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ENH: Show memory usage, too#523

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larsoner merged 6 commits intosphinx-gallery:masterfrom
larsoner:mem
Aug 12, 2019
Merged

ENH: Show memory usage, too#523
larsoner merged 6 commits intosphinx-gallery:masterfrom
larsoner:mem

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@larsoner
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@larsoner larsoner commented Aug 1, 2019

Closes #522.

@banesullivan feel free to try it and open a PR into my branch with any aesthetic tweaks you want (e.g., a header).

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larsoner commented Aug 1, 2019

Example output currently, for tinybuild:

computation time summary:
    - examples/plot_svg.py:                     0.18 sec   11.2 MB
    - examples/plot_numpy_matplotlib.py:        0.18 sec    9.6 MB
    - examples/plot_future_imports.py:          0.11 sec    9.4 MB
    - examples/plot_second_future_imports.py:   0.08 sec    9.4 MB
    - examples/plot_future_imports_broken.py:   0.06 sec    9.4 MB
    - examples/local_module.py:                 0.00 sec    0.0 MB

and for SG:

computation time summary:
    - ../tutorials/seaborn/plot_seaborn_notebook.py:       48.32 sec    11.7 MB
    - ../examples/plot_seaborn.py:                         22.96 sec    59.0 MB
    - ../tutorials/plot_notebook.py:                        2.39 sec    14.3 MB
    - ../mayavi_examples/plot_3d.py:                        1.88 sec   114.1 MB
    - ../examples/plot_quantum.py:                          1.03 sec     9.4 MB
    - ../examples/plot_function_identifier.py:              0.92 sec     9.5 MB
    - ../examples/plot_colors.py:                           0.83 sec    25.4 MB
    - ../examples/plot_unicode_everywhere.py:               0.74 sec     9.5 MB
    - ../tutorials/plot_parse.py:                           0.64 sec     9.4 MB
    - ../examples/sin_func/plot_sin_black_background.py:    0.46 sec     9.4 MB
    - ../examples/plot_choose_thumbnail.py:                 0.43 sec     9.4 MB
    - ../examples/no_output/plot_raise.py:                  0.41 sec     9.4 MB
    - ../examples/plot_exp.py:                              0.38 sec     9.4 MB
    - ../examples/plot_gallery_version.py:                  0.33 sec     9.5 MB
    - ../examples/sin_func/plot_sin.py:                     0.31 sec     9.4 MB
    - ../examples/no_output/plot_strings.py:                0.26 sec     9.5 MB
    - ../examples/no_output/plot_syntaxerror.py:            0.16 sec     9.4 MB
    - ../examples/plot_sys_argv.py:                         0.14 sec     9.4 MB
    - ../examples/local_module.py:                          0.00 sec     0.0 MB
    - ../examples/no_output/just_code.py:                   0.00 sec     0.0 MB

And the HTML file, courtesy CircleCI:

https://969-25860190-gh.circle-artifacts.com/0/rtd_html/auto_examples/sg_execution_times.html

Looks like AppVeyor is broken on master and failing on this PR, will probably try to fix that mess separately.

@larsoner larsoner added this to the 0.5.0 milestone Aug 1, 2019
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codecov-io commented Aug 1, 2019

Codecov Report

Merging #523 into master will increase coverage by 0.37%.
The diff coverage is 97.22%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #523      +/-   ##
==========================================
+ Coverage   96.25%   96.63%   +0.37%     
==========================================
  Files          29       29              
  Lines        2695     2731      +36     
==========================================
+ Hits         2594     2639      +45     
+ Misses        101       92       -9
Impacted Files Coverage Δ
sphinx_gallery/tests/test_gen_gallery.py 98.78% <100%> (+0.06%) ⬆️
sphinx_gallery/tests/test_full.py 100% <100%> (ø) ⬆️
sphinx_gallery/gen_rst.py 97.58% <100%> (ø) ⬆️
sphinx_gallery/gen_gallery.py 95.87% <96.15%> (+3.51%) ⬆️

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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larsoner commented Aug 5, 2019

@choldgraf this one should be good to go. We can improve aesthetics in subsequent PRs if people are motivated, but they are already a nice upgrade.

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@banesullivan have you given this one a chance?

