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kalininalab / DataSAIL

DataSAIL is a tool to split datasets while reducing information leakage.
https://datasail.readthedocs.io
MIT License
18 stars 1 forks source link

MAC M1 issue to install DataSAIL #12

Closed EasternCaveMan closed 7 months ago

EasternCaveMan commented 8 months ago

Hi Roman, I did following step to install DataSAIL on mac m1, 1- conda create -n sail python=3.10 2- conda activate sail 3- conda install -c conda-forge mamba 4- mamba install -c kalininalab -c conda-forge -c mosek -c bioconda datasail then I got this error:

(sail) vahidatabaigi@vahids-MacBook-Pro ~ % mamba install -c kalininalab -c conda-forge -c bioconda datasail

Looking for: ['datasail']

kalininalab/osx-arm64 (check zst)                   Checked  0.3s
kalininalab/noarch (check zst)                      Checked  0.2s
bioconda/osx-arm64 (check zst)                      Checked  0.2s
bioconda/noarch (check zst)                         Checked  0.2s
pkgs/main/osx-arm64 (check zst)                    Checked  0.1s
pkgs/main/noarch (check zst)                       Checked  0.0s
pkgs/r/osx-arm64 (check zst)                       Checked  0.0s
pkgs/r/noarch (check zst)                          Checked  0.0s
bioconda/osx-arm64                                 124.0 B @   1.3kB/s  0.1s
kalininalab/osx-arm64                                1.4kB @   3.9kB/s  0.4s
kalininalab/noarch                                 116.0 B @ 227.0 B/s  0.5s
pkgs/r/osx-arm64                                   108.0 B @ 102.0 B/s  0.5s
pkgs/main/noarch                                   702.3kB @ 182.0kB/s  3.5s
pkgs/r/noarch                                        2.1MB @ 183.6kB/s 11.1s
pkgs/main/osx-arm64                                  2.1MB @ 152.1kB/s 12.6s
bioconda/noarch                                      5.1MB @ 230.8kB/s 18.3s
conda-forge/osx-arm64                                8.3MB @ 279.6kB/s 29.6s
conda-forge/noarch                                  13.3MB @ 376.9kB/s 35.3s

Pinned packages:
  - python 3.10.*

Could not solve for environment specs
The following package could not be installed
└─ datasail is not installable because it requires
   └─ cd-hit, which does not exist (perhaps a missing channel).

then I tried to install cd-hit directly from bioconda/conda-forge channels in none of them was available for mac m1. I alos tried with pip, wasnt available

(sail) vahidatabaigi@vahids-MacBook-Pro ~ % conda install bioconda::cd-hit
Channels:
 - bioconda
 - defaults
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - bioconda::cd-hit

Current channels:

  - https://conda.anaconda.org/bioconda
  - defaults
  - https://conda.anaconda.org/conda-forge
  - https://conda.anaconda.org/bioconda

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

(sail) vahidatabaigi@vahids-MacBook-Pro ~ % pip install cd-hit
ERROR: Could not find a version that satisfies the requirement cd-hit (from versions: none)
ERROR: No matching distribution found for cd-hit

However, I have installed cd-hit through brew as recomended in cd-hit github https://github.com/weizhongli/cdhit However it seems that datasil still can not recognised 

(sail) vahidatabaigi@vahids-MacBook-Pro ~ % brew install cd-hit
==> Downloading https://formulae.brew.sh/api/formula.jws.json
##################################################################################################################################################################################################### 100.0%
==> Downloading https://formulae.brew.sh/api/cask.jws.json
##################################################################################################################################################################################################### 100.0%
Warning: brewsci/bio/cd-hit 4.8.1_1 is already installed and up-to-date.
To reinstall 4.8.1_1, run:
  brew reinstall cd-hit
(sail) vahidatabaigi@vahids-MacBook-Pro ~ % mamba install -c kalininalab -c conda-forge -c bioconda datasail

Looking for: ['datasail']

conda-forge/osx-arm64                                       Using cache
conda-forge/noarch                                          Using cache
bioconda/noarch                                             Using cache
pkgs/main/noarch                                              No change
pkgs/main/osx-arm64                                           No change
pkgs/r/noarch                                                 No change
bioconda/osx-arm64                                            No change
pkgs/r/osx-arm64                                              No change
kalininalab/osx-arm64                                         No change
kalininalab/noarch                                            No change

Pinned packages:
  - python 3.10.*

Could not solve for environment specs
The following package could not be installed
└─ datasail is not installable because it requires
   └─ cd-hit, which does not exist (perhaps a missing channel).

