Update conda environment to include rpy2

environment-3.11-win.yml

@@ -1,12 +1,13 @@
 name: sage-dev
 # Generated by conda-lock.
 # platform: win-64
-# input_hash: 156826b2f92d7be0a661413409cfa8bd1e1da81d7d917a2f51768e3647266991
+# input_hash: 4fdb24f38d982c64e642758c2d1bc7cb5650283337eec99d95ba6badde1db52a
 
 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
@@ -15,19 +16,21 @@ dependencies:
   - backports=1.0=pyhd8ed1ab_5
   - backports.tarfile=1.2.0=pyhd8ed1ab_1
   - beautifulsoup4=4.13.4=pyha770c72_0
-  - blas=2.131=openblas
-  - blas-devel=3.9.0=31_hc0f8095_openblas
-  - boltons=24.0.0=pyhd8ed1ab_1
+  - binutils_impl_win-64=2.44=h095e170_0
+  - blas=2.132=openblas
+  - blas-devel=3.9.0=32_hc0f8095_openblas
+  - boltons=25.0.0=pyhd8ed1ab_0
   - boost-cpp=1.85.0=ha5ead02_4
-  - brotli=1.1.0=h2466b09_2
-  - brotli-bin=1.1.0=h2466b09_2
-  - brotli-python=1.1.0=py311hda3d55a_2
+  - brotli=1.1.0=h2466b09_3
+  - brotli-bin=1.1.0=h2466b09_3
+  - brotli-python=1.1.0=py311hda3d55a_3
+  - bwidget=1.10.1=h57928b3_1
   - bzip2=1.0.8=h2466b09_7
-  - ca-certificates=2025.4.26=h4c7d964_0
+  - ca-certificates=2025.6.15=h4c7d964_0
   - cachecontrol=0.14.3=pyha770c72_0
   - cachecontrol-with-filecache=0.14.3=pyhd8ed1ab_0
   - cairo=1.18.4=h5782bbf_0
-  - certifi=2025.4.26=pyhd8ed1ab_0
+  - certifi=2025.6.15=pyhd8ed1ab_0
   - cffi=1.17.1=py311he736701_0
   - charset-normalizer=3.4.2=pyhd8ed1ab_0
   - clang=19.1.7=default_hec7ea82_3
@@ -38,17 +41,18 @@ dependencies:
   - comm=0.2.2=pyhd8ed1ab_1
   - compiler-rt=19.1.7=hc790b64_0
   - compiler-rt_win-64=19.1.7=hc790b64_0
-  - conda-lock=3.0.2=pyha6a9232_1
+  - conda-lock=3.0.4=pyha6a9232_1
   - conda-souschef=2.2.3=pyhd8ed1ab_0
   - contourpy=1.3.2=py311h3257749_0
   - conway-polynomials=0.10=pyhd8ed1ab_1
-  - coverage=7.8.2=py311h5082efb_0
+  - coverage=7.9.2=py311h3f79411_0
   - cpython=3.11.13=py311hd8ed1ab_0
   - crashtest=0.4.1=pyhd8ed1ab_1
-  - cryptography=45.0.3=py311hfd75b31_0
+  - cryptography=45.0.5=py311h5e0b3ae_0
+  - curl=8.14.1=h88aaa65_0
   - cycler=0.12.1=pyhd8ed1ab_1
   - cysignals=1.12.3=py311hda3d55a_0
-  - cython=3.1.1=py311h34f20a9_1
+  - cython=3.1.2=py311h34f20a9_2
   - debugpy=1.8.14=py311hda3d55a_0
   - decorator=5.2.1=pyhd8ed1ab_0
   - deprecated=1.2.18=pyhd8ed1ab_0
@@ -62,7 +66,7 @@ dependencies:
   - executing=2.2.0=pyhd8ed1ab_0
   - expat=2.7.0=he0c23c2_0
   - filelock=3.18.0=pyhd8ed1ab_0
-  - flake8=7.2.0=pyhd8ed1ab_0
+  - flake8=7.3.0=pyhd8ed1ab_0
   - flake8-rst-docstrings=0.3.1=pyhd8ed1ab_0
   - flang=19.1.7=hbeecb71_0
   - flang_impl_win-64=19.1.7=h719f0c7_0
@@ -74,31 +78,34 @@ dependencies:
