pin pymatgen to v2024.10.29 to avoid bug introduced in pseudos

abinit · Dec 14, 2024 · e74ccab · e74ccab
1 parent 256d219
commit e74ccab
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Showing 5 changed files with 123 additions and 114 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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",