Update environment.yml: reorganize dependencies, remove specific versioning, and add missing packages for improved compatibility

Envs/environment.yml

@@ -1,152 +1,171 @@
 name: tesisEnv
 channels:
   - bioconda
-  - conda-forge
   - anaconda
-  - https://repo.anaconda.com/pkgs/main
-  - https://repo.anaconda.com/pkgs/r
+  - conda-forge
+  - defaults
 dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - asttokens=3.0.0=py310h06a4308_0
-  - blas=1.0=mkl
-  - bzip2=1.0.8=h5eee18b_6
-  - c-ares=1.19.1=h5eee18b_0
-  - ca-certificates=2025.2.25=h06a4308_0
-  - comm=0.2.2=pyhd8ed1ab_1
-  - cyrus-sasl=2.1.28=h52b45da_1
-  - debugpy=1.8.11=py310h6a678d5_0
-  - decorator=5.2.1=pyhd8ed1ab_0
-  - entrypoints=0.4=py310h06a4308_0
-  - exceptiongroup=1.2.2=pyhd8ed1ab_1
-  - expat=2.7.1=h6a678d5_0
-  - font-ttf-dejavu-sans-mono=2.37=hd3eb1b0_0
-  - font-ttf-inconsolata=2.001=hcb22688_0
-  - font-ttf-source-code-pro=2.030=hd3eb1b0_0
-  - font-ttf-ubuntu=0.83=h8b1ccd4_0
-  - fontconfig=2.14.1=h55d465d_3
-  - fonts-anaconda=1=h8fa9717_0
-  - freetype=2.13.3=h4a9f257_0
-  - icu=73.1=h6a678d5_0
-  - importlib-metadata=8.5.0=py310h06a4308_0
-  - intel-openmp=2023.1.0=hdb19cb5_46306
-  - ipykernel=6.29.5=py310h06a4308_1
-  - ipython=8.33.0=pyh907856f_0
-  - ipywidgets=8.1.5=py310h06a4308_0
-  - jedi=0.19.2=py310h06a4308_0
-  - jpeg=9e=h5eee18b_3
-  - jsonschema=4.23.0=py310h06a4308_0
-  - jsonschema-specifications=2023.7.1=py310h06a4308_0
-  - jupyter_client=7.3.4=py310h06a4308_0
-  - jupyter_core=5.7.2=py310h06a4308_0
-  - jupyterlab_widgets=3.0.13=py310h06a4308_0
-  - kaleido-core=0.2.1=h7c8854e_0
-  - krb5=1.20.1=h143b758_1
-  - ld_impl_linux-64=2.40=h12ee557_0
-  - libabseil=20250127.0=cxx17_h6a678d5_0
-  - libcups=2.4.2=h2d74bed_1
-  - libcurl=8.12.1=hc9e6f67_0
-  - libedit=3.1.20230828=h5eee18b_0
-  - libev=4.33=h7f8727e_1
-  - libffi=3.4.4=h6a678d5_1
-  - libgcc-ng=11.2.0=h1234567_1
-  - libglib=2.78.4=hdc74915_0
-  - libgomp=11.2.0=h1234567_1
-  - libiconv=1.16=h5eee18b_3
-  - libnghttp2=1.57.0=h2d74bed_0
-  - libpng=1.6.39=h5eee18b_0
-  - libpq=17.4=hdbd6064_0
-  - libprotobuf=5.29.3=hc99497a_0
-  - libsodium=1.0.18=h7b6447c_0
-  - libssh2=1.11.1=h251f7ec_0
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - libuuid=1.41.5=h5eee18b_0
-  - libxcb=1.15=h7f8727e_0
-  - libxkbcommon=1.0.1=h097e994_2
-  - libxml2=2.13.7=hfdd30dd_0
-  - lz4-c=1.9.4=h6a678d5_1
-  - mathjax=2.7.5=h06a4308_0
-  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
-  - mkl=2023.1.0=h213fc3f_46344
-  - mkl-service=2.4.0=py310h5eee18b_2
-  - mkl_fft=1.3.11=py310h5eee18b_0
-  - mkl_random=1.2.8=py310h1128e8f_0
-  - mysql=8.4.0=h721767e_2
-  - narwhals=1.31.0=py310h06a4308_1
-  - nbformat=5.10.4=py310h06a4308_0
-  - ncurses=6.4=h6a678d5_0
-  - nest-asyncio=1.6.0=py310h06a4308_0
-  - nspr=4.35=h6a678d5_0
-  - nss=3.89.1=h6a678d5_0
-  - numpy=1.26.4=py310h5f9d8c6_0
-  - numpy-base=1.26.4=py310hb5e798b_0
-  - openldap=2.6.4=h42fbc30_0
-  - openssl=3.0.16=h5eee18b_0
-  - packaging=24.2=py310h06a4308_0
