Update environment configuration and improve conda update script

- Updated `environment-3.13-win.yml` with new dependencies and version updates.
- Added several new packages including `annotated-types`, `backports`, `click`, and others.
- Updated Python version from 3.13.7 to 3.13.8 and adjusted related dependencies.
- Enhanced `update-conda.py` to use threading for processing platforms and Python versions concurrently.
- Refactored dependency retrieval logic to improve clarity and maintainability.
- Removed unnecessary comments and cleaned up the code for better readability.

Author: cxzhong

environment-3.11-linux-aarch64.yml

@@ -1,44 +1,63 @@
 name: sage-dev
 # Generated by conda-lock.
 # platform: win-64
-# input_hash: 09061bd7178b454e63f96588295918d9acd5d4a774c0494fd52ded2a1f3d2429
+# input_hash: 05392857041fcece022a7cd1e9e184595622367e31876b83969474947b49a5df
 
 channels:
   - conda-forge
 dependencies:
   - _openmp_mutex=4.5=2_gnu
   - _r-mutex=1.0.1=anacondar_1
   - alabaster=1.0.0=pyhd8ed1ab_1
+  - annotated-types=0.7.0=pyhd8ed1ab_1
+  - appdirs=1.4.4=pyhd8ed1ab_1
+  - archspec=0.2.5=pyhd8ed1ab_0
   - asttokens=3.0.0=pyhd8ed1ab_1
   - attrs=25.4.0=pyh71513ae_0
   - babel=2.17.0=pyhd8ed1ab_0
+  - backports=1.0=pyhd8ed1ab_5
+  - backports.tarfile=1.2.0=pyhd8ed1ab_1
   - beautifulsoup4=4.14.2=pyha770c72_0
   - binutils_impl_win-64=2.44=h095e170_2
   - blas=2.137=openblas
   - blas-devel=3.9.0=37_ha590de0_openblas
   - bleach=6.2.0=pyh29332c3_4
   - bleach-with-css=6.2.0=h82add2a_4
+  - boltons=25.0.0=pyhd8ed1ab_0
   - boost-cpp=1.85.0=ha5ead02_4
   - brotli=1.1.0=hfd05255_4
   - brotli-bin=1.1.0=hfd05255_4
   - brotli-python=1.1.0=py311h3e6a449_4
   - bwidget=1.10.1=h57928b3_1
   - bzip2=1.0.8=h0ad9c76_8
   - ca-certificates=2025.10.5=h4c7d964_0
+  - cachecontrol=0.14.3=pyha770c72_0
+  - cachecontrol-with-filecache=0.14.3=pyhd8ed1ab_0
   - cairo=1.18.4=h5782bbf_0
   - certifi=2025.10.5=pyhd8ed1ab_0
   - cffi=2.0.0=py311h3485c13_0
   - charset-normalizer=3.4.3=pyhd8ed1ab_0
   - clang=19.1.7=default_hac490eb_5
   - clang-19=19.1.7=default_hac490eb_5
+  - click=8.1.8=pyh7428d3b_0
+  - click-default-group=1.2.4=pyhd8ed1ab_1
   - colorama=0.4.6=pyhd8ed1ab_1
   - comm=0.2.3=pyhe01879c_0
   - compiler-rt=19.1.7=h49e36cd_1
   - compiler-rt_win-64=19.1.7=h49e36cd_1
+  - conda=25.9.1=py311h1ea47a8_0
+  - conda-libmamba-solver=25.4.0=pyhd8ed1ab_0
+  - conda-lock=3.0.4=pyha6a9232_1
