From 8d3902a828ed6676249fdcbcbbdc7a1d87b3d446 Mon Sep 17 00:00:00 2001 From: "Martin D. Weinberg" Date: Wed, 12 Mar 2025 14:09:05 -0400 Subject: [PATCH 01/22] Added Jupyter notebooks rather than Markdown examples --- conf.py | 9 +- doxyxml/Doxyfile.xml | 4 +- doxyxml/_add_disk_8_h.xml | 71 +- doxyxml/_add_spheres_8_h.xml | 71 +- doxyxml/_axisymmetric_basis_8_h.xml | 52 +- doxyxml/_basis_8_h.xml | 62 +- doxyxml/_biorth_cube_8_h.xml | 96 +- doxyxml/_biorth_cyl_8_h.xml | 198 +-- doxyxml/_component_8_h.xml | 1222 ++++++++-------- doxyxml/_component_container_8_h.xml | 65 +- doxyxml/_cyl_disk_8_h.xml | 167 +-- doxyxml/_cyl_e_x_p_8_h.xml | 145 +- doxyxml/_cyl_two_d_8_h.xml | 453 +++--- doxyxml/_cylinder_8_h.xml | 1005 ++++++------- doxyxml/_data_grid_8_h.xml | 90 +- doxyxml/_direct_8_h.xml | 51 +- doxyxml/_disk2d_8_h.xml | 22 +- doxyxml/_disk2d_halo_8_h.xml | 172 +-- doxyxml/_disk_eval_8_h.xml | 20 + doxyxml/_disk_halo_8_h.xml | 167 +-- doxyxml/_disk_models_8_h.xml | 113 +- doxyxml/_disk_with_halo_8_h.xml | 227 +-- doxyxml/_e_jcom_8_h.xml | 411 +++--- doxyxml/_e_x_pini_8_h.xml | 101 +- doxyxml/_e_x_pmath_8_h.xml | 59 +- doxyxml/_ellipsoid_force_8_h.xml | 137 +- doxyxml/_emp_cyl2d_8_h.xml | 671 ++++++--- doxyxml/_emp_cyl_s_l_8_h.xml | 35 +- doxyxml/_external_collection_8_h.xml | 71 +- doxyxml/_external_force_8_h.xml | 70 +- doxyxml/_flat_disk_8_h.xml | 282 ++-- doxyxml/_gen_poly_8_h.xml | 71 +- doxyxml/_halo_bulge_8_h.xml | 47 +- doxyxml/_hunter_x_8_h.xml | 75 +- doxyxml/_k_dtree_8_h.xml | 667 +++++---- doxyxml/_make_model_8_h.xml | 59 +- doxyxml/_mixture_basis_8_h.xml | 411 +++--- doxyxml/_monot_cubic_interpolator_8_h.xml | 116 +- doxyxml/_n_v_t_x_8_h.xml | 95 +- doxyxml/_orient_8_h.xml | 305 ++-- doxyxml/_out_ascii_8_h.xml | 65 +- doxyxml/_out_calbr_8_h.xml | 61 +- doxyxml/_out_frac_8_h.xml | 61 +- doxyxml/_out_vel_8_h.xml | 73 +- doxyxml/_output_container_8_h.xml | 2 +- doxyxml/_periodic_b_c_8_h.xml | 51 +- doxyxml/_polar_basis_8_h.xml | 91 +- doxyxml/_pot_accel_8_h.xml | 144 +- doxyxml/_q_p_dist_f_8_h.xml | 201 +-- doxyxml/_s_l_grid_m_p2_8_h.xml | 263 ++-- doxyxml/_scatter_m_f_p_8_h.xml | 47 +- doxyxml/_shells_8_h.xml | 123 +- doxyxml/_slab_s_l_8_h.xml | 111 +- doxyxml/_sph_s_l_8_h.xml | 71 +- doxyxml/_sphere_8_h.xml | 125 +- doxyxml/_spherical_s_l_8_h.xml | 69 +- doxyxml/_string_tok_8_h.xml | 106 +- doxyxml/_three_d_grid_8_h.xml | 2 + doxyxml/_transform_f_f_t_8_h.xml | 69 +- doxyxml/_two_center_8_h.xml | 411 +++--- doxyxml/_user_bar_8_h.xml | 51 +- doxyxml/_user_disk_8_h.xml | 51 +- doxyxml/_user_halo_8_h.xml | 51 +- doxyxml/_user_log_pot_8_h.xml | 51 +- doxyxml/_user_m_ndisk_8_h.xml | 51 +- doxyxml/_user_m_w_8_h.xml | 51 +- doxyxml/_user_test_8_h.xml | 71 +- doxyxml/_user_test_cuda_8_h.xml | 47 +- doxyxml/_vtk_grid_8_h.xml | 292 ++-- doxyxml/_vtk_p_c_a_8_h.xml | 6 +- doxyxml/_yaml_check_8_h.xml | 144 +- doxyxml/_yaml_config_8_h.xml | 2 +- doxyxml/class_axi_sym_biorth.xml | 2 + doxyxml/class_axi_sym_model.xml | 567 +++++--- doxyxml/class_axi_sym_model_1_1_w_rgrid.xml | 6 +- doxyxml/class_axisymmetric_basis.xml | 16 +- doxyxml/class_b_w_data.xml | 2 +- doxyxml/class_basis.xml | 20 +- doxyxml/class_bessel_1_1_roots.xml | 2 +- doxyxml/class_biorth.xml | 3 + doxyxml/class_biorth_cyl.xml | 115 +- doxyxml/class_c_b_disk.xml | 1245 ++++++++++++++++- doxyxml/class_component.xml | 885 +++++++----- doxyxml/class_cube_1_1exe_timer.xml | 4 +- doxyxml/class_cyl_disk.xml | 46 +- doxyxml/class_cylinder.xml | 305 ++-- doxyxml/class_data_grid.xml | 25 +- doxyxml/class_disk_with_halo.xml | 76 +- doxyxml/class_e_l3.xml | 24 +- doxyxml/class_ellipsoid_force.xml | 108 +- doxyxml/class_embedded_disk_model.xml | 104 +- doxyxml/class_emp_cyl2d.xml | 228 ++- doxyxml/class_emp_cyl2d_1_1_basis2d.xml | 14 +- doxyxml/class_emp_cyl2d_1_1_mapping.xml | 16 +- doxyxml/class_emp_cyl2d_1_1_model_cyl.xml | 65 +- doxyxml/class_emp_cyl_s_l.xml | 4 +- doxyxml/class_emp_cyl_s_l_1_1_axi_disk.xml | 18 + doxyxml/class_exponential_disk.xml | 46 +- doxyxml/class_external_force.xml | 2 +- doxyxml/class_f_d_i_s_t.xml | 22 +- doxyxml/class_f_d_i_s_t_c.xml | 20 +- doxyxml/class_flat_disk.xml | 251 +++- doxyxml/class_generalized_polytrope.xml | 38 +- doxyxml/class_hernquist_sphere.xml | 40 +- doxyxml/class_hunter_disk.xml | 40 +- doxyxml/class_hunter_disk_x.xml | 40 +- doxyxml/class_isothermal_sphere.xml | 44 +- doxyxml/class_kalnajs_disk.xml | 38 +- doxyxml/class_king_sphere.xml | 34 +- doxyxml/class_low_sing_isothermal_sphere.xml | 44 +- doxyxml/class_mass_model.xml | 62 +- doxyxml/class_mestel_disk.xml | 32 +- doxyxml/class_orient.xml | 292 ++-- doxyxml/class_output_container.xml | 8 +- doxyxml/class_plummer_sphere.xml | 38 +- doxyxml/class_polar_basis.xml | 67 +- doxyxml/class_pot_accel.xml | 109 +- doxyxml/class_r_u_n.xml | 36 +- doxyxml/class_s_l_grid_slab.xml | 66 +- doxyxml/class_s_l_grid_slab_1_1_coord_map.xml | 26 +- .../class_s_l_grid_slab_1_1_linear_map.xml | 11 +- doxyxml/class_s_l_grid_slab_1_1_sech_map.xml | 11 +- doxyxml/class_s_l_grid_slab_1_1_tanh_map.xml | 11 +- doxyxml/class_s_l_grid_sph.xml | 4 +- doxyxml/class_sing_isothermal_sphere.xml | 50 +- doxyxml/class_spherical_basis.xml | 2 +- doxyxml/class_spherical_model_multi.xml | 232 +-- doxyxml/class_spherical_model_table.xml | 162 +-- doxyxml/class_tapered_mestel_disk.xml | 32 +- doxyxml/class_three_d_grid.xml | 18 +- doxyxml/class_timer.xml | 2 +- doxyxml/class_toomre_disk.xml | 38 +- doxyxml/class_transform_f_f_t.xml | 40 +- doxyxml/class_vtk_grid.xml | 141 +- doxyxml/class_zang_disk.xml | 50 +- doxyxml/classcxxopts_1_1_options.xml | 2 +- doxyxml/classnv_tracer.xml | 6 +- .../dir_68267d1309a1af8e8297ef4c3efbcdba.xml | 1 + .../dir_d44c64559bbebec7f509842c48db8b23.xml | 3 + doxyxml/expand_8_h.xml | 73 +- doxyxml/exponential_8_h.xml | 71 +- doxyxml/external_shock_8_h.xml | 31 +- doxyxml/fpetrap_8h.xml | 16 +- doxyxml/gauss_q_8_h.xml | 186 +-- doxyxml/global_8_h.xml | 30 +- doxyxml/hernquist__model_8_h.xml | 71 +- doxyxml/hunter_8_h.xml | 71 +- doxyxml/index.xml | 333 +++-- doxyxml/interp_8_h.xml | 116 +- doxyxml/isothermal_8_h.xml | 73 +- doxyxml/king_8_h.xml | 71 +- doxyxml/localmpi_8_h.xml | 241 ++-- doxyxml/massmodel1d_8_h.xml | 2 + doxyxml/massmodel_8_h.xml | 1136 ++++++++------- doxyxml/mestel_8_h.xml | 71 +- doxyxml/orbit_8_h.xml | 152 +- doxyxml/plummer_8_h.xml | 71 +- doxyxml/sphere_s_l_8_h.xml | 55 +- doxyxml/structlt_e_l3.xml | 6 +- doxyxml/toomre_8_h.xml | 71 +- intro/pyEXP-tutorial.rst | 138 +- 161 files changed, 12116 insertions(+), 8259 deletions(-) diff --git a/conf.py b/conf.py index 55b5d8f..7502419 100644 --- a/conf.py +++ b/conf.py @@ -27,7 +27,9 @@ 'sphinx.ext.inheritance_diagram', 'sphinx.ext.graphviz', 'breathe', - 'sphinx_copybutton' + 'sphinx_copybutton', + 'nbsphinx', + 'nbsphinx_link' ] @@ -46,3 +48,8 @@ # Turn on figure numering numfig = True + +# Grab files from pyEXP-examples +import os + +os.system("cd intro/notebook; rm *ipynb*; wget -L https://raw.githubusercontent.com/EXP-code/pyEXP-examples/refs/heads/main/Tutorials/Introduction/Part1-Coefficients.ipynb; wget -L https://raw.githubusercontent.com/EXP-code/pyEXP-examples/refs/heads/main/Tutorials/Introduction/Part2-Analysis.ipynb") diff --git a/doxyxml/Doxyfile.xml b/doxyxml/Doxyfile.xml index 9e444c9..bfe6dcf 100644 --- a/doxyxml/Doxyfile.xml +++ b/doxyxml/Doxyfile.xml @@ -2,7 +2,7 @@ - + @@ -132,8 +132,6 @@