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larsoner commented Aug 7, 2019

Here is the output on CircleCI for MNE:

Details
- ../examples/time_frequency/plot_source_power_spectrum_opm.py:                                    158.79 sec   2103.6 MB
- ../tutorials/source-modeling/plot_mne_solutions.py:                                              129.81 sec    434.4 MB
- ../examples/inverse/plot_covariance_whitening_dspm.py:                                            94.78 sec   1040.6 MB
- ../tutorials/source-modeling/plot_forward.py:                                                     91.85 sec   1135.5 MB
- ../examples/visualization/plot_montage.py:                                                        74.03 sec    309.8 MB
- ../tutorials/sample-datasets/plot_brainstorm_auditory.py:                                         65.71 sec    529.9 MB
- ../tutorials/source-modeling/plot_mne_dspm_source_localization.py:                                63.07 sec    114.6 MB
- ../examples/connectivity/plot_mne_inverse_envelope_correlation.py:                                60.42 sec    749.7 MB
- ../examples/inverse/plot_mixed_source_space_inverse.py:                                           49.15 sec   1347.9 MB
- ../examples/connectivity/plot_mixed_source_space_connectivity.py:                                 47.82 sec   1002.0 MB
- ../tutorials/stats-source-space/plot_stats_cluster_spatio_temporal_2samp.py:                      46.45 sec      8.6 MB
- ../examples/forward/plot_source_space_morphing.py:                                                46.43 sec    581.5 MB
- ../examples/visualization/plot_make_report.py:                                                    45.16 sec    663.9 MB
- ../examples/time_frequency/plot_time_frequency_global_field_power.py:                             45.12 sec   1519.0 MB
- ../tutorials/source-modeling/plot_eeg_no_mri.py:                                                  44.42 sec    441.5 MB
- ../examples/inverse/plot_dics_source_power.py:                                                    43.77 sec    453.0 MB
- ../tutorials/source-modeling/plot_dipole_orientations.py:                                         41.44 sec    454.2 MB
- ../tutorials/stats-source-space/plot_stats_cluster_spatio_temporal_repeated_measures_anova.py:    41.19 sec      8.3 MB
- ../tutorials/simulation/plot_dics.py:                                                             40.32 sec     79.8 MB
- ../tutorials/intro/plot_10_overview.py:                                                           39.86 sec    563.0 MB
- ../examples/preprocessing/plot_run_ica.py:                                                        39.72 sec    457.9 MB
- ../tutorials/preprocessing/plot_40_artifact_correction_ica.py:                                    38.74 sec    774.8 MB
- ../tutorials/simulation/plot_point_spread.py:                                                     38.16 sec    441.9 MB
- ../examples/connectivity/plot_mne_inverse_envelope_correlation_volume.py:                         36.39 sec    605.5 MB
- ../examples/simulation/plot_simulated_raw_data_using_subject_anatomy.py:                          34.82 sec    836.6 MB
- ../examples/preprocessing/plot_ica_comparison.py:                                                 34.54 sec    519.2 MB
- ../examples/inverse/plot_morph_volume_stc.py:                                                     33.79 sec    604.0 MB
- ../tutorials/sample-datasets/plot_sleep.py:                                                       31.99 sec    548.1 MB
- ../examples/decoding/plot_decoding_csp_timefreq.py:                                               31.44 sec      8.2 MB
- ../tutorials/source-modeling/plot_visualize_stc.py:                                               30.90 sec    657.1 MB
- ../tutorials/evoked/plot_whitened.py:                                                             29.18 sec    272.0 MB
- ../examples/decoding/plot_decoding_spoc_CMC.py:                                                   29.00 sec    962.6 MB
- ../examples/visualization/plot_xhemi.py:                                                          28.83 sec     88.8 MB
- ../tutorials/preprocessing/plot_45_ica_from_raw.py:                                               28.58 sec    455.3 MB
- ../tutorials/machine-learning/plot_sensors_decoding.py:                                           28.10 sec    487.1 MB
- ../tutorials/sample-datasets/plot_brainstorm_phantom_elekta.py:                                   26.81 sec    160.0 MB
- ../examples/inverse/plot_lcmv_beamformer_volume.py:                                               26.69 sec    845.0 MB
- ../tutorials/time-freq/plot_sensors_time_frequency.py:                                            23.86 sec    311.2 MB
- ../tutorials/source-modeling/plot_dipole_fit.py:                                                  23.61 sec      8.3 MB
- ../examples/inverse/plot_lcmv_beamformer.py:                                                      23.58 sec    798.9 MB
- ../tutorials/source-modeling/plot_compute_covariance.py:                                          22.60 sec      8.2 MB
- ../examples/inverse/plot_tf_dics.py:                                                              21.83 sec    486.6 MB
