Add packages to Anaconda module¶
Sometimes it is necessary to add packages to the default anaconda install, or update to a newer version.
Check the loaded module:
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!module list
!module list
Currently Loaded Modulefiles: 1) anaconda3/2020.07-gcc-8.4.1 3) proj/8.1.0-gcc-8.4.1 2) geos/3.9.1-gcc-8.4.1 >
Check the default packages in anaconda:
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!conda list
!conda list
# packages in environment at /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex: # # Name Version Build Channel _ipyw_jlab_nb_ext_conf 0.1.0 py38_0 _libgcc_mutex 0.1 main alabaster 0.7.12 py_0 anaconda 2020.07 py38_0 anaconda-client 1.7.2 py38_0 anaconda-navigator 1.9.12 py38_0 anaconda-project 0.8.4 py_0 argh 0.26.2 py38_0 asn1crypto 1.3.0 py38_0 astroid 2.4.2 py38_0 astropy 4.0.1.post1 py38h7b6447c_1 atomicwrites 1.4.0 py_0 attrs 19.3.0 py_0 autopep8 1.5.3 py_0 babel 2.8.0 py_0 backcall 0.2.0 py_0 backports 1.0 py_2 backports.functools_lru_cache 1.6.1 py_0 backports.shutil_get_terminal_size 1.0.0 py38_2 backports.tempfile 1.0 py_1 backports.weakref 1.0.post1 py_1 beautifulsoup4 4.9.1 py38_0 bitarray 1.4.0 py38h7b6447c_0 bkcharts 0.2 py38_0 blas 1.0 mkl bleach 3.1.5 py_0 blosc 1.19.0 hd408876_0 bokeh 2.1.1 py38_0 boto 2.49.0 py38_0 bottleneck 1.3.2 py38heb32a55_1 brotlipy 0.7.0 py38h7b6447c_1000 bzip2 1.0.8 h7b6447c_0 ca-certificates 2020.6.24 0 cairo 1.14.12 h8948797_3 certifi 2020.6.20 py38_0 cffi 1.14.0 py38he30daa8_1 chardet 3.0.4 py38_1003 click 7.1.2 py_0 cloudpickle 1.5.0 py_0 clyent 1.2.2 py38_1 colorama 0.4.3 py_0 conda 4.8.3 py38_0 conda-build 3.18.11 py38_0 conda-env 2.6.0 1 conda-package-handling 1.6.1 py38h7b6447c_0 conda-verify 3.4.2 py_1 contextlib2 0.6.0.post1 py_0 cryptography 2.9.2 py38h1ba5d50_0 curl 7.71.1 hbc83047_1 cycler 0.10.0 py38_0 cython 0.29.21 py38he6710b0_0 cytoolz 0.10.1 py38h7b6447c_0 dask 2.20.0 py_0 dask-core 2.20.0 py_0 dbus 1.13.16 hb2f20db_0 decorator 4.4.2 py_0 defusedxml 0.6.0 py_0 diff-match-patch 20200713 py_0 distributed 2.20.0 py38_0 docutils 0.16 py38_1 entrypoints 0.3 py38_0 et_xmlfile 1.0.1 py_1001 expat 2.2.9 he6710b0_2 fastcache 1.1.0 py38h7b6447c_0 filelock 3.0.12 py_0 flake8 3.8.3 py_0 flask 1.1.2 py_0 fontconfig 2.13.0 h9420a91_0 freetype 2.10.2 h5ab3b9f_0 fribidi 1.0.9 h7b6447c_0 fsspec 0.7.4 py_0 future 