From a191e0e114d89dc0922d82ab3702befc3d9e8b31 Mon Sep 17 00:00:00 2001
From: Cameron Mattson <camo@oak.ucdenver.pvt>
Date: Fri, 11 Aug 2023 15:31:18 -0600
Subject: [PATCH 1/3] Updated the environment file and remove an older
 environment

---
 analysis_env.yml | 147 --------------------------
 environment.yml  | 263 ++++-------------------------------------------
 2 files changed, 19 insertions(+), 391 deletions(-)
 delete mode 100644 analysis_env.yml

diff --git a/analysis_env.yml b/analysis_env.yml
deleted file mode 100644
index 2d7be15..0000000
--- a/analysis_env.yml
+++ /dev/null
@@ -1,147 +0,0 @@
-name: base
-channels:
-  - defaults
-dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - anaconda-client=1.11.1=py310h06a4308_0
-  - anaconda-navigator=2.4.0=py310h06a4308_0
-  - anaconda-project=0.11.1=py310h06a4308_0
-  - attrs=22.1.0=py310h06a4308_0
-  - backports=1.1=pyhd3eb1b0_0
-  - backports.functools_lru_cache=1.6.4=pyhd3eb1b0_0
-  - backports.tempfile=1.0=pyhd3eb1b0_1
-  - backports.weakref=1.0.post1=py_1
-  - beautifulsoup4=4.11.1=py310h06a4308_0
-  - boltons=23.0.0=py310h06a4308_0
-  - brotlipy=0.7.0=py310h7f8727e_1002
-  - bzip2=1.0.8=h7b6447c_0
-  - ca-certificates=2023.01.10=h06a4308_0
-  - certifi=2022.12.7=py310h06a4308_0
-  - cffi=1.15.1=py310h5eee18b_3
-  - chardet=4.0.0=py310h06a4308_1003
-  - charset-normalizer=2.0.4=pyhd3eb1b0_0
-  - click=8.0.4=py310h06a4308_0
-  - clyent=1.2.2=py310h06a4308_1
-  - conda=23.3.1=py310h06a4308_0
-  - conda-build=3.23.3=py310h06a4308_0
-  - conda-content-trust=0.1.3=py310h06a4308_0
-  - conda-pack=0.6.0=pyhd3eb1b0_0
-  - conda-package-handling=2.0.2=py310h06a4308_0
-  - conda-package-streaming=0.7.0=py310h06a4308_0
-  - conda-repo-cli=1.0.41=py310h06a4308_0
-  - conda-token=0.4.0=pyhd3eb1b0_0
-  - conda-verify=3.4.2=py_1
-  - cryptography=39.0.1=py310h9ce1e76_0
-  - dbus=1.13.18=hb2f20db_0
-  - defusedxml=0.7.1=pyhd3eb1b0_0
-  - expat=2.4.9=h6a678d5_0
-  - filelock=3.9.0=py310h06a4308_0
-  - fontconfig=2.14.1=h52c9d5c_1
-  - freetype=2.12.1=h4a9f257_0
-  - future=0.18.3=py310h06a4308_0
-  - giflib=5.2.1=h5eee18b_3
-  - glib=2.69.1=he621ea3_2
-  - glob2=0.7=pyhd3eb1b0_0
-  - gst-plugins-base=1.14.1=h6a678d5_1
-  - gstreamer=1.14.1=h5eee18b_1
-  - icu=58.2=he6710b0_3
-  - idna=3.4=py310h06a4308_0
-  - jinja2=3.1.2=py310h06a4308_0
-  - jpeg=9e=h5eee18b_1
-  - jsonpatch=1.32=pyhd3eb1b0_0
-  - jsonpointer=2.1=pyhd3eb1b0_0
-  - jsonschema=4.17.3=py310h06a4308_0
-  - jupyter_core=5.3.0=py310h06a4308_0
-  - krb5=1.19.4=h568e23c_0
-  - lcms2=2.12=h3be6417_0
-  - ld_impl_linux-64=2.38=h1181459_1
-  - lerc=3.0=h295c915_0
-  - libarchive=3.6.2=hab531cd_0
-  - libclang=10.0.1=default_hb85057a_2
-  - libdeflate=1.17=h5eee18b_0
-  - libedit=3.1.20221030=h5eee18b_0
-  - libevent=2.1.12=h8f2d780_0
