From 6d8bdb2918118870d74340a9333da5688960a8c7 Mon Sep 17 00:00:00 2001 From: Nitya Thakkar Date: Wed, 13 Sep 2023 09:29:12 -0700 Subject: [PATCH] reran notebook --- examples/evodiff.ipynb | 506 +---------------------------------------- 1 file changed, 8 insertions(+), 498 deletions(-) diff --git a/examples/evodiff.ipynb b/examples/evodiff.ipynb index 5bc8fbb..b13af6a 100644 --- a/examples/evodiff.ipynb +++ b/examples/evodiff.ipynb @@ -25,249 +25,13 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" } }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting evodiff\n", - " Obtaining dependency information for evodiff from https://files.pythonhosted.org/packages/40/1c/84e652ed9c83cbd9d826d03c8d1c80990f72ae790d3de119ab13d1885e6c/evodiff-1.1.0-py3-none-any.whl.metadata\n", - " Downloading evodiff-1.1.0-py3-none-any.whl.metadata (23 kB)\n", - "Collecting pandas (from evodiff)\n", - 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"Successfully installed Flask-2.3.3 GridDataFormats-1.0.1 Jinja2-3.1.2 Mako-1.2.4 MarkupSafe-2.1.3 Werkzeug-2.3.7 alembic-1.12.0 biopython-1.81 biotite-0.38.0 blinker-1.6.2 blosum-2.0.2 certifi-2023.7.22 charset-normalizer-3.2.0 click-8.1.7 cloudpickle-2.2.1 contourpy-1.1.0 cycler-0.11.0 databricks-cli-0.17.7 docker-6.1.3 entrypoints-0.4 evodiff-1.1.0 fair-esm-2.0.0 fasteners-0.18 fonttools-4.42.1 gitdb-4.0.10 gitpython-3.1.36 greenlet-2.0.2 gsd-3.1.1 gunicorn-21.2.0 idna-3.4 importlib-resources-6.0.1 itsdangerous-2.1.2 joblib-1.3.2 kiwisolver-1.4.5 lmdb-1.4.1 markdown-3.4.4 matplotlib-3.7.3 mdanalysis-2.4.3 mlflow-2.7.0 mmtf-python-1.1.3 mrcfile-1.4.3 msgpack-1.0.5 networkx-3.1 numpy-1.24.4 oauthlib-3.2.2 pandas-2.0.3 pdb-tools-2.5.0 pillow-10.0.0 protobuf-4.24.3 pyarrow-13.0.0 pyjwt-2.8.0 pyparsing-3.1.1 pytz-2023.3.post1 pyyaml-6.0.1 querystring-parser-1.2.4 requests-2.31.0 scikit-learn-1.3.0 scipy-1.10.1 seaborn-0.12.2 sequence-models-1.7.0 smmap-5.0.0 sqlalchemy-2.0.20 sqlparse-0.4.4 tabulate-0.9.0 threadpoolctl-3.2.0 tqdm-4.66.1 tzdata-2023.3 urllib3-1.26.16 websocket-client-1.6.3\n" - ] - } - ], + "outputs": [], "source": [ "import sys\n", "!{sys.executable} -m pip install evodiff" @@ -286,145 +50,13 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" } }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting package metadata (current_repodata.json): done\n", - "Solving environment: failed with initial frozen solve. Retrying with flexible solve.\n", - "Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.\n", - "Collecting package metadata (repodata.json): done\n", - "Solving environment: done\n", - "\n", - "\n", - "==> WARNING: A newer version of conda exists. <==\n", - " current version: 22.9.0\n", - " latest version: 23.7.4\n", - "\n", - "Please update conda by running\n", - "\n", - " $ conda update -n base -c defaults conda\n", - "\n", - "\n", - "\n", - "## Package Plan ##\n", - "\n", - " environment location: /Users/nityathakkar/opt/anaconda3/envs/evodiff\n", - "\n", - " added / updated specs:\n", - " - cpuonly\n", - " - pytorch\n", - " - torchaudio\n", - " - torchvision\n", - "\n", - "\n", - "The following packages will be downloaded:\n", - "\n", - " package | build\n", - " ---------------------------|-----------------\n", - " cryptography-41.0.3 | py38ha2381d6_0 1.2 MB\n", - " icu-73.1 | hcec6c5f_0 25.1 MB\n", - " libtiff-4.5.1 | hcec6c5f_0 