diff --git a/.Dockerfile b/.Dockerfile new file mode 100644 index 00000000..9588118c --- /dev/null +++ b/.Dockerfile @@ -0,0 +1,79 @@ +FROM condaforge/miniforge3:latest AS miniconda + +FROM texlive/texlive:latest-full + +COPY --from=miniconda /opt/conda /opt/conda + +ENV PATH=/opt/conda/bin:$PATH + +COPY analysis/environment-branch.yml /tmp/analysis/environment-branch.yml +COPY pyproject.toml /tmp/pyproject.toml +COPY package/src /tmp/package/src +COPY README.md /tmp/README.md +COPY LICENSE /tmp/LICENSE +COPY CITATION.cff /tmp/CITATION.cff + +# Build the Conda environment in three phases to work around the absence of +# libquadmath on aarch64: no native libquadmath package exists for arm64, yet +# gfortran still emits -lquadmath, which breaks capytaine's from-source build +# (capytaine ships no arm64 wheel). +# +# 1. Create the environment with the Conda packages only (strip the pip +# section), which installs the compiler toolchain. +RUN sed '/^[[:space:]]*- pip:/,$d' /tmp/analysis/environment-branch.yml \ + > /tmp/analysis/environment-nopip.yml \ + && mamba env create \ + -n openflash.openflash-on-branch-tex \ + -f /tmp/analysis/environment-nopip.yml + +# 2. If libquadmath is missing (i.e. on aarch64), drop an empty stub into the +# env so the linker is satisfied. capytaine references no quadmath symbols, +# and Conda links extensions with an rpath to $CONDA_PREFIX/lib, so the stub +# resolves at both link and run time. +RUN mamba run -n openflash.openflash-on-branch-tex bash -c '\ + if [ ! -e "$CONDA_PREFIX/lib/libquadmath.so" ]; then \ + echo "void __quadmath_stub(void){}" > /tmp/quadmath_stub.c \ + && "$CC" -shared -fPIC -Wl,-soname,libquadmath.so.0 \ + -o "$CONDA_PREFIX/lib/libquadmath.so.0" /tmp/quadmath_stub.c \ + && ln -sf libquadmath.so.0 "$CONDA_PREFIX/lib/libquadmath.so" \ + && rm /tmp/quadmath_stub.c; \ + fi' + +# 3. Install the pip packages; capytaine compiles its Fortran extension against +# the stub. +RUN mamba env update \ + -n openflash.openflash-on-branch-tex \ + -f /tmp/analysis/environment-branch.yml + +ENV PATH=/opt/conda/envs/openflash.openflash-on-branch-tex/bin:$PATH + +ENV PYTHONUNBUFFERED=1 +ENV PIP_DISABLE_PIP_VERSION_CHECK=1 +ENV PIP_NO_CACHE_DIR=1 + +RUN useradd -m openflash + +RUN mkdir -p /workspace \ + && chown -R openflash:openflash /workspace + +RUN mkdir -p /home/openflash/.ipython /home/openflash/.cache /home/openflash/.config \ + && chown -R openflash:openflash /home/openflash + +RUN mkdir -p /tmp/home/.local /tmp/home/.ipython /tmp/home/.cache /tmp/home/.config \ + /tmp/ipython /tmp/matplotlib /tmp/cache /tmp/jupyter \ + && chmod -R 777 /tmp/home /tmp/ipython /tmp/matplotlib /tmp/cache /tmp/jupyter + +RUN python -m ipykernel install \ + --prefix=/opt/conda/envs/openflash.openflash-on-branch-tex + +USER openflash +WORKDIR /workspace + +ENV HOME=/tmp/home +ENV IPYTHONDIR=/tmp/home/.ipython +ENV XDG_CACHE_HOME=/tmp/home/.cache +ENV XDG_CONFIG_HOME=/tmp/home/.config +ENV MPLCONFIGDIR=/tmp/matplotlib +ENV JUPYTER_DATA_DIR=/tmp/jupyter + +CMD ["bash"] diff --git a/.calkit/env-locks/openflash-on-branch-tex/amd64.json b/.calkit/env-locks/openflash-on-branch-tex/amd64.json new file mode 100644 index 00000000..7ce393aa --- /dev/null +++ b/.calkit/env-locks/openflash-on-branch-tex/amd64.json @@ -0,0 +1,47 @@ +{ + "RepoTags": [ + "openflash-on-branch-tex" + ], + "RepoDigests": [], + "Architecture": "amd64", + "Os": "linux", + "RootFS": { + "Type": "layers", + "Layers": [ + "sha256:4d416f5802b27e35b72bc7cf23b9a0135b5810f321b33213976f7b6e603004e2", + "sha256:1d70e638e6fc47166ab7f99695374817b8bd1a4f76f6855add9723e5d4600ad8", + "sha256:f6abbfcb16d15267190636a64d129388c1017c63e0ba88d6645cc7e2ba96cf71", + "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef", + "sha256:084a300d9aa225c7c8dddcf1f4b52943962a71f5293bfe315fb45b4979b26d98", + "sha256:94341c5a851fa791ecf9496f0d4b80d81d358681972644d599b088683ea29f60", + "sha256:64a8268e4aa9457c8301cc85de712ae83298f3cb67bd9e4e69a8b687e854963b", + "sha256:da4b7294439259ab23e03a525267ddfb3fda5dcf90094ca1657a402fcefdc76a", + "sha256:498fe8fca7f3a287f0e2d91505c4e2576f243fcf18175b0ee0b9a1bc64f8d340", + "sha256:0d1f4606c616748fae54b09ff503ad65a71d78f2fcd5b021fe0687620df8ea2f", + "sha256:081d458749d39610b2a48b06865f1dc02c33881b2eef43d92340bd1d9f7baf05", + "sha256:dd2cbea58177687881831968274f139b28a824be1b62d511d1dafa6bcf07c7bb", + "sha256:76b11e3c8b4ed6ba20c6f9c9d2a730fc43dff6dee005a328a2c9d50478bfd2ed", + "sha256:09d66d49f79d73649ee359f0e779424bf1ad2ae39e0cf6a2ca549ead8c72ea7b", + "sha256:5f0703082b86eda911eeeb51dad3bad9edb031dd036f7c2ff1741a6f9a8d5f48", + "sha256:57c7c0264d0699c6e96bff84a05897a7ec2f2858c59f5027c6d1a9dfe99ddb66", + "sha256:7000b23019a134e7b1d0bdb2fb2e5bf2117feb6bc3b660d65388c74df7c3a241", + "sha256:4c92e5e694696c39f1fbc9404a87c32e8fe8fec5f726bddde89911af56e8844a", + "sha256:69df376923a6706959fc106e1baeb3c4b1c3d41df6a090ef79046511490c4dde", + "sha256:5397c133875e96b819e46b889469d637e3821052f15f209b1ccb55369b8ac897", + "sha256:5ad73e56b66b7cf5f680a53edaf1188f76cfa8cc5f2bb5bc56b77d1d4622250c", + "sha256:48a6ff8201487f933d23983f02a3bdf238a1f0fae8fbfab065728b5b8848227e", + "sha256:957ef72c745080f61639ca84baaefe26f25d857b9e37a0caa98946f02cd033c3", + "sha256:033aa7700526dc25d2e8c8f2b4313a7d5c77f6ed154f0d02d3445ed75f2a9b1b", + "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef" + ] + }, + "DockerfileMD5": "8930fae8c7fef0feb3311446fba042be", + "DepsMD5s": { + "analysis/environment-branch.yml": "4be82009aeae596a40be0248e15d2f2f", + "package/src": "fb1d513041f63ba9e0fd9703f43b59ac", + "pyproject.toml": "c036c82893293e1fa9eae68f5731d451", + "README.md": "d4ecb4e9de12fcfac2094778ad29fbf5", + "LICENSE": "313afdf541ca2b338eaa77f1b698333c", + "CITATION.cff": "0ee89a93fb410b3526806206205500af" + } +} \ No newline at end of file diff --git a/.calkit/env-locks/openflash-on-branch/linux-64.yml b/.calkit/env-locks/openflash-on-branch/linux-64.yml index 44123a24..96105867 100644 --- a/.calkit/env-locks/openflash-on-branch/linux-64.yml +++ b/.calkit/env-locks/openflash-on-branch/linux-64.yml @@ -1,3 +1,4 @@ +name: openflash-openflash-on-branch channels: - conda-forge - defaults @@ -289,4 +290,3 @@ dependencies: - numpy==1.26.4 - -e ../../.. - scipy==1.13.1 -name: openflash-openflash-on-branch diff --git a/.calkit/env-locks/openflash-on-branch/osx-arm64.yml b/.calkit/env-locks/openflash-on-branch/osx-arm64.yml new file mode 100644 index 00000000..91d142f7 --- /dev/null +++ b/.calkit/env-locks/openflash-on-branch/osx-arm64.yml @@ -0,0 +1,221 @@ +name: openflash-openflash-on-branch +channels: + - conda-forge +dependencies: + - _openmp_mutex=4.5=7_kmp_llvm + - _python_abi3_support=1.0=hd8ed1ab_2 + - altair=6.1.0=pyhd8ed1ab_0 + - anyio=4.13.0=pyhcf101f3_0 + - appnope=0.1.4=pyhd8ed1ab_1 + - asttokens=3.0.1=pyhd8ed1ab_0 + - attrs=26.1.0=pyhcf101f3_0 + - aws-c-auth=0.10.1=ha7d4cc1_3 + - aws-c-cal=0.9.13=h6ee9776_1 + - aws-c-common=0.12.6=hc919400_0 + - aws-c-compression=0.3.2=h3e7f9b5_0 + - aws-c-event-stream=0.7.0=h351c84d_0 + - aws-c-http=0.10.13=h95cdebe_0 + - aws-c-io=0.26.3=h4137820_1 + - aws-c-mqtt=0.15.2=h8860bc9_2 + - aws-c-s3=0.12.2=h07b101a_1 + - aws-c-sdkutils=0.2.4=h16f91aa_4 + - aws-checksums=0.2.10=h3e7f9b5_0 + - aws-crt-cpp=0.38.3=hba17502_1 + - aws-sdk-cpp=1.11.747=h30a6df1_4 + - azure-core-cpp=1.16.2=he5ae378_0 + - azure-identity-cpp=1.13.3=h810541e_1 + - azure-storage-blobs-cpp=12.16.0=hc57151b_1 + - azure-storage-common-cpp=12.12.0=he467506_1 + - azure-storage-files-datalake-cpp=12.14.0=hf8a9d22_1 + - backports.zstd=1.4.0=py314h680f03e_0 + - blinker=1.9.0=pyhff2d567_0 + - brotli=1.2.0=h7d5ae5b_1 + - brotli-bin=1.2.0=hc919400_1 + - brotli-python=1.2.0=py314h3daef5d_1 + - bzip2=1.0.8=hd037594_9 + - c-ares=1.34.6=hc919400_0 + - ca-certificates=2026.4.22=hbd8a1cb_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cachetools=7.1.1=pyhd8ed1ab_0 + - certifi=2026.4.22=pyhd8ed1ab_0 + - charset-normalizer=3.4.7=pyhd8ed1ab_0 + - click=8.3.3=pyhc90fa1f_0 + - comm=0.2.3=pyhe01879c_0 + - contourpy=1.3.3=py314hf8a3a22_4 + - cpython=3.14.4=py314hd8ed1ab_100 + - cycler=0.12.1=pyhcf101f3_2 + - debugpy=1.8.20=py314he609de1_0 + - decorator=5.2.1=pyhd8ed1ab_0 + - exceptiongroup=1.3.1=pyhd8ed1ab_0 + - executing=2.2.1=pyhd8ed1ab_0 + - fonttools=4.62.1=pyh7db6752_0 + - freetype=2.14.3=hce30654_0 + - gflags=2.2.2=hf9b8971_1005 + - gitdb=4.0.12=pyhd8ed1ab_0 + - gitpython=3.1.50=pyhd8ed1ab_0 + - glog=0.7.1=heb240a5_0 + - h11=0.16.0=pyhcf101f3_1 + - h2=4.3.0=pyhcf101f3_0 + - h5netcdf=1.8.1=pyhd8ed1ab_0 + - h5py=3.16.0=nompi_py314h658a3ac_102 + - hdf5=2.1.0=nompi_he586413_105 + - hpack=4.1.0=pyhd8ed1ab_0 + - httptools=0.7.1=py314h0612a62_1 + - hyperframe=6.1.0=pyhd8ed1ab_0 + - idna=3.13=pyhcf101f3_0 + - importlib-metadata=8.8.0=pyhcf101f3_0 + - ipykernel=7.2.0=pyh5552912_1 + - ipython=9.13.0=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_core=5.9.1=pyhc90fa1f_0 + - kiwisolver=1.5.0=py314hf8a3a22_0 + - krb5=1.22.2=h385eeb1_0 + - lcms2=2.19.1=hdfa7624_0 + - lerc=4.1.0=h1eee2c3_0 + - libabseil=20260107.1=cxx17_h2062a1b_0 + - libaec=1.1.5=h8664d51_0 + - libarrow=24.0.0=h37fbca7_1_cpu + - libarrow-acero=24.0.0=hee8fe31_1_cpu + - libarrow-compute=24.0.0=h3b6a98a_1_cpu + - libarrow-dataset=24.0.0=hee8fe31_1_cpu + - libarrow-substrait=24.0.0=h05be00f_1_cpu + - libblas=3.11.0=6_h51639a9_openblas + - libbrotlicommon=1.2.0=hc919400_1 + - libbrotlidec=1.2.0=hc919400_1 + - libbrotlienc=1.2.0=hc919400_1 + - libcblas=3.11.0=6_hb0561ab_openblas + - libcrc32c=1.1.2=hbdafb3b_0 + - libcurl=8.20.0=hd5a2499_0 + - libcxx=22.1.5=h55c6f16_1 + - libdeflate=1.25=hc11a715_0 + - libedit=3.1.20250104=pl5321hafb1f1b_0 + - libev=4.33=h93a5062_2 + - libevent=2.1.12=h2757513_1 + - libexpat=2.8.0=hf6b4638_0 + - libffi=3.5.2=hcf2aa1b_0 + - libfreetype=2.14.3=hce30654_0 + - libfreetype6=2.14.3=hdfa99f5_0 + - libgcc=15.2.0=hcbb3090_19 + - libgfortran=15.2.0=h07b0088_19 + - libgfortran5=15.2.0=hdae7583_19 + - libgoogle-cloud=3.3.0=he41eb1d_1 + - libgoogle-cloud-storage=3.3.0=ha114238_1 + - libgrpc=1.78.1=h3e3f78d_0 + - libiconv=1.18=h23cfdf5_2 + - libjpeg-turbo=3.1.4.1=h84a0fba_0 + - liblapack=3.11.0=6_hd9741b5_openblas + - liblzma=5.8.3=h8088a28_0 + - libmpdec=4.0.0=h84a0fba_1 + - libnghttp2=1.68.1=h8f3e76b_0 + - libopenblas=0.3.32=openmp_he657e61_0 + - libopentelemetry-cpp=1.26.0=h08d5cc3_0 + - libopentelemetry-cpp-headers=1.26.0=hce30654_0 + - libparquet=24.0.0=h16c0493_1_cpu + - libpng=1.6.58=h132b30e_0 + - libprotobuf=6.33.5=h4a5acfd_0 + - libre2-11=2025.11.05=h4c27e2a_1 + - libsodium=1.0.21=h1a92334_3 + - libsqlite=3.53.1=h1b79a29_0 + - libssh2=1.11.1=h1590b86_0 + - libthrift=0.22.0=h1fb9c8a_2 + - libtiff=4.7.1=h4030677_1 + - libutf8proc=2.11.3=h2431656_0 + - libwebp-base=1.6.0=h07db88b_0 + - libxcb=1.17.0=hdb1d25a_0 + - libxml2=2.15.3=heed7d32_0 + - libxml2-16=2.15.3=h6967ea9_0 + - libzlib=1.3.2=h8088a28_2 + - llvm-openmp=22.1.5=hc7d1edf_1 + - lz4-c=1.10.0=h286801f_1 + - markupsafe=3.0.3=py314h6e9b3f0_1 + - matplotlib=3.10.9=py314he55896b_0 + - matplotlib-base=3.10.9=py314hc042b31_0 + - matplotlib-inline=0.2.2=pyhd8ed1ab_0 + - munkres=1.1.4=pyhd8ed1ab_1 + - narwhals=2.21.0=pyhcf101f3_0 + - ncurses=6.6=h1d4f5a5_0 + - nest-asyncio=1.6.0=pyhd8ed1ab_1 + - nlohmann_json=3.12.0=h784d473_1 + - numpy=2.4.3=py314h1569ea8_0 + - openjpeg=2.5.4=hd9e9057_0 + - openssl=3.6.2=hd24854e_0 + - orc=2.3.0=hd11884d_0 + - packaging=26.2=pyhc364b38_0 + - parso=0.8.7=pyhcf101f3_0 + - pexpect=4.9.0=pyhd8ed1ab_1 + - pillow=12.2.0=py314hab283cf_0 + - pip=26.1.1=pyh145f28c_0 + - platformdirs=4.9.6=pyhcf101f3_0 + - prometheus-cpp=1.3.0=h0967b3e_0 + - prompt-toolkit=3.0.52=pyha770c72_0 + - protobuf=6.33.5=py314he407d35_2 + - psutil=7.2.2=py314ha14b1ff_0 + - pthread-stubs=0.4=hd74edd7_1002 + - ptyprocess=0.7.0=pyhd8ed1ab_1 + - pure_eval=0.2.3=pyhd8ed1ab_1 + - pyarrow=24.0.0=py314he55896b_0 + - pyarrow-core=24.0.0=py314h109bba2_0_cpu + - pydeck=0.9.2=pyhd8ed1ab_0 + - pygments=2.20.0=pyhd8ed1ab_0 + - pyparsing=3.3.2=pyhcf101f3_0 + - pysocks=1.7.1=pyha55dd90_7 + - python=3.14.4=h4c637c5_100_cp314 + - 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=py314h6e9b3f0_1 + - pyzmq=27.1.0=py312h022ad19_2 + - qhull=2020.2=h420ef59_5 + - re2=2025.11.05=ha480c28_1 + - readline=8.3=h46df422_0 + - referencing=0.37.0=pyhcf101f3_0 + - requests=2.33.1=pyhcf101f3_1 + - rpds-py=0.30.0=py314haad56a0_0 + - scipy=1.17.1=py314hfc1f868_0 + - setuptools=82.0.1=pyh332efcf_0 + - six=1.17.0=pyhe01879c_1 + - smmap=5.0.3=pyhd8ed1ab_0 + - snappy=1.2.2=hada39a4_1 + - stack_data=0.6.3=pyhd8ed1ab_1 + - starlette=1.0.0=pyhcf101f3_0 + - streamlit=1.57.0=pyhd8ed1ab_0 + - tenacity=9.1.4=pyhcf101f3_0 + - tk=8.6.13=h010d191_3 + - toml=0.10.2=pyhcf101f3_3 + - tornado=6.5.5=py314h6c2aa35_0 + - traitlets=5.15.0=pyhcf101f3_0 + - typing-extensions=4.15.0=h396c80c_0 + - typing_extensions=4.15.0=pyhcf101f3_0 + - unicodedata2=17.0.1=py314h6c2aa35_0 + - urllib3=2.7.0=pyhd8ed1ab_0 + - uvicorn=0.46.0=pyhc90fa1f_0 + - watchdog=6.0.0=py314ha14b1ff_3 + - wcwidth=0.7.0=pyhd8ed1ab_0 + - websockets=16.0=py314ha14b1ff_1 + - wheel=0.47.0=pyhd8ed1ab_0 + - xarray=2026.4.0=pyhc364b38_0 + - xorg-libxau=1.0.12=hc919400_1 + - xorg-libxdmcp=1.1.5=hc919400_1 + - yaml=0.2.5=h925e9cb_3 + - zeromq=4.3.5=h4818236_10 + - zipp=3.23.1=pyhcf101f3_0 + - zlib=1.3.2=h8088a28_2 + - zlib-ng=2.3.3=hed4e4f5_1 + - zstd=1.5.7=hbf9d68e_6 + - pip: + - capytaine==2.3.1 + - markdown-it-py==4.2.0 + - mdurl==0.1.2 + - -e ../../.. + - pandas==2.3.3 + - pytz==2026.2 + - rich==15.0.0 + - tzdata==2026.2 diff --git a/.calkit/env-locks/openflash-on-main/linux-64.yml b/.calkit/env-locks/openflash-on-main/linux-64.yml index b13cbfff..21f6e292 100644 --- a/.calkit/env-locks/openflash-on-main/linux-64.yml +++ b/.calkit/env-locks/openflash-on-main/linux-64.yml @@ -1,6 +1,7 @@ +name: openflash-openflash-on-main channels: - - sea-lab - conda-forge + - sea-lab - defaults dependencies: - _openmp_mutex=4.5=20_gnu @@ -283,4 +284,3 @@ dependencies: - zlib=1.3.2=h25fd6f3_2 - zlib-ng=2.3.3=hceb46e0_1 - zstd=1.5.7=hb78ec9c_6 -name: openflash-openflash-on-main diff --git a/.calkit/env-locks/openflash-on-main/osx-arm64.yml b/.calkit/env-locks/openflash-on-main/osx-arm64.yml new file mode 100644 index 00000000..cae87c1f --- /dev/null +++ b/.calkit/env-locks/openflash-on-main/osx-arm64.yml @@ -0,0 +1,220 @@ +name: openflash-openflash-on-main +channels: + - conda-forge + - sea-lab +dependencies: + - _openmp_mutex=4.5=7_kmp_llvm + - _python_abi3_support=1.0=hd8ed1ab_2 + - altair=6.1.0=pyhd8ed1ab_0 + - anyio=4.13.0=pyhcf101f3_0 + - appnope=0.1.4=pyhd8ed1ab_1 + - asttokens=3.0.1=pyhd8ed1ab_0 + - attrs=26.1.0=pyhcf101f3_0 + - aws-c-auth=0.10.1=ha7d4cc1_3 + - aws-c-cal=0.9.13=h6ee9776_1 + - aws-c-common=0.12.6=hc919400_0 + - aws-c-compression=0.3.2=h3e7f9b5_0 + - aws-c-event-stream=0.7.0=h351c84d_0 + - aws-c-http=0.10.13=h95cdebe_0 + - aws-c-io=0.26.3=h4137820_1 + - aws-c-mqtt=0.15.2=h8860bc9_2 + - aws-c-s3=0.12.2=h07b101a_1 + - aws-c-sdkutils=0.2.4=h16f91aa_4 + - aws-checksums=0.2.10=h3e7f9b5_0 + - aws-crt-cpp=0.38.3=hba17502_1 + - aws-sdk-cpp=1.11.747=h30a6df1_4 + - azure-core-cpp=1.16.2=he5ae378_0 + - azure-identity-cpp=1.13.3=h810541e_1 + - azure-storage-blobs-cpp=12.16.0=hc57151b_1 + - azure-storage-common-cpp=12.12.0=he467506_1 + - azure-storage-files-datalake-cpp=12.14.0=hf8a9d22_1 + - backports.zstd=1.4.0=py314h680f03e_0 + - blinker=1.9.0=pyhff2d567_0 + - brotli=1.2.0=h7d5ae5b_1 + - brotli-bin=1.2.0=hc919400_1 + - brotli-python=1.2.0=py314h3daef5d_1 + - bzip2=1.0.8=hd037594_9 + - c-ares=1.34.6=hc919400_0 + - ca-certificates=2026.4.22=hbd8a1cb_0 + - cached-property=1.5.2=hd8ed1ab_1 + - cached_property=1.5.2=pyha770c72_1 + - cachetools=7.1.1=pyhd8ed1ab_0 + - certifi=2026.4.22=pyhd8ed1ab_0 + - charset-normalizer=3.4.7=pyhd8ed1ab_0 + - click=8.3.3=pyhc90fa1f_0 + - comm=0.2.3=pyhe01879c_0 + - contourpy=1.3.3=py314hf8a3a22_4 + - cpython=3.14.4=py314hd8ed1ab_100 + - cycler=0.12.1=pyhcf101f3_2 + - debugpy=1.8.20=py314he609de1_0 + - decorator=5.2.1=pyhd8ed1ab_0 + - exceptiongroup=1.3.1=pyhd8ed1ab_0 + - executing=2.2.1=pyhd8ed1ab_0 + - fonttools=4.62.1=pyh7db6752_0 + - freetype=2.14.3=hce30654_0 + - gflags=2.2.2=hf9b8971_1005 + - gitdb=4.0.12=pyhd8ed1ab_0 + - gitpython=3.1.50=pyhd8ed1ab_0 + - glog=0.7.1=heb240a5_0 + - h11=0.16.0=pyhcf101f3_1 + - h2=4.3.0=pyhcf101f3_0 + - h5netcdf=1.8.1=pyhd8ed1ab_0 + - h5py=3.16.0=nompi_py314h658a3ac_102 + - hdf5=2.1.0=nompi_he586413_105 + - hpack=4.1.0=pyhd8ed1ab_0 + - httptools=0.7.1=py314h0612a62_1 + - hyperframe=6.1.0=pyhd8ed1ab_0 + - idna=3.13=pyhcf101f3_0 + - importlib-metadata=8.8.0=pyhcf101f3_0 + - ipykernel=7.2.0=pyh5552912_1 + - ipython=9.13.0=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_core=5.9.1=pyhc90fa1f_0 + - kiwisolver=1.5.0=py314hf8a3a22_0 + - krb5=1.22.2=h385eeb1_0 + - lcms2=2.19.1=hdfa7624_0 + - lerc=4.1.0=h1eee2c3_0 + - libabseil=20260107.1=cxx17_h2062a1b_0 + - libaec=1.1.5=h8664d51_0 + - libarrow=24.0.0=h37fbca7_1_cpu + - libarrow-acero=24.0.0=hee8fe31_1_cpu + - libarrow-compute=24.0.0=h3b6a98a_1_cpu + - libarrow-dataset=24.0.0=hee8fe31_1_cpu + - libarrow-substrait=24.0.0=h05be00f_1_cpu + - libblas=3.11.0=6_h51639a9_openblas + - libbrotlicommon=1.2.0=hc919400_1 + - libbrotlidec=1.2.0=hc919400_1 + - libbrotlienc=1.2.0=hc919400_1 + - libcblas=3.11.0=6_hb0561ab_openblas + - libcrc32c=1.1.2=hbdafb3b_0 + - libcurl=8.20.0=hd5a2499_0 + - libcxx=22.1.5=h55c6f16_1 + - libdeflate=1.25=hc11a715_0 + - libedit=3.1.20250104=pl5321hafb1f1b_0 + - libev=4.33=h93a5062_2 + - libevent=2.1.12=h2757513_1 + - libexpat=2.8.0=hf6b4638_0 + - libffi=3.5.2=hcf2aa1b_0 + - libfreetype=2.14.3=hce30654_0 + - libfreetype6=2.14.3=hdfa99f5_0 + - libgcc=15.2.0=hcbb3090_19 + - libgfortran=15.2.0=h07b0088_19 + - libgfortran5=15.2.0=hdae7583_19 + - libgoogle-cloud=3.3.0=he41eb1d_1 + - libgoogle-cloud-storage=3.3.0=ha114238_1 + - libgrpc=1.78.1=h3e3f78d_0 + - libiconv=1.18=h23cfdf5_2 + - libjpeg-turbo=3.1.4.1=h84a0fba_0 + - liblapack=3.11.0=6_hd9741b5_openblas + - liblzma=5.8.3=h8088a28_0 + - libmpdec=4.0.0=h84a0fba_1 + - libnghttp2=1.68.1=h8f3e76b_0 + - libopenblas=0.3.32=openmp_he657e61_0 + - libopentelemetry-cpp=1.26.0=h08d5cc3_0 + - libopentelemetry-cpp-headers=1.26.0=hce30654_0 + - libparquet=24.0.0=h16c0493_1_cpu + - libpng=1.6.58=h132b30e_0 + - libprotobuf=6.33.5=h4a5acfd_0 + - libre2-11=2025.11.05=h4c27e2a_1 + - libsodium=1.0.21=h1a92334_3 + - libsqlite=3.53.1=h1b79a29_0 + - libssh2=1.11.1=h1590b86_0 + - libthrift=0.22.0=h1fb9c8a_2 + - libtiff=4.7.1=h4030677_1 + - libutf8proc=2.11.3=h2431656_0 + - libwebp-base=1.6.0=h07db88b_0 + - libxcb=1.17.0=hdb1d25a_0 + - libxml2=2.15.3=heed7d32_0 + - libxml2-16=2.15.3=h6967ea9_0 + - libzlib=1.3.2=h8088a28_2 + - llvm-openmp=22.1.5=hc7d1edf_1 + - lz4-c=1.10.0=h286801f_1 + - markupsafe=3.0.3=py314h6e9b3f0_1 + - matplotlib=3.10.9=py314he55896b_0 + - matplotlib-base=3.10.9=py314hc042b31_0 + - matplotlib-inline=0.2.2=pyhd8ed1ab_0 + - munkres=1.1.4=pyhd8ed1ab_1 + - narwhals=2.21.0=pyhcf101f3_0 + - ncurses=6.6=h1d4f5a5_0 + - nest-asyncio=1.6.0=pyhd8ed1ab_1 + - nlohmann_json=3.12.0=h784d473_1 + - numpy=2.4.3=py314h1569ea8_0 + - open-flash=v1.0.28=py_0 + - openjpeg=2.5.4=hd9e9057_0 + - openssl=3.6.2=hd24854e_0 + - orc=2.3.0=hd11884d_0 + - packaging=26.2=pyhc364b38_0 + - parso=0.8.7=pyhcf101f3_0 + - pexpect=4.9.0=pyhd8ed1ab_1 + - pillow=12.2.0=py314hab283cf_0 + - pip=26.1.1=pyh145f28c_0 + - platformdirs=4.9.6=pyhcf101f3_0 + - prometheus-cpp=1.3.0=h0967b3e_0 + - prompt-toolkit=3.0.52=pyha770c72_0 + - protobuf=6.33.5=py314he407d35_2 + - psutil=7.2.2=py314ha14b1ff_0 + - pthread-stubs=0.4=hd74edd7_1002 + - ptyprocess=0.7.0=pyhd8ed1ab_1 + - pure_eval=0.2.3=pyhd8ed1ab_1 + - pyarrow=24.0.0=py314he55896b_0 + - pyarrow-core=24.0.0=py314h109bba2_0_cpu + - pydeck=0.9.2=pyhd8ed1ab_0 + - pygments=2.20.0=pyhd8ed1ab_0 + - pyparsing=3.3.2=pyhcf101f3_0 + - pysocks=1.7.1=pyha55dd90_7 + - python=3.14.4=h4c637c5_100_cp314 + - 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=py314h6e9b3f0_1 + - pyzmq=27.1.0=py312h022ad19_2 + - qhull=2020.2=h420ef59_5 + - re2=2025.11.05=ha480c28_1 + - readline=8.3=h46df422_0 + - referencing=0.37.0=pyhcf101f3_0 + - requests=2.33.1=pyhcf101f3_1 + - rpds-py=0.30.0=py314haad56a0_0 + - scipy=1.17.1=py314hfc1f868_0 + - six=1.17.0=pyhe01879c_1 + - smmap=5.0.3=pyhd8ed1ab_0 + - snappy=1.2.2=hada39a4_1 + - stack_data=0.6.3=pyhd8ed1ab_1 + - starlette=1.0.0=pyhcf101f3_0 + - streamlit=1.57.0=pyhd8ed1ab_0 + - tenacity=9.1.4=pyhcf101f3_0 + - tk=8.6.13=h010d191_3 + - toml=0.10.2=pyhcf101f3_3 + - tornado=6.5.5=py314h6c2aa35_0 + - traitlets=5.15.0=pyhcf101f3_0 + - typing-extensions=4.15.0=h396c80c_0 + - typing_extensions=4.15.0=pyhcf101f3_0 + - unicodedata2=17.0.1=py314h6c2aa35_0 + - urllib3=2.7.0=pyhd8ed1ab_0 + - uvicorn=0.46.0=pyhc90fa1f_0 + - watchdog=6.0.0=py314ha14b1ff_3 + - wcwidth=0.7.0=pyhd8ed1ab_0 + - websockets=16.0=py314ha14b1ff_1 + - xarray=2026.4.0=pyhc364b38_0 + - xorg-libxau=1.0.12=hc919400_1 + - xorg-libxdmcp=1.1.5=hc919400_1 + - yaml=0.2.5=h925e9cb_3 + - zeromq=4.3.5=h4818236_10 + - zipp=3.23.1=pyhcf101f3_0 + - zlib=1.3.2=h8088a28_2 + - zlib-ng=2.3.3=hed4e4f5_1 + - zstd=1.5.7=hbf9d68e_6 + - pip: + - capytaine==2.3.1 + - markdown-it-py==4.2.0 + - mdurl==0.1.2 + - pandas==2.3.3 + - pytz==2026.2 + - rich==15.0.0 + - tzdata==2026.2 diff --git a/.calkit/env-locks/tex/arm64.json b/.calkit/env-locks/tex/arm64.json new file mode 100644 index 00000000..238401f5 --- /dev/null +++ b/.calkit/env-locks/tex/arm64.json @@ -0,0 +1,26 @@ +{ + "RepoTags": [ + "texlive/texlive:latest-full" + ], + "RepoDigests": [ + "texlive/texlive@sha256:6b683746cafd8e0022dea6e4a086aab21f1d9c179189767b3b424d2fb6d40002" + ], + "Architecture": "arm64", + "Os": "linux", + "RootFS": { + "Type": "layers", + "Layers": [ + "sha256:0518588c72fb6646e9e19a608ac235b16d6bcf393e529ffda582ea487919bcd2", + "sha256:89c68a8082a74f6fb6b5e8fea5ebf2c6f6389ff410ace68415e9b90002fa3833", + "sha256:319931a6c5bb3446bb840fc974762786ec01a16604cae7324d5d8fc40e92c307", + "sha256:5f70bf18a086007016e948b04aed3b82103a36bea41755b6cddfaf10ace3c6ef", + "sha256:6d0e1eb4feb4ee30e00d578b6cc2ab3873434b34a67a89620b47d0af1ec3425a", + "sha256:171f8fa7ef4d769ee6083e694da6276c7b6faefefd9bf9e8d4cfed29e54a6ab3", + "sha256:983a2813960f80aa14261eb67da88a4475f9ec3fc4fedafcf5a3cf3e8e9af090", + "sha256:3eeb6e6978a1422e92732e5cb12987f46893be5db9f84e00731bc2f481858474", + "sha256:385f4d063f1f9315140f5d1f1a237a3bb58338b2c351aa8bfea7cd910d9129d5" + ] + }, + "DockerfileMD5": null, + "DepsMD5s": {} +} \ No newline at end of file diff --git a/.calkit/notebooks/executed/analysis/test-latex.ipynb b/.calkit/notebooks/executed/analysis/test-latex.ipynb new file mode 100644 index 00000000..efc7a237 --- /dev/null +++ b/.calkit/notebooks/executed/analysis/test-latex.ipynb @@ -0,0 +1,179 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "ddf92cde", + "metadata": { + "execution": { + "iopub.execute_input": "2026-06-15T21:41:44.137328Z", + "iopub.status.busy": "2026-06-15T21:41:44.137142Z", + "iopub.status.idle": "2026-06-15T21:41:44.141533Z", + "shell.execute_reply": "2026-06-15T21:41:44.140508Z" + }, + "papermill": { + "duration": 0.0071, + "end_time": "2026-06-15T21:41:44.142215+00:00", + "exception": false, + "start_time": "2026-06-15T21:41:44.135115+00:00", + "status": "completed" + }, + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "/usr/bin/latex\n", + "/opt/conda/envs/openflash.openflash-on-branch-tex/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin\n" + ] + } + ], + "source": [ + "import os\n", + "import shutil\n", + "import subprocess\n", + "\n", + "print(shutil.which(\"latex\"))\n", + "print(os.environ[\"PATH\"])\n", + "\n", + "# subprocess.run([\"latex\", \"--version\"], check=True)" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "fd4e8d5a", + "metadata": { + "execution": { + "iopub.execute_input": "2026-06-15T21:41:44.145388Z", + "iopub.status.busy": "2026-06-15T21:41:44.145236Z", + "iopub.status.idle": "2026-06-15T21:41:44.148587Z", + "shell.execute_reply": "2026-06-15T21:41:44.147862Z" + }, + "papermill": { + "duration": 0.005804, + "end_time": "2026-06-15T21:41:44.149337+00:00", + "exception": false, + "start_time": "2026-06-15T21:41:44.143533+00:00", + "status": "completed" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "import sys\n", + "from pathlib import Path\n", + "HERE = Path.cwd().resolve()\n", + "utils_path = str((HERE / \"sea-lab-utils\").resolve())\n", + "# Define the path to the directory containing the package\n", + "if utils_path not in sys.path:\n", + " sys.path.insert(0, utils_path)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "9c14e4a4", + "metadata": { + "execution": { + "iopub.execute_input": "2026-06-15T21:41:44.152209Z", + "iopub.status.busy": "2026-06-15T21:41:44.152035Z", + "iopub.status.idle": "2026-06-15T21:41:45.237623Z", + "shell.execute_reply": "2026-06-15T21:41:45.236632Z" + }, + "papermill": { + "duration": 1.087907, + "end_time": "2026-06-15T21:41:45.238311+00:00", + "exception": false, + "start_time": "2026-06-15T21:41:44.150404+00:00", + "status": "completed" + }, + "tags": [] + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "#CC79A7\n" + ] + } + ], + "source": [ + "# Now you can import from the folder structure\n", + "# Assuming 'pyplotutilities' is a folder inside 'sea-lab-utils'\n", + "from pyplotutilities import colors\n", + "from pyplotutilities import fonts\n", + "colors.get_colors()\n", + "print(colors.purple)\n", + "fonts.get_fonts()" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "1000b71d", + "metadata": { + "execution": { + "iopub.execute_input": "2026-06-15T21:41:45.241716Z", + "iopub.status.busy": "2026-06-15T21:41:45.241481Z", + "iopub.status.idle": "2026-06-15T21:41:45.244416Z", + "shell.execute_reply": "2026-06-15T21:41:45.243621Z" + }, + "papermill": { + "duration": 0.005408, + "end_time": "2026-06-15T21:41:45.245009+00:00", + "exception": false, + "start_time": "2026-06-15T21:41:45.239601+00:00", + "status": "completed" + }, + "tags": [] + }, + "outputs": [], + "source": [ + "# import matplotlib.pyplot as plt\n", + "# fig, ax = plt.subplots()\n", + "# ax.plot([1, 2, 3], [1, 4, 9], color=colors.purple, label='Quadratic')\n", + "# ax.set_title('Sample Plot')\n", + "# ax.set_xlabel('$\\mathbf{X}$-axis')\n", + "# ax.set_ylabel('$\\phi$')\n", + "#fig.savefig('sample_plot.pdf', format='pdf', dpi=300, bbox_inches='tight')" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "python3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.13" + }, + "papermill": { + 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b/.calkit/systems/d58a9aaa4840d09b08058ac571cbe818a2630e69.json @@ -0,0 +1,28 @@ +{ + "os": "Linux", + "os_version": "6.17.0-1018-azure", + "python_version": "3.12.3", + "calkit_version": "0.41.16", + "calkit_git_rev": null, + "hostname": "runnervm1li68", + "processor": "x86_64", + "platform": "Linux-6.17.0-1018-azure-x86_64-with-glibc2.39", + "machine": "x86_64", + "python_implementation": "CPython", + "python_compiler": "GCC 13.3.0", + "memory_gb": 15.614948272705078, + "cpu_count": 4, + "node_id": 136469683209593, + "git_version": "git version 2.54.0", + "docker_version": "Docker version 28.0.4, build b8034c0", + "conda_version": "conda 26.3.2", + "mamba_version": null, + "uv_version": "uv 0.11.21 (x86_64-unknown-linux-gnu)", + "pixi_version": null, + "Rscript_version": null, + "juliaup_version": null, + "julia_version": "julia version 1.12.6", + "apt_version": "apt 2.8.3 (amd64)", + "yum_version": null, + "id": "d58a9aaa4840d09b08058ac571cbe818a2630e69" +} \ No newline at end of file diff --git a/.dvc/config b/.dvc/config index 48998f48..dd5656a1 100644 --- a/.dvc/config +++ b/.