🎨 environment files cleaned

Author: marcoreverenna

environment.linux.yml

@@ -1,45 +1,42 @@
 name: instanexus
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
+
 dependencies:
+  # core runtime dependencies
+  - python=3.11
   - biopython=1.85
-  - pcre2=10.42
-  - bzip2=1.0.8
-  - zlib=1.2.13
-  - wheel=0.45.1
-  - ncurses=6.5
-  - readline=8.2
-  - xz=5.6.4
-  - gettext=0.21.0
-  - ca-certificates=2025.2.25
-  - wget=1.25.0
-  - llvm-openmp=17.0.6
-  - openssl==3.0.17
-  - libxml2=2.13.8
-  - python=3.9.21
-  - libexpat=2.7.0
-  - setuptools=80.9.0
-  - icu=73.1
-  - libffi=3.4.6
-  - libiconv=1.16
   - pandas=2.3.1
-  - pip=25.1.1
-  - gawk=5.3.1
-  - tk=8.6.14
-  - libcxx=17.0.6
-  - sqlite=3.45.3
+  - upsetplot
   - tqdm=4.67.1
-  - libidn2=2.3.4
-  - libunistring=0.9.10
-  - clustalo=1.2.4
-  - matplotlib-base
   - seaborn=0.13.2
+  - matplotlib-base
   - plotly=6.2.0
   - logomaker=0.8
   - networkx
   - mmseqs2
+  - sbl::clustalomega
+  - gawk
+  - wget
+
+  # notebook
+  - ipykernel
+  - nbformat
+
+  # development tools
+  - black
+  - pytest
+  - coverage
+  - mypy
+  - pre-commit
+
+  # packaging
   - pip
   - pip:
-      - kaleido==0.2.1
+      - build
+      - twine
+      - hatchling
+      - wheel
+      - sphinx

environment.osx-arm64.yaml

@@ -35,7 +35,6 @@ dependencies:
   # packaging
   - pip
   - pip:
-      - kaleido==0.2.1
       - build
       - twine
       - hatchling