Jfm dissertation

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

@@ -3,46 +3,46 @@ channels:
   - defaults
 dependencies:
   - _openmp_mutex=4.5=20_gnu
-  - _python_abi3_support=1.0=hd8ed1ab_2
-  - 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
+  - _python_abi3_support=1.0=hd8ed1ab_3
+  - alsa-lib=1.2.16.1=hb03c661_0
+  - altair=6.2.2=pyhd8ed1ab_0
+  - anyio=4.14.2=pyhcf101f3_0
+  - asttokens=3.0.2=pyhd8ed1ab_0
   - attrs=26.1.0=pyhcf101f3_0
-  - aws-c-auth=0.10.1=ha62d5e7_3
-  - aws-c-cal=0.9.13=h2c9d079_1
-  - aws-c-common=0.12.6=hb03c661_0
-  - 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=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
-  - aws-checksums=0.2.10=h8b1a151_0
-  - aws-crt-cpp=0.38.3=h745e52d_1
-  - 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=12.17.0=hf824e48_1
-  - azure-storage-common-cpp=12.13.0=ha7a2c86_0
-  - azure-storage-files-datalake-cpp=12.15.0=h1e5b466_0
-  - backports.zstd=1.5.0=py312h90b7ffd_0
+  - aws-c-auth=0.10.4=hb7a77c6_1
+  - aws-c-cal=0.9.14=h2aa3ae6_4
+  - aws-c-common=0.14.2=hb03c661_0
+  - aws-c-compression=0.3.2=h720e601_4
+  - aws-c-event-stream=0.7.1=h6ffeea8_4
+  - aws-c-http=0.11.0=h38ae05a_4
+  - aws-c-io=0.27.3=h6f4d18d_1
+  - aws-c-mqtt=0.16.0=h21f4ec5_2
+  - aws-c-s3=0.12.8=h46fcd08_1
+  - aws-c-sdkutils=0.2.7=h720e601_2
+  - aws-checksums=0.2.10=h720e601_4
+  - aws-crt-cpp=0.40.1=h102d43b_3
+  - aws-sdk-cpp=1.11.833=hc7390e0_9
+  - azure-core-cpp=1.16.3=h206d751_0
+  - azure-identity-cpp=1.13.3=h71f81a8_2
+  - azure-storage-blobs-cpp=12.18.0=h74b55db_1
+  - azure-storage-common-cpp=12.14.0=hf596fc9_1
+  - azure-storage-files-datalake-cpp=12.16.0=h1f05bef_1
+  - backports.zstd=1.6.0=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=py312hdb49522_1
   - bzip2=1.0.8=hda65f42_9
-  - c-ares=1.34.6=hb03c661_0
-  - ca-certificates=2026.5.20=hbd8a1cb_0
-  - cached-property=1.5.2=hd8ed1ab_1
-  - cached_property=1.5.2=pyha770c72_1
+  - c-ares=1.34.8=hb03c661_0
+  - ca-certificates=2026.6.17=hbd8a1cb_0
+  - cached-property=1.5.2=hd8ed1ab_2
+  - cached_property=1.5.2=pyha770c72_2
   - cachetools=7.1.4=pyhd8ed1ab_0
   - cairo=1.18.4=he90730b_1
   - capytaine=2.3.1=py312h6a55c13_0
-  - certifi=2026.5.20=pyhd8ed1ab_0
-  - charset-normalizer=3.4.7=pyhd8ed1ab_0
-  - click=8.4.1=pyhc90fa1f_0
+  - certifi=2026.6.17=pyhd8ed1ab_0
+  - charset-normalizer=3.4.9=pyhd8ed1ab_0
+  - click=8.4.2=pyhc90fa1f_0
   - comm=0.2.3=pyhe01879c_0
   - contourpy=1.3.3=py312h0a2e395_4
   - cpython=3.12.13=py312hd8ed1ab_0
@@ -63,63 +63,65 @@ dependencies:
   - fonts-conda-forge=1=hc364b38_1
   - fonttools=4.63.0=py312h8a5da7c_0
   - freetype=2.14.3=ha770c72_0
