update dependencies (#82)

* update dependencies

* Update tests.yaml

* Update formatting.yaml

* Update pyproject.toml

* Update pyproject.toml

* Update pyproject.toml

.github/workflows/formatting.yaml

@@ -40,5 +40,9 @@ jobs:
       - name: Setup Python
         uses: actions/setup-python@v4
 
-      - name: Interrogate
-        uses: JackMcKew/python-interrogate-check@main
+      - name: Install interrogate
+        run: python -m pip install interrogate
+
+      - name: Run interrogate
+        run: interrogate .
+

.github/workflows/tests.yaml

@@ -45,14 +45,12 @@ jobs:
       max-parallel: 6
       matrix:
         config:
-          - { python-version: 3.8, os: ubuntu-latest }
-          - { python-version: 3.9, os: ubuntu-latest }
           - { python-version: "3.10", os: ubuntu-latest }
           - { python-version: "3.11", os: ubuntu-latest }
-          - { python-version: 3.8, os: macos-latest }
-          - { python-version: 3.9, os: macos-latest }
+          - { python-version: "3.12", os: ubuntu-latest }
           - { python-version: "3.10", os: macos-latest }
           - { python-version: "3.11", os: macos-latest }
+          - { python-version: "3.12", os: macos-latest }
     runs-on: ${{ matrix.config.os }}
     env:
       TZ: UTC

pyproject.toml

@@ -24,14 +24,15 @@ readme = "README.rst"
 include = ["LICENSE"]
 
 [tool.poetry.dependencies]
-python = "^3.8"
+python = ">=3.10"
 pandas = ">=1.5,<3.0"
-numpy = "^1.23.5"
-plotnine = "^0.12.0"
+numpy = "<=2.1.3"
+plotnine = "<=0.12.4"
 seaborn = ">=0.12,<0.14"
-requests = "^2.28.0"
-python-circos = "^0.3.0"
-anndata = { optional = true, version = ">=0.7.6,<0.10.0" }
+requests = ">=2.28.0"
+python-circos = ">=0.3.0"
+setuptools = "*"
+anndata = { optional = true, version = ">=0.7.6,<0.11.2" }
 black = { optional = true, version = "*" }
 pytest-cov = { optional = true, version = "*" }
 sphinx = { optional = true, version = "<8" }                         # see issue at https://github.com/readthedocs/readthedocs.org/issues/10279