Bump pytest-cov from 6.1.0 to 7.0.0

.github/workflows/ci.yml

@@ -21,10 +21,10 @@ jobs:
     runs-on: ${{matrix.os}}
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Install uv and set up Python ${{ matrix.python-version }}
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
 

.github/workflows/combine-prs.yml

@@ -30,7 +30,7 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      - uses: actions/github-script@v7
+      - uses: actions/github-script@v8
         id: create-combined-pr
         name: Create Combined PR
         with:

.github/workflows/publish-to-pypi.yml

@@ -14,12 +14,12 @@ jobs:
     needs: test
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
       - name: Build
         run: uv build
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           path: dist/*.*
 
@@ -31,7 +31,7 @@ jobs:
       id-token: write
     steps:
       - name: Get build artifacts
-        uses: actions/download-artifact@v4
+        uses: actions/download-artifact@v6
         with:
           name: artifact
           path: dist

.github/workflows/update-changelog.yml

@@ -12,7 +12,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Set up Git user
         run: |
@@ -36,7 +36,7 @@ jobs:
           github_changelog_generator -u WMD-group -p SMACT --token $CHANGELOG_GITHUB_TOKEN --output docs/CHANGELOG.md --exclude-labels dependencies
 
       - name: Set up Python
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: "3.12"
 

README.md

@@ -10,7 +10,7 @@
 ![dependencies](https://img.shields.io/librariesio/release/pypi/smact)
 [![CI Status](https://github.com/WMD-group/SMACT/actions/workflows/ci.yml/badge.svg)](https://github.com/WMD-group/SMACT/actions/workflows/ci.yml)
 [![codecov](https://codecov.io/gh/WMD-group/SMACT/branch/master/graph/badge.svg?token=UtgVxjoYNP)](https://codecov.io/gh/WMD-group/SMACT)
-![PyPI - Downloads](https://img.shields.io/pypi/dm/smact)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/smact) [![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/WMD-group/SMACT)
 
 # SMACT
 

pyproject.toml

@@ -346,6 +346,7 @@ exclude_also = [
 
 [dependency-groups]
 dev = [
+    "coverage>=7.10.6",
     "jupyter>=1.1.1",
     "jupyter-client>=8.6.3",
     "notebook>=7.3.3",