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 diff --git a/.github/workflows/calkit-pull-with-retries.sh b/.github/workflows/calkit-pull-with-retries.sh new file mode 100644 index 00000000..51a1b53c --- /dev/null +++ b/.github/workflows/calkit-pull-with-retries.sh @@ -0,0 +1,26 @@ +#!/usr/bin/env bash +set -u + +max_tries=10 +try=1 + +while (( try <= max_tries )); do + echo "=== Attempt $try / $max_tries ===" + + # Run pull and capture ALL output (stdout+stderr) + out="$(calkit pull 2>&1)" + echo "$out" + + # Check for the specific retry-able error pattern + if echo "$out" | grep -Eq 'ERROR: failed to pull data from the cloud - [0-9]+ files failed to download'; then + echo "Retryable error detected. Retrying..." + ((try++)) + sleep 2 + else + echo "No matching error found. Done." + exit 0 + fi +done + +echo "ERROR: exceeded maximum retries ($max_tries)." +exit 1 diff --git a/.github/workflows/calkit-run.yml b/.github/workflows/calkit-run.yml new file mode 100644 index 00000000..11f917c7 --- /dev/null +++ b/.github/workflows/calkit-run.yml @@ -0,0 +1,84 @@ +name: Run calkit pipeline + +on: + push: + branches: + - main + pull_request: + workflow_dispatch: +permissions: + contents: write + id-token: write + +# Make sure we only ever run one per branch so we don't have issues pushing +# after running the pipeline +concurrency: + group: calkit-run-${{ github.ref }} + cancel-in-progress: false + +jobs: + main: + name: Run + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v6 + with: + # For PRs, checkout the head ref to avoid detached HEAD + ref: ${{ github.head_ref || github.ref_name }} + token: ${{ secrets.GITHUB_TOKEN }} + submodules: true + persist-credentials: false + - name: Configure Git credentials + run: | + git config user.name github-actions[bot] + git config user.email 41898282+github-actions[bot]@users.noreply.github.com + git remote set-url origin https://github-actions[bot]:${{ secrets.GITHUB_TOKEN }}@github.com/${{ github.repository }}.git + - name: Setup uv + uses: astral-sh/setup-uv@v7 + - name: Install Calkit + run: uv tool install --upgrade calkit-python + - name: Setup jq + uses: dcarbone/install-jq-action@v3 + # - name: pull with retries + # run: bash .github/workflows/calkit_pull_with_retries.sh + # continue-on-error: true + - name: Run Calkit + id: run_calkit + continue-on-error: true + uses: calkit/run-action@v2 + with: + run_args: --keep-going --log + pull_dvc: true + save: false + cache_dvc: false + - name: calkit save + run: | + if ! git status --porcelain | grep -vE '^.. \.calkit/' | grep -q . && dvc status -q --no-updates; then + exit 0 # Exit without saving if nothing changed, or if the only changes are in .calkit/ + fi + + set +e # Continue even if pull fails + git pull --recurse-submodules + PULL_STATUS=$? + + if [ $PULL_STATUS -ne 0 ]; then + BRANCH="calkit-run-${{github.run_number}}-${{github.run_id}}" + echo "Pull failed due to merge conflict. Creating a new branch $BRANCH." + git checkout -b "$BRANCH" + # git config below does the equivalent of the --set-upstream option of git push + git config branch."$BRANCH".remote origin + git config branch."$BRANCH".merge refs/heads/"$BRANCH" + fi + + calkit dvc pull + calkit save dvc.lock dvc.yaml .calkit/ calkit.yaml -m "Run pipeline" + PUSH_STATUS=$? + + if [ $PUSH_STATUS -ne 0 ]; then + echo "Push failed, perhaps due to dvc push timeout. Retrying." + calkit dvc push + git push || true + fi + - run: | + echo "Errors from latex:" + grep -E "^!" pubs/JFM/FLMguide.log || true diff --git a/.github/workflows/calkit_pull_with_retries.sh b/.github/workflows/calkit_pull_with_retries.sh new file mode 100644 index 00000000..51a1b53c --- /dev/null +++ b/.github/workflows/calkit_pull_with_retries.sh @@ -0,0 +1,26 @@ +#!/usr/bin/env bash +set -u + +max_tries=10 +try=1 + +while (( try <= max_tries )); do + echo "=== Attempt $try / $max_tries ===" + + # Run pull and capture ALL output (stdout+stderr) + out="$(calkit pull 2>&1)" + echo "$out" + + # Check for the specific retry-able error pattern + if echo "$out" | grep -Eq 'ERROR: failed to pull data from the cloud - [0-9]+ files failed to download'; then + echo "Retryable error detected. Retrying..." + ((try++)) + sleep 2 + else + echo "No matching error found. Done." + exit 0 + fi +done + +echo "ERROR: exceeded maximum retries ($max_tries)." +exit 1 diff --git a/.github/workflows/pr-tagging.yml b/.github/workflows/pr-tagging.yml index 29dff58f..0557cc4a 100644 --- a/.github/workflows/pr-tagging.yml +++ b/.github/workflows/pr-tagging.yml @@ -24,6 +24,8 @@ permissions: jobs: manage-pr-tags: + # Don't run on forks + if: ${{ github.event_name != 'pull_request' || !github.event.pull_request.head.repo.fork }} runs-on: ubuntu-latest steps: - name: Checkout @@ -68,7 +70,7 @@ jobs: commit_sha: ${{ github.event.pull_request.merge_commit_sha }} - name: Dispatch docs deploy and publish package workflows - if: ${{ github.event.action == 'closed' && github.event.pull_request.merged == false }} == false + if: ${{ github.event.action != 'closed' || github.event.pull_request.merged }} uses: actions/github-script@v7 with: github-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore index 53041235..a11262c9 100644 --- a/.gitignore +++ b/.gitignore @@ -211,7 +211,6 @@ html/ .calkit/overleaf # Calkit build artifacts -.calkit/env-locks/ .calkit/logs/ .calkit/notebooks/executed/ .calkit/notebooks/cleaned/ diff --git a/.gitmodules b/.gitmodules index 4f9fca08..ed556264 100644 --- a/.gitmodules +++ b/.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 \ No newline at end of file diff --git a/analysis/convergence-results.ipynb b/analysis/convergence-results.ipynb index 202aa5fd..a6069ad7 100644 --- a/analysis/convergence-results.ipynb +++ b/analysis/convergence-results.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "fc78e665", "metadata": {}, "outputs": [ @@ -62,7 +62,7 @@ "\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", @@ -776,7 +776,7 @@ "# hmdr, m0h, right_ratio = vars\n", "# alpha = a1 * (log_like(1, b1, c1, right_ratio)) * (np.exp(-a2 * m0h) + b2) # need b2 >= 0\n", "# beta = a3 * (np.exp(-a4 * right_ratio) + b4) * (hmdr + b3) * ((m0h ** 0.5) * (m0h > 5) + m0h/(5**0.5) * (m0h <=5))\n", - "# # b4 = 0 in previous \u2014 assumed it trended to zero\n", + "# # b4 = 0 in previous — assumed it trended to zero\n", "# return alpha, beta\n", "# variables_used = [\"(h-d)/radwidth\", \"m0h\", \"h/(h-d)\"]\n", "# guess = [0.5, 0.016, 0, 0.01, 0, 0.09, 2, 0.1, 0]\n", @@ -951,4 +951,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/analysis/environment-branch.yml b/analysis/environment-branch.yml index fad8eb00..31a50acd 100644 --- a/analysis/environment-branch.yml +++ b/analysis/environment-branch.yml @@ -14,7 +14,13 @@ dependencies: - xarray - streamlit - ipykernel - - capytaine - seaborn + # Compiler toolchain so pip can build capytaine's Fortran extension from + # source (no prebuilt arm64 wheel exists). Sets CC/FC during env activation. + # Note: on aarch64 these don't provide libquadmath, which gfortran still + # links against; .Dockerfile supplies an empty stub to satisfy the linker. + - c-compiler + - fortran-compiler - pip: + - capytaine - -e .. diff --git a/analysis/environment-main.yml b/analysis/environment-main.yml index afd6e790..f2e318ad 100644 --- a/analysis/environment-main.yml +++ b/analysis/environment-main.yml @@ -3,4 +3,5 @@ channels: - conda-forge dependencies: - sea-lab::open-flash>=v1.0.25 - - capytaine + - pip: + - capytaine diff --git a/analysis/low_m0_plots.ipynb b/analysis/low_m0_plots.ipynb index 802a5631..a7ff42d2 100644 --- a/analysis/low_m0_plots.ipynb +++ b/analysis/low_m0_plots.