-  - libffi=3.4.2=h6a678d5_6
-  - libgcc-ng=11.2.0=h1234567_1
-  - libgomp=11.2.0=h1234567_1
-  - liblief=0.12.3=h6a678d5_0
-  - libllvm10=10.0.1=hbcb73fb_5
-  - libpng=1.6.39=h5eee18b_0
-  - libpq=12.9=h16c4e8d_3
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - libtiff=4.5.0=h6a678d5_2
-  - libuuid=1.41.5=h5eee18b_0
-  - libwebp=1.2.4=h11a3e52_1
-  - libwebp-base=1.2.4=h5eee18b_1
-  - libxcb=1.15=h7f8727e_0
-  - libxkbcommon=1.0.1=hfa300c1_0
-  - libxml2=2.9.14=h74e7548_0
-  - libxslt=1.1.35=h4e12654_0
-  - lz4-c=1.9.4=h6a678d5_0
-  - markupsafe=2.1.1=py310h7f8727e_0
-  - navigator-updater=0.3.0=py310h06a4308_0
-  - nbformat=5.7.0=py310h06a4308_0
-  - ncurses=6.4=h6a678d5_0
-  - nspr=4.33=h295c915_0
-  - nss=3.74=h0370c37_0
-  - openssl=1.1.1t=h7f8727e_0
-  - packaging=23.0=py310h06a4308_0
-  - patch=2.7.6=h7b6447c_1001
-  - patchelf=0.17.2=h6a678d5_0
-  - pathlib=1.0.1=pyhd3eb1b0_1
-  - pcre=8.45=h295c915_0
-  - pillow=9.4.0=py310h6a678d5_0
-  - pip=22.3.1=py310h06a4308_0
-  - pkginfo=1.9.6=py310h06a4308_0
-  - platformdirs=2.5.2=py310h06a4308_0
-  - pluggy=1.0.0=py310h06a4308_1
-  - ply=3.11=py310h06a4308_0
-  - psutil=5.9.0=py310h5eee18b_0
-  - py-lief=0.12.3=py310h6a678d5_0
-  - pycosat=0.6.4=py310h5eee18b_0
-  - pycparser=2.21=pyhd3eb1b0_0
-  - pyjwt=2.4.0=py310h06a4308_0
-  - pyopenssl=23.0.0=py310h06a4308_0
-  - pyqt=5.15.7=py310h6a678d5_1
-  - pyrsistent=0.18.0=py310h7f8727e_0
-  - pysocks=1.7.1=py310h06a4308_0
-  - python=3.10.9=h7a1cb2a_1
-  - python-dateutil=2.8.2=pyhd3eb1b0_0
-  - python-fastjsonschema=2.16.2=py310h06a4308_0
-  - python-libarchive-c=2.9=pyhd3eb1b0_1
-  - pytz=2022.7=py310h06a4308_0
-  - pyyaml=6.0=py310h5eee18b_1
-  - qt-main=5.15.2=h327a75a_7
-  - qt-webengine=5.15.9=hd2b0992_4
-  - qtpy=2.2.0=py310h06a4308_0
-  - qtwebkit=5.212=h4eab89a_4
-  - readline=8.2=h5eee18b_0
-  - requests=2.28.1=py310h06a4308_1
-  - ripgrep=13.0.0=hbdeaff8_0
-  - ruamel.yaml=0.17.21=py310h5eee18b_0
-  - ruamel.yaml.clib=0.2.6=py310h5eee18b_1
-  - ruamel_yaml=0.17.21=py310h5eee18b_0
-  - setuptools=65.6.3=py310h06a4308_0
-  - sip=6.6.2=py310h6a678d5_0
-  - six=1.16.0=pyhd3eb1b0_1
-  - soupsieve=2.4=py310h06a4308_0
-  - sqlite=3.41.1=h5eee18b_0
-  - tk=8.6.12=h1ccaba5_0
-  - toml=0.10.2=pyhd3eb1b0_0
-  - toolz=0.12.0=py310h06a4308_0
-  - tornado=6.2=py310h5eee18b_0
-  - tqdm=4.65.0=py310h2f386ee_0
-  - traitlets=5.7.1=py310h06a4308_0
-  - tzdata=2023c=h04d1e81_0
-  - ujson=5.4.0=py310h6a678d5_0
-  - urllib3=1.26.15=py310h06a4308_0
-  - wheel=0.38.4=py310h06a4308_0
-  - xz=5.2.10=h5eee18b_1
-  - yaml=0.2.5=h7b6447c_0
-  - zlib=1.2.13=h5eee18b_0
-  - zstandard=0.19.0=py310h5eee18b_0
-  - zstd=1.5.4=hc292b87_0
-  - pip:
-      - pyqt5-sip==12.11.0
-prefix: /home/camo/anaconda3
diff --git a/environment.yml b/environment.yml