0.18.2 py38_1 get_terminal_size 1.0.0 haa9412d_0 gevent 20.6.2 py38h7b6447c_0 glib 2.65.0 h3eb4bd4_0 glob2 0.7 py_0 gmp 6.1.2 h6c8ec71_1 gmpy2 2.0.8 py38hd5f6e3b_3 graphite2 1.3.14 h23475e2_0 greenlet 0.4.16 py38h7b6447c_0 gst-plugins-base 1.14.0 hbbd80ab_1 gstreamer 1.14.0 hb31296c_0 h5py 2.10.0 py38h7918eee_0 harfbuzz 2.4.0 hca77d97_1 hdf5 1.10.4 hb1b8bf9_0 heapdict 1.0.1 py_0 html5lib 1.1 py_0 icu 58.2 he6710b0_3 idna 2.10 py_0 imageio 2.9.0 py_0 imagesize 1.2.0 py_0 importlib-metadata 1.7.0 py38_0 importlib_metadata 1.7.0 0 intel-openmp 2020.1 217 intervaltree 3.0.2 py_1 ipykernel 5.3.2 py38h5ca1d4c_0 ipython 7.16.1 py38h5ca1d4c_0 ipython_genutils 0.2.0 py38_0 ipywidgets 7.5.1 py_0 isort 4.3.21 py38_0 itsdangerous 1.1.0 py_0 jbig 2.1 hdba287a_0 jdcal 1.4.1 py_0 jedi 0.17.1 py38_0 jeepney 0.4.3 py_0 jinja2 2.11.2 py_0 joblib 0.16.0 py_0 jpeg 9b h024ee3a_2 json5 0.9.5 py_0 jsonschema 3.2.0 py38_0 jupyter 1.0.0 py38_7 jupyter_client 6.1.6 py_0 jupyter_console 6.1.0 py_0 jupyter_core 4.6.3 py38_0 jupyterlab 2.1.5 py_0 jupyterlab_server 1.2.0 py_0 keyring 21.2.1 py38_0 kiwisolver 1.2.0 py38hfd86e86_0 krb5 1.18.2 h173b8e3_0 lazy-object-proxy 1.4.3 py38h7b6447c_0 lcms2 2.11 h396b838_0 ld_impl_linux-64 2.33.1 h53a641e_7 libarchive 3.4.2 h62408e4_0 libcurl 7.71.1 h20c2e04_1 libedit 3.1.20191231 h14c3975_1 libffi 3.3 he6710b0_2 libgcc-ng 9.1.0 hdf63c60_0 libgfortran-ng 7.3.0 hdf63c60_0 liblief 0.10.1 he6710b0_0 libllvm9 9.0.1 h4a3c616_1 libpng 1.6.37 hbc83047_0 libsodium 1.0.18 h7b6447c_0 libspatialindex 1.9.3 he6710b0_0 libssh2 1.9.0 h1ba5d50_1 libstdcxx-ng 9.1.0 hdf63c60_0 libtiff 4.1.0 h2733197_1 libtool 2.4.6 h7b6447c_5 libuuid 1.0.3 h1bed415_2 libxcb 1.14 h7b6447c_0 libxml2 2.9.10 he19cac6_1 libxslt 1.1.34 hc22bd24_0 llvmlite 0.33.0 py38hc6ec683_1 locket 0.2.0 py38_1 lxml 4.5.2 py38hefd8a0e_0 lz4-c 1.9.2 he6710b0_0 lzo 2.10 h7b6447c_2 markupsafe 1.1.1 py38h7b6447c_0 matplotlib 3.2.2 0 matplotlib-base 3.2.2 py38hef1b27d_0 mccabe 0.6.1 py38_1 mistune 0.8.4 py38h7b6447c_1000 mkl 2020.1 217 mkl-service 2.3.0 py38he904b0f_0 mkl_fft 1.1.0 py38h23d657b_0 mkl_random 1.1.1 py38h0573a6f_0 mock 4.0.2 py_0 more-itertools 8.4.0 py_0 mpc 1.1.0 h10f8cd9_1 mpfr 4.0.2 hb69a4c5_1 mpmath 1.1.0 py38_0 msgpack-python 1.0.0 py38hfd86e86_1 multipledispatch 0.6.0 py38_0 navigator-updater 0.2.1 py38_0 nbconvert 5.6.1 py38_0 nbformat 5.0.7 py_0 ncurses 6.2 he6710b0_1 networkx 2.4 py_1 nltk 3.5 py_0 nose 1.3.7 py38_2 notebook 6.0.3 py38_0 numba 0.50.1 py38h0573a6f_1 numexpr 2.7.1 py38h423224d_0 numpy 1.18.5 py38ha1c710e_0 numpy-base 1.18.5 py38hde5b4d6_0 numpydoc 1.1.0 py_0 olefile 0.46 py_0 openpyxl 3.0.4 py_0 openssl 1.1.1g h7b6447c_0 packaging 20.4 py_0 pandas 1.0.5 py38h0573a6f_0 pandoc 2.10 0 pandocfilters 1.4.2 py38_1 pango 1.45.3 hd140c19_0 parso 0.7.0 py_0 partd 1.1.0 py_0 patchelf 0.11 he6710b0_0 path 13.1.0 py38_0 path.py 12.4.0 0 pathlib2 2.3.5 py38_0 pathtools 0.1.2 py_1 patsy 0.5.1 py38_0 pcre 8.44 he6710b0_0 pep8 1.7.1 py38_0 pexpect 4.8.0 py38_0 pickleshare 0.7.5 py38_1000 pillow 7.2.0 py38hb39fc2d_0 pip 20.1.1 py38_1 pixman 0.40.0 h7b6447c_0 pkginfo 1.5.0.1 py38_0 pluggy 0.13.1 py38_0 ply 3.11 py38_0 prometheus_client 0.8.0 py_0 prompt-toolkit 3.0.5 py_0 prompt_toolkit 3.0.5 0 psutil 5.7.0 py38h7b6447c_0 ptyprocess 0.6.0 py38_0 py 1.9.0 py_0 py-lief 0.10.1 py38h403a769_0 pycodestyle 2.6.0 py_0 pycosat 0.6.3 py38h7b6447c_1 pycparser 2.20 py_2 pycurl 7.43.0.5 py38h1ba5d50_0 pydocstyle 5.0.2 py_0 pyflakes 2.2.0 py_0 pygments 2.6.1 py_0 pylint 2.5.3 py38_0 pyodbc 4.0.30 py38he6710b0_0 pyopenssl 19.1.0 py_1 pyparsing 2.4.7 py_0 pyqt 5.9.2 py38h05f1152_4 pyrsistent 0.16.0 py38h7b6447c_0 pysocks 1.7.1 py38_0 pytables 3.6.1 py38h9fd0a39_0 pytest 5.4.3 py38_0 python 3.8.3 hcff3b4d_2 python-dateutil 2.8.1 py_0 python-jsonrpc-server 0.3.4 py_1 python-language-server 0.34.1 py38_0 python-libarchive-c 2.9 py_0 pytz 2020.1 py_0 pywavelets 1.1.1 py38h7b6447c_0 pyxdg 0.26 py_0 pyyaml 5.3.1 py38h7b6447c_1 pyzmq 19.0.1 py38he6710b0_1 qdarkstyle 2.8.1 py_0 qt 5.9.7 h5867ecd_1 qtawesome 0.7.2 py_0 qtconsole 4.7.5 py_0 qtpy 1.9.0 py_0 readline 8.0 h7b6447c_0 regex 2020.6.8 py38h7b6447c_0 requests 2.24.0 py_0 ripgrep 11.0.2 he32d670_0 rope 0.17.0 py_0 rtree 0.9.4 py38_1 ruamel_yaml 0.15.87 py38h7b6447c_1 scikit-image 0.16.2 py38h0573a6f_0 scikit-learn 0.23.1 py38h423224d_0 scipy 1.5.0 py38h0b6359f_0 seaborn 0.10.1 py_0 secretstorage 3.1.2 py38_0 send2trash 1.5.0 py38_0 setuptools 49.2.0 py38_0 simplegeneric 0.8.1 py38_2 singledispatch 3.4.0.3 py38_0 sip 4.19.13 py38he6710b0_0 six 1.15.0 py_0 snappy 1.1.8 he6710b0_0 snowballstemmer 2.0.0 py_0 sortedcollections 1.2.1 py_0 sortedcontainers 2.2.2 py_0 soupsieve 2.0.1 py_0 sphinx 3.1.2 py_0 sphinxcontrib 1.0 py38_1 