GEOPY-2731: Replace InputFile for BaseUIJson class

docs/source/api_reference.rst → docs/source/api/api_reference.rst

@@ -1,24 +1,15 @@
 API Reference
 =============
 
+
 Subpackages
 -----------
 
 .. toctree::
    :maxdepth: 4
 
    surface_apps.iso_surfaces
-
-Submodules
-----------
-
-surface\_apps.driver module
----------------------------
-
-.. automodule:: surface_apps.driver
-   :members:
-   :undoc-members:
-   :show-inheritance:
+   surface_apps.surface_normals
 
 Module contents
 ---------------

docs/source/surface_apps.iso_surfaces.rst → docs/source/api/surface_apps.iso_surfaces.rst

@@ -12,10 +12,10 @@ surface\_apps.iso\_surfaces.driver module
    :undoc-members:
    :show-inheritance:
 
-surface\_apps.iso\_surfaces.params module
------------------------------------------
+surface\_apps.iso\_surfaces.options module
+------------------------------------------
 
-.. automodule:: surface_apps.iso_surfaces.params
+.. automodule:: surface_apps.iso_surfaces.options
    :members:
    :undoc-members:
    :show-inheritance:

docs/source/api/surface_apps.surface_normals.rst

@@ -0,0 +1,29 @@
+surface\_apps.surface\_normals package
+======================================
+
+Submodules
+----------
+
+surface\_apps.surface\_normals.driver module
+--------------------------------------------
+
+.. automodule:: surface_apps.surface_normals.driver
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+surface\_apps.surface\_normals.options module
+---------------------------------------------
+
+.. automodule:: surface_apps.surface_normals.options
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: surface_apps.surface_normals
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/source/index.rst

@@ -24,7 +24,7 @@ Content
    getting_started
    usage
    iso_surfaces
-   api_reference
+   api/api_reference
    release_notes
    THIRD_PARTY_SOFTWARE
 

environments/py-3.12-linux-64-dev.conda.lock.yml

@@ -1,59 +1,60 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: 042bb6f2771b0982a365cf34829041d6282dbb90cae2d960ed023844fc384968
+# input_hash: 3d272b222479b1ff3d111c77b7d1a98087ce85a745ecd23d8d382912cb8b5e1d
 