requirements.txt

@@ -10,7 +10,7 @@ alabaster==1.0.0
     # via sphinx
 annotated-types==0.7.0
     # via pydantic
-appnope==0.1.4 ; platform_system == 'Darwin'
+appnope==0.1.4 ; sys_platform == 'darwin'
     # via ipykernel
 ase==3.24.0
     # via smact (pyproject.toml)
@@ -30,15 +30,17 @@ bcrypt==4.3.0
     # via paramiko
 beautifulsoup4==4.13.3
     # via pydata-sphinx-theme
+bibtexparser==1.4.3
+    # via pymatgen
 black==25.1.0
     # via blacken-docs
 blacken-docs==1.19.1
     # via smact (pyproject.toml)
 blinker==1.9.0
     # via flask
-boto3==1.35.71
+boto3==1.40.42
     # via maggma
-botocore==1.35.71
+botocore==1.40.42
     # via
     #   boto3
     #   s3transfer
@@ -60,7 +62,7 @@ cloudpickle==3.1.1
     # via shap
 codespell==2.4.1
     # via smact (pyproject.toml)
-colorama==0.4.6 ; sys_platform == 'win32' or platform_system == 'Windows'
+colorama==0.4.6 ; sys_platform == 'win32'
     # via
     #   click
     #   ipython
@@ -71,27 +73,22 @@ comm==0.2.2
     # via ipykernel
 contourpy==1.2.0
     # via matplotlib
-coverage==7.8.0
+coverage==7.11.3
     # via pytest-cov
 cryptography==44.0.1
     # via paramiko
 cycler==0.12.1
     # via matplotlib
 dash==3.0.2
     # via smact (pyproject.toml)
-dash-core-components==2.0.0
-    # via dash
-dash-html-components==2.0.0
-    # via dash
-dash-table==5.0.0
-    # via dash
 debugpy==1.8.13
     # via ipykernel
 decorator==5.2.1
     # via ipython
 dill==0.3.8
     # via
     #   multiprocess
+    #   pandarallel
     #   pathos
 dnspython==2.7.0
     # via
@@ -107,10 +104,6 @@ elementembeddings==0.6.1
     # via smact (pyproject.toml)
 emmet-core==0.84.5
     # via mp-api
-exceptiongroup==1.2.2 ; python_full_version < '3.11'
-    # via
-    #   ipython
-    #   pytest
 executing==2.2.0
     # via stack-data
 fastjsonschema==2.21.1
@@ -171,7 +164,7 @@ jupyter-client==8.6.3
     # via
     #   ipykernel
     #   nbclient
-jupyter-core==5.7.2
+jupyter-core==5.8.1
     # via
     #   ipykernel
     #   jupyter-client
@@ -205,13 +198,16 @@ matplotlib==3.9.3
     #   adjusttext
     #   ase
     #   elementembeddings
+    #   matplotlib-venn
     #   pymatgen
     #   pymatviz
     #   seaborn
 matplotlib-inline==0.1.7
     # via
     #   ipykernel
     #   ipython
+matplotlib-venn==1.1.2
+    # via smact (pyproject.toml)
 mdit-py-plugins==0.4.2
     # via myst-parser
 mdurl==0.1.2
@@ -277,6 +273,7 @@ numpy==1.26.2
     #   maggma
     #   matminer
     #   matplotlib
+    #   matplotlib-venn
     #   monty
     #   numba
     #   opentsne
@@ -287,10 +284,11 @@ numpy==1.26.2
     #   scipy
     #   seaborn
     #   shap
+    #   shapely
     #   spglib
     #   umap-learn
     #   xgboost
-nvidia-nccl-cu12==2.26.2 ; platform_machine != 'aarch64' and platform_system == 'Linux'
+nvidia-nccl-cu12==2.26.2 ; platform_machine != 'aarch64' and sys_platform == 'linux'
     # via xgboost
 opentsne==1.0.2
     # via elementembeddings
@@ -308,11 +306,14 @@ packaging==24.0
     #   sphinx
 palettable==3.3.3
     # via pymatgen
+pandarallel==1.6.5
+    # via smact (pyproject.toml)
 pandas==2.2.3
     # via
     #   smact (pyproject.toml)
     #   maggma
     #   matminer
+    #   pandarallel
     #   pymatgen
     #   pymatviz
     #   seaborn
@@ -339,23 +340,25 @@ plotly==5.24.1
     #   pymatgen
     #   pymatviz
 pluggy==1.5.0
-    # via pytest
+    # via
+    #   pytest
+    #   pytest-cov
 pox==0.3.4
     # via pathos
 ppft==1.7.6.8
     # via pathos
 prompt-toolkit==3.0.50
     # via ipython
 psutil==7.0.0
-    # via ipykernel
+    # via
+    #   ipykernel
+    #   pandarallel
 ptyprocess==0.7.0 ; sys_platform != 'emscripten' and sys_platform != 'win32'
     # via pexpect
 pure-eval==0.2.3
     # via stack-data
 pybtex==0.24.0
-    # via
-    #   emmet-core
-    #   pymatgen
+    # via emmet-core
 pycparser==2.22
     # via cffi
 pydantic==2.9.2
@@ -399,14 +402,16 @@ pynacl==1.5.0
 pynndescent==0.5.13
     # via umap-learn
 pyparsing==3.1.1
-    # via matplotlib
+    # via
+    #   bibtexparser
+    #   matplotlib
 pyright==1.1.398
     # via smact (pyproject.toml)
 pytest==8.3.5
     # via
     #   smact (pyproject.toml)
     #   pytest-cov
-pytest-cov==6.1.0
+pytest-cov==7.0.0
     # via smact (pyproject.toml)
 python-dateutil==2.9.0.post0
     # via
@@ -415,7 +420,7 @@ python-dateutil==2.9.0.post0
     #   maggma
     #   matplotlib
     #   pandas
-python-dotenv==1.0.1
+python-dotenv==1.1.1
     # via pydantic-settings
 pytz==2024.1
     # via
@@ -440,7 +445,7 @@ referencing==0.35.1
     # via
     #   jsonschema
     #   jsonschema-specifications
-requests==2.32.3
+requests==2.32.4
     # via
     #   dash
     #   matminer
@@ -462,7 +467,7 @@ ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_imple
     # via ruamel-yaml
 ruff==0.11.2
     # via smact (pyproject.toml)
-s3transfer==0.10.4
+s3transfer==0.14.0
     # via boto3
 scikit-learn==1.5.2
     # via
@@ -479,6 +484,7 @@ scipy==1.14.1
     #   adjusttext
     #   ase
     #   elementembeddings
+    #   matplotlib-venn
     #   opentsne
     #   pymatgen
     #   pymatviz
@@ -500,6 +506,8 @@ setuptools==78.1.1
     #   mp-api
 shap==0.46.0
     # via smact (pyproject.toml)
+shapely==2.1.2
+    # via matplotlib-venn
 six==1.16.0
     # via
     #   latexcodec
@@ -551,7 +559,7 @@ sshtunnel==0.4.0
     # via maggma
 stack-data==0.6.3
     # via ipython
-sympy==1.12
+sympy==1.14.0
     # via
     #   matminer
     #   pymatgen
@@ -565,11 +573,7 @@ tenacity==8.2.3
 threadpoolctl==3.6.0
     # via scikit-learn
 tomli==2.2.1 ; python_full_version <= '3.11'
-    # via
-    #   black
-    #   coverage
-    #   pytest
-    #   sphinx
+    # via coverage
 tornado==6.5.1
     # via
     #   ipykernel
@@ -595,7 +599,6 @@ typing-extensions==4.12.2
     # via
     #   smact (pyproject.toml)
     #   beautifulsoup4
-    #   black
     #   dash
     #   elementembeddings
     #   emmet-core
@@ -617,7 +620,7 @@ umap-learn==0.5.7
     #   elementembeddings
 uncertainties==3.2.2
     # via pymatgen
-urllib3==2.2.2
+urllib3==2.5.0
     # via
     #   botocore
     #   requests