I am sure that I installed cd-hit successfully, becuase i did clustering with it. Best, Vahid

EasternCaveMan commented 8 months ago

Hi Roman, I added one more step , I installed DataSAIL but there is an error when I call it in CLI. 1- conda create -n sail python=3.10 2- conda activate sail 3- conda install -c conda-forge mamba 4- conda config --env --set subdir osx-64 5- mamba install -c kalininalab -c conda-forge -c mosek -c bioconda datasail

(base) vahidatabaigi@vahids-MBP ~ % conda create -n sail python=3.10
Channels:
 - bioconda
 - defaults
 - conda-forge
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/vahidatabaigi/anaconda3/envs/sail

  added / updated specs:
    - python=3.10

The following NEW packages will be INSTALLED:

  bzip2              pkgs/main/osx-arm64::bzip2-1.0.8-h620ffc9_4
  ca-certificates    pkgs/main/osx-arm64::ca-certificates-2023.12.12-hca03da5_0
  libffi             pkgs/main/osx-arm64::libffi-3.4.4-hca03da5_0
  ncurses            pkgs/main/osx-arm64::ncurses-6.4-h313beb8_0
  openssl            pkgs/main/osx-arm64::openssl-3.0.12-h1a28f6b_0
  pip                pkgs/main/osx-arm64::pip-23.3.1-py310hca03da5_0
  python             pkgs/main/osx-arm64::python-3.10.13-hb885b13_0
  readline           pkgs/main/osx-arm64::readline-8.2-h1a28f6b_0
  setuptools         pkgs/main/osx-arm64::setuptools-68.2.2-py310hca03da5_0
  sqlite             pkgs/main/osx-arm64::sqlite-3.41.2-h80987f9_0
  tk                 pkgs/main/osx-arm64::tk-8.6.12-hb8d0fd4_0
  tzdata             pkgs/main/noarch::tzdata-2023d-h04d1e81_0
  wheel              pkgs/main/osx-arm64::wheel-0.41.2-py310hca03da5_0
  xz                 pkgs/main/osx-arm64::xz-5.4.5-h80987f9_0
  zlib               pkgs/main/osx-arm64::zlib-1.2.13-h5a0b063_0

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate sail
#
# To deactivate an active environment, use
#
#     $ conda deactivate
(base) vahidatabaigi@vahids-MBP ~ % conda activate sail
(sail) vahidatabaigi@vahids-MBP ~ % conda install -c conda-forge mamba
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /Users/vahidatabaigi/anaconda3/envs/sail

  added / updated specs:
    - mamba

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    c-ares-1.26.0              |       h93a5062_0         142 KB  conda-forge
    ------------------------------------------------------------
                                           Total:         142 KB

The following NEW packages will be INSTALLED:

  archspec           conda-forge/noarch::archspec-0.2.2-pyhd8ed1ab_0
  boltons            conda-forge/noarch::boltons-23.1.1-pyhd8ed1ab_0
  brotli-python      conda-forge/osx-arm64::brotli-python-1.1.0-py310h1253130_1
  c-ares             conda-forge/osx-arm64::c-ares-1.26.0-h93a5062_0
  certifi            conda-forge/noarch::certifi-2023.11.17-pyhd8ed1ab_0
  cffi               conda-forge/osx-arm64::cffi-1.16.0-py310hdcd7c05_0
  charset-normalizer conda-forge/noarch::charset-normalizer-3.3.2-pyhd8ed1ab_0
  colorama           conda-forge/noarch::colorama-0.4.6-pyhd8ed1ab_0
  conda              conda-forge/osx-arm64::conda-23.11.0-py310hbe9552e_1
  conda-libmamba-so~ conda-forge/noarch::conda-libmamba-solver-23.12.0-pyhd8ed1ab_0
  conda-package-han~ conda-forge/noarch::conda-package-handling-2.2.0-pyh38be061_0
  conda-package-str~ conda-forge/noarch::conda-package-streaming-0.9.0-pyhd8ed1ab_0
  distro             conda-forge/noarch::distro-1.9.0-pyhd8ed1ab_0
  fmt                conda-forge/osx-arm64::fmt-10.2.1-h2ffa867_0
  icu                conda-forge/osx-arm64::icu-73.2-hc8870d7_0
  idna               conda-forge/noarch::idna-3.6-pyhd8ed1ab_0
  jsonpatch          conda-forge/noarch::jsonpatch-1.33-pyhd8ed1ab_0
  jsonpointer        conda-forge/osx-arm64::jsonpointer-2.4-py310hbe9552e_3
  krb5               conda-forge/osx-arm64::krb5-1.21.2-h92f50d5_0
  libarchive         conda-forge/osx-arm64::libarchive-3.7.2-hcacb583_1
  libcurl            conda-forge/osx-arm64::libcurl-8.5.0-h2d989ff_0
  libcxx             conda-forge/osx-arm64::libcxx-16.0.6-h4653b0c_0
  libedit            conda-forge/osx-arm64::libedit-3.1.20191231-hc8eb9b7_2
  libev              conda-forge/osx-arm64::libev-4.33-h93a5062_2
  libiconv           conda-forge/osx-arm64::libiconv-1.17-h0d3ecfb_2
  libmamba           conda-forge/osx-arm64::libmamba-1.5.6-h90c426b_0
  libmambapy         conda-forge/osx-arm64::libmambapy-1.5.6-py310h5e0a2f6_0
  libnghttp2         conda-forge/osx-arm64::libnghttp2-1.58.0-ha4dd798_1
  libsolv            conda-forge/osx-arm64::libsolv-0.7.27-h9e231a4_0
  libsqlite          conda-forge/osx-arm64::libsqlite-3.44.2-h091b4b1_0
  libssh2            conda-forge/osx-arm64::libssh2-1.11.0-h7a5bd25_0
  libxml2            conda-forge/osx-arm64::libxml2-2.12.4-h0d0cfa8_1
  libzlib            conda-forge/osx-arm64::libzlib-1.2.13-h53f4e23_5
  lz4-c              conda-forge/osx-arm64::lz4-c-1.9.4-hb7217d7_0
  lzo                conda-forge/osx-arm64::lzo-2.10-h642e427_1000
  mamba              conda-forge/osx-arm64::mamba-1.5.6-py310ha5d4528_0
  menuinst           conda-forge/osx-arm64::menuinst-2.0.2-py310hbe9552e_0
  packaging          conda-forge/noarch::packaging-23.2-pyhd8ed1ab_0
  platformdirs       conda-forge/noarch::platformdirs-4.1.0-pyhd8ed1ab_0
  pluggy             conda-forge/noarch::pluggy-1.4.0-pyhd8ed1ab_0
  pybind11-abi       conda-forge/noarch::pybind11-abi-4-hd8ed1ab_3
  pycosat            conda-forge/osx-arm64::pycosat-0.6.6-py310h2aa6e3c_0
  pycparser          conda-forge/noarch::pycparser-2.21-pyhd8ed1ab_0
  pysocks            conda-forge/noarch::pysocks-1.7.1-pyha2e5f31_6
  python_abi         conda-forge/osx-arm64::python_abi-3.10-4_cp310
  reproc             conda-forge/osx-arm64::reproc-14.2.4.post0-h93a5062_1
  reproc-cpp         conda-forge/osx-arm64::reproc-cpp-14.2.4.post0-h965bd2d_1
  requests           conda-forge/noarch::requests-2.31.0-pyhd8ed1ab_0
  ruamel.yaml        conda-forge/osx-arm64::ruamel.yaml-0.18.5-py310hd125d64_0
  ruamel.yaml.clib   conda-forge/osx-arm64::ruamel.yaml.clib-0.2.7-py310h2aa6e3c_2
  tqdm               conda-forge/noarch::tqdm-4.66.1-pyhd8ed1ab_0
  truststore         conda-forge/noarch::truststore-0.8.0-pyhd8ed1ab_0
  urllib3            conda-forge/noarch::urllib3-2.1.0-pyhd8ed1ab_0
  yaml-cpp           conda-forge/osx-arm64::yaml-cpp-0.8.0-h13dd4ca_0
  zstandard          conda-forge/osx-arm64::zstandard-0.22.0-py310h6289e41_0
  zstd               conda-forge/osx-arm64::zstd-1.5.5-h4f39d0f_0

The following packages will be UPDATED:

  openssl              pkgs/main::openssl-3.0.12-h1a28f6b_0 --> conda-forge::openssl-3.2.0-h0d3ecfb_1
  python               pkgs/main::python-3.10.13-hb885b13_0 --> conda-forge::python-3.10.13-h2469fbe_1_cpython
  tk                        pkgs/main::tk-8.6.12-hb8d0fd4_0 --> conda-forge::tk-8.6.13-h5083fa2_1
  zlib                    pkgs/main::zlib-1.2.13-h5a0b063_0 --> conda-forge::zlib-1.2.13-h53f4e23_5

Proceed ([y]/n)? y

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(sail) vahidatabaigi@vahids-MBP ~ % conda config --env --set subdir osx-64
(sail) vahidatabaigi@vahids-MBP ~ % mamba install -c kalininalab -c conda-forge -c mosek -c bioconda datasail