- ../tutorials/evoked/plot_visualize_evoked.py:                                                     21.69 sec     31.8 MB
- ../examples/inverse/plot_tf_lcmv.py:                                                              21.33 sec    473.8 MB
- ../examples/visualization/plot_eeg_on_scalp.py:                                                   20.98 sec     51.6 MB
- ../examples/inverse/plot_gamma_map_inverse.py:                                                    20.72 sec     69.8 MB
- ../examples/datasets/plot_opm_data.py:                                                            20.67 sec    944.9 MB
- ../examples/time_frequency/plot_compute_csd.py:                                                   20.39 sec    230.2 MB
- ../tutorials/discussions/plot_background_statistics.py:                                           20.36 sec      8.8 MB
- ../examples/inverse/plot_morph_surface_stc.py:                                                    19.77 sec      8.6 MB
- ../examples/visualization/plot_evoked_arrowmap.py:                                                19.44 sec     15.0 MB
- ../tutorials/sample-datasets/plot_brainstorm_phantom_ctf.py:                                      18.53 sec    391.5 MB
- ../examples/inverse/plot_time_frequency_mixed_norm_inverse.py:                                    18.10 sec      8.5 MB
- ../tutorials/discussions/plot_background_filtering.py:                                            18.10 sec      8.5 MB
- ../examples/decoding/plot_decoding_spatio_temporal_source.py:                                     17.51 sec     91.1 MB
- ../tutorials/source-modeling/plot_source_alignment.py:                                            17.31 sec      9.2 MB
- ../tutorials/epochs/plot_epoching_and_averaging.py:                                               17.26 sec    100.9 MB
- ../examples/connectivity/plot_mne_inverse_psi_visual.py:                                          17.19 sec      8.5 MB
- ../tutorials/machine-learning/plot_receptive_field.py:                                            17.02 sec      8.4 MB
- ../examples/connectivity/plot_mne_inverse_coherence_epochs.py:                                    16.94 sec      8.6 MB
- ../tutorials/stats-sensor-space/plot_stats_spatio_temporal_cluster_sensors.py:                    16.92 sec      8.6 MB
- ../examples/preprocessing/plot_otp.py:                                                            16.44 sec     44.8 MB
- ../tutorials/stats-source-space/plot_stats_cluster_spatio_temporal.py:                            16.31 sec      8.3 MB
- ../tutorials/epochs/plot_visualize_epochs.py:                                                     15.98 sec    219.4 MB
- ../tutorials/evoked/plot_eeg_erp.py:                                                              15.46 sec    127.7 MB
- ../tutorials/source-modeling/plot_object_source_estimate.py:                                      15.12 sec      8.6 MB
- ../tutorials/raw/plot_40_visualize_raw.py:                                                        14.71 sec   1868.5 MB
- ../tutorials/preprocessing/plot_15_handling_bad_channels.py:                                      14.32 sec     15.4 MB
- ../tutorials/stats-sensor-space/plot_stats_cluster_erp.py:                                        14.19 sec      8.5 MB
- ../examples/datasets/plot_brainstorm_data.py:                                                     13.84 sec   1450.3 MB
- ../examples/time_frequency/plot_source_label_time_frequency.py:                                   13.65 sec    171.8 MB
- ../examples/visualization/plot_topo_customized.py:                                                13.40 sec    216.9 MB
- ../tutorials/raw/plot_10_raw_overview.py:                                                         13.40 sec    214.9 MB
- ../tutorials/preprocessing/plot_10_preprocessing_overview.py:                                     12.76 sec    318.7 MB
- ../examples/inverse/plot_mixed_norm_inverse.py:                                                   12.72 sec     25.3 MB
- ../tutorials/epochs/plot_object_epochs.py:                                                        12.66 sec    829.3 MB
- ../examples/preprocessing/plot_interpolate_bad_channels.py:                                       12.63 sec      8.1 MB
- ../examples/decoding/plot_receptive_field_mtrf.py:                                                12.41 sec      8.5 MB
- ../examples/io/plot_elekta_epochs.py:                                                             11.84 sec     97.5 MB
- ../tutorials/misc/plot_ecog.py:                                                                   11.59 sec      9.0 MB
- ../examples/forward/plot_left_cerebellum_volume_source.py:                                        11.43 sec     47.4 MB
- ../tutorials/stats-source-space/plot_stats_cluster_time_frequency_repeated_measures_anova.py:     11.24 sec    160.7 MB
- ../tutorials/preprocessing/plot_50_artifact_correction_ssp.py:                                    11.14 sec    247.4 MB
- ../examples/datasets/plot_limo_data.py:                                                           10.41 sec    577.9 MB
- ../tutorials/intro/plot_40_projectors_background.py:                                               9.65 sec    211.7 MB
- ../examples/time_frequency/plot_time_frequency_erds.py:                                            9.56 sec      8.3 MB
