From e74ccab606798e1f3b3c9dad8046ec07e6310d3d Mon Sep 17 00:00:00 2001 From: Matteo Giantomassi Date: Sat, 14 Dec 2024 16:00:12 +0100 Subject: [PATCH] pin pymatgen to v2024.10.29 to avoid bug introduced in pseudos --- docs/Makefile | 21 ++-- docs/conf.py | 11 +- docs/sg_execution_times.rst | 200 ++++++++++++++++++------------------ requirements.txt | 2 +- setup.py | 3 +- 5 files changed, 123 insertions(+), 114 deletions(-) diff --git a/docs/Makefile b/docs/Makefile index 5674fe324..31dcc56b0 100644 --- a/docs/Makefile +++ b/docs/Makefile @@ -2,13 +2,16 @@ # # You can set these variables from the command line. -#SPHINXOPTS = -j6 -SPHINXOPTS = -#SPHINXBUILD = sphinx-build +#SPHINXOPTS = -j6 +#SPHINXOPTS = -v -W --show-traceback --pdb +#SPHINXOPTS = -j1 -v -W --show-traceback --pdb +SPHINXOPTS = # Verbose mode #SPHINXBUILD = sphinx-build -v # Sphinx may treat warnings as errors, halting HTML generation. -SPHINXBUILD = sphinx-build -v -W --keep-going +#SPHINXBUILD = sphinx-build -v -W --keep-going +#SPHINXBUILD = sphinx-build -v -W --show-traceback --pdb +SPHINXBUILD = sphinx-build PAPER = BUILDDIR = _build @@ -51,12 +54,16 @@ clean: -rm -rf flow_gallery/* html: - ./generate_rst_files.py - rm -rf ../abipy/examples/flows/flow_* + @echo "Generating RST files..." + ./generate_rst_files.py || { echo "Error: Failed to generate RST files"; exit 1; } + @echo "Cleaning old flow examples..." + rm -rf ../abipy/examples/flows/flow_* || { echo "Error: Failed to clean old flows"; exit 1; } export READTHEDOCS=1 - $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + #export READTHEDOCS=0 + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html || { echo "Error: Sphinx build failed"; exit 1; } @echo @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + #open $(BUILDDIR)/html/index.html || { echo "Error: Failed to open index.html"; exit 1; } dirhtml: $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml diff --git a/docs/conf.py b/docs/conf.py index eea581fb8..cf485111a 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -142,19 +142,20 @@ def load_mod(filepath): from sphinx_gallery.sorting import ExampleTitleSortKey sphinx_gallery_conf = { - #'only_warn_on_example_error': True, - 'abort_on_example_error': True, - 'log_level': {'backreference_missing': 'warning'}, + 'only_warn_on_example_error': True, + #'abort_on_example_error': True, + #'log_level': {'backreference_missing': 'warning'}, + 'log_level': {'backreference_missing': 'error'}, # # path to your examples scripts 'examples_dirs': [ - "../abipy/examples/plot", "../abipy/examples/flows", + "../abipy/examples/plot", ], # path where to save gallery generated examples 'gallery_dirs': [ - "gallery", "flow_gallery", + "gallery", ], 'filename_pattern': "(/plot*|/run_*)", 'default_thumb_file': '_static/abipy_logo.png', diff --git a/docs/sg_execution_times.rst b/docs/sg_execution_times.rst index d729f4222..3a9e41ae2 100644 --- a/docs/sg_execution_times.rst +++ b/docs/sg_execution_times.rst @@ -6,7 +6,7 @@ Computation times ================= -**00:57.535** total execution time for 66 files **from all galleries**: +**00:55.409** total execution time for 66 files **from all galleries**: .. container:: @@ -33,200 +33,200 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_gallery_plot_qha_vs_qmesh.py` (``../abipy/examples/plot/plot_qha_vs_qmesh.py``) - - 00:10.030 + - 00:10.444 - 0.0 * - :ref:`sphx_glr_gallery_plot_ddb_asr.py` (``../abipy/examples/plot/plot_ddb_asr.py``) - - 00:04.754 + - 00:04.728 - 0.0 * - :ref:`sphx_glr_gallery_plot_phonons_msqd.py` (``../abipy/examples/plot/plot_phonons_msqd.py``) - - 00:03.998 + - 00:04.034 - 0.0 * - :ref:`sphx_glr_gallery_plot_qha_v-ZSISA.py` (``../abipy/examples/plot/plot_qha_v-ZSISA.py``) - - 00:03.154 + - 00:03.341 - 0.0 * - :ref:`sphx_glr_gallery_plot_lumi_1D_nv_center.py` (``../abipy/examples/plot/plot_lumi_1D_nv_center.py``) - - 00:02.889 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_qha_2d.py` (``../abipy/examples/plot/plot_qha_2d.py``) - - 00:02.652 + - 00:02.918 - 0.0 * - :ref:`sphx_glr_gallery_plot_phbands_nkpt_tsmear.py` (``../abipy/examples/plot/plot_phbands_nkpt_tsmear.py``) - - 00:02.369 + - 00:02.459 - 0.0 * - :ref:`sphx_glr_gallery_plot_efatbands_spin.py` (``../abipy/examples/plot/plot_efatbands_spin.py``) - - 00:01.966 + - 00:02.046 - 0.0 - * - :ref:`sphx_glr_gallery_plot_mdf.py` (``../abipy/examples/plot/plot_mdf.py``) - - 00:01.696 + * - :ref:`sphx_glr_gallery_plot_qha_2d.py` (``../abipy/examples/plot/plot_qha_2d.py``) + - 00:02.017 - 0.0 - * - :ref:`sphx_glr_gallery_plot_ebands.py` (``../abipy/examples/plot/plot_ebands.py``) - - 00:01.572 + * - :ref:`sphx_glr_gallery_plot_mdf.py` (``../abipy/examples/plot/plot_mdf.py``) + - 00:01.759 - 0.0 * - :ref:`sphx_glr_gallery_plot_a2f.py` (``../abipy/examples/plot/plot_a2f.py``) - - 00:01.388 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_ebands_boxplot.py` (``../abipy/examples/plot/plot_ebands_boxplot.py``) - - 00:01.173 + - 00:01.369 - 0.0 * - :ref:`sphx_glr_gallery_plot_efatbands.py` (``../abipy/examples/plot/plot_efatbands.py``) - - 00:01.112 + - 00:01.156 - 0.0 * - :ref:`sphx_glr_gallery_plot_phbands_grid.py` (``../abipy/examples/plot/plot_phbands_grid.py``) - - 00:01.081 + - 00:01.110 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_ebands_spin.py` (``../abipy/examples/plot/plot_ebands_spin.py``) + - 00:00.825 - 0.0 * - :ref:`sphx_glr_gallery_plot_qpbands_with_interpolation.py` (``../abipy/examples/plot/plot_qpbands_with_interpolation.py``) - - 00:00.790 + - 00:00.817 - 0.0 * - :ref:`sphx_glr_gallery_plot_speed_of_sound.py` (``../abipy/examples/plot/plot_speed_of_sound.py``) - - 00:00.776 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_ebands_spin.py` (``../abipy/examples/plot/plot_ebands_spin.py``) - - 00:00.770 + - 00:00.755 - 0.0 * - :ref:`sphx_glr_gallery_plot_ebands_grid.py` (``../abipy/examples/plot/plot_ebands_grid.py``) - - 00:00.730 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_qha.py` (``../abipy/examples/plot/plot_qha.py``) - - 00:00.728 + - 00:00.731 - 0.0 * - :ref:`sphx_glr_gallery_plot_lumi_1D_Eu_doped.py` (``../abipy/examples/plot/plot_lumi_1D_Eu_doped.py``) - - 00:00.712 + - 00:00.702 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_qha.py` (``../abipy/examples/plot/plot_qha.py``) + - 00:00.686 - 0.0 * - :ref:`sphx_glr_gallery_plot_phonons_infrared.py` (``../abipy/examples/plot/plot_phonons_infrared.py``) - - 00:00.680 + - 00:00.657 - 0.0 * - :ref:`sphx_glr_gallery_plot_qpbands_with_scissor.py` (``../abipy/examples/plot/plot_qpbands_with_scissor.py``) - - 00:00.610 + - 00:00.626 - 0.0 * - :ref:`sphx_glr_gallery_plot_gruneisen.py` (``../abipy/examples/plot/plot_gruneisen.py``) - - 00:00.597 + - 00:00.594 - 0.0 * - :ref:`sphx_glr_gallery_plot_efatbands_lm.py` (``../abipy/examples/plot/plot_efatbands_lm.py``) - - 00:00.545 + - 00:00.567 - 0.0 - * - :ref:`sphx_glr_gallery_plot_wannier90_abiwan.py` (``../abipy/examples/plot/plot_wannier90_abiwan.py``) - - 00:00.521 + * - :ref:`sphx_glr_gallery_plot_phonon_fatbands.py` (``../abipy/examples/plot/plot_phonon_fatbands.py``) + - 00:00.546 - 0.0 * - :ref:`sphx_glr_gallery_plot_qps.py` (``../abipy/examples/plot/plot_qps.py``) - - 00:00.518 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_ebands_edos.py` (``../abipy/examples/plot/plot_ebands_edos.py``) - - 00:00.503 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_phonon_fatbands.py` (``../abipy/examples/plot/plot_phonon_fatbands.py``) - - 00:00.486 + - 00:00.537 - 0.0 * - :ref:`sphx_glr_gallery_plot_qpconvergence.py` (``../abipy/examples/plot/plot_qpconvergence.py``) - - 00:00.449 + - 00:00.465 - 0.0 * - :ref:`sphx_glr_gallery_plot_ifcs.py` (``../abipy/examples/plot/plot_ifcs.py``) - - 00:00.408 + - 00:00.431 - 0.0 * - :ref:`sphx_glr_gallery_plot_kpath_from_ibz.py` (``../abipy/examples/plot/plot_kpath_from_ibz.py``) - - 00:00.392 + - 00:00.400 - 0.0 - * - :ref:`sphx_glr_gallery_plot_phonons.py` (``../abipy/examples/plot/plot_phonons.py``) - - 00:00.368 + * - :ref:`sphx_glr_gallery_plot_edos_vs_broad.py` (``../abipy/examples/plot/plot_edos_vs_broad.py``) + - 00:00.387 - 0.0 - * - :ref:`sphx_glr_gallery_plot_multiple_mdf.py` (``../abipy/examples/plot/plot_multiple_mdf.py``) - - 00:00.362 + * - :ref:`sphx_glr_gallery_plot_ebands.py` (``../abipy/examples/plot/plot_ebands.py``) + - 00:00.381 - 0.0 * - :ref:`sphx_glr_gallery_plot_scqpgw.py` (``../abipy/examples/plot/plot_scqpgw.py``) - - 00:00.354 + - 00:00.370 - 0.0 - * - :ref:`sphx_glr_gallery_plot_edos_vs_broad.py` (``../abipy/examples/plot/plot_edos_vs_broad.py``) - - 00:00.349 + * - :ref:`sphx_glr_gallery_plot_multiple_mdf.py` (``../abipy/examples/plot/plot_multiple_mdf.py``) + - 00:00.370 - 0.0 - * - :ref:`sphx_glr_gallery_plot_optic.py` (``../abipy/examples/plot/plot_optic.py``) - - 00:00.348 + * - :ref:`sphx_glr_gallery_plot_wannier90_abiwan.py` (``../abipy/examples/plot/plot_wannier90_abiwan.py``) + - 00:00.367 - 0.0 * - :ref:`sphx_glr_gallery_plot_phbands_and_dos.py` (``../abipy/examples/plot/plot_phbands_and_dos.py``) - - 00:00.335 + - 00:00.358 