Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/pace-neutrons__Euphonic__0.0 && ls -R
.:
CHANGELOG.rst  __pycache__  euphonic.egg-info  tests_and_analysis
CITATION.cff   build        release.py         tox.ini
LICENSE        c            release_tox.ini    versioneer.py
MANIFEST.in    doc          setup.cfg
README.rst     euphonic     setup.py

./__pycache__:
versioneer.cpython-39.pyc

./build:
lib  temp.linux-x86_64-cpython-39

./build/lib:
euphonic

./build/lib/euphonic:
_euphonic.cpython-39-x86_64-linux-gnu.so

./build/temp.linux-x86_64-cpython-39:
c

./build/temp.linux-x86_64-cpython-39/c:
_euphonic.o  dyn_mat.o  load_libs.o  py_util.o  util.o

./c:
_euphonic.c  dyn_mat.h    load_libs.h  py_util.h  util.h
dyn_mat.c    load_libs.c  py_util.c    util.c

./doc:
Makefile  make.bat  requirements.txt  source

./doc/source:
brille-convergence-script.rst  installation.rst
brille-interpolator.rst        intensity-map-script.rst
changelog.rst                  plotting.rst
cite.rst                       powder-map-script.rst
cl-tools.rst                   powder.rst
conf.py                        python-api.rst
crystal.rst                    qpoint-frequencies.rst
debye-waller.rst               qpoint-phonon-modes.rst
dipole-parameter-script.rst    sampling-script.rst
disp-script.rst                sampling.rst
dos-script.rst                 scattering-intensities.rst
dos.rst                        spectra.rst
figures                        structure-factor.rst
force-constants.rst            styling.rst
howto.rst                      units.rst
index.rst                      utils.rst

./doc/source/figures:
euphonic-brille-convergence-lzo-fig1.png
euphonic-brille-convergence-lzo-fig2.png
euphonic-brille-convergence-lzo-fig3.png
euphonic-brille-convergence-lzo-fig4.png
euphonic-dispersion-nacl.png
euphonic-dispersion-quartz.png
euphonic-dos-nacl.png
euphonic-dos-quartz.png
euphonic-intensity-map-lzo.png
euphonic-intensity-map-quartz.png
euphonic-powder-map-nacl.png
euphonic-powder-map-quartz-kinematic.png
euphonic-powder-map-quartz.png
euphonic-show-sampling.png
fc-incommensurate-scell-arrows.png
fc-incommensurate-scell.png
howto
plot-styling-custom-1.png
plot-styling-custom-2.png
plot-styling-seaborn.png

./doc/source/figures/howto:
dos.png  pdos.png  powder-map.png

./euphonic:
__init__.py                               plot.py
_euphonic.cpython-39-x86_64-linux-gnu.so  powder.py
_version.py                               qpoint_frequencies.py
brille.py                                 qpoint_phonon_modes.py
broadening.py                             readers
cli                                       sampling.py
crystal.py                                spectra.py
data                                      structure_factor.py
debye_waller.py                           styles
force_constants.py                        util.py
io.py                                     validate.py

./euphonic/cli:
__init__.py            dos.py                        powder_map.py
brille_convergence.py  intensity_map.py              show_sampling.py
dispersion.py          optimise_dipole_parameter.py  utils.py

./euphonic/data:
__init__.py  bluebook.json  sears-1992.json

./euphonic/readers:
__init__.py  castep.py  phonopy.py

./euphonic/styles:
__init__.py  base.mplstyle  intensity_widget.mplstyle

./euphonic.egg-info:
PKG-INFO     dependency_links.txt  requires.txt
SOURCES.txt  entry_points.txt      top_level.txt

./tests_and_analysis:
__init__.py          minimum_euphonic_requirements.txt  tox_requirements.txt
ci_requirements.txt  test

./tests_and_analysis/test:
__init__.py  euphonic_test  run_tests.py  utils.py
data         pytest.ini     script_tests

./tests_and_analysis/test/data:
brille_grid   force_constants      readers               spectrum2d
castep_files  phonopy_files        script_data           structure_factor
crystal       qpoint_frequencies   spectrum1d            util
debye_waller  qpoint_phonon_modes  spectrum1dcollection

./tests_and_analysis/test/data/brille_grid:
lzo_trellis_10.hdf5  quartz_mesh_10.hdf5  quartz_mesh_10_unfilled.hdf5

./tests_and_analysis/test/data/castep_files:
LZO  NaH  Si2-sc-skew  ZnS  graphite  h-BN  quartz

./tests_and_analysis/test/data/castep_files/LZO:
La2Zr2O7-222-full.phonon_dos  La2Zr2O7.castep_bin  La2Zr2O7.param
La2Zr2O7-666-grid.phonon      La2Zr2O7.cell        La2Zr2O7.phonon

./tests_and_analysis/test/data/castep_files/NaH:
NaH.phonon

./tests_and_analysis/test/data/castep_files/Si2-sc-skew:
Si2-sc-skew-666-grid.phonon  Si2-sc-skew.cell   Si2-sc-skew.phonon
Si2-sc-skew.castep_bin       Si2-sc-skew.param

./tests_and_analysis/test/data/castep_files/ZnS:
loto_directions.phonon

./tests_and_analysis/test/data/castep_files/graphite:
graphite.castep_bin  graphite.cell  graphite.param

./tests_and_analysis/test/data/castep_files/h-BN:
h-BN_no_force_constants.castep_bin

./tests_and_analysis/test/data/castep_files/quartz:
quartz-554-full.phonon_dos  quartz.castep_bin  quartz_nosplit.phonon
quartz-666-grid.phonon      quartz.cell        quartz_split_qpts.phonon
quartz-777-grid.phonon      quartz.param

./tests_and_analysis/test/data/crystal:
crystal_LZO.json     crystal_quartz_cv_only.json  quartz_equiv_atoms.json
crystal_quartz.json  lzo_equiv_atoms.json

./tests_and_analysis/test/data/debye_waller:
CaHgO2  Si2-sc-skew  quartz

./tests_and_analysis/test/data/debye_waller/CaHgO2:
CaHgO2_666_300K_debye_waller.json

./tests_and_analysis/test/data/debye_waller/Si2-sc-skew:
Si2-sc-skew_666_300K_debye_waller.json
Si2-sc-skew_666_300K_symm_debye_waller.json

./tests_and_analysis/test/data/debye_waller/quartz:
quartz_666_0K_debye_waller.json
quartz_666_0K_debye_waller_10mev_lim.json
quartz_666_300K_debye_waller.json
quartz_666_300K_symm_debye_waller.json
quartz_777_300K_debye_waller.json

./tests_and_analysis/test/data/force_constants:
CaHgO2_convert_fc_data.json
CaHgO2_force_constants.json
LZO_force_constants.json
NaCl_QE_force_constants.json
NaCl_convert_full_fc_data.json
NaCl_default_force_constants.json
NaCl_force_constants.json
NaCl_phonopy_2.19_force_constants.json
NaCl_prim_force_constants.json
NaCl_total_with_dipole_force_constants.json
Si2-sc-skew_force_constants.json
graphite_force_constants.json
lzo_222_full_mode_gradients.json
lzo_222_full_mode_widths.json
quartz_554_full_mode_gradients.json
quartz_554_full_mode_widths.json
quartz_force_constants.json
quartz_random_force_constants.json
toy_quartz_mode_widths.json

./tests_and_analysis/test/data/phonopy_files:
CaHgO2   NaCl     NaCl_cli_test  NaCl_phonopy_2.19  README
LICENSE  NaCl_QE  NaCl_default   NaCl_prim

./tests_and_analysis/test/data/phonopy_files/CaHgO2:
CaHgO2-666-grid.yaml       mp-7041-20180417.yaml  phonopy_nofc.yaml
FULL_FORCE_CONSTANTS       phonopy_au_units.yaml  qpoints.yaml
full_force_constants.hdf5  phonopy_fullfc.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl:
BORN_nacl                           mesh
BORN_nacl_nofactor                  phonopy_full_fc.yaml
FORCE_CONSTANTS_nacl                phonopy_nacl.yaml
FULL_FORCE_CONSTANTS                phonopy_nacl_no_units.yaml
FULL_FORCE_CONSTANTS_single_number  phonopy_nofc.yaml
band                                phonopy_nofc_noborn.yaml
force_constants.hdf5                phonopy_nofc_noborn_nofactor.yaml
force_constants_hdf5.test           phonopy_nofc_noborn_wrongfactor.yaml
full_force_constants.hdf5           qpoints

./tests_and_analysis/test/data/phonopy_files/NaCl/band:
band.conf  band.hdf5  band.yaml  band_no_evec.hdf5  phonopy.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl/mesh:
mesh.conf  mesh.hdf5  mesh.yaml  mesh_no_evec.yaml  phonopy.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl/qpoints:
phonopy.yaml  qpoints.hdf5  qpoints_hdf5.test     qpoints_no_evec.yaml
qpoints.conf  qpoints.yaml  qpoints_no_evec.hdf5  qpoints_yaml.test

./tests_and_analysis/test/data/phonopy_files/NaCl_QE:
phonopy.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl_cli_test:
BORN  force_constants.hdf5  phonopy.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl_default:
BORN  FORCE_CONSTANTS  phonopy.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl_phonopy_2.19:
phonopy_2.19_nacl.yaml

./tests_and_analysis/test/data/phonopy_files/NaCl_prim:
phonopy_nacl.yaml

./tests_and_analysis/test/data/qpoint_frequencies:
CaHgO2  LZO  NaCl  quartz

./tests_and_analysis/test/data/qpoint_frequencies/CaHgO2:
CaHgO2_666_qpoint_frequencies.json  CaHgO2_from_phonopy_qpoint_frequencies.json

./tests_and_analysis/test/data/qpoint_frequencies/LZO:
LZO_no_asr_qpoint_frequencies.json  LZO_realspace_qpoint_frequencies.json
LZO_qpoint_frequencies.json         lzo_222_full_qpoint_frequencies.json

./tests_and_analysis/test/data/qpoint_frequencies/NaCl:
NaCl_band_no_evec_hdf5_from_phonopy_qpoint_frequencies.json
NaCl_band_yaml_from_phonopy_qpoint_frequencies.json
NaCl_mesh_hdf5_from_phonopy_qpoint_frequencies.json
NaCl_mesh_yaml_from_phonopy_qpoint_frequencies.json
NaCl_qpoints_hdf5_from_phonopy_qpoint_frequencies.json
NaCl_qpoints_yaml_from_phonopy_qpoint_frequencies.json
NaCl_trellis_10_qpoint_frequencies.json

./tests_and_analysis/test/data/qpoint_frequencies/quartz:
quartz_554_full_qpoint_frequencies.json
quartz_666_cv_only_qpoint_frequencies.json
quartz_666_qpoint_frequencies.json
quartz_bandstructure_cv_only_qpoint_frequencies.json
quartz_bandstructure_qpoint_frequencies.json
quartz_mesh_200_qpoint_frequencies.json
quartz_reciprocal_qpoint_frequencies.json
quartz_split_from_castep_qpoint_frequencies.json
quartz_split_reciprocal_qpoint_frequencies.json
toy_quartz_qpoint_frequencies.json

./tests_and_analysis/test/data/qpoint_phonon_modes:
CaHgO2  LZO  NaCl  Si2-sc-skew  quartz

./tests_and_analysis/test/data/qpoint_phonon_modes/CaHgO2:
CaHgO2_from_phonopy_qpoint_phonon_modes.json
CaHgO2_reciprocal_qpoint_phonon_modes.json

./tests_and_analysis/test/data/qpoint_phonon_modes/LZO:
LZO_from_castep_qpoint_phonon_modes.json
LZO_no_asr_qpoint_phonon_modes.json
LZO_realspace_qpoint_phonon_modes.json
LZO_reciprocal_qpoint_phonon_modes.json
La2Zr2O7_after_reorder_qpoint_phonon_modes.json
La2Zr2O7_before_reorder_qpoint_phonon_modes.json
lzo_222_full_qpoint_phonon_modes.json

./tests_and_analysis/test/data/qpoint_phonon_modes/NaCl:
NaCl_band_hdf5_from_phonopy_qpoint_phonon_modes.json
NaCl_band_yaml_from_phonopy_qpoint_phonon_modes.json
NaCl_mesh_hdf5_from_phonopy_qpoint_phonon_modes.json
NaCl_mesh_yaml_from_phonopy_qpoint_phonon_modes.json
NaCl_qpoints_hdf5_from_phonopy_qpoint_phonon_modes.json
NaCl_qpoints_yaml_from_phonopy_qpoint_phonon_modes.json
NaCl_reciprocal_qpoint_phonon_modes.json

./tests_and_analysis/test/data/qpoint_phonon_modes/Si2-sc-skew:
Si2-sc-skew_from_castep_qpoint_phonon_modes.json
Si2-sc-skew_no_asr_qpoint_phonon_modes.json
Si2-sc-skew_realspace_qpoint_phonon_modes.json
Si2-sc-skew_reciprocal_qpoint_phonon_modes.json

./tests_and_analysis/test/data/qpoint_phonon_modes/quartz:
quartz_554_full_qpoint_phonon_modes.json
quartz_after_reorder_nogamma_qpoint_phonon_modes.json
quartz_bandstructure_qpoint_phonon_modes.json
quartz_before_reorder_qpoint_phonon_modes.json
quartz_from_castep_qpoint_phonon_modes.json
quartz_no_asr_qpoint_phonon_modes.json
quartz_reciprocal_qpoint_phonon_modes.json
quartz_single_qpoint_phonon_modes.json
quartz_split_from_castep_qpoint_phonon_modes.json
quartz_split_reciprocal_qpoint_phonon_modes.json