 channels:
   - conda-forge
   - nodefaults
 dependencies:
   - _openmp_mutex=4.5=20_gnu
   - alabaster=1.0.0=pyhd8ed1ab_1
-  - annotated-types=0.7.0=pyhd8ed1ab_1
+  - annotated-types=0.8.0=pyhd8ed1ab_0
   - aom=3.14.1=pl5321h039972f_1
   - astroid=4.0.4=py312h7900ff3_0
-  - aws-c-auth=0.10.3=hea842a7_2
-  - aws-c-cal=0.9.14=h78948cc_2
-  - aws-c-common=0.14.0=hb03c661_0
-  - aws-c-compression=0.3.2=haa0cbde_2
-  - aws-c-http=0.11.0=h6488f85_2
-  - aws-c-io=0.26.3=h5b668fc_4
-  - aws-c-s3=0.12.5=hb916526_1
-  - aws-c-sdkutils=0.2.4=haa0cbde_6
-  - aws-checksums=0.2.10=haa0cbde_2
+  - aws-c-auth=0.10.4=h4610da3_2
+  - aws-c-cal=0.9.15=h6bbde05_1
+  - aws-c-common=0.14.3=hb03c661_0
+  - aws-c-compression=0.3.2=h01ee8f8_5
+  - aws-c-http=0.11.0=hbe094ff_5
+  - aws-c-io=0.27.5=h4f381ba_1
+  - aws-c-s3=0.13.1=h7508075_1
+  - aws-c-sdkutils=0.2.7=h01ee8f8_3
+  - aws-checksums=0.2.10=h01ee8f8_5
   - babel=2.18.0=pyhcf101f3_1
   - backports.zstd=1.6.0=py312h90b7ffd_0
   - blosc=1.21.6=he440d0b_1
   - brotli=1.2.0=hed03a55_1
   - brotli-bin=1.2.0=hb03c661_1
   - brotli-python=1.2.0=py312hdb49522_1
   - brunsli=0.1=hd1e3526_2
-  - bzip2=1.0.8=hda65f42_9
-  - c-ares=1.34.6=hb03c661_0
-  - c-blosc2=3.1.3=hc31b594_0
-  - ca-certificates=2026.5.20=hbd8a1cb_0
-  - cached-property=1.5.2=hd8ed1ab_1
-  - cached_property=1.5.2=pyha770c72_1
-  - certifi=2026.5.20=pyhd8ed1ab_0
+  - bzip2=1.0.8=hda65f42_10
+  - c-ares=1.34.8=h280c20c_1
+  - c-blosc2=3.3.2=hc31b594_0
+  - ca-certificates=2026.7.22=hbd8a1cb_0
+  - cached-property=1.5.2=hd8ed1ab_2
+  - cached_property=1.5.2=pyha770c72_2
+  - certifi=2026.7.22=pyhd8ed1ab_0
   - charls=2.4.4=hecca717_0
-  - charset-normalizer=3.4.7=pyhd8ed1ab_0
+  - charset-normalizer=3.4.9=pyhd8ed1ab_0
   - colorama=0.4.6=pyhd8ed1ab_1
   - contourpy=1.3.3=py312h0a2e395_4
-  - coverage=7.14.1=py312h8a5da7c_0
+  - coverage=7.15.4=py312h589e9ff_1
   - cycler=0.12.1=pyhcf101f3_2
   - dav1d=1.2.1=hd590300_0
   - dill=0.4.1=pyhcf101f3_0
-  - docutils=0.21.2=pyhd8ed1ab_1
+  - docutils=0.22.4=pyhd8ed1ab_0
   - exceptiongroup=1.3.1=pyhd8ed1ab_0
   - fonttools=4.63.0=py312h8a5da7c_0
-  - freetype=2.14.3=ha770c72_0
-  - giflib=5.2.2=hd590300_0
-  - h2=4.3.0=pyhcf101f3_0
+  - freetype=2.14.3=ha770c72_1
+  - giflib=5.2.2=ha257d8a_1
+  - h2=4.4.1=pyhcf101f3_0
   - h5py=3.16.0=nompi_py312ha829cd9_102
-  - hdf5=2.1.0=nompi_h735b18d_107
-  - hpack=4.1.0=pyhd8ed1ab_0
+  - hdf5=2.2.0=nompi_hc529623_100
+  - hpack=4.2.0=pyhd8ed1ab_0
   - hyperframe=6.1.0=pyhd8ed1ab_0
-  - idna=3.17=pyhcf101f3_0
-  - imagecodecs=2026.6.6=py312h71e39d9_1
+  - icu=78.3=h54a6638_2
+  - idna=3.18=pyhcf101f3_0
+  - imagecodecs=2026.6.26=py312h5b112d2_4
   - imageio=2.37.0=pyhfb79c49_0
   - imagesize=2.0.0=pyhd8ed1ab_0
   - importlib-metadata=9.0.0=pyhcf101f3_0
@@ -63,76 +64,77 @@ dependencies:
   - jxrlib=1.1=hd590300_3
   - keyutils=1.6.3=hb9d3cd8_0
   - kiwisolver=1.5.0=py312h0a2e395_0
-  - krb5=1.22.2=ha1258a1_0
+  - krb5=1.22.2=hbde042b_1
   - lazy-loader=0.5=pyhd8ed1ab_0
   - lcms2=2.19.1=h0c24ade_1
-  - ld_impl_linux-64=2.45.1=default_hbd61a6d_102