+  - conda-package-handling=2.4.0=pyh7900ff3_2
+  - conda-package-streaming=0.12.0=pyhd8ed1ab_0
+  - conda-recipe-manager=0.7.1=pyhd8ed1ab_0
+  - conda-souschef=2.2.3=pyhd8ed1ab_0
   - contourpy=1.3.3=py311h3fd045d_2
   - conway-polynomials=0.10=pyhd8ed1ab_1
   - coverage=7.10.7=py311h3f79411_0
+  - cpp-expected=1.3.1=h477610d_0
   - cpython=3.11.14=py311hd8ed1ab_1
+  - crashtest=0.4.1=pyhd8ed1ab_1
   - cryptography=46.0.2=py311h5e0b3ae_0
   - curl=8.14.1=h88aaa65_0
   - cycler=0.12.1=pyhd8ed1ab_1
@@ -48,17 +67,23 @@ dependencies:
   - decorator=5.2.1=pyhd8ed1ab_0
   - defusedxml=0.7.1=pyhd8ed1ab_0
   - deprecated=1.2.18=pyhd8ed1ab_0
+  - distlib=0.4.0=pyhd8ed1ab_0
+  - distro=1.9.0=pyhd8ed1ab_1
   - docutils=0.21.2=pyhd8ed1ab_1
   - double-conversion=3.3.1=he0c23c2_0
+  - dulwich=0.22.8=py311h533ab2d_0
+  - ensureconda=1.6.0=pyhcf101f3_0
   - exceptiongroup=1.3.0=pyhd8ed1ab_0
   - execnet=2.1.1=pyhd8ed1ab_1
   - executing=2.2.1=pyhd8ed1ab_0
   - expat=2.7.1=hac47afa_0
+  - filelock=3.20.0=pyhd8ed1ab_0
   - flake8=7.3.0=pyhd8ed1ab_0
   - flake8-rst-docstrings=0.4.0=pyhd8ed1ab_0
   - flang=19.1.7=hbeecb71_0
   - flang_impl_win-64=19.1.7=h719f0c7_0
   - flang_win-64=19.1.7=h719f0c7_0
+  - fmt=11.2.0=h1d4551f_0
   - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
   - font-ttf-inconsolata=3.000=h77eed37_0
   - font-ttf-source-code-pro=2.038=h77eed37_0
@@ -69,14 +94,22 @@ dependencies:
   - fonttools=4.60.1=py311h3f79411_0
   - fortran-compiler=1.11.0=h95e3450_0
   - freetype=2.14.1=h57928b3_0
+  - fribidi=1.0.16=hfd05255_0
+  - frozendict=2.4.6=py311h3485c13_1
   - furo=2024.8.6=pyhd8ed1ab_2
   - gcc_impl_win-64=15.2.0=h90e0b34_7
+  - getopt-win32=0.1=h6a83c73_3
   - gfortran_impl_win-64=15.2.0=hd3d1e43_7
+  - gitdb=4.0.12=pyhd8ed1ab_0
+  - gitpython=3.1.45=pyhff2d567_0
   - glpk=5.0=h8ffe710_0
   - gmp=6.3.0=hfeafd45_2
   - gmpy2=2.1.5=py311hb8385e8_3
   - graphite2=1.3.14=hac47afa_2
+  - graphviz=13.1.2=ha5e8f4b_0
+  - grayskull=2.9.1=pyhcf101f3_1
   - gsl=2.7=hdfb1a43_0
+  - gts=0.7.6=h6b5321d_4
   - gxx_impl_win-64=15.2.0=h4517dcd_7
   - h2=4.3.0=pyhcf101f3_0
   - harfbuzz=12.1.0=h5f2951f_0
@@ -87,25 +120,33 @@ dependencies:
   - igraph=1.0.0=h9eeb67d_0
   - imagesize=1.4.1=pyhd8ed1ab_0
   - importlib-metadata=8.7.0=pyhe01879c_1
+  - importlib_resources=6.5.2=pyhd8ed1ab_0
   - iniconfig=2.0.0=pyhd8ed1ab_1
-  - ipykernel=6.30.1=pyh3521513_0
+  - ipykernel=7.0.0=pyh6dadd2b_0
   - ipython=9.6.0=pyh6be1c34_0
   - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
   - ipywidgets=8.1.7=pyhd8ed1ab_0
+  - jaraco.classes=3.4.0=pyhd8ed1ab_2
+  - jaraco.context=6.0.1=pyhd8ed1ab_0
+  - jaraco.functools=4.3.0=pyhd8ed1ab_0
   - jedi=0.19.2=pyhd8ed1ab_1
   - jinja2=3.1.6=pyhd8ed1ab_0
+  - jsonpatch=1.33=pyhd8ed1ab_1
+  - jsonpointer=3.0.0=py311h1ea47a8_2
   - jsonschema=4.25.1=pyhe01879c_0
   - jsonschema-specifications=2025.9.1=pyhcf101f3_0
   - jupyter-sphinx=0.5.3=pyha770c72_5
   - jupyter_client=8.6.3=pyhd8ed1ab_1
   - jupyter_core=5.8.1=pyh5737063_0
   - jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
   - jupyterlab_widgets=3.0.15=pyhd8ed1ab_0
+  - keyring=25.6.0=pyh7428d3b_0
   - kiwisolver=1.4.9=py311h275cad7_1
   - krb5=1.21.3=hdf4eb48_0
   - lcms2=2.17=hbcf6048_0
   - ld_impl_win-64=2.44=hae1bf67_2
   - lerc=4.0.0=h6470a55_1
+  - libarchive=3.8.1=gpl_h26aea39_101
   - libblas=3.9.0=37_h0adab6e_openblas
   - libboost=1.85.0=h444863b_4
   - libboost-devel=1.85.0=h91493d7_4
@@ -138,9 +179,12 @@ dependencies:
   - libllvm19=19.1.7=h830ff33_2
   - liblzma=5.8.1=h2466b09_2
   - liblzma-devel=5.8.1=h2466b09_2
+  - libmamba=2.3.2=hd264f3a_2
+  - libmambapy=2.3.2=py311h1350bce_2
   - libopenblas=0.3.30=pthreads_ha4fe6b2_2
   - libpng=1.6.50=h7351971_1
   - libsodium=1.0.20=hc70643c_0
+  - libsolv=0.7.35=h8883371_0
   - libsqlite=3.50.4=hf5d6505_0
   - libssh2=1.11.1=h9aa295b_0
   - libstdcxx=15.2.0=h904f734_7
@@ -157,6 +201,8 @@ dependencies:
   - libzlib=1.3.1=h2466b09_2
   - lld=21.1.3=hc465015_0
   - llvm-tools=19.1.7=h752b59f_2
+  - lz4-c=1.10.0=h2466b09_1
+  - lzo=2.10=h6a83c73_1002
   - m2-conda-epoch=20250515=0_x86_64
   - m2w64-sysroot_win-64=12.0.0.r4.gg4f2fc60ca=hd8ed1ab_10
   - m4ri=20250128=h26c196c_0
@@ -166,16 +212,19 @@ dependencies:
   - matplotlib-inline=0.1.7=pyhd8ed1ab_1
   - mccabe=0.7.0=pyhd8ed1ab_1
   - memory-allocator=0.1.3=py311h3485c13_2
+  - menuinst=2.4.0=py311h3e6a449_0
   - meson=1.9.0=pyhcf101f3_0
   - meson-python=0.18.0=pyh70fd9c4_0
   - mingw-w64-ucrt-x86_64-crt-git=12.0.0.r4.gg4f2fc60ca=hd8ed1ab_10
   - mingw-w64-ucrt-x86_64-headers-git=12.0.0.r4.gg4f2fc60ca=hd8ed1ab_10
   - mingw-w64-ucrt-x86_64-windows-default-manifest=6.4=he206cdd_7
   - mingw-w64-ucrt-x86_64-winpthreads-git=12.0.0.r4.gg4f2fc60ca=hd8ed1ab_10
   - mistune=3.1.4=pyhcf101f3_0
+  - more-itertools=10.8.0=pyhd8ed1ab_0
   - mpc=1.3.1=h72bc38f_1
   - mpfr=4.2.1=hbc20e70_3
   - mpmath=1.3.0=pyhd8ed1ab_1