./tests_and_analysis/test/data/readers:
loto_directions_average.json  lzo_222_full_phonon_dos.json
loto_directions_no_loto.json  quartz_554_full_phonon_dos.json

./tests_and_analysis/test/data/script_data:
brille-convergence.json  dos.json            powder-map.json
dispersion.json          intensity-map.json  sphere_sampling.json

./tests_and_analysis/test/data/spectrum1d:
CaHgO2_666_dos.json
La2Zr2O7_trellis_100_sf_1d_average.json
gan_bands_index_2.json
gan_bands_index_2_3_add.json
gan_bands_index_3.json
gan_bands_index_4.json
lzo_222_full_adaptive_dos.json
lzo_222_full_adaptive_dos_fast.json
lzo_222_full_castep_total_adaptive_dos.json
lzo_222_full_castep_zr_adaptive_dos.json
methane_pdos_index_1.json
methane_pdos_index_1_1meV_gauss_broaden.json
methane_pdos_index_2.json
methane_pdos_index_3.json
quartz_554_full_adaptive_dos.json
quartz_554_full_adaptive_dos_fast.json
quartz_554_full_castep_si_adaptive_dos.json
quartz_554_full_castep_total_adaptive_dos.json
quartz_666_1meV_gauss_broaden_dos.json
quartz_666_1meV_lorentz_broaden_dos.json
quartz_666_300K_sf_1d_average_noweights.json
quartz_666_300K_sf_1d_average_with_weights.json
quartz_666_dos.json
quartz_666_dos_from_text.json
quartz_666_split_11_0.json
quartz_666_split_11_1.json
quartz_dos_collection_index_2.json
toy_band.json
toy_band_btol10_split_0.json
toy_band_btol10_split_1.json
toy_band_btol10_split_2.json
toy_band_btol22_split_0.json
toy_band_btol22_split_1.json
toy_quartz_adaptive_dos.json
toy_quartz_cropped_dos.json
toy_quartz_cropped_uneven_broaden_dos.json
toy_quartz_cropped_uneven_dos.json
toy_quartz_cropped_uneven_hartree_dos.json
toy_quartz_dos.json
toy_quartz_uneven_adaptive_dos.json
xsq_bin_edges_spectrum1d.json
xsq_spectrum1d.json
xsq_split38_0.json
xsq_split38_1.json
xsq_split38_2.json

./tests_and_analysis/test/data/spectrum1dcollection:
LZO_cut_dispersion.json
La2Zr2O7_666_coh_incoh_species_append_pdos.json
La2Zr2O7_666_coh_pdos.json
La2Zr2O7_666_coh_species_pdos.json
La2Zr2O7_666_incoh_pdos.json
La2Zr2O7_666_incoh_species_pdos.json
NaCl_band_yaml_dispersion.json
gan_bands.json
gan_bands_bin_centres.npy
gan_bands_bin_edges.npy
gan_bands_from_text_file.json
gan_bands_index_2_5.json
lzo_222_full_adaptive_coh_pdos.json
lzo_222_full_adaptive_fast_coh_pdos.json
lzo_222_full_castep_adaptive_dos.json
methane_pdos.json
methane_pdos_from_text_file_fmt.json
methane_pdos_index_1_4.json
methane_pdos_split50_0.json
methane_pdos_split50_1.json
quartz_554_full_castep_adaptive_dos.json
quartz_666_coh_pdos.json
quartz_666_coh_pdos_from_text_file_fmt.json
quartz_666_coherent_plus_incoherent_pdos.json
quartz_666_cs_dict_pdos.json
quartz_666_pdos.json
quartz_bandstructure_cv_only_dispersion.json
quartz_bandstructure_dispersion.json
quartz_dos_collection.json
quartz_dos_collection_bin_centres.npy
quartz_dos_collection_bin_edges.npy
xsq_from_single_spectrum1d.json

./tests_and_analysis/test/data/spectrum2d:
CaHgO2_300K_bose_negative_e_sqw.json
CaHgO2_300K_bose_sqw.json
La2Zr2O7_cut_sqw_uneven_bins.json
NaCl_band_yaml_dos_map.json
NaCl_constrained_ef_32_cm_angle_45_135.json
NaCl_constrained_ei_100_cm_angle_20_275.json
NaCl_constrained_ei_300_cm.json
NaCl_constrained_ei_30_meV_angle_-20_30.json
example_spectrum2d.json
example_spectrum2d_split4_0.json
example_spectrum2d_split4_1.json
example_xbin_edges_spectrum2d.json
example_xybin_edges_spectrum2d.json
lzo_57L_1.5meV_0.1ang_gauss_sqw.json
lzo_57L_1.5meV_0.1ang_lorentz_sqw.json
lzo_57L_bragg_sqw.json
quartz_bandstructure_0.1ang_xbroaden_sqw.json
quartz_bandstructure_100K_bose_no_dw_sqw.json
quartz_bandstructure_2meV_0.1ang_xybroaden_sqw.json
quartz_bandstructure_2meV_ybroaden_sqw.json
quartz_bandstructure_dos_map.json
quartz_bandstructure_dos_map_uneven_bins.json
quartz_bandstructure_sqw.json
quartz_bandstructure_xybroaden_lorentz_sqw.json
synthetic_x.json
synthetic_x_poly_broadened.json
synthetic_x_poly_broadened_cheby.json

./tests_and_analysis/test/data/structure_factor:
CaHgO2  LZO  Si2-sc-skew  quartz

./tests_and_analysis/test/data/structure_factor/CaHgO2:
CaHgO2_300K_fc_structure_factor.json  CaHgO2_300K_structure_factor.json

./tests_and_analysis/test/data/structure_factor/LZO:
La2Zr2O7_cut_structure_factor.json

./tests_and_analysis/test/data/structure_factor/Si2-sc-skew:
Si2-sc-skew_300K_fc_structure_factor.json
Si2-sc-skew_300K_structure_factor.json

./tests_and_analysis/test/data/structure_factor/quartz:
quartz_0K_fc_structure_factor.json
quartz_0K_structure_factor.json
quartz_300K_fc_structure_factor.json
quartz_300K_structure_factor.json
quartz_666_300K_structure_factor.json
quartz_666_300K_structure_factor_noweights.json
quartz_666_weights.npy
quartz_bandstructure_structure_factor.json
quartz_fc_structure_factor.json
quartz_recip_asr_300K_fc_structure_factor.json
quartz_structure_factor.json

./tests_and_analysis/test/data/util:
qgrid_444.txt

./tests_and_analysis/test/euphonic_test:
__init__.py
test_brille_interpolator.py
test_broadening.py
test_calculate_structure_factor.py
test_castep_reader.py
test_crystal.py
test_debye_waller.py
test_force_constants.py
test_force_constants_calculate_qpoint_frequencies.py
test_force_constants_calculate_qpoint_phonon_modes.py
test_install.py
test_plot.py
test_powder.py
test_qpoint_frequencies.py
test_qpoint_phonon_modes.py
test_ref_data.py
test_sampling.py
test_spectrum1d.py
test_spectrum1dcollection.py
test_spectrum2d.py
test_structure_factor.py
test_util.py

./tests_and_analysis/test/script_tests:
__init__.py                 test_intensity_map.py              test_styling.py
test_brille_convergence.py  test_optimise_dipole_parameter.py  utils.py
test_dispersion.py          test_powder_map.py
test_dos.py                 test_sphere_sampling.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/pace-neutrons__Euphonic__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
ls -R /workspace/robertwayne__cogwatch__0.0
/workspace/robertwayne__cogwatch__0.0:
CHANGELOG.md     LICENSE.md  cogwatch  poetry.lock     tests
CONTRIBUTING.md  README.md   examples  pyproject.toml

/workspace/robertwayne__cogwatch__0.0/cogwatch:
__init__.py  cogwatch.py

/workspace/robertwayne__cogwatch__0.0/examples:
classless_bot.py  subclassed_bot.py

