LICENSE
MANIFEST.in
README.md
logo.png
setup.py
src/aegis/__init__.py
src/aegis/__main__.py
src/aegis/log.py
src/aegis/parse.py
src/aegis/documentation/1 gallery.md
src/aegis/documentation/1 getting started.md
src/aegis/documentation/1 welcome.md
src/aegis/documentation/1 what is aegis for.md
src/aegis/documentation/1 who is aegis for.md
src/aegis/documentation/2 odd.md
src/aegis/documentation/3 user guide.md
src/aegis/documentation/4 about us and community.md
src/aegis/documentation/documenter.py
src/aegis/documentation/dynamic/default_parameters.md
src/aegis/documentation/dynamic/output_specifications.md
src/aegis/documentation/dynamic/submodel_specifications.md
src/aegis/documentation/dynamic/write.py
src/aegis/performance/utilities.py
src/aegis_gui/__init__.py
src/aegis_gui/app.py
src/aegis_gui/layout.py
src/aegis_gui/offcanvas.py
src/aegis_gui/assets/aegis-ager.svg
src/aegis_gui/assets/aegis.svg
src/aegis_gui/assets/bootstrap.min.css
src/aegis_gui/assets/favicon-group.ico
src/aegis_gui/assets/favicon.ico
src/aegis_gui/assets/list.svg
src/aegis_gui/assets/logo.svg
src/aegis_gui/assets/plot.svg
src/aegis_gui/assets/sim.svg
src/aegis_gui/assets/styles.css
src/aegis_gui/assets/styles_buttons.css
src/aegis_gui/assets/styles_colors.css
src/aegis_gui/assets/styles_dcc.css
src/aegis_gui/assets/styles_dropdown.css
src/aegis_gui/assets/styles_figures.css
src/aegis_gui/assets/styles_general.css
src/aegis_gui/assets/styles_header_footer.css
src/aegis_gui/assets/styles_inputs.css
src/aegis_gui/assets/styles_structure.css
src/aegis_gui/assets/styles_tab_specific.css
src/aegis_gui/assets/styles_tables.css
src/aegis_gui/assets/bootstrap-icons/font/bootstrap-icons.css
src/aegis_gui/assets/bootstrap-icons/font/bootstrap-icons.json
src/aegis_gui/assets/bootstrap-icons/font/bootstrap-icons.min.css
src/aegis_gui/assets/bootstrap-icons/font/bootstrap-icons.scss
src/aegis_gui/assets/bootstrap-icons/font/fonts/bootstrap-icons.woff
src/aegis_gui/assets/bootstrap-icons/font/fonts/bootstrap-icons.woff2
src/aegis_gui/assets/fonts/Inter.ttf
src/aegis_gui/assets/fonts/Quicksand.ttf
src/aegis_gui/docs/domains.py
src/aegis_gui/docs/specifications.py
src/aegis_gui/guisettings/GuiSettings.py
src/aegis_gui/guisettings/gui_settings.yml
src/aegis_gui/pages/tab_config/config_input.py
src/aegis_gui/pages/tab_config/copy_config.py
src/aegis_gui/pages/tab_config/foldable.py
src/aegis_gui/pages/tab_config/page.py
src/aegis_gui/pages/tab_config/run_simulation_button.py
src/aegis_gui/pages/tab_config/use_prerun.py
src/aegis_gui/pages/tab_config/valid_range.py
src/aegis_gui/pages/tab_landing/jumbotron.py
src/aegis_gui/pages/tab_landing/page.py
src/aegis_gui/pages/tab_landing/usecases.py
src/aegis_gui/pages/tab_plot/download.py
src/aegis_gui/pages/tab_plot/draw.py
src/aegis_gui/pages/tab_plot/graph.py
src/aegis_gui/pages/tab_plot/page.py
src/aegis_gui/pages/tab_plot/refresh.py
src/aegis_gui/pages/tab_plot/select_graph.py
src/aegis_gui/pages/tab_plot/select_sims.py
src/aegis_gui/pages/tab_plot/slider.py
src/aegis_gui/pages/tab_plot/plot/gen_fig.py
src/aegis_gui/pages/tab_plot/plot/prep_fig.py
src/aegis_gui/pages/tab_plot/plot/prep_setup.py
src/aegis_gui/pages/tab_plot/plot/prep_x.py