+  - msgpack-python=1.1.2=py311h3fd045d_0
   - munkres=1.1.4=pyhd8ed1ab_1
   - nauty=2.6.11=h2fa13f4_1
   - nbclient=0.10.2=pyhd8ed1ab_0
@@ -186,13 +235,15 @@ dependencies:
   - nest-asyncio=1.6.0=pyhd8ed1ab_1
   - networkx=3.5=pyhe01879c_0
   - ninja=1.13.1=h477610d_0
+  - nlohmann_json-abi=3.12.0=h0f90c79_1
   - numpy=2.3.3=py311h80b3fa1_0
   - openblas=0.3.30=pthreads_h4a7f399_2
   - openjpeg=2.5.4=h24db6dd_0
   - openssl=3.5.4=h725018a_0
   - packaging=25.0=pyh29332c3_1
   - pandoc=3.8.2=h57928b3_0
   - pandocfilters=1.5.0=pyhd8ed1ab_0
+  - pango=1.56.4=h03d888a_0
   - pari=2.17.2=h637a547_5_pthread
   - pari-elldata=0.0.20161017=0
   - pari-galdata=0.0.20180411=0
@@ -208,53 +259,76 @@ dependencies:
   - pixman=0.46.4=h5112557_1
   - pkg-config=0.29.2=h88c491f_1009
   - pkgconfig=1.5.5=pyhd8ed1ab_5
+  - pkginfo=1.12.1.2=pyhd8ed1ab_0
   - planarity=4.0.0.0=hfd05255_0
   - platformdirs=4.5.0=pyhcf101f3_0
   - pluggy=1.6.0=pyhd8ed1ab_0
   - primesieve=12.8=he0c23c2_0
+  - progressbar2=4.5.0=pyhd8ed1ab_1
   - prompt-toolkit=3.0.52=pyha770c72_0
   - psutil=7.1.0=py311h3485c13_0
   - pthread-stubs=0.4=h0e40799_1002
   - ptyprocess=0.7.0=pyhd8ed1ab_1
   - pure_eval=0.2.3=pyhd8ed1ab_1
+  - pybind11-abi=4=hd8ed1ab_3
   - pycodestyle=2.14.0=pyhd8ed1ab_0
   - pycosat=0.6.6=py311h3485c13_3
   - pycparser=2.22=pyh29332c3_1
+  - pydantic=2.12.0=pyh3cfb1c2_0
+  - pydantic-core=2.41.1=py311hf51aa87_0
   - pyflakes=3.4.0=pyhd8ed1ab_0
   - pygithub=2.8.1=pyhd8ed1ab_0
   - pygments=2.19.2=pyhd8ed1ab_0
+  - pygraphviz=1.14=py311hb614d00_2
   - pyjwt=2.10.1=pyhd8ed1ab_0
   - pynacl=1.6.0=py311h3485c13_0
   - pyparsing=3.2.5=pyhcf101f3_0
   - pyproject-metadata=0.9.1=pyhd8ed1ab_0
+  - pyproject_hooks=1.2.0=pyhd8ed1ab_1
   - pyside6=6.9.3=py311hf70c7b4_1
   - pysocks=1.7.1=pyh09c184e_7
   - pytest=8.4.2=pyhd8ed1ab_0
   - pytest-xdist=3.8.0=pyhd8ed1ab_0
   - python=3.11.14=h30ce641_1_cpython
+  - python-build=1.3.0=pyhff2d567_0
   - python-dateutil=2.9.0.post0=pyhe01879c_2
   - python-fastjsonschema=2.21.2=pyhe01879c_0
+  - python-installer=0.7.0=pyhff2d567_1
   - python-symengine=0.14.0=py311h17a871d_1
+  - python-utils=3.9.1=pyhff2d567_1
   - python_abi=3.11=8_cp311
   - pytz=2025.2=pyhd8ed1ab_0
   - pywin32=311=py311hefeebc8_1
+  - pywin32-ctypes=0.2.3=py311h1ea47a8_2
+  - pyyaml=6.0.3=py311h3f79411_0
   - pyzmq=27.1.0=py311hb77b9c8_0
   - qhull=2020.2=hc790b64_5
   - qt6-main=6.9.3=ha0de62e_0
