update notebooks

mctools · Mar 1, 2025 · c0739e8 · c0739e8
1 parent f696187
commit c0739e8
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Showing 18 changed files with 32 additions and 62 deletions.
diff --git a/.github/resources/run_notebooks.x b/.github/resources/run_notebooks.x
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/usr/bin/env bash
 set -eu
 export REPOROOT="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )/../../" && pwd )"
 CODCACHE_SRC="${REPOROOT}/.github/resources/codcache"
@@ -19,22 +19,26 @@ for notebookfile in `find "${REPOROOT}"/notebooks/ -name '*.ipynb'`; do
     cp -rp "${CODCACHE_SRC}" ./ncrystal_onlinedb_filecache
     python3 -mvenv create ./venv
     . ./venv/bin/activate
+
+    if [ "x${NCNOTEBOOKS_USE_NCRYSTAL_REPO}" != "x" ]; then
+        time python3 -m pip install "${NCNOTEBOOKS_USE_NCRYSTAL_REPO}/ncrystal_core"
+        python3 -m pip install "${NCNOTEBOOKS_USE_NCRYSTAL_REPO}/ncrystal_python"
+        python3 -m pip install "${NCNOTEBOOKS_USE_NCRYSTAL_REPO}/ncrystal_metapkg"
+    fi
+
+    #Workaround for https://github.com/spglib/spglib/issues/553 :
+    TMPPYVER=$(python3 -c 'import sys; print("%i.%i"%sys.version_info[0:2])')
+    if [ "${TMPPYVER}" == "3.13" ]; then
+        python3 -mpip install git+https://github.com/tkittel/spglib.git
+    fi
+
     python3 -mpip install jupyter ipython
     echo "   .. converting to script"
     cat "${notebookfile}" | \
         sed 's#always_do_pip_installs = False#always_do_pip_installs = True#' \
         > ./thenotebook.ipynb
     jupyter nbconvert --to script ./thenotebook.ipynb --output="${PWD}/thenotebook_converted"
     test -f ./thenotebook_converted.py
-    #For now, the texture plugin notebook should only be run on linux and not in
-    #NCrystal 4 before it has been ported:
-    DO_RUN_PLUGIN_NOTEBOOKS=0
-    if [ -e /proc ]; then
-        DO_RUN_PLUGIN_NOTEBOOKS=1
-    fi
-    if [ "x${NCNOTEBOOKS_FORCE_SKIP_PLUGIN_NB:-0}" == "x1" ]; then
-        DO_RUN_PLUGIN_NOTEBOOKS=0
-    fi
     if [ "x${bn}" == "xNEUWAVE_12_Examples_Transmission_with_NCrystal_and_McStas.ipynb" ]; then
         echo
         echo

diff --git a/.github/workflows/run_notebooks.yml b/.github/workflows/run_notebooks.yml
@@ -27,8 +27,8 @@ jobs:
       with:
         python-version: ${{ matrix.python }}
 
-    - name: Pip install
-      run: python3 -m pip install ncrystal[all]>=4.0.0
+#    - name: Pip install
+#      run: python3 -m pip install ncrystal[all]>=4.0.0
 
