Updates for 2026 spring

- New pytest major version (9.x.x, testing)
- sphinx 9.* didn't resolve with conda-forge with sphinx_rtd_theme
  even though it theoretically should have, according to the
  source. (documentation)
- New myst-parser major version (5.x.x, documentation)
- New pandas major version (probably not too relevant to coderefinery)

Author: rkdarst

environment.yml

@@ -4,20 +4,20 @@ channels:
   - bioconda
 dependencies:
   - python>=3.10,<3.14
-  - click=8.1.7
-  - ipywidgets=8.1.5
-  - jupyterlab=4.4.0
-  - jupyterlab-git=0.51.1
-  - matplotlib=3.10.1
-  - myst-parser=4.0.1
+  - click=8.3.1
+  - ipywidgets=8.1.8
+  - jupyterlab=4.5.3
+  - jupyterlab-git=0.51.4
+  - matplotlib=3.10.8
+  - myst-parser=5.0.0
   - nbdime=4.0.2
-  - numpy=2.2.4
-  - pandas=2.2.3
-  - pytest=8.3.5
-  - pytest-cov=6.0.0
+  - numpy=2.4.1
+  - pandas=3.0.0
+  - pytest=9.0.2
+  - pytest-cov=7.0.0
   - seaborn=0.13.2
-  - snakemake-minimal=9.1.7
+  - snakemake-minimal=9.14.8
   - sphinx=8.2.3
-  - sphinx-autobuild=2024.10.3
-  - sphinx_rtd_theme=3.0.1
+  - sphinx-autobuild=2025.8.25
+  - sphinx_rtd_theme=3.1.0
   - sphinx-autodoc2=0.5.0

requirements.txt

@@ -1,17 +1,17 @@
-click==8.1.7
-ipywidgets==8.1.5
-jupyterlab==4.4.0
-jupyterlab-git==0.51.1
-matplotlib==3.10.1
-myst-parser==4.0.1
+click==8.3.1
+ipywidgets==8.1.8
+jupyterlab==4.5.3
+jupyterlab-git==0.51.4
+matplotlib==3.10.8
+myst-parser==5.0.0
 nbdime==4.0.2
-numpy==2.2.4
-pandas==2.2.3
-pytest==8.3.5
-pytest-cov==6.0.0
+numpy==2.4.1
+pandas==3.0.0
+pytest==9.0.2
+pytest-cov==7.0.0
 seaborn==0.13.2
-snakemake==9.1.7
+snakemake==9.14.8
 sphinx==8.2.3
-sphinx-autobuild==2024.10.3
-sphinx_rtd_theme==3.0.1
+sphinx-autobuild==2025.8.25
+sphinx_rtd_theme==3.1.0
 sphinx-autodoc2==0.5.0