Looking for: ['datasail']

kalininalab/osx-64 (check zst)                      Checked  0.3s
kalininalab/noarch (check zst)                      Checked  0.2s
mosek/osx-64 (check zst)                            Checked  0.2s
mosek/noarch (check zst)                            Checked  0.6s
bioconda/osx-64 (check zst)                         Checked  0.4s
bioconda/noarch (check zst)                         Checked  0.2s
pkgs/main/osx-64 (check zst)                       Checked  0.1s
pkgs/main/noarch (check zst)                       Checked  0.0s
pkgs/r/osx-64 (check zst)                          Checked  0.0s
pkgs/r/noarch (check zst)                          Checked  0.0s
kalininalab/noarch                                 116.0 B @ 410.0 B/s  0.3s
kalininalab/osx-64                                   2.4kB @   5.9kB/s  0.5s
conda-forge/noarch                                  13.3MB @  24.1MB/s  0.6s
pkgs/main/noarch                                   702.3kB @   1.3MB/s  0.2s
mosek/osx-64                                        39.0kB @  64.5kB/s  0.6s
pkgs/r/osx-64                                      694.3kB @   1.1MB/s  0.1s
mosek/noarch                                       116.0 B @ 180.0 B/s  0.2s
pkgs/r/noarch                                        2.1MB @   2.3MB/s  0.4s
pkgs/main/osx-64                                     5.5MB @   5.5MB/s  0.4s
conda-forge/osx-64                                  28.5MB @  28.1MB/s  1.0s
bioconda/osx-64                                      4.4MB @   2.7MB/s  1.0s
bioconda/noarch                                      5.1MB @   2.8MB/s  1.2s

Pinned packages:
  - python 3.10.*

Transaction

  Prefix: /Users/vahidatabaigi/anaconda3/envs/sail

  Updating specs:

   - datasail
   - ca-certificates
   - certifi
   - openssl

  Package                           Version  Build               Channel          Size
────────────────────────────────────────────────────────────────────────────────────────
  Install:
────────────────────────────────────────────────────────────────────────────────────────