508 KB\n", - " libxml2-2.10.4 | h1bd7e62_1 665 KB\n", - " ------------------------------------------------------------\n", - " Total: 27.4 MB\n", - "\n", - "The following NEW packages will be INSTALLED:\n", - "\n", - " blas pkgs/main/osx-64::blas-1.0-mkl None\n", - " brotlipy pkgs/main/osx-64::brotlipy-0.7.0-py38h9ed2024_1003 None\n", - " bzip2 pkgs/main/osx-64::bzip2-1.0.8-h1de35cc_0 None\n", - " certifi pkgs/main/osx-64::certifi-2023.7.22-py38hecd8cb5_0 None\n", - " cffi pkgs/main/osx-64::cffi-1.15.1-py38hc55c11b_0 None\n", - " charset-normalizer pkgs/main/noarch::charset-normalizer-2.0.4-pyhd3eb1b0_0 None\n", - " cpuonly pytorch/noarch::cpuonly-2.0-0 None\n", - " cryptography pkgs/main/osx-64::cryptography-41.0.3-py38ha2381d6_0 None\n", - " ffmpeg pytorch/osx-64::ffmpeg-4.3-h0a44026_0 None\n", - " filelock pkgs/main/osx-64::filelock-3.9.0-py38hecd8cb5_0 None\n", - " freetype pkgs/main/osx-64::freetype-2.12.1-hd8bbffd_0 None\n", - " gettext pkgs/main/osx-64::gettext-0.21.0-he85b6c0_1 None\n", - " giflib pkgs/main/osx-64::giflib-5.2.1-h6c40b1e_3 None\n", - " gmp pkgs/main/osx-64::gmp-6.2.1-he9d5cce_3 None\n", - " gmpy2 pkgs/main/osx-64::gmpy2-2.1.2-py38hd5de756_0 None\n", - " gnutls pkgs/main/osx-64::gnutls-3.6.15-hed9c0bf_0 None\n", - " icu pkgs/main/osx-64::icu-73.1-hcec6c5f_0 None\n", - " idna pkgs/main/osx-64::idna-3.4-py38hecd8cb5_0 None\n", - " intel-openmp pkgs/main/osx-64::intel-openmp-2023.1.0-ha357a0b_43547 None\n", - " jinja2 pkgs/main/osx-64::jinja2-3.1.2-py38hecd8cb5_0 None\n", - " jpeg pkgs/main/osx-64::jpeg-9e-h6c40b1e_1 None\n", - " lame pkgs/main/osx-64::lame-3.100-h1de35cc_0 None\n", - " lcms2 pkgs/main/osx-64::lcms2-2.12-hf1fd2bf_0 None\n", - " lerc pkgs/main/osx-64::lerc-3.0-he9d5cce_0 None\n", - " libdeflate pkgs/main/osx-64::libdeflate-1.17-hb664fd8_0 None\n", - " libiconv pkgs/main/osx-64::libiconv-1.16-hca72f7f_2 None\n", - " libidn2 pkgs/main/osx-64::libidn2-2.3.4-h6c40b1e_0 None\n", - " libpng pkgs/main/osx-64::libpng-1.6.39-h6c40b1e_0 None\n", - " libtasn1 pkgs/main/osx-64::libtasn1-4.19.0-h6c40b1e_0 None\n", - " libtiff pkgs/main/osx-64::libtiff-4.5.1-hcec6c5f_0 None\n", - " libunistring pkgs/main/osx-64::libunistring-0.9.10-h9ed2024_0 None\n", - " libwebp pkgs/main/osx-64::libwebp-1.2.4-hf6ce154_1 None\n", - " libwebp-base pkgs/main/osx-64::libwebp-base-1.2.4-h6c40b1e_1 None\n", - " libxml2 pkgs/main/osx-64::libxml2-2.10.4-h1bd7e62_1 None\n", - " llvm-openmp pkgs/main/osx-64::llvm-openmp-14.0.6-h0dcd299_0 None\n", - " lz4-c pkgs/main/osx-64::lz4-c-1.9.4-hcec6c5f_0 None\n", - " markupsafe pkgs/main/osx-64::markupsafe-2.1.1-py38hca72f7f_0 None\n", - " mkl pkgs/main/osx-64::mkl-2023.1.0-h8e150cf_43559 None\n", - " mkl-service pkgs/main/osx-64::mkl-service-2.4.0-py38h6c40b1e_1 None\n", - " mkl_fft pkgs/main/osx-64::mkl_fft-1.3.6-py38h07fba90_1 None\n", - " mkl_random pkgs/main/osx-64::mkl_random-1.2.2-py38h07fba90_1 None\n", - " mpc pkgs/main/osx-64::mpc-1.1.0-h6ef4df4_1 None\n", - " mpfr pkgs/main/osx-64::mpfr-4.0.2-h9066e36_1 None\n", - " mpmath pkgs/main/osx-64::mpmath-1.3.0-py38hecd8cb5_0 None\n", - " nettle pkgs/main/osx-64::nettle-3.7.3-h230ac6f_1 None\n", - " networkx pkgs/main/osx-64::networkx-3.1-py38hecd8cb5_0 None\n", - " numpy pkgs/main/osx-64::numpy-1.23.5-py38h47b59a4_1 None\n", - " numpy-base pkgs/main/osx-64::numpy-base-1.23.5-py38hcfaf2c3_1 