/workspace/robertwayne__cogwatch__0.0/tests:
__init__.py  test_cogwatch.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/robertwayne__cogwatch__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/michaelhush__M-LOOP__0.0 && find . -name "*.py"
./docs/conf.py
./setup.py
./.eggs/pytest_runner-6.0.1-py3.9.egg/ptr/__init__.py
./examples/python_controlled_experiment.py
./mloop/utilities.py
./mloop/__init__.py
./mloop/neuralnet.py
./mloop/testing.py
./mloop/interfaces.py
./mloop/learners.py
./mloop/launchers.py
./mloop/controllers.py
./mloop/cmd.py
./mloop/visualizations.py
./tests/test_examples.py
./tests/shell_script.py
./tests/test_units.py
./tools/landscape_vis.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/michaelhush__M-LOOP__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/lanl__scico__0.0 && find . -type f -name "*.py"
./docs/source/pyfigures/xray_3d_vec.py
./docs/source/pyfigures/xray_2d_geom.py
./docs/source/pyfigures/spheregrad.py
./docs/source/pyfigures/cylindgrad.py
./docs/source/pyfigures/polargrad.py
./docs/source/pyfigures/xray_3d_ang.py
./docs/source/pyfigures/xray_3d_vol.py
./docs/source/docsutil.py
./docs/source/conf.py
./docs/source/conf/55-nbsphinx.py
./docs/source/conf/70-latex.py
./docs/source/conf/25-napoleon.py
./docs/source/conf/15-theme.py
./docs/source/conf/40-intersphinx.py
./docs/source/conf/20-extensions.py
./docs/source/conf/10-project.py
./docs/source/conf/81-scico_scipy.py
./docs/source/conf/30-autodoc.py
./docs/source/conf/71-texinfo.py
./docs/source/conf/80-scico_numpy.py
./docs/source/conf/60-rtd.py
./docs/source/conf/85-dtype_typehints.py
./docs/source/conf/72-man_page.py
./docs/source/conf/50-graphviz.py
./docs/source/conf/45-mathjax.py
./setup.py
./scico/data/__init__.py
./scico/functional/_denoiser.py
./scico/functional/__init__.py
./scico/functional/_proxavg.py
./scico/functional/_tvnorm.py
./scico/functional/_dist.py
./scico/functional/_indicator.py
./scico/functional/_functional.py
./scico/functional/_norm.py
./scico/random.py
./scico/_version.py
./scico/diagnostics.py
./scico/_autograd.py
./scico/function.py
./scico/numpy/__init__.py
./scico/numpy/linalg.py
./scico/numpy/_wrapped_function_lists.py
./scico/numpy/_wrappers.py
./scico/numpy/testing.py
./scico/numpy/_blockarray.py
./scico/numpy/util.py
./scico/numpy/fft.py
./scico/__init__.py
./scico/typing.py
./scico/linop/_func.py
./scico/linop/abel.py
./scico/linop/xray/svmbir.py
./scico/linop/xray/astra.py
./scico/linop/xray/__init__.py
./scico/linop/xray/_xray.py
./scico/linop/__init__.py
./scico/linop/_matrix.py
./scico/linop/_stack.py
./scico/linop/_diag.py
./scico/linop/_diff.py
./scico/linop/_grad.py
./scico/linop/optics.py
./scico/linop/_dft.py
./scico/linop/_linop.py
./scico/linop/_circconv.py
./scico/linop/_util.py
./scico/linop/_convolve.py
./scico/operator/_func.py
./scico/operator/__init__.py
./scico/operator/_stack.py
./scico/operator/_operator.py
./scico/operator/biconvolve.py
./scico/flax/_models.py
./scico/flax/__init__.py
./scico/flax/examples/__init__.py
./scico/flax/examples/typed_dict.py
./scico/flax/examples/examples.py
./scico/flax/examples/data_generation.py
./scico/flax/examples/data_preprocessing.py
./scico/flax/inverse.py
./scico/flax/_flax.py
./scico/flax/train/clu_utils.py
./scico/flax/train/diagnostics.py
./scico/flax/train/steps.py
./scico/flax/train/traversals.py
./scico/flax/train/spectral.py
./scico/flax/train/__init__.py
./scico/flax/train/trainer.py
./scico/flax/train/checkpoints.py
./scico/flax/train/apply.py
./scico/flax/train/state.py
./scico/flax/train/typed_dict.py
./scico/flax/train/learning_rate.py
./scico/flax/train/losses.py
./scico/flax/train/input_pipeline.py
./scico/flax/blocks.py
./scico/test/functional/test_tvnorm.py
./scico/test/functional/test_proxavg.py
./scico/test/functional/test_separable.py
./scico/test/functional/test_misc.py
./scico/test/functional/prox.py
./scico/test/functional/test_norm.py
./scico/test/functional/test_denoiser_func.py
./scico/test/functional/test_loss.py
./scico/test/functional/test_core.py
./scico/test/test_util.py
./scico/test/test_metric.py
./scico/test/test_examples.py
./scico/test/osver.py
./scico/test/numpy/test_numpy.py
./scico/test/numpy/test_blockarray.py
./scico/test/numpy/test_numpy_util.py
./scico/test/test_data.py
./scico/test/linop/test_abel.py
./scico/test/linop/xray/test_svmbir.py
./scico/test/linop/xray/test_xray_2d.py
./scico/test/linop/xray/test_xray_3d.py
./scico/test/linop/xray/test_astra.py
./scico/test/linop/test_grad.py
./scico/test/linop/test_diag.py
./scico/test/linop/test_binop.py
./scico/test/linop/test_convolve.py
./scico/test/linop/test_circconv.py
./scico/test/linop/test_dft.py
./scico/test/linop/test_func.py
./scico/test/linop/test_diff.py
./scico/test/linop/test_optics.py
./scico/test/linop/test_matrix.py
./scico/test/linop/test_conversions.py
./scico/test/linop/test_linop.py
./scico/test/linop/test_linop_util.py
./scico/test/linop/test_linop_stack.py
./scico/test/operator/test_op_stack.py
./scico/test/operator/test_operator.py
./scico/test/operator/test_biconvolve.py
./scico/test/test_ray_tune.py
./scico/test/flax/test_checkpoints.py
./scico/test/flax/test_spectral.py
./scico/test/flax/test_flax.py
./scico/test/flax/test_train_aux.py
./scico/test/flax/test_trainer.py
./scico/test/flax/test_clu.py
./scico/test/flax/test_traversal.py
./scico/test/flax/test_apply.py
./scico/test/flax/test_inv.py
./scico/test/flax/test_examples_flax.py
./scico/test/flax/test_steps.py
./scico/test/test_denoiser.py
./scico/test/test_diagnostics.py
./scico/test/test_random.py
./scico/test/optimize/test_ladmm.py
./scico/test/optimize/test_padmm.py
./scico/test/optimize/test_pgm.py
./scico/test/optimize/test_pdhg.py
./scico/test/optimize/test_admm.py
./scico/test/test_version.py
./scico/test/test_solver.py
./scico/test/conftest.py
./scico/test/test_autograd.py
./scico/test/test_scipy_special.py
./scico/test/test_function.py
./scico/metric.py
./scico/scipy/__init__.py
./scico/scipy/special.py
./scico/loss.py
./scico/optimize/_admmaux.py
./scico/optimize/__init__.py
./scico/optimize/_ladmm.py
./scico/optimize/_primaldual.py
./scico/optimize/_padmm.py
./scico/optimize/admm.py
./scico/optimize/_admm.py
./scico/optimize/_pgmaux.py
./scico/optimize/_common.py
./scico/optimize/_pgm.py
./scico/optimize/pgm.py
./scico/solver.py
./scico/examples.py
./scico/util.py
./scico/plot.py
./scico/ray/tune.py
./scico/ray/__init__.py
./scico/denoiser.py
./examples/jnb.py
./examples/scripts/ct_projector_comparison_3d.py
./examples/scripts/ct_odp_train_foam2.py
./examples/scripts/sparsecode_nn_admm.py
./examples/scripts/deconv_ppp_bm4d_admm.py
./examples/scripts/deconv_ppp_bm3d_admm.py
./examples/scripts/deconv_tv_admm.py
./examples/scripts/deconv_circ_tv_admm.py
./examples/scripts/denoise_dncnn_train_bsds.py
./examples/scripts/deconv_ppp_dncnn_padmm.py
./examples/scripts/ct_astra_tv_admm.py
./examples/scripts/ct_astra_3d_tv_admm.py
./examples/scripts/denoise_ptv_pdhg.py
./examples/scripts/sparsecode_nn_apgm.py
./examples/scripts/sparsecode_apgm.py
./examples/scripts/ct_svmbir_tv_multi.py
./examples/scripts/sparsecode_poisson_apgm.py
./examples/scripts/ct_svmbir_ppp_bm3d_admm_prox.py
./examples/scripts/deconv_microscopy_tv_admm.py
./examples/scripts/denoise_l1tv_admm.py
./examples/scripts/ct_datagen_foam2.py
./examples/scripts/deconv_datagen_bsds.py
./examples/scripts/deconv_tv_padmm.py
./examples/scripts/ct_astra_noreg_pcg.py
./examples/scripts/denoise_tv_apgm.py
./examples/scripts/denoise_tv_multi.py
./examples/scripts/video_rpca_admm.py
./examples/scripts/deconv_microscopy_allchn_tv_admm.py
./examples/scripts/ct_unet_train_foam2.py
./examples/scripts/ct_astra_3d_tv_padmm.py
./examples/scripts/ct_svmbir_ppp_bm3d_admm_cg.py
./examples/scripts/denoise_cplx_tv_pdhg.py
./examples/scripts/denoise_dncnn_universal.py
./examples/scripts/sparsecode_conv_md_admm.py
./examples/scripts/ct_astra_weighted_tv_admm.py
./examples/scripts/deconv_tv_admm_tune.py
./examples/scripts/denoise_tv_admm.py
./examples/scripts/denoise_cplx_tv_nlpadmm.py
./examples/scripts/deconv_modl_train_foam1.py
./examples/scripts/superres_ppp_dncnn_admm.py
./examples/scripts/deconv_ppp_bm3d_apgm.py
./examples/scripts/deconv_datagen_foam1.py
./examples/scripts/ct_modl_train_foam2.py
./examples/scripts/sparsecode_conv_admm.py
./examples/scripts/ct_multi_tv_admm.py
./examples/scripts/ct_abel_tv_admm.py
./examples/scripts/denoise_datagen_bsds.py
./examples/scripts/deconv_ppp_dncnn_admm.py
./examples/scripts/ct_projector_comparison_2d.py
./examples/scripts/deconv_odp_train_foam1.py
./examples/scripts/denoise_approx_tv_multi.py
./examples/scripts/ct_fan_svmbir_ppp_bm3d_admm_prox.py
./examples/scripts/ct_tv_admm.py
./examples/scripts/ct_abel_tv_admm_tune.py
./examples/scripts/diffusercam_tv_admm.py
./examples/scripts/demosaic_ppp_bm3d_admm.py
./examples/makeindex.py
./examples/removejnberr.py
./examples/makenotebooks.py
./examples/updatejnbcode.py
./examples/updatejnbmd.py
./misc/gpu/availgpu.py
./misc/gpu/envinfo.py
./conftest.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/lanl__scico__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/mtik00__yamicache__0.0 && ls -R
.:
CONTRIBUTING.rst  NOTES.md    manage.py             tests
HISTORY.rst       README.rst  requirements_dev.txt  yamicache
LICENSE           __manage    setup.cfg             yamicache.egg-info
MANIFEST.in       docs        setup.py

./__manage:
__init__.py  docs.py  version.py

./docs:
Makefile  contributing.rst  installation.rst  sphinx-reload.py
_static   history.rst       make.bat          usage.rst
conf.py   index.rst         readme.rst

./docs/_static:

./tests:
__init__.py         test_exceptions.py  test_serialization.py
test_class.py       test_gc.py          test_threading.py
test_clear_deco.py  test_init.py
test_collide.py     test_noclass.py

./yamicache:
__init__.py  yamicache.py

./yamicache.egg-info:
PKG-INFO  SOURCES.txt  dependency_links.txt  top_level.txt  zip-safe[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/mtik00__yamicache__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/sdv-dev__RDT__0.0 && tree -L 3
bash: tree: command not found[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/sdv-dev__RDT__0.0 #
[Command finished with exit code 127]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/google__mobly__0.0 && find . -name "*.py" -not -path "*/tests/*" -not -path "*/test/*"
./tools/sl4a_shell.py
./tools/snippet_shell.py
./mobly/controllers/sniffer_lib/__init__.py
./mobly/controllers/sniffer_lib/local/__init__.py
./mobly/controllers/sniffer_lib/local/tcpdump.py
./mobly/controllers/sniffer_lib/local/local_base.py
./mobly/controllers/sniffer_lib/local/tshark.py
./mobly/controllers/android_device.py
./mobly/controllers/__init__.py
./mobly/controllers/android_device_lib/jsonrpc_shell_base.py
./mobly/controllers/android_device_lib/sl4a_client.py
./mobly/controllers/android_device_lib/__init__.py
./mobly/controllers/android_device_lib/callback_handler.py
./mobly/controllers/android_device_lib/event_dispatcher.py
./mobly/controllers/android_device_lib/adb.py
./mobly/controllers/android_device_lib/snippet_client.py
./mobly/controllers/android_device_lib/fastboot.py
./mobly/controllers/android_device_lib/jsonrpc_client_base.py
./mobly/controllers/attenuator_lib/minicircuits.py
./mobly/controllers/attenuator_lib/__init__.py
./mobly/controllers/attenuator_lib/telnet_scpi_client.py
./mobly/controllers/sniffer.py
./mobly/controllers/attenuator.py
./mobly/controllers/iperf_server.py
./mobly/controllers/monsoon.py
./mobly/__init__.py
./mobly/asserts.py
./mobly/utils.py
./mobly/logger.py
./mobly/records.py
./mobly/test_runner.py
./mobly/base_test.py
./mobly/config_parser.py
./mobly/keys.py
./mobly/signals.py
./docs/conf.py
./setup.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/google__mobly__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/sdv-dev__RDT__0.0 && ls -l
total 180
-rw-rw-r-- 1 root root    56 Jan 24 01:11 AUTHORS.rst
-rw-rw-r-- 1 root root 22494 Jan 24 01:11 CONTRIBUTING.rst
-rw-rw-r-- 1 root root 16969 Jan 24 01:11 DEVELOPMENT.rst
-rw-rw-r-- 1 root root 59290 Jan 24 01:11 HISTORY.md
-rw-rw-r-- 1 root root  1716 Jan 24 01:11 INSTALL.md
-rw-rw-r-- 1 root root  4872 Jan 24 01:11 LICENSE
-rw-rw-r-- 1 root root  6532 Jan 24 01:11 Makefile
-rw-rw-r-- 1 root root  7132 Jan 24 01:11 README.md
-rw-rw-r-- 1 root root  6508 Jan 24 01:11 RELEASE.md
-rw-rw-r-- 1 root root    91 Jan 24 01:11 latest_requirements.txt
-rw-rw-r-- 1 root root  5658 Jan 24 01:11 pyproject.toml
drwxr-xr-x 4 root root  4096 Jan 24 01:11 rdt
drwxrwxr-x 2 root root  4096 Jan 24 01:19 rdt.egg-info
-rw-rw-r-- 1 root root   427 Jan 24 01:11 static_code_analysis.txt
-rw-rw-r-- 1 root root  3755 Jan 24 01:11 tasks.py
drwxr-xr-x 6 root root  4096 Jan 24 01:11 tests
-rw-rw-r-- 1 root root   491 Jan 24 01:11 tox.ini[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/sdv-dev__RDT__0.0 #
[Command finished with exit code 0]


Prompt:
Please continue working on the task on whatever approach you think is suitable.
If you think you have solved the task, please first send your answer to user through message and then finish the interaction.
IMPORTANT: YOU SHOULD NEVER ASK FOR HUMAN HELP.


