rerun with python 3.12

Author: rebeccamccabe

.calkit/env-locks/openflash-on-branch/linux-64.yml

@@ -4,7 +4,7 @@ channels:
 dependencies:
   - _openmp_mutex=4.5=20_gnu
   - _python_abi3_support=1.0=hd8ed1ab_2
-  - alsa-lib=1.2.15.3=hb03c661_0
+  - alsa-lib=1.2.16=hb03c661_0
   - altair=6.1.0=pyhd8ed1ab_0
   - anyio=4.13.0=pyhcf101f3_0
   - asttokens=3.0.1=pyhd8ed1ab_0
@@ -15,7 +15,7 @@ dependencies:
   - aws-c-compression=0.3.2=h8b1a151_0
   - aws-c-event-stream=0.7.0=h9b893ba_0
   - aws-c-http=0.10.13=h4bacb7b_0
-  - aws-c-io=0.26.3=h692f434_1
+  - aws-c-io=0.26.3=hb18f61d_2
   - aws-c-mqtt=0.15.2=hc1936db_2
   - aws-c-s3=0.12.2=he6ee468_1
   - aws-c-sdkutils=0.2.4=h8b1a151_4
@@ -24,238 +24,236 @@ dependencies:
   - aws-sdk-cpp=1.11.747=h41c0014_4
   - azure-core-cpp=1.16.2=h206d751_0
   - azure-identity-cpp=1.13.3=hed0cdb0_1
-  - azure-storage-blobs-cpp=12.16.0=hf824e48_2
+  - azure-storage-blobs-cpp=12.17.0=hf824e48_1
   - azure-storage-common-cpp=12.13.0=ha7a2c86_0
-  - azure-storage-files-datalake-cpp=12.14.0=h539c000_2
-  - backports.zstd=1.5.0=py314h680f03e_0
+  - azure-storage-files-datalake-cpp=12.15.0=h1e5b466_0
+  - backports.zstd=1.5.0=py312h90b7ffd_0
   - blinker=1.9.0=pyhff2d567_0
   - brotli=1.2.0=hed03a55_1
   - brotli-bin=1.2.0=hb03c661_1
-  - brotli-python=1.2.0=py314h3de4e8d_1
+  - brotli-python=1.2.0=py312hdb49522_1
   - bzip2=1.0.8=hda65f42_9
   - c-ares=1.34.6=hb03c661_0
-  - ca-certificates=2026.4.22=hbd8a1cb_0
+  - ca-certificates=2026.5.20=hbd8a1cb_0
   - cached-property=1.5.2=hd8ed1ab_1
   - cached_property=1.5.2=pyha770c72_1
-  - cachetools=7.1.2=pyhd8ed1ab_0
+  - cachetools=7.1.4=pyhd8ed1ab_0
   - cairo=1.18.4=he90730b_1
-  - capytaine=2.3.1=py314hacf7208_0
-  - certifi=2026.4.22=pyhd8ed1ab_0
+  - capytaine=2.3.1=py312h6a55c13_0
+  - certifi=2026.5.20=pyhd8ed1ab_0
   - charset-normalizer=3.4.7=pyhd8ed1ab_0
-  - click=8.3.3=pyhc90fa1f_0
+  - click=8.4.1=pyhc90fa1f_0
   - comm=0.2.3=pyhe01879c_0
-  - contourpy=1.3.3=py314h97ea11e_4
-  - cpython=3.14.4=py314hd8ed1ab_100
+  - contourpy=1.3.3=py312h0a2e395_4
+  - cpython=3.12.13=py312hd8ed1ab_0
   - cycler=0.12.1=pyhcf101f3_2
   - cyrus-sasl=2.1.28=hac629b4_1
   - dbus=1.16.2=h24cb091_1
-  - debugpy=1.8.20=py314h42812f9_0
-  - decorator=5.2.1=pyhd8ed1ab_0
+  - debugpy=1.8.21=py312h8285ef7_0
+  - decorator=5.3.1=pyhd8ed1ab_0
   - double-conversion=3.4.0=hecca717_0
   - exceptiongroup=1.3.1=pyhd8ed1ab_0