sphinxcontrib-applehelp 1.0.2 py_0 sphinxcontrib-devhelp 1.0.2 py_0 sphinxcontrib-htmlhelp 1.0.3 py_0 sphinxcontrib-jsmath 1.0.1 py_0 sphinxcontrib-qthelp 1.0.3 py_0 sphinxcontrib-serializinghtml 1.1.4 py_0 sphinxcontrib-websupport 1.2.3 py_0 spyder 4.1.4 py38_0 spyder-kernels 1.9.2 py38_0 sqlalchemy 1.3.18 py38h7b6447c_0 sqlite 3.32.3 h62c20be_0 statsmodels 0.11.1 py38h7b6447c_0 sympy 1.6.1 py38_0 tbb 2020.0 hfd86e86_0 tblib 1.6.0 py_0 terminado 0.8.3 py38_0 testpath 0.4.4 py_0 threadpoolctl 2.1.0 pyh5ca1d4c_0 tk 8.6.10 hbc83047_0 toml 0.10.1 py_0 toolz 0.10.0 py_0 tornado 6.0.4 py38h7b6447c_1 tqdm 4.47.0 py_0 traitlets 4.3.3 py38_0 typing_extensions 3.7.4.2 py_0 ujson 1.35 py38h7b6447c_0 unicodecsv 0.14.1 py38_0 unixodbc 2.3.7 h14c3975_0 urllib3 1.25.9 py_0 watchdog 0.10.3 py38_0 wcwidth 0.2.5 py_0 webencodings 0.5.1 py38_1 werkzeug 1.0.1 py_0 wheel 0.34.2 py38_0 widgetsnbextension 3.5.1 py38_0 wrapt 1.11.2 py38h7b6447c_0 wurlitzer 2.0.1 py38_0 xlrd 1.2.0 py_0 xlsxwriter 1.2.9 py_0 xlwt 1.3.0 py38_0 xmltodict 0.12.0 py_0 xz 5.2.5 h7b6447c_0 yaml 0.2.5 h7b6447c_0 yapf 0.30.0 py_0 zeromq 4.3.2 he6710b0_2 zict 2.0.0 py_0 zipp 3.1.0 py_0 zlib 1.2.11 h7b6447c_3 zope 1.0 py38_1 zope.event 4.4 py38_0 zope.interface 4.7.1 py38h7b6447c_0 zstd 1.4.5 h0b5b093_0
Add a new package¶
It is easily possible to add packages to a module installed anaconda distribution. These additional pacakges are stored in your $HOME/.local directory.
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# Check what version you are using?
import sys
print(sys.version)
# Check what version you are using?
import sys
print(sys.version)
3.8.3 (default, Jul 2 2020, 16:21:59) [GCC 7.3.0]
Based on that version you might already have a directory in your local directory. Within these directories your manually installed packages will be stored. These are default paths, and your python interpreter will always look there.
Special Note: If you want to ignore these user directories use export PYTHONNOUSERSITE=True
This variable must be set manually. Default is to use user directories.
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!ls $HOME/.local/lib
!ls $HOME/.local/lib
python3.7 python3.8
Now let's install the package metpy doc
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# Note that using --user might not be necessary for you, but it's a good reminder.