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/getnikola__nikola__0.0 && find . -type f -name "*.py" | grep -v "test"
./scripts/langstatus.py
./scripts/document_path_handlers.py
./scripts/getpyver.py
./scripts/langmatrix.py
./scripts/jinjify.py
./scripts/import_po.py
./scripts/github-release.py
./scripts/debug_rebuilds/step1_build_and_dumpdb.py
./scripts/debug_rebuilds/step2_analyze_py_files.py
./nikola/image_processing.py
./nikola/filters.py
./nikola/packages/pygments_better_html/__init__.py
./nikola/packages/__init__.py
./nikola/packages/datecond/__init__.py
./nikola/packages/tzlocal/win32.py
./nikola/packages/tzlocal/__init__.py
./nikola/packages/tzlocal/windows_tz.py
./nikola/packages/tzlocal/unix.py
./nikola/post.py
./nikola/__init__.py
./nikola/hierarchy_utils.py
./nikola/log.py
./nikola/plugins/misc/taxonomies_classifier.py
./nikola/plugins/misc/__init__.py
./nikola/plugins/misc/scan_posts.py
./nikola/plugins/compile/html.py
./nikola/plugins/compile/pandoc.py
./nikola/plugins/compile/php.py
./nikola/plugins/compile/rest/gist.py
./nikola/plugins/compile/rest/doc.py
./nikola/plugins/compile/rest/__init__.py
./nikola/plugins/compile/rest/thumbnail.py
./nikola/plugins/compile/rest/listing.py
./nikola/plugins/compile/rest/chart.py
./nikola/plugins/compile/rest/youtube.py
./nikola/plugins/compile/rest/post_list.py
./nikola/plugins/compile/rest/soundcloud.py
./nikola/plugins/compile/rest/media.py
./nikola/plugins/compile/rest/vimeo.py
./nikola/plugins/compile/__init__.py
./nikola/plugins/compile/markdown/mdx_gist.py
./nikola/plugins/compile/markdown/mdx_podcast.py
./nikola/plugins/compile/markdown/__init__.py
./nikola/plugins/compile/markdown/mdx_nikola.py
./nikola/plugins/compile/ipynb.py
./nikola/plugins/__init__.py
./nikola/plugins/task/redirect.py
./nikola/plugins/task/indexes.py
./nikola/plugins/task/taxonomies.py
./nikola/plugins/task/archive.py
./nikola/plugins/task/page_index.py
./nikola/plugins/task/copy_assets.py
./nikola/plugins/task/__init__.py
./nikola/plugins/task/gzip.py
./nikola/plugins/task/listings.py
./nikola/plugins/task/sitemap.py
./nikola/plugins/task/robots.py
./nikola/plugins/task/tags.py
./nikola/plugins/task/posts.py
./nikola/plugins/task/copy_files.py
./nikola/plugins/task/sources.py
./nikola/plugins/task/pages.py
./nikola/plugins/task/scale_images.py
./nikola/plugins/task/authors.py
./nikola/plugins/task/categories.py
./nikola/plugins/task/galleries.py
./nikola/plugins/task/bundles.py
./nikola/plugins/command/deploy.py
./nikola/plugins/command/new_post.py
./nikola/plugins/command/orphans.py
./nikola/plugins/command/auto/__init__.py
./nikola/plugins/command/__init__.py
./nikola/plugins/command/status.py
./nikola/plugins/command/subtheme.py
./nikola/plugins/command/theme.py
./nikola/plugins/command/version.py
./nikola/plugins/command/check.py
./nikola/plugins/command/new_page.py
./nikola/plugins/command/console.py
./nikola/plugins/command/rst2html/__init__.py
./nikola/plugins/command/init.py
./nikola/plugins/command/import_wordpress.py
./nikola/plugins/command/default_config.py
./nikola/plugins/command/plugin.py
./nikola/plugins/command/serve.py
./nikola/plugins/command/github_deploy.py
./nikola/plugins/shortcode/gist.py
./nikola/plugins/shortcode/thumbnail.py
./nikola/plugins/shortcode/listing.py
./nikola/plugins/shortcode/chart.py
./nikola/plugins/shortcode/post_list.py
./nikola/plugins/shortcode/emoji/__init__.py
./nikola/plugins/basic_import.py
./nikola/plugins/template/__init__.py
./nikola/plugins/template/jinja.py
./nikola/plugins/template/mako.py
./nikola/winutils.py
./nikola/utils.py
./nikola/data/samplesite/listings/hello.py
./nikola/data/themes/base/messages/messages_uk.py
./nikola/data/themes/base/messages/messages_az.py
./nikola/data/themes/base/messages/messages_nl.py
./nikola/data/themes/base/messages/messages_pl.py
./nikola/data/themes/base/messages/messages_fr.py
./nikola/data/themes/base/messages/messages_mi.py
./nikola/data/themes/base/messages/messages_es.py
./nikola/data/themes/base/messages/messages_tzm.py
./nikola/data/themes/base/messages/messages_fi.py
./nikola/data/themes/base/messages/messages_pa.py
./nikola/data/themes/base/messages/messages_id.py
./nikola/data/themes/base/messages/messages_fa.py
./nikola/data/themes/base/messages/messages_bs.py
./nikola/data/themes/base/messages/messages_ml.py
./nikola/data/themes/base/messages/messages_fur.py
./nikola/data/themes/base/messages/messages_lt.py
./nikola/data/themes/base/messages/messages_pt.py
./nikola/data/themes/base/messages/messages_af.py
./nikola/data/themes/base/messages/messages_sr_latin.py
./nikola/data/themes/base/messages/messages_ko.py
./nikola/data/themes/base/messages/messages_vi.py
./nikola/data/themes/base/messages/messages_he.py
./nikola/data/themes/base/messages/messages_bg.py
./nikola/data/themes/base/messages/messages_pt_br.py
./nikola/data/themes/base/messages/messages_oc.py
./nikola/data/themes/base/messages/messages_hr.py
./nikola/data/themes/base/messages/messages_el.py
./nikola/data/themes/base/messages/messages_da.py
./nikola/data/themes/base/messages/messages_hi.py
./nikola/data/themes/base/messages/messages_cs.py
./nikola/data/themes/base/messages/messages_it.py
./nikola/data/themes/base/messages/messages_ur.py
./nikola/data/themes/base/messages/messages_ru.py
./nikola/data/themes/base/messages/messages_en.py
./nikola/data/themes/base/messages/messages_tr.py
./nikola/data/themes/base/messages/messages_hu.py
./nikola/data/themes/base/messages/messages_eu.py
./nikola/data/themes/base/messages/messages_sv.py
./nikola/data/themes/base/messages/messages_sr.py
./nikola/data/themes/base/messages/messages_ca.py
./nikola/data/themes/base/messages/messages_et.py
./nikola/data/themes/base/messages/messages_eo.py
./nikola/data/themes/base/messages/messages_th.py
./nikola/data/themes/base/messages/messages_ja.py
./nikola/data/themes/base/messages/messages_ar.py
./nikola/data/themes/base/messages/messages_gl.py
./nikola/data/themes/base/messages/messages_zh_cn.py
./nikola/data/themes/base/messages/messages_zh_tw.py
./nikola/data/themes/base/messages/messages_br.py
./nikola/data/themes/base/messages/messages_de.py
./nikola/data/themes/base/messages/messages_te.py
./nikola/data/themes/base/messages/messages_nb.py
./nikola/data/themes/base/messages/messages_mr.py
./nikola/data/themes/base/messages/messages_sq.py
./nikola/data/themes/base/messages/messages_sl.py
./nikola/data/themes/base/messages/messages_ia.py
./nikola/data/themes/base/messages/messages_sk.py
./nikola/shortcodes.py
./nikola/plugin_categories.py
./nikola/state.py
./nikola/__main__.py
./nikola/metadata_extractors.py
./nikola/nikola.py
./docs/sphinx/conf.py
./docs/sphinx/nikola_titles_for_sphinx.py
./setup.py
./dodo.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/getnikola__nikola__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/sisl__CEEM__0.0 && ls -R
.:
CEEM.egg-info  ceem      experiments        requirements.txt
LICENSE        docs      pretrained_models  setup.py
README.md      examples  pyproject.toml     tests

./CEEM.egg-info:
PKG-INFO     dependency_links.txt  top_level.txt
SOURCES.txt  requires.txt          zip-safe

./ceem:
__init__.py        dynamics.py   nested.py        particleem.py
baseline_utils.py  exp_utils.py  nn.py            smoother.py
ceem.py            learner.py    odesolver.py     systems
data_utils.py      logger.py     opt_criteria.py  utils.py

./ceem/systems:
__init__.py        lorenzattractor.py  maglev.py
discretelinear.py  lorenzsystem.py     springmassdamper.py

./docs:
Makefile  README.rst  conf.py  index.rst  make.bat

./examples:
COVIDExample.ipynb  germany.csv

./experiments:
heli  lorenz

./experiments/heli:
baselines.py        evaluations.pkl  prepare_residual_dataset.py  trajectories
ceemnl.py           n4sid.py         run_n4sid.m
evaluate_models.py  plotting         train_lstm.py

./experiments/heli/plotting:
plot_trajectories.py  plotbar.py

./experiments/heli/trajectories:
evaluations.pkl  h25pred  lstmpred  naivepred  nlpred  sidpred

./experiments/lorenz:
bias_experiment.py  convergence_experiment_ceem.py
comp_ceem.py        convergence_experiment_pem.py
comp_pem.py         plotting

./experiments/lorenz/plotting:
process_bias.py  process_comp.py  process_convergence.py

./pretrained_models:
NL_model.th  SID  h25_baseline.th  lstm.th  naive_baseline.th

./pretrained_models/SID:
SID_10D.mat    SID_10D_10.mat  SID_10D_4.mat  SID_10D_7.mat  SID_20D.mat
SID_10D_0.mat  SID_10D_2.mat   SID_10D_5.mat  SID_10D_8.mat  SID_5D.mat
SID_10D_1.mat  SID_10D_3.mat   SID_10D_6.mat  SID_10D_9.mat

./tests:
ceem_test.py       ekf_test.py       ls_learner_test.py    systems
criterion_test.py  ekf_test_data.pt  nls_smoother_test.py
dynamics_test.py   learner_test.py   pem_test.py

./tests/systems:
lorenzattractor_test.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/sisl__CEEM__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/betcode-org__flumine__0.0 && ls -R
.:
HISTORY.rst  docs      flumine.egg-info        requirements-test.txt  tests
LICENSE      examples  mkdocs.yml              requirements.txt
README.md    flumine   requirements-speed.txt  setup.py

./docs:
advanced.md      controls.md  index.md        quickstart.md  trades.md
architecture.md  help.md      markets.md      sportsdata.md  workers.md
clients.md       images       performance.md  strategies.md

./docs/images:
jupyterloggingcontrol-screenshot.png  logo.png         uml_packages.png
logo-full.png                         uml_classes.png

./examples:
__init__.py            example-sportsdata.py  simulate-sportsdata.py  workers
controls               example.py             simulate.py
example-betconnect.py  marketrecorder.py      strategies
example-single.py      middleware             tennisexample.py

./examples/controls:
__init__.py     backtestloggingcontrol.py
analysis.ipynb  jupyterloggingcontrol.py

./examples/middleware:
__init__.py  marketcatalogue.py  orders.py

./examples/strategies:
__init__.py     marketrecorder.py  pricerecorder.py
lowestlayer.py  priceblockage.py

./examples/workers:
__init__.py  inplayservice.py  terminate.py

./flumine:
__init__.py     clients    events         flumine.py  patching.py  streams
__version__.py  config.py  exceptions.py  markets     simulation   utils.py
baseflumine.py  controls   execution      order       strategy     worker.py

./flumine/clients:
__init__.py    betconnectclient.py  clients.py
baseclient.py  betfairclient.py     simulatedclient.py

./flumine/controls:
__init__.py  clientcontrols.py  loggingcontrols.py  tradingcontrols.py

./flumine/events:
__init__.py  events.py

./flumine/execution:
__init__.py       betfairexecution.py    transaction.py
baseexecution.py  simulatedexecution.py

./flumine/markets:
__init__.py  blotter.py  market.py  markets.py  middleware.py

./flumine/order:
__init__.py  orderpackage.py  process.py    trade.py
order.py     ordertype.py     responses.py

./flumine/simulation:
__init__.py  simulatedorder.py  simulation.py  utils.py

./flumine/strategy:
__init__.py  runnercontext.py  strategy.py

./flumine/streams:
__init__.py    historicalstream.py  simulatedorderstream.py
basestream.py  marketstream.py      sportsdatastream.py
datastream.py  orderstream.py       streams.py

./flumine.egg-info:
PKG-INFO  SOURCES.txt  dependency_links.txt  requires.txt  top_level.txt

./tests:
__init__.py                test_integration.py      test_simulated_utils.py
resources                  test_loggingcontrols.py  test_simulatedorder.py
test_baseflumine.py        test_markets.py          test_strategy.py
test_blotter.py            test_middleware.py       test_streams.py
test_clientcontrols.py     test_order.py            test_trade.py
test_clients.py            test_orderpackage.py     test_tradingcontrols.py
test_config.py             test_ordertype.py        test_transaction.py
test_events.py             test_process.py          test_utils.py
test_execution.py          test_release.py          test_worker.py
test_flumine.py            test_responses.py
test_fluminesimulation.py  test_runnercontext.py

./tests/resources:
1.197931750  BASIC-1.132153978     SELF-1.181223994  sportsdata
1.197931751  BASIC-1.132153978.gz  SELF-1.181223995
1.200806927  PRO-1.170258213       catalogues

./tests/resources/catalogues:
1.197931750.json  1.197931751.json

./tests/resources/sportsdata:
1.200806927[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/betcode-org__flumine__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
ls -la /workspace/ICB-DCM__pyABC__0.0
total 84
drwxr-xr-x 10 root root 4096 Jan 17 15:49 .
drwxrwxr-x  3 root root 4096 Jan 17 15:37 ..
drwxr-xr-x  8 root root 4096 Jan 17 15:49 .git
drwxr-xr-x  3 root root 4096 Jan 17 15:48 .github
-rw-rw-r--  1 root root  821 Jan 17 15:48 .gitignore
-rw-rw-r--  1 root root  389 Jan 17 15:48 .readthedocs.yml
-rw-rw-r--  1 root root  154 Jan 17 15:48 .rtd_conda_env.yml
-rw-rw-r--  1 root root    1 Jan 17 15:48 .rtd_pip_reqs.txt
-rw-rw-r--  1 root root  176 Jan 17 15:48 CONTRIBUTING.md
-rw-rw-r--  1 root root 1465 Jan 17 15:48 LICENSE.txt
-rw-rw-r--  1 root root  107 Jan 17 15:48 MANIFEST.in
-rw-rw-r--  1 root root 2086 Jan 17 15:48 README.rst
drwxr-xr-x  6 root root 4096 Jan 17 15:48 doc
drwxr-xr-x 15 root root 4096 Jan 17 15:48 pyabc
drwxrwxr-x  2 root root 4096 Jan 17 15:49 pyabc.egg-info
-rwxrwxr-x  1 root root  138 Jan 17 15:48 run_flake8.sh
-rw-rw-r--  1 root root 2744 Jan 17 15:48 setup.cfg
-rw-rw-r--  1 root root  283 Jan 17 15:48 setup.py
drwxr-xr-x  6 root root 4096 Jan 17 15:48 test
drwxr-xr-x  2 root root 4096 Jan 17 15:48 test_nondeterministic
drwxr-xr-x  2 root root 4096 Jan 17 15:48 test_performance[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/ICB-DCM__pyABC__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
ls -la /workspace/HXLStandard__libhxl-python__0.0
total 88
drwxr-xr-x 8 root root  4096 Feb  5 11:21 .
drwxrwxr-x 3 root root  4096 Feb  5 10:45 ..
drwxr-xr-x 5 root root  4096 Feb  5 11:21 .git
-rw-rw-r-- 1 root root   140 Feb  5 11:21 .gitignore
-rw-rw-r-- 1 root root    91 Feb  5 11:21 .travis.yml
-rw-rw-r-- 1 root root 18947 Feb  5 11:21 CHANGELOG
-rw-rw-r-- 1 root root  1210 Feb  5 11:21 LICENSE.md
-rw-rw-r-- 1 root root    28 Feb  5 11:21 MANIFEST.in
-rw-rw-r-- 1 root root  1868 Feb  5 11:21 Makefile
-rw-rw-r-- 1 root root  6000 Feb  5 11:21 README.md
drwxr-xr-x 3 root root  4096 Feb  5 11:21 docs
drwxr-xr-x 3 root root  4096 Feb  5 11:21 hxl
drwxrwxr-x 2 root root  4096 Feb  5 11:21 libhxl.egg-info
drwxr-xr-x 3 root root  4096 Feb  5 11:21 profile
-rw-rw-r-- 1 root root   111 Feb  5 11:21 requirements.txt
-rwxrwxr-x 1 root root  2336 Feb  5 11:21 setup.py
drwxr-xr-x 3 root root  4096 Feb  5 11:21 tests[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/HXLStandard__libhxl-python__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/alan-turing-institute__mogp-emulator__0.0 && ls -R
.:
CODE_OF_CONDUCT.md  README.md      mogp_gpu                   requirements.txt
CONTRIBUTING.md     docs           requirements-dev.txt       setup.py
LICENSE             mogp_emulator  requirements-optional.txt