- ../examples/preprocessing/plot_resample.py:                                                        9.51 sec    588.7 MB
- ../tutorials/sample-datasets/plot_phantom_4DBTi.py:                                                9.48 sec      8.3 MB
- ../examples/inverse/plot_mne_crosstalk_function.py:                                                9.48 sec      9.3 MB
- ../examples/inverse/plot_mne_point_spread_function.py:                                             9.41 sec      8.6 MB
- ../examples/preprocessing/plot_metadata_query.py:                                                  9.38 sec    581.1 MB
- ../examples/forward/plot_forward_sensitivity_maps.py:                                              9.35 sec      8.3 MB
- ../examples/preprocessing/plot_virtual_evoked.py:                                                  9.26 sec      8.2 MB
- ../examples/time_frequency/plot_time_frequency_simulated.py:                                       9.13 sec     11.0 MB
- ../tutorials/preprocessing/plot_20_rejecting_bad_data.py:                                          8.72 sec    176.4 MB
- ../tutorials/epochs/plot_metadata_epochs.py:                                                       8.59 sec      8.3 MB
- ../tutorials/raw/plot_30_annotate_raw.py:                                                          8.46 sec    216.7 MB
- ../examples/visualization/plot_evoked_whitening.py:                                                8.40 sec    127.9 MB
- ../examples/inverse/plot_label_from_stc.py:                                                        8.40 sec      8.8 MB
- ../examples/visualization/plot_parcellation.py:                                                    8.21 sec      8.8 MB
- ../tutorials/misc/plot_sensor_locations.py:                                                        7.49 sec    486.9 MB
- ../tutorials/intro/plot_50_configure_mne.py:                                                       7.47 sec      8.1 MB
- ../examples/simulation/plot_simulate_raw_data.py:                                                  7.43 sec    275.0 MB
- ../examples/connectivity/plot_mne_inverse_label_connectivity.py:                                   7.27 sec      9.4 MB
- ../tutorials/preprocessing/plot_60_maxwell_filtering_sss.py:                                       7.24 sec    486.8 MB
- ../examples/inverse/plot_vector_mne_solution.py:                                                   7.04 sec     12.4 MB
- ../examples/inverse/plot_rap_music.py:                                                             6.88 sec      8.3 MB
- ../tutorials/raw/plot_20_event_arrays.py:                                                          6.81 sec    111.5 MB
- ../examples/time_frequency/plot_compute_source_psd_epochs.py:                                      6.81 sec     86.0 MB
- ../tutorials/intro/plot_20_events_from_raw.py:                                                     6.64 sec    214.9 MB
- ../examples/visualization/plot_3d_to_2d.py:                                                        6.57 sec      8.4 MB
- ../examples/time_frequency/plot_source_space_time_frequency.py:                                    6.52 sec    586.1 MB
- ../tutorials/evoked/plot_object_evoked.py:                                                         6.19 sec      8.2 MB
- ../tutorials/intro/plot_30_info.py:                                                                6.16 sec      8.1 MB
- ../examples/simulation/plot_simulate_evoked_data.py:                                               5.93 sec    383.0 MB
- ../examples/decoding/plot_linear_model_patterns.py:                                                5.81 sec   1033.0 MB
- ../examples/visualization/plot_ssp_projs_sensitivity_map.py:                                       5.76 sec    148.1 MB
- ../examples/inverse/plot_compute_mne_inverse_volume.py:                                            5.75 sec    581.1 MB
- ../tutorials/misc/plot_modifying_data_inplace.py:                                                  5.69 sec    464.8 MB
- ../examples/decoding/plot_decoding_unsupervised_spatial_filter.py:                                 5.62 sec      8.4 MB
- ../examples/decoding/plot_decoding_time_generalization_conditions.py:                              5.60 sec      8.5 MB
- ../examples/connectivity/plot_sensor_connectivity.py:                                              5.59 sec      9.8 MB
- ../examples/preprocessing/plot_xdawn_denoising.py:                                                 5.56 sec    127.9 MB
- ../tutorials/simulation/plot_creating_data_structures.py:                                          5.50 sec      8.1 MB
- ../examples/preprocessing/plot_movement_compensation.py:                                           5.47 sec     15.4 MB
- ../examples/time_frequency/plot_source_power_spectrum.py:                                          5.35 sec    108.0 MB
- ../examples/connectivity/plot_cwt_sensor_connectivity.py:                                          5.04 sec      8.1 MB
- ../examples/visualization/plot_meg_sensors.py:                                                     5.02 sec      9.3 MB
- ../examples/decoding/plot_decoding_xdawn_eeg.py:                                                   4.71 sec      8.2 MB
- ../examples/time_frequency/plot_compute_raw_data_spectrum.py:                                      4.59 sec    318.3 MB