src/aegis_gui/pages/tab_plot/plot/prep_y.py
src/aegis_gui/pages/tab_simlog/delete.py
src/aegis_gui/pages/tab_simlog/download.py
src/aegis_gui/pages/tab_simlog/dropdown.py
src/aegis_gui/pages/tab_simlog/goplot.py
src/aegis_gui/pages/tab_simlog/open_folder.py
src/aegis_gui/pages/tab_simlog/page.py
src/aegis_gui/pages/tab_simlog/table.py
src/aegis_gui/pages/tab_simlog/terminate.py
src/aegis_gui/pages/tab_simlog/zipp.py
src/aegis_gui/pages/tab_simlog copy/goplot.py
src/aegis_gui/pages/tab_wiki/page.py
src/aegis_gui/utilities/log.py
src/aegis_gui/utilities/manipulate.py
src/aegis_gui/utilities/ps_list.py
src/aegis_gui/utilities/sim_tracker.py
src/aegis_gui/utilities/utilities.py
src/aegis_sim/__init__.py
src/aegis_sim/bioreactor.py
src/aegis_sim/constants.py
src/aegis_sim/variables.py
src/aegis_sim/dataclasses/__init__.py
src/aegis_sim/dataclasses/genomes.py
src/aegis_sim/dataclasses/phenotypes.py
src/aegis_sim/dataclasses/population.py
src/aegis_sim/parameterization/__init__.py
src/aegis_sim/parameterization/default_parameters.py
src/aegis_sim/parameterization/parameter.py
src/aegis_sim/parameterization/parametermanager.py
src/aegis_sim/parameterization/trait.py
src/aegis_sim/recording/__init__.py
src/aegis_sim/recording/configrecorder.py
src/aegis_sim/recording/featherrecorder.py
src/aegis_sim/recording/flushrecorder.py
src/aegis_sim/recording/intervalrecorder.py
src/aegis_sim/recording/phenomaprecorder.py
src/aegis_sim/recording/picklerecorder.py
src/aegis_sim/recording/popgenstatsrecorder.py
src/aegis_sim/recording/popsizerecorder.py
src/aegis_sim/recording/progressrecorder.py
src/aegis_sim/recording/recorder.py
src/aegis_sim/recording/recordingmanager.py
src/aegis_sim/recording/simpleprogressrecorder.py
src/aegis_sim/recording/summaryrecorder.py
src/aegis_sim/recording/terecorder.py
src/aegis_sim/recording/ticker.py
src/aegis_sim/submodels/__init__.py
src/aegis_sim/submodels/abiotic.py
src/aegis_sim/submodels/frailty.py
src/aegis_sim/submodels/infection.py
src/aegis_sim/submodels/predation.py
src/aegis_sim/submodels/genetics/__init__.py
src/aegis_sim/submodels/genetics/architect.py
src/aegis_sim/submodels/genetics/doc.md
src/aegis_sim/submodels/genetics/envdrift.py
src/aegis_sim/submodels/genetics/ploider.py
src/aegis_sim/submodels/genetics/composite/__init__.py
src/aegis_sim/submodels/genetics/composite/architecture.py
src/aegis_sim/submodels/genetics/composite/interpreter.py
src/aegis_sim/submodels/genetics/modifying/__init__.py
src/aegis_sim/submodels/genetics/modifying/architecture.py
src/aegis_sim/submodels/genetics/modifying/gpm.py
src/aegis_sim/submodels/genetics/modifying/gpm_decoder.py
src/aegis_sim/submodels/reproduction/__init__.py
src/aegis_sim/submodels/reproduction/matingmanager.py
src/aegis_sim/submodels/reproduction/mutation.py
src/aegis_sim/submodels/reproduction/pairing.py
src/aegis_sim/submodels/reproduction/recombination.py
src/aegis_sim/submodels/reproduction/reproduction.py
src/aegis_sim/submodels/reproduction/sexsystem.py
src/aegis_sim/submodels/resources/__init__.py
src/aegis_sim/submodels/resources/resources.py
src/aegis_sim/submodels/resources/starvation.py
src/aegis_sim/utilities/__init__.py