./docs:
Makefile    conf.py  implementation  intro    requirements.txt
benchmarks  demos    index.rst       methods

./docs/benchmarks:
benchmarks.rst  gkdr_benchmark.rst       mice_benchmark.rst   rosenbrock.rst
branin.rst      histmatch_benchmark.rst  pivot_benchmark.rst  tsunami.rst

./docs/demos:
excalibur_workshop_demo.rst  gp_demos.rst            kdr_demos.rst
gp_demoGPU.rst               gp_kernel_demos.rst     mice_demos.rst
gp_demoR.rst                 historymatch_demos.rst

./docs/implementation:
DimensionReduction.rst  HistoryMatching.rst  SequentialDesign.rst
ExperimentalDesign.rst  Kernel.rst           fitting.rst
GPParams.rst            MeanFunction.rst     formula.rst
GaussianProcess.rst     MultiOutputGP.rst    implementation.rst
GaussianProcessGPU.rst  Priors.rst           linalg.rst

./docs/intro:
installation.rst   overview.rst    tutorial.rst       uq_workflow.png
methoddetails.rst  projectile.png  tutorial_nroy.png

./docs/methods:
alt  def  disc  exam  meta  methods.rst  proc  thread

./docs/methods/alt:
AltBLPriors.rst
AltBasisFunctions.rst
AltCoreDesign.rst
AltCorrelationFunction.rst
AltDynamicEmulationApproach.rst
AltEstimateDelta.rst
AltGPPriors.rst
AltGPorBLEmulator.rst
AltImplausibilityMeasure.rst
AltIteratingSingleStepEmulators.rst
AltMeanFunction.rst
AltMeanFunctionMultivariate.rst
AltMultipleOutputsApproach.rst
AltMultivariateCovarianceStructures.rst
AltMultivariateGPPriors.rst
AltNumericalSolutionForKarhunenLoeveExpansion.rst
AltOptimalCriteria.rst
AltOptimalDesignAlgorithms.rst
AltScreeningChoice.rst

./docs/methods/def:
DefActiveInput.rst            DefModelBasedDesign.rst
DefAdjoint.rst                DefModelDiscrepancy.rst
DefAssessment.rst             DefMultilevelEmulation.rst
DefBLAdjust.rst               DefMultivariateGP.rst
DefBLVarianceLearning.rst     DefMultivariateTProcess.rst
DefBasisFunctions.rst         DefNugget.rst
DefBayesLinear.rst            DefPrincipalComponentAnalysis.rst
DefBayesian.rst               DefProper.rst
DefBestInput.rst              DefRegularity.rst
DefCalibration.rst            DefReification.rst
DefCodeUncertainty.rst        DefScreening.rst
DefConjugate.rst              DefSecondOrderExch.rst
DefCorrelationLength.rst      DefSecondOrderSpec.rst
DefDataAssimilation.rst       DefSensitivityAnalysis.rst
DefDecisionBasedSA.rst        DefSeparable.rst
DefDesign.rst                 DefSimulator.rst
DefDeterministic.rst          DefSingleStepFunction.rst
DefDynamic.rst                DefSmoothingKernel.rst
DefElicitation.rst            DefSmoothness.rst
DefEmulator.rst               DefSpaceFillingDesign.rst
DefExchangeability.rst        DefStateVector.rst
DefForcingInput.rst           DefStochastic.rst
DefGP.rst                     DefTProcess.rst
DefHistoryMatching.rst        DefTrainingSample.rst
DefHyperparameter.rst         DefUncertaintyAnalysis.rst
DefImplausibilityMeasure.rst  DefValidation.rst
DefInactiveInput.rst          DefVarianceBasedSA.rst
DefMUCM.rst                   DefWeakPrior.rst

./docs/methods/disc:
DiscActiveInputs.rst            DiscObservations.rst
DiscAdjustExchBeliefs.rst       DiscPostModeDelta.rst
DiscBayesLinearTheory.rst       DiscRealisationDesign.rst
DiscBestInput.rst               DiscReification
DiscBuildCoreGP.rst             DiscReification.rst
DiscCore.rst                    DiscReificationTheory
DiscCoreDesign.rst              DiscReificationTheory.rst
DiscCoreValidationDesign.rst    DiscSensitivityAndDecision.rst
DiscCovarianceFunction.rst      DiscSensitivityAndOutputUncertainty.rst
DiscDecisionBasedSA.rst         DiscSensitivityAndSimplification.rst
DiscExchangeableModels.rst      DiscSobol.rst
DiscExpertAssessMD.rst          DiscStructuredMD.rst
DiscFactorialDesign.rst         DiscStructuredMeanFunction.rst
DiscFormalAssessMD.rst          DiscToolkitSensitivityAnalysis.rst
DiscGPBasedEmulator.rst         DiscUANugget.rst
DiscGaussianAssumption.rst      DiscUncertaintyAnalysis.rst
DiscImplausibilityCutoff.rst    DiscVarianceBasedSA.rst
DiscInformalAssessMD.rst        DiscVarianceBasedSATheory.rst
DiscIterativeRefocussing.rst    DiscWhyModelDiscrepancy.rst
DiscKarhunenLoeveExpansion.rst  DiscWhyProbabilisticSA.rst
DiscMonteCarlo.rst

./docs/methods/disc/DiscReification:
ReifNetwork1.png

./docs/methods/disc/DiscReificationTheory:
ReifNetwork2.png  ReifNetwork3.png

./docs/methods/exam:
Exam1DHistoryMatch       ExamMultipleOutputsPCA
Exam1DHistoryMatch.rst   ExamMultipleOutputsPCA.rst
ExamCoreGP1Dim           ExamScreeningAutomaticRelevanceDetermination
ExamCoreGP1Dim.rst       ExamScreeningAutomaticRelevanceDetermination.rst
ExamCoreGP2Dim           ExamScreeningMorris
ExamCoreGP2Dim.rst       ExamScreeningMorris.rst
ExamDecisionBasedSA.rst  ExamVariantWithDerivatives1Dim
ExamMultipleOutputs      ExamVariantWithDerivatives1Dim.rst
ExamMultipleOutputs.rst

./docs/methods/exam/Exam1DHistoryMatch:
GradPoints14.pdf  GradPoints14.png  GradPoints17.pdf  GradPoints17.png

./docs/methods/exam/ExamCoreGP1Dim:
Figure1.png  Figure3.png  Figure5.png  Figure7.png
Figure2.png  Figure4.png  Figure6.png  Figure8.png

./docs/methods/exam/ExamCoreGP2Dim:
Figure1.png  Figure3.png  Figure5.png  Figure7.png
Figure2.png  Figure4.png  Figure6.png

./docs/methods/exam/ExamMultipleOutputs:
CONVpreds.png  LMCpreds.png  ellipse_samescale.png  output1.png
INDpreds.png   SEPpreds.png  ellipse_zoom.png       output2.png

./docs/methods/exam/ExamMultipleOutputsPCA:
pca.png  z-scores-dist.png  z-scores.png

./docs/methods/exam/ExamScreeningAutomaticRelevanceDetermination:
exampleARD.png  exampleARD2D.png

./docs/methods/exam/ExamScreeningMorris:
morrisToolkitExample.png

./docs/methods/exam/ExamVariantWithDerivatives1Dim:
Figure1.png  Figure2.png  Figure3.png  Figure4.png  Figure5.png  Figure6.png

./docs/methods/meta:
MetaComments.rst         MetaNotation.rst            MetaToolkitStructure.rst
MetaCopyrightNotice.rst  MetaSoftwareDisclaimer.rst  MetaToolkitTutorial
MetaHomePage.rst         MetaToolkitPageList.rst     MetaToolkitTutorial.rst

./docs/methods/meta/MetaToolkitTutorial:
Fig1.png  Fig2.png

./docs/methods/proc:
ProcASCM.rst
ProcApproxDeltaPosterior.rst
ProcApproximateIterateSingleStepEmulator.rst
ProcApproximateUpdateDynamicMeanandVariance.rst
ProcAutomaticRelevanceDetermination.rst
ProcBLAdjust.rst
ProcBLPredict.rst
ProcBLVarianceLearning.rst
ProcBranchAndBoundAlgorithm.rst
ProcBuildCoreBL.rst
ProcBuildCoreBLEmpirical.rst
ProcBuildCoreGP.rst
ProcBuildEmulateDerivsGP.rst
ProcBuildMultiOutputGP.rst
ProcBuildMultiOutputGPSep.rst
ProcBuildWithDerivsGP.rst
ProcDataPreProcessing.rst
ProcExactIterateSingleStepEmulator.rst
ProcExchangeAlgorithm.rst
ProcExploreFullSimulatorDesignRegion.rst
ProcFourierExpansionForKL.rst
ProcHaarWaveletExpansionForKL.rst
ProcHaltonDesign.rst
ProcLHC.rst
ProcLatticeDesign.rst
ProcMCMCDeltaCoreGP.rst
ProcMorris.rst
ProcOptimalLHC.rst
ProcOutputSample.rst
ProcOutputTransformation.rst
ProcOutputsPrincipalComponents.rst
ProcPivotedCholesky.rst
ProcPredictGP.rst
ProcPredictMultiOutputFunction.rst
ProcPredictMultipleEmulators.rst
ProcSimulationBasedInference.rst
ProcSobolSequence.rst
ProcUABL.rst
ProcUADynamicEmulator.rst
ProcUAGP.rst
ProcUAMultipleEmulators.rst
ProcUpdateDynamicMeanAndVariance.rst
ProcValidateCoreGP.rst
ProcVarSAGP.rst
ProcVariogram.rst
ProcWeylDesign.rst

./docs/methods/thread:
ThreadCoreBL.rst                     ThreadTopicSensitivityAnalysis.rst
ThreadCoreGP.rst                     ThreadVariantDynamic.rst
ThreadGenericEmulateDerivatives.rst  ThreadVariantModelDiscrepancy.rst
ThreadGenericHistoryMatching.rst     ThreadVariantMultipleOutputs.rst
ThreadGenericMultipleEmulators.rst   ThreadVariantTwoLevelEmulation.rst
ThreadTopicExperimentalDesign.rst    ThreadVariantWithDerivatives.rst
ThreadTopicScreening.rst

./mogp_emulator:
DimensionReduction.py  Kernel.py             SequentialDesign.py  linalg
ExperimentalDesign.py  LibGPGPU.py           __init__.py          tests
GPParams.py            MeanFunction.py       benchmarks           utils.py
GaussianProcess.py     MultiOutputGP.py      demos
GaussianProcessGPU.py  MultiOutputGP_GPU.py  fitting.py
HistoryMatching.py     Priors.py             formula.py

./mogp_emulator/benchmarks:
Makefile             benchmark_gpu_parallel.py     benchmark_rosenbrock.py
__init__.py          benchmark_historymatching.py  benchmark_tsunami.py
benchmark_MICE.py    benchmark_kdr_GP.py           timingtestdata.npz
benchmark_branin.py  benchmark_pivot.py            tsunamidata.npz

./mogp_emulator/demos:
__init__.py                 gp_demos.py            mice_demos.py
excalibur_workshop_demo.py  gp_kernel_demos.py     projectile.py
gp_demo.R                   historymatch_demos.py  tutorial.py
gp_demo_gpu.py              kdr_demos.py

./mogp_emulator/linalg:
__init__.py  cholesky.py  linalg_utils.py

./mogp_emulator/tests:
Makefile                      test_GPUMeanFunction.py
__init__.py                   test_GaussianProcess.py
benchmark_MICE.py             test_HistoryMatching.py
benchmark_branin.py           test_Kernel.py
benchmark_historymatching.py  test_MeanFunction.py
benchmark_kdr_GP.py           test_MultiOutputGP.py
benchmark_rosenbrock.py       test_Priors.py
benchmark_tsunami.py          test_SequentialDesign.py
test_DimensionReduction.py    test_fitting.py
test_ExperimentalDesign.py    test_formula.py
test_GPParams.py              test_linalg.py

