {GitHub repository}
 }
 ```
-Link: [Drudge on GitHub](https://github.com/DrudgeCAS/drudge)
 
 **2. Jinmo Zhao’s Ph.D. thesis**  
 ```bibtex

From 6d3c954678c5a178f5d9b01c374c5d156447f111 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 22:51:12 -0500
Subject: [PATCH 40/47] Remove debugging blocks

---
 .github/workflows/windows.yml | 13 -------------
 1 file changed, 13 deletions(-)

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
index bb4c900..978d875 100644
--- a/.github/workflows/windows.yml
+++ b/.github/workflows/windows.yml
@@ -26,14 +26,6 @@ jobs:
     - name: Install uv
       uses: astral-sh/setup-uv@v6
 
-    - name: Check Python and environment
-      run: |
-        python --version
-        python -c "import sys; print('Platform:', sys.platform)"
-        echo "MSVC environment variables:"
-        echo "INCLUDE: $env:INCLUDE"
-        echo "LIB: $env:LIB"
-
     - name: Install the project
       run: |
         uv sync --locked --extra dev
@@ -65,11 +57,6 @@ jobs:
     - name: Install uv
       uses: astral-sh/setup-uv@v6
 
-    - name: Check Python and environment
-      run: |
-        python --version
-        python -c "import sys; print('Platform:', sys.platform)"
-
     - name: Install the project
       run: |
         uv sync --locked --extra dev

From e621f99ad8df707011d405e5dd5646623a9f81be Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Sun, 14 Sep 2025 23:03:52 -0500
Subject: [PATCH 41/47] Combine the Ubuntu and MacOS CI into one workflow

---
 .github/workflows/ci.yml     | 78 ++++++++++++++++++++++++++++++++++++
 .github/workflows/macos.yml  | 63 -----------------------------
 .github/workflows/ubuntu.yml | 70 --------------------------------
 CITATION.cff                 |  1 -
 4 files changed, 78 insertions(+), 134 deletions(-)
 create mode 100644 .github/workflows/ci.yml
 delete mode 100644 .github/workflows/macos.yml
 delete mode 100644 .github/workflows/ubuntu.yml

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 0000000..5b8ed13
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,78 @@
+name: CI (Ubuntu + macOS)
+
+on: [push]
+
+jobs:
+  build:
+    name: ${{ matrix.plat.name }} Build
+    runs-on: ${{ matrix.plat.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        plat:
+          - { os: ubuntu-latest, name: Ubuntu }
+          - { os: macos-latest,  name: macOS }
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Download submodules
+        shell: bash
+        run: git submodule update --init --recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install the project
+        run: |
+          uv sync --locked --extra dev
+          uv build
+
+  test:
+    name: ${{ matrix.plat.name }} Tests
+    runs-on: ${{ matrix.plat.os }}
+    needs: build
+    strategy:
+      fail-fast: false
+      matrix:
+        plat:
+          - { os: ubuntu-latest, name: Ubuntu }
+          - { os: macos-latest,  name: macOS }
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Download submodules
+        shell: bash
+        run: git submodule update --init --recursive
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Install the project
+        run: uv sync --locked --extra dev
+
+      - name: Install coverage tools
+        run: uv pip install coverage coveralls
+
+      - name: Run tests with coverage
+        env:
+          DUMMY_SPARK: 1
+        run: uv run coverage run --source=drudge -m pytest tests
+
+      - name: Upload coverage to Coveralls (Ubuntu only)
+        if: ${{ always() && matrix.plat.os == 'ubuntu-latest' }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: uv run coveralls --service=github
+
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
deleted file mode 100644
index 5517088..0000000
--- a/.github/workflows/macos.yml
+++ /dev/null
@@ -1,63 +0,0 @@
-name: macOS
-
-on: [push]
-
-jobs:
-  build:
-    name: macOS Build
-    runs-on: macos-latest
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Download submodules
-      shell: bash
-      run: |
-        git submodule update --init --recursive
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version-file: "pyproject.toml"
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-
-    - name: Install the project
-      run: |
-        uv sync --locked --extra dev
-        uv build
-
-  test:
-    name: macOS Tests
-    runs-on: macos-latest
-    needs: build
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Download submodules
-      shell: bash
-      run: |
-        git submodule update --init --recursive
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version-file: "pyproject.toml"
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-
-    - name: Install the project
-      run: |
-        uv sync --locked --extra dev
-
-    - name: Install coverage tools
-      run: |
-        uv pip install coverage coveralls
-
-    - name: Run tests with coverage
-      env:
-        DUMMY_SPARK: 1
-      run: uv run coverage run --source=drudge -m pytest tests
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
deleted file mode 100644
index bf01b7a..0000000
--- a/.github/workflows/ubuntu.yml
+++ /dev/null
@@ -1,70 +0,0 @@
-name: Ubuntu
-
-on: [push]
-
-jobs:
-  build:
-    name: Ubuntu Build
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Download submodules
-      shell: bash
-      run: |
-        git submodule update --init --recursive
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version-file: "pyproject.toml"
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-
-    - name: Install the project
-      run: |
-        uv sync --locked --extra dev
-        uv build
-
-  test:
-    name: Ubuntu Tests
-    runs-on: ubuntu-latest
-    needs: build
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Download submodules
-      shell: bash
-      run: |
-        git submodule update --init --recursive
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version-file: "pyproject.toml"
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-
-    - name: Install the project
-      run: |
-        uv sync --locked --extra dev
-
-    - name: Install coverage tools
-      run: |
-        uv pip install coverage coveralls
-
-    - name: Run tests with coverage
-      env:
-        DUMMY_SPARK: 1
-      run: uv run coverage run --source=drudge -m pytest tests
-
-    - name: Upload coverage to Coveralls
-      if: always()
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      run: uv run coveralls --service=github
- 
diff --git a/CITATION.cff b/CITATION.cff
index 9411309..62183b9 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -1,4 +1,3 @@
-# CITATION.cff
 cff-version: 1.2.0
 message: "If you use Drudge, please cite the following works."
 authors:

