Merge pull request #43 from coderefinery/radovan/update-software-environment

update software environment

Author: rkdarst

environment.yml

@@ -1,25 +1,23 @@
 name: coderefinery
 channels:
   - conda-forge
-  - defaults
   - bioconda
 dependencies:
-  - python>=3.10
+  - python>=3.10,<3.14
   - click=8.1.7
-  - ipywidgets=8.1.2
-  - jupyterlab=4.1.2
-  - jupyterlab-git=0.50.0
-  - matplotlib=3.8.3
-  - myst-parser=2.0.0
-  - nbdime=4.0.1
-  - numpy=1.26.4
-  - pandas=2.2.1
-  - pytest=8.0.2
-  - pytest-cov=4.1.0
+  - ipywidgets=8.1.5
+  - jupyterlab=4.4.0
+  - jupyterlab-git=0.51.1
+  - matplotlib=3.10.1
+  - myst-parser=4.0.1
+  - nbdime=4.0.2
+  - numpy=2.2.4
+  - pandas=2.2.3
+  - pytest=8.3.5
+  - pytest-cov=6.0.0
   - seaborn=0.13.2
-  - snakemake-minimal=8.5.3
-  - pulp<2.8.0
-  - sphinx=7.2.6
-  - sphinx-autobuild=2024.2.4
-  - sphinx_rtd_theme=2.0.0
-  - sphinx-autodoc2
+  - snakemake-minimal=9.1.7
+  - sphinx=8.2.3
+  - sphinx-autobuild=2024.10.3
+  - sphinx_rtd_theme=3.0.1
+  - sphinx-autodoc2=0.5.0

requirements.txt

@@ -1,17 +1,17 @@
 click==8.1.7
-ipywidgets==8.1.2
-jupyterlab==4.1.2
-jupyterlab-git==0.50.0
-matplotlib==3.8.3
-myst-parser==2.0.0
-nbdime==4.0.1
-numpy==1.26.4
-pandas==2.2.1
-pytest==8.0.2
-pytest-cov==4.1.0
+ipywidgets==8.1.5
+jupyterlab==4.4.0
+jupyterlab-git==0.51.1
+matplotlib==3.10.1
+myst-parser==4.0.1
+nbdime==4.0.2
+numpy==2.2.4
+pandas==2.2.3
+pytest==8.3.5
+pytest-cov==6.0.0
 seaborn==0.13.2
-snakemake==8.5.3
-pulp<2.8.0
-sphinx==7.2.6
-sphinx-autobuild==2024.2.4
-sphinx_rtd_theme==2.0.0
+snakemake==9.1.7
+sphinx==8.2.3
+sphinx-autobuild==2024.10.3
+sphinx_rtd_theme==3.0.1
+sphinx-autodoc2==0.5.0