   - fontconfig=2.15.0=h765892d_1
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=0
-  - fonttools=4.58.1=py311h5082efb_0
-  - fortran-compiler=1.9.0=h95e3450_0
+  - fonttools=4.58.5=py311h3f79411_0
+  - fortran-compiler=1.10.0=h95e3450_0
   - freetype=2.13.3=h57928b3_1
   - furo=2024.8.6=pyhd8ed1ab_2
+  - gcc_impl_win-64=15.1.0=hb5bc704_3
+  - gfortran_impl_win-64=15.1.0=h792c6fe_3
   - gitdb=4.0.12=pyhd8ed1ab_0
   - gitpython=3.1.44=pyhff2d567_0
   - glpk=5.0=h8ffe710_0
   - gmp=6.3.0=hfeafd45_2
   - gmpy2=2.1.5=py311hb8385e8_3
-  - graphite2=1.3.13=h63175ca_1003
+  - graphite2=1.3.14=he0c23c2_0
   - grayskull=2.9.1=pyhd8ed1ab_0
-  - gsl=2.8=h5b8d9c4_1
+  - gsl=2.7=hdfb1a43_0
+  - gxx_impl_win-64=15.1.0=h91e354b_3
   - h2=4.2.0=pyhd8ed1ab_0
   - harfbuzz=11.2.1=h8796e6f_0
   - hpack=4.1.0=pyhd8ed1ab_0
   - hyperframe=6.1.0=pyhd8ed1ab_0
   - icu=75.1=he0c23c2_0
   - idna=3.10=pyhd8ed1ab_1
-  - igraph=0.10.15=h43210b2_1
+  - igraph=0.10.16=h9f42cb0_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=6.29.5=pyh4bbf305_0
-  - ipython=9.3.0=pyh6be1c34_0
+  - ipython=9.4.0=pyh6be1c34_0
   - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
   - ipywidgets=8.1.7=pyhd8ed1ab_0
   - jaraco.classes=3.4.0=pyhd8ed1ab_2
@@ -110,74 +117,87 @@ dependencies:
   - jupyter_core=5.8.1=pyh5737063_0
   - jupyterlab_widgets=3.0.15=pyhd8ed1ab_0
   - keyring=25.6.0=pyh7428d3b_0
-  - kiwisolver=1.4.7=py311h3257749_0
+  - kiwisolver=1.4.8=py311h3fd045d_1
   - krb5=1.21.3=hdf4eb48_0
   - lcms2=2.17=hbcf6048_0
+  - ld_impl_win-64=2.44=hae1bf67_0
   - lerc=4.0.0=h6470a55_1
-  - libblas=3.9.0=31_h11dc60a_openblas
+  - libblas=3.9.0=32_h11dc60a_openblas
   - libboost=1.85.0=h444863b_4
   - libboost-devel=1.85.0=h91493d7_4
   - libboost-headers=1.85.0=h57928b3_4
-  - libbrotlicommon=1.1.0=h2466b09_2
-  - libbrotlidec=1.1.0=h2466b09_2
-  - libbrotlienc=1.1.0=h2466b09_2
-  - libcblas=3.9.0=31_h9bd4c3b_openblas
-  - libclang13=20.1.6=default_h6e92b77_0
+  - libbrotlicommon=1.1.0=h2466b09_3
+  - libbrotlidec=1.1.0=h2466b09_3
+  - libbrotlienc=1.1.0=h2466b09_3
+  - libcblas=3.9.0=32_h9bd4c3b_openblas
+  - libclang13=20.1.7=default_h6e92b77_0
+  - libcurl=8.14.1=h88aaa65_0
   - libdeflate=1.24=h76ddb4d_0
   - libexpat=2.7.0=he0c23c2_0
   - libffi=3.4.6=h537db12_1
   - libflang=19.1.7=he0c23c2_0
   - libflint=3.2.2=h4de658f_0
   - libfreetype=2.13.3=h57928b3_1
   - libfreetype6=2.13.3=h0b5ce68_1
-  - libgcc=15.1.0=h1383e82_2
+  - libgcc=15.1.0=h1383e82_3
+  - libgcc-devel_win-64=15.1.0=hec057c1_103
   - libgd=2.3.3=h7208af6_11
+  - libgfortran=15.1.0=h719f0c7_3
+  - libgfortran5=15.1.0=h997fb6f_3
   - libglib=2.84.2=hbc94333_0