From de45b735ac2a275d6ae53751d36385a9ebc23d2c Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Mon, 15 Sep 2025 09:13:19 -0500
Subject: [PATCH 42/47] Update the description in `pyproject.toml`

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b75477d..95ed970 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "drudge"
 version = "0.11.0"
-description = "A CAS based on sympy focusing on tensor and noncommutative algebras"
+description = "A symbolic algebra system for tensorial and noncommutative algebras"
 requires-python = ">=3.12"
 dependencies = [
   "sympy>=1.14",

From f97c7a98a13c99bec09f2f3d951ba590223e5439 Mon Sep 17 00:00:00 2001
From: "Guo P. Chen" <peizhi.chen@gmail.com>
Date: Tue, 16 Sep 2025 11:09:57 -0500
Subject: [PATCH 43/47] Streamline CI and update the badges in README (#27)

---
 .github/workflows/ci.yml      | 39 ++---------------
 .github/workflows/windows.yml | 79 ++++++++++-------------------------
 README.md                     |  4 +-
 pyproject.toml                |  2 +-
 uv.lock                       |  4 +-
 5 files changed, 31 insertions(+), 97 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 5b8ed13..3da4919 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -3,8 +3,8 @@ name: CI (Ubuntu + macOS)
 on: [push]
 
 jobs:
-  build:
-    name: ${{ matrix.plat.name }} Build
+  ci:
+    name: ${{ matrix.plat.name }} Build + Test
     runs-on: ${{ matrix.plat.os }}
     strategy:
       fail-fast: false
@@ -23,43 +23,12 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version-file: "pyproject.toml"
+          python-version-file: pyproject.toml
 
       - name: Install uv
         uses: astral-sh/setup-uv@v6
 
-      - name: Install the project
-        run: |
-          uv sync --locked --extra dev
-          uv build
-
-  test:
-    name: ${{ matrix.plat.name }} Tests
-    runs-on: ${{ matrix.plat.os }}
-    needs: build
-    strategy:
-      fail-fast: false
-      matrix:
-        plat:
-          - { os: ubuntu-latest, name: Ubuntu }
-          - { os: macos-latest,  name: macOS }
-
-    steps:
-      - uses: actions/checkout@v5
-
-      - name: Download submodules
-        shell: bash
-        run: git submodule update --init --recursive
-
-      - name: Set up Python
-        uses: actions/setup-python@v5
-        with:
-          python-version-file: "pyproject.toml"
-
-      - name: Install uv
-        uses: astral-sh/setup-uv@v6
-
-      - name: Install the project
+      - name: Build Drudge
         run: uv sync --locked --extra dev
 