  + networkx                          3.2.1  pyhd8ed1ab_0        conda-forge       1MB
  + toml                             0.10.2  pyhd8ed1ab_0        conda-forge      18kB
  + makefun                          1.15.2  pyhd8ed1ab_0        conda-forge      26kB
  + exceptiongroup                    1.2.0  pyhd8ed1ab_2        conda-forge      21kB
  + iniconfig                         2.0.0  pyhd8ed1ab_0        conda-forge      11kB
  + tomli                             2.0.1  pyhd8ed1ab_0        conda-forge      16kB
  + joblib                            1.3.2  pyhd8ed1ab_0        conda-forge     221kB
  + threadpoolctl                     3.2.0  pyha21a80b_0        conda-forge      21kB
  + python-tzdata                    2023.4  pyhd8ed1ab_0        conda-forge     146kB
  + pytz                       2023.3.post1  pyhd8ed1ab_0        conda-forge     187kB
  + cycler                           0.12.1  pyhd8ed1ab_0        conda-forge      13kB
  + pyparsing                         3.1.1  pyhd8ed1ab_0        conda-forge      90kB
  + munkres                           1.1.4  pyh9f0ad1d_0        conda-forge      12kB
  + six                              1.16.0  pyh6c4a22f_0        conda-forge      14kB
  + font-ttf-dejavu-sans-mono          2.37  hab24e00_0          conda-forge     397kB
  + font-ttf-inconsolata              3.000  h77eed37_0          conda-forge      97kB
  + font-ttf-source-code-pro          2.038  h77eed37_0          conda-forge     701kB
  + font-ttf-ubuntu                    0.83  h77eed37_1          conda-forge       2MB
  + typing_extensions                 4.9.0  pyha770c72_0        conda-forge      36kB
  + decopatch                        1.4.10  pyhd8ed1ab_0        conda-forge      19kB
  + pytest                            7.4.4  pyhd8ed1ab_0        conda-forge     245kB
  + python-dateutil                   2.8.2  pyhd8ed1ab_0        conda-forge     246kB
  + fonts-conda-forge                     1  0                   conda-forge       4kB
  + typing-extensions                 4.9.0  hd8ed1ab_0          conda-forge      10kB
  + pytest-cases                      3.8.2  pyhd8ed1ab_0        conda-forge      87kB
  + fonts-conda-ecosystem                 1  0                   conda-forge       4kB
  + cppad                        20210000.6  he49afe7_0          conda-forge     445kB
  + gmp                               6.3.0  h93d8f39_0          conda-forge     521kB
  + tbb                              2020.2  h940c156_4          conda-forge     136kB
  + metis                             5.1.0  he965462_1007       conda-forge       4MB
  + unixodbc                         2.3.12  he8a5cf4_0          conda-forge     259kB
  + llvm-openmp                      17.0.6  hb6ac08f_0          conda-forge     300kB
  + gettext                          0.21.1  h8a4c099_0          conda-forge       4MB
  + perl                             5.32.1  7_h10d778d_perl5    conda-forge      12MB
  + capnproto                         0.9.1  hd991315_4          conda-forge       4MB
  + yaml                              0.2.5  h0d85af4_2          conda-forge      84kB
  + libjpeg-turbo                     3.0.0  h0dc2134_1          conda-forge     580kB
  + lerc                              4.0.0  hb486fe8_0          conda-forge     290kB
  + libdeflate                         1.19  ha4e1b8e_0          conda-forge      69kB
  + libwebp-base                      1.3.2  h0dc2134_0          conda-forge     347kB
  + libpng                           1.6.39  ha978bb4_0          conda-forge     272kB
  + kiwisolver                        1.4.5  py310h88cfcbd_1     conda-forge      60kB
  + tornado                           6.3.3  py310h6729b98_1     conda-forge     643kB
  + xorg-libxau                      1.0.11  h0dc2134_0          conda-forge      13kB
  + unicodedata2                     15.1.0  py310h6729b98_0     conda-forge     367kB
  + libexpat                          2.5.0  hf0c8a7f_1          conda-forge      70kB
  + clarabel                          0.6.0  py310h1c65b78_1     conda-forge     407kB
  + pixman                           0.43.0  h73e2aa4_0          conda-forge     326kB
  + mumps-include                     5.2.1  h694c41f_14         conda-forge      25kB
  + greenlet                          3.0.3  py310h5daac23_0     conda-forge     200kB
  + chardet                           5.2.0  py310h2ec42d9_1     conda-forge     246kB
  + pcre2                             10.42  h0ad2156_0          conda-forge     900kB
  + libqdldl                          0.1.7  hf0c8a7f_0          conda-forge      18kB
  + libboost                         1.82.0  h99d8d82_6          conda-forge       2MB
  + pthread-stubs                       0.4  hc929b4f_1001       conda-forge       6kB
  + xorg-libxdmcp                     1.1.3  h35c211d_0          conda-forge      17kB
  + libunistring                     0.9.10  h0d85af4_0          conda-forge       1MB
  + brotli                            1.0.9  he49afe7_4          conda-forge     436kB
  + scotch                            6.0.9  h3da7401_2          conda-forge       1MB
  + coverage                          7.4.1  py310hb372a2b_0     conda-forge     288kB
  + aria2                            1.37.0  hd891fde_1          conda-forge       1MB