-  - lerc=4.1.0=hdb68285_0
+  - ld_impl_linux-64=2.46.1=default_hbd61a6d_102
+  - lerc=4.2.0=hdb68285_0
   - libaec=1.1.5=h088129d_0
-  - libavif16=1.4.2=hf998032_1
-  - libblas=3.11.0=8_h4a7cf45_openblas
+  - libavif16=1.4.2=h0ed3d04_3
+  - libblas=3.11.0=9_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
-  - libcurl=8.20.0=hcf29cc6_0
-  - libdeflate=1.25=h17f619e_0
+  - libcblas=3.11.0=9_h0358290_openblas
+  - libcurl=8.21.0=heca4667_4
+  - libdeflate=1.25=hd45a770_1
   - libedit=3.1.20250104=pl5321h7949ede_0
-  - libev=4.33=hd590300_2
+  - libev=4.33=h280c20c_3
   - libexpat=2.8.1=hecca717_1
   - 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
-  - libgomp=15.2.0=he0feb66_19
-  - libhwy=1.4.0=h10be129_0
-  - libjpeg-turbo=3.1.4.1=hb03c661_0
-  - libjxl=0.11.2=h174a0a3_1
-  - liblapack=3.11.0=8_h47877c9_openblas
-  - liblzma=5.8.3=hb03c661_0
+  - libfreetype=2.14.3=ha770c72_1
+  - libfreetype6=2.14.3=h73754d4_1
+  - libgcc=16.1.0=ha9f2e26_1
+  - libgcc-ng=16.1.0=h69a702a_1
+  - libgfortran=16.1.0=h69a702a_1
+  - libgfortran5=16.1.0=h79bb938_1
+  - libgomp=16.1.0=he0feb66_1
+  - libhwy=1.4.0=h3a9caae_0
+  - libjpeg-turbo=3.2.0=hb03c661_1
+  - libjxl=0.12.0=h174a0a3_1
+  - liblapack=3.11.0=9_h47877c9_openblas
+  - liblzma=5.8.3=hb03c661_1
   - libnghttp2=1.68.1=h877daf1_0
   - libnsl=2.0.1=hb9d3cd8_1
-  - libopenblas=0.3.33=pthreads_h94d23a6_0
+  - libopenblas=0.3.34=pthreads_h94d23a6_0
   - libpng=1.6.58=h421ea60_0
-  - libsqlite=3.53.2=h0c1763c_0
+  - libpsl=0.23.0=hf670292_0
+  - libsqlite=3.53.4=hf4e2dac_0
   - libssh2=1.11.1=hcf80075_0
-  - libstdcxx=15.2.0=h934c35e_19
-  - libstdcxx-ng=15.2.0=hdf11a46_19
-  - libtiff=4.7.1=h9d88235_1
-  - libuuid=2.42.1=h5347b49_0
-  - libwebp-base=1.6.0=hd42ef1d_0
+  - libstdcxx=16.1.0=h934c35e_1
+  - libstdcxx-ng=16.1.0=hdf11a46_1
+  - libtiff=4.7.2=h9d88235_0
+  - libuuid=2.42.2=h5347b49_0
+  - libwebp-base=1.6.0=hd42ef1d_1
   - libxcb=1.17.0=h8a09558_0
-  - libxcrypt=4.4.36=hd590300_1
-  - libzlib=1.3.2=h25fd6f3_2
+  - libxcrypt=4.4.38=h280c20c_0
+  - libzlib=1.3.2=h25fd6f3_3
   - libzopfli=1.0.3=h9c3ff4c_0
   - lz4-c=1.10.0=h5888daf_1
   - markupsafe=3.0.3=py312h8a5da7c_1
   - matplotlib-base=3.10.9=py312he3d6523_0
   - mccabe=0.7.0=pyhd8ed1ab_1
   - munkres=1.1.4=pyhd8ed1ab_1
-  - ncurses=6.6=hdb14827_0
+  - ncurses=6.6=hdb14827_1
   - networkx=3.6.1=pyhcf101f3_0
   - numpy=2.4.6=py312h33ff503_0
   - openjpeg=2.5.4=h55fea9a_0
-  - openjph=0.28.1=h8d634f6_0
-  - openssl=3.6.3=h35e630c_0
-  - packaging=26.2=pyhc364b38_0
-  - pillow=12.2.0=py312h50c33e8_0
-  - pip=26.1.2=pyh8b19718_0
-  - platformdirs=4.10.0=pyhcf101f3_0
+  - openjph=0.31.0=h8d634f6_0
+  - openssl=3.6.3=h35e630c_1
+  - packaging=26.3=pyhc364b38_0
+  - pillow=12.3.0=py312h50c33e8_0
+  - pip=26.2.1=pyh8b19718_0
+  - platformdirs=4.11.1=pyhcf101f3_0
   - pluggy=1.6.0=pyhf9edf01_1
   - psutil=7.2.2=py312h5253ce2_0
-  - pthread-stubs=0.4=hb9d3cd8_1002
+  - pthread-stubs=0.4=hb03c661_1003
   - pydantic=2.12.5=pyhcf101f3_1
   - pydantic-core=2.41.5=py312h868fb18_1