       - name: Install coverage tools
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
index 978d875..0abfdd3 100644
--- a/.github/workflows/windows.yml
+++ b/.github/workflows/windows.yml
@@ -1,71 +1,38 @@
-name: Windows
+name: CI (Windows)
 
 on: [push]
 
 jobs:
-  build:
-    name: Windows Build
+  windows:
+    name: Windows Build + Test
     runs-on: windows-latest
 
     steps:
-    - uses: actions/checkout@v5
+      - uses: actions/checkout@v5
 
-    - name: Download submodules
-      shell: bash
-      run: |
-        git submodule update --init --recursive
+      - name: Download submodules
+        shell: bash
+        run: git submodule update --init --recursive
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version-file: "pyproject.toml"
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: pyproject.toml
 
-    - name: Setup MSVC
-      uses: ilammy/msvc-dev-cmd@v1
+      - name: Setup MSVC
+        uses: ilammy/msvc-dev-cmd@v1
 
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
 
-    - name: Install the project
-      run: |
-        uv sync --locked --extra dev
-        echo "Dependencies installed successfully"
-        uv build
-        echo "Package build completed successfully"
+      - name: Build Drudge
+        run: uv sync --locked --extra dev
 
-  test:
-    name: Windows Tests
-    runs-on: windows-latest
-    needs: build
-
-    steps:
-    - uses: actions/checkout@v5
-
-    - name: Download submodules
-      shell: bash
-      run: |
-        git submodule update --init --recursive
-
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version-file: "pyproject.toml"
-
-    - name: Setup MSVC
-      uses: ilammy/msvc-dev-cmd@v1
-
-    - name: Install uv
-      uses: astral-sh/setup-uv@v6
-
-    - name: Install the project
-      run: |
-        uv sync --locked --extra dev
+      - name: Install coverage tools
+        run: uv pip install coverage
 
-    - name: Install coverage tools
-      run: |
-        uv pip install coverage coveralls
+      - name: Run tests with coverage
+        env:
+          DUMMY_SPARK: 1
+        run: uv run coverage run --source=drudge -m pytest tests
 
-    - name: Run tests with coverage
-      env:
-        DUMMY_SPARK: 1
-      run: uv run coverage run --source=drudge -m pytest tests
diff --git a/README.md b/README.md
index c39bedb..65a5bae 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,4 @@
-[![Ubuntu](https://github.com/DrudgeCAS/drudge/workflows/Ubuntu/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/ubuntu.yml)
-[![macOS](https://github.com/DrudgeCAS/drudge/workflows/macOS/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/macos.yml)
-[![Windows](https://github.com/DrudgeCAS/drudge/workflows/Windows/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/windows.yml)
+[![CI](https://github.com/DrudgeCAS/drudge/actions/workflows/ci.yml/badge.svg)](https://github.com/DrudgeCAS/drudge/actions/workflows/ci.yml)
 [![Coveralls](https://coveralls.io/repos/github/DrudgeCAS/drudge/badge.svg?branch=master)](https://coveralls.io/github/DrudgeCAS/drudge?branch=master)
 [![Cite this repo](https://img.shields.io/badge/Cite-this_repo-blue.svg)](./CITATION.cff)
 
diff --git a/pyproject.toml b/pyproject.toml
index 95ed970..cc1c1b6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ dependencies = [
   "jinja2",
   "pyspark>=3.5,<3.6",
   "ipython>=9.0",
-  "dummyrdd @ git+https://github.com/tschijnmo/DummyRDD.git@master"
+  "dummyrdd @ git+https://github.com/DrudgeCAS/DummyRDD.git@master"
 ]
 classifiers = [
   'Development Status :: 4 - Beta',
diff --git a/uv.lock b/uv.lock
index 1766c26..aa03206 100644
--- a/uv.lock
+++ b/uv.lock
@@ -128,7 +128,7 @@ docs = [
 