src/aegis_sim/utilities/container.py
src/aegis_sim/utilities/funcs.py
src/aegis_sim/utilities/get_folder_size.py
src/aegis_sim/utilities/popgenstats.py
src/aegis_sim/utilities/analysis/__init__.py
src/aegis_sim/utilities/analysis/genome.py
src/aegis_sim/utilities/analysis/leslie.py
src/aegis_sim/utilities/analysis/reproduction.py
src/aegis_sim/utilities/analysis/survival.py
tests/test_gui.py
tests/test_sim.py
tests/test_sim.yml
tests/__pycache__/test_dash.cpython-38-pytest-6.2.4.pyc
tests/__pycache__/test_dash.cpython-38-pytest-8.3.3.pyc
tests/__pycache__/test_dash.cpython-38.pyc
tests/__pycache__/test_gpm.cpython-38-pytest-6.2.4.pyc
tests/__pycache__/test_gpm.cpython-38-pytest-8.2.0.pyc
tests/__pycache__/test_gpm.cpython-38-pytest-8.2.2.pyc
tests/__pycache__/test_gpm.cpython-38-pytest-8.3.3.pyc
tests/__pycache__/test_gpm_initial.cpython-38-pytest-6.2.4.pyc
tests/__pycache__/test_gpm_initial.cpython-38-pytest-8.2.0.pyc
tests/__pycache__/test_gpm_initial.cpython-38-pytest-8.2.2.pyc
tests/__pycache__/test_gpm_initial.cpython-38-pytest-8.3.3.pyc
tests/__pycache__/test_gui.cpython-38-pytest-6.2.4.pyc
tests/__pycache__/test_gui.cpython-38-pytest-8.3.3.pyc
tests/__pycache__/test_sim.cpython-38-pytest-6.2.4.pyc
tests/__pycache__/test_sim.cpython-38-pytest-8.3.3.pyc
tests/test_sim/final_config.yml
tests/test_sim/input_summary.json
tests/test_sim/output_summary.json
tests/test_sim/popsize_after_reproduction.csv
tests/test_sim/popsize_before_reproduction.csv
tests/test_sim/progress.log
tests/test_sim/simpleprogress.log
tests/test_sim/ticker.txt
tests/test_sim/gui/genotypes.csv
tests/test_sim/gui/phenotypes.csv
tests/test_sim/gui/spectra/additive_age_structure.csv
tests/test_sim/gui/spectra/age_at_abiotic.csv
tests/test_sim/gui/spectra/age_at_age_limit.csv
tests/test_sim/gui/spectra/age_at_birth.csv
tests/test_sim/gui/spectra/age_at_infection.csv
tests/test_sim/gui/spectra/age_at_intrinsic.csv
tests/test_sim/gui/spectra/age_at_predation.csv
tests/test_sim/gui/spectra/age_at_starvation.csv
tests/test_sim/pickles/1
tests/test_sim/pickles/1000
tests/test_sim/popgen/allele_frequencies.csv
tests/test_sim/popgen/genotype_frequencies.csv
tests/test_sim/popgen/mean_h_per_bit.csv
tests/test_sim/popgen/mean_h_per_bit_expected.csv
tests/test_sim/popgen/mean_h_per_locus.csv
tests/test_sim/popgen/reference_genome.csv
tests/test_sim/popgen/reference_genome_gsample.csv
tests/test_sim/popgen/sfs.csv
tests/test_sim/popgen/simple.csv
tests/test_sim/snapshots/demography/0.feather
tests/test_sim/snapshots/demography/1.feather
tests/test_sim/snapshots/demography/1000.feather
tests/test_sim/snapshots/demography/998.feather
tests/test_sim/snapshots/demography/999.feather
tests/test_sim/snapshots/genotypes/0.feather
tests/test_sim/snapshots/genotypes/1.feather
tests/test_sim/snapshots/genotypes/1000.feather
tests/test_sim/snapshots/genotypes/998.feather
tests/test_sim/snapshots/genotypes/999.feather
tests/test_sim/snapshots/phenotypes/0.feather
tests/test_sim/snapshots/phenotypes/1.feather
tests/test_sim/snapshots/phenotypes/1000.feather
tests/test_sim/snapshots/phenotypes/998.feather
tests/test_sim/snapshots/phenotypes/999.feather
tests/test_sim/te/0.csv
tests/test_sim/te/1.csv