girip commented on issue #30:
URL:
https://github.com/apache/airavata-cerebrum/issues/30#issuecomment-4698901263
Thank you @srirampc
Apologies that earlier error was from wrong environment.
I now tried with the fresh environment and got another error on
installation. Note, this is after following the installation procedure of
creating a new environment as specified in readme (the results of conda install
is below the error message).
(cerebrum) ~ pip install airavata-cerebrum
Collecting airavata-cerebrum
Downloading airavata_cerebrum-0.1.2-py3-none-any.whl.metadata (5.8 kB)
Collecting allensdk>=2.16 (from airavata-cerebrum)
Downloading allensdk-2.16.2-py3-none-any.whl.metadata (1.9 kB)
Collecting altair>=6.0 (from airavata-cerebrum)
Downloading altair-6.2.1-py3-none-any.whl.metadata (11 kB)
Collecting anndata>=0.10 (from airavata-cerebrum)
Downloading anndata-0.11.4-py3-none-any.whl.metadata (9.3 kB)
Collecting anywidget>=0.9 (from airavata-cerebrum)
Downloading anywidget-0.11.0-py3-none-any.whl.metadata (8.9 kB)
Collecting awitree>=0.1 (from airavata-cerebrum)
Downloading awitree-0.1.0-py2.py3-none-any.whl.metadata (2.4 kB)
Collecting duckdb>=1.2 (from airavata-cerebrum)
Downloading duckdb-1.5.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (4.2
kB)
Collecting fastexcel>=0.13 (from airavata-cerebrum)
Downloading fastexcel-0.20.2-cp310-abi3-macosx_11_0_arm64.whl.metadata
(7.2 kB)
Collecting h5py>=3.15 (from airavata-cerebrum)
Downloading h5py-3.16.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (3.0 kB)
Collecting ipytree>=0.2 (from airavata-cerebrum)
Downloading ipytree-0.2.2-py2.py3-none-any.whl.metadata (849 bytes)
Collecting ipywidgets>=8.1 (from airavata-cerebrum)
Downloading ipywidgets-8.1.8-py3-none-any.whl.metadata (2.4 kB)
Collecting jupyter (from airavata-cerebrum)
Downloading jupyter-1.1.1-py2.py3-none-any.whl.metadata (2.0 kB)
Collecting lmfit (from airavata-cerebrum)
Downloading lmfit-1.3.4-py3-none-any.whl.metadata (8.8 kB)
Collecting matplotlib>=3.7 (from airavata-cerebrum)
Downloading matplotlib-3.10.9-cp310-cp310-macosx_11_0_arm64.whl.metadata
(52 kB)
Collecting neuroanalysis>=0.0.7 (from airavata-cerebrum)
Downloading neuroanalysis-0.0.7.tar.gz (1.8 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 3.2 MB/s 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Collecting numba>=0.63 (from airavata-cerebrum)
Downloading numba-0.65.1-cp310-cp310-macosx_12_0_arm64.whl.metadata (2.9
kB)
Collecting numpy>=1.23 (from airavata-cerebrum)
Downloading numpy-2.2.6-cp310-cp310-macosx_14_0_arm64.whl.metadata (62 kB)
Collecting openpyxl>=3.1 (from airavata-cerebrum)
Downloading openpyxl-3.1.5-py2.py3-none-any.whl.metadata (2.5 kB)
Collecting pandas>=1.5 (from airavata-cerebrum)
Downloading pandas-2.3.3-cp310-cp310-macosx_11_0_arm64.whl.metadata (91 kB)
Collecting parse>=1.20 (from airavata-cerebrum)
Downloading parse-1.22.1-py2.py3-none-any.whl.metadata (21 kB)
Collecting pillow (from airavata-cerebrum)
Downloading pillow-12.2.0-cp310-cp310-macosx_11_0_arm64.whl.metadata (8.8
kB)
Collecting polars>=1.26 (from airavata-cerebrum)
Downloading polars-1.41.2-py3-none-any.whl.metadata (10 kB)
Collecting psutil>=7.0 (from airavata-cerebrum)
Downloading psutil-7.2.2-cp36-abi3-macosx_11_0_arm64.whl.metadata (22 kB)
Collecting psycopg2 (from airavata-cerebrum)
Downloading psycopg2-2.9.12.tar.gz (379 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [34 lines of output]
/private/var/folders/xb/7s9bzr7s4pn88h222dpgpw3c0000gs/T/pip-build-env-ykc7hmeb/overlay/lib/python3.10/site-packages/setuptools/dist.py:765:
SetuptoolsDeprecationWarning: License classifiers are deprecated.
!!
********************************************************************************
Please consider removing the following classifiers in favor of
a SPDX license expression:
License :: OSI Approved :: GNU Library or Lesser General
Public License (LGPL)
See
https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license
for details.
********************************************************************************
!!
self._finalize_license_expression()
running egg_info
writing psycopg2.egg-info/PKG-INFO
writing dependency_links to psycopg2.egg-info/dependency_links.txt
writing top-level names to psycopg2.egg-info/top_level.txt
Error: pg_config executable not found.
pg_config is required to build psycopg2 from source. Please add the
directory
containing pg_config to the $PATH or specify the full executable path
with the
option:
python setup.py build_ext --pg-config /path/to/pg_config build ...
or with the pg_config option in 'setup.cfg'.
If you prefer to avoid building psycopg2 from source, please install
the PyPI
'psycopg2-binary' package instead.
For further information please check the 'doc/src/install.rst' file
(also at
<https://www.psycopg.org/docs/install.html>).
[end of output]
note: This error originates from a subprocess, and is likely not a problem
with pip.