./mogp_gpu:
Makefile  src  test

./mogp_gpu/src:
bindings.cu      kernel.cu     multioutputgp_gpu.hpp  util.cu
densegp_gpu.hpp  kernel.hpp    strided_range.hpp      util.hpp
fitting.hpp      meanfunc.hpp  types.hpp

./mogp_gpu/test:
test_basic_fitting.cu  test_gpu_basic.cu     test_gpu_utils.cu  test_openmp.cu
test_densegp_gpu.cu    test_gpu_cholesky.cu  test_meanfunc.cu
test_gp_fitting.cu     test_gpu_kernel.cu    test_mogp_gpu.cu[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/alan-turing-institute__mogp-emulator__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/KnowledgeCaptureAndDiscovery__somef__0.0 && ls -R
.:
CITATION.cff  LICENSE    config.json  experiments  notebook        setup.py
Dockerfile    README.md  docs         mkdocs.yml   pyproject.toml  src

./docs:
index.md    links.csv  logo_big.png  objective.md  paper.pdf         usage.md
install.md  logo.png   logo_old.png  output.md     requirements.txt

./experiments:
'Classifier Pipelines.ipynb'   helper_scripts           trained_models
 TFidf-Logistic.ipynb          initial_baseline.ipynb   training_allen
 TFidf-NB.ipynb                ranking                  training_corpus
 create_models.py              readme.md
 header_analysis               setup_corpus.py

./experiments/header_analysis:
Wordnet.ipynb  header.csv  header_evaluation  md_split

./experiments/header_analysis/header_evaluation:
header_evaluation_new.csv
header_evaluation_new_header_content_annotated.csv
header_evaluation_new_header_only_annotated.csv
header_evaluation_predicted_2021-03-10.csv
header_evaluation_predicted_2021-07-04.csv
header_evaluation_summary_2021-03-10.csv
header_evaluation_summary_2021-07-04.csv
old_evaluations
readme.md

./experiments/header_analysis/header_evaluation/old_evaluations:
header_evaluation.csv            header_evaluation_summary_2021-03-10_old.csv
header_evaluation_predicted.csv  header_evaluation_summary_old.csv

./experiments/header_analysis/md_split:
common_name.csv  common_name_grouped.csv  md_section.csv

./experiments/helper_scripts:
environment.yml         gitmydoc.py                    splitcsvcategory.py
fetchgithubmetadata.py  minegithubrepodescriptions.py  synthRepoData.py
githubrepo2readme.py    printprogressbar.py

./experiments/ranking:
citation_classifier.csv     installation_classifier.csv
description_classifier.csv  invocation_classifier.csv

./experiments/trained_models:
citcvbb.p   cittfrfc.p  destflr.p   inscvnb.p   instfxgb.p  invtfper.p
citcvlr.p   cittfsgd.p  destfnb.p   instfada.p  invcvbb.p   invtfrfc.p
citcvnb.p   cittfxgb.p  destfper.p  instfdtc.p  invcvlr.p   invtfsgd.p
cittfada.p  descvbb.p   destfrfc.p  instflr.p   invcvnb.p   invtfxgb.p
cittfdtc.p  descvlr.p   destfsgd.p  instfnb.p   invtfada.p
cittflr.p   descvnb.p   destfxgb.p  instfper.p  invtfdtc.p
cittfnb.p   destfada.p  inscvbb.p   instfrfc.p  invtflr.p
cittfper.p  destfdtc.p  inscvlr.p   instfsgd.p  invtfnb.p

./experiments/training_allen:
experiment.json  testing.py  training.py

./experiments/training_corpus:
citation.csv            description.csv   invocation.csv  repos
count_distributions.py  installation.csv  none.csv        repos_summary.csv

./experiments/training_corpus/repos:
3D-ResNets-PyTorch-README.md
CU-Net-README.md
DBNet-README.md
DCPDN-README.md
DID-MDN-README.md
DaSiamRPN-README.md
DeepGuidedFilter-README.md
DeepMVS-README.md
Detectron-README.md
Fiona-README.md
Flow-Guided-Feature-Aggregation-README.md
GAN_stability-README.md
GANimation-README.md
GPRPy-README.md
ICNet-README.md
LapSRN-README.md
LibGEOS.jl-README.md
PRM-README.md
PVGeo-README.md
RDN-README.md
RESCAN-README.md
SRN-Deblur-README.md
Shapely-README.md
apsg-README.md
bootstrap-README.md
cltk-cltk-README.md
d3-README.md
da-faster-rcnn-README.md
empymod-README.md
facebookresearch-DensePose-README.md
facebookresearch-ResNeXt-README.md
facebookresearch-pyrobot-README.md
facebookresearch-wav2letter-README.md
gdal-docker-README.md
gempy-README.md
generator-arcgis-js-app-README.md
geojson-vt-README.md
geonotebook-README.md
gitbucket-gitbucket-README.md
gitfolio-README.md
gprMax-README.md
harismuneer-Ultimate-Facebook-Scraper-README.md
hmr-README.md
hyvr-README.md
integral-human-pose-README.md
ipyleaflet-README.md
iter-reason-README.md
kosmtik-README.md
lasio-README.md
map-vectorizer-README.md
mapshaper-README.md
microsoft-malmo-README.md
mplleaflet-README.md
mplstereonet-README.md
neural-motifs-README.md
neural_renderer-README.md
nextflow-io-nextflow-README.md
node-qa-masker-README.md
omfvista-README.md
pose-residual-network-pytorch-README.md
puppeteer-README.md
pyGeoPressure-README.md
pyansys-README.md
pylops-README.md
pymeshfix-README.md
pyro-ppl-pyro-README.md
pysal-README.md
pyvista-README.md
rasterio-README.md
react-README.md
readgssi-README.md
reduxjs-react-redux-README.md
scikit-image-scikit-image-README.md
scikit-learn-scikit-learn-README.md
segyio-README.md
sentinelsat-README.md
sequelize-sequelize-README.md
sg2im-README.md
striplog-README.md
tensorflow-README.md
tensorflow-magenta-README.md
tetgen-README.md
tilelive-mapnik-README.md
tilematrix-README.md
tippecanoe-README.md
two-stream-dyntex-synth-README.md
vid2vid-README.md
vue-README.md
vue-devtools-README.md

./notebook:
'SOMEF Usage Example.ipynb'   test.json

./src:
somef

./src/somef:
__init__.py               extract_workflows.py   process_results.py
__main__.py               header_analysis.py     regular_expressions.py
configuration.py          mapping                rolf
evaluation                models                 somef_cli.py
export                    parser                 supervised_classification.py
extract_ontologies.py     process_files.py       test
extract_software_type.py  process_repository.py  utils

./src/somef/evaluation:
create_header_corpus.py           output_header_evaluation_summary.py
header_evaluation_interactive.py  update_evaluation.py

./src/somef/export:
__init__.py  json_export.py  turtle_export.py

./src/somef/mapping:
__init__.py  rml.ttl  yarrrml.yml

./src/somef/models:
citation.p  deprecated  description.p  installation.p  invocation.p

./src/somef/models/deprecated:
citation.sk  description.sk  installation.sk  invocation.sk

./src/somef/parser:
__init__.py  create_excerpts.py  mardown_parser.py

./src/somef/rolf:
__init__.py  models  models_test  preprocessing.py

./src/somef/rolf/models:
audio.sav            natural_language_processing.sav
computer_vision.sav  reinforcement_learning.sav
graphs.sav           semantic_web.sav

./src/somef/rolf/models_test:
astrophysics.sav  rationale.md  sequential.sav

./src/somef/test:
__init__.py                 test_parser_somef.py
test_JSON_export.py         test_process_repository.py
test_cli.py                 test_process_results.py
test_configuration.py       test_regular_expressions.py
test_data                   test_software_type.py
test_extract_ontologies.py  test_supervised_classification.py
test_extract_workflows.py   test_turtle_export.py
test_header_analysis.py

./src/somef/test/test_data:
README-GENI.md              rasterio-README.md
README-OBA-SPARQL.md        repositories
README-OWL-To-OAS.md        repostatus-README.md
README-PPool.md             test_465.md
README-TINTO.md             test_arxiv_links.txt
README-base-images.md       test_extract_bibtex.txt
README-devilog.md           test_extract_binder_links.txt
README-easytv-annotator.md  test_extract_dois.txt
README-epw2rdf-contents.md  test_extract_gitter_chat.txt
README-epw2rdf.md           test_extract_header_content_hash.txt
README-fair-ontologies.md   test_extract_header_content_hash_complex.txt
README-kgtk-notebooks.md    test_extract_header_content_underline.txt
README-licensius.md         test_extract_readthedocs_1.txt
README-loupe-api.md         test_extract_readthedocs_2.txt
README-manim.md             test_extract_readthedocs_3.txt
README-mapeathor.md         test_extract_title_hash.txt
README-mapshaper.md         test_extract_title_underline.txt
README-pylops.md            test_extract_title_with_md.txt
README-pytorch.md           test_images.txt
README-raidologist.md       test_issue_181.txt
README-tada-gam.md          test_issue_181_2.txt
README-tensorflow-2.6.0.md  test_issue_181_3.txt
README-tokei.md             test_issue_270.txt
README-urllib3.md           test_issue_images.txt
README-widoco.md            test_logo.txt
README-wothive.md           test_logo2.txt
README-ya2o.md              test_logo_tensorflow.txt
SimulatedReads2Map.wdl      test_logo_uscisii2.txt
export_test.json            test_pypi.md
extract_bash_code.txt       test_repo_status.txt
input-test.txt              test_wiki.md
pyansys-README.rst          widoco_readme.md

./src/somef/test/test_data/repositories:
A-Dynamic-E-Commerce-Website-master    ipynb-master
Clamp                                  kgtk-notebooks
Fermi                                  mir_eval
JAFFA-master                           probot-12.1.1
OWL-To-OAS-Specification-master        rdflib-6.0.2
RDFChess                               repos_oeg
Widoco                                 resolver_deco
ack                                    software_catalog
auroral-ontology-core                  sprint-main
basis_functions_approach_to_GP-master  wav2letter
bimerr-epw                             website-static-master
captum                                 wot-hive
corpuser

./src/somef/test/test_data/repositories/A-Dynamic-E-Commerce-Website-master:
README.md  admin.php  admin_orders.php  delete_from_cart.php  mangola.sql

./src/somef/test/test_data/repositories/Clamp:
README.md

./src/somef/test/test_data/repositories/Fermi:
README.md

./src/somef/test/test_data/repositories/JAFFA-master:
README  README.md  cwl

./src/somef/test/test_data/repositories/JAFFA-master/cwl:
converter.cwl  smcFusion-jaffa-workflow.cwl  tar.cwl  twoBitToFa.cwl

./src/somef/test/test_data/repositories/OWL-To-OAS-Specification-master:
README.md  mkdocs.yml  requirements.txt

./src/somef/test/test_data/repositories/RDFChess:
README.md  pom.xml  rdfchess.config  run.bat

./src/somef/test/test_data/repositories/Widoco:
CITATION.cff     Dockerfile  README.md     license.md
CONTRIBUTING.md  LICENSE     example_onto  test

./src/somef/test/test_data/repositories/Widoco/example_onto:
ontology.nt  ontology.ttl  test.ttl

./src/somef/test/test_data/repositories/Widoco/test:
CITATION.cff  test

./src/somef/test/test_data/repositories/Widoco/test/test:
CITATION.cff  test

./src/somef/test/test_data/repositories/Widoco/test/test/test:
CITATION.cff

./src/somef/test/test_data/repositories/ack:
ACKNOWLEDGMENT.md  README.md

./src/somef/test/test_data/repositories/auroral-ontology-core:
ontology.rdf  ontology.xml  readme.md

./src/somef/test/test_data/repositories/basis_functions_approach_to_GP-master:
BF_1D_notebook.Rmd  Diagnosis_HSGP_v2.Rmd  Rnb_case3D_diagnosis.Rmd

./src/somef/test/test_data/repositories/bimerr-epw:
LICENSE  README.md

./src/somef/test/test_data/repositories/captum:
AWESOME_LIST.md  CODE_OF_CONDUCT.md  LICENSE    environment.yml  setup.cfg
CITATION         CONTRIBUTING.md     README.md  pyproject.toml   setup.py

./src/somef/test/test_data/repositories/corpuser:
README.md

./src/somef/test/test_data/repositories/ipynb-master:
__init__.py  bogus_ipynb.ipynb  r_notebook.ipynb

./src/somef/test/test_data/repositories/kgtk-notebooks:
LICENSE  README.md  tutorial  use-cases

./src/somef/test/test_data/repositories/kgtk-notebooks/tutorial:
01-kgtk-introduction.ipynb       05-kg-enrichment-with-lod.ipynb
02-kg-profiling.ipynb            06-kg-network-analysis.ipynb
03-kg-graph-embeddings.ipynb     07-kg-constraint-validation.ipynb
04-kg-enrichment-with-csv.ipynb  kgtk-browser.ipynb

./src/somef/test/test_data/repositories/kgtk-notebooks/use-cases:
Visualize-force-graph-example.ipynb  ontology-examples.ipynb
browser-profiling.ipynb              properties-for-this-type.ipynb
class-visualization.ipynb

./src/somef/test/test_data/repositories/mir_eval:
LICENSE.txt  README.rst  setup.py

./src/somef/test/test_data/repositories/probot-12.1.1:
CODE_OF_CONDUCT.md  LICENSE    README.pt-br.md
CONTRIBUTING.md     README.md  codecov.yml