   - r-base=4.5.1=h4076d79_3
   - r-lattice=0.22_7=r45heceb674_1
+  - rapidfuzz=3.14.1=py311h3e6a449_0
   - referencing=0.36.2=pyh29332c3_0
+  - reproc=14.2.5.post0=h2466b09_0
+  - reproc-cpp=14.2.5.post0=he0c23c2_0
   - requests=2.32.5=pyhd8ed1ab_0
+  - requests-toolbelt=1.0.0=pyhd8ed1ab_1
   - restructuredtext_lint=1.4.0=pyhd8ed1ab_1
   - roman-numerals-py=3.1.0=pyhd8ed1ab_0
   - rpds-py=0.27.1=py311hf51aa87_1
+  - ruamel.yaml=0.18.15=py311h3485c13_1
+  - ruamel.yaml.clib=0.2.12=py311h3485c13_1
+  - ruamel.yaml.jinja2=0.2.7=pyhd8ed1ab_1
   - ruff=0.14.0=h3e3edff_0
   - sagemath-db-elliptic-curves=0.8.1=hecc5488_0
   - sagemath-db-graphs=20210214=hd8ed1ab_0
   - sagemath-db-polytopes=20170220=1
   - scipy=1.16.2=py311h9a1c30b_0
+  - semver=3.0.4=pyhd8ed1ab_0
   - setuptools=80.9.0=pyhff2d567_0
+  - shellingham=1.5.4=pyhd8ed1ab_1
+  - simdjson=4.0.7=h49e36cd_0
   - six=1.17.0=pyhe01879c_1
+  - smmap=5.0.2=pyhd8ed1ab_0
   - snowballstemmer=3.0.1=pyhd8ed1ab_0
   - soupsieve=2.8=pyhd8ed1ab_0
   - sphinx=8.2.3=pyhd8ed1ab_0
@@ -269,17 +343,23 @@ dependencies:
   - sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_1
   - sqlite=3.50.4=hdb435a2_0
   - stack_data=0.6.3=pyhd8ed1ab_1
+  - stdlib-list=0.11.1=pyhd8ed1ab_0
   - symengine=0.14.0=h1ba984b_1
   - symmetrica=3.1.0=h1056bf2_0
   - sympy=1.14.0=pyh04b8f61_5
   - tinycss2=1.4.0=pyhd8ed1ab_0
   - tk=8.6.13=h2c6b04d_2
   - tktable=2.10=h7e9e0db_7
   - tomli=2.3.0=pyhcf101f3_0
+  - tomli-w=1.2.0=pyhd8ed1ab_0
+  - tomlkit=0.13.3=pyha770c72_0
   - tornado=6.5.2=py311h3485c13_1
   - tqdm=4.67.1=pyhd8ed1ab_1
   - traitlets=5.14.3=pyhd8ed1ab_1
+  - trove-classifiers=2025.9.11.17=pyhd8ed1ab_0
+  - truststore=0.10.3=pyhe01879c_0
   - typing-extensions=4.15.0=h396c80c_0
+  - typing-inspection=0.4.2=pyhd8ed1ab_0
   - typing_extensions=4.15.0=pyhcf101f3_0
   - tzdata=2025b=h78e105d_0
   - ucrt=10.0.26100.0=h57928b3_0
@@ -289,6 +369,7 @@ dependencies:
   - vc=14.3=h41ae7f8_31
   - vc14_runtime=14.44.35208=h818238b_31
   - vcomp14=14.44.35208=h818238b_31
+  - virtualenv=20.35.3=pyhd8ed1ab_0
   - vs2015_runtime=14.44.35208=h38c0c73_31
   - vs2022_win-64=19.44.35207=ha74f236_31
   - vswhere=3.1.7=h40126e0_1
@@ -309,6 +390,8 @@ dependencies:
   - xorg-libxt=1.3.1=h0e40799_0
   - xz=5.8.1=h208afaa_2
   - xz-tools=5.8.1=h2466b09_2
+  - yaml=0.2.5=h6a83c73_3
+  - yaml-cpp=0.8.0=he0c23c2_0
   - zeromq=4.3.5=h5bddc39_9
   - zipp=3.23.0=pyhd8ed1ab_0
   - zlib=1.3.1=h2466b09_2