None\n", - " openh264 pkgs/main/osx-64::openh264-2.1.1-h8346a28_0 None\n", - " pillow pkgs/main/osx-64::pillow-9.4.0-py38hcec6c5f_0 None\n", - " pycparser pkgs/main/noarch::pycparser-2.21-pyhd3eb1b0_0 None\n", - " pyopenssl pkgs/main/osx-64::pyopenssl-23.2.0-py38hecd8cb5_0 None\n", - " pysocks pkgs/main/osx-64::pysocks-1.7.1-py38_1 None\n", - " pytorch pytorch/osx-64::pytorch-2.0.1-py3.8_0 None\n", - " pytorch-mutex pytorch/noarch::pytorch-mutex-1.0-cpu None\n", - " requests pkgs/main/osx-64::requests-2.31.0-py38hecd8cb5_0 None\n", - " sympy pkgs/main/osx-64::sympy-1.11.1-py38hecd8cb5_0 None\n", - " tbb pkgs/main/osx-64::tbb-2021.8.0-ha357a0b_0 None\n", - " torchaudio pytorch/osx-64::torchaudio-2.0.2-py38_cpu None\n", - " torchvision pytorch/osx-64::torchvision-0.15.2-py38_cpu None\n", - " urllib3 pkgs/main/osx-64::urllib3-1.26.16-py38hecd8cb5_0 None\n", - " zstd pkgs/main/osx-64::zstd-1.5.5-hc035e20_0 None\n", - "\n", - "The following packages will be UPDATED:\n", - "\n", - " ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 None\n", - "\n", - "The following packages will be SUPERSEDED by a higher-priority channel:\n", - "\n", - " openssl conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-1.1.1w-hca72f7f_0 None\n", - "\n", - "\n", - "\n", - "Downloading and Extracting Packages\n", - "libxml2-2.10.4 | 665 KB | ##################################### | 100% \n", - "cryptography-41.0.3 | 1.2 MB | ##################################### | 100% \n", - "libtiff-4.5.1 | 508 KB | ##################################### | 100% \n", - "icu-73.1 | 25.1 MB | ##################################### | 100% \n", - "Preparing transaction: done\n", - "Verifying transaction: done\n", - "Executing transaction: done\n", - "Retrieving notices: ...working... done\n", - "\n", - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], + "outputs": [], "source": [ "conda install pytorch torchvision torchaudio cpuonly -c pytorch" ] @@ -442,148 +74,26 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" } }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting package metadata (current_repodata.json): done\n", - "Solving environment: done\n", - "\n", - "\n", - "==> WARNING: A newer version of conda exists. <==\n", - " current version: 22.9.0\n", - " latest version: 23.7.4\n", - "\n", - "Please update conda by running\n", - "\n", - " $ conda update -n base -c defaults conda\n", - "\n", - "\n", - "\n", - "## Package Plan ##\n", - "\n", - " environment location: /Users/nityathakkar/opt/anaconda3/envs/evodiff\n", - "\n", - " added / updated specs:\n", - " - pyg\n", - "\n", - "\n", - "The following NEW packages will be INSTALLED:\n", - "\n", - " appdirs pkgs/main/noarch::appdirs-1.4.4-pyhd3eb1b0_0 None\n", - " joblib pkgs/main/osx-64::joblib-1.2.0-py38hecd8cb5_0 None\n", - " libgfortran pkgs/main/osx-64::libgfortran-5.0.0-11_3_0_hecd8cb5_28 None\n", - " libgfortran5 pkgs/main/osx-64::libgfortran5-11.3.0-h9dfd629_28 None\n", - " pooch pkgs/main/noarch::pooch-1.4.0-pyhd3eb1b0_0 None\n", - " pyg pyg/osx-64::pyg-2.3.1-py38_torch_2.0.0_cpu None\n", - " pyparsing pkgs/main/osx-64::pyparsing-3.0.9-py38hecd8cb5_0 None\n", - " scikit-learn pkgs/main/osx-64::scikit-learn-1.2.2-py38hcec6c5f_0 None\n", - " scipy pkgs/main/osx-64::scipy-1.10.1-py38hf241641_1 None\n", - " threadpoolctl pkgs/main/noarch::threadpoolctl-2.2.0-pyh0d69192_0 