   - executing=2.2.1=pyhd8ed1ab_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
   - font-ttf-ubuntu=0.83=h77eed37_3
-  - fontconfig=2.17.1=h27c8c51_0
+  - fontconfig=2.18.1=h27c8c51_0
   - fonts-conda-ecosystem=1=0
   - fonts-conda-forge=1=hc364b38_1
-  - fonttools=4.63.0=pyh7db6752_0
+  - fonttools=4.63.0=py312h8a5da7c_0
   - freetype=2.14.3=ha770c72_0
   - gflags=2.2.2=h5888daf_1005
   - gitdb=4.0.12=pyhd8ed1ab_0
   - gitpython=3.1.50=pyhd8ed1ab_0
   - glog=0.7.1=hbabe93e_0
-  - graphite2=1.3.14=hecca717_2
+  - graphite2=1.3.15=hecca717_0
   - h11=0.16.0=pyhcf101f3_1
   - h2=4.3.0=pyhcf101f3_0
   - h5netcdf=1.8.1=pyhd8ed1ab_0
-  - h5py=3.16.0=nompi_py314hddf7a69_102
-  - harfbuzz=14.2.0=h6083320_0
+  - h5py=3.16.0=nompi_py312ha829cd9_102
+  - harfbuzz=14.2.1=h6083320_0
   - hdf5=2.1.0=nompi_h87a9417_105
   - hpack=4.1.0=pyhd8ed1ab_0
-  - httptools=0.7.1=py314h5bd0f2a_1
+  - httptools=0.8.0=py312h4c3975b_0
   - hyperframe=6.1.0=pyhd8ed1ab_0
   - icu=78.3=h33c6efd_0
-  - idna=3.13=pyhcf101f3_0
-  - importlib-metadata=8.8.0=pyhcf101f3_0
+  - idna=3.17=pyhcf101f3_0
+  - importlib-metadata=9.0.0=pyhcf101f3_0
   - ipykernel=7.2.0=pyha191276_1
-  - ipython=9.13.0=pyh53cf698_0
+  - ipython=9.14.1=pyh53cf698_0
   - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
   - itsdangerous=2.2.0=pyhd8ed1ab_1
   - jedi=0.19.2=pyhd8ed1ab_1
   - jinja2=3.1.6=pyhcf101f3_1
   - jsonschema=4.26.0=pyhcf101f3_0
   - jsonschema-specifications=2025.9.1=pyhcf101f3_0
-  - jupyter_client=8.8.0=pyhcf101f3_0
+  - jupyter_client=8.9.0=pyhcf101f3_0
   - jupyter_core=5.9.1=pyhc90fa1f_0
   - keyutils=1.6.3=hb9d3cd8_0
-  - kiwisolver=1.5.0=py314h97ea11e_0
+  - kiwisolver=1.5.0=py312h0a2e395_0
   - krb5=1.22.2=ha1258a1_0
-  - lcms2=2.19.1=h0c24ade_0
+  - lcms2=2.19.1=h0c24ade_1
   - ld_impl_linux-64=2.45.1=default_hbd61a6d_102
   - lerc=4.1.0=hdb68285_0
   - libabseil=20260107.1=cxx17_h7b12aa8_0
   - libaec=1.1.5=h088129d_0
-  - libarrow=24.0.0=h0935d00_1_cpu
-  - libarrow-acero=24.0.0=h635bf11_1_cpu
-  - libarrow-compute=24.0.0=h53684a4_1_cpu
-  - libarrow-dataset=24.0.0=h635bf11_1_cpu
-  - libarrow-substrait=24.0.0=hb4dd7c2_1_cpu
-  - libblas=3.11.0=7_h4a7cf45_openblas
+  - libarrow=24.0.0=h61d77b5_4_cpu
+  - libarrow-acero=24.0.0=h635bf11_4_cpu
+  - libarrow-compute=24.0.0=h53684a4_4_cpu
+  - libarrow-dataset=24.0.0=h635bf11_4_cpu
+  - libarrow-substrait=24.0.0=hb4dd7c2_4_cpu
+  - libblas=3.11.0=8_h4a7cf45_openblas