  + mpfr                              4.2.1  h0c69b56_0          conda-forge     377kB
  + glpk                                5.0  h3cb5acd_0          conda-forge       1MB
  + libgfortran5                     13.2.0  h2873a65_2          conda-forge       2MB
  + pyyaml                            6.0.1  py310h6729b98_1     conda-forge     160kB
  + libtiff                           4.6.0  h684deea_2          conda-forge     267kB
  + freetype                         2.12.1  h60636b9_2          conda-forge     599kB
  + expat                             2.5.0  hf0c8a7f_1          conda-forge     120kB
  + sqlalchemy                       2.0.25  py310hb372a2b_0     conda-forge       3MB
  + libglib                          2.78.3  h198397b_0          conda-forge       2MB
  + libxcb                             1.15  hb7f2c08_0          conda-forge     314kB
  + libidn2                           2.3.7  h10d778d_0          conda-forge     133kB
  + fonttools                        4.47.2  py310hb372a2b_0     conda-forge       2MB
  + gawk                              5.3.0  h2c496e9_0          conda-forge       1MB
  + libgfortran                       5.0.0  13_2_0_h97931a8_2   conda-forge     110kB
  + openjpeg                          2.5.0  ha4da562_3          conda-forge     336kB
  + lcms2                              2.16  ha2f27b4_0          conda-forge     224kB
  + fontconfig                       2.14.2  h5bb23bf_0          conda-forge     237kB
  + wget                             1.20.3  hd3787cc_1          conda-forge     831kB
  + fftw                             3.3.10  nompi_h4fa670e_108  conda-forge       2MB
  + ampl-mp                           3.1.0  h2beb688_1006       conda-forge       1MB
  + libopenblas                      0.3.26  openmp_hfef2a42_0   conda-forge       6MB
  + pillow                           10.2.0  py310he65384d_0     conda-forge      41MB
  + cairo                            1.18.0  h99e66fa_0          conda-forge     885kB
  + libblas                           3.9.0  21_osx64_openblas   conda-forge      15kB
  + pycairo                          1.25.1  py310h9878b33_0     conda-forge     103kB
  + libcblas                          3.9.0  21_osx64_openblas   conda-forge      15kB
  + liblapack                         3.9.0  21_osx64_openblas   conda-forge      15kB
  + gsl                                 2.7  h93259b0_0          conda-forge       3MB
  + dsdp                                5.8  h6e329d1_1203       conda-forge     226kB
  + mumps-seq                         5.2.1  hea8e22a_11         conda-forge       3MB
  + suitesparse                      5.10.1  h68a9093_0          conda-forge       3MB
  + numpy                            1.26.3  py310h4bfa8fc_0     conda-forge       6MB
  + ipopt                            3.14.1  hc501a57_0          conda-forge     948kB
  + cvxopt                            1.3.2  py310ha550498_1     conda-forge     472kB
  + libboost-python                  1.82.0  py310h8ef98ee_6     conda-forge     105kB
  + contourpy                         1.2.0  py310ha697434_0     conda-forge     232kB
  + scipy                            1.12.0  py310hdfaad59_2     conda-forge      16MB
  + pandas                            2.2.0  py310h276d7da_0     conda-forge      12MB
  + scip                              7.0.3  hc6291ea_1          conda-forge       9MB
  + matplotlib-base                   3.8.2  py310hec49e92_0     conda-forge       7MB
  + qdldl-python                0.1.7.post0  py310h276d7da_1     conda-forge     105kB
  + scs                         3.2.4.post1  py310hf7a4035_0     conda-forge      81kB
  + ecos                             2.0.11  py310h91862f5_1     conda-forge     101kB
  + scikit-learn                      1.4.0  py310h38ce860_0     conda-forge       8MB
  + cvxpy-base                        1.4.2  py310h276d7da_0     conda-forge       1MB
  + pyscipopt                         3.5.0  py310hba3363e_0     conda-forge     682kB
  + matplotlib                        3.8.2  py310h2ec42d9_0     conda-forge       9kB
  + cd-hit                            4.8.1  h0100bc9_9          bioconda        195kB
  + tmalign                        20170708  h868d4ab_6          bioconda         82kB
  + mmseqs2                        15.6f452  pl5321hf590d3d_0    bioconda          4MB
  + foldseek                      8.ef4e960  pl5321h79102bb_0    bioconda          7MB
  + mash                                2.3  hf785b45_2          bioconda        615kB
  + libosqp                           0.6.3  hcec6c5f_0          pkgs/main        80kB
  + pytest-cov                        4.1.0  pyhd8ed1ab_0        conda-forge      25kB
  + freetype-py                       2.3.0  pyhd8ed1ab_0        conda-forge      59kB
  + rlpycairo                         0.2.0  pyhd8ed1ab_0        conda-forge      15kB
  + osqp                              0.6.3  py310hdba192b_2     conda-forge     114kB
  + reportlab                         4.0.9  py310hb372a2b_0     conda-forge       2MB
  + cvxpy                             1.4.2  py310h2ec42d9_0     conda-forge     126kB
  + rdkit                         2023.09.4  py310hbbc110b_0     conda-forge      35MB
  + datasail                          0.2.2  py310_0             kalininalab      35MB