-  - libgomp=15.1.0=h1383e82_2
+  - libgomp=15.1.0=h1383e82_3
   - libiconv=1.18=h135ad9c_1
   - libintl=0.22.5=h5728263_3
   - libjpeg-turbo=3.1.0=h2466b09_0
-  - liblapack=3.9.0=31_h2526c6b_openblas
-  - liblapacke=3.9.0=31_h1d0e49f_openblas
+  - liblapack=3.9.0=32_h2526c6b_openblas
+  - liblapacke=3.9.0=32_h1d0e49f_openblas
   - libllvm19=19.1.7=h3089188_1
-  - liblzma=5.8.1=h2466b09_1
-  - liblzma-devel=5.8.1=h2466b09_1
-  - libopenblas=0.3.29=pthreads_head3c61_0
-  - libpng=1.6.47=h7a4582a_0
+  - liblzma=5.8.1=h2466b09_2
+  - liblzma-devel=5.8.1=h2466b09_2
+  - libopenblas=0.3.30=pthreads_ha4fe6b2_0
+  - libpng=1.6.50=h95bef1e_0
   - libsodium=1.0.20=hc70643c_0
-  - libsqlite=3.50.0=h67fdade_0
+  - libsqlite=3.50.2=hf5d6505_0
+  - libssh2=1.11.1=h9aa295b_0
+  - libstdcxx=15.1.0=h904f734_3
+  - libstdcxx-devel_win-64=15.1.0=hec057c1_103
   - libtiff=4.7.0=h05922d8_5
   - libwebp-base=1.5.0=h3b0e114_0
   - libwinpthread=12.0.0.r4.gg4f2fc60ca=h57928b3_9
   - libxcb=1.17.0=h0e4246c_0
   - libxml2=2.13.8=h442d1da_0
   - libxslt=1.1.39=h3df6e99_0
   - libzlib=1.3.1=h2466b09_2
-  - lld=20.1.6=he99c172_0
+  - lld=20.1.7=he99c172_0
   - llvm-tools=19.1.7=h2a44499_1
+  - m2w64-sysroot_win-64=12.0.0.r4.gg4f2fc60ca=h7428d3b_9
   - m4ri=20240729=h4afdad8_1
   - markupsafe=3.0.2=py311h5082efb_1
   - matplotlib=3.10.3=py311h1ea47a8_0
   - matplotlib-base=3.10.3=py311h8f1b1e4_0
   - matplotlib-inline=0.1.7=pyhd8ed1ab_1
   - mccabe=0.7.0=pyhd8ed1ab_1
   - memory-allocator=0.1.3=py311he736701_1
-  - meson=1.8.1=pyhe01879c_0
+  - meson=1.8.2=pyhe01879c_0
   - meson-python=0.18.0=pyh70fd9c4_0
+  - mingw-w64-ucrt-x86_64-crt-git=12.0.0.r4.gg4f2fc60ca=h7428d3b_9
+  - mingw-w64-ucrt-x86_64-headers-git=12.0.0.r4.gg4f2fc60ca=h7428d3b_9
+  - mingw-w64-ucrt-x86_64-windows-default-manifest=6.4=he206cdd_7
+  - mingw-w64-ucrt-x86_64-winpthreads-git=12.0.0.r4.gg4f2fc60ca=h7428d3b_9
   - more-itertools=10.7.0=pyhd8ed1ab_0
   - mpc=1.3.1=h72bc38f_1
   - mpfr=4.2.1=hbc20e70_3
   - mpmath=1.3.0=pyhd8ed1ab_1
-  - msgpack-python=1.1.0=py311h3257749_0
-  - munkres=1.1.4=pyh9f0ad1d_0
+  - msgpack-python=1.1.1=py311h3257749_0
+  - munkres=1.1.4=pyhd8ed1ab_1
   - nauty=2.6.11=h2fa13f4_1
   - nest-asyncio=1.6.0=pyhd8ed1ab_1
   - networkx=3.5=pyhe01879c_0
-  - ninja=1.12.1=hc790b64_1
-  - numpy=2.2.6=py311h5e411d1_0
-  - openblas=0.3.29=pthreads_h4a7f399_0
+  - ninja=1.13.0=h79cd779_0
+  - numpy=2.3.1=py311haedcf98_0
+  - openblas=0.3.30=pthreads_h4a7f399_0
   - openjpeg=2.5.3=h4d64b90_0
-  - openssl=3.5.0=ha4e3fda_1
+  - openssl=3.5.1=h725018a_0
   - packaging=25.0=pyh29332c3_1
   - pari=2.17.2=h7f476ce_4_single