   - libbrotlicommon=1.2.0=hb03c661_1
   - libbrotlidec=1.2.0=hb03c661_1
   - libbrotlienc=1.2.0=hb03c661_1
-  - libcblas=3.11.0=7_h0358290_openblas
-  - libclang13=22.1.5=default_h746c552_1
+  - libcblas=3.11.0=8_h0358290_openblas
+  - libclang13=22.1.7=default_h746c552_1
   - libcrc32c=1.1.2=h9c3ff4c_0
   - libcups=2.3.3=h7a8fb5f_6
   - libcurl=8.20.0=hcf29cc6_0
   - libdeflate=1.25=h17f619e_0
   - libdrm=2.4.127=hb03c661_0
   - libedit=3.1.20250104=pl5321h7949ede_0
-  - libegl=1.7.0=ha4b6fd6_2
-  - libegl-devel=1.7.0=ha4b6fd6_2
+  - libegl=1.7.0=ha4b6fd6_3
+  - libegl-devel=1.7.0=ha4b6fd6_3
   - libev=4.33=hd590300_2
   - libevent=2.1.12=hf998b51_1
-  - libexpat=2.8.0=hecca717_0
+  - libexpat=2.8.1=hecca717_0
   - libffi=3.5.2=h3435931_0
   - libfreetype=2.14.3=ha770c72_0
   - libfreetype6=2.14.3=h73754d4_0
   - libgcc=15.2.0=he0feb66_19
   - libgcc-ng=15.2.0=h69a702a_19
   - libgfortran=15.2.0=h69a702a_19
   - libgfortran5=15.2.0=h68bc16d_19
-  - libgl=1.7.0=ha4b6fd6_2
-  - libgl-devel=1.7.0=ha4b6fd6_2
+  - libgl=1.7.0=ha4b6fd6_3
+  - libgl-devel=1.7.0=ha4b6fd6_3
   - libglib=2.88.1=h0d30a3d_2
-  - libglvnd=1.7.0=ha4b6fd6_2
-  - libglx=1.7.0=ha4b6fd6_2
-  - libglx-devel=1.7.0=ha4b6fd6_2
+  - libglvnd=1.7.0=ha4b6fd6_3
+  - libglx=1.7.0=ha4b6fd6_3
+  - libglx-devel=1.7.0=ha4b6fd6_3
   - libgomp=15.2.0=he0feb66_19
-  - libgoogle-cloud=3.3.0=h25dbb67_1
-  - libgoogle-cloud-storage=3.3.0=hdbdcf42_1
+  - libgoogle-cloud=3.5.0=h8d2ee43_1
+  - libgoogle-cloud-storage=3.5.0=hdbdcf42_1
   - libgrpc=1.78.1=h1d1128b_0
   - libiconv=1.18=h3b78370_2
   - libjpeg-turbo=3.1.4.1=hb03c661_0
-  - liblapack=3.11.0=7_h47877c9_openblas
-  - libllvm22=22.1.5=hf7376ad_1
+  - liblapack=3.11.0=8_h47877c9_openblas
+  - libllvm22=22.1.7=hf7376ad_0
   - liblzma=5.8.3=hb03c661_0
-  - libmpdec=4.0.0=hb03c661_1
   - libnghttp2=1.68.1=h877daf1_0
+  - libnsl=2.0.1=hb9d3cd8_1
   - libntlm=1.8=hb9d3cd8_0
   - libopenblas=0.3.33=pthreads_h94d23a6_0
-  - libopengl=1.7.0=ha4b6fd6_2
-  - libopentelemetry-cpp=1.26.0=h9692893_0
-  - libopentelemetry-cpp-headers=1.26.0=ha770c72_0
-  - libparquet=24.0.0=h7376487_1_cpu
+  - libopengl=1.7.0=ha4b6fd6_3
+  - libopentelemetry-cpp=1.27.0=h9692893_0
+  - libopentelemetry-cpp-headers=1.27.0=ha770c72_0
+  - libparquet=24.0.0=h7376487_4_cpu
   - libpciaccess=0.19=hb03c661_0
   - libpng=1.6.58=h421ea60_0
   - libpq=18.4=hd5a49e9_0
-  - libprotobuf=6.33.5=h2b00c02_0