- ../examples/visualization/plot_evoked_topomap.py:                                                  4.56 sec      8.3 MB
- ../tutorials/preprocessing/plot_30_filtering_resampling.py:                                        4.29 sec      8.1 MB
- ../examples/inverse/plot_custom_inverse_solver.py:                                                 4.25 sec      8.4 MB
- ../examples/simulation/plot_source_simulator.py:                                                   4.19 sec    113.8 MB
- ../examples/visualization/plot_roi_erpimage_by_rt.py:                                              4.19 sec      8.1 MB
- ../examples/inverse/plot_read_inverse.py:                                                          4.13 sec      8.4 MB
- ../examples/stats/plot_linear_regression_raw.py:                                                   4.08 sec      9.3 MB
- ../examples/decoding/plot_decoding_csp_eeg.py:                                                     3.86 sec      8.5 MB
- ../tutorials/epochs/plot_epochs_to_data_frame.py:                                                  3.79 sec      9.3 MB
- ../examples/inverse/plot_read_source_space.py:                                                     3.74 sec      8.3 MB
- ../examples/stats/plot_sensor_permutation_test.py:                                                 3.65 sec    251.5 MB
- ../examples/decoding/plot_ems_filtering.py:                                                        3.63 sec      8.1 MB
- ../examples/io/plot_read_proj.py:                                                                  3.56 sec     14.0 MB
- ../examples/io/plot_objects_from_arrays.py:                                                        3.53 sec     75.6 MB
- ../tutorials/stats-sensor-space/plot_stats_cluster_time_frequency.py:                              3.43 sec      8.1 MB
- ../examples/stats/plot_sensor_regression.py:                                                       3.41 sec     11.0 MB
- ../examples/visualization/plot_topo_compare_conditions.py:                                         3.29 sec      8.2 MB
- ../examples/stats/plot_fdr_stats_evoked.py:                                                        3.26 sec      8.6 MB
- ../examples/inverse/plot_compute_mne_inverse_epochs_in_label.py:                                   3.25 sec      8.2 MB
- ../examples/connectivity/plot_mne_inverse_connectivity_spectrum.py:                                3.21 sec      8.7 MB
- ../examples/stats/plot_cluster_stats_evoked.py:                                                    3.15 sec      8.7 MB
- ../tutorials/stats-sensor-space/plot_stats_cluster_1samp_test_time_frequency.py:                   3.11 sec      8.5 MB
- ../examples/datasets/plot_hf_sef_data.py:                                                          2.86 sec      8.2 MB
- ../examples/preprocessing/plot_find_ecg_artifacts.py:                                              2.83 sec      8.1 MB
- ../examples/preprocessing/plot_rereference_eeg.py:                                                 2.28 sec    127.8 MB
- ../examples/preprocessing/plot_define_target_events.py:                                            2.19 sec      8.1 MB
- ../examples/io/plot_read_and_write_raw_data.py:                                                    2.18 sec     32.4 MB
- ../examples/io/plot_read_evoked.py:                                                                2.06 sec      8.4 MB
- ../examples/time_frequency/plot_temporal_whitening.py:                                             2.06 sec      8.2 MB
- ../examples/inverse/plot_compute_mne_inverse_raw_in_label.py:                                      1.91 sec      8.2 MB
- ../examples/visualization/plot_channel_epochs_image.py:                                            1.84 sec     11.6 MB
- ../examples/inverse/plot_snr_estimate.py:                                                          1.80 sec      8.6 MB
- ../examples/visualization/plot_sensor_noise_level.py:                                              1.72 sec    166.9 MB
- ../examples/preprocessing/plot_head_positions.py:                                                  1.71 sec      8.1 MB
- ../examples/preprocessing/plot_eog_artifact_histogram.py:                                          1.67 sec    127.8 MB
- ../examples/inverse/plot_label_source_activations.py:                                              1.62 sec      8.2 MB
- ../examples/io/plot_read_epochs.py:                                                                1.53 sec     22.2 MB
- ../examples/preprocessing/plot_find_eog_artifacts.py:                                              1.31 sec      8.1 MB
- ../examples/preprocessing/plot_shift_evoked.py:                                                    1.26 sec      8.2 MB
- ../examples/inverse/plot_read_stc.py:                                                              1.23 sec      8.1 MB
- ../examples/io/plot_read_events.py:                                                                1.19 sec      8.1 MB
- ../examples/inverse/plot_label_activation_from_stc.py:                                             1.13 sec      8.1 MB
- ../examples/io/plot_read_noise_covariance_matrix.py:                                               1.09 sec      8.2 MB
</details>