   - pari-elldata=0.0.20161017=0
@@ -189,9 +209,9 @@ dependencies:
   - perl=5.32.1.1=7_h57928b3_strawberry
   - pexpect=4.9.0=pyhd8ed1ab_1
   - pickleshare=0.7.5=pyhd8ed1ab_1004
-  - pillow=11.2.1=py311h43e43bb_0
+  - pillow=11.3.0=py311h0f9b5fc_0
   - pip=25.1.1=pyh8b19718_0
-  - pixman=0.46.0=had0cd8c_0
+  - pixman=0.46.2=had0cd8c_0
   - pkg-config=0.29.2=h88c491f_1009
   - pkgconfig=1.5.5=pyhd8ed1ab_5
   - pkginfo=1.12.1.2=pyhd8ed1ab_0
@@ -205,26 +225,26 @@ dependencies:
   - pthread-stubs=0.4=h0e40799_1002
   - ptyprocess=0.7.0=pyhd8ed1ab_1
   - pure_eval=0.2.3=pyhd8ed1ab_1
-  - pycodestyle=2.13.0=pyhd8ed1ab_0
+  - pycodestyle=2.14.0=pyhd8ed1ab_0
   - pycosat=0.6.6=py311he736701_2
   - pycparser=2.22=pyh29332c3_1
-  - pydantic=2.11.4=pyh3cfb1c2_0
+  - pydantic=2.11.7=pyh3cfb1c2_0
   - pydantic-core=2.33.2=py311hc4022dc_0
-  - pyflakes=3.3.2=pyhd8ed1ab_0
+  - pyflakes=3.4.0=pyhd8ed1ab_0
   - pygithub=2.6.1=pyhd8ed1ab_0
-  - pygments=2.19.1=pyhd8ed1ab_0
+  - pygments=2.19.2=pyhd8ed1ab_0
   - pyjwt=2.10.1=pyhd8ed1ab_0
   - pynacl=1.5.0=py311h984d3dc_4
   - pyparsing=3.2.3=pyhd8ed1ab_1
   - pyproject-metadata=0.9.1=pyhd8ed1ab_0
   - pyproject_hooks=1.2.0=pyhd8ed1ab_1
   - pyside6=6.9.1=py311h5d1a980_0
   - pysocks=1.7.1=pyh09c184e_7
-  - pytest=8.4.0=pyhd8ed1ab_0
-  - pytest-xdist=3.7.0=pyhd8ed1ab_0
+  - pytest=8.4.1=pyhd8ed1ab_0
+  - pytest-xdist=3.8.0=pyhd8ed1ab_0
   - python=3.11.13=h3f84c4b_0_cpython
   - python-build=1.2.2.post1=pyhff2d567_1
-  - python-dateutil=2.9.0.post0=pyhff2d567_1
+  - python-dateutil=2.9.0.post0=pyhe01879c_2
   - python-fastjsonschema=2.21.1=pyhd8ed1ab_0
   - python-installer=0.7.0=pyhff2d567_1
   - python-symengine=0.14.0=py311h17a871d_1
@@ -234,22 +254,24 @@ dependencies:
   - pywin32=307=py311hda3d55a_3
   - pywin32-ctypes=0.2.3=py311h1ea47a8_1
   - pyyaml=6.0.2=py311h5082efb_2
-  - pyzmq=26.4.0=py311h484c95c_0
+  - pyzmq=27.0.0=py311h484c95c_0
   - qhull=2020.2=hc790b64_5
-  - qt6-main=6.9.1=h02ddd7d_0
+  - qt6-main=6.9.1=h02ddd7d_1
+  - r-base=4.4.3=h80eeea9_2
+  - r-lattice=0.22_7=r44h11b023d_0
   - rapidfuzz=3.13.0=py311hda3d55a_0
-  - requests=2.32.3=pyhd8ed1ab_1
+  - requests=2.32.4=pyhd8ed1ab_0
   - requests-toolbelt=1.0.0=pyhd8ed1ab_1
   - restructuredtext_lint=1.4.0=pyhd8ed1ab_1
   - roman-numerals-py=3.1.0=pyhd8ed1ab_0
-  - ruamel.yaml=0.18.12=py311he736701_0
+  - ruamel.yaml=0.18.14=py311he736701_0
   - ruamel.yaml.clib=0.2.8=py311he736701_1
   - ruamel.yaml.jinja2=0.2.7=pyhd8ed1ab_1
-  - ruff=0.11.12=py311hfc2f1ad_0
+  - ruff=0.12.2=hd40eec1_0
   - sagemath-db-elliptic-curves=0.8.1=hecc5488_0
   - sagemath-db-graphs=20210214=hd8ed1ab_0