-  - gflags=2.2.2=h5888daf_1005
+  - fribidi=1.0.16=hb03c661_0
+  - gflags=2.3.0=h54a6638_0
   - gitdb=4.0.12=pyhd8ed1ab_0
-  - gitpython=3.1.50=pyhd8ed1ab_0
-  - glog=0.7.1=hbabe93e_0
+  - gitpython=3.1.52=pyhd8ed1ab_0
+  - glog=0.7.1=hb7133d2_1
   - 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_py312ha829cd9_102
-  - harfbuzz=14.2.1=h6083320_0
-  - hdf5=2.1.0=nompi_h87a9417_105
-  - hpack=4.1.0=pyhd8ed1ab_0
+  - harfbuzz=14.2.1=ha770c72_1
+  - hdf5=2.1.0=nompi_h654f344_110
+  - hpack=4.2.0=pyhd8ed1ab_0
   - httptools=0.8.0=py312h4c3975b_0
   - hyperframe=6.1.0=pyhd8ed1ab_0
   - icu=78.3=h33c6efd_0
-  - idna=3.17=pyhcf101f3_0
+  - idna=3.18=pyhcf101f3_0
   - importlib-metadata=9.0.0=pyhcf101f3_0
-  - ipykernel=7.2.0=pyha191276_1
-  - ipython=9.14.1=pyh53cf698_0
+  - ipykernel=7.3.0=pyha191276_0
+  - ipython=9.15.0=pyh53cf698_0
   - ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
   - itsdangerous=2.2.0=pyhd8ed1ab_1
-  - jedi=0.19.2=pyhd8ed1ab_1
+  - jedi=0.20.0=pyhcf101f3_0
   - jinja2=3.1.6=pyhcf101f3_1
   - jsonschema=4.26.0=pyhcf101f3_0
   - jsonschema-specifications=2025.9.1=pyhcf101f3_0
-  - jupyter_client=8.9.0=pyhcf101f3_0
+  - jupyter_client=8.9.1=pyhcf101f3_0
   - jupyter_core=5.9.1=pyhc90fa1f_0
   - keyutils=1.6.3=hb9d3cd8_0
   - kiwisolver=1.5.0=py312h0a2e395_0
-  - krb5=1.22.2=ha1258a1_0
+  - krb5=1.22.2=hbde042b_1
   - lcms2=2.19.1=h0c24ade_1
-  - ld_impl_linux-64=2.45.1=default_hbd61a6d_102
+  - ld_impl_linux-64=2.46.1=default_hbd61a6d_102
   - lerc=4.1.0=hdb68285_0
-  - libabseil=20260107.1=cxx17_h7b12aa8_0
+  - libabseil=20260526.0=cxx17_h7b12aa8_1
   - libaec=1.1.5=h088129d_0
-  - 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
+  - libarrow=24.0.0=hcdbc531_10_cpu
+  - libarrow-acero=24.0.0=h635bf11_10_cpu
+  - libarrow-compute=24.0.0=h53684a4_10_cpu
+  - libarrow-dataset=24.0.0=h635bf11_10_cpu
+  - libarrow-substrait=24.0.0=h66fbfdd_10_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=8_h0358290_openblas
-  - libclang13=22.1.7=default_h746c552_1
+  - libclang-cpp22.1=22.1.8=default_h6c227bf_3
+  - libclang13=22.1.8=default_h9692865_3
   - libcrc32c=1.1.2=h9c3ff4c_0
   - libcups=2.3.3=h7a8fb5f_6
-  - libcurl=8.20.0=hcf29cc6_0
+  - libcurl=8.21.0=hae6b9f4_2
   - libdeflate=1.25=h17f619e_0
   - libdrm=2.4.127=hb03c661_0
   - libedit=3.1.20250104=pl5321h7949ede_0
   - 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=2.8.1=hecca717_0
+  - libexpat=2.8.1=hecca717_1
   - libffi=3.5.2=h3435931_0
   - libfreetype=2.14.3=ha770c72_0
   - libfreetype6=2.14.3=h73754d4_0
@@ -129,41 +131,45 @@ dependencies:
   - libgfortran5=15.2.0=h68bc16d_19
   - libgl=1.7.0=ha4b6fd6_3
