diff --git a/.docs/Notebooks/mfusg_transport_tutorial07c_ChainDecay.py b/.docs/Notebooks/mfusg_transport_07c_ChainDecay_dev.py similarity index 100% rename from .docs/Notebooks/mfusg_transport_tutorial07c_ChainDecay.py rename to .docs/Notebooks/mfusg_transport_07c_ChainDecay_dev.py diff --git a/.docs/Notebooks/mfusg_transport_tutorial08_Lake.py b/.docs/Notebooks/mfusg_transport_08_Lake_dev.py similarity index 100% rename from .docs/Notebooks/mfusg_transport_tutorial08_Lake.py rename to .docs/Notebooks/mfusg_transport_08_Lake_dev.py diff --git a/.docs/conf.py b/.docs/conf.py index a88ef3b9ab..a254d30019 100644 --- a/.docs/conf.py +++ b/.docs/conf.py @@ -92,13 +92,15 @@ print(" ".join(cmd)) os.system(" ".join(cmd)) -# -- convert tutorial scripts and run example notebooks ---------------------- +# -- convert and run tutorial and example notebooks ---------------------- if not on_rtd: - nbs_py = Path("Notebooks").glob("*.py") - for py in nbs_py: + for py in Path("Notebooks").glob("*.py"): + if not ("tutorial" in py.name or "example" in py.name): + print(f"skipping {py}") + continue ipynb = py.with_suffix(".ipynb") if ipynb.exists(): - print(f"{ipynb} already exists, skipping") + print(f"Notebook {ipynb} already exists, skipping") continue cmd = ("jupytext", "--to", "ipynb", "--execute", str(py)) print(" ".join(cmd)) diff --git a/.docs/create_rstfiles.py b/.docs/create_rstfiles.py index fc37bdfcc9..b63a70c567 100644 --- a/.docs/create_rstfiles.py +++ b/.docs/create_rstfiles.py @@ -50,6 +50,7 @@ def create_tutorials_rst(): "mf2005": {"title": "MODFLOW-2005", "files": []}, "lgr": {"title": "MODFLOW-LGR", "files": []}, "nwt": {"title": "MODFLOW-NWT", "files": []}, + "mfusg": {"title": "MODFLOW USG", "files": []}, "mt3dms": {"title": "MT3DMS", "files": []}, "pest": {"title": "PEST", "files": []}, "misc": {"title": "Miscellaneous", "files": []}, diff --git a/.docs/examples.rst b/.docs/examples.rst deleted file mode 100644 index f3c467381d..0000000000 --- a/.docs/examples.rst +++ /dev/null @@ -1,151 +0,0 @@ -Examples gallery -================ - -The following examples illustrate the functionality of Flopy. After the `tutorials `_, the examples are the best resource for learning the underlying capabilities of FloPy. - -The basic set of MODFLOW executables as well as the `optional` dependency group are both required to run the tutorials. - -If the tutorial/example scripts detect that they are running within the repository, they will use local example data. -Otherwise they will download example data files where necessary from GitHub. - -Preprocessing and Discretization --------------------------------- - -.. nbgallery:: - :name: dis - - Notebooks/dis_triangle_example - Notebooks/dis_voronoi_example - Notebooks/grid_intersection_example - Notebooks/gridgen_example - Notebooks/modelgrid_examples - Notebooks/raster_intersection_example - - -Postprocessing and Visualization --------------------------------- - -.. nbgallery:: - :name: viz - - Notebooks/load_swr_binary_data_example - Notebooks/plot_array_example - Notebooks/plot_cross_section_example - Notebooks/plot_map_view_example - - -Exporting data --------------- - -.. nbgallery:: - :name: export - - Notebooks/shapefile_export_example - - -Other FloPy features --------------------- - -.. nbgallery:: - :name: flopy - - Notebooks/feat_working_stack_examples - Notebooks/get_transmissivities_example - Notebooks/save_binary_data_file_example - Notebooks/shapefile_feature_examples - - -MODFLOW 6 examples ------------------- - -.. nbgallery:: - :name: mf6 - - Notebooks/mf6_complex_model_example - Notebooks/mf6_parallel_model_splitting_example - Notebooks/mf6_simple_model_example - Notebooks/mf6_support_example - - -MODFLOW USG examples --------------------- - -.. nbgallery:: - :name: mfusg - - Notebooks/mfusg_conduit_examples - Notebooks/mfusg_freyberg_example - Notebooks/mfusg_zaidel_example - - -MODFLOW-2005/MODFLOW-NWT examples ---------------------------------- - -.. nbgallery:: - :name: mf2005 - - Notebooks/drain_return_example - Notebooks/lake_example - Notebooks/mf_watertable_recharge_example - Notebooks/modflow_postprocessing_example - Notebooks/sfrpackage_example - Notebooks/swi2package_example1 - Notebooks/swi2package_example2 - Notebooks/swi2package_example3 - Notebooks/swi2package_example4 - Notebooks/swi2package_example5 - Notebooks/uzf_example - - -MODPATH examples ----------------- - -.. nbgallery:: - :name: modpath - - Notebooks/modpath6_example - Notebooks/modpath7_create_simulation_example - Notebooks/modpath7_structured_example - Notebooks/modpath7_structured_transient_example - Notebooks/modpath7_unstructured_example - Notebooks/modpath7_unstructured_lateral_example - Notebooks/vtk_pathlines_example - - -MT3D and SEAWAT examples ------------------------- - -.. nbgallery:: - :name: mt3d - - Notebooks/mt3d-usgs_example - Notebooks/mt3dms_examples - - -Examples from Bakker and others (2016) --------------------------------------- - -.. nbgallery:: - :name: 2016gw-paper - - Notebooks/groundwater_paper_example_1 - Notebooks/groundwater_paper_uspb_example - - -Examples from Hughes and others (2023) --------------------------------------- - -.. nbgallery:: - :name: 2023gw-paper - - Notebooks/groundwater2023_watershed_example - - -Miscellaneous examples ----------------------- - -.. nbgallery:: - :name: misc - - Notebooks/seawat_henry_example - Notebooks/zonebudget_example diff --git a/.docs/main.rst b/.docs/main.rst index bea538a3d4..557e3fd15b 100644 --- a/.docs/main.rst +++ b/.docs/main.rst @@ -8,7 +8,7 @@ FloPy .. image:: _images/flopylogo.png -**Documentation for version 3.6.0.dev0** +**Documentation for version 3.10.0.dev4** Documentation is generated with Sphinx from the `FloPy repository `_. diff --git a/.docs/tutorials.rst b/.docs/tutorials.rst deleted file mode 100644 index 8f3e6d318d..0000000000 --- a/.docs/tutorials.rst +++ /dev/null @@ -1,102 +0,0 @@ -Tutorials -========= - -The following tutorials demonstrate basic FloPy features and usage with MODFLOW 2005, MODFLOW 6, and related programs. - -The basic set of MODFLOW executables as well as the `optional` dependency group are both required to run the tutorials. - -If the tutorial/example scripts detect that they are running within the repository, they will use local example data. -Otherwise they will download example data files where necessary from GitHub. - -FloPy ------ - -.. toctree:: - :maxdepth: 2 - - Notebooks/array_output_tutorial - Notebooks/export_tutorial - Notebooks/export_vtk_tutorial - Notebooks/external_file_handling_tutorial - - -MODFLOW 6 ---------- - -.. toctree:: - :maxdepth: 2 - - Notebooks/mf6_data_tutorial01 - Notebooks/mf6_data_tutorial02 - Notebooks/mf6_data_tutorial03 - Notebooks/mf6_data_tutorial04 - Notebooks/mf6_data_tutorial05 - Notebooks/mf6_data_tutorial06 - Notebooks/mf6_data_tutorial07 - Notebooks/mf6_data_tutorial08 - Notebooks/mf6_data_tutorial09 - Notebooks/mf6_data_tutorial10 - Notebooks/mf6_output_tutorial01 - Notebooks/mf6_tutorial01 - Notebooks/mf6_lgr_tutorial01 - - -MODFLOW-2005 ------------- - -.. toctree:: - :maxdepth: 2 - - Notebooks/mf_boundaries_tutorial - Notebooks/mf_error_tutorial01 - Notebooks/mf_load_tutorial - Notebooks/mf_tutorial01 - Notebooks/mf_tutorial02 - Notebooks/mf_mnw2_tutorial01 - Notebooks/mf_sfr_tutorial01 - - -MODFLOW-NWT ------------ - -.. toctree:: - :maxdepth: 2 - - Notebooks/nwt_option_blocks_tutorial - - -MODFLOW-USG ------------ - -.. toctree:: - :maxdepth: 2 - - Notebooks/mfusg_transport_tutorial01_1D - Notebooks/mfusg_transport_tutorial02_Radial - Notebooks/mfusg_transport_tutorial03_Conduit - Notebooks/mfusg_transport_tutorial04_DualDomain - Notebooks/mfusg_transport_tutorial05_Henry - Notebooks/mfusg_transport_tutorial06_StallmanHeatTransport - Notebooks/mfusg_transport_tutorial07a_DiscreteFracture - Notebooks/mfusg_transport_tutorial07b_SandBox - Notebooks/mfusg_transport_tutorial09_PFAS - - -MT3DMS ------- - -.. toctree:: - :maxdepth: 2 - - Notebooks/mt3dms_sft_lkt_uzt_tutorial - Notebooks/mt3dms_ssm_package_tutorial - Notebooks/seawat_tutorial01 - - -PEST ----- - -.. toctree:: - :maxdepth: 2 - - Notebooks/pest_tutorial01 diff --git a/autotest/test_example_notebooks.py b/autotest/test_example_notebooks.py index e7c673adf7..9ce750c086 100644 --- a/autotest/test_example_notebooks.py +++ b/autotest/test_example_notebooks.py @@ -10,8 +10,8 @@ EXCLUDE = [ "mf6_lgr", - "mfusg_transport_tutorial07c_ChainDecay", - "mfusg_transport_tutorial08_Lake", + "mfusg_transport_07c_ChainDecay", + "mfusg_transport_08_Lake", ] # skip pyvista notebooks on windows/mac in CI due to persistent issues # first with offscreen rendering, then with finding pyvista even after