None\n", - " tqdm pkgs/main/osx-64::tqdm-4.65.0-py38h01d92e1_0 None\n", - "\n", - "The following packages will be UPDATED:\n", - "\n", - " ca-certificates conda-forge::ca-certificates-2023.7.2~ --> pkgs/main::ca-certificates-2023.08.22-hecd8cb5_0 None\n", - "\n", - "The following packages will be SUPERSEDED by a higher-priority channel:\n", - "\n", - " certifi conda-forge/noarch::certifi-2023.7.22~ --> pkgs/main/osx-64::certifi-2023.7.22-py38hecd8cb5_0 None\n", - " openssl conda-forge::openssl-1.1.1w-h8a1eda9_0 --> pkgs/main::openssl-1.1.1w-hca72f7f_0 None\n", - "\n", - "\n", - "Preparing transaction: done\n", - "Verifying transaction: done\n", - "Executing transaction: | \n", - "\n", - " Installed package of scikit-learn can be accelerated using scikit-learn-intelex.\n", - " More details are available here: https://intel.github.io/scikit-learn-intelex\n", - "\n", - " For example:\n", - "\n", - " $ conda install scikit-learn-intelex\n", - " $ python -m sklearnex my_application.py\n", - "\n", - " \n", - "\n", - "done\n", - "Retrieving notices: ...working... done\n", - "\n", - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], + "outputs": [], "source": [ "conda install pyg -c pyg" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": { "pycharm": { "name": "#%%\n" } }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Collecting package metadata (current_repodata.json): \\ WARNING conda.models.version:get_matcher(542): Using .* with relational operator is superfluous and deprecated and will be removed in a future version of conda. Your spec was 1.7.1.*, but conda is ignoring the .* and treating it as 1.7.1\n", - "done\n", - "Solving environment: done\n", - "\n", - "\n", - "==> WARNING: A newer version of conda exists. <==\n", - " current version: 22.9.0\n", - " latest version: 23.7.4\n", - "\n", - "Please update conda by running\n", - "\n", - " $ conda update -n base -c defaults conda\n", - "\n", - "\n", - "\n", - "## Package Plan ##\n", - "\n", - " environment location: /Users/nityathakkar/opt/anaconda3/envs/evodiff\n", - "\n", - " added / updated specs:\n", - " - torch-scatter\n", - "\n", - "\n", - "The following NEW packages will be INSTALLED:\n", - "\n", - " libprotobuf pkgs/main/osx-64::libprotobuf-3.20.3-hfff2838_0 None\n", - " libuv conda-forge/osx-64::libuv-1.46.0-h0c2f820_0 None\n", - " ninja conda-forge/osx-64::ninja-1.11.1-hb8565cd_0 None\n", - " torch-scatter conda-forge/osx-64::torch-scatter-2.1.1-py38hf47b5ae_1 None\n", - "\n", - "The following packages will be SUPERSEDED by a higher-priority channel:\n", - "\n", - " ca-certificates pkgs/main::ca-certificates-2023.08.22~ --> conda-forge::ca-certificates-2023.7.22-h8857fd0_0 None\n", - " certifi pkgs/main/osx-64::certifi-2023.7.22-p~ --> conda-forge/noarch::certifi-2023.7.22-pyhd8ed1ab_0 None\n", - " openssl pkgs/main::openssl-1.1.1w-hca72f7f_0 --> conda-forge::openssl-1.1.1w-h8a1eda9_0 None\n", - " pytorch pytorch::pytorch-2.0.1-py3.8_0 --> pkgs/main::pytorch-2.0.1-cpu_py38h77673e4_0 None\n", - "\n", - "\n", - "Preparing transaction: done\n", - "Verifying transaction: done\n", - "Executing transaction: done\n", - "Retrieving notices: ...working... done\n", - "\n", - "Note: you may need to restart the kernel to use updated packages.\n" - ] - } - ], + "outputs": [], "source": [ "conda install -c conda-forge torch-scatter" ]