./src/somef/test/test_data/repositories/rdflib-6.0.2:
CHANGELOG.md  black.toml                run_tests.sh
CONTRIBUTORS  docker-compose.tests.yml  run_tests_with_coverage_report.sh
LICENSE       pull_request_template.md  setup.cfg
MANIFEST.in   requirements.dev.txt      setup.py
Makefile      requirements.txt          skiptests.list
README.md     run_tests.py              tox.ini

./src/somef/test/test_data/repositories/repos_oeg:
bimerr-core

./src/somef/test/test_data/repositories/repos_oeg/bimerr-core:
README.md

./src/somef/test/test_data/repositories/resolver_deco:
LICENSE.txt  README.txt  resolver_deco.py  setup.py

./src/somef/test/test_data/repositories/software_catalog:
LICENSE  README.md  repo_icons

./src/somef/test/test_data/repositories/software_catalog/repo_icons:
acknowledgement.png  citation.png

./src/somef/test/test_data/repositories/sprint-main:
netex_accounting_version.xsd.rdf  setup.sh

./src/somef/test/test_data/repositories/wav2letter:
CMakeLists.txt      CONTRIBUTING.md  LICENSE    Test.cpp   docs
CODE_OF_CONDUCT.md  Decode.cpp       README.md  Train.cpp  scripts

./src/somef/test/test_data/repositories/wav2letter/docs:
DecoderSketch.png  arch.md  decoder.md  installation.md  train.md

./src/somef/test/test_data/repositories/wav2letter/scripts:
OptimizeSortParams.cpp  imgcat                         wavextract
Seq2SeqAnalysis.cpp     launch_distributed_chronos.sh  wavplot
arrayfire_parser.py     tensorboard.py                 wavstatus
fair_cluster            wavdiff

./src/somef/test/test_data/repositories/wav2letter/scripts/fair_cluster:
w2l_fair_cluster_build.sh   w2l_fair_cluster_distributed_training_benchmarks.sh
w2l_fair_cluster_decode.sh  w2l_fair_cluster_train.sh

./src/somef/test/test_data/repositories/website-static-master:
fonts.css  header.js  image.js  index.js  layout.js  privacy.js  terms.js

./src/somef/test/test_data/repositories/wot-hive:
README.md  docker

./src/somef/test/test_data/repositories/wot-hive/docker:
auroral-hive  docker-compose.yml  fuseki

./src/somef/test/test_data/repositories/wot-hive/docker/auroral-hive:
Dockerfile

./src/somef/test/test_data/repositories/wot-hive/docker/fuseki:
Dockerfile

./src/somef/utils:
__init__.py  constants.py  markdown_utils.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/KnowledgeCaptureAndDiscovery__somef__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/HXLStandard__libhxl-python__0.0 && ls -R
.:
CHANGELOG   MANIFEST.in  README.md  hxl              profile           setup.py
LICENSE.md  Makefile     docs       libhxl.egg-info  requirements.txt  tests

./docs:
converters.html  formulas    input.html    util.html
datatypes.html   geo.html    model.html    validation.html
filters.html     index.html  scripts.html

./docs/formulas:
eval.html  functions.html  index.html  lexer.html  parser.html  parsetab.html

./hxl:
__init__.py    filters.py  hxl-default-schema.json  scripts.py
converters.py  formulas    input.py                 util.py
datatypes.py   geo.py      model.py                 validation.py

./hxl/formulas:
__init__.py  eval.py  functions.py  lexer.py  parser.py

./libhxl.egg-info:
PKG-INFO     dependency_links.txt  requires.txt
SOURCES.txt  entry_points.txt      top_level.txt

./profile:
data  validation-profile.py

./profile/data:
unhcr_popstats_export_persons_of_concern_all_data.hxl

./tests:
__init__.py         test_datatypes.py  test_geo.py    test_scripts.py
files               test_filters.py    test_input.py  test_validation.py
test_converters.py  test_formulas.py   test_model.py

./tests/files:
mock  test_converters  test_io  test_scripts  test_validation

./tests/files/mock:
append-source-1.csv  append-source-2.csv  append-source-list.csv  taxonomy.csv

./tests/files/test_converters:
wide-tagging-test.csv

./tests/files/test_io:
input-broken.xlsx               input-valid-json.txt
input-fuzzy.csv                 input-valid-latin1.csv
input-invalid.csv               input-valid-nested.json
input-invalid.png               input-valid-objects.json
input-merged.xlsx               input-valid-xlsx.NOEXT
input-multiline.csv             input-valid.csv
input-multiple-headers.csv      input-valid.json
input-notag1.html               input-valid.ssv
input-notag2.html               input-valid.tsv
input-quality.xls               input-valid.xls
input-quality.xlsx              input-valid.xlsx
input-untagged-csv.zip          input-zip-invalid.zip
input-untagged-objects.json     output-valid-objects.json
input-untagged.json             output-valid.csv
input-valid-csv.zip             output-valid.json
input-valid-json-selector.json

./tests/files/test_scripts:
add-output-before.csv             rename-output-multiple.csv
add-output-default.csv            rename-output-single.csv
add-output-headers.csv            select-output-eq.csv
append-dataset.csv                select-output-ge.csv
clean-output-headers.csv          select-output-gt.csv
clean-output-lower.csv            select-output-le.csv
clean-output-noheaders.csv        select-output-lt.csv
clean-output-upper.csv            select-output-multiple.csv
clean-output-whitespace-all.csv   select-output-ne.csv
clean-output-whitespace-tags.csv  select-output-nre.csv
count-output-aggregated.csv       select-output-re.csv
count-output-colspec.csv          select-output-reverse.csv
count-output-simple.csv           sort-output-date.csv
cut-output-excludes.csv           sort-output-default.csv
cut-output-includes.csv           sort-output-numeric.csv
input-date.csv                    sort-output-reverse.csv
input-merge.csv                   sort-output-tags.csv
input-simple.csv                  tag-output-ambiguous.csv
input-status.csv                  tag-output-default.csv
input-untagged.csv                tag-output-full.csv
input-whitespace.csv              tag-output-notsubstrings.csv
merge-output-basic.csv            tag-output-partial.csv
merge-output-overwrite.csv        validation-schema-invalid.csv
merge-output-replace.csv          validation-schema-valid.csv
rename-output-header.csv

./tests/files/test_validation:
truthy-schema.json[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/HXLStandard__libhxl-python__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/kontron__python-ipmi__0.0 && ls -R
.:
AUTHORS  README.rst  docs      pyipmi                setup.cfg  tests
COPYING  bin         examples  python_ipmi.egg-info  setup.py

./bin:
supported_cmds.py

./docs:
commands.rst  source

./docs/source:
bmcWatchdog_cmd.rst  conf.py    introduction.rst      ipmiMsgSupport_cmd.rst
chassis_cmd.rst      index.rst  ipmDevGlobal_cmd.rst  quick_start.rst

./examples:
dcmi.py  interface_aardvark.py  interface_rmcp.py

./pyipmi:
__init__.py   errors.py  hpm.py       messaging.py  sensor.py
bmc.py        event.py   interfaces   msgs          session.py
chassis.py    fields.py  ipmitool.py  picmg.py      state.py
constants.py  fru.py     lan.py       sdr.py        utils.py
dcmi.py       helper.py  logger.py    sel.py        version.py

./pyipmi/interfaces:
__init__.py  aardvark.py  ipmb.py  ipmitool.py  mock.py  rmcp.py

./pyipmi/msgs:
__init__.py  constants.py         event.py  lan.py      registry.py  sensor.py
bmc.py       dcmi.py              fru.py    message.py  sdr.py       session.py
chassis.py   device_messaging.py  hpm.py    picmg.py    sel.py       vita.py

./python_ipmi.egg-info:
PKG-INFO     dependency_links.txt  requires.txt
SOURCES.txt  entry_points.txt      top_level.txt

./tests:
__init__.py  msgs             test_fields.py  test_ipmi.py   test_sensor.py
fru_bin      test_bmc.py      test_fru.py     test_picmg.py  test_utils.py
hpm_bin      test_chassis.py  test_helper.py  test_sdr.py
interfaces   test_errors.py   test_hpm.py     test_sel.py

./tests/fru_bin:
kontron_am4010.bin  kontron_am4904.bin  vadatech_utc017.bin

./tests/hpm_bin:
firmware.hpm

./tests/interfaces:
__init__.py  test_aardvark.py  test_ipmb.py  test_ipmitool.py  test_rmcp.py

./tests/msgs:
__init__.py               test_event.py    test_picmg.py     test_sensor.py
test_bmc.py               test_fru.py      test_registry.py
test_chassis.py           test_hpm.py      test_sdr.py
test_device_messaging.py  test_message.py  test_sel.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/kontron__python-ipmi__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
ls -R /workspace/python-lsp__python-lsp-ruff__0.0
/workspace/python-lsp__python-lsp-ruff__0.0:
LICENSE    pylsp_ruff      python_lsp_ruff.egg-info  tests
README.md  pyproject.toml  setup.py

/workspace/python-lsp__python-lsp-ruff__0.0/pylsp_ruff:
__init__.py  ruff_lint.py

/workspace/python-lsp__python-lsp-ruff__0.0/python_lsp_ruff.egg-info:
PKG-INFO     dependency_links.txt  requires.txt
SOURCES.txt  entry_points.txt      top_level.txt

/workspace/python-lsp__python-lsp-ruff__0.0/tests:
test_ruff_lint.py[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/python-lsp__python-lsp-ruff__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/ppizarror__PyDetex__0.0 && ls -R
.:
LICENSE      README.rst  codecov.yml  gui.py   pydetex.egg-info  setup.py  test
MANIFEST.in  build.py    docs         pydetex  requirements.txt  specs

./docs:
Makefile  _source  _static  conf.py  index.rst  make.bat

./docs/_source:
contributors.rst  license.rst  parsers.rst  pipelines.rst  utils.rst

./docs/_static:
example_simple.png  example_strict.png  pydetex_windows.png

./pydetex:
__init__.py    _fonts.py         _symbols.py     gui.py        res
__pycache__    _gui_settings.py  _utils_lang.py  parsers.py    utils.py
__pyinstaller  _gui_utils.py     _utils_tex.py   pipelines.py  version.py

./pydetex/__pycache__:
__init__.cpython-39.pyc  version.cpython-39.pyc

./pydetex/__pyinstaller:
__init__.py  hook-pydetex.py

./pydetex/res:
cog.ico         icon.png            u_superscripts.txt  u_textfrak.txt
dictionary.ico  placeholder_en.tex  u_symbols.txt       u_textit.txt
icon.gif        placeholder_es.tex  u_textbb.txt        u_textmono.txt
icon.icns       stopwords.json      u_textbf.txt
icon.ico        u_subscripts.txt    u_textcal.txt

./pydetex.egg-info:
PKG-INFO     dependency_links.txt  requires.txt
SOURCES.txt  entry_points.txt      top_level.txt

./specs:
PyDetex_Win.spec  PyDetex_Win_Single.spec  PyDetex_macOS.spec  __init__.py

./test:
__init__.py  data         test_parsers.py    test_utils.py
_base.py     test_gui.py  test_pipelines.py

./test/data:
example.tex                          example_simple_comments.txt
example_complex_envs.txt             example_simple_comments_output.txt
example_complex_envs_output.txt      example_simple_figure_caption.txt
example_complex_template.txt         example_simple_figure_caption_output.txt
example_complex_template_output.txt  example_simple_itemize.txt
example_placeholder.txt              example_simple_itemize_output.txt
example_placeholder_output.txt       example_tables_strict.txt
example_simple_cite.txt              example_tables_strict_output.txt
example_simple_cite_output.txt       simple.tex[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/ppizarror__PyDetex__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/CSchoel__nolds__0.0 && ls -R
.:
CHANGELOG.md  MANIFEST.in  TODO.md  nolds           notes.txt
LICENSE.txt   README.rst   doc      nolds.egg-info  setup.py

./doc:
Makefile  make.bat  source

./doc/source:
conf.py  examples.rst  index.rst  nolds.rst  tests.rst

./nolds:
__init__.py  datasets  datasets.py  examples.py  measures.py  test_measures.py

./nolds/datasets:
'^JKSE.csv'  '^N225.csv'  '^NDX.csv'   brown72.npy   qrandom.npy