   - libgl-devel=1.7.0=ha4b6fd6_3
-  - libglib=2.88.1=h0d30a3d_2
+  - libglib=2.88.2=h0d30a3d_0
   - 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=3.5.0=h8d2ee43_1
-  - libgoogle-cloud-storage=3.5.0=hdbdcf42_1
-  - libgrpc=1.78.1=h1d1128b_0
+  - libgoogle-cloud=3.6.0=hbc29df5_1
+  - libgoogle-cloud-storage=3.6.0=hdbdcf42_1
+  - libgrpc=1.82.1=h792040b_0
+  - libharfbuzz=14.2.1=h17a8019_1
+  - libharfbuzz-devel=14.2.1=h17a8019_1
   - libiconv=1.18=h3b78370_2
-  - libjpeg-turbo=3.1.4.1=hb03c661_0
+  - libjpeg-turbo=3.2.0=hb03c661_0
   - liblapack=3.11.0=8_h47877c9_openblas
-  - libllvm22=22.1.7=hf7376ad_0
+  - libllvm22=22.1.8=hf7376ad_1
   - liblzma=5.8.3=hb03c661_0
   - 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_3
-  - libopentelemetry-cpp=1.27.0=h9692893_0
-  - libopentelemetry-cpp-headers=1.27.0=ha770c72_0
-  - libparquet=24.0.0=h7376487_4_cpu
+  - libopentelemetry-cpp=1.27.0=h3133023_1
+  - libopentelemetry-cpp-headers=1.27.0=ha770c72_1
+  - libparquet=24.0.0=h7376487_10_cpu
   - libpciaccess=0.19=hb03c661_0
   - libpng=1.6.58=h421ea60_0
-  - libpq=18.4=hd5a49e9_0
-  - libprotobuf=6.33.5=h6eeba95_1
-  - libre2-11=2025.11.05=h0dc7533_1
+  - libpq=18.4=hd5a49e9_1
+  - libprotobuf=7.35.1=h2840a7c_2
+  - libpsl=0.22.0=h49b2146_1
+  - libraqm=0.10.5=h6406941_1
+  - libre2-11=2025.11.05=h60473fc_2
   - libsodium=1.0.22=h280c20c_1
-  - libsqlite=3.53.2=h0c1763c_0
+  - libsqlite=3.53.3=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
+  - libtiff=4.7.2=h9d88235_0
   - libutf8proc=2.11.3=hfe17d71_0
-  - libuuid=2.42.1=h5347b49_0
+  - libuuid=2.42.2=h5347b49_0
   - libvulkan-loader=1.4.341.0=h5279c79_0
   - libwebp-base=1.6.0=hd42ef1d_0
   - libxcb=1.17.0=h8a09558_0
@@ -176,39 +182,39 @@ dependencies:
   - lz4-c=1.10.0=h5888daf_1
   - markdown-it-py=4.2.0=pyhd8ed1ab_0
   - markupsafe=3.0.3=py312h8a5da7c_1
-  - matplotlib=3.10.9=py312h7900ff3_0
-  - matplotlib-base=3.10.9=py312he3d6523_0
+  - matplotlib=3.11.0=py312h7900ff3_1
+  - matplotlib-base=3.11.0=py312hc1765e9_1
   - matplotlib-inline=0.2.2=pyhd8ed1ab_0
   - mdurl=0.1.2=pyhd8ed1ab_1
   - munkres=1.1.4=pyhd8ed1ab_1
-  - narwhals=2.22.1=pyhcf101f3_0
+  - narwhals=2.24.0=pyhcf101f3_0
   - ncurses=6.6=hdb14827_0
-  - nest-asyncio=1.6.0=pyhd8ed1ab_1
+  - nest-asyncio2=1.7.2=pyhcf101f3_0
   - nlohmann_json=3.12.0=h54a6638_1
   - openjpeg=2.5.4=h55fea9a_0
   - openldap=2.6.13=hbde042b_0
-  - openssl=3.6.2=h35e630c_0
-  - orc=2.3.0=h21090e2_0
+  - openssl=3.6.3=h35e630c_0
+  - orc=2.3.0=h443056b_2
   - packaging=26.2=pyhc364b38_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=py312h50c33e8_0
+  - pillow=12.3.0=py312h50c33e8_0
   - pip=26.1.2=pyh8b19718_0