index a45d6dd..fcb1b2e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -1,247 +1,22 @@
 name: nf1_analysis
 channels:
-  - defaults
+  - conda-forge
 dependencies:
-  - _libgcc_mutex=0.1=main
-  - _openmp_mutex=5.1=1_gnu
-  - _sysroot_linux-64_curr_repodata_hack=3=haa98f57_10
-  - binutils_impl_linux-64=2.38=h2a08ee3_1
-  - binutils_linux-64=2.38.0=hc2dff05_0
-  - ca-certificates=2023.01.10=h06a4308_0
-  - certifi=2022.12.7=py39h06a4308_0
-  - gcc_impl_linux-64=11.2.0=h1234567_1
-  - gcc_linux-64=11.2.0=h5c386dc_0
-  - gxx_impl_linux-64=11.2.0=h1234567_1
-  - gxx_linux-64=11.2.0=hc2dff05_0
-  - kernel-headers_linux-64=3.10.0=h57e8cba_10
-  - ld_impl_linux-64=2.38=h1181459_1
-  - libffi=3.4.2=h6a678d5_6
-  - libgcc-devel_linux-64=11.2.0=h1234567_1
-  - libgcc-ng=11.2.0=h1234567_1
-  - libgomp=11.2.0=h1234567_1
-  - libstdcxx-devel_linux-64=11.2.0=h1234567_1
-  - libstdcxx-ng=11.2.0=h1234567_1
-  - ncurses=6.4=h6a678d5_0
-  - openssl=1.1.1t=h7f8727e_0
-  - pcre=8.45=h295c915_0
-  - pip=23.0.1=py39h06a4308_0
-  - python=3.9.16=h7a1cb2a_2
-  - readline=8.2=h5eee18b_0
-  - setuptools=65.6.3=py39h06a4308_0
-  - sqlite=3.41.1=h5eee18b_0
-  - swig=4.0.2=h295c915_4
-  - sysroot_linux-64=2.17=h57e8cba_10
-  - tk=8.6.12=h1ccaba5_0
-  - wheel=0.38.4=py39h06a4308_0
-  - xz=5.2.10=h5eee18b_1
-  - zlib=1.2.13=h5eee18b_0
-  - pip:
-      - aiofiles==22.1.0
-      - aiosqlite==0.18.0
-      - anyio==3.6.2
-      - argon2-cffi==21.3.0
-      - argon2-cffi-bindings==21.2.0
-      - arrow==1.2.3
-      - astroid==2.15.2
-      - asttokens==2.2.1
-      - attrs==22.2.0
-      - auto-sklearn==0.15.0
-      - autopep8==2.0.2
-      - babel==2.12.1
-      - backcall==0.2.0
-      - beautifulsoup4==4.12.2
-      - bleach==6.0.0
-      - blinker==1.6.2
-      - cffi==1.15.1
-      - cfgv==3.3.1
-      - charset-normalizer==3.1.0
-      - click==8.1.3
-      - cloudpickle==2.2.1
-      - comm==0.1.3
-      - configspace==0.4.21
-      - contourpy==1.0.7
-      - cycler==0.11.0
-      - cython==0.29.34
-      - dash==2.9.3
-      - dash-core-components==2.0.0
-      - dash-cytoscape==0.3.0
-      - dash-html-components==2.0.0
-      - dash-table==5.0.0
-      - dask==2023.3.2
-      - debugpy==1.6.7
-      - decorator==5.1.1
-      - defusedxml==0.7.1
-      - dill==0.3.6
-      - distlib==0.3.6
-      - distributed==2023.3.2.1
-      - distro==1.8.0
-      - docstring-to-markdown==0.12
-      - emcee==3.1.4
-      - executing==1.2.0
-      - fastjsonschema==2.16.3
-      - fastkde==1.0.24
-      - filelock==3.12.0
-      - flake8==6.0.0
-      - flask==2.3.2
-      - fonttools==4.39.3
-      - fqdn==1.5.1
-      - fsspec==2023.4.0
-      - gevent==22.10.2
-      - greenlet==2.0.2
-      - heapdict==1.0.1
-      - identify==2.5.24
-      - idna==3.4
-      - imageio==2.28.1