-  - parso=0.8.4=py310h06a4308_0
-  - pcre2=10.42=hebb0a14_1
-  - pexpect=4.9.0=pyhd8ed1ab_1
-  - pickleshare=0.7.5=pyhd3eb1b0_1003
-  - pip=25.0=py310h06a4308_0
-  - platformdirs=4.3.6=pyhd8ed1ab_1
-  - plotly=6.0.1=py310he3bba80_0
-  - prompt-toolkit=3.0.50=pyha770c72_0
-  - psutil=5.9.1=py310h5764c6d_0
-  - ptyprocess=0.7.0=pyhd3eb1b0_2
-  - pure_eval=0.2.3=pyhd8ed1ab_1
-  - pyfaidx=0.8.1.3=pyhdfd78af_0
-  - pygments=2.19.1=py310h06a4308_0
-  - pyqt=6.7.1=py310h6a678d5_1
-  - pyqt6-sip=13.9.1=py310h5eee18b_1
-  - python=3.10.16=he870216_1
-  - python-dateutil=2.9.0.post0=py310h06a4308_1
-  - python-fastjsonschema=2.20.0=py310h06a4308_0
-  - python-kaleido=0.2.1=py310h06a4308_0
-  - python_abi=3.10=2_cp310
-  - pyvcf3=1.0.3=pyhdfd78af_0
-  - pyzmq=26.2.0=py310h6a678d5_0
-  - qtbase=6.7.3=hdaa5aa8_0
-  - qtdeclarative=6.7.3=h6a678d5_0
-  - qtsvg=6.7.3=he621ea3_0
-  - qttools=6.7.3=h80c7b02_0
-  - qtwebchannel=6.7.3=h6a678d5_0
-  - qtwebsockets=6.7.3=h6a678d5_0
-  - readline=8.2=h5eee18b_0
-  - referencing=0.30.2=py310h06a4308_0
-  - rpds-py=0.22.3=py310h4aa5aa6_0
-  - setuptools=75.8.0=py310h06a4308_0
-  - sip=6.10.0=py310h6a678d5_0
-  - six=1.17.0=py310h06a4308_0
-  - sqlite=3.45.3=h5eee18b_0
-  - stack_data=0.6.3=pyhd8ed1ab_1
-  - tbb=2021.8.0=hdb19cb5_0
-  - tk=8.6.14=h39e8969_0
-  - tomli=2.0.1=py310h06a4308_0
-  - tornado=6.1=py310h7f8727e_0
-  - traitlets=5.14.3=py310h06a4308_0
-  - typing_extensions=4.12.2=py310h06a4308_0
-  - wcwidth=0.2.13=pyhd8ed1ab_1
-  - wheel=0.45.1=py310h06a4308_0
-  - widgetsnbextension=4.0.13=py310h06a4308_0
-  - xcb-util-cursor=0.1.4=h5eee18b_0
-  - xz=5.6.4=h5eee18b_1
-  - zeromq=4.3.5=h6a678d5_0
-  - zipp=3.21.0=py310h06a4308_0
-  - zlib=1.2.13=h5eee18b_1
+  - _libgcc_mutex=0.1
+  - _openmp_mutex=5.1
+  - asttokens=3.0.0
+  - blas=1.0
+  - bottleneck=1.4.2
+  - brotli-python=1.0.9
+  - bzip2=1.0.8
+  - c-ares=1.19.1
+  - ca-certificates=2025.2.25
+  - certifi=2025.4.26
+  - comm=0.2.2
+  - contourpy=1.3.1
+  - cyrus-sasl=2.1.28
+  - debugpy=1.8.11
+  - decorator=5.2.1
+  - entrypoints=0.4
+  - exceptiongroup=1.2.2
+  - executing=2.2.0
+  - expat=2.7.1
+  - font-ttf-dejavu-sans-mono=2.37
+  - font-ttf-inconsolata=2.001
+  - font-ttf-source-code-pro=2.030
+  - font-ttf-ubuntu=0.83
+  - fontconfig=2.14.1
+  - fonts-anaconda=1
+  - freetype=2.13.3
+  - icu=73.1
+  - importlib-metadata=8.5.0
+  - intel-openmp=2023.1.0
+  - ipykernel=6.29.5
+  - ipython=8.33.0
+  - ipywidgets=8.1.5
+  - jedi=0.19.2
+  - jpeg=9e
+  - jsonschema=4.23.0
+  - jsonschema-specifications=2023.7.1
+  - jupyter_client=7.3.4
+  - jupyter_core=5.7.2
+  - jupyterlab_widgets=3.0.13
+  - kaleido-core=0.2.1
+  - kiwisolver=1.4.8
+  - krb5=1.20.1
+  - lcms2=2.16
+  - ld_impl_linux-64=2.40
+  - lerc=4.0.0
+  - libabseil=20250127.0
+  - libcups=2.4.2
+  - libcurl=8.12.1
+  - libdeflate=1.22
+  - libedit=3.1.20230828
+  - libev=4.33
+  - libffi=3.4.4
+  - libgcc-ng=11.2.0
+  - libglib=2.78.4
+  - libgomp=11.2.0
+  - libiconv=1.16
+  - libnghttp2=1.57.0