-  - pixman=0.46.4=h54a6638_1
-  - platformdirs=4.10.0=pyhcf101f3_0
+  - pixman=0.46.4=h54a6638_2
+  - platformdirs=4.10.1=pyhcf101f3_0
   - prometheus-cpp=1.3.0=ha5d0236_0
   - prompt-toolkit=3.0.52=pyha770c72_0
-  - protobuf=6.33.5=py312ha7b3241_2
+  - protobuf=7.35.1=py312h7bd0bee_1
   - 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=py312h7900ff3_0
   - pyarrow-core=24.0.0=py312h2054cf2_0_cpu
-  - pydeck=0.9.2=pyhd8ed1ab_0
+  - pydeck=0.9.3=pyhd8ed1ab_0
   - pygments=2.20.0=pyhd8ed1ab_0
   - pyparsing=3.3.2=pyhcf101f3_0
   - pyside6=6.11.1=py312h50ac2ff_1
@@ -222,47 +228,47 @@ dependencies:
   - pyzmq=27.1.0=py312hda471dd_3
   - qhull=2020.2=h434a139_5
   - qt6-main=6.11.1=pl5321h16c4a6b_1
-  - re2=2025.11.05=h5301d42_1
+  - re2=2025.11.05=h94463f1_2
   - 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=2026.5.1=py312h192e038_0
-  - s2n=1.7.3=hc5a330e_0
+  - rpds-py=2026.6.3=py312h192e038_0
+  - s2n=1.7.5=h7e3ee7f_1
   - seaborn=0.13.2=hd8ed1ab_3
   - seaborn-base=0.13.2=pyhd8ed1ab_3
-  - setuptools=82.0.1=pyh332efcf_0
+  - setuptools=83.0.0=pyh332efcf_0
   - six=1.17.0=pyhe01879c_1
-  - smmap=5.0.3=pyhd8ed1ab_0
+  - smmap=5.0.3=pyhcf101f3_1
   - snappy=1.2.2=h03e3b7b_1
   - stack_data=0.6.3=pyhd8ed1ab_1
-  - starlette=1.2.1=pyhcf101f3_0
+  - starlette=1.3.1=pyhcf101f3_0
   - statsmodels=0.14.6=py312h4f23490_0
-  - streamlit=1.58.0=pyhd8ed1ab_0
+  - streamlit=1.59.2=pyhd8ed1ab_0
   - tenacity=9.1.4=pyhcf101f3_0
-  - tk=8.6.13=noxft_h366c992_103
+  - tk=8.6.13=noxft_hd70dff1_3
   - toml=0.10.2=pyhcf101f3_3
-  - tornado=6.5.6=py312h4c3975b_0
+  - tornado=6.5.7=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
+  - typing-extensions=4.16.0=h69aa097_0
+  - typing_extensions=4.16.0=pyhcf101f3_0
+  - tzdata=2026c=h151e31d_0
   - unicodedata2=17.0.1=py312h4c3975b_0
   - urllib3=2.7.0=pyhd8ed1ab_0
-  - uvicorn=0.49.0=pyhc90fa1f_0
+  - uvicorn=0.51.0=pyhc90fa1f_0
   - watchdog=6.0.0=py312h20c3967_3
-  - wayland=1.25.0=hd6090a7_0
-  - wcwidth=0.7.0=pyhd8ed1ab_0
-  - websockets=16.0=py312h5253ce2_1
+  - wayland=1.26.0=hd6090a7_0
+  - wcwidth=0.8.2=pyhd8ed1ab_0
+  - websockets=16.1.1=py312h574c966_0
   - wheel=0.47.0=pyhd8ed1ab_0
-  - xarray=2026.4.0=pyhc364b38_0
+  - xarray=2026.7.0=pyhc364b38_0
   - xcb-util=0.4.1=h4f16b4b_2
   - xcb-util-cursor=0.1.6=hb03c661_0
   - xcb-util-image=0.4.0=hb711507_2
   - xcb-util-keysyms=0.4.1=hb711507_0
   - xcb-util-renderutil=0.3.10=hb711507_0
   - xcb-util-wm=0.4.2=hb711507_0
-  - xkeyboard-config=2.47=hb03c661_0
+  - xkeyboard-config=2.48=h280c20c_0
   - xorg-libice=1.1.2=hb9d3cd8_0
   - xorg-libsm=1.2.6=he73a12e_0
   - xorg-libx11=1.8.13=he1eb515_0