+  - libprotobuf=6.33.5=h6eeba95_1
   - libre2-11=2025.11.05=h0dc7533_1
-  - libsodium=1.0.21=h280c20c_3
-  - libsqlite=3.53.1=h0c1763c_0
+  - libsodium=1.0.22=h280c20c_1
+  - libsqlite=3.53.2=h0c1763c_0
   - libssh2=1.11.1=hcf80075_0
   - libstdcxx=15.2.0=h934c35e_19
   - libstdcxx-ng=15.2.0=hdf11a46_19
   - libthrift=0.22.0=h7d032f7_2
   - libtiff=4.7.1=h9d88235_1
   - libutf8proc=2.11.3=hfe17d71_0
-  - libuuid=2.42=h5347b49_0
+  - libuuid=2.42.1=h5347b49_0
   - libvulkan-loader=1.4.341.0=h5279c79_0
   - libwebp-base=1.6.0=hd42ef1d_0
   - libxcb=1.17.0=h8a09558_0
   - libxcrypt=4.4.36=hd590300_1
-  - libxkbcommon=1.13.1=hca5e8e5_0
+  - libxkbcommon=1.13.2=hca5e8e5_0
   - libxml2=2.15.3=h49c6c72_0
   - libxml2-16=2.15.3=hca6bf5a_0
   - libxslt=1.1.43=h711ed8c_1
   - libzlib=1.3.2=h25fd6f3_2
   - lz4-c=1.10.0=h5888daf_1
   - markdown-it-py=4.2.0=pyhd8ed1ab_0
-  - markupsafe=3.0.3=py314h67df5f8_1
-  - matplotlib=3.10.9=py314hdafbbf9_0
-  - matplotlib-base=3.10.9=py314h1194b4b_0
+  - markupsafe=3.0.3=py312h8a5da7c_1
+  - matplotlib=3.10.9=py312h7900ff3_0
+  - matplotlib-base=3.10.9=py312he3d6523_0
   - matplotlib-inline=0.2.2=pyhd8ed1ab_0
   - mdurl=0.1.2=pyhd8ed1ab_1
   - munkres=1.1.4=pyhd8ed1ab_1
-  - narwhals=2.21.2=pyhcf101f3_0
+  - narwhals=2.22.1=pyhcf101f3_0
   - ncurses=6.6=hdb14827_0
   - nest-asyncio=1.6.0=pyhd8ed1ab_1
   - nlohmann_json=3.12.0=h54a6638_1
-  - numpy=2.4.5=py314h2b28147_0
   - openjpeg=2.5.4=h55fea9a_0
   - openldap=2.6.13=hbde042b_0
   - openssl=3.6.2=h35e630c_0
   - orc=2.3.0=h21090e2_0
   - packaging=26.2=pyhc364b38_0
-  - pandas=3.0.3=py314hb4ffadd_0
+  - pandas=3.0.3=py312h8ecdadd_0
   - parso=0.8.7=pyhcf101f3_0
   - patsy=1.0.2=pyhcf101f3_0
   - pcre2=10.47=haa7fec5_0
   - pexpect=4.9.0=pyhd8ed1ab_1
-  - pillow=12.2.0=py314h8ec4b1a_0
-  - pip=26.1.1=pyh145f28c_0
+  - pillow=12.2.0=py312h50c33e8_0
+  - pip=26.1.2=pyh8b19718_0
   - pixman=0.46.4=h54a6638_1
-  - platformdirs=4.9.6=pyhcf101f3_0
+  - platformdirs=4.10.0=pyhcf101f3_0
   - prometheus-cpp=1.3.0=ha5d0236_0
   - prompt-toolkit=3.0.52=pyha770c72_0
-  - protobuf=6.33.5=py314h61e7c5f_2
-  - psutil=7.2.2=py314h0f05182_0
+  - protobuf=6.33.5=py312ha7b3241_2
+  - psutil=7.2.2=py312h5253ce2_0
   - pthread-stubs=0.4=hb9d3cd8_1002
   - ptyprocess=0.7.0=pyhd8ed1ab_1
   - pure_eval=0.2.3=pyhd8ed1ab_1
-  - pyarrow=24.0.0=py314hdafbbf9_0
-  - pyarrow-core=24.0.0=py314h969be7f_0_cpu