   - pygments=2.20.0=pyhd8ed1ab_0
-  - pylint=4.0.6=pyhcf101f3_0
+  - pylint=4.0.7=pyhcf101f3_0
   - pyparsing=3.3.2=pyhcf101f3_0
   - pysocks=1.7.1=pyha55dd90_7
-  - pytest=9.0.3=pyhc364b38_1
+  - pytest=9.1.1=pyhc364b38_2
   - pytest-cov=7.1.0=pyhcf101f3_0
   - python=3.12.13=hd63d673_0_cpython
   - python-dateutil=2.9.0.post0=pyhe01879c_2
@@ -143,48 +145,47 @@ dependencies:
   - readline=8.3=h853b02a_0
   - requests=2.34.2=pyhcf101f3_0
   - roman-numerals=4.1.0=pyhd8ed1ab_0
-  - roman-numerals-py=4.1.0=pyhd8ed1ab_0
-  - s2n=1.7.3=hc5a330e_0
+  - s2n=1.7.6=h7e3ee7f_0
   - scikit-image=0.26.0=np2py312h4ae17e4_0
   - scipy=1.17.1=py312h54fa4ab_1
-  - setuptools=82.0.1=pyh332efcf_0
+  - setuptools=84.0.0=pyh332efcf_0
   - six=1.17.0=pyhe01879c_1
   - snappy=1.2.2=h03e3b7b_1
   - snowballstemmer=3.1.1=pyhd8ed1ab_0
-  - sphinx=8.3.0=pyhd8ed1ab_0
-  - sphinx-autodoc-typehints=3.5.2=pyhd8ed1ab_0
-  - sphinx-rtd-theme=3.1.0=hd8ed1ab_0
-  - sphinx_rtd_theme=3.1.0=pyha770c72_0
+  - sphinx=9.1.0=pyhd8ed1ab_0
+  - sphinx-autodoc-typehints=3.13.2=pyhd8ed1ab_0
+  - sphinx-rtd-theme=3.1.0=h9eada29_2
+  - sphinx_rtd_theme=3.1.0=pyhcf101f3_2
   - sphinxcontrib-applehelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-devhelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-htmlhelp=2.1.0=pyhd8ed1ab_1
   - sphinxcontrib-jquery=4.1=pyhd8ed1ab_1
   - sphinxcontrib-jsmath=1.0.1=pyhd8ed1ab_1
   - sphinxcontrib-qthelp=2.0.0=pyhd8ed1ab_1
   - sphinxcontrib-serializinghtml=2.0.0=pyhd8ed1ab_0
-  - svt-av1=4.0.1=hecca717_0
-  - tifffile=2026.6.1=pyhd8ed1ab_0
-  - tk=8.6.13=noxft_h366c992_103
+  - svt-av1=4.2.0=hecca717_0
+  - tifffile=2026.7.31=pyhd8ed1ab_0
+  - tk=8.6.13=noxft_hd70dff1_3
   - tomli=2.4.1=pyhcf101f3_0
-  - tomlkit=0.15.0=pyha770c72_0
-  - tqdm=4.68.2=pyh8f84b5b_1
-  - typing-extensions=4.15.0=h396c80c_0
-  - typing-inspection=0.4.2=pyhcf101f3_2
-  - typing_extensions=4.15.0=pyhcf101f3_0
-  - tzdata=2025c=hc9c84f9_1
+  - tomlkit=0.15.1=pyhcf101f3_0
+  - tqdm=4.70.0=pyh8f84b5b_0
+  - typing-extensions=4.16.0=h69aa097_0
+  - typing-inspection=0.4.3=pyhcf101f3_0
+  - typing_extensions=4.16.0=pyhcf101f3_0
+  - tzdata=2026c=h151e31d_0
   - unicodedata2=17.0.1=py312h4c3975b_0
   - urllib3=2.7.0=pyhd8ed1ab_0
   - wheel=0.47.0=pyhd8ed1ab_0
-  - xorg-libxau=1.0.12=hb03c661_1
-  - xorg-libxdmcp=1.1.5=hb03c661_1
+  - xorg-libxau=1.0.12=hb03c661_2
+  - xorg-libxdmcp=1.1.5=hb03c661_2
   - yaml=0.2.5=h280c20c_3
   - zfp=1.0.1=h909a3a2_5
   - zipp=4.1.0=pyhcf101f3_0
   - zlib-ng=2.3.3=hceb46e0_1
   - zstd=1.5.7=hb78ec9c_6
   - pip:
-    - geoapps-utils @ git+https://github.com/MiraGeoscience/geoapps-utils.git@31e1f71c37347154e97e6b07e068f7979a67832c
-    - geoh5py @ git+https://github.com/MiraGeoscience/geoh5py.git@37016b8cbe1db7d880c9c2ae724d48ab09962c28
+    - geoapps-utils @ git+https://github.com/MiraGeoscience/geoapps-utils.git@76a52e34cf92ec343bbba3e1399f008cdc2daf99
+    - geoh5py @ git+https://github.com/MiraGeoscience/geoh5py.git@0c2186088c98fdb08cfadbad5723d096ee46f189
 
 variables:
   KMP_WARNINGS: 0