.dvc/config

@@ -2,5 +2,4 @@
     remote = calkit
     autostage = true
 ['remote "calkit"']
-    url = https://api.calkit.io/projects/symbiotic-engineering/openflash/dvc
-    auth = custom
+    url = ck://symbiotic-engineering/openflash

.github/workflows/pr-tagging.yml

@@ -44,7 +44,7 @@ jobs:
           rc_tag="${{ steps.compute_base.outputs.base }}rc${{ github.event.pull_request.number }}"
           if git rev-parse "$rc_tag" >/dev/null 2>&1; then
             devN=$(git rev-list --count $rc_tag..HEAD)
-            rc_dev_tag="${rc_tag}dev${devN}"
+            rc_dev_tag="${rc_tag}.dev${devN}"
           else
             rc_dev_tag="${rc_tag}"
           fi

.gitmodules

@@ -1,7 +1,4 @@
-[submodule "src/sea-lab-utils"]
-	path = src/sea-lab-utils
-	url = https://github.com/symbiotic-engineering/sea-lab-utils.git
-[submodule "sea-lab-utils"]
-	path = sea-lab-utils
+[submodule "analysis/sea-lab-utils"]
+	path = analysis/sea-lab-utils
 	url = https://github.com/symbiotic-engineering/sea-lab-utils.git
 	branch = main

analysis/convergence-results.ipynb

@@ -13,13 +13,7 @@
       "<class 'module'>\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"
-     ]
-    },
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
+      "OpenFLASH modules imported successfully!\n",
       "#CC79A7\n"
      ]
     }
@@ -62,7 +56,7 @@
     "\n",
     "dir_path_1_str = str((HERE / \"..\" / \"dev\" / \"python\" / \"convergence-study\"))\n",
     "dir_path_2_str = str((HERE / \"..\" / \"dev\" / \"python\"))\n",
-    "dir_path_3_str = str((HERE / \"..\" / \"sea-lab-utils\").resolve())\n",
+    "dir_path_3_str = str((HERE / \"sea-lab-utils\").resolve())\n",
     "dir_path_4_str = str((HERE / \"..\" / \"dev\" / \"python\" / \"convergence-study\" / \"prediction\"))\n",
     "\n",
     "data_1_str = str((HERE / \"..\" / \"dev\" / \"python\" / \"convergence-study\" / \"i-region-convergence\" / \"middle-region\" / \"data\" / \"predetermined-4.pkl\"))\n",