+  - pyarrow=24.0.0=py312h7900ff3_0
+  - pyarrow-core=24.0.0=py312h2054cf2_0_cpu
   - pydeck=0.9.2=pyhd8ed1ab_0
   - pygments=2.20.0=pyhd8ed1ab_0
   - pyparsing=3.3.2=pyhcf101f3_0
-  - pyside6=6.11.1=py314h3987850_1
+  - pyside6=6.11.1=py312h50ac2ff_1
   - pysocks=1.7.1=pyha55dd90_7
-  - python=3.14.4=habeac84_100_cp314
+  - python=3.12.13=hd63d673_0_cpython
   - python-dateutil=2.9.0.post0=pyhe01879c_2
-  - python-gil=3.14.4=h4df99d1_100
-  - python-multipart=0.0.28=pyhcf101f3_0
-  - python_abi=3.14=8_cp314
-  - pyyaml=6.0.3=py314h67df5f8_1
-  - pyzmq=27.1.0=py312hda471dd_2
+  - python-gil=3.12.13=hd8ed1ab_0
+  - python-multipart=0.0.32=pyhcf101f3_0
+  - python_abi=3.12=8_cp312
+  - pyyaml=6.0.3=py312h8a5da7c_1
+  - pyzmq=27.1.0=py312hda471dd_3
   - qhull=2020.2=h434a139_5
-  - qt6-main=6.11.1=pl5321h16c4a6b_0
+  - qt6-main=6.11.1=pl5321h16c4a6b_1
   - re2=2025.11.05=h5301d42_1
   - readline=8.3=h853b02a_0
   - referencing=0.37.0=pyhcf101f3_0
   - requests=2.34.2=pyhcf101f3_0
   - rich=15.0.0=pyhcf101f3_0
-  - rpds-py=0.30.0=py314h2e6c369_0
-  - s2n=1.7.2=hc5a330e_1
-  - scipy=1.17.1=py314hf07bd8e_0
+  - rpds-py=2026.5.1=py312h192e038_0
+  - s2n=1.7.3=hc5a330e_0
   - seaborn=0.13.2=hd8ed1ab_3
   - seaborn-base=0.13.2=pyhd8ed1ab_3
   - setuptools=82.0.1=pyh332efcf_0
   - six=1.17.0=pyhe01879c_1
   - smmap=5.0.3=pyhd8ed1ab_0
   - snappy=1.2.2=h03e3b7b_1
   - stack_data=0.6.3=pyhd8ed1ab_1
-  - starlette=1.0.0=pyhcf101f3_0
-  - statsmodels=0.14.6=py314hc02f841_0
-  - streamlit=1.57.0=pyhd8ed1ab_0
+  - starlette=1.2.1=pyhcf101f3_0
+  - statsmodels=0.14.6=py312h4f23490_0
+  - streamlit=1.58.0=pyhd8ed1ab_0
   - tenacity=9.1.4=pyhcf101f3_0
   - tk=8.6.13=noxft_h366c992_103
   - toml=0.10.2=pyhcf101f3_3
-  - tornado=6.5.5=py314h5bd0f2a_0
-  - traitlets=5.15.0=pyhcf101f3_0
+  - tornado=6.5.6=py312h4c3975b_0
+  - traitlets=5.15.1=pyhcf101f3_0
   - typing-extensions=4.15.0=h396c80c_0
   - typing_extensions=4.15.0=pyhcf101f3_0
   - tzdata=2025c=hc9c84f9_1
-  - unicodedata2=17.0.1=py314h5bd0f2a_0
+  - unicodedata2=17.0.1=py312h4c3975b_0
   - urllib3=2.7.0=pyhd8ed1ab_0
-  - uvicorn=0.47.0=pyhc90fa1f_0
-  - watchdog=6.0.0=py314h9e666f3_3
+  - uvicorn=0.49.0=pyhc90fa1f_0
+  - watchdog=6.0.0=py312h20c3967_3
   - wayland=1.25.0=hd6090a7_0
   - wcwidth=0.7.0=pyhd8ed1ab_0
-  - websockets=16.0=py314h0f05182_1
+  - websockets=16.0=py312h5253ce2_1
   - wheel=0.47.0=pyhd8ed1ab_0
   - xarray=2026.4.0=pyhc364b38_0