   - sagemath-db-polytopes=20170220=1
-  - scipy=1.15.2=py311h99d06ae_0
+  - scipy=1.16.0=py311h0e21e1b_0
   - semver=3.0.4=pyhd8ed1ab_0
   - setuptools=80.9.0=pyhff2d567_0
   - shellingham=1.5.4=pyhd8ed1ab_1
@@ -259,20 +281,22 @@ dependencies:
   - soupsieve=2.7=pyhd8ed1ab_0
   - sphinx=8.2.3=pyhd8ed1ab_0
   - sphinx-basic-ng=1.0.0b2=pyhd8ed1ab_3
+  - sphinx-copybutton=0.5.2=pyhd8ed1ab_1
   - sphinx-inline-tabs=2023.4.21=pyhd8ed1ab_1
   - sphinxcontrib-applehelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-devhelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-htmlhelp=2.1.0=pyhd8ed1ab_1
   - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_1
   - sphinxcontrib-qthelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-serializinghtml=1.1.10=pyhd8ed1ab_1
-  - sqlite=3.50.0=h2466b09_0
+  - sqlite=3.50.2=hdb435a2_0
   - stack_data=0.6.3=pyhd8ed1ab_1
   - stdlib-list=0.11.1=pyhd8ed1ab_0
   - symengine=0.14.0=h1ba984b_1
   - symmetrica=3.0.1=h1537add_0
   - sympy=1.14.0=pyh04b8f61_5
   - tk=8.6.13=h2c6b04d_2
+  - tktable=2.10=h7e9e0db_7
   - toml=0.10.2=pyhd8ed1ab_1
   - tomli=2.2.1=pyhd8ed1ab_1
   - tomli-w=1.2.0=pyhd8ed1ab_0
@@ -281,18 +305,19 @@ dependencies:
   - tqdm=4.67.1=pyhd8ed1ab_1
   - traitlets=5.14.3=pyhd8ed1ab_1
   - trove-classifiers=2025.5.9.12=pyhd8ed1ab_0
-  - typing-extensions=4.14.0=h32cad80_0
+  - typing-extensions=4.14.1=h4440ef1_0
   - typing-inspection=0.4.1=pyhd8ed1ab_0
-  - typing_extensions=4.14.0=pyhe01879c_0
+  - typing_extensions=4.14.1=pyhe01879c_0
   - tzdata=2025b=h78e105d_0
   - ucrt=10.0.22621.0=h57928b3_1
   - unicodedata2=16.0.0=py311he736701_0
-  - urllib3=2.4.0=pyhd8ed1ab_0
-  - vc=14.3=h2b53caa_26
-  - vc14_runtime=14.42.34438=hfd919c2_26
+  - urllib3=2.5.0=pyhd8ed1ab_0
+  - uv=0.7.19=h579f82e_0
+  - vc=14.3=h41ae7f8_26
+  - vc14_runtime=14.44.35208=h818238b_26
   - virtualenv=20.31.2=pyhd8ed1ab_0
-  - vs2015_runtime=14.42.34438=h7142326_26
-  - vs2022_win-64=19.43.34604=h070f0e0_26
+  - vs2015_runtime=14.44.35208=h38c0c73_26
+  - vs2022_win-64=19.44.35207=ha74f236_26
   - vswhere=3.1.7=h40126e0_1
   - wcwidth=0.2.13=pyhd8ed1ab_1
   - wheel=0.45.1=pyhd8ed1ab_1
@@ -308,11 +333,11 @@ dependencies:
   - xorg-libxext=1.3.6=h0e40799_0
   - xorg-libxpm=3.5.17=h0e40799_1
   - xorg-libxt=1.3.1=h0e40799_0
-  - xz=5.8.1=h208afaa_1
-  - xz-tools=5.8.1=h2466b09_1
+  - xz=5.8.1=h208afaa_2
+  - xz-tools=5.8.1=h2466b09_2
   - yaml=0.2.5=h8ffe710_2
   - zeromq=4.3.5=ha9f60a1_7
-  - zipp=3.22.0=pyhd8ed1ab_0
+  - zipp=3.23.0=pyhd8ed1ab_0
   - zlib=1.3.1=h2466b09_2
   - zstandard=0.23.0=py311he736701_2
   - zstd=1.5.7=hbeecb71_2