+  - libpng=1.6.39
+  - libpq=17.4
+  - libprotobuf=5.29.3
+  - libsodium=1.0.18
+  - libssh2=1.11.1
+  - libstdcxx-ng=11.2.0
+  - libtiff=4.7.0
+  - libuuid=1.41.5
+  - libwebp-base=1.3.2
+  - libxcb=1.15
+  - libxkbcommon=1.0.1
+  - libxml2=2.13.7
+  - llvmlite=0.44.0
+  - lz4-c=1.9.4
+  - mathjax=2.7.5
+  - matplotlib-base=3.10.0
+  - matplotlib-inline=0.1.7
+  - mkl=2023.1.0
+  - mkl-service=2.4.0
+  - mkl_fft=1.3.11
+  - mkl_random=1.2.8
+  - mysql=8.4.0
+  - narwhals=1.31.0
+  - nbformat=5.10.4
+  - ncurses=6.4
+  - nest-asyncio=1.6.0
+  - nspr=4.35
+  - nss=3.89.1
+  - numba=0.61.0
+  - numexpr=2.10.1
+  - numpy=1.26.4
+  - numpy-base=1.26.4
+  - openjpeg=2.5.2
+  - openldap=2.6.4
+  - openssl=3.0.16
+  - packaging=24.2
+  - pandas=2.2.3
+  - parso=0.8.4
+  - pcre2=10.42
+  - pexpect=4.9.0
+  - pickleshare=0.7.5
+  - pillow=11.1.0
+  - pip=25.0
+  - platformdirs=4.3.6
+  - plotly=6.0.1
+  - prompt-toolkit=3.0.50
+  - psutil=5.9.1
+  - ptyprocess=0.7.0
+  - pure_eval=0.2.3
+  - pyfaidx=0.8.1.3
+  - pygments=2.19.1
+  - pynndescent=0.5.10
+  - pyqt=6.7.1
+  - pyqt6-sip=13.9.1
+  - python=3.10.16
+  - python-dateutil=2.9.0.post0
+  - python-fastjsonschema=2.20.0
+  - python-kaleido=0.2.1
+  - python-tzdata=2025.2
+  - python_abi=3.10
+  - pyvcf3=1.0.3
+  - pyzmq=26.2.0
+  - qtbase=6.7.3
+  - qtdeclarative=6.7.3
+  - qtsvg=6.7.3
+  - qttools=6.7.3
+  - qtwebchannel=6.7.3
+  - qtwebsockets=6.7.3
+  - readline=8.2
+  - referencing=0.30.2
+  - rpds-py=0.22.3
+  - seaborn=0.13.2
+  - setuptools=75.8.0
+  - sip=6.10.0
+  - six=1.17.0
+  - sqlite=3.45.3
+  - stack_data=0.6.3
+  - tbb=2021.8.0
+  - tk=8.6.14
+  - tomli=2.0.1
+  - tornado=6.1
+  - traitlets=5.14.3
+  - typing_extensions=4.12.2
+  - umap-learn=0.5.7
+  - unicodedata2=15.1.0
+  - wcwidth=0.2.13
+  - wheel=0.45.1
+  - widgetsnbextension=4.0.13
+  - xcb-util-cursor=0.1.4
+  - xz=5.6.4
+  - zeromq=4.3.5
+  - zipp=3.21.0
+  - zlib=1.2.13
   - pip:
       - attrs==25.1.0
       - biopython==1.85
       - biotite==0.41.2
       - brotli==1.1.0
-      - certifi==2025.1.31
       - charset-normalizer==3.4.1
       - cloudpathlib==0.20.0
-      - contourpy==1.3.1
       - cycler==0.12.1
       - dna-features-viewer==3.1.4
       - einops==0.8.1
       - esm==3.1.4
-      - executing==2.2.0
       - filelock==3.17.0
       - fonttools==4.56.0
       - fsspec==2025.2.0
@@ -156,7 +175,6 @@ dependencies:
       - idna==3.10
       - jinja2==3.1.5
       - joblib==1.4.2
-      - kiwisolver==1.4.8
       - markupsafe==3.0.2
       - matplotlib==3.10.1
       - mpmath==1.3.0
@@ -176,8 +194,6 @@ dependencies:
       - nvidia-nccl-cu12==2.21.5
       - nvidia-nvjitlink-cu12==12.4.127
       - nvidia-nvtx-cu12==12.4.127
-      - pandas==2.2.3
-      - pillow==11.1.0
       - protobuf==6.31.0
       - py3dmol==2.4.2
       - pyparsing==3.2.1
@@ -205,4 +221,3 @@ dependencies:
       - uniprot-id-mapper==1.1.4
       - urllib3==2.3.0
       - zstd==1.5.6.5
-prefix: /home/jpuglia/miniconda3/envs/tesisEnv