   - xcb-util=0.4.1=h4f16b4b_2
@@ -275,18 +273,20 @@ dependencies:
   - xorg-libxdmcp=1.1.5=hb03c661_1
   - xorg-libxext=1.3.7=hb03c661_0
   - xorg-libxfixes=6.0.2=hb03c661_0
-  - xorg-libxi=1.8.2=hb9d3cd8_0
+  - xorg-libxi=1.8.3=hb03c661_0
   - xorg-libxrandr=1.5.5=hb03c661_0
   - xorg-libxrender=0.9.12=hb9d3cd8_0
   - xorg-libxtst=1.2.5=hb9d3cd8_3
   - xorg-libxxf86vm=1.1.7=hb03c661_0
   - xorg-xorgproto=2025.1=hb03c661_0
   - yaml=0.2.5=h280c20c_3
-  - zeromq=4.3.5=h41580af_10
-  - zipp=3.23.1=pyhcf101f3_0
+  - zeromq=4.3.5=h09e67af_11
+  - zipp=4.1.0=pyhcf101f3_0
   - zlib=1.3.2=h25fd6f3_2
   - zlib-ng=2.3.3=hceb46e0_1
   - zstd=1.5.7=hb78ec9c_6
   - pip:
+      - numpy==1.26.4
       - -e ../../..
+      - scipy==1.13.1
 name: openflash-openflash-on-branch

analysis/convergence-results.ipynb

@@ -2,7 +2,7 @@ name: openflash-openflash-on-branch
 channels:
   - conda-forge
 dependencies:
-  - python
+  - python=3.12
   - pip
   - setuptools
   - wheel

analysis/environment-branch.yml

@@ -11,8 +11,8 @@
      "output_type": "stream",
      "text": [
       "<class 'module'>\n",
-      "['/home/becca/Documents/git/OpenFLASH/package/src/openflash']\n",
-      "/home/becca/Documents/git/OpenFLASH/package/src/openflash/__init__.py\n",
+      "['/home/becca/Documents/git/MDOcean-worktrees/review/mdocean/simulation/modules/OpenFLASH/package/src/openflash']\n",
+      "/home/becca/Documents/git/MDOcean-worktrees/review/mdocean/simulation/modules/OpenFLASH/package/src/openflash/__init__.py\n",
       "OpenFLASH modules imported successfully!\n",
       "#CC79A7\n"
      ]
@@ -623,7 +623,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/tmp/ipykernel_505275/3246268765.py:67: MatplotlibDeprecationWarning: Since Matplotlib 3.10 indicate_inset_[zoom] returns a single InsetIndicator artist with a rectangle property and a connectors property.  From 3.12 it will no longer be possible to unpack the return value into two elements.\n",
+      "/tmp/ipykernel_1472529/3246268765.py:67: MatplotlibDeprecationWarning: Since Matplotlib 3.10 indicate_inset_[zoom] returns a single InsetIndicator artist with a rectangle property and a connectors property.  From 3.12 it will no longer be possible to unpack the return value into two elements.\n",
       "  rect, connectors = axs[0, i].indicate_inset_zoom(axs[1, i], edgecolor=\"black\", alpha=1.0, linestyle='-', linewidth=0.8)\n"
      ]
     },