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "d5e23a34", "metadata": {}, "outputs": [ @@ -44,7 +44,7 @@ " sys.path.insert(0, str(low_m0_dir))\n", "from low_m0 import low_get_hydros\n", "\n", - "utils_path = (HERE / \"..\" / \"sea-lab-utils\").resolve()\n", + "utils_path = (HERE / \"sea-lab-utils\").resolve()\n", "utils_str = str(utils_path)\n", "if utils_str not in sys.path:\n", " sys.path.insert(0, utils_str)\n", @@ -295,4 +295,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/analysis/sea-lab-utils b/analysis/sea-lab-utils new file mode 160000 index 00000000..f9d69427 --- /dev/null +++ b/analysis/sea-lab-utils @@ -0,0 +1 @@ +Subproject commit f9d69427a24304292c4a140b272e63122df9b6cf diff --git a/analysis/slant_data_plots.ipynb b/analysis/slant_data_plots.ipynb index d886cd95..df705107 100644 --- a/analysis/slant_data_plots.ipynb +++ b/analysis/slant_data_plots.ipynb @@ -46,7 +46,7 @@ "import sys\n", "from pathlib import Path\n", "HERE = Path.cwd().resolve()\n", - "utils_str = str((HERE / \"..\" / \"sea-lab-utils\").resolve())\n", + "utils_str = str((HERE / \"sea-lab-utils\").resolve())\n", "prob_path = str((HERE / \"..\" / \"dev\" / \"python\").resolve())\n", "modified_meem_path = str((HERE / \"..\" / \"dev\" / \"python\" / \"slants\" / \"a-matrix-b-vector-changes\").resolve())\n", "\n", @@ -937,4 +937,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/analysis/test-latex.ipynb b/analysis/test-latex.ipynb new file mode 100644 index 00000000..def49141 --- /dev/null +++ b/analysis/test-latex.ipynb @@ -0,0 +1,76 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "ddf92cde", + "metadata": {}, + "outputs": [], + "source": [ + "import os\n", + "import shutil\n", + "import subprocess\n", + "\n", + "print(shutil.which(\"latex\"))\n", + "print(os.environ[\"PATH\"])\n", + "\n", + "# subprocess.run([\"latex\", \"--version\"], check=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "fd4e8d5a", + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "from pathlib import Path\n", + "HERE = Path.cwd().resolve()\n", + "utils_path = str((HERE / \"sea-lab-utils\").resolve())\n", + "# Define the path to the directory containing the package\n", + "if utils_path not in sys.path:\n", + " sys.path.insert(0, utils_path)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9c14e4a4", + "metadata": {}, + "outputs": [], + "source": [ + "# Now you can import from the folder structure\n", + "# Assuming 'pyplotutilities' is a folder inside 'sea-lab-utils'\n", + "from pyplotutilities import colors\n", + "from pyplotutilities import fonts\n", + "colors.get_colors()\n", + "print(colors.purple)\n", + "fonts.get_fonts()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1000b71d", + "metadata": {}, + "outputs": [], + "source": [ + "# import matplotlib.pyplot as plt\n", + "# fig, ax = plt.subplots()\n", + "# ax.plot([1, 2, 3], [1, 4, 9], color=colors.purple, label='Quadratic')\n", + "# ax.set_title('Sample Plot')\n", + "# ax.set_xlabel('$\\mathbf{X}$-axis')\n", + "# ax.set_ylabel('$\\phi$')\n", + "#fig.savefig('sample_plot.pdf', format='pdf', dpi=300, bbox_inches='tight')" + ] + } + ], + "metadata": { + "language_info": { + "name": "python" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/analysis/timing_data_generation.ipynb b/analysis/timing_data_generation.ipynb index 68104f37..e5940a03 100644 --- a/analysis/timing_data_generation.ipynb +++ b/analysis/timing_data_generation.ipynb @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "9ddd15c3", "metadata": {}, "outputs": [ @@ -69,7 +69,6 @@ "\n", "\n", "# Now you can import from the folder structure\n", - "# Assuming 'pyplotutilities' is a folder inside 'sea-lab-utils'\n", "import sys\n", "from pathlib import Path\n", "HERE = Path.cwd().resolve()\n", diff --git a/analysis/timing_plots.ipynb b/analysis/timing_plots.ipynb index 891f777e..844a6a2b 100644 --- a/analysis/timing_plots.ipynb +++ b/analysis/timing_plots.ipynb @@ -27,7 +27,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "ed2439b5", "metadata": {}, "outputs": [ @@ -69,7 +69,7 @@ "import sys\n", "from pathlib import Path\n", "HERE = Path.cwd().resolve()\n", - "utils_path = (HERE / \"..\" / \"sea-lab-utils\").resolve()\n", + "utils_path = (HERE / \"sea-lab-utils\").resolve()\n", "utils_str = str(utils_path)\n", "if utils_str not in sys.path:\n", " sys.path.insert(0, utils_str)\n", @@ -582,4 +582,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/analysis/validation_with_capytaine_plots.ipynb b/analysis/validation_with_capytaine_plots.ipynb index 94827805..4c296651 100644 --- a/analysis/validation_with_capytaine_plots.ipynb +++ b/analysis/validation_with_capytaine_plots.ipynb @@ -48,7 +48,7 @@ "import sys\n", "from pathlib import Path\n", "HERE = Path.cwd().resolve()\n", - "utils_path = str((HERE / \"..\" / \"sea-lab-utils\").resolve())\n", + "utils_path = str((HERE / \"sea-lab-utils\").resolve())\n", "# Define the path to the directory containing the package\n", "if utils_path not in sys.path:\n", " sys.path.insert(0, utils_path)\n", @@ -994,4 +994,4 @@ }, "nbformat": 4, "nbformat_minor": 5 -} \ No newline at end of file +} diff --git a/calkit.yaml b/calkit.yaml index 1cce0a36..306579aa 100644 --- a/calkit.yaml +++ b/calkit.yaml @@ -13,40 +13,57 @@ environments: openflash-on-branch: path: analysis/environment-branch.yml kind: conda + deps: + - package/src + - pyproject.toml + openflash-on-branch-tex: + kind: docker + path: .Dockerfile + image: openflash-on-branch-tex + description: openflash-on-branch conda environment with TeXlive via Docker. + deps: + - analysis/environment-branch.yml + - package/src + - pyproject.toml + - README.md + - LICENSE + - CITATION.cff openflash-on-main: path: analysis/environment-main.yml kind: conda openflash-dev: path: analysis/environment-dev.yml kind: conda - + pipeline: stages: validate-w-capy: kind: jupyter-notebook notebook_path: analysis/validation_with_capytaine_plots.ipynb - environment: openflash-on-branch + environment: openflash-on-branch-tex + inputs: + - analysis/sea-lab-utils outputs: - pubs/JFM/figs/MEEM_vs_Capytaine_Nonslant_Validation.pdf low-m0-figs: kind: jupyter-notebook notebook_path: analysis/low_m0_plots.ipynb - environment: openflash-on-branch + environment: openflash-on-branch-tex inputs: - package/src/ - dev/python/limiting-cases/low_m0.py - - sea-lab-utils + - analysis/sea-lab-utils outputs: - pubs/JFM/figs/MEEM-Low-Freq.pdf slant-figs: kind: jupyter-notebook notebook_path: analysis/slant_data_plots.ipynb - environment: openflash-on-branch + environment: openflash-on-branch-tex inputs: - analysis/data/slants.pkl - analysis/data/slope-slants.pkl - analysis/data/potential-slants.pkl - - sea-lab-utils + - analysis/sea-lab-utils outputs: - pubs/JFM/figs/MEEM-CPT-Slant-Freq.pdf - pubs/JFM/figs/Vary-Slopes.pdf @@ -55,10 +72,10 @@ pipeline: timing-figs: kind: jupyter-notebook notebook_path: analysis/timing_plots.ipynb - environment: openflash-on-branch + environment: openflash-on-branch-tex inputs: - analysis/data/timing.pkl - - sea-lab-utils + - analysis/sea-lab-utils outputs: - pubs/JFM/figs/MEEM-Comp-Distribution.pdf - pubs/JFM/figs/MEEM-CPT-Speed-Comparison.pdf @@ -66,9 +83,9 @@ pipeline: convergence-figs: kind: jupyter-notebook notebook_path: analysis/convergence-results.ipynb - environment: openflash-on-branch + environment: openflash-on-branch-tex inputs: - - sea-lab-utils + - analysis/sea-lab-utils outputs: - pubs/JFM/figs/alpha-beta-explanation.pdf - pubs/JFM/figs/alpha-beta-to-trend.pdf @@ -81,6 +98,13 @@ pipeline: - pubs/JFM/figs/A_sparsity_plot.pdf - pubs/JFM/figs/B_sparsity_plot.pdf - pubs/JFM/figs/C_sparsity_plot.pdf + test-latex: + kind: jupyter-notebook + notebook_path: analysis/test-latex.ipynb + environment: openflash-on-branch-tex + inputs: + - analysis/sea-lab-utils + executed_ipynb_storage: git graphical-abstract: kind: latex target_path: pubs/JFM/figs/graph_abstract.tex diff --git a/dev/python/validation_with_capytaine_plots.ipynb b/dev/python/validation_with_capytaine_plots.ipynb index a71f5774..1ccb404a 100644 --- a/dev/python/validation_with_capytaine_plots.ipynb +++ b/dev/python/validation_with_capytaine_plots.