@banesullivan
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@choldgraf - I haven't given it a try yet, apologies! I'll try experimenting with it today!

@choldgraf
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@banesullivan sounds good - once I get a 👍 from you then I think we should merge, please feel free to give a code review as well!

@larsoner
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... and for matplotlib:

computation time summary:
    - ../examples/animation/animation_demo.py:                                     8.51 sec   0.0 MB
    - ../tutorials/intermediate/constrainedlayout_guide.py:                        5.82 sec   0.0 MB
    - ../examples/style_sheets/style_sheets_reference.py:                          5.44 sec   0.0 MB
    - ../tutorials/colors/colormaps.py:                                            3.92 sec   0.0 MB
    - ../tutorials/intermediate/gridspec.py:                                       3.74 sec   0.0 MB
    - ../examples/lines_bars_and_markers/markevery_demo.py:                        3.71 sec   0.0 MB
    - ../examples/showcase/mandelbrot.py:                                          3.01 sec   0.0 MB
    - ../examples/userdemo/demo_gridspec06.py:                                     1.41 sec   0.0 MB
    - ../tutorials/intermediate/tight_layout_guide.py:                             1.40 sec   0.0 MB
    - ../examples/subplots_axes_and_figures/secondary_axis.py:                     1.39 sec   0.0 MB
    - ../examples/text_labels_and_annotations/demo_text_rotation_mode.py:          1.09 sec   0.0 MB
    - ../examples/subplots_axes_and_figures/demo_tight_layout.py:                  1.08 sec   0.0 MB
    - ../examples/images_contours_and_fields/plot_streamplot.py:                   1.04 sec   0.0 MB
    - ../examples/subplots_axes_and_figures/subplots_demo.py:                      1.03 sec   0.0 MB

Given it works on each of these repos I'll go ahead and merge @banesullivan. We can always iterate in subsequent PRs if we want to tweak things!

@larsoner larsoner merged commit 9d66dbd into sphinx-gallery:master Aug 12, 2019
@larsoner larsoner deleted the mem branch August 12, 2019 20:12
@banesullivan
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Thanks, @larsoner and apologies for not getting around to this! I'll iterate back when I have free time

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Show memory usage in build output

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