ERROR: Failed to build 'psycopg2' when getting requirements to build wheel
---------------------------------------------------------------------------------------
~ conda config --add channels conda-forge
conda create -n cerebrum python=3.10 nodejs
conda activate cerebrum
/opt/anaconda3/lib/python3.12/site-packages/conda/base/context.py:198:
FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and
will be removed in 25.9.
To remove this warning, please choose a default channel explicitly with
conda's regular configuration system, e.g. by adding 'defaults' to the list of
channels:
conda config --add channels defaults
For more information see
https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html
deprecated.topic(
Retrieving notices: done
Channels:
- conda-forge
- defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: done
## Package Plan ##
environment location: /opt/anaconda3/envs/cerebrum
added / updated specs:
- nodejs
- python=3.10
The following packages will be downloaded:
package | build
---------------------------|-----------------
bzip2-1.0.8 | hd037594_9 122 KB conda-forge
c-ares-1.34.6 | hc919400_0 176 KB conda-forge
ca-certificates-2026.5.20 | hbd8a1cb_0 127 KB conda-forge
icu-78.3 | hef89b57_0 11.8 MB conda-forge
libabseil-20260107.1 | cxx17_h2062a1b_0 1.2 MB conda-forge
libbrotlicommon-1.2.0 | hc919400_1 78 KB conda-forge
libbrotlidec-1.2.0 | hc919400_1 29 KB conda-forge
libbrotlienc-1.2.0 | hc919400_1 284 KB conda-forge
libcxx-22.1.7 | h55c6f16_0 555 KB conda-forge
libexpat-2.8.1 | hf6b4638_1 68 KB conda-forge
libffi-3.5.2 | hcf2aa1b_0 40 KB conda-forge
liblzma-5.8.3 | h8088a28_0 90 KB conda-forge
libnghttp2-1.68.1 | h8f3e76b_0 563 KB conda-forge
libsqlite-3.53.2 | h1ae2325_0 906 KB conda-forge
libuv-1.52.1 | h1a92334_0 120 KB conda-forge
libzlib-1.3.2 | h8088a28_2 47 KB conda-forge
ncurses-6.6 | h1d4f5a5_0 787 KB conda-forge
nodejs-26.3.0 | h7039424_0 17.2 MB conda-forge
openssl-3.6.3 | hd24854e_0 3.0 MB conda-forge
packaging-26.2 | pyhc364b38_0 89 KB conda-forge
pip-26.1.2 | pyh8b19718_0 1.1 MB conda-forge
python-3.10.20 |hac0b6dc_1_cpython 12.3 MB
conda-forge
readline-8.3 | h46df422_0 307 KB conda-forge
setuptools-82.0.1 | pyh332efcf_0 625 KB conda-forge
tk-8.6.13 | h010d191_3 3.0 MB conda-forge
tzdata-2025c | hc9c84f9_1 116 KB conda-forge
wheel-0.47.0 | pyhd8ed1ab_0 33 KB conda-forge
zstd-1.5.7 | hbf9d68e_6 423 KB conda-forge
------------------------------------------------------------
Total: 55.0 MB
The following NEW packages will be INSTALLED:
bzip2 conda-forge/osx-arm64::bzip2-1.0.8-hd037594_9
c-ares conda-forge/osx-arm64::c-ares-1.34.6-hc919400_0
ca-certificates conda-forge/noarch::ca-certificates-2026.5.20-hbd8a1cb_0
icu conda-forge/osx-arm64::icu-78.3-hef89b57_0
libabseil
conda-forge/osx-arm64::libabseil-20260107.1-cxx17_h2062a1b_0
libbrotlicommon conda-forge/osx-arm64::libbrotlicommon-1.2.0-hc919400_1
libbrotlidec conda-forge/osx-arm64::libbrotlidec-1.2.0-hc919400_1
libbrotlienc conda-forge/osx-arm64::libbrotlienc-1.2.0-hc919400_1
libcxx conda-forge/osx-arm64::libcxx-22.1.7-h55c6f16_0
libev conda-forge/osx-arm64::libev-4.33-h93a5062_2
libexpat conda-forge/osx-arm64::libexpat-2.8.1-hf6b4638_1
libffi conda-forge/osx-arm64::libffi-3.5.2-hcf2aa1b_0
liblzma conda-forge/osx-arm64::liblzma-5.8.3-h8088a28_0
libnghttp2 conda-forge/osx-arm64::libnghttp2-1.68.1-h8f3e76b_0
libsqlite conda-forge/osx-arm64::libsqlite-3.53.2-h1ae2325_0
libuv conda-forge/osx-arm64::libuv-1.52.1-h1a92334_0
libzlib conda-forge/osx-arm64::libzlib-1.3.2-h8088a28_2
ncurses conda-forge/osx-arm64::ncurses-6.6-h1d4f5a5_0
nodejs conda-forge/osx-arm64::nodejs-26.3.0-h7039424_0
openssl conda-forge/osx-arm64::openssl-3.6.3-hd24854e_0
packaging conda-forge/noarch::packaging-26.2-pyhc364b38_0
pip conda-forge/noarch::pip-26.1.2-pyh8b19718_0
python conda-forge/osx-arm64::python-3.10.20-hac0b6dc_1_cpython
readline conda-forge/osx-arm64::readline-8.3-h46df422_0
setuptools conda-forge/noarch::setuptools-82.0.1-pyh332efcf_0
tk conda-forge/osx-arm64::tk-8.6.13-h010d191_3
tzdata conda-forge/noarch::tzdata-2025c-hc9c84f9_1
wheel conda-forge/noarch::wheel-0.47.0-pyhd8ed1ab_0
zstd conda-forge/osx-arm64::zstd-1.5.7-hbf9d68e_6
Proceed ([y]/n)? y
Downloading and Extracting Packages:
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate cerebrum
#
# To deactivate an active environment, use
#
# $ conda deactivate
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