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "id": "d8810371", "metadata": {}, "outputs": [ @@ -48,7 +48,7 @@ "import os\n", "\n", "# Define the path to the directory containing the package\n", - "utils_path = r\"C:\\Users\\15183\\OpenFLASH\\sea-lab-utils\"\n", + "utils_path = r\"C:\\Users\\15183\\OpenFLASH\\analysis\\sea-lab-utils\"\n", "\n", "if utils_path not in sys.path:\n", " sys.path.append(utils_path)\n", diff --git a/dvc.lock b/dvc.lock index c12f3cf7..96b90272 100644 --- a/dvc.lock +++ b/dvc.lock @@ -24,9 +24,9 @@ stages: deps: - path: .calkit/env-locks/tex hash: md5 - md5: 1d20723629fc752e4776c7e1d6cb328e.dir - size: 1147 - nfiles: 1 + md5: b404863b132f96ede5eaceb8cc787b66.dir + size: 2294 + nfiles: 2 - path: pubs/JFM/FLMguide.tex hash: md5 md5: b18ab48f6a2a2b07053d9fad57307dfa @@ -45,13 +45,13 @@ stages: size: 3942 - path: pubs/JFM/figs/ hash: md5 - md5: 946c4054a6e3f57f6370510717616bb1.dir - size: 3030216 - nfiles: 30 + md5: 02e8935adcb25ade89b1d8bbbfe696ee.dir + size: 3057061 + nfiles: 34 - path: pubs/JFM/jfm-appendix.tex hash: md5 - md5: 52770e0cffdb81b9601fd8a08032dd55 - size: 29074 + md5: 59854076d75ccb3d68e204bbe2b302cc + size: 28854 - path: pubs/JFM/jfm.bib hash: md5 md5: 94debb13be1e536dfceb909122f78e97 @@ -71,36 +71,41 @@ stages: outs: - path: pubs/JFM/FLMguide.pdf hash: md5 - md5: 8a85411ba9f03859b8c4a6fd6079f03e - size: 1471009 + md5: 5bd4911566aa33441471766e9c2678a5 + size: 1470985 validate-w-capy: - cmd: calkit nb execute --environment openflash-on-branch --no-check --to + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/validation_with_capytaine_plots.ipynb" deps: - - path: .calkit/env-locks/openflash-on-branch + - path: .calkit/env-locks/openflash-on-branch-tex hash: md5 - md5: 6fee7550c7f8d298fc987043523e190e.dir - size: 9764 + md5: ac0655df47557fc89aae3e74f4e0cbab.dir + size: 2838 nfiles: 1 - path: .calkit/notebooks/cleaned/analysis/validation_with_capytaine_plots.ipynb hash: md5 - md5: cb24277a46743be663ca11d97c5ccc66 - size: 29270 + md5: e592214a6e8b43b22060431f6412ad04 + size: 29261 + - path: analysis/sea-lab-utils + hash: md5 + md5: 22cff2f89b0191c779029f1a327c6977.dir + size: 16569 + nfiles: 22 outs: - path: .calkit/notebooks/executed/analysis/validation_with_capytaine_plots.ipynb hash: md5 - md5: f5d56751fbddd58583df31cab8f4fe56 - size: 874326 + md5: 229bce83cf419734d521652aae41bddf + size: 874832 - path: .calkit/notebooks/html/analysis/validation_with_capytaine_plots.html hash: md5 - md5: db1b9525ad6d75cd4bd6742934de5917 - size: 1191408 + md5: bae0db1cffa14d6a90af0fa41a4a997e + size: 1199208 - path: pubs/JFM/figs/MEEM_vs_Capytaine_Nonslant_Validation.pdf hash: md5 - md5: ac37fee7716bda0ff7e4f4cb62823d2a - size: 167991 + md5: 49df974ed2886c24daa885d4b452d935 + size: 167999 _check-env-openflash-on-branch: cmd: calkit check environment --name openflash-on-branch deps: @@ -174,45 +179,45 @@ stages: md5: 6a832537745ca618c89db30ddffa8e5d size: 11041 low-m0-figs: - cmd: calkit nb execute --environment openflash-on-branch --no-check --to + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/low_m0_plots.ipynb" deps: - - path: .calkit/env-locks/openflash-on-branch + - path: .calkit/env-locks/openflash-on-branch-tex hash: md5 - md5: 6fee7550c7f8d298fc987043523e190e.dir - size: 9764 + md5: ac0655df47557fc89aae3e74f4e0cbab.dir + size: 2838 nfiles: 1 - path: .calkit/notebooks/cleaned/analysis/low_m0_plots.ipynb hash: md5 - md5: b4dbb74d88dfa46140698a49a87947d4 - size: 11593 + md5: ea093bc530b8589101fad2355fc53a04 + size: 11584 + - path: analysis/sea-lab-utils + hash: md5 + md5: 22cff2f89b0191c779029f1a327c6977.dir + size: 16569 + nfiles: 22 - path: dev/python/limiting-cases/low_m0.py hash: md5 md5: 14c26f7e714c57e0de0a9b507a4a8091 size: 5745 - path: package/src/ hash: md5 - md5: d5e40e2f0a2e7b547d3e8ec700c6a269.dir - size: 228300 - nfiles: 27 - - path: sea-lab-utils - hash: md5 - md5: bee8da5063bc568e5251764466d97f5c.dir - size: 18456 - nfiles: 24 + md5: d4d82c0b73d7851bdad2f7252251875f.dir + size: 92043 + nfiles: 11 outs: - path: .calkit/notebooks/executed/analysis/low_m0_plots.ipynb hash: md5 - md5: a8547653d62e3711ba5ed8ee05f647d3 - size: 79695 + md5: ceab0818f0ad6834560c42b96c46f66f + size: 80405 - path: .calkit/notebooks/html/analysis/low_m0_plots.html hash: md5 - md5: f523c9b99747fc1d795116283f48806a - size: 384476 + md5: d7c4a98d2188c5ecd90f1a123bdcc059 + size: 392480 - path: pubs/JFM/figs/MEEM-Low-Freq.pdf hash: md5 - md5: 2642f708fe85c22730dd626452dd3ac8 - size: 402985 + md5: 1275e1c8bd4a42bb2a95f9571098ecbc + size: 402979 _clean-nb-slant-figs: cmd: calkit nb clean "analysis/slant_data_plots.ipynb" deps: @@ -226,18 +231,18 @@ stages: md5: d0f3626ddf4a5f876f6e028ec1ea5ca4 size: 10931 slant-figs: - cmd: calkit nb execute --environment openflash-on-branch --no-check --to + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/slant_data_plots.ipynb" deps: - - path: .calkit/env-locks/openflash-on-branch + - path: .calkit/env-locks/openflash-on-branch-tex hash: md5 - md5: 6fee7550c7f8d298fc987043523e190e.dir - size: 9764 + md5: ac0655df47557fc89aae3e74f4e0cbab.dir + size: 2838 nfiles: 1 - path: .calkit/notebooks/cleaned/analysis/slant_data_plots.ipynb hash: md5 - md5: effb86232aa402753c74bf7fd4ffaa1a - size: 44500 + md5: 86dbc507ee974a6d95b27bc18c2a2391 + size: 44491 - path: analysis/data/potential-slants.pkl hash: md5 md5: 31cd3c8c05c5951db5f91ef631c166a0 @@ -250,36 +255,36 @@ stages: hash: md5 md5: 3cb581a4d2a2774c678c1ab000b5bcdc size: 6664 - - path: sea-lab-utils + - path: analysis/sea-lab-utils hash: md5 - md5: bee8da5063bc568e5251764466d97f5c.dir - size: 18456 - nfiles: 24 + md5: 22cff2f89b0191c779029f1a327c6977.dir + size: 16569 + nfiles: 22 outs: - path: .calkit/notebooks/executed/analysis/slant_data_plots.ipynb hash: md5 - md5: e0dec938a208e9500fa799ed8031c277 - size: 469931 + md5: b8dd48656232d88cce9c239f0e1fb7cf + size: 470469 - path: .calkit/notebooks/html/analysis/slant_data_plots.html hash: md5 - md5: 9a3e09badb1f42fa46c4e3676fe17de2 - size: 881760 + md5: e4d8ac76a00d535d17dae63d9c16fc79 + size: 889593 - path: pubs/JFM/figs/Along-Outline.pdf hash: md5 - md5: d7bdf9c9285573974252d475e3cf8a79 - size: 109531 + md5: 9cc71561d25519436159c2f39b3c2925 + size: 109525 - path: pubs/JFM/figs/Cross-Section-Potential-Slant.pdf hash: md5 - md5: 03325e72175cbeffe3a038a6efe86794 - size: 363449 + md5: 5f66e7d5d77d0f9c53d737b29f8760e8 + size: 363443 - path: pubs/JFM/figs/MEEM-CPT-Slant-Freq.pdf hash: md5 - md5: 87632752d88b4acd04e25368ff5541ea - size: 137300 + md5: 0a995f31d8f77e5c04e919121923342d + size: 137294 - path: pubs/JFM/figs/Vary-Slopes.pdf hash: md5 - md5: d870c74ff963d9b5d0ac909657d86f31 - size: 178446 + md5: e4b4fc6d45dcf5164714e1f79ef4c8b4 + size: 178440 _clean-nb-timing-figs: cmd: calkit nb clean "analysis/timing_plots.ipynb" deps: @@ -293,57 +298,57 @@ stages: md5: 6b1b55ca488e86706de62d5caab79a13 size: 20403 timing-figs: - cmd: calkit nb execute --environment openflash-on-branch --no-check --to + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/timing_plots.ipynb" deps: - - path: .calkit/env-locks/openflash-on-branch + - path: .calkit/env-locks/openflash-on-branch-tex hash: md5 - md5: 6fee7550c7f8d298fc987043523e190e.dir - size: 9764 + md5: ac0655df47557fc89aae3e74f4e0cbab.dir + size: 2838 nfiles: 1 - path: .calkit/notebooks/cleaned/analysis/timing_plots.ipynb hash: md5 - md5: 3d8acfcba713200795b331612bbb3d1e - size: 22441 + md5: 246e8563b970cb9963fdd816baadc47a + size: 22432 - path: analysis/data/timing.pkl hash: md5 md5: 8f44378ee5eed677e435c38ac905d0af size: 4035 - - path: sea-lab-utils + - path: analysis/sea-lab-utils hash: md5 - md5: bee8da5063bc568e5251764466d97f5c.dir - size: 18456 - nfiles: 24 + md5: 22cff2f89b0191c779029f1a327c6977.dir + size: 16569 + nfiles: 22 outs: - path: .calkit/notebooks/executed/analysis/timing_plots.ipynb hash: md5 - md5: 06854bad21c3244180cab6fba4f884db - size: 358957 + md5: e285e78bfb80cd8c5c7537e022328cdb + size: 358735 - path: .calkit/notebooks/html/analysis/timing_plots.html hash: md5 - md5: 35b5a43d18ba7232476414935e17c72b - size: 699004 + md5: 0a9c6545f1fce6f651868dbf0ea72459 + size: 706070 - path: pubs/JFM/figs/MEEM-CPT-Speed-Comparison.pdf hash: md5 - md5: 045f6fb53f9cb56bdcf6153110d4574d - size: 136511 + md5: 1e9eb7738380bccdf596ec78da5d8fbe + size: 136505 - path: pubs/JFM/figs/MEEM-CPT-Time-Matrix-Comparison.pdf hash: md5 - md5: 136f64c475df70c3a029d8c96d3ea507 - size: 104576 + md5: f3839a8a42af7a0287e670ae1b7380c1 + size: 104570 - path: pubs/JFM/figs/MEEM-Comp-Distribution.pdf hash: md5 - md5: d05d914346cd03a9b4662b36903a423d - size: 137530 + md5: c58f151d7213e12e807a43c0bc4caa97 + size: 137524 sparsity-figs: cmd: calkit nb execute --environment openflash-on-main --no-check --to html "analysis/sparsity_plots.ipynb" deps: - path: .calkit/env-locks/openflash-on-main hash: md5 - md5: f54044d40708eae49d172a85254513fa.dir - size: 9592 - nfiles: 1 + md5: 98482ae17ceccf2fb913dca62c3c1c8d.dir + size: 16887 + nfiles: 2 - path: .calkit/notebooks/cleaned/analysis/sparsity_plots.ipynb hash: md5 md5: ee07dfad96a7d0196a3b895c62bc6502 @@ -351,71 +356,71 @@ stages: outs: - path: .calkit/notebooks/executed/analysis/sparsity_plots.ipynb hash: md5 - md5: 9f677e417bc9f3bc1489082de1ac3c7e + md5: b52f7cce4519baf4d43702f3f3c05add size: 109739 - path: .calkit/notebooks/html/analysis/sparsity_plots.html hash: md5 - md5: 81ffac3dae40fbb64803344eedfcfb20 - size: 416883 + md5: bdc6bfa41a308a72bb96a6fbde91384a + size: 424173 - path: pubs/JFM/figs/A_sparsity_plot.pdf hash: md5 - md5: 51308691ed65e0f0324b836298183256 - size: 12561 + md5: a50e3735d603490c6d452660bdd21829 + size: 12555 - path: pubs/JFM/figs/B_sparsity_plot.pdf hash: md5 - md5: 5e51a27b563089ec5a0f50f6d830a573 - size: 9202 + md5: e96ff0df15997d1299f9cb14d4c0695b + size: 9196 - path: pubs/JFM/figs/C_sparsity_plot.pdf hash: md5 - md5: 736a8d4aa4366f94204eeeef422ece15 - size: 9863 + md5: 5a1dc95ecb3ca3a5a7d2c5dd3372099e + size: 9857 convergence-figs: - cmd: calkit nb execute --environment openflash-on-branch --no-check --to + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/convergence-results.ipynb" deps: - - path: .calkit/env-locks/openflash-on-branch + - path: .calkit/env-locks/openflash-on-branch-tex hash: md5 - md5: 6fee7550c7f8d298fc987043523e190e.dir - size: 9764 + md5: ac0655df47557fc89aae3e74f4e0cbab.dir + size: 2838 nfiles: 1 - path: .calkit/notebooks/cleaned/analysis/convergence-results.ipynb hash: md5 - md5: 8cf6a258c632999e7b933e7dcdff214a - size: 45478 - - path: sea-lab-utils + md5: 4cd2afb7b3d65985bde73850590d2e49 + size: 45469 + - path: analysis/sea-lab-utils hash: md5 - md5: bee8da5063bc568e5251764466d97f5c.dir - size: 18456 - nfiles: 24 + md5: 22cff2f89b0191c779029f1a327c6977.dir + size: 16569 + nfiles: 22 outs: - path: .calkit/notebooks/executed/analysis/convergence-results.ipynb hash: md5 - md5: acf2047d06b687e067222f7d6392dcc6 - size: 232924 + md5: 5445112241e21d97349d2c0f3e1ea977 + size: 232695 - path: .calkit/notebooks/html/analysis/convergence-results.html hash: md5 - md5: ea60e8624fe5133832c957c460f6232c - size: 609842 + md5: bc2f89a8da3403c8acde90f6ff558be9 + size: 616908 - path: pubs/JFM/figs/alpha-beta-explanation.pdf hash: md5 - md5: c5ccd7b1c7f815aeca90c3e5dfc0b0f4 - size: 380172 + md5: 96bb0c76660c0b2a431c06951e936536 + size: 380162 - path: pubs/JFM/figs/alpha-beta-to-trend.pdf hash: md5 - md5: fc2a573dbc4458d901d43f22c3d40ce7 - size: 403400 + md5: 21a70e0dd0c6cb605c684c1bb64a648b + size: 403379 - path: pubs/JFM/figs/convergence-fit-assessment.pdf hash: md5 - md5: e61b9659ab6a5593c1ec1e62f388dd56 - size: 209396 + md5: 5eeba467250e37dd2cf68b7f3534d65b + size: 209390 graphical-abstract: cmd: calkit latex build -e tex --no-check pubs/JFM/figs/graph_abstract.tex deps: - path: .calkit/env-locks/tex hash: md5 - md5: 1d20723629fc752e4776c7e1d6cb328e.dir - size: 1147 - nfiles: 1 + md5: b404863b132f96ede5eaceb8cc787b66.dir + size: 2294 + nfiles: 2 - path: pubs/JFM/figs/graph_abstract.tex hash: md5 md5: ec8dbe649b3b67812906d82d7a78ce23 @@ -423,9 +428,36 @@ stages: outs: - path: pubs/JFM/figs/graph_abstract.log hash: md5 - md5: a9b22b3b8142f53823030431b128ca89 + md5: bd6c96400ddc73af24ef25723bb87d9c size: 16701 - path: pubs/JFM/figs/graph_abstract.pdf hash: md5 - md5: ab6898db6da82271616f7b82ad05056a + md5: 0410b888c57ee3da4d4deb1f69979613 size: 11873 + test-latex: + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to + html "analysis/test-latex.ipynb" + deps: + - path: .calkit/env-locks/openflash-on-branch-tex + hash: md5 + md5: ac0655df47557fc89aae3e74f4e0cbab.dir + size: 2838 + nfiles: 1 + - path: .calkit/notebooks/cleaned/analysis/test-latex.ipynb + hash: md5 + md5: 42b2bcc4fc7904f7320328006a722e72 + size: 2044 + - path: analysis/sea-lab-utils + hash: md5 + md5: 22cff2f89b0191c779029f1a327c6977.dir + size: 16569 + nfiles: 22 + outs: + - path: .calkit/notebooks/executed/analysis/test-latex.ipynb + hash: md5 + md5: 329a5516b384390108939537b49e0948 + size: 4897 + - path: .calkit/notebooks/html/analysis/test-latex.html + hash: md5 + md5: 3044494d054f0b335da1c0bc691d9c3d + size: 282704 diff --git a/dvc.yaml b/dvc.yaml index 90d4e2f6..848b91b5 100644 --- a/dvc.yaml +++ b/dvc.yaml @@ -1,11 +1,12 @@ stages: validate-w-capy: - cmd: calkit nb execute --environment openflash-on-branch + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/validation_with_capytaine_plots.ipynb" deps: - .calkit/notebooks/cleaned/analysis/validation_with_capytaine_plots.ipynb - - .calkit/env-locks/openflash-on-branch + - analysis/sea-lab-utils + - .calkit/env-locks/openflash-on-branch-tex outs: - pubs/JFM/figs/MEEM_vs_Capytaine_Nonslant_Validation.pdf - .calkit/notebooks/executed/analysis/validation_with_capytaine_plots.ipynb: @@ -15,14 +16,14 @@ stages: desc: Automatically generated from the 'validate-w-capy' stage in calkit.yaml. Changes made here will be overwritten. low-m0-figs: - cmd: calkit nb execute --environment openflash-on-branch + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/low_m0_plots.ipynb" deps: - .calkit/notebooks/cleaned/analysis/low_m0_plots.ipynb - package/src/ - dev/python/limiting-cases/low_m0.py - - sea-lab-utils - - .calkit/env-locks/openflash-on-branch + - analysis/sea-lab-utils + - .calkit/env-locks/openflash-on-branch-tex outs: - pubs/JFM/figs/MEEM-Low-Freq.pdf - .calkit/notebooks/executed/analysis/low_m0_plots.ipynb: @@ -32,15 +33,15 @@ stages: desc: Automatically generated from the 'low-m0-figs' stage in calkit.yaml. Changes made here will be overwritten. slant-figs: - cmd: calkit nb execute --environment openflash-on-branch + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/slant_data_plots.ipynb" deps: - .calkit/notebooks/cleaned/analysis/slant_data_plots.ipynb - analysis/data/slants.pkl - analysis/data/slope-slants.pkl - analysis/data/potential-slants.pkl - - sea-lab-utils - - .calkit/env-locks/openflash-on-branch + - analysis/sea-lab-utils + - .calkit/env-locks/openflash-on-branch-tex outs: - pubs/JFM/figs/MEEM-CPT-Slant-Freq.pdf - pubs/JFM/figs/Vary-Slopes.pdf @@ -53,13 +54,13 @@ stages: desc: Automatically generated from the 'slant-figs' stage in calkit.yaml. Changes made here will be overwritten. timing-figs: - cmd: calkit nb execute --environment openflash-on-branch + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/timing_plots.ipynb" deps: - .calkit/notebooks/cleaned/analysis/timing_plots.ipynb - analysis/data/timing.pkl - - sea-lab-utils - - .calkit/env-locks/openflash-on-branch + - analysis/sea-lab-utils + - .calkit/env-locks/openflash-on-branch-tex outs: - pubs/JFM/figs/MEEM-Comp-Distribution.pdf - pubs/JFM/figs/MEEM-CPT-Speed-Comparison.pdf @@ -71,12 +72,12 @@ stages: desc: Automatically generated from the 'timing-figs' stage in calkit.yaml. Changes made here will be overwritten. convergence-figs: - cmd: calkit nb execute --environment openflash-on-branch + cmd: calkit nb execute --environment openflash-on-branch-tex --no-check --to html "analysis/convergence-results.ipynb" deps: - .calkit/notebooks/cleaned/analysis/convergence-results.ipynb - - sea-lab-utils - - .calkit/env-locks/openflash-on-branch + - analysis/sea-lab-utils + - .calkit/env-locks/openflash-on-branch-tex outs: - pubs/JFM/figs/alpha-beta-explanation.pdf - pubs/JFM/figs/alpha-beta-to-trend.pdf @@ -103,6 +104,20 @@ stages: cache: true desc: Automatically generated from the 'sparsity-figs' stage in calkit.yaml. Changes made here will be overwritten. + test-latex: + cmd: calkit nb execute --environment openflash-on-branch-tex + --no-check --to html "analysis/test-latex.ipynb" + deps: + - .calkit/notebooks/cleaned/analysis/test-latex.ipynb + - analysis/sea-lab-utils + - .calkit/env-locks/openflash-on-branch-tex + outs: + - .calkit/notebooks/executed/analysis/test-latex.ipynb: + cache: false + - .calkit/notebooks/html/analysis/test-latex.html: + cache: true + desc: Automatically generated from the 'test-latex' stage in + calkit.yaml. Changes made here will be overwritten. graphical-abstract: cmd: calkit latex build -e tex --no-check pubs/JFM/figs/graph_abstract.tex diff --git a/pubs/JFM/jfm-appendix.tex b/pubs/JFM/jfm-appendix.tex index e0200754..bf323208 100644 --- a/pubs/JFM/jfm-appendix.tex +++ b/pubs/JFM/jfm-appendix.tex @@ -115,13 +115,13 @@ \section{Matching Equations}\label{jfm:appB} \begin{multline}\label{jfm:eq:velocity matching vector equations} \boldsymbol{\mathcal{Z}}^\mathrm{ts} \odot \mathbf{1}_{N^\mathrm{t}1}\vec{R}_1^\mathrm{s}(a)\vec{C}_1^\mathrm{s}+\boldsymbol{\mathcal{Z}}^\mathrm{ts} \odot \mathbf{1}_{N^\mathrm{t}1}\vec{R}_2^\mathrm{s}(a)\vec{C}_2^\mathrm{s}\\ -(h-d_\mathrm{t})\mathrm{diag}\left( \frac{\partial}{\partial r} \vec{R}_1^\mathrm{t}(a)\right)\vec{C}_1^\mathrm{t} -(h-d_\mathrm{t})\mathrm{diag}\left( \frac{\partial}{\partial r} \vec{R}_2^\mathrm{t}(a)\right)\vec{C}_2^\mathrm{t} \\ = \int_{-h}^{-d_\mathrm{t}}\frac{\partial \phi_\mathrm{p}^\mathrm{t}}{\partial r}(a,z) \vec{Z}^\mathrm{t}{}(z) \mathrm{d}z-\int_{-h}^{-d_\mathrm{s}}\frac{\partial \phi_\mathrm{p}^\mathrm{s}}{\partial r}(a,z) \vec{Z}^\mathrm{t}{}(z) \mathrm{d}z \end{multline} -where +where \begin{equation} \vec{R}_1^\ell(r)=[R_{10}^\ell(r), R_{11}^\ell(r),\dots, R_{1(N^\ell-1)}^\ell(r) ] \end{equation} and \begin{equation} - \vec{R}_2^\ell(r)=[R_{20}^\ell(r), R_{21}^\ell(r),\dots, R_{2(N^\ell-1)}^\ell(r) ] + \vec{R}_2^\ell(r)=[R_{20}^\ell(r), R_{21}^\ell(r),\dots, R_{2(N^\ell-1)}^\ell(r) ] \end{equation} are row vectors of radial eigenfunctions; \begin{equation} @@ -134,10 +134,10 @@ \section{Matching Equations}\label{jfm:appB} are column vectors of eigencoefficients; and \begin{equation} \begin{aligned} - &\vec{Z}^\ell(z)=[Z_0^\ell(z),Z_1^\ell(z),\dots, Z_{(N^\ell-1)}^\ell(z)]^T + &\vec{Z}^\ell(z)=[Z_0^\ell(z),Z_1^\ell(z),\dots, Z_{(N^\ell-1)}^\ell(z)]^T \end{aligned} \end{equation} -are column vectors of vertical eigenfunctions, where $\ell$ is $\mathrm{s}$ or $\mathrm{t}$. Additionally, +are column vectors of vertical eigenfunctions, where $\ell$ is $\mathrm{s}$ or $\mathrm{t}$. Additionally, \begin{equation} \begin{aligned} &\boldsymbol{\mathcal{Z}}^\mathrm{st}=\boldsymbol{\mathcal{Z}}^\mathrm{ts}{}^T=\int_{-h}^{-d_\mathrm{s}} \vec{Z}^\mathrm{s}{}(z) \otimes \vec{Z}^\mathrm{t}(z) \mathrm{d}z \end{aligned} @@ -192,60 +192,60 @@ \section{Forms of Matrix A}\label{jfm:sec:Forms of Matrix A} \centering \begin{tabular}{|>{\centering\arraybackslash}p{0.18\linewidth}|c||c|c|c|c|c|} \hline - & & + & & $\vec{C}_{1}^{i_m}$ - & + & $\vec{C}_{2}^{i_m}$ - & - $\vec{C}_{1}^{i_{m+1}}$ - & - $\vec{C}_{2}^{i_{m+1}}$ - \\\hline + & + $\vec{C}_{1}^{i_{m+1}}$ + & + $\vec{C}_{2}^{i_{m+1}}$ + \\\hline & size - & + & $N^{i_m}$ - & + & $N^{i_m}$ - & + & $N^{i_{m+1}}$ - & + & $N^{i_{m+1}}$ - \\ \hline \hline - + \\ \hline \hline + % Row 1 \shortstack{ - $\phi^{i_m}=\phi^{i_{m+1}}$ - \\ at $r=a_m$} - & - $N^{i_m}$ - & - $\mathbf{1}_{N^{i_m}1} \vec{R}_1^{i_m}$ - & - $\mathbf{1}_{N^{i_m}1} \vec{R}_2^{i_m}$ - & - $ \mathbf{1}_{N^{i_m}1} \vec{R}_1^{i_{m+1}}$ - & - $ \mathbf{1}_{N^{i_m}1} \vec{R}_2^{i_{m+1}}$ + $\phi^{i_m}=\phi^{i_{m+1}}$ + \\ at $r=a_m$} + & + $N^{i_m}$ + & + $\mathbf{1}_{N^{i_m}1} \vec{R}_1^{i_m}$ + & + $\mathbf{1}_{N^{i_m}1} \vec{R}_2^{i_m}$ + & + $ \mathbf{1}_{N^{i_m}1} \vec{R}_1^{i_{m+1}}$ + & + $ \mathbf{1}_{N^{i_m}1} \vec{R}_2^{i_{m+1}}$ \\ \hline - + % Row 2 \shortstack{ - $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ - \\ at $r=a_m$} - & + $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ + \\ at $r=a_m$} + & $N^{i_{m+1}}$ - & - $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_1^{i_{m}}$ - & - $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_2^{i_{m}}$ - & - $\mathbf{1}_{N^{i_{m+1}}1} \frac{\partial}{\partial r} \vec{R}_1^{i_{m+1}}$ - & - $\mathbf{1}_{N^{i_{m+1}}1} \frac{\partial}{\partial r} \vec{R}_2^{i_{m+1}}$ + & + $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_1^{i_{m}}$ + & + $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_2^{i_{m}}$ + & + $\mathbf{1}_{N^{i_{m+1}}1} \frac{\partial}{\partial r} \vec{R}_1^{i_{m+1}}$ + & + $\mathbf{1}_{N^{i_{m+1}}1} \frac{\partial}{\partial r} \vec{R}_2^{i_{m+1}}$ \\ \hline \end{tabular} - \caption{MEEM $\mathbf{A}_{m,r}$ sub-matrix when $d_m>d_{m+1}$ ($i_m = \mathrm{s}$ and $i_{m+1} = \mathrm{t}$). + \caption{MEEM $\mathbf{A}_{m,r}$ sub-matrix when $d_m>d_{m+1}$ ($i_m = \mathrm{s}$ and $i_{m+1} = \mathrm{t}$). Note all radial eigenfunctions and their derivatives are evaluated at $r=a_m$.} \label{jfm:tab:MEEM-A_mr-matrix-case-1} \end{table} @@ -256,59 +256,59 @@ \section{Forms of Matrix A}\label{jfm:sec:Forms of Matrix A} \centering \begin{tabular}{|>{\centering\arraybackslash}p{0.18\linewidth}|c||c|c|c|c|c|} \hline - & & + & & $\vec{C}_{1}^{i_m}$ - & + & $\vec{C}_{2}^{i_m}$ - & - $\vec{C}_{1}^{i_{m+1}}$ - & - $\vec{C}_{2}^{i_{m+1}}$ - \\\hline - &size& + & + $\vec{C}_{1}^{i_{m+1}}$ + & + $\vec{C}_{2}^{i_{m+1}}$ + \\\hline + &size& $N^{i_m}$ - & + & $N^{i_m}$ - & + & $N^{i_{m+1}}$ - & + & $N^{i_{m+1}}$ - \\ \hline \hline - + \\ \hline \hline + % Row 1 \shortstack{ - $\phi^{i_m}=\phi^{i_{m+1}}$ - \\ + $\phi^{i_m}=\phi^{i_{m+1}}$ + \\ at $r=a_m$ - } - & - $N^{i_{m+1}}$ - & - $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_1^{i_{m}}$ - & - $\mathbf{1}_{N^{i_{m+1}}1} \vec{R}_2^{i_{m}}$ - & - $\mathbf{1}_{N^{i_{m+1}}1} \vec{R}_1^{i_{m+1}}$ - & - $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_2^{i_{m+1}}$ + } + & + $N^{i_{m+1}}$ + & + $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_1^{i_{m}}$ + & + $\mathbf{1}_{N^{i_{m+1}}1} \vec{R}_2^{i_{m}}$ + & + $\mathbf{1}_{N^{i_{m+1}}1} \vec{R}_1^{i_{m+1}}$ + & + $ \mathbf{1}_{N^{i_{m+1}}1} \vec{R}_2^{i_{m+1}}$ \\ \hline - + % Row 2 \shortstack{ - $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ - \\ + $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ + \\ at $r=a_m$ - } - & + } + & $N^{i_{m}}$ - & - $\mathbf{1}_{N^{i_{m}}1} \frac{\partial}{\partial r} \vec{R}_1^{i_{m}}$ - & - $\mathbf{1}_{N^{i_{m}}1} \frac{\partial}{\partial r} \vec{R}_2^{i_{m}}$ - & - $ \mathbf{1}_{N^{i_{m}}1} \vec{R}_1^{i_{m+1}}$ - & - $ \mathbf{1}_{N^{i_{m}}1} \vec{R}_2^{i_{m+1}}$ + & + $\mathbf{1}_{N^{i_{m}}1} \frac{\partial}{\partial r} \vec{R}_1^{i_{m}}$ + & + $\mathbf{1}_{N^{i_{m}}1} \frac{\partial}{\partial r} \vec{R}_2^{i_{m}}$ + & + $ \mathbf{1}_{N^{i_{m}}1} \vec{R}_1^{i_{m+1}}$ + & + $ \mathbf{1}_{N^{i_{m}}1} \vec{R}_2^{i_{m+1}}$ \\ \hline \end{tabular} \caption{MEEM $\mathbf{A}_{m,r}$ sub-matrix when $d_m{\centering\arraybackslash}p{0.18\linewidth}|c||c|c|c|c|c|} \hline & - & + & $\vec{C}_{1}^{i_m}$ - & + & $\vec{C}_{2}^{i_m}$ - & - $\vec{C}_{1}^{i_{m+1}}$ - & - $\vec{C}_{2}^{i_{m+1}}$ - \\\hline + & + $\vec{C}_{1}^{i_{m+1}}$ + & + $\vec{C}_{2}^{i_{m+1}}$ + \\\hline & size - & + & $N^{i_m}$ - & + & $N^{i_m}$ - & + & $N^{i_{m+1}}$ - & + & $N^{i_{m+1}}$ - \\ \hline \hline - + \\ \hline \hline + % Row 1 \shortstack{ - $\phi^{i_m}=\phi^{i_{m+1}}$ - \\ - at $r=a_m$} - & - $N^{i_m}$ - & - $(h-d_m) \mathbf{I}^{i_m}$ - & - $(h-d_m) \mathbf{I}^{i_m}$ - & - $-\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}}$ - & - $-\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}}$ + $\phi^{i_m}=\phi^{i_{m+1}}$ + \\ + at $r=a_m$} + & + $N^{i_m}$ + & + $(h-d_m) \mathbf{I}^{i_m}$ + & + $(h-d_m) \mathbf{I}^{i_m}$ + & + $-\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}}$ + & + $-\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}}$ \\ \hline - + % Row 2 \shortstack{ - $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ - \\ + $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ + \\ at $r=a_m$ - } - & + } + & $N^{i_{m+1}}$ - & - $\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m}$ - & - $\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m}$ - & - $-(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ - & - $-(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ + & + $\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m}$ + & + $\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m}$ + & + $-(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ + & + $-(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ \\ \hline \end{tabular} \caption{MEEM $\mathbf{A}_{m,z}$ sub-matrix when $d_m>d_{m+1}$ ($i_m = \mathrm{s}$ and $i_{m+1} = \mathrm{t}$). @@ -391,59 +391,59 @@ \section{Forms of Matrix A}\label{jfm:sec:Forms of Matrix A} \centering \begin{tabular}{|>{\centering\arraybackslash}p{0.18\linewidth}|c||c|c|c|c|c|} \hline - & & + & & $\vec{C}_{1}^{i_m}$ - & + & $\vec{C}_{2}^{i_m}$ - & - $\vec{C}_{1}^{i_{m+1}}$ - & - $\vec{C}_{2}^{i_{m+1}}$ - \\\hline + & + $\vec{C}_{1}^{i_{m+1}}$ + & + $\vec{C}_{2}^{i_{m+1}}$ + \\\hline & size - & + & $N^{i_m}$ - & + & $N^{i_m}$ - & + & $N^{i_{m+1}}$ - & + & $N^{i_{m+1}}$ - \\ \hline \hline - + \\ \hline \hline + % Row 1 \shortstack{ - $\phi^{i_m}=\phi^{i_{m+1}}$ - \\ - at $r=a_m$} - & - $N^{i_{m+1}}$ - & - $-\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m} $ - & - $-\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m}$ - & - $(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ - & - $(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ + $\phi^{i_m}=\phi^{i_{m+1}}$ + \\ + at $r=a_m$} + & + $N^{i_{m+1}}$ + & + $-\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m} $ + & + $-\boldsymbol{\mathcal{Z}}^{i_{m+1}i_m}$ + & + $(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ + & + $(h-d_{m+1}) \mathbf{I}^{i_{m+1}}$ \\ \hline - + % Row 2 \shortstack{ - $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ - \\ - at $r=a_m$} - & + $\frac{\partial}{\partial r}\phi^{i_m}=\frac{\partial}{\partial r}\phi^{i_{m+1}}$ + \\ + at $r=a_m$} + & $N^{i_{m}}$ - & - $-(h-d_{m}) \mathbf{I}^{i_{m}}$ - & - $-(h-d_{m}) \mathbf{I}^{i_{m}}$ - & - $\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}} $ - & - $\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}} $ + & + $-(h-d_{m}) \mathbf{I}^{i_{m}}$ + & + $-(h-d_{m}) \mathbf{I}^{i_{m}}$ + & + $\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}} $ + & + $\boldsymbol{\mathcal{Z}}^{i_mi_{m+1}} $ \\ \hline \end{tabular} \caption{MEEM $\mathbf{A}_{m,z}$ sub-matrix when $d_m