!pip install --user metpy
# Note that using --user might not be necessary for you, but it's a good reminder.
!pip install --user metpy
Collecting metpy
Downloading MetPy-1.1.0-py3-none-any.whl (361 kB)
|████████████████████████████████| 361 kB 14.9 MB/s eta 0:00:01
Collecting pint>=0.10.1
Downloading Pint-0.17-py2.py3-none-any.whl (204 kB)
|████████████████████████████████| 204 kB 81.4 MB/s eta 0:00:01
Requirement already satisfied: matplotlib>=3.0.1 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from metpy) (3.2.2)
Requirement already satisfied: pyproj>=2.3.0 in /home/spack/.local/lib/python3.8/site-packages (from metpy) (3.2.1)
Collecting importlib-resources>=1.3.0; python_version < "3.9"
Downloading importlib_resources-5.2.2-py3-none-any.whl (27 kB)
Collecting pooch>=0.1
Downloading pooch-1.5.2-py3-none-any.whl (57 kB)
|████████████████████████████████| 57 kB 15.4 MB/s eta 0:00:01
Collecting xarray>=0.14.1
Using cached xarray-0.19.0-py3-none-any.whl (827 kB)
Requirement already satisfied: traitlets>=4.3.0 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from metpy) (4.3.3)
Requirement already satisfied: scipy>=1.2.0 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from metpy) (1.5.0)
Requirement already satisfied: numpy>=1.17.0 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from metpy) (1.18.5)
Requirement already satisfied: pandas>=0.24.0 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from metpy) (1.0.5)
Requirement already satisfied: packaging in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from pint>=0.10.1->metpy) (20.4)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from matplotlib>=3.0.1->metpy) (2.4.7)
Requirement already satisfied: python-dateutil>=2.1 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from matplotlib>=3.0.1->metpy) (2.8.1)
Requirement already satisfied: cycler>=0.10 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from matplotlib>=3.0.1->metpy) (0.10.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from matplotlib>=3.0.1->metpy) (1.2.0)
Requirement already satisfied: certifi in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from pyproj>=2.3.0->metpy) (2020.6.20)
Requirement already satisfied: zipp>=3.1.0; python_version < "3.10" in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from importlib-resources>=1.3.0; python_version < "3.9"->metpy) (3.1.0)
Collecting appdirs
Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Requirement already satisfied: requests in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from pooch>=0.1->metpy) (2.24.0)
Requirement already satisfied: setuptools>=40.4 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from xarray>=0.14.1->metpy) (49.2.0.post20200714)
Requirement already satisfied: six in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from traitlets>=4.3.0->metpy) (1.15.0)
Requirement already satisfied: ipython-genutils in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from traitlets>=4.3.0->metpy) (0.2.0)
Requirement already satisfied: decorator in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from traitlets>=4.3.0->metpy) (4.4.2)
Requirement already satisfied: pytz>=2017.2 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from pandas>=0.24.0->metpy) (2020.1)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from requests->pooch>=0.1->metpy) (1.25.9)
Requirement already satisfied: idna<3,>=2.5 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from requests->pooch>=0.1->metpy) (2.10)
Requirement already satisfied: chardet<4,>=3.0.2 in /home/swd/spack/opt/spack/linux-rhel8-skylake_avx512/gcc-8.4.1/anaconda3-2020.07-4onhdcbnvyvwfdxxbelrplxjihjsknex/lib/python3.8/site-packages (from requests->pooch>=0.1->metpy) (3.0.4)
Installing collected packages: pint, importlib-resources, appdirs, pooch, xarray, metpy
Successfully installed appdirs-1.4.4 importlib-resources-5.2.2 metpy-1.1.0 pint-0.17 pooch-1.5.2 xarray-0.19.0
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# check if metpy is installed?
!pip list | grep -i metpy
# check if metpy is installed?
!pip list | grep -i metpy
MetPy 1.1.0
Note: conda won't show the packages as listed
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import metpy
import metpy
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# this shows where the python module is installed, in your .local directory.
metpy.__file__
# this shows where the python module is installed, in your .local directory.
metpy.__file__
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'/home/spack/.local/lib/python3.8/site-packages/metpy/__init__.py'
Last update:
March 13, 2023
Created: March 8, 2023
Created: March 8, 2023