 [package.metadata]
 requires-dist = [
-    { name = "dummyrdd", git = "https://github.com/tschijnmo/DummyRDD.git?rev=master" },
+    { name = "dummyrdd", git = "https://github.com/DrudgeCAS/DummyRDD.git?rev=master" },
     { name = "ipython", specifier = ">=9.0" },
     { name = "jinja2" },
     { name = "pyspark", specifier = ">=3.5,<3.6" },
@@ -140,7 +140,7 @@ requires-dist = [
 [[package]]
 name = "dummyrdd"
 version = "0.0.8.dev0"
-source = { git = "https://github.com/tschijnmo/DummyRDD.git?rev=master#aff7b0101ca557625bd560d41ada0fc8d72a849a" }
+source = { git = "https://github.com/DrudgeCAS/DummyRDD.git?rev=master#0f53b93b64ef5e9db38aa8d2dc3d5bf025a581d6" }
 
 [[package]]
 name = "executing"

From 225325234576aa5ecf0a77b2bd5ddf882a338140 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 16 Sep 2025 11:19:52 -0500
Subject: [PATCH 44/47] Rename the GitHub workflows

---
 .github/workflows/ci.yml      | 2 +-
 .github/workflows/windows.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 3da4919..a84ac06 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -1,4 +1,4 @@
-name: CI (Ubuntu + macOS)
+name: CI
 
 on: [push]
 
diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
index 0abfdd3..7cdb583 100644
--- a/.github/workflows/windows.yml
+++ b/.github/workflows/windows.yml
@@ -1,4 +1,4 @@
-name: CI (Windows)
+name: CI
 
 on: [push]
 

From a743687d7c1639e6234bfedfe148824fca09e10b Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 16 Sep 2025 11:20:07 -0500
Subject: [PATCH 45/47] Ask the users to use WSL on Windows for now

---
 README.md | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/README.md b/README.md
index 65a5bae..ec9f5c2 100644
--- a/README.md
+++ b/README.md
@@ -66,6 +66,9 @@ or [pip](https://pypi.org/project/pip/)
 pip install git+https://github.com/DrudgeCAS/drudge.git
 ```
 
+> **Note:** Native Windows builds are currently not working. Please use WSL
+> (Windows Subsystem for Linux) to install and run Drudge on Windows.
+
 
 ## Citation
 

From 83919aa703632a0d796f5469d8411ec9e0850cb8 Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 16 Sep 2025 11:30:56 -0500
Subject: [PATCH 46/47] Revise the README

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ec9f5c2..cec3266 100644
--- a/README.md
+++ b/README.md
@@ -67,7 +67,7 @@ pip install git+https://github.com/DrudgeCAS/drudge.git
 ```
 
 > **Note:** Native Windows builds are currently not working. Please use WSL
-> (Windows Subsystem for Linux) to install and run Drudge on Windows.
+> (Windows Subsystem for Linux) to install and run Drudge on Windows for now.
 
 
 ## Citation

From 3c8f641cb726b67646f2fb5c7f2a1773a6935b8f Mon Sep 17 00:00:00 2001
From: Guo Chen <peizhi.chen@gmail.com>
Date: Tue, 16 Sep 2025 11:56:25 -0500
Subject: [PATCH 47/47] Add a Documentation section in the README

---
 README.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/README.md b/README.md
index cec3266..4cb5bad 100644
--- a/README.md
+++ b/README.md
@@ -70,6 +70,13 @@ pip install git+https://github.com/DrudgeCAS/drudge.git
 > (Windows Subsystem for Linux) to install and run Drudge on Windows for now.
 
 
+## Documentation
+
+Please refer to the documentation at
+[https://drudgecas.github.io/drudge/](https://drudgecas.github.io/drudge/).
+Additional examples can be found in the `./docs/examples` directory.
+
+
 ## Citation
 
 If you use Drudge in your work, please cite this repository and Jinmo Zhao's