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update docs readme and add docs_env.yml
docs_env.yml is a conda environment for building the docs locally
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‎docs/README.md‎

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‎docs/docs_env.yml‎

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name: pyopenms_viz_docs_env
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channels:
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- conda-forge
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- bioconda
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- defaults
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dependencies:
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- _libgcc_mutex=0.1=conda_forge
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- _openmp_mutex=4.5=2_gnu
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- anyio=4.8.0=pyhd8ed1ab_0
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- argon2-cffi=23.1.0=pyhd8ed1ab_1
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- argon2-cffi-bindings=21.2.0=py312h66e93f0_5
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- arrow=1.3.0=pyhd8ed1ab_1
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- asttokens=3.0.0=pyhd8ed1ab_1
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- async-lru=2.0.4=pyhd8ed1ab_1
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- bleach=6.2.0=pyh29332c3_4
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- bleach-with-css=6.2.0=h82add2a_4
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- brotli-python=1.1.0=py312h2ec8cdc_2
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- bzip2=1.0.8=h4bc722e_7
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- ca-certificates=2025.1.31=hbcca054_0
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- cached-property=1.5.2=hd8ed1ab_1
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- cached_property=1.5.2=pyha770c72_1
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- cffi=1.17.1=py312h06ac9bb_0
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- comm=0.2.2=pyhd8ed1ab_1
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- debugpy=1.8.13=py312h2ec8cdc_0
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- decorator=5.2.1=pyhd8ed1ab_0
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- defusedxml=0.7.1=pyhd8ed1ab_0
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- exceptiongroup=1.2.2=pyhd8ed1ab_1
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- executing=2.1.0=pyhd8ed1ab_1
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- fqdn=1.5.1=pyhd8ed1ab_1
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- h11=0.14.0=pyhd8ed1ab_1
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- h2=4.2.0=pyhd8ed1ab_0
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- hpack=4.1.0=pyhd8ed1ab_0
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- httpcore=1.0.7=pyh29332c3_1
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- httpx=0.28.1=pyhd8ed1ab_0
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- hyperframe=6.1.0=pyhd8ed1ab_0
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- idna=3.10=pyhd8ed1ab_1
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- importlib-metadata=8.6.1=pyha770c72_0
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- importlib_resources=6.5.2=pyhd8ed1ab_0
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- ipykernel=6.29.5=pyh3099207_0
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- ipython=9.0.0=pyhfb0248b_1
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- ipython_pygments_lexers=1.1.1=pyhd8ed1ab_0
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- isoduration=20.11.0=pyhd8ed1ab_1
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- jedi=0.19.2=pyhd8ed1ab_1
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- json5=0.10.0=pyhd8ed1ab_1
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- jsonpointer=3.0.0=py312h7900ff3_1
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- jsonschema=4.23.0=pyhd8ed1ab_1
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- jsonschema-specifications=2024.10.1=pyhd8ed1ab_1
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- jsonschema-with-format-nongpl=4.23.0=hd8ed1ab_1
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- jupyter-lsp=2.2.5=pyhd8ed1ab_1
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- jupyter_client=8.6.3=pyhd8ed1ab_1
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- jupyter_core=5.7.2=pyh31011fe_1
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- jupyter_events=0.12.0=pyh29332c3_0
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- jupyter_server=2.15.0=pyhd8ed1ab_0
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- jupyter_server_terminals=0.5.3=pyhd8ed1ab_1
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- jupyterlab=4.3.5=pyhd8ed1ab_0
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- jupyterlab_pygments=0.3.0=pyhd8ed1ab_2
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- jupyterlab_server=2.27.3=pyhd8ed1ab_1
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- keyutils=1.6.1=h166bdaf_0
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- krb5=1.21.3=h659f571_0
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- ld_impl_linux-64=2.43=h712a8e2_4
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- libedit=3.1.20250104=pl5321h7949ede_0
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- libexpat=2.6.4=h5888daf_0
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- libffi=3.4.6=h2dba641_0
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- libgcc=14.2.0=h767d61c_2
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- libgcc-ng=14.2.0=h69a702a_2
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- libgomp=14.2.0=h767d61c_2
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- liblzma=5.6.4=hb9d3cd8_0
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- libnsl=2.0.1=hd590300_0
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- libsodium=1.0.20=h4ab18f5_0
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- libsqlite=3.49.1=hee588c1_1
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- libstdcxx=14.2.0=h8f9b012_2
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- libstdcxx-ng=14.2.0=h4852527_2
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- libuuid=2.38.1=h0b41bf4_0
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- libxcrypt=4.4.36=hd590300_1
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- libzlib=1.3.1=hb9d3cd8_2
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- markupsafe=3.0.2=py312h178313f_1
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- matplotlib-inline=0.1.7=pyhd8ed1ab_1
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- nbclient=0.10.2=pyhd8ed1ab_0
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- nbconvert-core=7.16.6=pyh29332c3_0
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- nbformat=5.10.4=pyhd8ed1ab_1
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- ncurses=6.5=h2d0b736_3
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- nest-asyncio=1.6.0=pyhd8ed1ab_1
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- notebook-shim=0.2.4=pyhd8ed1ab_1
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- openssl=3.4.1=h7b32b05_0
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- overrides=7.7.0=pyhd8ed1ab_1
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- pandoc=3.6.3=ha770c72_0
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- parso=0.8.4=pyhd8ed1ab_1
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- pexpect=4.9.0=pyhd8ed1ab_1
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- pickleshare=0.7.5=pyhd8ed1ab_1004
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- pip=25.0.1=pyh8b19718_0
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- pkgutil-resolve-name=1.3.10=pyhd8ed1ab_2
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- platformdirs=4.3.6=pyhd8ed1ab_1
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- prometheus_client=0.21.1=pyhd8ed1ab_0
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- prompt-toolkit=3.0.50=pyha770c72_0
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- psutil=7.0.0=py312h66e93f0_0
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- ptyprocess=0.7.0=pyhd8ed1ab_1
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- pure_eval=0.2.3=pyhd8ed1ab_1
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- pycparser=2.22=pyh29332c3_1
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- pysocks=1.7.1=pyha55dd90_7
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- python=3.12.9=h9e4cc4f_1_cpython
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- python-dateutil=2.9.0.post0=pyhff2d567_1