./nolds.egg-info:
PKG-INFO  SOURCES.txt  dependency_links.txt  requires.txt  top_level.txt[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/CSchoel__nolds__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/SPARC-X__SPARC-X-API__0.0 && find . -type f
./setup.py
./.github/ISSUE_TEMPLATE/bug_report.md
./.github/ISSUE_TEMPLATE/feature_request.md
./.github/workflows/update_api.yml
./.github/workflows/publish_doc_pages.yml
./.github/workflows/unit_test.yml
./.github/workflows/api_version_probe.py
./.github/workflows/joss_paper.yml
./.github/workflows/publish-pypi.yml
./.conda/meta.yaml
./.git/ORIG_HEAD
./.git/logs/refs/heads/master
./.git/logs/HEAD
./.git/refs/heads/master
./.git/index
./.git/objects/pack/pack-e25a6da39db4f98e3ae6d54782006b725367aa1b.idx
./.git/objects/pack/pack-e25a6da39db4f98e3ae6d54782006b725367aa1b.pack
./.git/packed-refs
./.git/config
./.git/HEAD
./.gitignore
./README.md
./examples/simple_examples/ex1-ase-optimize.py
./examples/simple_examples/ex0-eos.py
./examples/socket/singlepoint/spin-polarized/run.py
./examples/socket/singlepoint/spin-paired/run.py
./examples/socket/md/mlff/plumed/run.py
./examples/socket/md/ab-initio/ase/run.py
./examples/socket/md/ab-initio/plumed/run.py
./examples/socket/relax/mlff/coords/run.py
./examples/socket/relax/ab-initio/cell/run.py
./examples/socket/relax/ab-initio/coords/run.py
./examples/FileIO/md/mlff/run.py
./examples/FileIO/md/ab-initio/run.py
./examples/FileIO/relax/relax_coords/mlff/run.py
./examples/FileIO/relax/relax_coords/ab-initio/run.py
./examples/FileIO/relax/relax_cell/ab-initio/run.py
./examples/active_learning/ft_config_gemnet_gpu.yml
./examples/active_learning/example_finetuna_minimal.py
./examples/env.sh
./.pre-commit-config.yaml
./paper/paper.md
./paper/README.md
./paper/paper.bib
./paper/fig/fig_sparc_api_overview.svg
./paper/fig/fig_socket_hetero.svg
./LICENSE
./tests/test_psp.py
./tests/test_read_all_examples.py
./tests/test_ion_parser.py
./tests/archive/read_input.ion
./tests/archive/test.py
./tests/archive/read_input.inpt
./tests/test_import.py
./tests/test_calculator.py
./tests/test_downloader.py
./tests/test_000_ase_io.py
./tests/test_bundle_to_calc.py
./tests/test_quicktest.py
./tests/sparc-latex-doc-202302/System.tex
./tests/sparc-latex-doc-202302/Print.tex
./tests/sparc-latex-doc-202302/Electrostatics.tex
./tests/sparc-latex-doc-202302/Manual.tex
./tests/sparc-latex-doc-202302/highT/SQ.tex
./tests/sparc-latex-doc-202302/highT/Manual_highT.tex
./tests/sparc-latex-doc-202302/highT/Introduction.tex
./tests/sparc-latex-doc-202302/SCF.tex
./tests/sparc-latex-doc-202302/MD.tex
./tests/sparc-latex-doc-202302/Optimization.tex
./tests/sparc-latex-doc-202302/Introduction.tex
./tests/sparc-latex-doc-202302/Paral.tex
./tests/sparc-latex-doc-202302/Stress.tex
./tests/test_inpt_parser.py
./tests/test_output_parser.py
./tests/outputs/Cu_FCC.sparc/Cu_FCC.inpt
./tests/outputs/Cu_FCC.sparc/Cu_FCC.static
./tests/outputs/Cu_FCC.sparc/Cu_FCC.out
./tests/outputs/Cu_FCC.sparc/Cu_FCC.ion
./tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.geopt
./tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.out
./tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.ion
./tests/outputs/Alloy_geopt_ppd_bc.sparc/SPARC.inpt
./tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.ion
./tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.inpt
./tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.static
./tests/outputs/Fe2_spin_scan_gamma.sparc/Fe2_spin_scan_gamma.out
./tests/outputs/H2O_socket_incomplete.sparc/01_H_1_1.0_1.0_pbe_v1.0.psp8
./tests/outputs/H2O_socket_incomplete.sparc/SPARC.out
./tests/outputs/H2O_socket_incomplete.sparc/SPARC.static
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./tests/outputs/H2O_socket_incomplete.sparc/sparc.log
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./tests/outputs/H2O_socket_incomplete.sparc/08_O_6_1.2_1.4_pbe_n_v1.0.psp8
./tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.geopt
./tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.inpt
./tests/outputs/AlSi_primitive_quick_relax.sparc/output.sparc
./tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.ion
./tests/outputs/AlSi_primitive_quick_relax.sparc/AlSi_primitive_quick_relax.out
./tests/outputs/TiO2_orthogonal_quick_md.sparc/TiO2_orthogonal_quick_md.ion
./tests/outputs/TiO2_orthogonal_quick_md.sparc/TiO2_orthogonal_quick_md.out
./tests/outputs/TiO2_orthogonal_quick_md.sparc/TiO2_orthogonal_quick_md.inpt
./tests/outputs/TiO2_orthogonal_quick_md.sparc/TiO2_orthogonal_quick_md.aimd
./tests/outputs/Si8_cell_geopt_relax2.sparc/Si8_cell_geopt.inpt
./tests/outputs/Si8_cell_geopt_relax2.sparc/Si8_cell_geopt.geopt
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./tests/outputs/Si8_cell_geopt_relax2.sparc/Si8_cell_geopt.out
./tests/outputs/SiH4_quick.sparc/SiH4_quick.out
./tests/outputs/SiH4_quick.sparc/SiH4_quick.inpt
./tests/outputs/SiH4_quick.sparc/SiH4_quick.ion
./tests/outputs/SiH4_quick.sparc/SiH4_quick.static
./tests/outputs/Al_socket_bfgs.sparc/13_Al_3_1.9_1.9_pbe_n_v1.0.psp8
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./tests/outputs/Al_socket_volchange.sparc/single-points/sp_image00/SPARC.out
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./tests/outputs/Al_socket_volchange.sparc/single-points/sp_image09/SPARC.out
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./tests/outputs/Al_socket_volchange.sparc/single-points/sp_image08/SPARC.out
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./tests/outputs/Al_socket_volchange.sparc/single-points/sp_image04/SPARC.out
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./tests/outputs/Al_socket_volchange.sparc/single-points/sp_image05/SPARC.out
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./tests/outputs/Al_socket_volchange.sparc/single-points/sp_image06/SPARC.out
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./tests/outputs/H2O_wire_z.sparc/H2O_wire.inpt
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./tests/outputs/Al_multi_geopt.sparc/SPARC.geopt
./tests/outputs/Al_multi_geopt.sparc/SPARC.geopt_01
./tests/outputs/Al_multi_geopt.sparc/SPARC.out_02
./tests/outputs/Al_multi_geopt.sparc/SPARC.ion
./tests/outputs/Al_multi_geopt.sparc/SPARC.inpt
./tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.static
./tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.inpt
./tests/outputs/H2O_sheet_yz.sparc/output.sparc
./tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.ion
./tests/outputs/H2O_sheet_yz.sparc/H2O_sheet.out
./tests/outputs/NH3_sort_lbfgs_opt.sparc/SPARC.restart
./tests/outputs/NH3_sort_lbfgs_opt.sparc/SPARC.geopt
./tests/outputs/NH3_sort_lbfgs_opt.sparc/01_H_1_1.0_1.0_pbe_v1.0.psp8
./tests/outputs/NH3_sort_lbfgs_opt.sparc/SPARC.out
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./tests/outputs/NH3_sort_lbfgs_opt.sparc/07_N_5_1.2_1.4_pbe_n_v1.0.psp8
./tests/test_api_version.py
./tests/test_parse_atoms.py
./tests/test_socket.py
./tests/test_sparc_bundle.py
./tests/psps/As-pbe-bad.psp8
./tests/psps/33_As_15_1.8_2.1_pbe_n_v1.0.psp8
./tests/psps/47_Ag_19_1.9_2.5_pbe_n_v1.0.psp8
./tests/psps/Ag-PBE.pot
./tests/psps/Ag-LDA.pot
./tests/test_static_parser.py
./tests/test_parser_utils.py
./tests/sparc-latex-socket-202401/System.tex
./tests/sparc-latex-socket-202401/Print.tex
./tests/sparc-latex-socket-202401/Electrostatics.tex
./tests/sparc-latex-socket-202401/Manual.tex
./tests/sparc-latex-socket-202401/BandStructure.tex
./tests/sparc-latex-socket-202401/highT/SQ.tex
./tests/sparc-latex-socket-202401/highT/Manual_highT.tex
./tests/sparc-latex-socket-202401/highT/Introduction.tex
./tests/sparc-latex-socket-202401/SCF.tex
./tests/sparc-latex-socket-202401/MD.tex
./tests/sparc-latex-socket-202401/Optimization.tex
./tests/sparc-latex-socket-202401/Introduction.tex
./tests/sparc-latex-socket-202401/Paral.tex
./tests/sparc-latex-socket-202401/cyclix/cyclix.tex
./tests/sparc-latex-socket-202401/cyclix/FAQs.tex
./tests/sparc-latex-socket-202401/cyclix/Introduction.tex
./tests/sparc-latex-socket-202401/cyclix/Manual_cyclix.tex
./tests/sparc-latex-socket-202401/Stress.tex
./tests/sparc-latex-socket-202401/Socket.tex
./tests/test_aimd_parser.py
./tests/test_geopt_parser.py
./tests/test_docparser.py
./tests/test_sparc_input_api.py
./tests/test_read_sparc.py
./tests/test_gui.py
./sparc/client.py
./sparc/sparc_parsers/__init__.py
./sparc/sparc_parsers/atoms.py
./sparc/sparc_parsers/geopt.py
./sparc/sparc_parsers/ion.py
./sparc/sparc_parsers/inpt.py
./sparc/sparc_parsers/pseudopotential.py
./sparc/sparc_parsers/out.py
./sparc/sparc_parsers/utils.py
./sparc/sparc_parsers/static.py
./sparc/sparc_parsers/aimd.py
./sparc/__init__.py
./sparc/sparc_json_api/parameters.json
./sparc/io.py
./sparc/download_data.py
./sparc/cli.py
./sparc/calculator.py
./sparc/api.py
./sparc/common.py
./sparc/socketio.py
./sparc/psp/README.md
./sparc/utils.py
./sparc/quicktest.py
./sparc/docparser.py
./doc/maintainers/sparc-c-c++.md
./doc/maintainers/sparc-x-api.md
./doc/maintainers/github.md
./doc/make.bat
./doc/Makefile
./doc/examples.md
./doc/index.md
./doc/maintainers.md
./doc/examples/internal_mlff.md
./doc/examples/geopt_compare.md
./doc/examples/external_mlff.md
./doc/examples/simple_dft.md
./doc/api_changes.md
./doc/package_components.md
./doc/img/scheme_socket_hetero.svg
./doc/img/scheme-SPARC-socket-modes.png
./doc/img/scheme_sparc_protocol.svg
./doc/img/scheme_sparc_protocol.png
./doc/img/screenshots/coverage_example.png
./doc/img/screenshots/github_pages_setting.png
./doc/img/screenshots/github_action_dispatch.png
./doc/img/screenshots/api_update_pr_github.png
./doc/img/screenshots/pypi_publisher_setup.png
./doc/img/scheme_socket_hetero.png
./doc/img/scheme_api_architecture.svg
./doc/img/scheme-SPARC-socke-modes.svg
./doc/img/fig_sparc_api_overview.svg
./doc/img/scheme_api_architecture.png
./doc/advanced_topics.md
./doc/basic_usage.md
./doc/introduction.md
./doc/setup_environment.md
./doc/troubleshooting.md
./doc/advanced_socket.md
./doc/contribute.md
./doc/installation.md
./doc/test_coverage.md
./doc/conf.py
./sparc_x_api.egg-info/SOURCES.txt
./sparc_x_api.egg-info/entry_points.txt
./sparc_x_api.egg-info/requires.txt
./sparc_x_api.egg-info/dependency_links.txt
./sparc_x_api.egg-info/top_level.txt
./sparc_x_api.egg-info/PKG-INFO[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/SPARC-X__SPARC-X-API__0.0 #
[Command finished with exit code 0]


Prompt:
EXECUTION RESULT of [execute_bash]:
cd /workspace/adafruit__Adafruit_CircuitPython_HTTPServer__0.0 && ls -R
.:
CODE_OF_CONDUCT.md                          adafruit_httpserver
LICENSE                                     docs
LICENSES                                    examples
README.rst                                  optional_requirements.txt
README.rst.license                          pyproject.toml
adafruit_circuitpython_httpserver.egg-info  requirements.txt

./LICENSES:
CC-BY-4.0.txt  MIT.txt  Unlicense.txt

./adafruit_circuitpython_httpserver.egg-info:
PKG-INFO  SOURCES.txt  dependency_links.txt  requires.txt  top_level.txt

./adafruit_httpserver:
__init__.py        headers.py     mime_types.py  route.py
authentication.py  interfaces.py  request.py     server.py
exceptions.py      methods.py     response.py    status.py

./docs:
_static          conf.py               index.rst
api.rst          examples.rst          index.rst.license
api.rst.license  examples.rst.license  requirements.txt

./docs/_static:
favicon.ico  favicon.ico.license

./examples:
directory_listing.tpl.html             httpserver_multiple_servers.py
home.html                              httpserver_neopixel.py
httpserver_authentication_handlers.py  httpserver_redirects.py
httpserver_authentication_server.py    httpserver_simpletest_auto.py
httpserver_chunked.py                  httpserver_simpletest_manual.py
httpserver_cookies.py                  httpserver_sse.py
httpserver_cpu_information.py          httpserver_start_and_poll.py
httpserver_cpython.py                  httpserver_start_and_poll_asyncio.py
httpserver_ethernet_simpletest.py      httpserver_static_files_serving.py
httpserver_form_data.py                httpserver_templates.py
httpserver_handler_serves_file.py      httpserver_url_parameters.py
httpserver_mdns.py                     httpserver_websocket.py
httpserver_methods.py                  settings.toml[Python Interpreter: /usr/bin/python]
root@openhands-workspace:/workspace/adafruit__Adafruit_CircuitPython_HTTPServer__0.0 #
[Command finished with exit code 0]