fix: setting lower bound of spglib

For some reason the lower bound in ncrystal is not picked
up properly by uv.
Might have to do with the dependency being optional, but not sure.

Author: jokasimr

pyproject.toml

@@ -32,7 +32,8 @@ requires-python = ">=3.11"
 dependencies = [
   "dask>=2022.1.0",
   "essreduce>=25.12.1",
-  "graphviz",
+  "essreduce>=25.11.0",
+  "graphviz>=0.20",
   "numpy>=1.25",
   "plopp>=25.07.0",
   "pythreejs>=2.4.1",
@@ -42,7 +43,10 @@ dependencies = [
   "scippnexus>=23.12.0",
   "tof>=25.11.1",
   "ncrystal[cif]>=4.1.0",
-  "spglib!=2.7",  # https://github.com/mctools/ncrystal/issues/320
+  # For some reason the spglib lower bound
+  # in ncrystal is not picked up by uv,
+  # so it's repeated here.
+  "spglib!=2.7,>=2.1",  # https://github.com/mctools/ncrystal/issues/320
 ]
 
 dynamic = ["version"]

requirements/base.in

@@ -4,13 +4,15 @@
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask>=2022.1.0
 essreduce>=25.12.1
-graphviz
+essreduce>=25.11.0
+graphviz>=0.20
 numpy>=1.25
 plopp>=25.07.0
 pythreejs>=2.4.1
 sciline>=25.04.1
-scipp>=25.05.1
+scipp>=25.11.0
 scippneutron>=25.02.0
 scippnexus>=23.12.0
 tof>=25.11.1
 ncrystal[cif]>=4.1.0
+spglib!=2.7,>=2.1

requirements/base.txt

@@ -1,4 +1,4 @@
-# SHA1:211d5471bcbe9da722143b751c4a5cb05f6e5be4
+# SHA1:9c368525af8f5625e6995c2622c272af6d2dbe59
 #
 # This file was generated by pip-compile-multi.
 # To update, run:
@@ -7,11 +7,11 @@
 #
 annotated-types==0.7.0
     # via pydantic
-ase==3.26.0
+ase==3.27.0
     # via ncrystal
 asttokens==3.0.1
     # via stack-data
-certifi==2025.11.12
+certifi==2026.1.4
     # via requests
 charset-normalizer==3.4.4
     # via requests
@@ -27,19 +27,19 @@ cyclebane==24.10.0
     # via sciline
 cycler==0.12.1
     # via matplotlib
-dask==2025.11.0
+dask==2025.12.0
     # via -r base.in
 decorator==5.2.1
     # via ipython
 dnspython==2.8.0
     # via email-validator
 email-validator==2.3.0
     # via scippneutron
-essreduce==25.12.1
+essreduce==26.1.0
     # via -r base.in
 executing==2.2.1
     # via stack-data
-fonttools==4.61.0
+fonttools==4.61.1
     # via matplotlib
 fsspec==2025.12.0
     # via dask
@@ -55,11 +55,11 @@ idna==3.11
     # via
     #   email-validator
     #   requests
-importlib-metadata==8.7.0
+importlib-metadata==8.7.1
     # via dask
 ipydatawidgets==4.3.5
     # via pythreejs
-ipython==9.8.0
+ipython==9.9.0
     # via ipywidgets
 ipython-pygments-lexers==1.1.1
     # via ipython
@@ -80,7 +80,7 @@ lazy-loader==0.4
     #   tof
 locket==1.0.0
     # via partd
-matplotlib==3.10.7
+matplotlib==3.10.8
     # via
     #   ase
     #   mpltoolbox
@@ -97,7 +97,7 @@ ncrystal-python==4.2.10
     # via ncrystal
 networkx==3.6.1
     # via cyclebane
-numpy==2.3.5
+numpy==2.4.0
     # via
     #   -r base.in
     #   ase
@@ -123,7 +123,7 @@ partd==1.4.2
     # via dask
 pexpect==4.9.0
     # via ipython
-pillow==12.0.0
+pillow==12.1.0
     # via matplotlib
 platformdirs==4.5.1
     # via pooch
@@ -148,7 +148,7 @@ pygments==2.19.2
     # via
     #   ipython
     #   ipython-pygments-lexers
-pyparsing==3.2.5
+pyparsing==3.3.1
     # via matplotlib
 python-dateutil==2.9.0.post0
     # via
@@ -188,7 +188,9 @@ scipy==1.16.3
 six==1.17.0
     # via python-dateutil
 spglib==2.6.0
-    # via ncrystal
+    # via
+    #   -r base.in
+    #   ncrystal
 stack-data==0.6.3
     # via ipython
 tof==25.12.1
@@ -215,7 +217,7 @@ typing-extensions==4.15.0
     #   typing-inspection
 typing-inspection==0.4.2
     # via pydantic
-urllib3==2.6.1
+urllib3==2.6.2
     # via requests
 wcwidth==0.2.14
     # via prompt-toolkit