  Summary:

  Install: 122 packages

  Total download: 264MB

────────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y
exceptiongroup                                      20.6kB @ 157.5kB/s  0.1s
makefun                                             26.3kB @ 170.0kB/s  0.2s
iniconfig                                           11.1kB @  71.6kB/s  0.2s
toml                                                18.4kB @ 112.9kB/s  0.2s
cycler                                              13.5kB @  69.4kB/s  0.1s
networkx                                             1.1MB @   5.7MB/s  0.2s
six                                                 14.3kB @  69.2kB/s  0.1s
font-ttf-dejavu-sans-mono                          397.4kB @   1.7MB/s  0.1s
fonts-conda-forge                                    4.1kB @  17.2kB/s  0.0s
typing-extensions                                   10.2kB @  41.6kB/s  0.0s
font-ttf-ubuntu                                      1.6MB @   5.9MB/s  0.1s
lerc                                               290.3kB @ 968.3kB/s  0.1s
llvm-openmp                                        299.7kB @ 939.9kB/s  0.1s
libpng                                             271.7kB @ 818.3kB/s  0.1s
xorg-libxau                                         13.1kB @  35.7kB/s  0.1s
gettext                                              4.2MB @  10.0MB/s  0.2s
libqdldl                                            17.7kB @  41.3kB/s  0.1s
xorg-libxdmcp                                       17.2kB @  37.6kB/s  0.0s
mpfr                                               376.5kB @ 721.7kB/s  0.1s
tbb                                                135.6kB @ 254.5kB/s  0.3s
clarabel                                           407.1kB @ 753.0kB/s  0.2s
greenlet                                           199.9kB @ 351.0kB/s  0.2s
pyyaml                                             160.1kB @ 280.5kB/s  0.0s
expat                                              120.3kB @ 206.2kB/s  0.1s
libxcb                                             313.8kB @ 515.0kB/s  0.1s
libgfortran                                        110.1kB @ 177.4kB/s  0.1s
scotch                                               1.3MB @   1.9MB/s  0.2s
pycairo                                            102.7kB @ 150.9kB/s  0.1s
fftw                                                 1.8MB @   2.6MB/s  0.1s
gawk                                                 1.2MB @   1.6MB/s  0.2s
gsl                                                  3.2MB @   4.2MB/s  0.1s
dsdp                                               226.5kB @ 254.6kB/s  0.2s
ipopt                                              948.5kB @ 910.4kB/s  0.3s
ecos                                               101.0kB @  92.4kB/s  0.2s
scipy                                               15.8MB @  12.1MB/s  0.5s
pandas                                              12.1MB @   8.8MB/s  0.6s
mash                                               614.9kB @ 437.3kB/s  0.1s
pyscipopt                                          681.8kB @ 468.1kB/s  0.4s
tmalign                                             82.0kB @  56.2kB/s  0.4s
freetype-py                                         58.9kB @  39.6kB/s  0.1s
cvxpy                                              126.1kB @  79.6kB/s  0.1s
python-tzdata                                      146.0kB @  92.0kB/s  0.1s
pillow                                              41.2MB @  25.6MB/s  1.0s
typing_extensions                                   36.1kB @  22.0kB/s  0.1s
font-ttf-source-code-pro                           700.8kB @ 420.1kB/s  0.1s
python-dateutil                                    246.0kB @ 147.2kB/s  0.1s
reportlab                                            2.4MB @   1.4MB/s  0.3s
yaml                                                84.2kB @  48.5kB/s  0.1s
pixman                                             326.3kB @ 182.0kB/s  0.1s
tornado                                            642.8kB @ 348.7kB/s  0.1s
metis                                                3.9MB @   2.0MB/s  0.3s
libboost                                             2.0MB @   1.0MB/s  0.2s
aria2                                                1.1MB @ 561.8kB/s  0.1s
libgfortran5                                         1.6MB @ 754.9kB/s  0.1s
glpk                                                 1.0MB @ 491.3kB/s  0.1s
openjpeg                                           335.6kB @ 152.5kB/s  0.1s
lcms2                                              224.4kB @ 101.9kB/s  0.1s
cairo                                              885.3kB @ 388.0kB/s  0.1s
libblas                                             14.8kB @   6.5kB/s  0.1s
mumps-seq                                            3.3MB @   1.4MB/s  0.2s
capnproto                                            4.0MB @   1.6MB/s  0.8s
pcre2                                              899.8kB @ 348.0kB/s  0.7s
rdkit                                               34.9MB @  13.4MB/s  1.1s
qdldl-python                                       104.7kB @  39.7kB/s  0.2s
pytest-cov                                          25.4kB @   9.6kB/s  0.0s
threadpoolctl                                       21.0kB @   7.8kB/s  0.0s
munkres                                             12.5kB @   4.5kB/s  0.0s
scs                                                 81.2kB @  29.3kB/s  0.3s
suitesparse                                          2.6MB @ 936.1kB/s  0.5s
pytest                                             244.6kB @  87.3kB/s  0.1s
libjpeg-turbo                                      579.7kB @ 200.7kB/s  0.1s
libexpat                                            69.6kB @  23.4kB/s  0.1s
pthread-stubs                                        5.7kB @   1.9kB/s  0.1s
perl                                                12.3MB @   4.0MB/s  0.3s
coverage                                           288.1kB @  92.3kB/s  0.1s
fonttools                                            2.2MB @ 692.3kB/s  0.1s
cppad                                              445.2kB @ 138.9kB/s  0.4s
sqlalchemy                                           2.8MB @ 831.6kB/s  0.3s
libopenblas                                          6.0MB @   1.8MB/s  0.2s
contourpy                                          231.8kB @  67.7kB/s  0.1s
ampl-mp                                              1.1MB @ 314.2kB/s  0.2s
matplotlib                                           8.5kB @   2.4kB/s  0.1s
joblib                                             221.2kB @  61.9kB/s  0.1s
libboost-python                                    104.8kB @  29.1kB/s  0.2s
font-ttf-inconsolata                                96.5kB @  26.6kB/s  0.1s
fonts-conda-ecosystem                                3.7kB @   1.0kB/s  0.0s
libdeflate                                          69.0kB @  18.8kB/s  0.0s
unicodedata2                                       366.6kB @  99.4kB/s  0.1s
libosqp                                             79.8kB @  21.4kB/s  0.3s
libunistring                                         1.4MB @ 372.0kB/s  0.1s
freetype                                           599.3kB @ 158.5kB/s  0.1s
liblapack                                           14.7kB @   3.9kB/s  0.0s
cvxpy-base                                           1.2MB @ 302.0kB/s  0.1s
fontconfig                                         237.1kB @  59.9kB/s  0.2s
pyparsing                                           89.5kB @  22.1kB/s  0.1s
osqp                                               113.8kB @  27.9kB/s  0.2s
gmp                                                520.9kB @ 125.3kB/s  0.1s
kiwisolver                                          60.4kB @  14.5kB/s  0.1s
brotli                                             436.2kB @ 103.2kB/s  0.1s
libtiff                                            266.5kB @  62.4kB/s  0.1s
cvxopt                                             471.6kB @ 107.8kB/s  0.1s
scip                                                 8.7MB @   2.0MB/s  0.6s
numpy                                                6.4MB @   1.4MB/s  0.2s
rlpycairo                                           14.9kB @   3.3kB/s  0.1s
tomli                                               15.9kB @   3.5kB/s  0.1s
unixodbc                                           259.2kB @  57.6kB/s  0.1s
libglib                                              2.5MB @ 543.8kB/s  0.1s
libidn2                                            133.2kB @  29.0kB/s  0.1s
wget                                               831.3kB @ 178.3kB/s  0.2s
pytest-cases                                        86.9kB @  18.6kB/s  0.1s
libcblas                                            14.7kB @   3.1kB/s  0.0s
decopatch                                           19.2kB @   4.0kB/s  0.3s
datasail                                            34.5MB @   7.1MB/s  2.3s
matplotlib-base                                      7.0MB @   1.4MB/s  0.2s
mumps-include                                       25.3kB @   5.2kB/s  0.2s
mmseqs2                                              4.0MB @ 807.9kB/s  2.3s
libwebp-base                                       346.6kB @  70.0kB/s  0.1s
chardet                                            245.9kB @  49.5kB/s  0.1s
pytz                                               187.5kB @  37.4kB/s  0.1s
cd-hit                                             194.8kB @  37.5kB/s  0.3s
scikit-learn                                         8.1MB @   1.4MB/s  1.0s
foldseek                                             6.8MB @   1.0MB/s  1.6s

Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

(sail) vahidatabaigi@vahids-MBP ~ % datasail
Traceback (most recent call last):
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/__init__.py", line 24, in <module>
    from . import multiarray
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/multiarray.py", line 10, in <module>
    from . import overrides
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/overrides.py", line 8, in <module>
    from numpy.core._multiarray_umath import (
ImportError: dlopen(/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so, 0x0002): tried: '/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so' (no such file), '/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/__init__.py", line 130, in <module>
    from numpy.__config__ import show as show_config
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/__config__.py", line 4, in <module>
    from numpy.core._multiarray_umath import (
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/__init__.py", line 50, in <module>
    raise ImportError(msg)
ImportError:

IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE!

Importing the numpy C-extensions failed. This error can happen for
many reasons, often due to issues with your setup or how NumPy was
installed.

We have compiled some common reasons and troubleshooting tips at:

    https://numpy.org/devdocs/user/troubleshooting-importerror.html

Please note and check the following:

  * The Python version is: Python3.10 from "/Users/vahidatabaigi/anaconda3/envs/sail/bin/python"
  * The NumPy version is: "1.26.3"

and make sure that they are the versions you expect.
Please carefully study the documentation linked above for further help.

Original error was: dlopen(/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so, 0x0002): tried: '/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so' (no such file), '/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/core/_multiarray_umath.cpython-310-darwin.so' (mach-o file, but is an incompatible architecture (have 'x86_64', need 'arm64'))

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/vahidatabaigi/anaconda3/envs/sail/bin/datasail", line 7, in <module>
    from datasail.sail import sail
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/datasail/sail.py", line 5, in <module>
    from datasail.parsers import parse_datasail_args
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/datasail/parsers.py", line 9, in <module>
    from datasail.argparse_patch import insert_patch
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/datasail/argparse_patch.py", line 3, in <module>
    from datasail.settings import KW_E_ARGS, KW_F_ARGS
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/datasail/settings.py", line 8, in <module>
    import cvxpy
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/cvxpy/__init__.py", line 19, in <module>
    import cvxpy.interface.scipy_wrapper
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/cvxpy/interface/__init__.py", line 17, in <module>
    from cvxpy.interface.matrix_utilities import *
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/cvxpy/interface/matrix_utilities.py", line 19, in <module>
    import numpy as np
  File "/Users/vahidatabaigi/anaconda3/envs/sail/lib/python3.10/site-packages/numpy/__init__.py", line 135, in <module>
    raise ImportError(msg) from e
ImportError: Error importing numpy: you should not try to import numpy from
        its source directory; please exit the numpy source tree, and relaunch
        your python interpreter from there.
(sail) vahidatabaigi@vahids-MBP ~ %

I uninstalled numpy and installed it with env config to osx=64 but it didnot work. and same error

Old-Shatterhand commented 8 months ago

Hi @atabaigi the problem is that CD-Hit is not available for M1 chips, i.e. the osx-arm64 architecture. I'll check out ways to fix it and use other installations of CD-Hit for M1.

Old-Shatterhand commented 7 months ago

This is a duplicate to #16. A fix will be provided in version 1.0.0. More details in #16.