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- python-fastjsonschema=2.21.1=pyhd8ed1ab_0
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- python-json-logger=2.0.7=pyhd8ed1ab_0
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- python_abi=3.12=5_cp312
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- pyyaml=6.0.2=py312h178313f_2
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- readline=8.2=h8c095d6_2
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- requests=2.32.3=pyhd8ed1ab_1
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- rfc3339-validator=0.1.4=pyhd8ed1ab_1
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- rfc3986-validator=0.1.1=pyh9f0ad1d_0
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- send2trash=1.8.3=pyh0d859eb_1
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- setuptools=75.8.2=pyhff2d567_0
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- sniffio=1.3.1=pyhd8ed1ab_1
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- stack_data=0.6.3=pyhd8ed1ab_1
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- terminado=0.18.1=pyh0d859eb_0
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- tinycss2=1.4.0=pyhd8ed1ab_0
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- tk=8.6.13=noxft_h4845f30_101
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- tomli=2.2.1=pyhd8ed1ab_1
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- tornado=6.4.2=py312h66e93f0_0
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- traitlets=5.14.3=pyhd8ed1ab_1
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- types-python-dateutil=2.9.0.20241206=pyhd8ed1ab_0
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- typing-extensions=4.12.2=hd8ed1ab_1
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- typing_extensions=4.12.2=pyha770c72_1
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- typing_utils=0.1.0=pyhd8ed1ab_1
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- uri-template=1.3.0=pyhd8ed1ab_1
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- wcwidth=0.2.13=pyhd8ed1ab_1
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- webcolors=24.11.1=pyhd8ed1ab_0
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- webencodings=0.5.1=pyhd8ed1ab_3
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- websocket-client=1.8.0=pyhd8ed1ab_1
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- wheel=0.45.1=pyhd8ed1ab_1
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- yaml=0.2.5=h7f98852_2
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- zeromq=4.3.5=h3b0a872_7
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- zipp=3.21.0=pyhd8ed1ab_1
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- zstandard=0.23.0=py312hef9b889_1
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- zstd=1.5.6=ha6fb4c9_0
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- pip:
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- accessible-pygments==0.0.5
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- alabaster==1.0.0
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- alphatims==1.0.8
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- attrs==24.3.0
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- babel==2.16.0
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- beautifulsoup4==4.12.3
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- bokeh==3.6.0
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- cairocffi==1.7.1
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- cairosvg==2.7.1
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- certifi==2024.12.14
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- charset-normalizer==3.4.0
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- click==8.1.8
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- contourpy==1.3.0
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- cssselect2==0.8.0
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- cycler==0.12.1
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- docutils==0.21.2
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- fonttools==4.54.1
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- h5py==3.13.0
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- imagesize==1.4.1
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- iniconfig==2.0.0
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- jinja2==3.1.4
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- kiwisolver==1.4.7
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- llvmlite==0.44.0
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- lxml==5.3.1
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- matplotlib==3.9.2
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- mistune==3.1.0
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- nbconvert==7.16.4
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- nbsphinx==0.9.6
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- numba==0.61.0
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- numpy==1.26.4
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- packaging==24.1
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- pandas==2.1.4
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- pandocfilters==1.5.1
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- pillow==11.0.0
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- plotly==5.24.1
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- pluggy==1.5.0
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- pydata-sphinx-theme==0.16.1
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- pygments==2.18.0
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- pymzml==2.5.11
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- pyopenms==3.3.0
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- pyopenms-viz==1.0.0
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- pyparsing==3.2.0
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- pyteomics==4.7.5
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- pytest==8.3.3
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- pytz==2024.2
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- pyzmq==26.2.0
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- pyzstd==0.16.2
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- rdkit==2024.9.5
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- referencing==0.35.1
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- regex==2024.11.6
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- rpds-py==0.22.3
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- six==1.16.0
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- snowballstemmer==2.2.0
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- soupsieve==2.6
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- sphinx==8.1.3
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- sphinx-copybutton==0.5.2
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- sphinx-gallery==0.18.0
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- sphinxcontrib-applehelp==2.0.0
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- sphinxcontrib-devhelp==2.0.0
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- sphinxcontrib-htmlhelp==2.1.0
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- sphinxcontrib-jsmath==1.0.1
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- sphinxcontrib-qthelp==2.0.0
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- sphinxcontrib-serializinghtml==2.0.0
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- syrupy==4.7.2
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- tenacity==9.0.0
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- tqdm==4.67.1
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- tzdata==2024.2
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- urllib3==2.2.3
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- xyzservices==2024.9.0
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prefix: /home/joshua/mambaforge/envs/test5

‎docs/readme.md‎

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# Documentation
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## Building Docs Locally
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1. Create a new conda environment based on the docs_env.yml file
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`conda env create -f docs_env.yml`
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This environment contains requirements.txt jupyter-lab pandoc, cairo_svg and rdkit
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2. Build docs with sphinx-build
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`sphinx-build -b html ./ ./_build` ensure this is executed in the docs folder

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