-      - importlib-metadata==6.1.0
-      - importlib-resources==5.12.0
-      - interpret==0.3.2
-      - interpret-core==0.3.2
-      - ipykernel==6.22.0
-      - ipython==8.12.0
-      - ipython-genutils==0.2.0
-      - isoduration==20.11.0
-      - isort==5.12.0
-      - itsdangerous==2.1.2
-      - jedi==0.18.2
-      - jinja2==3.1.2
-      - joblib==1.2.0
-      - json5==0.9.11
-      - jsonpointer==2.3
-      - jsonschema==4.17.3
-      - jupyter-client==8.1.0
-      - jupyter-core==5.3.0
-      - jupyter-events==0.6.3
-      - jupyter-lsp==2.0.1
-      - jupyter-server==2.5.0
-      - jupyter-server-fileid==0.8.0
-      - jupyter-server-terminals==0.4.4
-      - jupyter-server-ydoc==0.8.0
-      - jupyter-ydoc==0.2.3
-      - jupyterlab==3.6.3
-      - jupyterlab-lsp==4.0.1
-      - jupyterlab-pygments==0.2.2
-      - jupyterlab-server==2.22.0
-      - kiwisolver==1.4.4
-      - lazy-loader==0.2
-      - lazy-object-proxy==1.9.0
-      - liac-arff==2.5.0
-      - lime==0.2.0.1
-      - llvmlite==0.39.1
-      - locket==1.0.0
-      - markupsafe==2.1.2
-      - matplotlib==3.7.1
-      - matplotlib-inline==0.1.6
-      - mccabe==0.7.0
-      - mistune==2.0.5
-      - msgpack==1.0.5
-      - multiprocess==0.70.14
-      - nbclassic==0.5.5
-      - nbclient==0.7.3
-      - nbconvert==7.3.0
-      - nbformat==5.8.0
-      - nest-asyncio==1.5.6
-      - networkx==3.1
-      - nodeenv==1.8.0
-      - notebook==6.5.4
-      - notebook-shim==0.2.2
-      - numba==0.56.4
-      - numpy==1.23.0
-      - packaging==23.0
-      - pandas==2.0.0
-      - pandocfilters==1.5.0
-      - parso==0.8.3
-      - partd==1.4.0
-      - patsy==0.5.3
-      - pexpect==4.8.0
-      - pickleshare==0.7.5
-      - pillow==9.5.0
-      - platformdirs==3.2.0
-      - plotly==5.14.1
-      - pluggy==1.0.0
-      - pre-commit==3.3.1
-      - prometheus-client==0.16.0
-      - prompt-toolkit==3.0.38
-      - psutil==5.9.4
-      - ptyprocess==0.7.0
-      - pure-eval==0.2.2
-      - pyarrow==11.0.0
-      - pycodestyle==2.10.0
-      - pycparser==2.21
-      - pydocstyle==6.3.0
-      - pyflakes==3.0.1
-      - pygments==2.14.0
-      - pylint==2.17.2
-      - pynisher==0.6.4
-      - pynndescent==0.5.8
-      - pyparsing==3.0.9
-      - pyrfr==0.8.3
-      - pyrsistent==0.19.3
-      - python-dateutil==2.8.2
-      - python-dotenv==1.0.0
-      - python-json-logger==2.0.7
-      - python-lsp-jsonrpc==1.0.0
-      - python-lsp-server==1.7.2
-      - pytoolconfig==1.2.5
-      - pytz==2023.3
-      - pywavelets==1.4.1
-      - pyyaml==6.0
-      - pyzmq==25.0.2
-      - requests==2.28.2
-      - rfc3339-validator==0.1.4
-      - rfc3986-validator==0.1.1
-      - rope==1.7.0
-      - salib==1.4.7
-      - scikit-image==0.20.0
-      - scikit-learn==0.24.2