requirements/basetest.txt

@@ -7,7 +7,7 @@
 #
 asttokens==3.0.1
     # via stack-data
-certifi==2025.11.12
+certifi==2026.1.4
     # via requests
 charset-normalizer==3.4.4
     # via requests
@@ -21,7 +21,7 @@ idna==3.11
     # via requests
 iniconfig==2.3.0
     # via pytest
-ipython==9.8.0
+ipython==9.9.0
     # via ipywidgets
 ipython-pygments-lexers==1.1.1
     # via ipython
@@ -33,7 +33,7 @@ jupyterlab-widgets==3.0.16
     # via ipywidgets
 matplotlib-inline==0.2.1
     # via ipython
-numpy==2.3.5
+numpy==2.4.0
     # via pandas
 packaging==25.0
     # via
@@ -81,9 +81,9 @@ traitlets==5.14.3
     #   matplotlib-inline
 typing-extensions==4.15.0
     # via ipython
-tzdata==2025.2
+tzdata==2025.3
     # via pandas
-urllib3==2.6.1
+urllib3==2.6.2
     # via requests
 wcwidth==0.2.14
     # via prompt-toolkit

requirements/ci.txt

@@ -5,9 +5,9 @@
 #
 #    requirements upgrade
 #
-cachetools==6.2.2
+cachetools==6.2.4
     # via tox
-certifi==2025.11.12
+certifi==2026.1.4
     # via requests
 chardet==5.2.0
     # via tox
@@ -17,13 +17,13 @@ colorama==0.4.6
     # via tox
 distlib==0.4.0
     # via virtualenv
-filelock==3.20.0
+filelock==3.20.2
     # via
     #   tox
     #   virtualenv
 gitdb==4.0.12
     # via gitpython
-gitpython==3.1.45
+gitpython==3.1.46
     # via -r ci.in
 idna==3.11
     # via requests
@@ -44,9 +44,9 @@ requests==2.32.5
     # via -r ci.in
 smmap==5.0.2
     # via gitdb
-tox==4.32.0
+tox==4.33.0
     # via -r ci.in
-urllib3==2.6.1
+urllib3==2.6.2
     # via requests
 virtualenv==20.35.4
     # via tox

requirements/dev.txt

@@ -44,7 +44,7 @@ isoduration==20.11.0
     # via jsonschema
 jinja2-ansible-filters==1.3.2
     # via copier
-json5==0.12.1
+json5==0.13.0
     # via jupyterlab-server
 jsonpointer==3.0.0
     # via jsonschema
@@ -65,7 +65,7 @@ jupyter-server==2.17.0
     #   notebook-shim
 jupyter-server-terminals==0.5.3
     # via jupyter-server
-jupyterlab==4.5.0
+jupyterlab==4.5.1
     # via -r dev.in
 jupyterlab-server==2.28.0
     # via jupyterlab
@@ -99,7 +99,7 @@ rfc3986-validator==0.1.1
     #   jupyter-events
 rfc3987-syntax==1.1.0
     # via jsonschema
-send2trash==1.8.3
+send2trash==2.0.0
     # via jupyter-server
 terminado==0.18.1
     # via

requirements/docs.txt

@@ -26,7 +26,7 @@ beautifulsoup4==4.14.3
     #   pydata-sphinx-theme
 bleach[css]==6.3.0
     # via nbconvert
-debugpy==1.8.17
+debugpy==1.8.19
     # via ipykernel
 defusedxml==0.7.1
     # via nbconvert
@@ -83,11 +83,11 @@ mdit-py-plugins==0.5.0
     # via myst-parser
 mdurl==0.1.2
     # via markdown-it-py
-mistune==3.1.4
+mistune==3.2.0
     # via nbconvert
 myst-parser==4.0.1
     # via -r docs.in
-nbclient==0.10.2
+nbclient==0.10.4
     # via nbconvert
 nbconvert==7.16.6
     # via nbsphinx
@@ -104,7 +104,7 @@ pandas==2.3.3
     # via -r docs.in
 pandocfilters==1.5.1
     # via nbconvert
-psutil==7.1.3
+psutil==7.2.1
     # via ipykernel
 pyarrow==22.0.0
     # via -r docs.in
@@ -130,15 +130,17 @@ referencing==0.37.0
     # via
     #   jsonschema
     #   jsonschema-specifications
-roman-numerals-py==3.1.0
+roman-numerals==4.1.0
+    # via roman-numerals-py
+roman-numerals-py==4.1.0
     # via sphinx
 rpds-py==0.30.0
     # via
     #   jsonschema
     #   referencing
 snowballstemmer==3.0.1
     # via sphinx
-soupsieve==2.8
+soupsieve==2.8.1
     # via beautifulsoup4
 sphinx==8.2.3
     # via
@@ -173,11 +175,11 @@ sphinxcontrib-serializinghtml==2.0.0
     # via sphinx
 tinycss2==1.4.0
     # via bleach
-tornado==6.5.2
+tornado==6.5.4
     # via
     #   ipykernel
     #   jupyter-client
-tzdata==2025.2
+tzdata==2025.3
     # via pandas
 webencodings==0.5.1
     # via

requirements/mypy.txt

@@ -6,9 +6,9 @@
 #    requirements upgrade
 #
 -r test.txt
-librt==0.7.3
+librt==0.7.7
     # via mypy
-mypy==1.19.0
+mypy==1.19.1
     # via -r mypy.in
 mypy-extensions==1.1.0
     # via mypy

requirements/nightly.in

@@ -2,10 +2,11 @@
 # --- END OF CUSTOM SECTION ---
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask>=2022.1.0
-graphviz
+graphviz>=0.20
 numpy>=1.25
 pythreejs>=2.4.1
 ncrystal[cif]>=4.1.0
+spglib!=2.7,>=2.1
 pandas>=2.1.2
 pooch>=1.5
 pytest>=7.0