     - name: Check versions
       shell: bash

diff --git a/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Extinction_correction_exercise.ipynb b/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Extinction_correction_exercise.ipynb
@@ -52,9 +52,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl pandas\n",
+    "    %pip -q install ncrystal[plot] ipympl pandas\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_In_scattering.ipynb b/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_In_scattering.ipynb
@@ -56,9 +56,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl tqdm\n",
+    "    %pip -q install ncrystal[plot] ipympl tqdm\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/...ooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Installing_Plugins_Texture_exercise.ipynb b/...ooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Installing_Plugins_Texture_exercise.ipynb
@@ -56,11 +56,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip install -q ncrystal[all]\n",
-    "    if not all(_fs(m) for m in ['ipympl','pandas','pickleshare']):\n",
-    "        %pip install -q ipympl pandas pickleshare\n",
+    "    %pip install -q ncrystal[all] ipympl pandas pickleshare\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Neutron_filters_exercise.ipynb b/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Neutron_filters_exercise.ipynb
@@ -51,9 +51,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl pandas\n",
+    "    %pip -q install ncrystal[plot] ipympl pandas\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/...ributed/NEUWAVE-12/NEUWAVE_12_Examples_Polymers_with_Functional_Group_Approximation.ipynb b/...ributed/NEUWAVE-12/NEUWAVE_12_Examples_Polymers_with_Functional_Group_Approximation.ipynb
@@ -62,9 +62,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[all] ipympl\n",
+    "    %pip -q install ncrystal[all] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/...s/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Sample_container_transmission_exercise.ipynb b/...s/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Sample_container_transmission_exercise.ipynb
@@ -45,9 +45,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[all] ipympl\n",
+    "    %pip -q install ncrystal[all] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Water_Ice.ipynb b/notebooks/contributed/NEUWAVE-12/NEUWAVE_12_Examples_Water_Ice.ipynb
@@ -54,9 +54,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not all(_fs(m) for m in ['NCrystal','ipympl','pandas']):\n",
-    "        %pip -q install ncrystal[all] ipympl pandas\n",
+    "    %pip -q install ncrystal[all] ipympl pandas\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/misc/ncrystal_sapphire_filter.ipynb b/notebooks/misc/ncrystal_sapphire_filter.ipynb
@@ -54,9 +54,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl\n",
+    "    %pip -q install ncrystal[plot] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal1_basic_01_Introduction_and_Python_API.ipynb b/notebooks/ncrystal1_basic_01_Introduction_and_Python_API.ipynb
@@ -48,9 +48,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl\n",
+    "    %pip -q install ncrystal[plot] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal1_basic_02_Data_Infrastructure_and_StdDataLib.ipynb b/notebooks/ncrystal1_basic_02_Data_Infrastructure_and_StdDataLib.ipynb
@@ -48,9 +48,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl\n",
+    "    %pip -q install ncrystal[plot] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal1_basic_03_Scatter_patterns_with_the_builtin_MiniMC_framework.ipynb b/notebooks/ncrystal1_basic_03_Scatter_patterns_with_the_builtin_MiniMC_framework.ipynb
@@ -50,9 +50,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl numpy\n",
+    "    %pip -q install ncrystal[plot] ipympl numpy\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal1_basic_04_NCrystal_as_backend_for_third_party_apps.ipynb b/notebooks/ncrystal1_basic_04_NCrystal_as_backend_for_third_party_apps.ipynb
@@ -48,9 +48,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[plot] ipympl\n",
+    "    %pip -q install ncrystal[plot] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal2_advanced_01_Creating_materials_and_the_NCMATComposer.ipynb b/notebooks/ncrystal2_advanced_01_Creating_materials_and_the_NCMATComposer.ipynb
@@ -48,9 +48,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[all] ipympl\n",
+    "    %pip -q install ncrystal[all] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal2_advanced_02_Import_crystal_structure_from_CIF_or_databases.ipynb b/notebooks/ncrystal2_advanced_02_Import_crystal_structure_from_CIF_or_databases.ipynb
@@ -46,9 +46,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[all] ipympl\n",
+    "    %pip -q install ncrystal[all] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/...al2_advanced_03_Add_phonon_info_with_PhononDOSAnalyser_with_QuantumEspresso_example.ipynb b/...al2_advanced_03_Add_phonon_info_with_PhononDOSAnalyser_with_QuantumEspresso_example.ipynb
@@ -50,9 +50,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal[all] ipympl\n",
+    "    %pip -q install ncrystal[all] ipympl\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",

diff --git a/notebooks/ncrystal2_advanced_04_VDOS2KNL_Connecting_phonons_to_inelastic_scattering.ipynb b/notebooks/ncrystal2_advanced_04_VDOS2KNL_Connecting_phonons_to_inelastic_scattering.ipynb
@@ -59,9 +59,7 @@
     "except ModuleNotFoundError:\n",
     "    google_colab=None#not on google colab\n",
     "if always_do_pip_installs or google_colab:\n",
-    "    from importlib.util import find_spec as _fs\n",
-    "    if not _fs('NCrystal'):\n",
-    "        %pip -q install ncrystal ipympl numpy matplotlib\n",
+    "    %pip -q install ncrystal ipympl numpy matplotlib\n",
     "#enable inline and interactive matplotlib plots:\n",
     "if google_colab:\n",
     "    google_colab.output.enable_custom_widget_manager()\n",