-      - scikit-posthocs==0.7.0
-      - scipy==1.9.1
-      - seaborn==0.12.2
-      - send2trash==1.8.0
-      - shap==0.41.0
-      - six==1.16.0
-      - skope-rules==1.0.1
-      - slicer==0.0.7
-      - smac==1.2
-      - sniffio==1.3.0
-      - snowballstemmer==2.2.0
-      - sortedcontainers==2.4.0
-      - soupsieve==2.4
-      - stack-data==0.6.2
-      - statsmodels==0.13.5
-      - tblib==1.7.0
-      - tenacity==8.2.2
-      - terminado==0.17.1
-      - threadpoolctl==3.1.0
-      - tifffile==2023.4.12
-      - tinycss2==1.2.1
-      - toml==0.10.2
-      - tomli==2.0.1
-      - tomlkit==0.11.7
-      - toolz==0.12.0
-      - tornado==6.2
-      - tqdm==4.65.0
-      - traitlets==5.9.0
-      - treeinterpreter==0.2.3
-      - typing-extensions==4.5.0
-      - tzdata==2023.3
-      - ujson==5.7.0
-      - umap-learn==0.5.3
-      - uri-template==1.2.0
-      - urllib3==1.26.15
-      - virtualenv==20.23.0
-      - wcwidth==0.2.6
-      - webcolors==1.13
-      - webencodings==0.5.1
-      - websocket-client==1.5.1
-      - werkzeug==2.3.4
-      - whatthepatch==1.0.4
-      - wrapt==1.15.0
-      - xgboost==1.7.5
-      - y-py==0.5.9
-      - yapf==0.32.0
-      - ypy-websocket==0.8.2
-      - zict==2.2.0
-      - zipp==3.15.0
-      - zope-event==4.6
-      - zope-interface==6.0
-prefix: /home/camo/anaconda3/envs/nf1_analysis
+  - conda-forge::python=3.9
+  - umap-learn
+  - scikit-posthocs
+  - pandas
+  - numpy
+  - matplotlib
+  - scipy
+  - pathlib2
+  - scikit-learn
+  - requests
+  - seaborn
+  - pip
+  # R packages:
+  - r-base=4.2.2
+  - r-tidyr
+  - r-dplyr
+  - r-readr
+  - r-ggplot2

From a32e327ad32f558dd6066ea54e091d9eabf414d5 Mon Sep 17 00:00:00 2001
From: Cameron Mattson <camo@oak.ucdenver.pvt>
Date: Fri, 18 Aug 2023 17:50:01 -0600
Subject: [PATCH 2/3] Updated the conda environment from pr suggestions

---
 environment.yml | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/environment.yml b/environment.yml
index fcb1b2e..314164a 100644
--- a/environment.yml
+++ b/environment.yml
@@ -14,9 +14,7 @@ dependencies:
   - requests
   - seaborn
   - pip
+  - ipython
+  - notebook
   # R packages:
-  - r-base=4.2.2
-  - r-tidyr
-  - r-dplyr
-  - r-readr
-  - r-ggplot2
+  - r-essentials

From 737bbc0c370090ae53a945a015c513a316bdf136 Mon Sep 17 00:00:00 2001
From: Cameron Mattson <camo@oak.ucdenver.pvt>
Date: Fri, 18 Aug 2023 17:52:30 -0600
Subject: [PATCH 3/3] Updated pandas dependency

---
 environment.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/environment.yml b/environment.yml
index 314164a..e063e58 100644
--- a/environment.yml
+++ b/environment.yml
@@ -5,7 +5,7 @@ dependencies:
   - conda-forge::python=3.9
   - umap-learn
   - scikit-posthocs
-  - pandas
+  - pandas<2.0
   - numpy
   - matplotlib
   - scipy