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_optic.py` (``../abipy/examples/plot/plot_optic.py``) + - 00:00.336 - 0.0 * - :ref:`sphx_glr_gallery_plot_convergence.py` (``../abipy/examples/plot/plot_convergence.py``) - - 00:00.303 + - 00:00.325 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_ejdos.py` (``../abipy/examples/plot/plot_ejdos.py``) + - 00:00.313 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_multiple_hist.py` (``../abipy/examples/plot/plot_multiple_hist.py``) + - 00:00.306 - 0.0 * - :ref:`sphx_glr_gallery_plot_scr_matrix.py` (``../abipy/examples/plot/plot_scr_matrix.py``) - - 00:00.298 + - 00:00.303 - 0.0 - * - :ref:`sphx_glr_gallery_plot_ejdos.py` (``../abipy/examples/plot/plot_ejdos.py``) - - 00:00.295 + * - :ref:`sphx_glr_gallery_plot_ebands_boxplot.py` (``../abipy/examples/plot/plot_ebands_boxplot.py``) + - 00:00.283 - 0.0 * - :ref:`sphx_glr_gallery_plot_den.py` (``../abipy/examples/plot/plot_den.py``) - - 00:00.290 + - 00:00.271 - 0.0 - * - :ref:`sphx_glr_gallery_plot_multiple_hist.py` (``../abipy/examples/plot/plot_multiple_hist.py``) - - 00:00.283 + * - :ref:`sphx_glr_gallery_plot_ebands_edos.py` (``../abipy/examples/plot/plot_ebands_edos.py``) + - 00:00.264 - 0.0 - * - :ref:`sphx_glr_gallery_plot_dfpt_cycle.py` (``../abipy/examples/plot/plot_dfpt_cycle.py``) - - 00:00.262 + * - :ref:`sphx_glr_gallery_plot_phonons.py` (``../abipy/examples/plot/plot_phonons.py``) + - 00:00.261 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_phonons_lo_to.py` (``../abipy/examples/plot/plot_phonons_lo_to.py``) + - 00:00.257 - 0.0 * - :ref:`sphx_glr_gallery_plot_wfk.py` (``../abipy/examples/plot/plot_wfk.py``) - 00:00.254 - 0.0 - * - :ref:`sphx_glr_gallery_plot_lobster_files.py` (``../abipy/examples/plot/plot_lobster_files.py``) - - 00:00.242 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_potentials.py` (``../abipy/examples/plot/plot_potentials.py``) - - 00:00.228 + * - :ref:`sphx_glr_gallery_plot_dfpt_cycle.py` (``../abipy/examples/plot/plot_dfpt_cycle.py``) + - 00:00.250 - 0.0 * - :ref:`sphx_glr_gallery_plot_hist.py` (``../abipy/examples/plot/plot_hist.py``) - - 00:00.227 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_phonons_lo_to.py` (``../abipy/examples/plot/plot_phonons_lo_to.py``) - - 00:00.226 + - 00:00.241 - 0.0 * - :ref:`sphx_glr_gallery_plot_lobster_cohp.py` (``../abipy/examples/plot/plot_lobster_cohp.py``) - - 00:00.214 + - 00:00.225 - 0.0 - * - :ref:`sphx_glr_gallery_plot_ebands_scatter3d.py` (``../abipy/examples/plot/plot_ebands_scatter3d.py``) - - 00:00.201 + * - :ref:`sphx_glr_gallery_plot_lobster_files.py` (``../abipy/examples/plot/plot_lobster_files.py``) + - 00:00.223 - 0.0 - * - :ref:`sphx_glr_gallery_plot_bz.py` (``../abipy/examples/plot/plot_bz.py``) - - 00:00.187 + * - :ref:`sphx_glr_gallery_plot_potentials.py` (``../abipy/examples/plot/plot_potentials.py``) + - 00:00.209 - 0.0 * - :ref:`sphx_glr_gallery_plot_phonon_pjdos.py` (``../abipy/examples/plot/plot_phonon_pjdos.py``) - - 00:00.183 + - 00:00.206 - 0.0 - * - :ref:`sphx_glr_gallery_plot_gw_spectral_functions.py` (``../abipy/examples/plot/plot_gw_spectral_functions.py``) - - 00:00.174 + * - :ref:`sphx_glr_gallery_plot_ebands_scatter3d.py` (``../abipy/examples/plot/plot_ebands_scatter3d.py``) + - 00:00.205 - 0.0 * - :ref:`sphx_glr_gallery_plotly_phbands_and_dos.py` (``../abipy/examples/plot/plotly_phbands_and_dos.py``) - - 00:00.162 + - 00:00.172 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_gw_spectral_functions.py` (``../abipy/examples/plot/plot_gw_spectral_functions.py``) + - 00:00.169 - 0.0 * - :ref:`sphx_glr_gallery_plot_wannier90_wout.py` (``../abipy/examples/plot/plot_wannier90_wout.py``) - - 00:00.148 + - 00:00.145 - 0.0 * - :ref:`sphx_glr_gallery_plot_scr.py` (``../abipy/examples/plot/plot_scr.py``) - - 00:00.145 + - 00:00.140 - 0.0 * - :ref:`sphx_glr_gallery_plot_effmass.py` (``../abipy/examples/plot/plot_effmass.py``) - - 00:00.144 + - 00:00.140 - 0.0 * - :ref:`sphx_glr_gallery_plot_fold2bloch.py` (``../abipy/examples/plot/plot_fold2bloch.py``) - - 00:00.140 + - 00:00.135 - 0.0 * - :ref:`sphx_glr_gallery_plot_lruj.py` (``../abipy/examples/plot/plot_lruj.py``) - - 00:00.137 - - 0.0 - * - :ref:`sphx_glr_gallery_plot_edos_grid.py` (``../abipy/examples/plot/plot_edos_grid.py``) - 00:00.130 - 0.0 - * - :ref:`sphx_glr_gallery_plot_gscycle.py` (``../abipy/examples/plot/plot_gscycle.py``) - - 00:00.109 + * - :ref:`sphx_glr_gallery_plot_bz.py` (``../abipy/examples/plot/plot_bz.py``) + - 00:00.112 - 0.0 - * - :ref:`sphx_glr_gallery_plot_edos.py` (``../abipy/examples/plot/plot_edos.py``) - - 00:00.107 + * - :ref:`sphx_glr_gallery_plot_phdos_grid.py` (``../abipy/examples/plot/plot_phdos_grid.py``) + - 00:00.104 - 0.0 * - :ref:`sphx_glr_gallery_plot_phthermo.py` (``../abipy/examples/plot/plot_phthermo.py``) - - 00:00.095 + - 00:00.102 - 0.0 - * - :ref:`sphx_glr_gallery_plot_phdos_grid.py` (``../abipy/examples/plot/plot_phdos_grid.py``) - - 00:00.073 + * - :ref:`sphx_glr_gallery_plot_gscycle.py` (``../abipy/examples/plot/plot_gscycle.py``) + - 00:00.101 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_edos.py` (``../abipy/examples/plot/plot_edos.py``) + - 00:00.097 + - 0.0 + * - :ref:`sphx_glr_gallery_plot_edos_grid.py` (``../abipy/examples/plot/plot_edos_grid.py``) + - 00:00.084 - 0.0 * - :ref:`sphx_glr_gallery_plot_xrd.py` (``../abipy/examples/plot/plot_xrd.py``) - - 00:00.067 + - 00:00.049 - 0.0 * - :ref:`sphx_glr_gallery_plot_funcs.py` (``../abipy/examples/plot/plot_funcs.py``) - - 00:00.045 + - 00:00.046 - 0.0 diff --git a/requirements.txt b/requirements.txt index 722e85967..38afdd433 100644 --- a/requirements.txt +++ b/requirements.txt @@ -11,7 +11,7 @@ pandas numpy<2.0.0 sympy spglib -pymatgen +pymatgen==v2024.10.29 netCDF4 matplotlib seaborn diff --git a/setup.py b/setup.py index 2b134c21a..911e2e4a5 100755 --- a/setup.py +++ b/setup.py @@ -156,7 +156,8 @@ def cleanup(): "numpy<2.0.0", "scipy", "spglib", - "pymatgen>=2022.0.14", + #"pymatgen>=2022.0.14", + "pymatgen==v2024.10.29", "netCDF4", "matplotlib", "seaborn",