Merge pull request #352 from WMD-group/develop

Merge develop branch into master

docs/conf.py

@@ -73,7 +73,7 @@
 # The short X.Y version.
 version = "3.0"
 # The full version, including alpha/beta/rc tags.
-release = "3.0.0"
+release = "3.0.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "SMACT"
-version = "3.0"
+version = "3.0.1"
 description = "Semiconducting Materials by Analogy and Chemical Theory"
 readme = "README.md"
 authors = [
@@ -99,10 +99,9 @@ optional = [
     "seaborn>=0.13.2",
     "pymatgen>=2024.2.20",
     "matminer>=0.9.2",
-    "umap-learn>=0.5.3",
     "kaleido>=0.2.1",
     "ase>=3.22.0",
-    "numpy",
+    "llvmlite>=0.40",
     "ElementEmbeddings>=0.4",
     "dash>=2.18.2",
 

requirements.txt

@@ -1,17 +1,13 @@
-#
-# This file is autogenerated by pip-compile with Python 3.10
-# by the following command:
-#
-#    pip-compile --extra=strict --output-file=requirements.txt
-#
+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml --extra optional --universal --output-file=requirements.txt
 adjusttext==1.3.0
     # via elementembeddings
 aioitertools==0.12.0
     # via maggma
 annotated-types==0.7.0
     # via pydantic
 ase==3.23.0
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 attrs==24.2.0
     # via
     #   jsonlines
@@ -33,18 +29,23 @@ cffi==1.17.1
     # via
     #   cryptography
     #   pynacl
+    #   pyzmq
 charset-normalizer==3.3.2
     # via requests
 click==8.1.7
     # via flask
+colorama==0.4.6 ; platform_system == 'Windows'
+    # via
+    #   click
+    #   tqdm
 contourpy==1.2.0
     # via matplotlib
 cryptography==44.0.0
     # via paramiko
 cycler==0.12.1
     # via matplotlib
 dash==2.18.2
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 dash-core-components==2.0.0
     # via dash
 dash-html-components==2.0.0
@@ -60,7 +61,7 @@ dnspython==2.7.0
     #   maggma
     #   pymongo
 elementembeddings==0.6.1
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 emmet-core==0.84.3rc4
     # via mp-api
 flask==3.0.3
@@ -93,7 +94,7 @@ jsonschema==4.23.0
 jsonschema-specifications==2024.10.1
     # via jsonschema
 kaleido==0.2.1
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 kiwisolver==1.4.5
     # via matplotlib
 latexcodec==2.0.1
@@ -109,7 +110,7 @@ markupsafe==3.0.2
     #   jinja2
     #   werkzeug
 matminer==0.9.2
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 matplotlib==3.9.3
     # via
     #   adjusttext
@@ -128,7 +129,7 @@ monty==2024.10.21
     #   mp-api
     #   pymatgen
 mp-api==0.42.2
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 mpmath==1.3.0
     # via sympy
 msgpack==1.1.0
@@ -147,7 +148,7 @@ numba==0.60.0
     #   umap-learn
 numpy==1.26.2
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   adjusttext
     #   ase
     #   contourpy
@@ -178,9 +179,9 @@ packaging==24.0
     #   plotly
 palettable==3.3.3
     # via pymatgen
-pandas[output-formatting]==2.2.3
+pandas==2.2.3
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   maggma
     #   matminer
     #   pymatgen
@@ -189,7 +190,7 @@ pandas[output-formatting]==2.2.3
 paramiko==3.5.0
     # via sshtunnel
 pathos==0.3.2
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 pillow==10.4.0
     # via matplotlib
 plotly==5.24.1
@@ -209,7 +210,7 @@ pycparser==2.22
     # via cffi
 pydantic==2.9.2
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   emmet-core
     #   maggma
     #   pydantic-settings
@@ -223,14 +224,14 @@ pydash==8.0.4
     # via maggma
 pymatgen==2024.11.13
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   elementembeddings
     #   emmet-core
     #   matminer
     #   mp-api
     #   pymatviz
 pymatviz==0.14.0
-    # via SMACT (setup.py)
+    # via smact (pyproject.toml)
 pymongo==4.10.1
     # via
     #   maggma
@@ -278,7 +279,7 @@ ruamel-yaml==0.18.6
     #   maggma
     #   monty
     #   pymatgen
-ruamel-yaml-clib==0.2.8
+ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython'
     # via ruamel-yaml
 s3transfer==0.10.4
     # via boto3
@@ -292,7 +293,7 @@ scikit-learn==1.5.2
     #   umap-learn
 scipy==1.14.1
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   adjusttext
     #   ase
     #   elementembeddings
@@ -304,10 +305,15 @@ scipy==1.14.1
     #   umap-learn
 seaborn==0.13.2
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   elementembeddings
 sentinels==1.0.0
     # via mongomock
+setuptools==75.6.0
+    # via
+    #   dash
+    #   maggma
+    #   mp-api
 six==1.16.0
     # via
     #   latexcodec
@@ -318,7 +324,7 @@ smart-open==7.0.5
     # via mp-api
 spglib==2.5.0
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   pymatgen
 sshtunnel==0.4.0
     # via maggma
@@ -342,7 +348,7 @@ tqdm==4.66.4
     #   umap-learn
 typing-extensions==4.12.2
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   dash
     #   elementembeddings
     #   emmet-core
@@ -354,7 +360,7 @@ tzdata==2024.1
     # via pandas
 umap-learn==0.5.3
     # via
-    #   SMACT (setup.py)
+    #   smact (pyproject.toml)
     #   elementembeddings
 uncertainties==3.2.2
     # via pymatgen
@@ -370,6 +376,3 @@ wrapt==1.17.0
     # via smart-open
 zipp==3.21.0
     # via importlib-metadata
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools